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Sample records for synthetic microbial ecosystem

Synthetic microbial ecology and the dynamic interplay between microbial genotypes.

Science.gov (United States)

Dolinšek, Jan; Goldschmidt, Felix; Johnson, David R

2016-11-01

Assemblages of microbial genotypes growing together can display surprisingly complex and unexpected dynamics and result in community-level functions and behaviors that are not readily expected from analyzing each genotype in isolation. This complexity has, at least in part, inspired a discipline of synthetic microbial ecology. Synthetic microbial ecology focuses on designing, building and analyzing the dynamic behavior of ‘ecological circuits’ (i.e. a set of interacting microbial genotypes) and understanding how community-level properties emerge as a consequence of those interactions. In this review, we discuss typical objectives of synthetic microbial ecology and the main advantages and rationales of using synthetic microbial assemblages. We then summarize recent findings of current synthetic microbial ecology investigations. In particular, we focus on the causes and consequences of the interplay between different microbial genotypes and illustrate how simple interactions can create complex dynamics and promote unexpected community-level properties. We finally propose that distinguishing between active and passive interactions and accounting for the pervasiveness of competition can improve existing frameworks for designing and predicting the dynamics of microbial assemblages.
[Synthetic biology and rearrangements of microbial genetic material].

Science.gov (United States)

Liang, Quan-Feng; Wang, Qian; Qi, Qing-Sheng

2011-10-01

As an emerging discipline, synthetic biology has shown great scientific values and application prospects. Although there have been many reviews of various aspects on synthetic biology over the last years, this article, for the first time, attempted to discuss the relationship and difference between microbial genetics and synthetic biology. We summarized the recent development of synthetic biology in rearranging microbial genetic materials, including synthesis, design and reduction of genetic materials, standardization of genetic parts and modularization of genetic circuits. The relationship between synthetic biology and microbial genetic engineering was also discussed in the paper.
Synthetic Electric Microbial Biosensors

Science.gov (United States)

2017-06-10

domains and DNA-binding domains into a single protein for deregulation of down stream genes of have been favored [10]. Initially experiments with... Germany DISTRIBUTION A. Approved for public release: distribution unlimited. Talk title: “Synthetic biology based microbial biosensors for the...toolbox” in Heidelberg, Germany Poster title: “Anaerobic whole cell microbial biosensors” Link: http://phdsymposium.embl.org/#home September, 2014
Design and construction of synthetic microbial consortia in China

Directory of Open Access Journals (Sweden)

Ming-Zhu Ding

2016-12-01

Full Text Available The rapid development of synthetic biology enables the design, construction and optimization of synthetic microbial consortia to achieve specific functions. In China, the “973” project-“Design and Construction of Microbial Consortia” was funded by the National Basic Research Program of China in January 2014. It was proposed to address the fundamental challenges in engineering natural microbial consortia and reconstructing microbial consortia to meet industrial demands. In this review, we will introduce this “973” project, including the significance of microbial consortia, the fundamental scientific issues, the recent research progresses, and some case studies about synthetic microbial consortia in the past two and a half years.
Toward Understanding, Managing, and Protecting Microbial Ecosystems

Science.gov (United States)

Bodelier, Paul L. E.

2011-01-01

Microbial communities are at the very basis of life on earth, catalyzing biogeochemical reactions driving global nutrient cycles. However, unlike for plants and animals, microbial diversity is not on the biodiversity–conservation agenda. The latter, however, would imply that microbial diversity is not under any threat by anthropogenic disturbance or climate change. This maybe a misconception caused by the rudimentary knowledge we have concerning microbial diversity and its role in ecosystem functioning. This perspective paper identifies major areas with knowledge gaps within the field of environmental microbiology that preclude a comprehension of microbial ecosystems on the level we have for plants and animals. Opportunities and challenges are pointed out to open the microbial black box and to go from descriptive to predictive microbial ecology. PMID:21747797
Towards understanding, managing and protecting microbial ecosystems

Directory of Open Access Journals (Sweden)

Paul eBodelier

2011-04-01

Full Text Available Microbial communities are at the very basis of life on earth, catalysing biogeochemical reactions driving global nutrient cycles. However, unlike for plants and animals, microbial diversity is not on the biodiversity conservation agenda. The latter, however, would imply that microbial diversity is not under any threat by anthropogenic disturbance or climate change. This maybe a misconception caused by the rudimentary knowledge we have concerning microbial diversity and its role in ecosystem functioning. This perspective paper indentifies major areas with knowledge gaps within the field of environmental microbiology that preclude a comprehension of microbial ecosystems on the level we have for plants and animals. Opportunities and challenges are pointed out to open the microbial black box and to go from descriptive to predictive microbial ecology.
Toward understanding, managing, and protecting microbial ecosystems.

Science.gov (United States)

Bodelier, Paul L E

2011-01-01

Microbial communities are at the very basis of life on earth, catalyzing biogeochemical reactions driving global nutrient cycles. However, unlike for plants and animals, microbial diversity is not on the biodiversity-conservation agenda. The latter, however, would imply that microbial diversity is not under any threat by anthropogenic disturbance or climate change. This maybe a misconception caused by the rudimentary knowledge we have concerning microbial diversity and its role in ecosystem functioning. This perspective paper identifies major areas with knowledge gaps within the field of environmental microbiology that preclude a comprehension of microbial ecosystems on the level we have for plants and animals. Opportunities and challenges are pointed out to open the microbial black box and to go from descriptive to predictive microbial ecology.
Reprint of Design of synthetic microbial communities for biotechnological production processes.

Science.gov (United States)

Jagmann, Nina; Philipp, Bodo

2014-12-20

In their natural habitats microorganisms live in multi-species communities, in which the community members exhibit complex metabolic interactions. In contrast, biotechnological production processes catalyzed by microorganisms are usually carried out with single strains in pure cultures. A number of production processes, however, may be more efficiently catalyzed by the concerted action of microbial communities. This review will give an overview of organismic interactions between microbial cells and of biotechnological applications of microbial communities. It focuses on synthetic microbial communities that consist of microorganisms that have been genetically engineered. Design principles for such synthetic communities will be exemplified based on plausible scenarios for biotechnological production processes. These design principles comprise interspecific metabolic interactions via cross-feeding, regulation by interspecific signaling processes via metabolites and autoinducing signal molecules, and spatial structuring of synthetic microbial communities. In particular, the implementation of metabolic interdependencies, of positive feedback regulation and of inducible cell aggregation and biofilm formation will be outlined. Synthetic microbial communities constitute a viable extension of the biotechnological application of metabolically engineered single strains and enlarge the scope of microbial production processes. Copyright © 2014 Elsevier B.V. All rights reserved.
Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning.

Science.gov (United States)

He, Zhili; Zhang, Ping; Wu, Linwei; Rocha, Andrea M; Tu, Qichao; Shi, Zhou; Wu, Bo; Qin, Yujia; Wang, Jianjun; Yan, Qingyun; Curtis, Daniel; Ning, Daliang; Van Nostrand, Joy D; Wu, Liyou; Yang, Yunfeng; Elias, Dwayne A; Watson, David B; Adams, Michael W W; Fields, Matthew W; Alm, Eric J; Hazen, Terry C; Adams, Paul D; Arkin, Adam P; Zhou, Jizhong

2018-02-20

Contamination from anthropogenic activities has significantly impacted Earth's biosphere. However, knowledge about how environmental contamination affects the biodiversity of groundwater microbiomes and ecosystem functioning remains very limited. Here, we used a comprehensive functional gene array to analyze groundwater microbiomes from 69 wells at the Oak Ridge Field Research Center (Oak Ridge, TN), representing a wide pH range and uranium, nitrate, and other contaminants. We hypothesized that the functional diversity of groundwater microbiomes would decrease as environmental contamination (e.g., uranium or nitrate) increased or at low or high pH, while some specific populations capable of utilizing or resistant to those contaminants would increase, and thus, such key microbial functional genes and/or populations could be used to predict groundwater contamination and ecosystem functioning. Our results indicated that functional richness/diversity decreased as uranium (but not nitrate) increased in groundwater. In addition, about 5.9% of specific key functional populations targeted by a comprehensive functional gene array (GeoChip 5) increased significantly ( P contamination and ecosystem functioning. This study indicates great potential for using microbial functional genes to predict environmental contamination and ecosystem functioning. IMPORTANCE Disentangling the relationships between biodiversity and ecosystem functioning is an important but poorly understood topic in ecology. Predicting ecosystem functioning on the basis of biodiversity is even more difficult, particularly with microbial biomarkers. As an exploratory effort, this study used key microbial functional genes as biomarkers to provide predictive understanding of environmental contamination and ecosystem functioning. The results indicated that the overall functional gene richness/diversity decreased as uranium increased in groundwater, while specific key microbial guilds increased significantly as
Effect of ecosystems substitutions and CO2 increase of the atmosphere on the microbial ecosystems of forests

International Nuclear Information System (INIS)

Martin, F.

2007-01-01

Biological diversity is often exclusively considered at the level of plants and animals, whereas the bulk of global biodiversity is in fact at the microbial level. Although it is clear that the ecology of our planet is driven by microbial ecosystems, we are severely hampered by our limited understanding of the diversity and function of such microbial ecosystems. In the present project, teams in the disciplines of geochemistry, soil microbiology, genomics and ecosystem processes are assembled to study the relationship between environmental change, land use changes, biodiversity, and functioning of forest ecosystems. The network has a strong focus on developing and applying biochemical and genotyping methodologies to address key scientific issues in soil microbial ecology. These include assessing the impact of environmental- and land use changes on microbial diversity and function and exploring the evolutionary and mechanistic links between biological diversity and ecosystem function. In the present study, we have shown that: (1) The native mixed forest showed the highest microbial diversity (2) The mono specific plantations of tree species (e.g., oak, beech, pine, spruce) strikingly alter genetic and functional diversities of soil bacterial and fungal species. (3) Bacterial denitrification rates were dramatically modified by the planted species. Only by taking into account the impact of forest management on below-ground microbial diversity can one hope to get a full ecosystem-based understanding, and this must be addressed via modelling in order to provide relevant and useful information for conservation and policy making. (author)
Soil microbial community successional patterns during forest ecosystem restoration.

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Banning, Natasha C; Gleeson, Deirdre B; Grigg, Andrew H; Grant, Carl D; Andersen, Gary L; Brodie, Eoin L; Murphy, D V

2011-09-01

Soil microbial community characterization is increasingly being used to determine the responses of soils to stress and disturbances and to assess ecosystem sustainability. However, there is little experimental evidence to indicate that predictable patterns in microbial community structure or composition occur during secondary succession or ecosystem restoration. This study utilized a chronosequence of developing jarrah (Eucalyptus marginata) forest ecosystems, rehabilitated after bauxite mining (up to 18 years old), to examine changes in soil bacterial and fungal community structures (by automated ribosomal intergenic spacer analysis [ARISA]) and changes in specific soil bacterial phyla by 16S rRNA gene microarray analysis. This study demonstrated that mining in these ecosystems significantly altered soil bacterial and fungal community structures. The hypothesis that the soil microbial community structures would become more similar to those of the surrounding nonmined forest with rehabilitation age was broadly supported by shifts in the bacterial but not the fungal community. Microarray analysis enabled the identification of clear successional trends in the bacterial community at the phylum level and supported the finding of an increase in similarity to nonmined forest soil with rehabilitation age. Changes in soil microbial community structure were significantly related to the size of the microbial biomass as well as numerous edaphic variables (including pH and C, N, and P nutrient concentrations). These findings suggest that soil bacterial community dynamics follow a pattern in developing ecosystems that may be predictable and can be conceptualized as providing an integrated assessment of numerous edaphic variables.
Microbial ecosystem constructed in water for successful organic hydroponics

OpenAIRE

Makoto Shinohara; Hiromi Ohmori; Yoichi Uehara

2008-01-01

Conventional hydroponics systems generally use only chemical fertilisers, not organic ones, since there are no microbial ecosystems present in such systems to mineralise organic compounds to inorganic nutrients. Addition of organic compounds to the hydroponic solution generally has phytotoxic effects and causes poor plant growth. We developed a novel hydroponic culture method using organic fertiliser. A microbial ecosystem was constructed in hydroponic solution by regulating the amounts of or...
Soil Microbial Community Successional Patterns during Forest Ecosystem Restoration ▿†

OpenAIRE

Banning, Natasha C.; Gleeson, Deirdre B.; Grigg, Andrew H.; Grant, Carl D.; Andersen, Gary L.; Brodie, Eoin L.; Murphy, D. V.

2011-01-01

Soil microbial community characterization is increasingly being used to determine the responses of soils to stress and disturbances and to assess ecosystem sustainability. However, there is little experimental evidence to indicate that predictable patterns in microbial community structure or composition occur during secondary succession or ecosystem restoration. This study utilized a chronosequence of developing jarrah (Eucalyptus marginata) forest ecosystems, rehabilitated after bauxite mini...
A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems.

Science.gov (United States)

Budinich, Marko; Bourdon, Jérémie; Larhlimi, Abdelhalim; Eveillard, Damien

2017-01-01

Interplay within microbial communities impacts ecosystems on several scales, and elucidation of the consequent effects is a difficult task in ecology. In particular, the integration of genome-scale data within quantitative models of microbial ecosystems remains elusive. This study advocates the use of constraint-based modeling to build predictive models from recent high-resolution -omics datasets. Following recent studies that have demonstrated the accuracy of constraint-based models (CBMs) for simulating single-strain metabolic networks, we sought to study microbial ecosystems as a combination of single-strain metabolic networks that exchange nutrients. This study presents two multi-objective extensions of CBMs for modeling communities: multi-objective flux balance analysis (MO-FBA) and multi-objective flux variability analysis (MO-FVA). Both methods were applied to a hot spring mat model ecosystem. As a result, multiple trade-offs between nutrients and growth rates, as well as thermodynamically favorable relative abundances at community level, were emphasized. We expect this approach to be used for integrating genomic information in microbial ecosystems. Following models will provide insights about behaviors (including diversity) that take place at the ecosystem scale.
Allee effect: the story behind the stabilization or extinction of microbial ecosystem.

Science.gov (United States)

Goswami, Madhurankhi; Bhattacharyya, Purnita; Tribedi, Prosun

2017-03-01

A population exhibiting Allee effect shows a positive correlation between population fitness and population size or density. Allee effect decides the extinction or conservation of a microbial population and thus appears to be an important criterion in population ecology. The underlying factor of Allee effect that decides the stabilization and extinction of a particular population density is the threshold or the critical density of their abundance. According to Allee, microbial populations exhibit a definite, critical or threshold density, beyond which the population fitness of a particular population increases with the rise in population density and below it, the population fitness goes down with the decrease in population density. In particular, microbial population displays advantageous traits such as biofilm formation, expression of virulence genes, spore formation and many more only at a high population density. It has also been observed that microorganisms exhibiting a lower population density undergo complete extinction from the residual microbial ecosystem. In reference to Allee effect, decrease in population density or size introduces deleterious mutations among the population density through genetic drift. Mutations are carried forward to successive generations resulting in its accumulation among the population density thus reducing its microbial fitness and thereby increasing the risk of extinction of a particular microbial population. However, when the microbial load is high, the chance of genetic drift is less, and through the process of biofilm formation, the cooperation existing among the microbial population increases that increases the microbial fitness. Thus, the high microbial population through the formation of microbial biofilm stabilizes the ecosystem by increasing fitness. Taken together, microbial fitness shows positive correlation with the ecosystem conservation and negative correlation with ecosystem extinction.
A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems.

Directory of Open Access Journals (Sweden)

Marko Budinich

Full Text Available Interplay within microbial communities impacts ecosystems on several scales, and elucidation of the consequent effects is a difficult task in ecology. In particular, the integration of genome-scale data within quantitative models of microbial ecosystems remains elusive. This study advocates the use of constraint-based modeling to build predictive models from recent high-resolution -omics datasets. Following recent studies that have demonstrated the accuracy of constraint-based models (CBMs for simulating single-strain metabolic networks, we sought to study microbial ecosystems as a combination of single-strain metabolic networks that exchange nutrients. This study presents two multi-objective extensions of CBMs for modeling communities: multi-objective flux balance analysis (MO-FBA and multi-objective flux variability analysis (MO-FVA. Both methods were applied to a hot spring mat model ecosystem. As a result, multiple trade-offs between nutrients and growth rates, as well as thermodynamically favorable relative abundances at community level, were emphasized. We expect this approach to be used for integrating genomic information in microbial ecosystems. Following models will provide insights about behaviors (including diversity that take place at the ecosystem scale.
Microbial Fingerprints of Community Structure Correlate with Changes in Ecosystem Function Induced by Perturbing the Redox Environment

Science.gov (United States)

Mills, A. L.; Ford, R. M.; Vallino, J. J.; Herman, J. S.; Hornberger, G. M.

2001-12-01

Restoration of high-quality groundwater has been an elusive engineering goal. Consequently, natural microbially-mediated reactions are increasingly relied upon to degrade organic contaminants, including hydrocarbons and many synthetic compounds. Of concern is how the introduction of an organic chemical contaminant affects the indigenous microbial communities, the geochemistry of the aquifer, and the function of the ecosystem. The presence of functional redundancy in microbial communities suggests that recovery of the community after a disturbance such as a contamination event could easily result in a community that is similar in function to that which existed prior to the contamination, but which is compositionally quite different. To investigate the relationship between community structure and function we observed the response of a diverse microbial community obtained from raw sewage to a dynamic redox environment using an aerobic/anaerobic/aerobic cycle. To evaluate changes in community function CO2, pH, ammonium and nitrate levels were monitored. A phylogenetically-based DNA technique (tRFLP) was used to assess changes in microbial community structure. Principal component analysis of the tRFLP data revealed significant changes in the composition of the microbial community that correlated well with changes in community function. Results from our experiments will be discussed in the context of a metabolic model based the biogeochemistry of the system. The governing philosophy of this thermodynamically constrained metabolic model is that living systems synthesize and allocate cellular machinery in such a way as to "optimally" utilize available resources in the environment. The robustness of this optimization-based approach provides a powerful tool for studying relationships between microbial diversity and ecosystem function.
Microbial biodiversity of Sardinian oleic ecosystems.

Science.gov (United States)

Santona, Mario; Sanna, Maria Lina; Multineddu, Chiara; Fancello, Francesco; de la Fuente, Sara Audije; Dettori, Sandro; Zara, Severino

2018-04-01

The olives are rich in microorganisms that, during the extraction process may persist in the oils and can influence their physicochemical and sensory characteristics. In this work, and for the first time, we isolated and identified microbial species, yeast and bacteria, present during the production process in four Sardinian (Italy) oleic ecosystems. Among these varieties, we found that Nera di Gonnos was associated to the highest microbial biodiversity, which was followed by Bosana, Nocellara del Belice and Semidana. Among the different microbial species isolated, some are specific of olive ecological niches, such as Cryptococcus spp and Serratia spp; and others to olive oils such as Candida spp and Saccharomyces. Some other species identified in this work were not found before in oleic ecosystems. The enzymatic analyses of yeast and bacteria showed that they have good β-glucosidase activity and yeast also showed good β-glucanase activity. The majority of bacteria presented lipolytic and catalase activities while in yeast were species-specific. Interestingly, yeast and bacteria isolates presented a high resistance to bile acid, and about 65% of the yeast were able to resist at pH 2.5 for 2 h. Finally, bacteria showed no biofilm activity compared to yeast. Copyright © 2017 Elsevier Ltd. All rights reserved.
Soil Microbial Community Successional Patterns during Forest Ecosystem Restoration ▿†

Science.gov (United States)

Banning, Natasha C.; Gleeson, Deirdre B.; Grigg, Andrew H.; Grant, Carl D.; Andersen, Gary L.; Brodie, Eoin L.; Murphy, D. V.

2011-01-01

Soil microbial community characterization is increasingly being used to determine the responses of soils to stress and disturbances and to assess ecosystem sustainability. However, there is little experimental evidence to indicate that predictable patterns in microbial community structure or composition occur during secondary succession or ecosystem restoration. This study utilized a chronosequence of developing jarrah (Eucalyptus marginata) forest ecosystems, rehabilitated after bauxite mining (up to 18 years old), to examine changes in soil bacterial and fungal community structures (by automated ribosomal intergenic spacer analysis [ARISA]) and changes in specific soil bacterial phyla by 16S rRNA gene microarray analysis. This study demonstrated that mining in these ecosystems significantly altered soil bacterial and fungal community structures. The hypothesis that the soil microbial community structures would become more similar to those of the surrounding nonmined forest with rehabilitation age was broadly supported by shifts in the bacterial but not the fungal community. Microarray analysis enabled the identification of clear successional trends in the bacterial community at the phylum level and supported the finding of an increase in similarity to nonmined forest soil with rehabilitation age. Changes in soil microbial community structure were significantly related to the size of the microbial biomass as well as numerous edaphic variables (including pH and C, N, and P nutrient concentrations). These findings suggest that soil bacterial community dynamics follow a pattern in developing ecosystems that may be predictable and can be conceptualized as providing an integrated assessment of numerous edaphic variables. PMID:21724890
Synthetic biology for microbial heavy metal biosensors.

Science.gov (United States)

Kim, Hyun Ju; Jeong, Haeyoung; Lee, Sang Jun

2018-02-01

Using recombinant DNA technology, various whole-cell biosensors have been developed for detection of environmental pollutants, including heavy metal ions. Whole-cell biosensors have several advantages: easy and inexpensive cultivation, multiple assays, and no requirement of any special techniques for analysis. In the era of synthetic biology, cutting-edge DNA sequencing and gene synthesis technologies have accelerated the development of cell-based biosensors. Here, we summarize current technological advances in whole-cell heavy metal biosensors, including the synthetic biological components (bioparts), sensing and reporter modules, genetic circuits, and chassis cells. We discuss several opportunities for improvement of synthetic cell-based biosensors. First, new functional modules must be discovered in genome databases, and this knowledge must be used to upgrade specific bioparts through molecular engineering. Second, modules must be assembled into functional biosystems in chassis cells. Third, heterogeneity of individual cells in the microbial population must be eliminated. In the perspectives, the development of whole-cell biosensors is also discussed in the aspects of cultivation methods and synthetic cells.

Comparison of seasonal soil microbial process in snow-covered temperate ecosystems of northern China.

Directory of Open Access Journals (Sweden)

Xinyue Zhang

Full Text Available More than half of the earth's terrestrial surface currently experiences seasonal snow cover and soil frost. Winter compositional and functional investigations in soil microbial community are frequently conducted in alpine tundra and boreal forest ecosystems. However, little information on winter microbial biogeochemistry is known from seasonally snow-covered temperate ecosystems. As decomposer microbes may differ in their ability/strategy to efficiently use soil organic carbon (SOC within different phases of the year, understanding seasonal microbial process will increase our knowledge of biogeochemical cycling from the aspect of decomposition rates and corresponding nutrient dynamics. In this study, we measured soil microbial biomass, community composition and potential SOC mineralization rates in winter and summer, from six temperate ecosystems in northern China. Our results showed a clear pattern of increased microbial biomass C to nitrogen (N ratio in most winter soils. Concurrently, a shift in soil microbial community composition occurred with higher fungal to bacterial biomass ratio and gram negative (G- to gram positive (G+ bacterial biomass ratio in winter than in summer. Furthermore, potential SOC mineralization rate was higher in winter than in summer. Our study demonstrated a distinct transition of microbial community structure and function from winter to summer in temperate snow-covered ecosystems. Microbial N immobilization in winter may not be the major contributor for plant growth in the following spring.
An open source platform for multi-scale spatially distributed simulations of microbial ecosystems

Energy Technology Data Exchange (ETDEWEB)

Segre, Daniel [Boston Univ., MA (United States)

2014-08-14

The goal of this project was to develop a tool for facilitating simulation, validation and discovery of multiscale dynamical processes in microbial ecosystems. This led to the development of an open-source software platform for Computation Of Microbial Ecosystems in Time and Space (COMETS). COMETS performs spatially distributed time-dependent flux balance based simulations of microbial metabolism. Our plan involved building the software platform itself, calibrating and testing it through comparison with experimental data, and integrating simulations and experiments to address important open questions on the evolution and dynamics of cross-feeding interactions between microbial species.
Microbial ecology of fermentative hydrogen producing bioprocesses: useful insights for driving the ecosystem function.

Science.gov (United States)

Cabrol, Lea; Marone, Antonella; Tapia-Venegas, Estela; Steyer, Jean-Philippe; Ruiz-Filippi, Gonzalo; Trably, Eric

2017-03-01

One of the most important biotechnological challenges is to develop environment friendly technologies to produce new sources of energy. Microbial production of biohydrogen through dark fermentation, by conversion of residual biomass, is an attractive solution for short-term development of bioH2 producing processes. Efficient biohydrogen production relies on complex mixed communities working in tight interaction. Species composition and functional traits are of crucial importance to maintain the ecosystem service. The analysis of microbial community revealed a wide phylogenetic diversity that contributes in different-and still mostly unclear-ways to hydrogen production. Bridging this gap of knowledge between microbial ecology features and ecosystem functionality is essential to optimize the bioprocess and develop strategies toward a maximization of the efficiency and stability of substrate conversion. The aim of this review is to provide a comprehensive overview of the most up-to-date biodata available and discuss the main microbial community features of biohydrogen engineered ecosystems, with a special emphasis on the crucial role of interactions and the relationships between species composition and ecosystem service. The elucidation of intricate relationships between community structure and ecosystem function would make possible to drive ecosystems toward an improved functionality on the basis of microbial ecology principles. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
Guiding bioprocess design by microbial ecology.

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Volmer, Jan; Schmid, Andreas; Bühler, Bruno

2015-06-01

Industrial bioprocess development is driven by profitability and eco-efficiency. It profits from an early stage definition of process and biocatalyst design objectives. Microbial bioprocess environments can be considered as synthetic technical microbial ecosystems. Natural systems follow Darwinian evolution principles aiming at survival and reproduction. Technical systems objectives are eco-efficiency, productivity, and profitable production. Deciphering technical microbial ecology reveals differences and similarities of natural and technical systems objectives, which are discussed in this review in view of biocatalyst and process design and engineering strategies. Strategies for handling opposing objectives of natural and technical systems and for exploiting and engineering natural properties of microorganisms for technical systems are reviewed based on examples. This illustrates the relevance of considering microbial ecology for bioprocess design and the potential for exploitation by synthetic biology strategies. Copyright © 2015 Elsevier Ltd. All rights reserved.
Microbial mat ecosystems: Structure types, functional diversity, and biotechnological application

Directory of Open Access Journals (Sweden)

Cristina M. Prieto-Barajas

2018-01-01

Full Text Available Microbial mats are horizontally stratified microbial communities, exhibiting a structure defined by physiochemical gradients, which models microbial diversity, physiological activities, and their dynamics as a whole system. These ecosystems are commonly associated with aquatic habitats, including hot springs, hypersaline ponds, and intertidal coastal zones and oligotrophic environments, all of them harbour phototrophic mats and other environments such as acidic hot springs or acid mine drainage harbour non-photosynthetic mats. This review analyses the complex structure, diversity, and interactions between the microorganisms that form the framework of different types of microbial mats located around the globe. Furthermore, the many tools that allow studying microbial mats in depth and their potential biotechnological applications are discussed.
Shifts of microbial communities of wheat (Triticum aestivum L.) cultivation in a closed artificial ecosystem.

Science.gov (United States)

Qin, Youcai; Fu, Yuming; Dong, Chen; Jia, Nannan; Liu, Hong

2016-05-01

The microbial communities of plant ecosystems are in relation to plant growing environment, but the alteration in biodiversity of rhizosphere and phyllosphere microbial communities in closed and controlled environments is unknown. The purpose of this study is to analyze the change regularity of microbial communities with wheat plants dependent-cultivated in a closed artificial ecosystem. The microbial community structures in closed-environment treatment plants were investigated by a culture-dependent approach, polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE), and Illumina Miseq high-throughput sequencing. The results indicated that the number of microbes decreased along with time, and the magnitude of bacteria, fungi, and actinomycetes were 10(7)-10(8), 10(5), and 10(3)-10(4) CFU/g (dry weight), respectively. The analysis of PCR-DGGE and Illumina Miseq revealed that the wheat leaf surface and near-root substrate had different microbial communities at different periods of wheat ecosystem development and showed that the relative highest diversity of microbial communities appeared at late and middle periods of the plant ecosystem, respectively. The results also indicated that the wheat leaf and substrate had different microbial community compositions, and the wheat substrate had higher richness of microbial community than the leaf. Flavobacterium, Pseudomonas, Paenibacillus, Enterobacter, Penicillium, Rhodotorula, Acremonium, and Alternaria were dominant in the wheat leaf samples, and Pedobacter, Flavobacterium, Halomonas, Marinobacter, Salinimicrobium, Lysobacter, Pseudomonas, Halobacillus, Xanthomonas, Acremonium, Monographella, and Penicillium were dominant populations in the wheat near-root substrate samples.
Synthetic biology for microbial production of lipid-based biofuels.

Science.gov (United States)

d'Espaux, Leo; Mendez-Perez, Daniel; Li, Rachel; Keasling, Jay D

2015-12-01

The risks of maintaining current CO2 emission trends have led to interest in producing biofuels using engineered microbes. Microbial biofuels reduce emissions because CO2 produced by fuel combustion is offset by CO2 captured by growing biomass, which is later used as feedstock for biofuel fermentation. Hydrocarbons found in petroleum fuels share striking similarity with biological lipids. Here we review synthetic metabolic pathways based on fatty acid and isoprenoid metabolism to produce alkanes and other molecules suitable as biofuels. We further discuss engineering strategies to optimize engineered biosynthetic routes, as well as the potential of synthetic biology for sustainable manufacturing. Published by Elsevier Ltd.
Synthetic biology for microbial production of lipid-based biofuels

Energy Technology Data Exchange (ETDEWEB)

d' Espaux, L; Mendez-Perez, D; Li, R; Keasling, JD

2015-10-23

The risks of maintaining current CO₂ emission trends have led to interest in producing biofuels using engineered microbes. Microbial biofuels reduce emissions because CO₂ produced by fuel combustion is offset by CO2 captured by growing biomass, which is later used as feedstock for biofuel fermentation. Hydrocarbons found in petroleum fuels share striking similarity with biological lipids. Here in this paper we review synthetic metabolic pathways based on fatty acid and isoprenoid metabolism to produce alkanes and other molecules suitable as biofuels. Lastly, we further discuss engineering strategies to optimize engineered biosynthetic routes, as well as the potential of synthetic biology for sustainable manufacturing.
Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning

Science.gov (United States)

Zhang, Ping; Wu, Linwei; Rocha, Andrea M.; Shi, Zhou; Wu, Bo; Qin, Yujia; Wang, Jianjun; Yan, Qingyun; Curtis, Daniel; Ning, Daliang; Van Nostrand, Joy D.; Wu, Liyou; Watson, David B.; Adams, Michael W. W.; Alm, Eric J.; Adams, Paul D.; Arkin, Adam P.

2018-01-01

ABSTRACT Contamination from anthropogenic activities has significantly impacted Earth’s biosphere. However, knowledge about how environmental contamination affects the biodiversity of groundwater microbiomes and ecosystem functioning remains very limited. Here, we used a comprehensive functional gene array to analyze groundwater microbiomes from 69 wells at the Oak Ridge Field Research Center (Oak Ridge, TN), representing a wide pH range and uranium, nitrate, and other contaminants. We hypothesized that the functional diversity of groundwater microbiomes would decrease as environmental contamination (e.g., uranium or nitrate) increased or at low or high pH, while some specific populations capable of utilizing or resistant to those contaminants would increase, and thus, such key microbial functional genes and/or populations could be used to predict groundwater contamination and ecosystem functioning. Our results indicated that functional richness/diversity decreased as uranium (but not nitrate) increased in groundwater. In addition, about 5.9% of specific key functional populations targeted by a comprehensive functional gene array (GeoChip 5) increased significantly (P contamination and ecosystem functioning. This study indicates great potential for using microbial functional genes to predict environmental contamination and ecosystem functioning. PMID:29463661
Diversity and Function of Microbial Community in Chinese Strong-Flavor Baijiu Ecosystem: A Review

Directory of Open Access Journals (Sweden)

Wei Zou

2018-04-01

Full Text Available Strong flavor baijiu (SFB, also called Luzhou-flavor liquor, is the most popular Chinese baijiu. It is manufactured via solid fermentation, with daqu as the starter. Microbial diversity of the SFB ecosystem and the synergistic effects of the enzymes and compounds produced by them are responsible for the special flavor and mouthfeel of SFB. The present review covers research studies focused on microbial community analysis of the SFB ecosystem, including the culturable microorganisms, their metabolic functions, microbial community diversity and their interactions. The review specifically emphasizes on the most recently conducted culture-independent analysis of SFB microbial community diversity. Furthermore, the possible application of systems biology approaches for elucidating the molecular mechanisms of SFB production were also reviewed and prospected.
Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning

Directory of Open Access Journals (Sweden)

Zhili He

2018-02-01

Full Text Available Contamination from anthropogenic activities has significantly impacted Earth’s biosphere. However, knowledge about how environmental contamination affects the biodiversity of groundwater microbiomes and ecosystem functioning remains very limited. Here, we used a comprehensive functional gene array to analyze groundwater microbiomes from 69 wells at the Oak Ridge Field Research Center (Oak Ridge, TN, representing a wide pH range and uranium, nitrate, and other contaminants. We hypothesized that the functional diversity of groundwater microbiomes would decrease as environmental contamination (e.g., uranium or nitrate increased or at low or high pH, while some specific populations capable of utilizing or resistant to those contaminants would increase, and thus, such key microbial functional genes and/or populations could be used to predict groundwater contamination and ecosystem functioning. Our results indicated that functional richness/diversity decreased as uranium (but not nitrate increased in groundwater. In addition, about 5.9% of specific key functional populations targeted by a comprehensive functional gene array (GeoChip 5 increased significantly (P < 0.05 as uranium or nitrate increased, and their changes could be used to successfully predict uranium and nitrate contamination and ecosystem functioning. This study indicates great potential for using microbial functional genes to predict environmental contamination and ecosystem functioning.
Microbial diversity in sediment ecosystems (evaporites domes, microbial mats and crusts of hypersaline Laguna Tebenquiche, Salar de Atacama, Chile

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Ana Beatriz Fernandez

2016-08-01

Full Text Available We combined nucleic acid-based molecular methods, biogeochemical measurements and physicochemical characteristics to investigate microbial sedimentary ecosystems of Laguna Tebenquiche, Atacama Desert, Chile. Molecular diversity and biogeochemistry of hypersaline microbial mats, rhizome-associated concretions and an endoevaporite were compared with: The V4 hypervariable region of the 16S rRNA gene was amplified by pyrosequencing to analyze the total microbial diversity (i.e., bacteria and archaea in bulk samples and, in addition, in detail on a millimeter scale in one microbial mat and in one evaporite. Archaea were more abundant than bacteria. Euryarchaeota was one of the most abundant phyla in all samples, and particularly dominant (97% of total diversity in the most lithified ecosystem, the evaporite. Most of the euryarchaeal OTUs could be assigned to the class Halobacteria or anaerobic and methanogenic archaea. Planctomycetes potentially also play a key role in mats and rhizome-associated concretions, notably the aerobic organoheterotroph members of the class Phycisphaerae. In addition to cyanobacteria, members of Chromatiales and possibly the candidate family Chlorotrichaceae contributed to photosynthetic carbon fixation. Other abundant uncultured taxa such as the candidate division MSBL1, the uncultured MBGB and the phylum Acetothermia potentially play an important metabolic role in these ecosystems. Lithifying microbial mats contained calcium carbonate precipitates, whereas endoevoporites consisted of gypsum and halite. Biogeochemical measurements revealed that based on depth profiles of O2 and sulfide, metabolic activities were much higher in the non-lithifying mat (peaking in the least lithified systems than in lithifying mats with the lowest activity in endoevaporites. This trend in decreasing microbial activity reflects the increase in salinity, which may play an important role in the biodiversity.
Social interaction in synthetic and natural microbial communities.

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Xavier, Joao B

2011-04-12

Social interaction among cells is essential for multicellular complexity. But how do molecular networks within individual cells confer the ability to interact? And how do those same networks evolve from the evolutionary conflict between individual- and population-level interests? Recent studies have dissected social interaction at the molecular level by analyzing both synthetic and natural microbial populations. These studies shed new light on the role of population structure for the evolution of cooperative interactions and revealed novel molecular mechanisms that stabilize cooperation among cells. New understanding of populations is changing our view of microbial processes, such as pathogenesis and antibiotic resistance, and suggests new ways to fight infection by exploiting social interaction. The study of social interaction is also challenging established paradigms in cancer evolution and immune system dynamics. Finding similar patterns in such diverse systems suggests that the same 'social interaction motifs' may be general to many cell populations.
Soil Microbial Activity Responses to Fire in a Semi-arid Savannah Ecosystem Pre- and Post-Monsoon Season

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Jimenez, J. R.; Raub, H. D.; Jong, E. L.; Muscarella, C. R.; Smith, W. K.; Gallery, R. E.

2017-12-01

Extracellular enzyme activities (EEA) of soil microorganisms can act as important proxies for nutrient limitation and turnover in soil and provide insight into the biochemical requirements of microbes in terrestrial ecosystems. In semi-arid ecosystems, microbial activity is influenced by topography, disturbances such as fire, and seasonality from monsoon rains. Previous studies from forest ecosystems show that microbial communities shift to similar compositions after severe fires despite different initial conditions. In semi-arid ecosystems with high spatial heterogeniety, we ask does fire lead to patch intensification or patch homogenization and how do monsoon rains influence the successional trajectories of microbial responses? We analyzed microbial activity and soil biogeochemistry throughout the monsoon season in paired burned and unburned sites in the Santa Rita Experimental Range, AZ. Surface soil (5cm) from bare-ground patches, bole, canopy drip line, and nearby grass patches for 5 mesquite trees per site allowed tests of spatiotemporal responses to fire and monsoon rain. Microbial activity was low during the pre-monsoon season and did not differ between the burned and unburned sites. We found greater activity near mesquite trees that reflects soil water and nutrient availability. Fire increased soil alkalinity, though soils near mesquite trees were less affected. Soil water content was significantly higher in the burned sites post-monsoon, potentially reflecting greater hydrophobicity of burned soils. Considering the effects of fire in these semi-arid ecosystems is especially important in the context of the projected changing climate regime in this region. Assessing microbial community recovery pre-, during, and post-monsoon is important for testing predictions about whether successional pathways post-fire lead to recovery or novel trajectories of communities and ecosystem function.
Synthetic Microbial Ecology: Engineering Habitats for Modular Consortia.

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Ben Said, Sami; Or, Dani

2017-01-01

The metabolic diversity present in microbial communities enables cooperation toward accomplishing more complex tasks than possible by a single organism. Members of a consortium communicate by exchanging metabolites or signals that allow them to coordinate their activity through division of labor. In contrast with monocultures, evidence suggests that microbial consortia self-organize to form spatial patterns, such as observed in biofilms or in soil aggregates, that enable them to respond to gradient, to improve resource interception and to exchange metabolites more effectively. Current biotechnological applications of microorganisms remain rudimentary, often relying on genetically engineered monocultures (e.g., pharmaceuticals) or mixed-cultures of partially known composition (e.g., wastewater treatment), yet the vast potential of "microbial ecological power" observed in most natural environments, remains largely underused. In line with the Unified Microbiome Initiative (UMI) which aims to "discover and advance tools to understand and harness the capabilities of Earth's microbial ecosystems," we propose in this concept paper to capitalize on ecological insights into the spatial and modular design of interlinked microbial consortia that would overcome limitations of natural systems and attempt to optimize the functionality of the members and the performance of the engineered consortium. The topology of the spatial connections linking the various members and the regulated fluxes of media between those modules, while representing a major engineering challenge, would allow the microbial species to interact. The modularity of such spatially linked microbial consortia (SLMC) could facilitate the design of scalable bioprocesses that can be incorporated as parts of a larger biochemical network. By reducing the need for a compatible growth environment for all species simultaneously, SLMC will dramatically expand the range of possible combinations of microorganisms and their
Soil microbial communities drive the resistance of ecosystem multifunctionality to global change in drylands across the globe.

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Delgado-Baquerizo, Manuel; Eldridge, David J; Ochoa, Victoria; Gozalo, Beatriz; Singh, Brajesh K; Maestre, Fernando T

2017-10-01

The relationship between soil microbial communities and the resistance of multiple ecosystem functions linked to C, N and P cycling (multifunctionality resistance) to global change has never been assessed globally in natural ecosystems. We collected soils from 59 dryland ecosystems worldwide to investigate the importance of microbial communities as predictor of multifunctionality resistance to climate change and nitrogen fertilisation. Multifunctionality had a lower resistance to wetting-drying cycles than to warming or N deposition. Multifunctionality resistance was regulated by changes in microbial composition (relative abundance of phylotypes) but not by richness, total abundance of fungi and bacteria or the fungal: bacterial ratio. Our results suggest that positive effects of particular microbial taxa on multifunctionality resistance could potentially be controlled by altering soil pH. Together, our work demonstrates strong links between microbial community composition and multifunctionality resistance in dryland soils from six continents, and provides insights into the importance of microbial community composition for buffering effects of global change in drylands worldwide. © 2017 John Wiley & Sons Ltd/CNRS.
Linking microbial and ecosystem ecology using ecological stoichiometry: a synthesis of conceptual and empirical approaches

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Hall, E.K.; Maixner, F.; Franklin, O.; Daims, H.; Richter, A.; Battin, T.

2011-01-01

Currently, one of the biggest challenges in microbial and ecosystem ecology is to develop conceptual models that organize the growing body of information on environmental microbiology into a clear mechanistic framework with a direct link to ecosystem processes. Doing so will enable development of testable hypotheses to better direct future research and increase understanding of key constraints on biogeochemical networks. Although the understanding of phenotypic and genotypic diversity of microorganisms in the environment is rapidly accumulating, how controls on microbial physiology ultimately affect biogeochemical fluxes remains poorly understood. We propose that insight into constraints on biogeochemical cycles can be achieved by a more rigorous evaluation of microbial community biomass composition within the context of ecological stoichiometry. Multiple recent studies have pointed to microbial biomass stoichiometry as an important determinant of when microorganisms retain or recycle mineral nutrients. We identify the relevant cellular components that most likely drive changes in microbial biomass stoichiometry by defining a conceptual model rooted in ecological stoichiometry. More importantly, we show how X-ray microanalysis (XRMA), nanoscale secondary ion mass spectroscopy (NanoSIMS), Raman microspectroscopy, and in situ hybridization techniques (for example, FISH) can be applied in concert to allow for direct empirical evaluation of the proposed conceptual framework. This approach links an important piece of the ecological literature, ecological stoichiometry, with the molecular front of the microbial revolution, in an attempt to provide new insight into how microbial physiology could constrain ecosystem processes.
Mammalian engineers drive soil microbial communities and ecosystem functions across a disturbance gradient.

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Eldridge, David J; Delgado-Baquerizo, Manuel; Woodhouse, Jason N; Neilan, Brett A

2016-11-01

The effects of mammalian ecosystem engineers on soil microbial communities and ecosystem functions in terrestrial ecosystems are poorly known. Disturbance from livestock has been widely reported to reduce soil function, but disturbance by animals that forage in the soil may partially offset these negative effects of livestock, directly and/or indirectly by shifting the composition and diversity of soil microbial communities. Understanding the role of disturbance from livestock and ecosystem engineers in driving soil microbes and functions is essential for formulating sustainable ecosystem management and conservation policies. We compared soil bacterial community composition and enzyme concentrations within four microsites: foraging pits of two vertebrates, the indigenous short-beaked echidna (Tachyglossus aculeatus) and the exotic European rabbit (Oryctolagus cuniculus), and surface and subsurface soils along a gradient in grazing-induced disturbance in an arid woodland. Microbial community composition varied little across the disturbance gradient, but there were substantial differences among the four microsites. Echidna pits supported a lower relative abundance of Acidobacteria and Cyanobacteria, but a higher relative abundance of Proteobacteria than rabbit pits and surface microsites. Moreover, these microsite differences varied with disturbance. Rabbit pits had a similar profile to the subsoil or the surface soils under moderate and high, but not low disturbance. Overall, echidna foraging pits had the greatest positive effect on function, assessed as mean enzyme concentrations, but rabbits had the least. The positive effects of echidna foraging on function were indirectly driven via microbial community composition. In particular, increasing activity was positively associated with increasing relative abundance of Proteobacteria, but decreasing Acidobacteria. Our study suggests that soil disturbance by animals may offset, to some degree, the oft-reported negative
Earth's Earliest Ecosystems in the C: The Use of Microbial Mats to Demonstrate General Principles of Scientific Inquiry and Microbial Ecology

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Bebout, Brad M.; Bucaria, Robin

2006-01-01

Microbial mats are living examples of the most ancient biological communities on Earth. As Earth's earliest ecosystems, they are centrally important to understanding the history of life on our planet and are useful models for the search for life elsewhere. As relatively compact (but complete) ecosystems, microbial mats are also extremely useful for educational activities. Mats may be used to demonstrate a wide variety of concepts in general and microbial ecology, including the biogeochemical cycling of elements, photosynthesis and respiration, and the origin of the Earth's present oxygen containing atmosphere. Microbial mats can be found in a number of common environments accessible to teachers, and laboratory microbial mats can be constructed using materials purchased from biological supply houses. With funding from NASA's Exobiology program, we have developed curriculum and web-based activities centered on the use of microbial mats as tools for demonstrating general principles in ecology, and the scientific process. Our web site (http://microbes.arc.nasa.gov) includes reference materials, lesson plans, and a "Web Lab", featuring living mats maintained in a mini-aquarium. The site also provides information as to how research on microbial mats supports NASA's goals, and various NASA missions. A photo gallery contains images of mats, microscopic views of the organisms that form them, and our own research activities. An animated educational video on the web site uses computer graphic and video microscopy to take students on a journey into a microbial mat. These activities are targeted to a middle school audience and are aligned with the National Science Standards.
From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems.

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Garza, Daniel R; Dutilh, Bas E

2015-11-01

Microorganisms and the viruses that infect them are the most numerous biological entities on Earth and enclose its greatest biodiversity and genetic reservoir. With strength in their numbers, these microscopic organisms are major players in the cycles of energy and matter that sustain all life. Scientists have only scratched the surface of this vast microbial world through culture-dependent methods. Recent developments in generating metagenomes, large random samples of nucleic acid sequences isolated directly from the environment, are providing comprehensive portraits of the composition, structure, and functioning of microbial communities. Moreover, advances in metagenomic analysis have created the possibility of obtaining complete or nearly complete genome sequences from uncultured microorganisms, providing important means to study their biology, ecology, and evolution. Here we review some of the recent developments in the field of metagenomics, focusing on the discovery of genetic novelty and on methods for obtaining uncultured genome sequences, including through the recycling of previously published datasets. Moreover we discuss how metagenomics has become a core scientific tool to characterize eco-evolutionary patterns of microbial ecosystems, thus allowing us to simultaneously discover new microbes and study their natural communities. We conclude by discussing general guidelines and challenges for modeling the interactions between uncultured microorganisms and viruses based on the information contained in their genome sequences. These models will significantly advance our understanding of the functioning of microbial ecosystems and the roles of microbes in the environment.

Microbial Community Activity And Plant Biomass Are Insensitive To Passive Warming In A Semiarid Ecosystem

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Espinosa, N. J.; Fehmi, J. S.; Rasmussen, C.; Gallery, R. E.

2017-12-01

Soil microorganisms drive biogeochemical and nutrient cycling through the production of extracellular enzymes that facilitate organic matter decomposition and the flux of large amounts of carbon dioxide to the atmosphere. Although dryland ecosystems occupy over 40% of land cover and are projected to expand due to climate change, much of our current understanding of these processes comes from mesic temperate ecosystems. Understanding the responses of these globally predominant dryland ecosystems is therefore important yet complicated by co-occurring environmental changes. For example, the widespread and pervasive transition from grass to woody dominated landscapes is changing the hydrology, fire regimes, and carbon storage potential of semiarid ecosystems. In this study, we used a novel passive method of warming to conduct a warming experiment with added plant debris as either woodchip or biochar, to simulate different long-term carbon additions that accompany woody plant encroachment in semiarid ecosystems. The response of heterotrophic respiration, plant biomass, and microbial activity was monitored bi-annually. We hypothesized that the temperature manipulations would have direct and indirect effects on microbial activity. Warmer soils directly reduce the activity of soil extracellular enzymes through denaturation and dehydration of soil pores and indirectly through reducing microbe-available substrates and plant inputs. Overall, reduction in extracellular enzyme activity may reduce decomposition of coarse woody debris and potentially enhance soil carbon storage in semiarid ecosystems. For all seven hydrolytic enzymes examined as well as heterotrophic respiration, there was no consistent or significant response to experimental warming, regardless of seasonal climatic and soil moisture variation. The enzyme results observed here are consistent with the few other experimental results for warming in semiarid ecosystems and indicate that the controls over soil
Linking Soil Microbial Ecology to Ecosystem Functioning in Integrated Crop-Livestock Systems

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Enhanced soil stability, nutrient cycling and C sequestration potential are important ecosystem functions driven by soil microbial processes and are directly influenced by agricultural management. Integrated crop-livestock agroecosystems (ICL) can enhance these functions via high-residue returning c...
Soil microbial responses to nitrogen addition in arid ecosystems

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Robert L Sinsabaugh

2015-08-01

Full Text Available The N cycle of arid ecosystems is influenced by low soil organic matter, high soil pH and extremes in water potential and temperature that lead to open canopies and development of biological soil crusts (biocrusts. We investigated the effects of N amendment on soil microbial dynamics in a Larrea tridentata-Ambrosia dumosa shrubland site in southern Nevada USA. Sites were fertilized with a NO3-NH4 mix at 0, 7, and 15 kg ha-1 yr-1 from March 2012 to March 2013. In March 2013, biocrust (0-0.5 cm and bulk soils (0-10 cm were collected beneath Ambrosia canopies and in the interspaces between plants. Biomass responses were assessed as bacterial and fungal SSU rRNA gene copy number and chlorophyll a concentration. Metabolic responses were measured by five ecoenzyme activities (EEA and rates of N transformation. By most measures, nutrient availability, microbial biomass and process rates were greater in soils beneath the shrub canopy compared to the interspace between plants, and greater in the surface biocrust horizon compared to the deeper 10 cm soil profile. Most measures responded positively to experimental N addition. Effect sizes were generally greater for bulk soil than biocrust. Results were incorporated into a meta-analysis of arid ecosystem responses to N.
Stimulation of microbial nitrogen cycling in aquatic ecosystems by benthic macrofauna: mechanisms and environmental implications

OpenAIRE

P. Stief

2013-01-01

Invertebrate animals that live at the bottom of aquatic ecosystems (i.e., benthic macrofauna) are important mediators between nutrients in the water column and microbes in the benthos. The presence of benthic macrofauna stimulates microbial nutrient dynamics through different types of animal–microbe interactions, which potentially affect the trophic status of aquatic ecosystems. This review contrasts three types of animal–microbe interactions in the benthos of aquatic ecosystems: (i) e...
Microbial Communities in the Vertical Atmosphere: Effects of Urbanization and the Natural Environment in Four North American Ecosystems

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Docherty, K. M.; Lemmer, K. M.; Domingue, K. D.; Spring, A.; Kerber, T. V.; Mooney, M. M.

2017-12-01

Airborne transport of microbial communities is a key component of the global ecosystem because it serves as a mechanism for dispersing microbial life between all surface habitats on the planet. However, most of our understanding of airborne microbial distribution is derived from samples collected near the ground. Little is understood about how the vertical layers of the air may act as a habitat filter or how local terrestrial ecosystems contribute to a vast airborne microbial seedbank. Specifically, urbanization may fundamentally alter the terrestrial sources of airborne microbial biodiversity. To address this question, we conducted airborne sampling at minimally disturbed natural sites and paired urban sites in 4 different North American ecosystems: shortgrass steppe, desert scrub, eastern deciduous forest, and northern mesic forest. All natural area sites were co-located with NEON/Ameriflux tower sites collecting atmospheric data. We developed an airborne sampling platform that uses tethered helikites at 3 replicate locations within each ecosystem to launch remote-controlled sampler payloads. We designed sampler payloads to collect airborne bacteria and fungi from 150, 30 and 2 m above the ground. Payload requirements included: ability to be disinfected and remain contaminant-free during transport, remote open/close functionality, payload weight under 6 lbs and automated collection of weather data. After sampling for 6 hours at each location, we extracted DNA collected by the samplers. We also extracted DNA from soil and plant samples collected from each location, and characterized ground vegetation. We conducted bacterial 16S amplicon-based sequencing using Mi-Seq and sequence analysis using QIIME. We used ArcGIS to determine percent land use coverage. Our results demonstrate that terrestrial ecosystem type is the most important factor contributing to differences in airborne bacterial community composition, and that communities differed by ecosystem. The
Microbial characterization of toluene-degrading denitrifying consortia obtained from terrestrial and marine ecosystems.

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An, Y-J; Joo, Y-H; Hong, I-Y; Ryu, H-W; Cho, K-S

2004-10-01

The degradation characteristics of toluene coupled to nitrate reduction were investigated in enrichment culture and the microbial communities of toluene-degrading denitrifying consortia were characterized by denaturing gradient gel electrophoresis (DGGE) technique. Anaerobic nitrate-reducing bacteria were enriched from oil-contaminated soil samples collected from terrestrial (rice field) and marine (tidal flat) ecosystems. Enriched consortia degraded toluene in the presence of nitrate as a terminal electron acceptor. The degradation rate of toluene was affected by the initial substrate concentration and co-existence of other hydrocarbons. The types of toluene-degrading denitrifying consortia depended on the type of ecosystem. The clone RS-7 obtained from the enriched consortium of the rice field was most closely related to a toluene-degrading and denitrifying bacterium, Azoarcus denitrificians (A. tolulyticus sp. nov.). The clone TS-11 detected in the tidal flat enriched consortium was affiliated to Thauera sp. strain S2 (T. aminoaromatica sp. nov.) that was able to degrade toluene under denitrifying conditions. This indicates that environmental factors greatly influence microbial communities obtained from terrestrial (rice field) and marine (tidal flat) ecosystems.
Recent progress in synthetic biology for microbial production of C3-C10 alcohols

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Edna N. Lamsen

2012-06-01

Full Text Available The growing need to address current energy and environmental problems has sparked an interest in developing improved biological methods to produce liquid fuels from renewable sources. While microbial ethanol production is well established, higher chain alcohols possess chemical properties that are more similar to gasoline. Unfortunately, these alcohols (except 1-butanol are not produced efficiently in natural microorganisms, and thus economical production in industrial volumes remains a challenge. Synthetic biology, however, offers additional tools to engineer synthetic pathways in user-friendly hosts to help increase titers and productivity of these advanced biofuels. This review concentrates on recent developments in synthetic biology to produce higher-chain alcohols as viable renewable replacements for traditional fuel.
Microbial community dynamics and transformation of vascular plant detritus in two wetland ecosystems

International Nuclear Information System (INIS)

Moran, M.A.

1987-01-01

The microbial ecology of two wetland ecosystems in southeastern Georgia, USA, was studied with respect to microbial community dynamics and microbially-mediated transformations of vascular plant detritus. In the Okefenokee Swamp, biomass of microorganisms in the water column and sediments was generally lower in winter months and higher during spring and summer. Biomass and activity (measured as 14 C-lignocellulose mineralization) differed significantly among five habitats within the Okefenokee, and also among locations within each habitat. Significant heterogeneity in the structure of Okefenokee microbial communities was found at scales from 30 cm to 150 m. In field and laboratory studies of vascular plant decomposition in the Okefenokee and a salt marsh on Sapelo Island, the mathematical model which best describes decomposition kinetics is the decaying coefficient model
Spies and Bloggers: New Synthetic Biology Tools to Understand Microbial Processes in Soils and Sediments

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Masiello, C. A.; Silberg, J. J.; Cheng, H. Y.; Del Valle, I.; Fulk, E. M.; Gao, X.; Bennett, G. N.

2017-12-01

Microbes can be programmed through synthetic biology to report on their behavior, informing researchers when their environment has triggered changes in their gene expression (e.g. in response to shifts in O2 or H2O), or when they have participated in a specific step of an elemental cycle (e.g. denitrification). This use of synthetic biology has the potential to significantly improve our understanding of microbes' roles in elemental and water cycling, because it allows reporting on the environment from the perspective of a microbe, matching the measurement scale exactly to the scale that a microbe experiences. However, synthetic microbes have not yet seen wide use in soil and sediment laboratory experiments because synthetic organisms typically report by fluorescing, making their signals difficult to detect outside the petri dish. We are developing a new suite of microbial programs that report instead by releasing easily-detected gases, allowing the real-time, noninvasive monitoring of behaviors in sediments and soils. Microbial biosensors can, in theory, be programmed to detect dynamic processes that contribute to a wide range of geobiological processes, including C cycling (biofilm production, methanogenesis, and synthesis of extracellular enzymes that degrade organic matter), N cycling (expression of enzymes that underlie different steps of the N cycle) and potentially S cycling. We will provide an overview of the potential uses of gas-reporting biosensors in soil and sediment lab experiments, and will report the development of the systematics of these sensors. Successful development of gas biosensors for laboratory use will require addressing issues including: engineering the intensity and selectivity of microbial gas production to maximize the signal to noise ratio; normalizing the gas reporter signal to cell population size, managing gas diffusion effects on signal shape; and developing multiple gases that can be used in parallel.
Microbial communities, processes and functions in acid mine drainage ecosystems.

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Chen, Lin-xing; Huang, Li-nan; Méndez-García, Celia; Kuang, Jia-liang; Hua, Zheng-shuang; Liu, Jun; Shu, Wen-sheng

2016-04-01

Acid mine drainage (AMD) is generated from the oxidative dissolution of metal sulfides when water and oxygen are available largely due to human mining activities. This process can be accelerated by indigenous microorganisms. In the last several decades, culture-dependent researches have uncovered and validated the roles of AMD microorganisms in metal sulfides oxidation and acid generation processes, and culture-independent studies have largely revealed the diversity and metabolic potentials and activities of AMD communities, leading towards a full understanding of the microbial diversity, functions and interactions in AMD ecosystems. This review describes the diversity of microorganisms and their functions in AMD ecosystems, and discusses their biotechnological applications in biomining and AMD bioremediation according to their capabilities. Copyright © 2016 Elsevier Ltd. All rights reserved.
Effect of peristalsis in balance of intestinal microbial ecosystem

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Mirbagheri, Seyed Amir; Fu, Henry C.

2017-11-01

A balance of microbiota density in gastrointestinal tracts is necessary for health of the host. Although peristaltic flow made by intestinal muscles is constantly evacuating the lumen, bacterial density stay balanced. Some of bacteria colonize in the secreted mucus where there is no flow, but the rest resist the peristaltic flow in lumen and maintain their population. Using a coupled two-dimensional model of flow induced by large amplitude peristaltic waves, bacterial motility, reproduction, and diffusion, we address how bacterial growth and motility combined with peristaltic flow affect the balance of the intestinal microbial ecosystem.
Effect of salinity on carbon and sulfur cycles in Umm Alhool sabkha microbial mat ecosystem in Qatar

KAUST Repository

Alnajjar, Mohammad Ahmad

2012-10-19

Microbial mats are only present under extreme conditions, where grazing by higher organisms is limited. Therefore, microbial mats may provide insight into extraterrestrial life, due to their adaptations to extreme temperatures, desiccation or salinity. They are faced with a diurnal cycle with variable length based on their location, which exposes them to extreme salinity conditions (i.e., water withdrawal and high evaporation). Cyanobacteria in the photic zone of a mat ecosystem supply the other microorganism with the required organic material to produce energy and grow. Subsequently, this will reproduce the nutrients needed by the phototrophs through elemental re-mineralization. In this work, we investigated the effect of water salinity that covers the microbial mat ecosystem of Umm Alhool sabkha, Qatar, regarding the most important processes within microbial mats: photosynthesis and sulfate reduction (SR). Our results showed that both photosynthetic and sulfate reduction rates decreased with increasing the salinity. The microbial community structure, assessed by 454 pyro-sequencing, revealed that the cyanobacterial community structure changed in response to the change in salinity. This was not the case for the sulfate reducer community structure, which stayed as it is in the mats incubated at different salinities. Therefore, we speculate that salinity affects the photosynthetic community structure, and consequently affects the photosynthetic activity of the whole ecosystem. However, sulfate reduction rates decreased due to less organic material supply from the upper layers and not due to change in microbial community structure of SR. Other factors such as the activity of the enzymes could also have an effect on SRR, but it was not investigated in this study.
Effect of ecosystems substitutions and CO{sub 2} increase of the atmosphere on the microbial ecosystems of forests; Effet de substitutions d'essence et de l'augmentation en CO{sub 2} de l'atmosphere sur les communautes microbiennes intervenant dans le fonctionnement d'un ecosysteme forestier

Energy Technology Data Exchange (ETDEWEB)

Martin, F

2007-07-01

Biological diversity is often exclusively considered at the level of plants and animals, whereas the bulk of global biodiversity is in fact at the microbial level. Although it is clear that the ecology of our planet is driven by microbial ecosystems, we are severely hampered by our limited understanding of the diversity and function of such microbial ecosystems. In the present project, teams in the disciplines of geochemistry, soil microbiology, genomics and ecosystem processes are assembled to study the relationship between environmental change, land use changes, biodiversity, and functioning of forest ecosystems. The network has a strong focus on developing and applying biochemical and genotyping methodologies to address key scientific issues in soil microbial ecology. These include assessing the impact of environmental- and land use changes on microbial diversity and function and exploring the evolutionary and mechanistic links between biological diversity and ecosystem function. In the present study, we have shown that: (1) The native mixed forest showed the highest microbial diversity (2) The mono specific plantations of tree species (e.g., oak, beech, pine, spruce) strikingly alter genetic and functional diversities of soil bacterial and fungal species. (3) Bacterial denitrification rates were dramatically modified by the planted species. Only by taking into account the impact of forest management on below-ground microbial diversity can one hope to get a full ecosystem-based understanding, and this must be addressed via modelling in order to provide relevant and useful information for conservation and policy making. (author)
Population cycles and species diversity in dynamic Kill-the-Winner model of microbial ecosystems

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Maslov, Sergei; Sneppen, Kim

2017-01-01

Determinants of species diversity in microbial ecosystems remain poorly understood. Bacteriophages are believed to increase the diversity by the virtue of Kill-the-Winner infection bias preventing the fastest growing organism from taking over the community. Phage-bacterial ecosystems are traditionally described in terms of the static equilibrium state of Lotka-Volterra equations in which bacterial growth is exactly balanced by losses due to phage predation. Here we consider a more dynamic scenario in which phage infections give rise to abrupt and severe collapses of bacterial populations whenever they become sufficiently large. As a consequence, each bacterial population in our model follows cyclic dynamics of exponential growth interrupted by sudden declines. The total population of all species fluctuates around the carrying capacity of the environment, making these cycles cryptic. While a subset of the slowest growing species in our model is always driven towards extinction, in general the overall ecosystem diversity remains high. The number of surviving species is inversely proportional to the variation in their growth rates but increases with the frequency and severity of phage-induced collapses. Thus counter-intuitively we predict that microbial communities exposed to more violent perturbations should have higher diversity. PMID:28051127
Impact of Transgenic Brassica napus Harboring the Antifungal Synthetic Chitinase (NiC Gene on Rhizosphere Microbial Diversity and Enzyme Activities

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Mohammad S. Khan

2017-07-01

Full Text Available Transgenic Brassica napus harboring the synthetic chitinase (NiC gene exhibits broad-spectrum antifungal resistance. As the rhizosphere microorganisms play an important role in element cycling and nutrient transformation, therefore, biosafety assessment of NiC containing transgenic plants on soil ecosystem is a regulatory requirement. The current study is designed to evaluate the impact of NiC gene on the rhizosphere enzyme activities and microbial community structure. The transgenic lines with the synthetic chitinase gene (NiC showed resistance to Alternaria brassicicola, a common disease causing fungal pathogen. The rhizosphere enzyme analysis showed no significant difference in the activities of fivesoil enzymes: alkalyine phosphomonoestarase, arylsulphatase, β-glucosidase, urease and sucrase between the transgenic and non-transgenic lines of B. napus varieties, Durr-e-NIFA (DN and Abasyne-95 (AB-95. However, varietal differences were observed based on the analysis of molecular variance. Some individual enzymes were significantly different in the transgenic lines from those of non-transgenic but the results were not reproducible in the second trail and thus were considered as environmental effect. Genotypic diversity of soil microbes through 16S–23S rRNA intergenic spacer region amplification was conducted to evaluate the potential impact of the transgene. No significant diversity (4% for bacteria and 12% for fungal between soil microbes of NiC B. napus and the non-transgenic lines was found. However, significant varietal differences were observed between DN and AB-95 with 79% for bacterial and 54% for fungal diversity. We conclude that the NiC B. napus lines may not affect the microbial enzyme activities and community structure of the rhizosphere soil. Varietal differences might be responsible for minor changes in the tested parameters.
The perils and promises of microbial abundance: novel natures and model ecosystems, from artisanal cheese to alien seas.

Science.gov (United States)

Paxson, Heather; Helmreich, Stefan

2014-04-01

Microbial life has been much in the news. From outbreaks of Escherichia coli to discussions of the benefits of raw and fermented foods to recent reports of life forms capable of living in extreme environments, the modest microbe has become a figure for thinking through the presents and possible futures of nature, writ large as well as small. Noting that dominant representations of microbial life have shifted from an idiom of peril to one of promise, we argue that microbes--especially when thriving as microbial communities--are being upheld as model ecosystems in a prescriptive sense, as tokens of how organisms and human ecological relations with them could, should, or might be. We do so in reference to two case studies: the regulatory politics of artisanal cheese and the speculative research of astrobiology. To think of and with microbial communities as model ecosystems offers a corrective to the scientific determinisms we detect in some recent calls to attend to the materiality of scientific objects.
Soil microbial metabolic quotient (qCO2) of twelve ecosystems of Mt. Kilimanjaro

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Pabst, Holger; Gerschlauer, Friederike; Kiese, Ralf; Kuzyakov, Yakov

2014-05-01

Soil organic carbon, microbial biomass carbon (MBC) and the metabolic quotient qCO2 - as sensitive and important parameters for soil fertility and C turnover - are strongly affected by land-use changes all over the world. These effects are particularly distinct upon conversion of natural to agricultural ecosystems due to very fast carbon (C) and nutrient cycles and high vulnerability, especially in the tropics. In this study, we used an elevational gradient on Mt. Kilimanjaro to investigate the effects of land-use change and elevation on Corg, MBC and qCO2. Down to a soil depth of 18 cm we compared 4 natural (Helichrysum, Erica forest, Podocarpus forest, Ocotea forest), 5 seminatural (disturbed Podocarpus forest, disturbed Ocotea forest, lower montane forest, grassland, savannah), 1 sustainably used (homegarden) and 2 intensively used ecosystems (coffee plantation, maize field) on an elevation gradient from 950 to 3880 m a.s.l.. Using an incubation device, soil CO2-efflux of 18 cm deep soil cores was measured under field moist conditions and mean annual temperature. MBC to Corg ratios varied between 0.7 and 2.3%. qCO2 increased with magnitude of the disturbance, albeit this effect decreased with elevation. Following the annual precipitation of the ecosystems, both, Corg and MBC showed a hum-shaped distribution with elevation, whereas their maxima were between 2500 and 3000 m a.s.l.. Additionaly, Corg and MBC contents were significantly reduced in intensively used agricultural systems. We conclude that the soil microbial biomass and its activity in Mt. Kilimanjaro ecosystems are strongly altered by land-use. This effect is more distinct in lower than in higher elevated ecosystems and strongly dependent on the magnitude of disturbance.
Mapping microbial ecosystems and spoilage-gene flow in breweries highlights patterns of contamination and resistance.

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Bokulich, Nicholas A; Bergsveinson, Jordyn; Ziola, Barry; Mills, David A

2015-03-10

Distinct microbial ecosystems have evolved to meet the challenges of indoor environments, shaping the microbial communities that interact most with modern human activities. Microbial transmission in food-processing facilities has an enormous impact on the qualities and healthfulness of foods, beneficially or detrimentally interacting with food products. To explore modes of microbial transmission and spoilage-gene frequency in a commercial food-production scenario, we profiled hop-resistance gene frequencies and bacterial and fungal communities in a brewery. We employed a Bayesian approach for predicting routes of contamination, revealing critical control points for microbial management. Physically mapping microbial populations over time illustrates patterns of dispersal and identifies potential contaminant reservoirs within this environment. Habitual exposure to beer is associated with increased abundance of spoilage genes, predicting greater contamination risk. Elucidating the genetic landscapes of indoor environments poses important practical implications for food-production systems and these concepts are translatable to other built environments.
Burning fire-prone Mediterranean shrublands: immediate changes in soil microbial community structure and ecosystem functions.

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Goberna, M; García, C; Insam, H; Hernández, M T; Verdú, M

2012-07-01

Wildfires subject soil microbes to extreme temperatures and modify their physical and chemical habitat. This might immediately alter their community structure and ecosystem functions. We burned a fire-prone shrubland under controlled conditions to investigate (1) the fire-induced changes in the community structure of soil archaea, bacteria and fungi by analysing 16S or 18S rRNA gene amplicons separated through denaturing gradient gel electrophoresis; (2) the physical and chemical variables determining the immediate shifts in the microbial community structure; and (3) the microbial drivers of the change in ecosystem functions related to biogeochemical cycling. Prokaryotes and eukaryotes were structured by the local environment in pre-fire soils. Fire caused a significant shift in the microbial community structure, biomass C, respiration and soil hydrolases. One-day changes in bacterial and fungal community structure correlated to the rise in total organic C and NO(3)(-)-N caused by the combustion of plant residues. In the following week, bacterial communities shifted further forced by desiccation and increasing concentrations of macronutrients. Shifts in archaeal community structure were unrelated to any of the 18 environmental variables measured. Fire-induced changes in the community structure of bacteria, rather than archaea or fungi, were correlated to the enhanced microbial biomass, CO(2) production and hydrolysis of C and P organics. This is the first report on the combined effects of fire on the three biological domains in soils. We concluded that immediately after fire the biogeochemical cycling in Mediterranean shrublands becomes less conservative through the increased microbial biomass, activity and changes in the bacterial community structure.
Bioremediation in marine ecosystems: a computational study combining ecological modelling and flux balance analysis

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Marianna eTaffi

2014-09-01

Full Text Available The pressure to search effective bioremediation methodologies for contaminated ecosystems has led to the large-scale identification of microbial species and metabolic degradation pathways. However, minor attention has been paid to the study of bioremediation in marine food webs and to the definition of integrated strategies for reducing bioaccumulation in species. We propose a novel computational framework for analysing the multiscale effects of bioremediation at the ecosystem level, based on coupling food web bioaccumulation models and metabolic models of degrading bacteria. The combination of techniques from synthetic biology and ecological network analysis allows the specification of arbitrary scenarios of contaminant removal and the evaluation of strategies based on natural or synthetic microbial strains.In this study, we derive a bioaccumulation model of polychlorinated biphenyls (PCBs in the Adriatic food web, and we extend a metabolic reconstruction of Pseudomonas putida KT2440 (iJN746 with the aerobic pathway of PCBs degradation. We assess the effectiveness of different bioremediation scenarios in reducing PCBs concentration in species and we study indices of species centrality to measure their importance in the contaminant diffusion via feeding links.The analysis of the Adriatic sea case study suggests that our framework could represent a practical tool in the design of effective remediation strategies, providing at the same time insights into the ecological role of microbial communities within food webs.

Microbial communities in dark oligotrophic volcanic ice cave ecosystems of Mt. Erebus, Antarctica

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Bradley M. Tebo

2015-03-01

Full Text Available The Earth’s crust hosts a subsurface, dark, and oligotrophic biosphere that is poorly understood in terms of the energy supporting its biomass production and impact on food webs at the Earth’s surface. Dark oligotrophic volcanic ecosystems (DOVEs are good environments for investigations of life in the absence of sunlight as they are poor in organics, rich in chemical reactants and well known for chemical exchange with Earth’s surface systems. Ice caves near the summit of Mt. Erebus (Antarctica offer DOVEs in a polar alpine environment that is starved in organics and with oxygenated hydrothermal circulation in highly reducing host rock. We surveyed the microbial communities using PCR, cloning, sequencing and analysis of the small subunit (16S ribosomal and Ribulose-1,5-bisphosphate Carboxylase/Oxygenase (RubisCO genes in sediment samples from three different caves, two that are completely dark and one that receives snow-filtered sunlight seasonally. The microbial communities in all three caves are composed primarily of Bacteria and fungi; Archaea were not detected. The bacterial communities from these ice caves display low phylogenetic diversity, but with a remarkable diversity of RubisCO genes including new deeply branching Form I clades, implicating the Calvin-Benson-Bassham cycle as a pathway of CO2 fixation. The microbial communities in one of the dark caves, Warren Cave, which has a remarkably low phylogenetic diversity, were analyzed in more detail to gain a possible perspective on the energetic basis of the microbial ecosystem in the cave. Atmospheric carbon (CO2 and CO, including from volcanic emissions, likely supplies carbon and/or some of the energy requirements of chemoautotrophic microbial communities in Warren Cave and probably other Mt. Erebus ice caves. Our work casts a first glimpse at Mt. Erebus ice caves as natural laboratories for exploring carbon, energy and nutrient sources in the subsurface biosphere and the
Dynamics of microbial communities during decomposition of litter from pioneering plants in initial soil ecosystems

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J. Esperschütz

2013-07-01

Full Text Available In initial ecosystems, concentrations of all macro- and micronutrients can be considered as extremely low. Plant litter therefore strongly influences the development of a degrader's food web and is an important source for C and N input into soil in such ecosystems. In the present study, a 13C litter decomposition field experiment was performed for 30 weeks in initial soils from a post-mining area near the city of Cottbus (Germany. Two of this region's dominant but contrasting pioneering plant species (Lotus corniculatus L. and Calamagrostis epigejos L. were chosen to investigate the effects of litter quality on the litter decomposing microbial food web in initially nutrient-poor substrates. The results clearly indicate the importance of litter quality, as indicated by its N content, its bioavailability for the degradation process and the development of microbial communities in the detritusphere and soil. The degradation of the L. corniculatus litter, which had a low C / N ratio, was fast and showed pronounced changes in the microbial community structure 1–4 weeks after litter addition. The degradation of the C. epigejos litter material was slow and microbial community changes mainly occurred between 4 and 30 weeks after litter addition to the soil. However, for both litter materials a clear indication of the importance of fungi for the degradation process was observed both in terms of fungal abundance and activity (13C incorporation activity
Hadal biosphere: insight into the microbial ecosystem in the deepest ocean on Earth.

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Nunoura, Takuro; Takaki, Yoshihiro; Hirai, Miho; Shimamura, Shigeru; Makabe, Akiko; Koide, Osamu; Kikuchi, Tohru; Miyazaki, Junichi; Koba, Keisuke; Yoshida, Naohiro; Sunamura, Michinari; Takai, Ken

2015-03-17

Hadal oceans at water depths below 6,000 m are the least-explored aquatic biosphere. The Challenger Deep, located in the western equatorial Pacific, with a water depth of ∼11 km, is the deepest ocean on Earth. Microbial communities associated with waters from the sea surface to the trench bottom (0∼10,257 m) in the Challenger Deep were analyzed, and unprecedented trench microbial communities were identified in the hadal waters (6,000∼10,257 m) that were distinct from the abyssal microbial communities. The potentially chemolithotrophic populations were less abundant in the hadal water than those in the upper abyssal waters. The emerging members of chemolithotrophic nitrifiers in the hadal water that likely adapt to the higher flux of electron donors were also different from those in the abyssal waters that adapt to the lower flux of electron donors. Species-level niche separation in most of the dominant taxa was also found between the hadal and abyssal microbial communities. Considering the geomorphology and the isolated hydrotopographical nature of the Mariana Trench, we hypothesized that the distinct hadal microbial ecosystem was driven by the endogenous recycling of organic matter in the hadal waters associated with the trench geomorphology.
Synthetic Biology and Microbial Fuel Cells: Towards Self-Sustaining Life Support Systems

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Hogan, John Andrew

2014-01-01

NASA ARC and the J. Craig Venter Institute (JCVI) collaborated to investigate the development of advanced microbial fuels cells (MFCs) for biological wastewater treatment and electricity production (electrogenesis). Synthetic biology techniques and integrated hardware advances were investigated to increase system efficiency and robustness, with the intent of increasing power self-sufficiency and potential product formation from carbon dioxide. MFCs possess numerous advantages for space missions, including rapid processing, reduced biomass and effective removal of organics, nitrogen and phosphorus. Project efforts include developing space-based MFC concepts, integration analyses, increasing energy efficiency, and investigating novel bioelectrochemical system applications
Long-term reactive nitrogen loading alters soil carbon and microbial community properties in a subalpine forest ecosystem

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Boot, Claudia M.; Hall, Ed K.; Denef, Karolien; Baron, Jill S.

2016-01-01

Elevated nitrogen (N) deposition due to increased fossil fuel combustion and agricultural practices has altered global carbon (C) cycling. Additions of reactive N to N-limited environments are typically accompanied by increases in plant biomass. Soil C dynamics, however, have shown a range of different responses to the addition of reactive N that seem to be ecosystem dependent. We evaluated the effect of N amendments on biogeochemical characteristics and microbial responses of subalpine forest organic soils in order to develop a mechanistic understanding of how soils are affected by N amendments in subalpine ecosystems. We measured a suite of responses across three years (2011–2013) during two seasons (spring and fall). Following 17 years of N amendments, fertilized soils were more acidic (control mean 5.09, fertilized mean 4.68), and had lower %C (control mean 33.7% C, fertilized mean 29.8% C) and microbial biomass C by 22% relative to control plots. Shifts in biogeochemical properties in fertilized plots were associated with an altered microbial community driven by reduced arbuscular mycorrhizal (control mean 3.2 mol%, fertilized mean 2.5 mol%) and saprotrophic fungal groups (control mean 17.0 mol%, fertilized mean 15.2 mol%), as well as a decrease in N degrading microbial enzyme activity. Our results suggest that decreases in soil C in subalpine forests were in part driven by increased microbial degradation of soil organic matter and reduced inputs to soil organic matter in the form of microbial biomass.
Microbial Community Dynamics in Soil Depth Profiles Over 120,000 Years of Ecosystem Development

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Stephanie Turner

2017-05-01

Full Text Available Along a long-term ecosystem development gradient, soil nutrient contents and mineralogical properties change, therefore probably altering soil microbial communities. However, knowledge about the dynamics of soil microbial communities during long-term ecosystem development including progressive and retrogressive stages is limited, especially in mineral soils. Therefore, microbial abundances (quantitative PCR and community composition (pyrosequencing as well as their controlling soil properties were investigated in soil depth profiles along the 120,000 years old Franz Josef chronosequence (New Zealand. Additionally, in a microcosm incubation experiment the effects of particular soil properties, i.e., soil age, soil organic matter fraction (mineral-associated vs. particulate, O2 status, and carbon and phosphorus additions, on microbial abundances (quantitative PCR and community patterns (T-RFLP were analyzed. The archaeal to bacterial abundance ratio not only increased with soil depth but also with soil age along the chronosequence, coinciding with mineralogical changes and increasing phosphorus limitation. Results of the incubation experiment indicated that archaeal abundances were less impacted by the tested soil parameters compared to Bacteria suggesting that Archaea may better cope with mineral-induced substrate restrictions in subsoils and older soils. Instead, archaeal communities showed a soil age-related compositional shift with the Bathyarchaeota, that were frequently detected in nutrient-poor, low-energy environments, being dominant at the oldest site. However, bacterial communities remained stable with ongoing soil development. In contrast to the abundances, the archaeal compositional shift was associated with the mineralogical gradient. Our study revealed, that archaeal and bacterial communities in whole soil profiles are differently affected by long-term soil development with archaeal communities probably being better adapted to
A Synthesis of the Effects of Pesticides on Microbial Persistence in Aquatic Ecosystems

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Staley, Zachery R.; Harwood, Valerie J.; Rohr, Jason R.

2016-01-01

Pesticides are a pervasive presence in aquatic ecosystems throughout the world. While pesticides are intended to control fungi, insects, and other pests, their mechanisms of action are often not specific enough to prevent unintended effects, such as on non-target microbial populations. Microorganisms, including algae and cyanobacteria, protozoa, aquatic fungi, and bacteria, form the basis of many food webs and are responsible for crucial aspects of biogeochemical cycling; therefore, the potential for pesticides to alter microbial community structures must be understood to preserve ecosystem services. This review examines studies that focused on direct population-level effects and indirect community-level effects of pesticides on microorganisms. Generally, insecticides, herbicides, and fungicides were found to have adverse direct effects on algal and fungal species. Insecticides and fungicides also had deleterious direct effects in the majority of studies examining protozoa species, although herbicides were found to have inconsistent direct effects on protozoans. Our synthesis revealed mixed or no direct effects on bacterial species among all pesticide categories, with results highly dependent on the target species, chemical, and concentration used in the study. Examination of community-level, indirect effects revealed that all pesticide categories had a tendency to reduce higher trophic levels, thereby diminishing top-down pressures and favoring lower trophic levels. Often, indirect effects exerted greater influence than direct effects. However, few studies have been conducted to specifically address community-level effects of pesticides on microorganisms and further research is necessary to better understand and predict the net effects of pesticides on ecosystem health. PMID:26565685
Monitoring the fibrolytic potential of microbial ecosystems from domestic and wild ruminants browsing tanniferous forages

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Nokwethemba Nqobile Philile Msimango

2016-03-01

Full Text Available Although the rumen microbiome has been reported to synthesize a rich source of symbiotic enzymes (exocellulase, endocellulase, hemicellulase and cellobiase, the digestion of tropical C4 grasses and browses by ruminants is still limited. Therefore, this study aimed to unveil potential fibrolytic microbial ecosystems from giraffe, kudu, impala and consortia (A1 [giraffe + kudu], A2 [giraffe + impala], A3 [kudu + impala], and A4 [giraffe + kudu + impala] browsing tanniferous plants, which can be used to improve forage utilization in domesticated goat. Crude protein enzyme extracts (CPZ from fresh faecal samples were precipitated by 60% ammonium sulphate and assayed for exocellulase, endocellulase and hemicellulase by incubating with crystalline cellulose, carboxymethyl cellulose and xylan at 38 °C with optimum pH of 5.5 to 6.5 for 1, 2, and 48 h, respectively. Enzyme specific activities were defined as μg of reducing sugar/mg CPZ. In vitro fermentation study was done by transferring 33 mL of fresh faecal inoculum into 67 mL of salivary buffer containing 1 g Acacia sieberiana and incubating for 72 h at 38 °C. Apparent degradability (APDeg, true degradability (TD, neutral detergent fibre degradability (NDFdeg, acid detergent fibre degradability (ADFdeg, microbial yield (MY, metabolizable energy (ME and total gas emitted (Gas were measured. Exocellulase activities were higher (P < 0.05 in all wild animals and consortia than those in goat except for A4. Minimal differences in hemicellulase activities (P < 0.05 were observed among goat and wild animals and consortia, while endocellulase activity was generally higher (P < 0.05 in goat than that in the rest of the systems. Apart from A3, TDeg, NDFdeg and ADFdeg were higher (P < 0.05 in all microbial ecosystems from wild animals and consortia than those in goat. Apparent degradability, MY and ME also varied (P < 0.05 among these systems. Giraffe, Kudu and A3 produced lower (P�
A model for improving microbial biofuel production using a synthetic feedback loop

Energy Technology Data Exchange (ETDEWEB)

Dunlop, Mary; Keasling, Jay; Mukhopadhyay, Aindrila

2011-07-14

Cells use feedback to implement a diverse range of regulatory functions. Building synthetic feedback control systems may yield insight into the roles that feedback can play in regulation since it can be introduced independently of native regulation, and alternative control architectures can be compared. We propose a model for microbial biofuel production where a synthetic control system is used to increase cell viability and biofuel yields. Although microbes can be engineered to produce biofuels, the fuels are often toxic to cell growth, creating a negative feedback loop that limits biofuel production. These toxic effects may be mitigated by expressing efflux pumps that export biofuel from the cell. We developed a model for cell growth and biofuel production and used it to compare several genetic control strategies for their ability to improve biofuel yields. We show that controlling efflux pump expression directly with a biofuel-responsive promoter is a straight forward way of improving biofuel production. In addition, a feed forward loop controller is shown to be versatile at dealing with uncertainty in biofuel production rates.
Microbial functional diversity plays an important role in the degradation of polyhydroxybutyrate (PHB) in soil.

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Dey, Samrat; Tribedi, Prosun

2018-03-01

Towards bioremediation of recalcitrant materials like synthetic polymer, soil has been recognized as a traditional site for disposal and subsequent degradation as some microorganisms in soil can degrade the polymer in a non-toxic, cost-effective, and environment friendly way. Microbial functional diversity is a constituent of biodiversity that includes wide range of metabolic activities that can influence numerous aspects of ecosystem functioning like ecosystem stability, nutrient availability, ecosystem dynamics, etc. Thus, in the current study, we assumed that microbial functional diversity could play an important role in polymer degradation in soil. To verify this hypothesis, we isolated soil from five different sites of landfill and examined several microbiological parameters wherein we observed a significant variation in heterotrophic microbial count as well as microbial activities among the soil microcosms tested. Multivariate analysis (principle component analysis) based on the carbon sources utilization pattern revealed that soil microcosms showed different metabolic patterns suggesting the variable distribution of microorganisms among the soil microcosms tested. Since microbial functional diversity depends on both microbial richness and evenness, Shannon diversity index was determined to measure microbial richness and Gini coefficient was determined to measure microbial evenness. The tested soil microcosms exhibited variation in both microbial richness and evenness suggesting the considerable difference in microbial functional diversity among the tested microcosms. We then measured polyhydroxybutyrate (PHB) degradation in soil microcosms after desired period of incubation of PHB in soil wherein we found that soil microcosms having higher functional diversity showed enhanced PHB degradation and soil microcosms having lower functional diversity showed reduced PHB degradation. We also noticed that all the tested soil microcosms showed similar pattern in both
Rhizosphere soil microbial index of tree species in a coal mining ecosystem

Energy Technology Data Exchange (ETDEWEB)

Sinha, S.; Masto, R.E.; Ram, L.C.; Selvi, V.A.; Srivastava, N.K.; Tripathi, R.C.; George, J. [Central Institute of Mining & Fuel Research, Dhanbad (India)

2009-09-15

Microbial characterization of the tree rhizosphere provides important information relating to the screening of tree species for re-vegetation of degraded land. Rhizosphere soil samples collected from a few predominant tree species growing in the coal mining ecosystem of Dhanbad, India, were analyzed for soil organic carbon (SOC), mineralizable N, microbial biomass carbon (MBC), active microbial biomass carbon (AMBC), basal soil respiration (BSR), and soil enzyme activities (dehydrogenase, urease, catalase, phenol oxidase, and peroxidase). Principal component analysis was employed to derive a rhizosphere soil microbial index (RSMI) and accordingly, dehydrogenase, BSR/MBC, MBC/SOC, EC, phenol oxidase and AMBC were found to be the most critical properties. The observed values for the above properties were converted into a unitless score (0-1.00) and the scores were integrated into RSMI. The tree species could be arranged in decreasing order of the RSMI as: A. marmelos (0.718), A. indica (0.715), Bauhinia bauhinia (0.693), B. monosperma (0.611), E. jambolana (0.601), Moringa oleifera (0.565), Dalbergia sissoo (0.498), T indica (0.488), Morus alba (0.415), F religiosa (0.291), Eucalyptus sp. (0.232) and T grandis (0.181). It was concluded that tree species in coal mining areas had diverse effects on their respective rhizosphere microbial processes, which could directly or indirectly determine the survival and performance of the planted tree species in degraded coal mining areas. Tree species with higher RSMI values could be recommended for re-vegetation of degraded coal mining area.
Plant, microbial and ecosystem carbon use efficiencies interact to stabilize microbial growth as a fraction of gross primary production.

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Sinsabaugh, Robert L; Moorhead, Daryl L; Xu, Xiaofeng; Litvak, Marcy E

2017-06-01

The carbon use efficiency of plants (CUE a ) and microorganisms (CUE h ) determines rates of biomass turnover and soil carbon sequestration. We evaluated the hypothesis that CUE a and CUE h counterbalance at a large scale, stabilizing microbial growth (μ) as a fraction of gross primary production (GPP). Collating data from published studies, we correlated annual CUE a , estimated from satellite imagery, with locally determined soil CUE h for 100 globally distributed sites. Ecosystem CUE e , the ratio of net ecosystem production (NEP) to GPP, was estimated for each site using published models. At the ecosystem scale, CUE a and CUE h were inversely related. At the global scale, the apparent temperature sensitivity of CUE h with respect to mean annual temperature (MAT) was similar for organic and mineral soils (0.029°C -1 ). CUE a and CUE e were inversely related to MAT, with apparent sensitivities of -0.009 and -0.032°C -1 , respectively. These trends constrain the ratio μ : GPP (= (CUE a × CUE h )/(1 - CUE e )) with respect to MAT by counterbalancing the apparent temperature sensitivities of the component processes. At the ecosystem scale, the counterbalance is effected by modulating soil organic matter stocks. The results suggest that a μ : GPP value of c. 0.13 is a homeostatic steady state for ecosystem carbon fluxes at a large scale. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.
Too big or too narrow? Disturbance characteristics determine the functional resilience in virtual microbial ecosystems

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König, Sara; Firle, Anouk-Letizia; Koehnke, Merlin; Banitz, Thomas; Frank, Karin

2017-04-01

In general ecology, there is an ongoing debate about the influence of fragmentation on extinction thresholds. Whether this influence is positive or negative depends on the considered type of fragmentation: whereas habitat fragmentation often has a negative influence on population extinction thresholds, spatially fragmented disturbances are observed to have mostly positive effects on the extinction probability. Besides preventing population extinction, in soil systems ecology we are interested in analyzing how ecosystem functions are maintained despite disturbance events. Here, we analyzed the influence of disturbance size and fragmentation on the functional resilience of a microbial soil ecosystem. As soil is a highly heterogeneous environment exposed to disturbances of different spatial configurations, the identification of critical disturbance characteristics for maintaining its functions is crucial. We used the numerical simulation model eColony considering bacterial growth, degradation and dispersal for analyzing the dynamic response of biodegradation examplary for an important microbial ecosystem service to disturbance events of different spatial configurations. We systematically varied the size and the degree of fragmentation of the affected area (disturbance pattern). We found that the influence of the disturbance size on functional recovery and biodegradation performance highly depends on the spatial fragmentation of the disturbance. Generally, biodegradation performance decreases with increasing clumpedness and increasing size of the affected area. After spatially correlated disturbance events, biodegradation performance decreases linear with increasing disturbance size. After spatially fragmented disturbance events, on the other hand, an increase in disturbance size has no influence on the biodegradation performance until a critical disturbance size is reached. Is the affected area bigger than this critical size, the functional performance decreases
An examination of the biodiversity-ecosystem function relationship in arable soil microbial communities

DEFF Research Database (Denmark)

Griffiths, B.S.; Ritz, Karl; Wheatley, R.

2001-01-01

, nitrate accumulation, respiratory growth response, community level physiological profile and decomposition). Neither was there a direct effect of biodiversity on the variability of the processes, nor on the stability of decomposition when the soils were perturbed by heat or copper. The biodiversity of......Microbial communities differing in biodiversity were established by inoculating sterile agricultural soil with serially diluted soil suspensions prepared from the parent soil. Three replicate communities of each dilution were allowed to establish an equivalent microbial biomass by incubation for 9...... months at 15°C, after which the biodiversity-ecosystem function relationship was examined for a range of soil processes. Biodiversity was determined by monitoring cultivable bacterial and fungal morphotypes, directly extracted eubacterial DNA and protozoan taxa. In the context of this study biodiversity...
Spatial dynamics of synthetic microbial mutualists and their parasites.

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Daniel R Amor

2017-08-01

Full Text Available A major force contributing to the emergence of novelty in nature is the presence of cooperative interactions, where two or more components of a system act in synergy, sometimes leading to higher-order, emergent phenomena. Within molecular evolution, the so called hypercycle defines the simplest model of an autocatalytic cycle, providing major theoretical insights on the evolution of cooperation in the early biosphere. These closed cooperative loops have also inspired our understanding of how catalytic loops appear in ecological systems. In both cases, hypercycle and ecological cooperative loops, the role played by space seems to be crucial for their stability and resilience against parasites. However, it is difficult to test these ideas in natural ecosystems, where time and spatial scales introduce considerable limitations. Here, we use engineered bacteria as a model system to a variety of environmental scenarios identifying trends that transcend the specific model system, such an enhanced genetic diversity in environments requiring mutualistic interactions. Interestingly, we show that improved environments can slow down mutualistic range expansions as a result of genetic drift effects preceding local resource depletion. Moreover, we show that a parasitic strain is excluded from the population during range expansions (which acknowledges a classical prediction. Nevertheless, environmental deterioration can reshape population interactions, this same strain becoming part of a three-species mutualistic web in scenarios in which the two-strain mutualism becomes non functional. The evolutionary and ecological implications for the design of synthetic ecosystems are outlined.
Primary productivity as a control over soil microbial diversity along environmental gradients in a polar desert ecosystem

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Kevin M. Geyer

2017-07-01

Full Text Available Primary production is the fundamental source of energy to foodwebs and ecosystems, and is thus an important constraint on soil communities. This coupling is particularly evident in polar terrestrial ecosystems where biological diversity and activity is tightly constrained by edaphic gradients of productivity (e.g., soil moisture, organic carbon availability and geochemical severity (e.g., pH, electrical conductivity. In the McMurdo Dry Valleys of Antarctica, environmental gradients determine numerous properties of soil communities and yet relatively few estimates of gross or net primary productivity (GPP, NPP exist for this region. Here we describe a survey utilizing pulse amplitude modulation (PAM fluorometry to estimate rates of GPP across a broad environmental gradient along with belowground microbial diversity and decomposition. PAM estimates of GPP ranged from an average of 0.27 μmol O2/m2/s in the most arid soils to an average of 6.97 μmol O2/m2/s in the most productive soils, the latter equivalent to 217 g C/m2/y in annual NPP assuming a 60 day growing season. A diversity index of four carbon-acquiring enzyme activities also increased with soil productivity, suggesting that the diversity of organic substrates in mesic environments may be an additional driver of microbial diversity. Overall, soil productivity was a stronger predictor of microbial diversity and enzymatic activity than any estimate of geochemical severity. These results highlight the fundamental role of environmental gradients to control community diversity and the dynamics of ecosystem-scale carbon pools in arid systems.
A Synthetic Ecology Perspective: How Well Does Behavior of Model Organisms in the Laboratory Predict Microbial Activities in Natural Habitats?

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Yu, Zheng; Krause, Sascha M B; Beck, David A C; Chistoserdova, Ludmila

2016-01-01

In this perspective article, we question how well model organisms, the ones that are easy to cultivate in the laboratory and that show robust growth and biomass accumulation, reflect the dynamics and interactions of microbial communities observed in nature. Today's -omics toolbox allows assessing the genomic potential of microbes in natural environments in a high-throughput fashion and at a strain-level resolution. However, understanding of the details of microbial activities and of the mechanistic bases of community function still requires experimental validation in simplified and fully controlled systems such as synthetic communities. We have studied methane utilization in Lake Washington sediment for a few decades and have identified a number of species genetically equipped for this activity. We have also identified co-occurring satellite species that appear to form functional communities together with the methanotrophs. Here, we compare experimental findings from manipulation of natural communities involved in metabolism of methane in this niche with findings from manipulation of synthetic communities assembled in the laboratory of species originating from the same study site, from very simple (two-species) to rather complex (50-species) synthetic communities. We observe some common trends in community dynamics between the two types of communities, toward representation of specific functional guilds. However, we also identify strong discrepancies between the dominant methane oxidizers in synthetic communities compared to natural communities, under similar incubation conditions. These findings highlight the challenges that exist in using the synthetic community approach to modeling dynamics and species interactions in natural communities.
Microbial production of natural and non-natural flavonoids: Pathway engineering, directed evolution and systems/synthetic biology.

Science.gov (United States)

Pandey, Ramesh Prasad; Parajuli, Prakash; Koffas, Mattheos A G; Sohng, Jae Kyung

2016-01-01

In this review, we address recent advances made in pathway engineering, directed evolution, and systems/synthetic biology approaches employed in the production and modification of flavonoids from microbial cells. The review is divided into two major parts. In the first, various metabolic engineering and system/synthetic biology approaches used for production of flavonoids and derivatives are discussed broadly. All the manipulations/engineering accomplished on the microorganisms since 2000 are described in detail along with the biosynthetic pathway enzymes, their sources, structures of the compounds, and yield of each product. In the second part of the review, post-modifications of flavonoids by four major reactions, namely glycosylations, methylations, hydroxylations and prenylations using recombinant strains are described. Copyright © 2016 Elsevier Inc. All rights reserved.
Microbial and Functional Diversity within the Phyllosphere of Espeletia Species in an Andean High-Mountain Ecosystem.

Science.gov (United States)

Ruiz-Pérez, Carlos A; Restrepo, Silvia; Zambrano, María Mercedes

2016-01-08

Microbial populations residing in close contact with plants can be found in the rhizosphere, in the phyllosphere as epiphytes on the surface, or inside plants as endophytes. Here, we analyzed the microbiota associated with Espeletia plants, endemic to the Páramo environment of the Andes Mountains and a unique model for studying microbial populations and their adaptations to the adverse conditions of high-mountain neotropical ecosystems. Communities were analyzed using samples from the rhizosphere, necromass, and young and mature leaves, the last two analyzed separately as endophytes and epiphytes. The taxonomic composition determined by performing sequencing of the V5-V6 region of the 16S rRNA gene indicated differences among populations of the leaf phyllosphere, the necromass, and the rhizosphere, with predominance of some phyla but only few shared operational taxonomic units (OTUs). Functional profiles predicted on the basis of taxonomic affiliations differed from those obtained by GeoChip microarray analysis, which separated community functional capacities based on plant microenvironment. The identified metabolic pathways provided insight regarding microbial strategies for colonization and survival in these ecosystems. This study of novel plant phyllosphere microbiomes and their putative functional ecology is also the first step for future bioprospecting studies in search of enzymes, compounds, or microorganisms relevant to industry or for remediation efforts. Copyright © 2016, American Society for Microbiology. All Rights Reserved.
Stable isotope probing to study functional components of complex microbial ecosystems.

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Mazard, Sophie; Schäfer, Hendrik

2014-01-01

This protocol presents a method of dissecting the DNA or RNA of key organisms involved in a specific biochemical process within a complex ecosystem. Stable isotope probing (SIP) allows the labelling and separation of nucleic acids from community members that are involved in important biochemical transformations, yet are often not the most numerically abundant members of a community. This pure culture-independent technique circumvents limitations of traditional microbial isolation techniques or data mining from large-scale whole-community metagenomic studies to tease out the identities and genomic repertoires of microorganisms participating in biological nutrient cycles. SIP experiments can be applied to virtually any ecosystem and biochemical pathway under investigation provided a suitable stable isotope substrate is available. This versatile methodology allows a wide range of analyses to be performed, from fatty-acid analyses, community structure and ecology studies, and targeted metagenomics involving nucleic acid sequencing. SIP experiments provide an effective alternative to large-scale whole-community metagenomic studies by specifically targeting the organisms or biochemical transformations of interest, thereby reducing the sequencing effort and time-consuming bioinformatics analyses of large datasets.

The feasibility of automated online flow cytometry for in-situ monitoring of microbial dynamics in aquatic ecosystems

Science.gov (United States)

Besmer, Michael D.; Weissbrodt, David G.; Kratochvil, Bradley E.; Sigrist, Jürg A.; Weyland, Mathias S.; Hammes, Frederik

2014-01-01

Fluorescent staining coupled with flow cytometry (FCM) is often used for the monitoring, quantification and characterization of bacteria in engineered and environmental aquatic ecosystems including seawater, freshwater, drinking water, wastewater, and industrial bioreactors. However, infrequent grab sampling hampers accurate characterization and subsequent understanding of microbial dynamics in all of these ecosystems. A logic technological progression is high throughput and full automation of the sampling, staining, measurement, and data analysis steps. Here we assess the feasibility and applicability of automated FCM by means of actual data sets produced with prototype instrumentation. As proof-of-concept we demonstrate examples of microbial dynamics in (i) flowing tap water from a municipal drinking water supply network and (ii) river water from a small creek subject to two rainfall events. In both cases, automated measurements were done at 15-min intervals during 12–14 consecutive days, yielding more than 1000 individual data points for each ecosystem. The extensive data sets derived from the automated measurements allowed for the establishment of baseline data for each ecosystem, as well as for the recognition of daily variations and specific events that would most likely be missed (or miss-characterized) by infrequent sampling. In addition, the online FCM data from the river water was combined and correlated with online measurements of abiotic parameters, showing considerable potential for a better understanding of cause-and-effect relationships in aquatic ecosystems. Although several challenges remain, the successful operation of an automated online FCM system and the basic interpretation of the resulting data sets represent a breakthrough toward the eventual establishment of fully automated online microbiological monitoring technologies. PMID:24917858
Functional resilience of microbial ecosystems in soil: How important is a spatial analysis?

Science.gov (United States)

König, Sara; Banitz, Thomas; Centler, Florian; Frank, Karin; Thullner, Martin

2015-04-01

Microbial life in soil is exposed to fluctuating environmental conditions influencing the performance of microbially mediated ecosystem services such as biodegradation of contaminants. However, as this environment is typically very heterogeneous, spatial aspects can be expected to play a major role for the ability to recover from a stress event. To determine key processes for functional resilience, simple scenarios with varying stress intensities were simulated within a microbial simulation model and the biodegradation rate in the recovery phase monitored. Parameters including microbial growth and dispersal rates were varied over a typical range to consider microorganisms with varying properties. Besides an aggregated temporal monitoring, the explicit observation of the spatio-temporal dynamics proved essential to understand the recovery process. For a mechanistic understanding of the model system, scenarios were also simulated with selected processes being switched-off. Results of the mechanistic and the spatial view show that the key factors for functional recovery with respect to biodegradation after a simple stress event depend on the location of the observed habitats. The limiting factors near unstressed areas are spatial processes - the mobility of the bacteria as well as substrate diffusion - the longer the distance to the unstressed region the more important becomes the process growth. Furthermore, recovery depends on the stress intensity - after a low stress event the spatial configuration has no influence on the key factors for functional resilience. To confirm these results, we repeated the stress scenarios but this time including an additional dispersal network representing a fungal network in soil. The system benefits from an increased spatial performance due to the higher mobility of the degrading microorganisms. However, this effect appears only in scenarios where the spatial distribution of the stressed area plays a role. With these simulations we
Biodegradable Plastic Mulch Films: Impacts on Soil Microbial Communities and Ecosystem Functions

Directory of Open Access Journals (Sweden)

Sreejata Bandopadhyay

2018-04-01

Full Text Available Agricultural plastic mulch films are widely used in specialty crop production systems because of their agronomic benefits. Biodegradable plastic mulches (BDMs offer an environmentally sustainable alternative to conventional polyethylene (PE mulch. Unlike PE films, which need to be removed after use, BDMs are tilled into soil where they are expected to biodegrade. However, there remains considerable uncertainty about long-term impacts of BDM incorporation on soil ecosystems. BDMs potentially influence soil microbial communities in two ways: first, as a surface barrier prior to soil incorporation, indirectly affecting soil microclimate and atmosphere (similar to PE films and second, after soil incorporation, as a direct input of physical fragments, which add carbon, microorganisms, additives, and adherent chemicals. This review summarizes the current literature on impacts of plastic mulches on soil biological and biogeochemical processes, with a special emphasis on BDMs. The combined findings indicated that when used as a surface barrier, plastic mulches altered soil microbial community composition and functioning via microclimate modification, though the nature of these alterations varied between studies. In addition, BDM incorporation into soil can result in enhanced microbial activity and enrichment of fungal taxa. This suggests that despite the fact that total carbon input from BDMs is minuscule, a stimulatory effect on microbial activity may ultimately affect soil organic matter dynamics. To address the current knowledge gaps, long term studies and a better understanding of impacts of BDMs on nutrient biogeochemistry are needed. These are critical to evaluating BDMs as they relate to soil health and agroecosystem sustainability.
Biodegradable Plastic Mulch Films: Impacts on Soil Microbial Communities and Ecosystem Functions.

Science.gov (United States)

Bandopadhyay, Sreejata; Martin-Closas, Lluis; Pelacho, Ana M; DeBruyn, Jennifer M

2018-01-01

Agricultural plastic mulch films are widely used in specialty crop production systems because of their agronomic benefits. Biodegradable plastic mulches (BDMs) offer an environmentally sustainable alternative to conventional polyethylene (PE) mulch. Unlike PE films, which need to be removed after use, BDMs are tilled into soil where they are expected to biodegrade. However, there remains considerable uncertainty about long-term impacts of BDM incorporation on soil ecosystems. BDMs potentially influence soil microbial communities in two ways: first, as a surface barrier prior to soil incorporation, indirectly affecting soil microclimate and atmosphere (similar to PE films) and second, after soil incorporation, as a direct input of physical fragments, which add carbon, microorganisms, additives, and adherent chemicals. This review summarizes the current literature on impacts of plastic mulches on soil biological and biogeochemical processes, with a special emphasis on BDMs. The combined findings indicated that when used as a surface barrier, plastic mulches altered soil microbial community composition and functioning via microclimate modification, though the nature of these alterations varied between studies. In addition, BDM incorporation into soil can result in enhanced microbial activity and enrichment of fungal taxa. This suggests that despite the fact that total carbon input from BDMs is minuscule, a stimulatory effect on microbial activity may ultimately affect soil organic matter dynamics. To address the current knowledge gaps, long term studies and a better understanding of impacts of BDMs on nutrient biogeochemistry are needed. These are critical to evaluating BDMs as they relate to soil health and agroecosystem sustainability.
Statistical Physics Approaches to Microbial Ecology

Science.gov (United States)

Mehta, Pankaj

The unprecedented ability to quantitatively measure and probe complex microbial communities has renewed interest in identifying the fundamental ecological principles governing community ecology in microbial ecosystems. Here, we present work from our group and others showing how ideas from statistical physics can help us uncover these ecological principles. Two major lessons emerge from this work. First, large, ecosystems with many species often display new, emergent ecological behaviors that are absent in small ecosystems with just a few species. To paraphrase Nobel laureate Phil Anderson, ''More is Different'', especially in community ecology. Second, the lack of trophic layer separation in microbial ecology fundamentally distinguishes microbial ecology from classical paradigms of community ecology and leads to qualitative different rules for community assembly in microbes. I illustrate these ideas using both theoretical modeling and novel new experiments on large microbial ecosystems performed by our collaborators (Joshua Goldford and Alvaro Sanchez). Work supported by Simons Investigator in MMLS and NIH R35 R35 GM119461.
Soil ecology of a rock outcrop ecosystem: Abiotic stresses, soil respiration, and microbial community profiles in limestone cedar glades

Science.gov (United States)

Cartwright, Jennifer M.; Advised by Dzantor, E. Kudjo

2015-01-01

Limestone cedar glades are a type of rock outcrop ecosystem characterized by shallow soil and extreme hydrologic conditions—seasonally ranging from xeric to saturated—that support a number of plant species of conservation concern. Although a rich botanical literature exists on cedar glades, soil biochemical processes and the ecology of soil microbial communities in limestone cedar glades have largely been ignored. This investigation documents the abiotic stress regime of this ecosystem (shallow soil, extreme hydrologic fluctuations and seasonally high soil surface temperatures) as well as soil physical and chemical characteristics, and relates both types of information to ecological structures and functions including vegetation, soil respiration, and soil microbial community metabolic profiles and diversity. Methods used in this investigation include field observations and measurements of soil physical and chemical properties and processes, laboratory analyses, and microbiological assays of soil samples.
Microbes as engines of ecosystem function: when does community structure enhance predictions of ecosystem processes?

Directory of Open Access Journals (Sweden)

Emily B. Graham

2016-02-01

Full Text Available Microorganisms are vital in mediating the earth’s biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: ‘When do we need to understand microbial community structure to accurately predict function?’ We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology.
2012 Molecular Basis of Microbial One-Carbon Metabolism Gordon Research Conferences and Gordon Research Seminar, August 4-10,2012

Energy Technology Data Exchange (ETDEWEB)

Hanson, Thomas

2012-08-10

The 2012 Gordon Conference will present and discuss cutting-edge research in the field of microbial metabolism of C1 compounds. The conference will feature the roles and application of C1 metabolism in natural and synthetic systems at scales from molecules to ecosystems. The conference will stress molecular aspects of the unique metabolism exhibited by autotrophic bacteria, methanogens, methylotrophs, aerobic and anaerobic methanotrophs, and acetogens.
Adaptive long-term monitoring of soil health in metal phytostabilization: ecological attributes and ecosystem services based on soil microbial parameters.

Science.gov (United States)

Epelde, Lur; Becerril, José M; Alkorta, Itziar; Garbisu, Carlos

2014-01-01

Phytostabilization is a promising option for the remediation of metal contaminated soils which requires the implementation of long-term monitoring programs. We here propose to incorporate the paradigm of "adaptive monitoring", which enables monitoring programs to evolve iteratively as new information emerges and research questions change, to metal phytostabilization. Posing good questions that cover the chemical, toxicological and ecological concerns associated to metal contaminated soils is critical for an efficient long-term phytostabilization monitoring program. Regarding the ecological concerns, soil microbial parameters are most valuable indicators of the effectiveness of metal phytostabilization processes in terms of recovery of soil health. We suggest to group soil microbial parameters in higher-level categories such as "ecological attributes" (vigor, organization, stability) or "ecosystem services" in order to facilitate interpretation and, most importantly, to provide long-term phytostabilization monitoring programs with the required stability through time against changes in techniques, methods, interests, etc. that will inevitably occur during the monitoring program. Finally, a Phytostabilization Monitoring Card, based on both ecological attributes and ecosystem services, for soil microbial properties is provided.
Microbial ecology-based engineering of Microbial Electrochemical Technologies.

Science.gov (United States)

Koch, Christin; Korth, Benjamin; Harnisch, Falk

2018-01-01

Microbial ecology is devoted to the understanding of dynamics, activity and interaction of microorganisms in natural and technical ecosystems. Bioelectrochemical systems represent important technical ecosystems, where microbial ecology is of highest importance for their function. However, whereas aspects of, for example, materials and reactor engineering are commonly perceived as highly relevant, the study and engineering of microbial ecology are significantly underrepresented in bioelectrochemical systems. This shortfall may be assigned to a deficit on knowledge and power of these methods as well as the prerequisites for their thorough application. This article discusses not only the importance of microbial ecology for microbial electrochemical technologies but also shows which information can be derived for a knowledge-driven engineering. Instead of providing a comprehensive list of techniques from which it is hard to judge the applicability and value of information for a respective one, this review illustrates the suitability of selected techniques on a case study. Thereby, best practice for different research questions is provided and a set of key questions for experimental design, data acquisition and analysis is suggested. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.
Stimulation of microbial nitrogen cycling in aquatic ecosystems by benthic macrofauna: mechanisms and environmental implications

Science.gov (United States)

Stief, P.

2013-12-01

Invertebrate animals that live at the bottom of aquatic ecosystems (i.e., benthic macrofauna) are important mediators between nutrients in the water column and microbes in the benthos. The presence of benthic macrofauna stimulates microbial nutrient dynamics through different types of animal-microbe interactions, which potentially affect the trophic status of aquatic ecosystems. This review contrasts three types of animal-microbe interactions in the benthos of aquatic ecosystems: (i) ecosystem engineering, (ii) grazing, and (iii) symbiosis. Their specific contributions to the turnover of fixed nitrogen (mainly nitrate and ammonium) and the emission of the greenhouse gas nitrous oxide are evaluated. Published data indicate that ecosystem engineering by sediment-burrowing macrofauna stimulates benthic nitrification and denitrification, which together allows fixed nitrogen removal. However, the release of ammonium from sediments is enhanced more strongly than the sedimentary uptake of nitrate. Ecosystem engineering by reef-building macrofauna increases nitrogen retention and ammonium concentrations in shallow aquatic ecosystems, but allows organic nitrogen removal through harvesting. Grazing by macrofauna on benthic microbes apparently has small or neutral effects on nitrogen cycling. Animal-microbe symbioses provide abundant and distinct benthic compartments for a multitude of nitrogen-cycle pathways. Recent studies reveal that ecosystem engineering, grazing, and symbioses of benthic macrofauna significantly enhance nitrous oxide emission from shallow aquatic ecosystems. The beneficial effect of benthic macrofauna on fixed nitrogen removal through coupled nitrification-denitrification can thus be offset by the concurrent release of (i) ammonium that stimulates aquatic primary production and (ii) nitrous oxide that contributes to global warming. Overall, benthic macrofauna intensifies the coupling between benthos, pelagial, and atmosphere through enhanced turnover and
Effects of mushroom and herb polysaccharides, as alternative for an antibiotic, on the cecal microbial ecosystem in broiler chickens

NARCIS (Netherlands)

Guo, F.; Williams, B.A.; Kwakkel, R.P.; Li, H.S.; Li, X.P.; Luo, J.Y.; Li, W.K.; Verstegen, M.W.A.

2004-01-01

An in vivo experiment was conducted to study the potential prebiotic effects of mushroom and herb polysaccharide extracts, Lentinus edodes extract (LenE), Tremella fuciformis extract, and Astragalus membranaceus Radix extract, on chicken growth and the cecal microbial ecosystem, as compared with the
Does microbial biomass affect pelagic ecosystem efficiency? An experimental study.

Science.gov (United States)

Wehr, J D; Le, J; Campbell, L

1994-01-01

Bacteria and other microorganisms in the pelagic zone participate in the recycling of organic matter and nutrients within the water column. The microbial loop is thought to enhance ecosystem efficiency through rapid recycling and reduced sinking rates, thus reducing the loss of nutrients contained in organisms remaining within the photic zone. We conducted experiments with lake communities in 5400-liter mesocosms, and measured the flux of materials and nutrients out of the water column. A factorial design manipulated 8 nutrient treatments: 4 phosphorus levels × 2 nitrogen levels. Total sedimentation rates were greatest in high-N mesocosms; within N-surplus communities, [Symbol: see text]1 µM P resulted in 50% increase in total particulate losses. P additions without added N had small effects on nutrient losses from the photic zone; +2 µM P tanks received 334 mg P per tank, yet after 14 days lost only 69 mg more particulate-P than did control communities. Nutrient treatments resulted in marked differences in phytoplankton biomass (twofold N effect, fivefold P effect in +N mesocosms only), bacterioplankton densities (twofold N-effect, twofold P effects in -N and +N mesocosms), and the relative importance of autotrophic picoplankton (maximum in high NY mesocosms). Multiple regression analysis found that of 8 plankton and water chemistry variables, the ratio of autotrophic picoplankton to total phytoplankton (measured as chlorophyll α) explained the largest portion of the total variation in sedimentation loss rates (65% of P-flux, 57% of N-flux, 26% of total flux). In each case, systems with greater relative importance of autotrophic picoplankton had significantly reduced loss rates. In contrast, greater numbers of planktonic bacteria were associated with increased sedimentation rates and lower system efficiency. We suggest that different microbial components may have contrasting effects on the presumed enhanced efficiency provided by the microbial loop.
From bacteria to elephants: Effects of land-use legacies on biodiversity and ecosystem structure in the Serengeti-Mara ecosystem: Chapter 8

Science.gov (United States)

Verchot, Louis V.; Ward, Naomi L.; Belnap, Jayne; Bossio, Deborah; Coughenour, Michael; Gibson, John; Hanotte, Olivier; Muchiru, Andrew N.; Phillips, Susan L.; Steven, Blaire; Wall, Diana H.; Reid, Robin S.

2015-01-01

Generally, ecological research has considered the aboveground and belowground components of ecosystems separately. Consequently, frameworks for integrating the two components are not well developed. Integrating the microbial components into ecosystem ecology requires different approaches from those offered by plant ecology, partly because of the scales at which microbial processes operate and partly because of measurement constraints. Studies have begun to relate microbial community structure to ecosystem function. results suggest that excluding people and livestock from the MMNR, or preventing heavier livestock from grazing around settlements, may not change the general structure of the ecosystem (soils, plant structure), but can change the numbers and diversity of wildlife, nematodes and microbes in this ecosystem in subtle ways.
Carrot Juice Fermentations as Man-Made Microbial Ecosystems Dominated by Lactic Acid Bacteria.

Science.gov (United States)

Wuyts, Sander; Van Beeck, Wannes; Oerlemans, Eline F M; Wittouck, Stijn; Claes, Ingmar J J; De Boeck, Ilke; Weckx, Stefan; Lievens, Bart; De Vuyst, Luc; Lebeer, Sarah

2018-06-15

Spontaneous vegetable fermentations, with their rich flavors and postulated health benefits, are regaining popularity. However, their microbiology is still poorly understood, therefore raising concerns about food safety. In addition, such spontaneous fermentations form interesting cases of man-made microbial ecosystems. Here, samples from 38 carrot juice fermentations were collected through a citizen science initiative, in addition to three laboratory fermentations. Culturing showed that Enterobacteriaceae were outcompeted by lactic acid bacteria (LAB) between 3 and 13 days of fermentation. Metabolite-target analysis showed that lactic acid and mannitol were highly produced, as well as the biogenic amine cadaverine. High-throughput 16S rRNA gene sequencing revealed that mainly species of Leuconostoc and Lactobacillus (as identified by 8 and 20 amplicon sequence variants [ASVs], respectively) mediated the fermentations in subsequent order. The analyses at the DNA level still detected a high number of Enterobacteriaceae , but their relative abundance was low when RNA-based sequencing was performed to detect presumptive metabolically active bacterial cells. In addition, this method greatly reduced host read contamination. Phylogenetic placement indicated a high LAB diversity, with ASVs from nine different phylogenetic groups of the Lactobacillus genus complex. However, fermentation experiments with isolates showed that only strains belonging to the most prevalent phylogenetic groups preserved the fermentation dynamics. The carrot juice fermentation thus forms a robust man-made microbial ecosystem suitable for studies on LAB diversity and niche specificity. IMPORTANCE The usage of fermented food products by professional chefs is steadily growing worldwide. Meanwhile, this interest has also increased at the household level. However, many of these artisanal food products remain understudied. Here, an extensive microbial analysis was performed of spontaneous fermented
Meta genome-wide network from functional linkages of genes in human gut microbial ecosystems.

Science.gov (United States)

Ji, Yan; Shi, Yixiang; Wang, Chuan; Dai, Jianliang; Li, Yixue

2013-03-01

The human gut microbial ecosystem (HGME) exerts an important influence on the human health. In recent researches, meta-genomics provided deep insights into the HGME in terms of gene contents, metabolic processes and genome constitutions of meta-genome. Here we present a novel methodology to investigate the HGME on the basis of a set of functionally coupled genes regardless of their genome origins when considering the co-evolution properties of genes. By analyzing these coupled genes, we showed some basic properties of HGME significantly associated with each other, and further constructed a protein interaction map of human gut meta-genome to discover some functional modules that may relate with essential metabolic processes. Compared with other studies, our method provides a new idea to extract basic function elements from meta-genome systems and investigate complex microbial environment by associating its biological traits with co-evolutionary fingerprints encoded in it.
Vertical structure and pH as factors for chitinolytic and pectinolytic microbial community of soils and terrestrial ecosystems of different climatic zones

Science.gov (United States)

Lukacheva, Evgeniya; Natalia, Manucharova

2016-04-01

Chitin is a naturally occurring fibre-forming polymer that plays a protective role in many lower animals similar to that of cellulose in plants. Also it's a compound of cell walls of fungi. Chemically it is a long-chain unbranched polysaccharide made of N-acetylglucosamine residues; it is the second most abundant organic compound in nature, after cellulose. Pectin is a structural heteropolysaccharide contained in the primary cell walls of terrestrial plants. Roots of the plants and root crops contain pectin. Chitin and pectin are widely distributed throughout the natural world. Structural and functional features of the complex microbial degradation of biopolymers one of the most important direction in microbial ecology. But there is no a lot of data concerns degradation in vertical structure of terrestrial ecosystems and detailed studies concerning certain abiotic features as pH. Microbial complexes of natural areas were analyzed only as humus horizons (A1) of the soil profile. Only small part of microbial community could be studied with this approach. It is known that ecosystems have their own structure. It is possible to allocate some vertical tiers: phylloplane, litter (soil covering), soil. We investigated chitinolytic and pectinolytic microbial communities dedicated to different layers of the ecosystems. Also it was described depending on pH dominated in certain ecosystem with certain conditions. Quantity of eukaryote and procaryote organisms increased in the test samples with chitin and pectin. Increasing of eukaryote in samples with pectin was more then in samples with chitin. Also should be noted the significant increasing of actinomycet's quantity in the samples with chitin in comparison with samples with pectin. The variety and abundance of bacteria in the litter samples increased an order of magnitude as compared to other probes. Further prokaryote community was investigated by method FISH (fluorescence in situ hybridization). FISH is a cytogenetic
Impacts of radiation exposure on the experimental microbial ecosystem: a particle-based model simulation approach

International Nuclear Information System (INIS)

Doi, M.; Tanaka, N.; Fuma, S.; Kawabata, Z.

2004-01-01

Well-designed experimental model ecosystem could be a simple reference of the actual environment and complex ecological systems. For ecological toxicity test of radiation and other environmental toxicants, we investigated and aquatic microbial ecosystem (closed microcosm) in the test tube with initial substrates,autotroph flagellate algae (Euglena, G.), heterotroph ciliate protozoa (Tetrahymena T.) and saprotroph bacteria (E, coli). These species organizes by itself to construct the ecological system, that keeps the sustainable population dynamics for more than 2 years after inoculation only by adding light diurnally and controlling temperature at 25 degree Celsius. Objective of the study is to develop the particle-based computer simulation by reviewing interactions among microbes and environment, and analyze the ecological toxicities of radiation on the microcosm by replicating experimental results in the computer simulation. (Author) 14 refs
Cosmo Cassette: A Microfluidic Microgravity Microbial System For Synthetic Biology Unit Tests and Satellite Missions

Science.gov (United States)

Berliner, Aaron J.

2013-01-01

Although methods in the design-build-test life cycle of the synthetic biology field have grown rapidly, the expansion has been non-uniform. The design and build stages in development have seen innovations in the form of biological CAD and more efficient means for building DNA, RNA, and other biological constructs. The testing phase of the cycle remains in need of innovation. Presented will be both a theoretical abstraction of biological measurement and a practical demonstration of a microfluidics-based platform for characterizing synthetic biological phenomena. Such a platform demonstrates a design of additive manufacturing (3D printing) for construction of a microbial fuel cell (MFC) to be used in experiments carried out in space. First, the biocompatibility of the polypropylene chassis will be demonstrated. The novel MFCs will be cheaper, and faster to make and iterate through designs. The novel design will contain a manifold switchingdistribution system and an integrated in-chip set of reagent reservoirs fabricated via 3D printing. The automated nature of the 3D printing yields itself to higher resolution switching valves and leads to smaller sized payloads, lower cost, reduced power and a standardized platform for synthetic biology unit tests on Earth and in space. It will be demonstrated that the application of unit testing in synthetic biology will lead to the automatic construction and validation of desired constructs. Unit testing methodologies offer benefits of preemptive problem identification, change of facility, simplicity of integration, ease of documentation, and separation of interface from implementation, and automated design.
Molecular microbial ecology manual

NARCIS (Netherlands)

Kowalchuk, G.A.; Bruijn, de F.J.; Head, I.M.; Akkermans, A.D.L.

2004-01-01

The field of microbial ecology has been revolutionized in the past two decades by the introduction of molecular methods into the toolbox of the microbial ecologist. This molecular arsenal has helped to unveil the enormity of microbial diversity across the breadth of the earth's ecosystems, and has

Modern Microbial Ecosystems are a Key to Understanding Our Biosphere's Early Evolution and its Contributions To The Atmosphere and Rock Record

Science.gov (United States)

DesMarais, David J.; DeVincenzi, Donald L. (Technical Monitor)

2000-01-01

The survival of our early biosphere depended upon efficient coordination anion- diverse microbial populations. Microbial mats exhibit a 3.46-billion-year fossil record, thus they are the oldest known ecosystems. Photosynthetic microbial mats were key because, today, sunlight powers more than 99 percent of global primary productivity. Thus photosynthetic ecosystems have affected the atmosphere profoundly and have created the most pervasive, easily-detected fossils. Photosynthetic biospheres elsewhere will be most detectible via telescopes or spacecraft. As a part of the Astrobiology Institute, our Ames Microbial Ecosystems group examines the roles played by ecological processes in the early evolution of our biosphere, as recorded in geologic fossils and in the macromolecules of living cells: (1) We are defining the microbial mat microenvironment, which was an important milieu for early evolution. (2) We are comparing mats in contrasting environments to discern strategies of adaptation and diversification, traits that were key for long-term survival. (3) We have selected sites that mimic key environmental attributes of early Earth and thereby focus upon evolutionary adaptations to long-term changes in the global environment. (4) Our studies of gas exchange contribute to better estimates of biogenic gases in Earth's early atmosphere. This group therefore directly addresses the question: How have the Earth and its biosphere influenced each other over time Our studies strengthen the systematics for interpreting the microbial fossil record and thereby enhance astrobiological studies of martian samples. Our models of biogenic gas emissions will enhance models of atmospheres that might be detected on inhabited extrasolar planets. This work therefore also addresses the question: How can other biospheres be recogniZed" Our choice of field sites helps us explore Earth's evolving early environment. For example, modern mats that occupy thermal springs and certain freshwater
[Fibers as carriers of microbial particles].

Science.gov (United States)

Górny, Rafał L; Ławniczek-Wałczyk, Anna; Stobnicka, Agata; Gołofit-Szymczak, Małgorzata; Cyprowski, Marcin

2015-01-01

The aim of the study was to assess the ability of natural, synthetic and semi-synthetic fibers to transport microbial particles. The simultaneously settled dust and aerosol sampling was carried out in 3 industrial facilities processing natural (cotton, silk, flax, hemp), synthetic (polyamide, polyester, polyacrylonitrile, polypropylene) and semi-synthetic (viscose) fibrous materials; 2 stables where horses and sheep were bred; 4 homes where dogs or cats were kept and 1 zoo lion pavilion. All samples were laboratory analyzed for their microbiological purity. The isolated strains were qualitatively identified. To identify the structure and arrangement of fibers that may support transport of microbial particles, a scanning electron microscopy analysis was performed. Both settled and airborne fibers transported analogous microorganisms. All synthetic, semi-synthetic and silk fibers, present as separated threads with smooth surface, were free from microbial contamination. Natural fibers with loose packing and rough surface (e.g., wool, horse hair), sheaf packing and septated surface (e.g., flax, hemp) or present as twisted ribbons with corrugated surface (cotton) were able to carry up to 9×10(5) cfu/g aerobic bacteria, 3.4×10(4) cfu/g anaerobic bacteria and 6.3×10(4) cfu/g of fungi, including pathogenic strains classified by Directive 2000/54/EC in hazard group 2. As plant and animal fibers are contaminated with a significant number of microorganisms, including pathogens, all of them should be mechanically eliminated from the environment. In factories, if the manufacturing process allows, they should be replaced by synthetic or semi-synthetic fibers. To avoid unwanted exposure to harmful microbial agents on fibers, the containment measures that efficiently limit their presence and dissemination in both occupational and non-occupational environments should be introduced. This work is available in Open Access model and licensed under a CC BY-NC 3.0 PL license.
Fibers as carriers of microbial particles

Directory of Open Access Journals (Sweden)

Rafał L. Górny

2015-08-01

Full Text Available Background: The aim of the study was to assess the ability of natural, synthetic and semi-synthetic fibers to transport microbial particles. Material and Methods: The simultaneously settled dust and aerosol sampling was carried out in 3 industrial facilities processing natural (cotton, silk, flax, hemp, synthetic (polyamide, polyester, polyacrylonitrile, polypropylene and semi-synthetic (viscose fibrous materials; 2 stables where horses and sheep were bred; 4 homes where dogs or cats were kept and 1 zoo lion pavilion. All samples were laboratory analyzed for their microbiological purity. The isolated strains were qualitatively identified. To identify the structure and arrangement of fibers that may support transport of microbial particles, a scanning electron microscopy analysis was performed. Results: Both settled and airborne fibers transported analogous microorganisms. All synthetic, semi-synthetic and silk fibers, present as separated threads with smooth surface, were free from microbial contamination. Natural fibers with loose packing and rough surface (e.g., wool, horse hair, sheaf packing and septated surface (e.g., flax, hemp or present as twisted ribbons with corrugated surface (cotton were able to carry up to 9×105 cfu/g aerobic bacteria, 3.4×104 cfu/g anaerobic bacteria and 6.3×104 cfu/g of fungi, including pathogenic strains classified by Directive 2000/54/EC in hazard group 2. Conclusions: As plant and animal fibers are contaminated with a significant number of microorganisms, including pathogens, all of them should be mechanically eliminated from the environment. In factories, if the manufacturing process allows, they should be replaced by synthetic or semi-synthetic fibers. To avoid unwanted exposure to harmful microbial agents on fibers, the containment measures that efficiently limit their presence and dissemination in both occupational and non-occupational environments should be introduced. Med Pr 2015;66(4:511–523
Strong linkage between active microbial communities and microbial carbon usage in a deglaciated terrain of the High Arctic

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Kim, M.; Gyeong, H. R.; Lee, Y. K.

2017-12-01

Soil microorganisms play pivotal roles in ecosystem development and carbon cycling in newly exposed glacier forelands. However, little is known about carbon utilization pattern by metabolically active microbes over the course of ecosystem succession in these nutrient-poor environments. We investigated RNA-based microbial community dynamics and its relation to microbial carbon usage along the chronosequence of a High Arctic glacier foreland. Among microbial taxa surveyed (bacteria, archaea and fungi), bacteria are among the most metabolically active taxa with a dominance of Cyanobacteria and Actinobacteria. There was a strong association between microbial carbon usage and active Actinobacterial communities, suggesting that member of Actinobacteria are actively involved in organic carbon degradation in glacier forelands. Both bacterial community and microbial carbon usage are converged towards later stage of succession, indicating that the composition of soil organic carbon plays important roles in structuring bacterial decomposer communities during ecosystem development.
The YNP Metagenome Project: Environmental Parameters Responsible for Microbial Distribution in the Yellowstone Geothermal Ecosystem

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William P. Inskeep

2013-05-01

Full Text Available The Yellowstone geothermal complex contains over 10,000 diverse geothermal features that host numerous phylogenetically deeply-rooted and poorly understood archaea, bacteria and viruses. Microbial communities in high-temperature environments are generally less diverse than soil, marine, sediment or lake habitats and therefore offer a tremendous opportunity for studying the structure and function of different model microbial communities using environmental metagenomics. One of the broader goals of this study was to establish linkages among microbial distribution, metabolic potential and environmental variables. Twenty geochemically distinct geothermal ecosystems representing a broad spectrum of Yellowstone hot-spring environments were used for metagenomic and geochemical analysis and included approximately equal numbers of: (1 phototrophic mats, (2 ‘filamentous streamer’ communities, and (3 archaeal-dominated sediments. The metagenomes were analyzed using a suite of complementary and integrative bioinformatic tools, including phylogenetic and functional analysis of both individual sequence reads and assemblies of predominant phylotypes. This volume identifies major environmental determinants of a large number of thermophilic microbial lineages, many of which have not been fully described in the literature nor previously cultivated to enable functional and genomic analyses. Moreover, protein family abundance comparisons and in-depth analyses of specific genes and metabolic pathways relevant to these hot-spring environments reveal hallmark signatures of metabolic capabilities that parallel the distribution of phylotypes across specific types of geochemical environments.
Diversity of key players in the microbial ecosystems of the human body.

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Jordán, Ferenc; Lauria, Mario; Scotti, Marco; Nguyen, Thanh-Phuong; Praveen, Paurush; Morine, Melissa; Priami, Corrado

2015-10-30

Coexisting bacteria form various microbial communities in human body parts. In these ecosystems they interact in various ways and the properties of the interaction network can be related to the stability and functional diversity of the local bacterial community. In this study, we analyze the interaction network among bacterial OTUs in 11 locations of the human body. These belong to two major groups. One is the digestive system and the other is the female genital tract. In each local ecosystem we determine the key species, both the ones being in key positions in the interaction network and the ones that dominate by frequency. Beyond identifying the key players and discussing their biological relevance, we also quantify and compare the properties of the 11 networks. The interaction networks of the female genital system and the digestive system show totally different architecture. Both the topological properties and the identity of the key groups differ. Key groups represent four phyla of prokaryotes. Some groups appear in key positions in several locations, while others are assigned only to a single body part. The key groups of the digestive and the genital tracts are totally different.
Unravelling core microbial metabolisms in the hypersaline microbial mats of Shark Bay using high-throughput metagenomics

Energy Technology Data Exchange (ETDEWEB)

Ruvindy, Rendy; White III, Richard Allen; Neilan, Brett Anthony; Burns, Brendan Paul

2015-05-29

Modern microbial mats are potential analogues of some of Earth’s earliest ecosystems. Excellent examples can be found in Shark Bay, Australia, with mats of various morphologies. To further our understanding of the functional genetic potential of these complex microbial ecosystems, we conducted for the first time shotgun metagenomic analyses. We assembled metagenomic nextgeneration sequencing data to classify the taxonomic and metabolic potential across diverse morphologies of marine mats in Shark Bay. The microbial community across taxonomic classifications using protein-coding and small subunit rRNA genes directly extracted from the metagenomes suggests that three phyla Proteobacteria, Cyanobacteria and Bacteriodetes dominate all marine mats. However, the microbial community structure between Shark Bay and Highbourne Cay (Bahamas) marine systems appears to be distinct from each other. The metabolic potential (based on SEED subsystem classifications) of the Shark Bay and Highbourne Cay microbial communities were also distinct. Shark Bay metagenomes have a metabolic pathway profile consisting of both heterotrophic and photosynthetic pathways, whereas Highbourne Cay appears to be dominated almost exclusively by photosynthetic pathways. Alternative non-rubisco-based carbon metabolism including reductive TCA cycle and 3-hydroxypropionate/4-hydroxybutyrate pathways is highly represented in Shark Bay metagenomes while not represented in Highbourne Cay microbial mats or any other mat forming ecosystems investigated to date. Potentially novel aspects of nitrogen cycling were also observed, as well as putative heavy metal cycling (arsenic, mercury, copper and cadmium). Finally, archaea are highly represented in Shark Bay and may have critical roles in overall ecosystem function in these modern microbial mats.
Molecular ecology of microbial mats

NARCIS (Netherlands)

Bolhuis, H.; Cretoiu, M.S.; Stal, L.J.

2014-01-01

Phototrophic microbial mats are ideal model systems for ecological and evolutionary analysis of highly diverse microbial communities. Microbial mats are small-scale, nearly closed, and self-sustaining benthic ecosystems that comprise the major element cycles, trophic levels, and food webs. The steep
New directions in coral reef microbial ecology.

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Garren, Melissa; Azam, Farooq

2012-04-01

Microbial processes largely control the health and resilience of coral reef ecosystems, and new technologies have led to an exciting wave of discovery regarding the mechanisms by which microbial communities support the functioning of these incredibly diverse and valuable systems. There are three questions at the forefront of discovery: What mechanisms underlie coral reef health and resilience? How do environmental and anthropogenic pressures affect ecosystem function? What is the ecology of microbial diseases of corals? The goal is to understand the functioning of coral reefs as integrated systems from microbes and molecules to regional and ocean-basin scale ecosystems to enable accurate predictions of resilience and responses to perturbations such as climate change and eutrophication. This review outlines recent discoveries regarding the microbial ecology of different microenvironments within coral ecosystems, and highlights research directions that take advantage of new technologies to build a quantitative and mechanistic understanding of how coral health is connected through microbial processes to its surrounding environment. The time is ripe for natural resource managers and microbial ecologists to work together to create an integrated understanding of coral reef functioning. In the context of long-term survival and conservation of reefs, the need for this work is immediate. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.
Maintenance of Geobacter-dominated biofilms in microbial fuel cells treating synthetic wastewater.

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Commault, Audrey S; Lear, Gavin; Weld, Richard J

2015-12-01

Geobacter-dominated biofilms can be selected under stringent conditions that limit the growth of competing bacteria. However, in many practical applications, such stringent conditions cannot be maintained and the efficacy and stability of these artificial biofilms may be challenged. In this work, biofilms were selected on low-potential anodes (-0.36 V vs Ag/AgCl, i.e. -0.08 V vs SHE) in minimal acetate or ethanol media. Selection conditions were then relaxed by transferring the biofilms to synthetic wastewater supplemented with soil as a source of competing bacteria. We tracked community succession and functional changes in these biofilms. The Geobacter-dominated biofilms showed stability in their community composition and electrochemical properties, with Geobacter sp. being still electrically active after six weeks in synthetic wastewater with power densities of 100±19 mW·m(-2) (against 74±14 mW·m(-2) at week 0) for all treatments. After six weeks, the ethanol-selected biofilms, despite their high taxon richness and their efficiency at removing the chemical oxygen demand (0.8 g·L(-1) removed against the initial 1.3 g·L(-1) injected), were the least stable in terms of community structure. These findings have important implications for environmental microbial fuel cells based on Geobacter-dominated biofilms and suggest that they could be stable in challenging environments. Copyright © 2015 Elsevier B.V. All rights reserved.
Soil microbial responses to climate warming in Northern Andean alpine ecosystems

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Gallery, R. E.; Lasso, E.

2017-12-01

The historically cooler temperatures and waterlogged soils of tropical alpine grasslands (páramo) have resulted in low decomposition rates and a large buildup of organic matter, making páramo one of the most important carbon sinks in tropical biomes. The climatic factors that favored the carbon accumulation are changing, and as a result páramo could play a disproportionate role in driving climate feedbacks through increased carbon released from these large soil carbon stores. Open top chamber warming experiments were established in the Colombian Andes in 2016 to quantify the magnitude of climate change on carbon balance and identify microbial and plant traits that regulate these impacts. Two focal sites differ in mean annual temperature, precipitation, and plant community richness. Heterotrophic respiration (RH,) was measured from soil cores incubated at temperatures representing current and projected warming. The warming effect on RH was sensitive to soil moisture, which could reflect shifts in microbial community composition and/or extracellular enzyme production or efficiency as soils dry. Bacterial, archaeal, and fungal communities in ambient and warmed plots were measured through high-throughput amplicon sequencing of the 16S rRNA and ITS1 rRNA gene regions. Communities showed strong spatial structuring both within and among páramo, reflecting the topographic heterogeneity of these ecosystems. Significant differences in relative abundance of dominant microbial taxa between páramo could be largely explained by soil bulk density, water holding capacity, and non-vascular plant cover. Phototrophs common to anoxic soils (e.g., Rhodospirillaceae, Hyphomicrobiaceae) were abundant. Taxa within Euryarchaeota were recovered, suggesting methanogenesis potential. Exploration of the magnitude and temperature sensitivity of methane flux is needed in these seasonally anoxic soils whose dynamics could have significant implications for the global climate system.
Microbial ecology of mountain glacier ecosystems: biodiversity, ecological connections and implications of a warming climate.

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Hotaling, Scott; Hood, Eran; Hamilton, Trinity L

2017-08-01

Glacier ecosystems are teeming with life on, beneath, and to a lesser degree, within their icy masses. This conclusion largely stems from polar research, with less attention paid to mountain glaciers that overlap environmentally and ecologically with their polar counterparts in some ways, but diverge in others. One difference lies in the susceptibility of mountain glaciers to the near-term threat of climate change, as they tend to be much smaller in both area and volume. Moreover, mountain glaciers are typically steeper, more dependent upon basal sliding for movement, and experience higher seasonal precipitation. Here, we provide a modern synthesis of the microbial ecology of mountain glacier ecosystems, and particularly those at low- to mid-latitudes. We focus on five ecological zones: the supraglacial surface, englacial interior, subglacial bedrock-ice interface, proglacial streams and glacier forefields. For each, we discuss the role of microbiota in biogeochemical cycling and outline ecological and hydrological connections among zones, underscoring the interconnected nature of these ecosystems. Collectively, we highlight the need to: better document the biodiversity and functional roles of mountain glacier microbiota; describe the ecological implications of rapid glacial retreat under climate change and resolve the relative contributions of ecological zones to broader ecosystem function. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.
Genome-driven evolutionary game theory helps understand the rise of metabolic interdependencies in microbial communities.

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Zomorrodi, Ali R; Segrè, Daniel

2017-11-16

Metabolite exchanges in microbial communities give rise to ecological interactions that govern ecosystem diversity and stability. It is unclear, however, how the rise of these interactions varies across metabolites and organisms. Here we address this question by integrating genome-scale models of metabolism with evolutionary game theory. Specifically, we use microbial fitness values estimated by metabolic models to infer evolutionarily stable interactions in multi-species microbial "games". We first validate our approach using a well-characterized yeast cheater-cooperator system. We next perform over 80,000 in silico experiments to infer how metabolic interdependencies mediated by amino acid leakage in Escherichia coli vary across 189 amino acid pairs. While most pairs display shared patterns of inter-species interactions, multiple deviations are caused by pleiotropy and epistasis in metabolism. Furthermore, simulated invasion experiments reveal possible paths to obligate cross-feeding. Our study provides genomically driven insight into the rise of ecological interactions, with implications for microbiome research and synthetic ecology.
Long-term effects of irrigation with waste water on soil AM fungi diversity and microbial activities: the implications for agro-ecosystem resilience.

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Maria del Mar Alguacil

Full Text Available The effects of irrigation with treated urban wastewater (WW on the arbuscular mycorrhizal fungi (AMF diversity and soil microbial activities were assayed on a long-term basis in a semiarid orange-tree orchard. After 43 years, the soil irrigated with fresh water (FW had higher AMF diversity than soils irrigated with WW. Microbial activities were significantly higher in the soils irrigated with WW than in those irrigated with FW. Therefore, as no negative effects were observed on crop vitality and productivity, it seems that the ecosystem resilience gave rise to the selection of AMF species better able to thrive in soils with higher microbial activity and, thus, to higher soil fertility.
Reconstructing the Genetic Potential of the Microbially-Mediated Nitrogen Cycle in a Salt Marsh Ecosystem.

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Dini-Andreote, Francisco; Brossi, Maria Julia de L; van Elsas, Jan Dirk; Salles, Joana F

2016-01-01

Coastal ecosystems are considered buffer zones for the discharge of land-derived nutrients without accounting for potential negative side effects. Hence, there is an urgent need to better understand the ecological assembly and dynamics of the microorganisms that are involved in nitrogen (N) cycling in such systems. Here, we employed two complementary methodological approaches (i.e., shotgun metagenomics and quantitative PCR) to examine the distribution and abundance of selected microbial genes involved in N transformations. We used soil samples collected along a well-established pristine salt marsh soil chronosequence that spans over a century of ecosystem development at the island of Schiermonnikoog, The Netherlands. Across the examined soil successional stages, the structure of the populations of genes involved in N cycling processes was strongly related to (shifts in the) soil nitrogen levels (i.e., [Formula: see text], [Formula: see text]), salinity and pH (explaining 73.8% of the total variation, R (2) = 0.71). Quantification of the genes used as proxies for N fixation, nitrification and denitrification revealed clear successional signatures that corroborated the taxonomic assignments obtained by metagenomics. Notably, we found strong evidence for niche partitioning, as revealed by the abundance and distribution of marker genes for nitrification (ammonia-oxidizing bacteria and archaea) and denitrification (nitrite reductase nirK, nirS and nitrous oxide reductase nosZ clades I and II). This was supported by a distinct correlation between these genes and soil physico-chemical properties, such as soil physical structure, pH, salinity, organic matter, total N, [Formula: see text], [Formula: see text] and [Formula: see text], across four seasonal samplings. Overall, this study sheds light on the successional trajectories of microbial N cycle genes along a naturally developing salt marsh ecosystem. The data obtained serve as a foundation to guide the formulation of
Assessing Impacts of Unconventional Natural Gas Extraction on Microbial Communities in Headwater Stream Ecosystems in Northwestern Pennsylvania

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Ryan eTrexler

2014-11-01

Full Text Available Hydraulic fracturing and horizontal drilling have increased dramatically in Pennsylvania Marcellus shale formations, however the potential for major environmental impacts are still incompletely understood. High-throughput sequencing of the 16S rRNA gene was performed to characterize the microbial community structure of water, sediment, bryophyte, and biofilm samples from 26 headwater stream sites in northwestern Pennsylvania with different histories of fracking activity within Marcellus shale play. Further, we describe the relationship between microbial community structure and environmental parameters measured. Approximately 3.2 million 16S rRNA gene sequences were retrieved from a total of 58 samples. Microbial community analyses showed significant reductions in species richness as well as evenness in sites with Marcellus shale activity (MSA+. Beta diversity analyses revealed distinct microbial community structure between sites with and without Marcellus shale activity (MSA-. For example, OTUs within the Acetobacteracea, Methylocystaceae, Acidobacteriaceae, and Phenylobacterium were greater than three log-fold more abundant in MSA+ sites as compared to MSA- sites. Further, several of these OTUs were strongly negatively correlated with pH and positively correlated with the number of wellpads in a watershed. It should be noted that many of the OTUs enriched in MSA+ sites are putative acidophilic and/or methanotrophic populations. This study revealed apparent shifts in the autochthonous microbial communities and highlighted potential members that could be responding to changing stream conditions as a result of nascent industrial activity in these aquatic ecosystems.
Assessing impacts of unconventional natural gas extraction on microbial communities in headwater stream ecosystems in Northwestern Pennsylvania

Science.gov (United States)

Trexler, Ryan; Solomon, Caroline; Brislawn, Colin J.; Wright, Justin R.; Rosenberger, Abigail; McClure, Erin E.; Grube, Alyssa M.; Peterson, Mark P.; Keddache, Mehdi; Mason, Olivia U.; Hazen, Terry C.; Grant, Christopher J.; Lamendella, Regina

2014-01-01

Hydraulic fracturing and horizontal drilling have increased dramatically in Pennsylvania Marcellus shale formations, however the potential for major environmental impacts are still incompletely understood. High-throughput sequencing of the 16S rRNA gene was performed to characterize the microbial community structure of water, sediment, bryophyte, and biofilm samples from 26 headwater stream sites in northwestern Pennsylvania with different histories of fracking activity within Marcellus shale formations. Further, we describe the relationship between microbial community structure and environmental parameters measured. Approximately 3.2 million 16S rRNA gene sequences were retrieved from a total of 58 samples. Microbial community analyses showed significant reductions in species richness as well as evenness in sites with Marcellus shale activity. Beta diversity analyses revealed distinct microbial community structure between sites with and without Marcellus shale activity. For example, operational taxonomic units (OTUs) within the Acetobacteracea, Methylocystaceae, Acidobacteriaceae, and Phenylobacterium were greater than three log-fold more abundant in MSA+ sites as compared to MSA− sites. Further, several of these OTUs were strongly negatively correlated with pH and positively correlated with the number of wellpads in a watershed. It should be noted that many of the OTUs enriched in MSA+ sites are putative acidophilic and/or methanotrophic populations. This study revealed apparent shifts in the autochthonous microbial communities and highlighted potential members that could be responding to changing stream conditions as a result of nascent industrial activity in these aquatic ecosystems. PMID:25408683
Microbial ecology of terrestrial Antarctica: Are microbial systems at risk from human activities?

Energy Technology Data Exchange (ETDEWEB)

White, G.J.

1996-08-01

Many of the ecological systems found in continental Antarctica are comprised entirely of microbial species. Concerns have arisen that these microbial systems might be at risk either directly through the actions of humans or indirectly through increased competition from introduced species. Although protection of native biota is covered by the Protocol on Environmental Protection to the Antarctic Treaty, strict measures for preventing the introduction on non-native species or for protecting microbial habitats may be impractical. This report summarizes the research conducted to date on microbial ecosystems in continental Antarctica and discusses the need for protecting these ecosystems. The focus is on communities inhabiting soil and rock surfaces in non-coastal areas of continental Antarctica. Although current polices regarding waste management and other operations in Antarctic research stations serve to reduce the introduction on non- native microbial species, importation cannot be eliminated entirely. Increased awareness of microbial habitats by field personnel and protection of certain unique habitats from physical destruction by humans may be necessary. At present, small-scale impacts from human activities are occurring in certain areas both in terms of introduced species and destruction of habitat. On a large scale, however, it is questionable whether the introduction of non-native microbial species to terrestrial Antarctica merits concern.
Microbial bioenergetics of coral-algal interactions

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Ty N.F. Roach

2017-06-01

Full Text Available Human impacts are causing ecosystem phase shifts from coral- to algal-dominated reef systems on a global scale. As these ecosystems undergo transition, there is an increased incidence of coral-macroalgal interactions. Mounting evidence indicates that the outcome of these interaction events is, in part, governed by microbially mediated dynamics. The allocation of available energy through different trophic levels, including the microbial food web, determines the outcome of these interactions and ultimately shapes the benthic community structure. However, little is known about the underlying thermodynamic mechanisms involved in these trophic energy transfers. This study utilizes a novel combination of methods including calorimetry, flow cytometry, and optical oxygen measurements, to provide a bioenergetic analysis of coral-macroalgal interactions in a controlled aquarium setting. We demonstrate that the energetic demands of microbial communities at the coral-algal interaction interface are higher than in the communities associated with either of the macroorganisms alone. This was evident through higher microbial power output (energy use per unit time and lower oxygen concentrations at interaction zones compared to areas distal from the interface. Increases in microbial power output and lower oxygen concentrations were significantly correlated with the ratio of heterotrophic to autotrophic microbes but not the total microbial abundance. These results suggest that coral-algal interfaces harbor higher proportions of heterotrophic microbes that are optimizing maximal power output, as opposed to yield. This yield to power shift offers a possible thermodynamic mechanism underlying the transition from coral- to algal-dominated reef ecosystems currently being observed worldwide. As changes in the power output of an ecosystem are a significant indicator of the current state of the system, this analysis provides a novel and insightful means to quantify
Microbially derived biosensors for diagnosis, monitoring and epidemiology.

Science.gov (United States)

Chang, Hung-Ju; Voyvodic, Peter L; Zúñiga, Ana; Bonnet, Jérôme

2017-09-01

Living cells have evolved to detect and process various signals and can self-replicate, presenting an attractive platform for engineering scalable and affordable biosensing devices. Microbes are perfect candidates: they are inexpensive and easy to manipulate and store. Recent advances in synthetic biology promise to streamline the engineering of microbial biosensors with unprecedented capabilities. Here we review the applications of microbially-derived biosensors with a focus on environmental monitoring and healthcare applications. We also identify critical challenges that need to be addressed in order to translate the potential of synthetic microbial biosensors into large-scale, real-world applications. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Microbial ecology of deep-water mid-Atlantic canyons

Science.gov (United States)

Kellogg, Christina A.

2011-01-01

The research described in this fact sheet will be conducted from 2012 to 2014 as part of the U.S. Geological Survey's DISCOVRE (DIversity, Systematics, and COnnectivity of Vulnerable Reef Ecosystems) Program. This integrated, multidisciplinary effort will be investigating a variety of topics related to unique and fragile deep-sea ecosystems from the microscopic level to the ecosystem level. One goal is to improve understanding, at the microbiological scale, of the benthic communities (including corals) that reside in and around mid-Atlantic canyon habitats and their associated environments. Specific objectives include identifying and characterizing the microbial associates of deep-sea corals, characterizing the microbial biofilms on hard substrates to better determine their role in engineering the ecosystem, and adding a microbial dimension to benthic community structure and function assessments by characterizing micro-eukaryotes, bacteria, and archaea in deep-sea sediments.
Recent applications of synthetic biology tools for yeast metabolic engineering

DEFF Research Database (Denmark)

Jensen, Michael Krogh; Keasling, Jay

2015-01-01

to engineer microbial chemical factories has steadily decreased, improvement is still needed. Through the development of synthetic biology tools for key microbial hosts, it should be possible to further decrease the development times and improve the reliability of the resulting microorganism. Together...... with continuous decreases in price and improvements in DNA synthesis, assembly and sequencing, synthetic biology tools will rationalize time-consuming strain engineering, improve control of metabolic fluxes, and diversify screening assays for cellular metabolism. This review outlines some recently developed...... synthetic biology tools and their application to improve production of chemicals and fuels in yeast. Finally, we provide a perspective for the challenges that lie ahead....
Effects of Elevated Carbon Dioxide and Salinity on the Microbial Diversity in Lithifying Microbial Mats

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Steven R. Ahrendt

2014-03-01

Full Text Available Atmospheric levels of carbon dioxide (CO2 are rising at an accelerated rate resulting in changes in the pH and carbonate chemistry of the world’s oceans. However, there is uncertainty regarding the impact these changing environmental conditions have on carbonate-depositing microbial communities. Here, we examine the effects of elevated CO2, three times that of current atmospheric levels, on the microbial diversity associated with lithifying microbial mats. Lithifying microbial mats are complex ecosystems that facilitate the trapping and binding of sediments, and/or the precipitation of calcium carbonate into organosedimentary structures known as microbialites. To examine the impact of rising CO2 and resulting shifts in pH on lithifying microbial mats, we constructed growth chambers that could continually manipulate and monitor the mat environment. The microbial diversity of the various treatments was compared using 16S rRNA gene pyrosequencing. The results indicated that elevated CO2 levels during the six month exposure did not profoundly alter the microbial diversity, community structure, or carbonate precipitation in the microbial mats; however some key taxa, such as the sulfate-reducing bacteria Deltasulfobacterales, were enriched. These results suggest that some carbonate depositing ecosystems, such as the microbialites, may be more resilient to anthropogenic-induced environmental change than previously thought.
Insights into the Processing of Carbon by Early Microbial Ecosystems

Science.gov (United States)

DesMarais, D.; Bebout, B.; Carpenter, S.; Discipulo, S.; Londry, K.; Habicht, K.; Turk, K.

2003-01-01

Interactions between Earth and the biosphere that were crucial for early biological evolution also influenced substantially the processes that circulate C between its reservoirs in the atmosphere, ocean, crust and mantle. The C-13 C-12 values of crustal carbonates and organics have recorded changes both in biological discrimination and in the relative rates of burial of organics and carbonates. A full interpretation of these patterns needs further isotopic studies of microbial ecosystems and individual anaerobes. Thus we measured carbon isotope discrimination during autotrophic and heterotrophic growth of pure cultures of sulfate-reducing bacteria and archaea (SRB and SRA). Discrimination during CO2 assimilation is significantly larger than during heterotrophic growth on lactate or acetate. SRB grown lithoautotrophically consumed less than 3% of available CO2 and exhibited substantial discrimination, as follows: Desulfobacterium autotrophicum (alpha 1.0100 to 1.0123), Desulfobacter hydrogenophilus (alpha = 0.0138), and Desulfotomuculum acetoxidans (alpha = 1.0310). Mixotrophic growth of Desulfovibrio desulfuricans on acetate and CO2 resulted in biomass with delta C-13 composition intermediate to that of the substrates. We have recently extended these experiments to include the thermophilic SRA Archeoglobus spp. Ecological forces also influence isotopic discrimination. Accordingly, we quantified the flow of C and other constituents in modern marine cyanobacterial mats, whose ancestry extends back billions of years. Such ecosystem processes shaped the biosignatures that entered sediments and atmospheres. At Guerrero Negro, BCS, Mexico, we examined mats dominated by Microcoleus (subtidal) and Lyngbya (intertidal to supratidal) cyanobacteria. During 24 hour cycles, we observed the exchange of O2 and dissolved inorganic C (DIC) between mats and the overlying water. Microcoleus mats assimilated near-equal amounts of DIC during the day as they released at night, but
Stream microbial diversity responds to environmental changes: Review and synthesis of existing research

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Lydia eZeglin

2015-05-01

Full Text Available The importance of microbial activity to ecosystem function in aquatic ecosystems is well established, but microbial diversity has been less frequently addressed. This review and synthesis of the hundreds of published studies on stream microbial diversity shows that factors known to drive ecosystem processes, such as nutrient availability, hydrology, metal contamination, contrasting land-use and temperature, also cause heterogeneity in bacterial diversity. Temporal heterogeneity in stream bacterial diversity was frequently observed, reflecting the dynamic nature of both stream ecosystems and microbial community composition. However, within-stream spatial differences in stream bacterial diversity were more commonly observed, driven specifically by different organic matter compartments. Bacterial phyla showed similar patterns in relative abundance with regard to compartment type across different streams. For example, surface water contained the highest relative abundance of Actinobacteria, while epilithon contained the highest relative abundance of Cyanobacteria and Bacteroidetes. This suggests that contrasting physical and/or nutritional habitats characterized by different stream organic matter compartment types may select for certain bacterial lineages. When comparing the prevalence of physicochemical effects on stream bacterial diversity, effects of changing metal concentrations were most, while effects of differences in nutrient concentrations were least frequently observed. This may indicate that although changing nutrient concentrations do tend to affect microbial diversity, other environmental factors are more likely to alter stream microbial diversity and function. The common observation of connections between ecosystem process drivers and microbial diversity suggests that microbial taxonomic turnover could mediate ecosystem-scale responses to changing environmental conditions, including both microbial habitat distribution and
Seasonal microbial and nutrient responses during a 5-year reduction in the daily temperature range of soil in a Chihuahuan Desert ecosystem.

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van Gestel, Natasja C; Dhungana, Nirmala; Tissue, David T; Zak, John C

2016-01-01

High daily temperature range of soil (DTRsoil) negatively affects soil microbial biomass and activity, but its interaction with seasonal soil moisture in regulating ecosystem function remains unclear. For our 5-year field study in the Chihuahuan Desert, we suspended shade cloth 15 cm above the soil surface to reduce daytime temperature and increase nighttime soil temperature compared to unshaded plots, thereby reducing DTRsoil (by 5 ºC at 0.2 cm depth) without altering mean temperatures. Microbial biomass production was primarily regulated by seasonal precipitation with the magnitude of the response dependent on DTRsoil. Reduced DTRsoil more consistently increased microbial biomass nitrogen (MBN; +38%) than microbial biomass carbon (MBC) with treatment responses being similar in spring and summer. Soil respiration depended primarily on soil moisture with responses to reduced DTRsoil evident only in wetter summer soils (+53%) and not in dry spring soils. Reduced DTRsoil had no effect on concentrations of dissolved organic C, soil organic matter (SOM), nor soil inorganic N (extractable NO3 (-)-N + NH4 (+)-N). Higher MBN without changes in soil inorganic N suggests faster N cycling rates or alternate sources of N. If N cycling rates increased without a change to external N inputs (atmospheric N deposition or N fixation), then productivity in this desert system, which is N-poor and low in SOM, could be negatively impacted with continued decreases in daily temperature range. Thus, the future N balance in arid ecosystems, under conditions of lower DTR, seems linked to future precipitation regimes through N deposition and regulation of soil heat load dynamics.
A multitrophic model to quantify the effects of marine viruses on microbial food webs and ecosystem processes

DEFF Research Database (Denmark)

Weitz, Joshua S.; Stock, Charles A.; Wilhelm, Steven W.

2015-01-01

Viral lysis of microbial hosts releases organic matter that can then be assimilated by nontargeted microorganisms. Quantitative estimates of virus-mediated recycling of carbon in marine waters, first established in the late 1990s, were originally extrapolated from marine host and virus densities......, host carbon content and inferred viral lysis rates. Yet, these estimates did not explicitly incorporate the cascade of complex feedbacks associated with virus-mediated lysis. To evaluate the role of viruses in shaping community structure and ecosystem functioning, we extend dynamic multitrophic...
[Progress in synthetic biology of "973 Funding Program" in China].

Science.gov (United States)

Chen, Guoqiang; Wang, Ying

2015-06-01

This paper reviews progresses made in China from 2011 in areas of "Synthetic Biology" supported by State Basic Research 973 Program. Till the end of 2014, 9 "synthetic biology" projects have been initiated with emphasis on "microbial manufactures" with the 973 Funding Program. Combined with the very recent launch of one project on "mammalian cell synthetic biology" and another on "plant synthetic biology", Chinese "synthetic biology" research reflects its focus on "manufactures" while not giving up efforts on "synthetic biology" of complex systems.
WISB: Warwick Integrative Synthetic Biology Centre.

Science.gov (United States)

McCarthy, John

2016-06-15

Synthetic biology promises to create high-impact solutions to challenges in the areas of biotechnology, human/animal health, the environment, energy, materials and food security. Equally, synthetic biologists create tools and strategies that have the potential to help us answer important fundamental questions in biology. Warwick Integrative Synthetic Biology (WISB) pursues both of these mutually complementary 'build to apply' and 'build to understand' approaches. This is reflected in our research structure, in which a core theme on predictive biosystems engineering develops underpinning understanding as well as next-generation experimental/theoretical tools, and these are then incorporated into three applied themes in which we engineer biosynthetic pathways, microbial communities and microbial effector systems in plants. WISB takes a comprehensive approach to training, education and outreach. For example, WISB is a partner in the EPSRC/BBSRC-funded U.K. Doctoral Training Centre in synthetic biology, we have developed a new undergraduate module in the subject, and we have established five WISB Research Career Development Fellowships to support young group leaders. Research in Ethical, Legal and Societal Aspects (ELSA) of synthetic biology is embedded in our centre activities. WISB has been highly proactive in building an international research and training network that includes partners in Barcelona, Boston, Copenhagen, Madrid, Marburg, São Paulo, Tartu and Valencia. © 2016 The Author(s).
Biogeography of serpentinite-hosted microbial ecosystems

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Brazelton, W.; Cardace, D.; Fruh-Green, G.; Lang, S. Q.; Lilley, M. D.; Morrill, P. L.; Szponar, N.; Twing, K. I.; Schrenk, M. O.

2012-12-01

Ultramafic rocks in the Earth's mantle represent a tremendous reservoir of carbon and reducing power. Upon tectonic uplift and exposure to fluid flow, serpentinization of these materials generates copious energy, sustains abiogenic synthesis of organic molecules, and releases hydrogen gas (H2). To date, however, the "serpentinite microbiome" is poorly constrained- almost nothing is known about the microbial diversity endemic to rocks actively undergoing serpentinization. Through the Census of Deep Life, we have obtained 16S rRNA gene pyrotag sequences from fluids and rocks from serpentinizing ophiolites in California, Canada, and Italy. The samples include high pH serpentinite springs, presumably representative of deeper environments within the ophiolite complex, wells which directly access subsurface aquifers, and rocks obtained from drill cores into serpentinites. These data represent a unique opportunity to examine biogeographic patterns among a restricted set of microbial taxa that are adapted to similar environmental conditions and are inhabiting sites with related geological histories. In general, our results point to potentially H2-utilizing Betaproteobacteria thriving in shallow, oxic-anoxic transition zones and anaerobic Clostridia thriving in anoxic, deep subsurface habitats. These general taxonomic and biogeochemical trends were also observed in seafloor Lost City hydrothermal chimneys, indicating that we are beginning to identify a core serpentinite microbial community that spans marine and continental settings.
Synthetic control of a fitness tradeoff in yeast nitrogen metabolism

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Lee Jack J

2009-01-01

Full Text Available Abstract Background Microbial communities are involved in many processes relevant to industrial and medical biotechnology, such as the formation of biofilms, lignocellulosic degradation, and hydrogen production. The manipulation of synthetic and natural microbial communities and their underlying ecological parameters, such as fitness, evolvability, and variation, is an increasingly important area of research for synthetic biology. Results Here, we explored how synthetic control of an endogenous circuit can be used to regulate a tradeoff between fitness in resource abundant and resource limited environments in a population of Saccharomyces cerevisiae. We found that noise in the expression of a key enzyme in ammonia assimilation, Gdh1p, mediated a tradeoff between growth in low nitrogen environments and stress resistance in high ammonia environments. We implemented synthetic control of an endogenous Gdh1p regulatory network to construct an engineered strain in which the fitness of the population was tunable in response to an exogenously-added small molecule across a range of ammonia environments. Conclusion The ability to tune fitness and biological tradeoffs will be important components of future efforts to engineer microbial communities.
Glycoside Hydrolases across Environmental Microbial Communities.

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Renaud Berlemont

2016-12-01

Full Text Available Across many environments microbial glycoside hydrolases support the enzymatic processing of carbohydrates, a critical function in many ecosystems. Little is known about how the microbial composition of a community and the potential for carbohydrate processing relate to each other. Here, using 1,934 metagenomic datasets, we linked changes in community composition to variation of potential for carbohydrate processing across environments. We were able to show that each ecosystem-type displays a specific potential for carbohydrate utilization. Most of this potential was associated with just 77 bacterial genera. The GH content in bacterial genera is best described by their taxonomic affiliation. Across metagenomes, fluctuations of the microbial community structure and GH potential for carbohydrate utilization were correlated. Our analysis reveals that both deterministic and stochastic processes contribute to the assembly of complex microbial communities.
Industrial systems biology and its impact on synthetic biology of yeast cell factories

DEFF Research Database (Denmark)

Fletcher, Eugene; Krivoruchko, Anastasia; Nielsen, Jens

2016-01-01

Engineering industrial cell factories to effectively yield a desired product while dealing with industrially relevant stresses is usually the most challenging step in the development of industrial production of chemicals using microbial fermentation processes. Using synthetic biology tools......, microbial cell factories such as Saccharomyces cerevisiae can be engineered to express synthetic pathways for the production of fuels, biopharmaceuticals, fragrances, and food flavors. However, directing fluxes through these synthetic pathways towards the desired product can be demanding due to complex...... regulation or poor gene expression. Systems biology, which applies computational tools and mathematical modeling to understand complex biological networks, can be used to guide synthetic biology design. Here, we present our perspective on how systems biology can impact synthetic biology towards the goal...
DOC removal paradigms in highly humic aquatic ecosystems.

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Farjalla, Vinicius F; Amado, André M; Suhett, Albert L; Meirelles-Pereira, Frederico

2009-07-01

Dissolved humic substances (HS) usually comprise 50-80% of the dissolved organic carbon (DOC) in aquatic ecosystems. From a trophic and biogeochemical perspective, HS has been considered to be highly refractory and is supposed to accumulate in the water. The upsurge of the microbial loop paradigm and the studies on HS photo-degradation into labile DOC gave rise to the belief that microbial processing of DOC should sustain aquatic food webs in humic waters. However, this has not been extensively supported by the literature, since most HS and their photo-products are often oxidized by microbes through respiration in most nutrient-poor humic waters. Here, we review basic concepts, classical studies, and recent data on bacterial and photo-degradation of DOC, comparing the rates of these processes in highly humic ecosystems and other aquatic ecosystems. We based our review on classical and recent findings from the fields of biogeochemistry and microbial ecology, highlighting some odd results from highly humic Brazilian tropical lagoons, which can reach up to 160 mg C L(-1). Highly humic tropical lagoons showed proportionally lower bacterial production rates and higher bacterial respiration rates (i.e., lower bacterial growth efficiency) than other lakes. Zooplankton showed similar delta(13)C to microalgae but not to humic DOC in these highly humic lagoons. Thus, the data reviewed here do not support the microbial loop as an efficient matter transfer pathway in highly humic ecosystems, where it is supposed to play its major role. In addition, we found that some tropical humic ecosystems presented the highest potential DOC photo-chemical mineralization (PM) rates reported in the literature, exceeding up to threefold the rates reported for temperate humic ecosystems. We propose that these atypically high PM rates are the result of a joint effect of the seasonal dynamics of allochthonous humic DOC input to these ecosystems and the high sunlight incidence throughout the year
Synthetic biology for manufacturing chemicals: constraints drive the use of non-conventional microbial platforms.

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Czajka, Jeffrey; Wang, Qinhong; Wang, Yechun; Tang, Yinjie J

2017-10-01

Genetically modified microbes have had much industrial success producing protein-based products (such as antibodies and enzymes). However, engineering microbial workhorses for biomanufacturing of commodity compounds remains challenging. First, microbes cannot afford burdens with both overexpression of multiple enzymes and metabolite drainage for product synthesis. Second, synthetic circuits and introduced heterologous pathways are not yet as "robust and reliable" as native pathways due to hosts' innate regulations, especially under suboptimal fermentation conditions. Third, engineered enzymes may lack channeling capabilities for cascade-like transport of metabolites to overcome diffusion barriers or to avoid intermediate toxicity in the cytoplasmic environment. Fourth, moving engineered hosts from laboratory to industry is unreliable because genetic mutations and non-genetic cell-to-cell variations impair the large-scale fermentation outcomes. Therefore, synthetic biology strains often have unsatisfactory industrial performance (titer/yield/productivity). To overcome these problems, many different species are being explored for their metabolic strengths that can be leveraged to synthesize specific compounds. Here, we provide examples of non-conventional and genetically amenable species for industrial manufacturing, including the following: Corynebacterium glutamicum for its TCA cycle-derived biosynthesis, Yarrowia lipolytica for its biosynthesis of fatty acids and carotenoids, cyanobacteria for photosynthetic production from its sugar phosphate pathways, and Rhodococcus for its ability to biotransform recalcitrant feedstock. Finally, we discuss emerging technologies (e.g., genome-to-phenome mapping, single cell methods, and knowledge engineering) that may facilitate the development of novel cell factories.
Nitrogen transformations in stratified aquatic microbial ecosystems

DEFF Research Database (Denmark)

Revsbech, Niels Peter; Risgaard-Petersen, N.; Schramm, Andreas

2006-01-01

Abstract New analytical methods such as advanced molecular techniques and microsensors have resulted in new insights about how nitrogen transformations in stratified microbial systems such as sediments and biofilms are regulated at a µm-mm scale. A large and ever-expanding knowledge base about n...... performing dissimilatory reduction of nitrate to ammonium have given new dimensions to the understanding of nitrogen cycling in nature, and the occurrence of these organisms and processes in stratified microbial communities will be described in detail.......Abstract New analytical methods such as advanced molecular techniques and microsensors have resulted in new insights about how nitrogen transformations in stratified microbial systems such as sediments and biofilms are regulated at a µm-mm scale. A large and ever-expanding knowledge base about...... nitrogen fixation, nitrification, denitrification, and dissimilatory reduction of nitrate to ammonium, and about the microorganisms performing the processes, has been produced by use of these techniques. During the last decade the discovery of anammmox bacteria and migrating, nitrate accumulating bacteria...
Divergence of dominant factors in soil microbial communities and functions in forest ecosystems along a climatic gradient

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Xu, Zhiwei; Yu, Guirui; Zhang, Xinyu; He, Nianpeng; Wang, Qiufeng; Wang, Shengzhong; Xu, Xiaofeng; Wang, Ruili; Zhao, Ning

2018-03-01

Soil microorganisms play an important role in regulating nutrient cycling in terrestrial ecosystems. Most of the studies conducted thus far have been confined to a single forest biome or have focused on one or two controlling factors, and few have dealt with the integrated effects of climate, vegetation, and soil substrate availability on soil microbial communities and functions among different forests. In this study, we used phospholipid-derived fatty acid (PLFA) analysis to investigate soil microbial community structure and extracellular enzymatic activities to evaluate the functional potential of soil microbes of different types of forests in three different climatic zones along the north-south transect in eastern China (NSTEC). Both climate and forest type had significant effects on soil enzyme activities and microbial communities with considerable interactive effects. Except for soil acid phosphatase (AP), the other three enzyme activities were much higher in the warm temperate zone than in the temperate and the subtropical climate zones. The soil total PLFAs and bacteria were much higher in the temperate zone than in the warm temperate and the subtropical zones. The soil β-glucosidase (BG) and N-acetylglucosaminidase (NAG) activities were highest in the coniferous forest. Except for the soil fungi and fungi-bacteria (F/B), the different groups of microbial PLFAs were much higher in the conifer broad-leaved mixed forests than in the coniferous forests and the broad-leaved forests. In general, soil enzyme activities and microbial PLFAs were higher in primary forests than in secondary forests in temperate and warm temperate regions. In the subtropical region, soil enzyme activities were lower in the primary forests than in the secondary forests and microbial PLFAs did not differ significantly between primary and secondary forests. Different compositions of the tree species may cause variations in soil microbial communities and enzyme activities. Our results
Bayesian analysis of non-linear differential equation models with application to a gut microbial ecosystem.

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Lawson, Daniel J; Holtrop, Grietje; Flint, Harry

2011-07-01

Process models specified by non-linear dynamic differential equations contain many parameters, which often must be inferred from a limited amount of data. We discuss a hierarchical Bayesian approach combining data from multiple related experiments in a meaningful way, which permits more powerful inference than treating each experiment as independent. The approach is illustrated with a simulation study and example data from experiments replicating the aspects of the human gut microbial ecosystem. A predictive model is obtained that contains prediction uncertainty caused by uncertainty in the parameters, and we extend the model to capture situations of interest that cannot easily be studied experimentally. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Anti-Bacterial and Anti-Fungal Activity of Xanthones Obtained via Semi-Synthetic Modification of α-Mangostin from Garcinia mangostana

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Srinivasan Narasimhan

2017-02-01

Full Text Available The microbial contamination in food packaging has been a major concern that has paved the way to search for novel, natural anti-microbial agents, such as modified α-mangostin. In the present study, twelve synthetic analogs were obtained through semi-synthetic modification of α-mangostin by Ritter reaction, reduction by palladium-carbon (Pd-C, alkylation, and acetylation. The evaluation of the anti-microbial potential of the synthetic analogs showed higher bactericidal activity than the parent molecule. The anti-microbial studies proved that I E showed high anti-bacterial activity whereas I I showed the highest anti-fungal activity. Due to their microbicidal potential, modified α-mangostin derivatives could be utilized as active anti-microbial agents in materials for the biomedical and food industry.
Microbial assessment of un-bottled synthetic juices sold in Peshawar

International Nuclear Information System (INIS)

Abid, H.; Ali, J.; Hussain, A.

2010-01-01

Un-bottled synthetic juices are sold by street vendors and hawkers raising the concern about their safety. To examine the quality of un-bottled synthetic beverages from different locations of Peshawar city using Standard techniques. A total of 56 samples of un-bottled synthetic juices were collected from 8 different locations of Peshawar City and analyzed for Total Plate Count, Total Coliform Bacteria, Total Fecal Coliform bacteria E. coli, Yeast and Mould. In all localities, the street vended un-bottled synthetic juices were found hygienically of poor quality as all had high total plate count which ranged from 2 x 102 to 5 x 107 and total coliform bacteria ranged from 110 MPN/ml. Total Fecal Coliform ranged from < 0.3 to 110M PN/ml. The presence of E coli, contamination was found in (25) 44 % Samples, while all the analyzed samples were contaminated with yeasts and moulds. All un-bottled synthetic juices sold on roadside were highly contaminated with disease causing microorganisms. Policy message: Periodic monitoring of street beverage should be carried out to make them safe for consumption. (author)

Determining the specific microbial populations and their spatial distribution within the stromatolite ecosystem of Shark Bay.

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Goh, Falicia; Allen, Michelle A; Leuko, Stefan; Kawaguchi, Tomohiro; Decho, Alan W; Burns, Brendan P; Neilan, Brett A

2009-04-01

The stromatolites at Shark Bay, Western Australia, are analogues of some of the oldest evidence of life on Earth. The aim of this study was to identify and spatially characterize the specific microbial communities associated with Shark Bay intertidal columnar stromatolites. Conventional culturing methods and construction of 16S rDNA clone libraries from community genomic DNA with both universal and specific PCR primers were employed. The estimated coverage, richness and diversity of stromatolite microbial populations were compared with earlier studies on these ecosystems. The estimated coverage for all clone libraries indicated that population coverage was comprehensive. Phylogenetic analyses of stromatolite and surrounding seawater sequences were performed in ARB with the Greengenes database of full-length non-chimaeric 16S rRNA genes. The communities identified exhibited extensive diversity. The most abundant sequences from the stromatolites were alpha- and gamma-proteobacteria (58%), whereas the cyanobacterial community was characterized by sequences related to the genera Euhalothece, Gloeocapsa, Gloeothece, Chroococcidiopsis, Dermocarpella, Acaryochloris, Geitlerinema and Schizothrix. All clones from the archaeal-specific clone libraries were related to the halophilic archaea; however, no archaeal sequence was identified from the surrounding seawater. Fluorescence in situ hybridization also revealed stromatolite surfaces to be dominated by unicellular cyanobacteria, in contrast to the sub-surface archaea and sulphate-reducing bacteria. This study is the first to compare the microbial composition of morphologically similar stromatolites over time and examine the spatial distribution of specific microorganismic groups in these intertidal structures and the surrounding seawater at Shark Bay. The results provide a platform for identifying the key microbial physiology groups and their potential roles in modern stromatolite morphogenesis and ecology.
Synthetic biology and metabolic engineering.

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Stephanopoulos, Gregory

2012-11-16

Metabolic engineering emerged 20 years ago as the discipline occupied with the directed modification of metabolic pathways for the microbial synthesis of various products. As such, it deals with the engineering (design, construction, and optimization) of native as well as non-natural routes of product synthesis, aided in this task by the availability of synthetic DNA, the core enabling technology of synthetic biology. The two fields, however, only partially overlap in their interest in pathway engineering. While fabrication of biobricks, synthetic cells, genetic circuits, and nonlinear cell dynamics, along with pathway engineering, have occupied researchers in the field of synthetic biology, the sum total of these areas does not constitute a coherent definition of synthetic biology with a distinct intellectual foundation and well-defined areas of application. This paper reviews the origins of the two fields and advances two distinct paradigms for each of them: that of unit operations for metabolic engineering and electronic circuits for synthetic biology. In this context, metabolic engineering is about engineering cell factories for the biological manufacturing of chemical and pharmaceutical products, whereas the main focus of synthetic biology is fundamental biological research facilitated by the use of synthetic DNA and genetic circuits.
Approaches to chemical synthetic biology.

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Chiarabelli, Cristiano; Stano, Pasquale; Anella, Fabrizio; Carrara, Paolo; Luisi, Pier Luigi

2012-07-16

Synthetic biology is first represented in terms of two complementary aspects, the bio-engineering one, based on the genetic manipulation of extant microbial forms in order to obtain forms of life which do not exist in nature; and the chemical synthetic biology, an approach mostly based on chemical manipulation for the laboratory synthesis of biological structures that do not exist in nature. The paper is mostly devoted to shortly review chemical synthetic biology projects currently carried out in our laboratory. In particular, we describe: the minimal cell project, then the "Never Born Proteins" and lastly the Never Born RNAs. We describe and critically analyze the main results, emphasizing the possible relevance of chemical synthetic biology for the progress in basic science and biotechnology. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.
Habitat constraints on the functional significance of soil microbial communities

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Nunan, Naoise; Leloup, Julie; Ruamps, Léo; Pouteau, Valérie; Chenu, Claire

2017-04-01

An underlying assumption of most ecosystem models is that soil microbial communities are functionally equivalent; in other words, that microbial activity under given set of conditions is not dependent on the composition or diversity of the communities. Although a number of studies have suggested that this assumption is incorrect, ecosystem models can adequately describe ecosystem processes, such as soil C dynamics, without an explicit description of microbial functioning. Here, we provide a mechanistic basis for reconciling this apparent discrepancy. In a reciprocal transplant experiment, we show that microbial communities are not always functionally equivalent. The data suggest that when the supply of substrate is restricted, then the functioning of different microbial communities cannot be distinguished, but when the supply is less restricted, the intrinsic functional differences among communities can be expressed. When the supply of C is restricted then C dynamics are related to the properties of the physical and chemical environment of the soil. We conclude that soil C dynamics may depend on microbial community structure or diversity in environments such as the rhizosphere or the litter layer, but are less likely to do so in oligotrophic environments such as the mineral layers of soil.
Microbial biotechnology addressing the plastic waste disaster.

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Narancic, Tanja; O'Connor, Kevin E

2017-09-01

Oceans are a major source of biodiversity, they provide livelihood, and regulate the global ecosystem by absorbing heat and CO 2 . However, they are highly polluted with plastic waste. We are discussing here microbial biotechnology advances with the view to improve the start and the end of life of biodegradable polymers, which could contribute to the sustainable use of marine and coastal ecosystems (UN Sustainability development goal 14). © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.
Proliferation of MISS-related microbial mats following the end-Permian mass extinction in terrestrial ecosystems: Evidence from the Lower Triassic of the Yiyang area, Henan Province, North China

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Tu, Chenyi; Chen, Zhong-Qiang; Retallack, Gregory J.; Huang, Yuangeng; Fang, Yuheng

2016-03-01

Microbially induced sedimentary structures (MISSs) are commonly present in siliciclastic shallow marine settings following the end-Permian mass extinction, but have been rarely reported in the post-extinction terrestrial ecosystems. Here, we present six types of well-preserved MISSs from the upper Sunjiagou Formation and lower Liujiagou Formation of Induan (Early Triassic) age in the Yiyang area, Henan Province, North China. These MISSs include: polygonal sand cracks, worm-like structures, wrinkle structures, sponge pore fabrics, gas domes, and leveled ripple marks. Microanalysis shows that these MISSs are characterized by thin clayey laminae and filamentous mica grains arranged parallel to bedding plane as well as oriented matrix supported quartz grains, which are indicative of biogenic origin. Facies analysis suggests that the MISS-hosting sediments were deposited in a fluvial sedimentary system during the Early Triassic, including lake delta, riverbeds/point bars, and flood plain paleoenvironments. Abundant MISSs from Yiyang indicate that microbes also proliferated in terrestrial ecosystems in the aftermath of the Permian-Triassic (P-Tr) biocrisis, like they behaved in marine ecosystems. Microbial blooms, together with dramatic loss of metazoans, may reflect environmental stress and degradation of terrestrial ecosystems or arid climate immediately after the severe Permian-Triassic ecologic crisis.
Environmental regulation in a network of simulated microbial ecosystems.

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Williams, Hywel T P; Lenton, Timothy M

2008-07-29

The Earth possesses a number of regulatory feedback mechanisms involving life. In the absence of a population of competing biospheres, it has proved hard to find a robust evolutionary mechanism that would generate environmental regulation. It has been suggested that regulation must require altruistic environmental alterations by organisms and, therefore, would be evolutionarily unstable. This need not be the case if organisms alter the environment as a selectively neutral by-product of their metabolism, as in the majority of biogeochemical reactions, but a question then arises: Why should the combined by-product effects of the biota have a stabilizing, rather than destabilizing, influence on the environment? Under certain conditions, selection acting above the level of the individual can be an effective adaptive force. Here we present an evolutionary simulation model in which environmental regulation involving higher-level selection robustly emerges in a network of interconnected microbial ecosystems. Spatial structure creates conditions for a limited form of higher-level selection to act on the collective environment-altering properties of local communities. Local communities that improve their environmental conditions achieve larger populations and are better colonizers of available space, whereas local communities that degrade their environment shrink and become susceptible to invasion. The spread of environment-improving communities alters the global environment toward the optimal conditions for growth and tends to regulate against external perturbations. This work suggests a mechanism for environmental regulation that is consistent with evolutionary theory.
Industrial systems biology and its impact on synthetic biology of yeast cell factories.

Science.gov (United States)

Fletcher, Eugene; Krivoruchko, Anastasia; Nielsen, Jens

2016-06-01

Engineering industrial cell factories to effectively yield a desired product while dealing with industrially relevant stresses is usually the most challenging step in the development of industrial production of chemicals using microbial fermentation processes. Using synthetic biology tools, microbial cell factories such as Saccharomyces cerevisiae can be engineered to express synthetic pathways for the production of fuels, biopharmaceuticals, fragrances, and food flavors. However, directing fluxes through these synthetic pathways towards the desired product can be demanding due to complex regulation or poor gene expression. Systems biology, which applies computational tools and mathematical modeling to understand complex biological networks, can be used to guide synthetic biology design. Here, we present our perspective on how systems biology can impact synthetic biology towards the goal of developing improved yeast cell factories. Biotechnol. Bioeng. 2016;113: 1164-1170. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.
Differential sensitivity of total and active soil microbial communities to drought and forest management.

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Bastida, Felipe; Torres, Irene F; Andrés-Abellán, Manuela; Baldrian, Petr; López-Mondéjar, Rubén; Větrovský, Tomáš; Richnow, Hans H; Starke, Robert; Ondoño, Sara; García, Carlos; López-Serrano, Francisco R; Jehmlich, Nico

2017-10-01

Climate change will affect semiarid ecosystems through severe droughts that increase the competition for resources in plant and microbial communities. In these habitats, adaptations to climate change may consist of thinning-that reduces competition for resources through a decrease in tree density and the promotion of plant survival. We deciphered the functional and phylogenetic responses of the microbial community to 6 years of drought induced by rainfall exclusion and how forest management affects its resistance to drought, in a semiarid forest ecosystem dominated by Pinus halepensis Mill. A multiOMIC approach was applied to reveal novel, community-based strategies in the face of climate change. The diversity and the composition of the total and active soil microbiome were evaluated by 16S rRNA gene (bacteria) and ITS (fungal) sequencing, and by metaproteomics. The microbial biomass was analyzed by phospholipid fatty acids (PLFAs), and the microbially mediated ecosystem multifunctionality was studied by the integration of soil enzyme activities related to the cycles of C, N, and P. The microbial biomass and ecosystem multifunctionality decreased in drought-plots, as a consequence of the lower soil moisture and poorer plant development, but this decrease was more notable in unthinned plots. The structure and diversity of the total bacterial community was unaffected by drought at phylum and order level, but did so at genus level, and was influenced by seasonality. However, the total fungal community and the active microbial community were more sensitive to drought and were related to ecosystem multifunctionality. Thinning in plots without drought increased the active diversity while the total diversity was not affected. Thinning promoted the resistance of ecosystem multifunctionality to drought through changes in the active microbial community. The integration of total and active microbiome analyses avoids misinterpretations of the links between the soil microbial
Key players and team play: anaerobic microbial communities in hydrocarbon-contaminated aquifers.

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Kleinsteuber, Sabine; Schleinitz, Kathleen M; Vogt, Carsten

2012-05-01

Biodegradation of anthropogenic pollutants in shallow aquifers is an important microbial ecosystem service which is mainly brought about by indigenous anaerobic microorganisms. For the management of contaminated sites, risk assessment and control of natural attenuation, the assessment of in situ biodegradation and the underlying microbial processes is essential. The development of novel molecular methods, "omics" approaches, and high-throughput techniques has revealed new insight into complex microbial communities and their functions in anoxic environmental systems. This review summarizes recent advances in the application of molecular methods to study anaerobic microbial communities in contaminated terrestrial subsurface ecosystems. We focus on current approaches to analyze composition, dynamics, and functional diversity of subsurface communities, to link identity to activity and metabolic function, and to identify the ecophysiological role of not yet cultured microbes and syntrophic consortia. We discuss recent molecular surveys of contaminated sites from an ecological viewpoint regarding degrader ecotypes, abiotic factors shaping anaerobic communities, and biotic interactions underpinning the importance of microbial cooperation for microbial ecosystem services such as contaminant degradation.
Distinct responses of soil microbial communities to elevated CO2 and O3 in a soybean agro-ecosystem.

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He, Zhili; Xiong, Jinbo; Kent, Angela D; Deng, Ye; Xue, Kai; Wang, Gejiao; Wu, Liyou; Van Nostrand, Joy D; Zhou, Jizhong

2014-03-01

The concentrations of atmospheric carbon dioxide (CO2) and tropospheric ozone (O3) have been rising due to human activities. However, little is known about how such increases influence soil microbial communities. We hypothesized that elevated CO2 (eCO2) and elevated O3 (eO3) would significantly affect the functional composition, structure and metabolic potential of soil microbial communities, and that various functional groups would respond to such atmospheric changes differentially. To test these hypotheses, we analyzed 96 soil samples from a soybean free-air CO2 enrichment (SoyFACE) experimental site using a comprehensive functional gene microarray (GeoChip 3.0). The results showed the overall functional composition and structure of soil microbial communities shifted under eCO2, eO3 or eCO2+eO3. Key functional genes involved in carbon fixation and degradation, nitrogen fixation, denitrification and methane metabolism were stimulated under eCO2, whereas those involved in N fixation, denitrification and N mineralization were suppressed under eO3, resulting in the fact that the abundance of some eO3-supressed genes was promoted to ambient, or eCO2-induced levels by the interaction of eCO2+eO3. Such effects appeared distinct for each treatment and significantly correlated with soil properties and soybean yield. Overall, our analysis suggests possible mechanisms of microbial responses to global atmospheric change factors through the stimulation of C and N cycling by eCO2, the inhibition of N functional processes by eO3 and the interaction by eCO2 and eO3. This study provides new insights into our understanding of microbial functional processes in response to global atmospheric change in soybean agro-ecosystems.
Multitrophic microbial interactions for eco- and agro-biotechnological processes: theory and practice.

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Saleem, Muhammad; Moe, Luke A

2014-10-01

Multitrophic level microbial loop interactions mediated by protist predators, bacteria, and viruses drive eco- and agro-biotechnological processes such as bioremediation, wastewater treatment, plant growth promotion, and ecosystem functioning. To what extent these microbial interactions are context-dependent in performing biotechnological and ecosystem processes remains largely unstudied. Theory-driven research may advance the understanding of eco-evolutionary processes underlying the patterns and functioning of microbial interactions for successful development of microbe-based biotechnologies for real world applications. This could also be a great avenue to test the validity or limitations of ecology theory for managing diverse microbial resources in an era of altering microbial niches, multitrophic interactions, and microbial diversity loss caused by climate and land use changes. Copyright © 2014 Elsevier Ltd. All rights reserved.
Proceedings of the 8. International Symposium on Microbial Ecology : microbial biosystems : new frontiers

International Nuclear Information System (INIS)

Bell, C.R.; Brylinsky, M.; Johnson-Green, P.

2000-01-01

A wide range of disciplines were presented at this conference which reflected the importance of microbial ecology and provided an understanding of the factors that determine the growth and activities of microorganisms. The conference attracted 1444 delegates from 54 countries. The research emerging from the rapidly expanding frontier of microbial ecosystems was presented in 62 oral presentation and 817 poster presentations. The two volumes of these proceedings presented a total of 27 areas in microbial ecology, some of which included terrestrial biosystems, aquatic, estuarine, surface and subsurface microbial ecology. Other topics included bioremediation, microbial ecology in industry and microbial ecology of oil fields. Some of the papers highlighted the research that is underway to determine the feasibility of using microorganisms for enhanced oil recovery (EOR). Research has shown that microbial EOR can increase production at lower costs than conventional oil recovery. The use of bacteria has also proven to be a feasible treatment method in the biodegradation of hydrocarbons associated with oil spills. refs., tabs., figs
Tropical forest carbon balance in a warmer world: a critical review spanning microbial- to ecosystem-scale processes

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Wood, Tana E.; Cavaleri, Molly A.; Reed, Sasha C.

2012-01-01

Tropical forests play a major role in regulating global carbon (C) fluxes and stocks, and even small changes to C cycling in this productive biome could dramatically affect atmospheric carbon dioxide (CO2) concentrations. Temperature is expected to increase over all land surfaces in the future, yet we have a surprisingly poor understanding of how tropical forests will respond to this significant climatic change. Here we present a contemporary synthesis of the existing data and what they suggest about how tropical forests will respond to increasing temperatures. Our goals were to: (i) determine whether there is enough evidence to support the conclusion that increased temperature will affect tropical forest C balance; (ii) if there is sufficient evidence, determine what direction this effect will take; and, (iii) establish what steps should to be taken to resolve the uncertainties surrounding tropical forest responses to increasing temperatures. We approach these questions from a mass-balance perspective and therefore focus primarily on the effects of temperature on inputs and outputs of C, spanning microbial- to ecosystem-scale responses. We found that, while there is the strong potential for temperature to affect processes related to C cycling and storage in tropical forests, a notable lack of data combined with the physical, biological and chemical diversity of the forests themselves make it difficult to resolve this issue with certainty. We suggest a variety of experimental approaches that could help elucidate how tropical forests will respond to warming, including large-scale in situ manipulation experiments, longer term field experiments, the incorporation of a range of scales in the investigation of warming effects (both spatial and temporal), as well as the inclusion of a diversity of tropical forest sites. Finally, we highlight areas of tropical forest research where notably few data are available, including temperature effects on: nutrient cycling
Dormancy contributes to the maintenance of microbial diversity.

Science.gov (United States)

Jones, Stuart E; Lennon, Jay T

2010-03-30

Dormancy is a bet-hedging strategy used by a variety of organisms to overcome unfavorable environmental conditions. By entering a reversible state of low metabolic activity, dormant individuals become members of a seed bank, which can determine community dynamics in future generations. Although microbiologists have documented dormancy in both clinical and natural settings, the importance of seed banks for the diversity and functioning of microbial communities remains untested. Here, we develop a theoretical model demonstrating that microbial communities are structured by environmental cues that trigger dormancy. A molecular survey of lake ecosystems revealed that dormancy plays a more important role in shaping bacterial communities than eukaryotic microbial communities. The proportion of dormant bacteria was relatively low in productive ecosystems but accounted for up to 40% of taxon richness in nutrient-poor systems. Our simulations and empirical data suggest that regional environmental cues and dormancy synchronize the composition of active communities across the landscape while decoupling active microbes from the total community at local scales. Furthermore, we observed that rare bacterial taxa were disproportionately active relative to common bacterial taxa, suggesting that microbial rank-abundance curves are more dynamic than previously considered. We propose that repeated transitions to and from the seed bank may help maintain the high levels of microbial biodiversity that are observed in nearly all ecosystems.
Simultaneous adsorption and biodegradation of synthetic melanoidin

African Journals Online (AJOL)

Being an antioxidant, melanoidin removal through purely biodegradation has been inadequate. Consequently, in the current study, simultaneous adsorption and biodegradation (SAB) was employed in a stirred tank system to remove melanoidin from synthetic wastewater. Mixed microbial consortium was immobilized onto ...
Diazotrophic microbial mats

NARCIS (Netherlands)

Severin, I.; Stal, L.J.; Seckbach, J.; Oren, A.

2010-01-01

Microbial mats have been the focus of scientific research for a few decades. These small-scale ecosystems are examples of versatile benthic communities of microorganisms, usually dominated by phototrophic bacteria (e.g., Krumbein et al., 1977; Jørgensen et al., 1983). They develop as vertically
Pathogen self defense: mechanisms to counteract microbial antagonism

NARCIS (Netherlands)

Duffy, B.K.; Schouten, A.; Raaijmakers, J.M.

2003-01-01

Natural and agricultural ecosystems harbor a wide variety of microorganisms that play an integral role in plant health, crop productivity, and preservation of multiple ecosystem functions. Interactions within and among microbial communities are numerous and range from synergistic and mutualistic to
Linking the development and functioning of a carnivorous pitcher plant's microbial digestive community.

Science.gov (United States)

Armitage, David W

2017-11-01

Ecosystem development theory predicts that successional turnover in community composition can influence ecosystem functioning. However, tests of this theory in natural systems are made difficult by a lack of replicable and tractable model systems. Using the microbial digestive associates of a carnivorous pitcher plant, I tested hypotheses linking host age-driven microbial community development to host functioning. Monitoring the yearlong development of independent microbial digestive communities in two pitcher plant populations revealed a number of trends in community succession matching theoretical predictions. These included mid-successional peaks in bacterial diversity and metabolic substrate use, predictable and parallel successional trajectories among microbial communities, and convergence giving way to divergence in community composition and carbon substrate use. Bacterial composition, biomass, and diversity positively influenced the rate of prey decomposition, which was in turn positively associated with a host leaf's nitrogen uptake efficiency. Overall digestive performance was greatest during late summer. These results highlight links between community succession and ecosystem functioning and extend succession theory to host-associated microbial communities.
Representing Microbial Dormancy in Soil Decomposition Models Improves Model Performance and Reveals Key Ecosystem Controls on Microbial Activity

Science.gov (United States)

He, Y.; Yang, J.; Zhuang, Q.; Wang, G.; Liu, Y.

2014-12-01

Climate feedbacks from soils can result from environmental change and subsequent responses of plant and microbial communities and nutrient cycling. Explicit consideration of microbial life history traits and strategy may be necessary to predict climate feedbacks due to microbial physiology and community changes and their associated effect on carbon cycling. In this study, we developed an explicit microbial-enzyme decomposition model and examined model performance with and without representation of dormancy at six temperate forest sites with observed soil efflux ranged from 4 to 10 years across different forest types. We then extrapolated the model to all temperate forests in the Northern Hemisphere (25-50°N) to investigate spatial controls on microbial and soil C dynamics. Both models captured the observed soil heterotrophic respiration (RH), yet no-dormancy model consistently exhibited large seasonal amplitude and overestimation in microbial biomass. Spatially, the total RH from temperate forests based on dormancy model amounts to 6.88PgC/yr, and 7.99PgC/yr based on no-dormancy model. However, no-dormancy model notably overestimated the ratio of microbial biomass to SOC. Spatial correlation analysis revealed key controls of soil C:N ratio on the active proportion of microbial biomass, whereas local dormancy is primarily controlled by soil moisture and temperature, indicating scale-dependent environmental and biotic controls on microbial and SOC dynamics. These developments should provide essential support to modeling future soil carbon dynamics and enhance the avenue for collaboration between empirical soil experiment and modeling in the sense that more microbial physiological measurements are needed to better constrain and evaluate the models.

Geochemical and physical drivers of microbial community structure in hot spring ecosystems

Science.gov (United States)

Havig, J. R.; Hamilton, T. L.; Boyd, E. S.; Meyer-Dombard, D. R.; Shock, E.

2012-12-01

Microbial communities in natural systems are typically characterized using samples collected from a single time point, thereby neglecting the temporal dynamics that characterize natural systems. The composition of these communities obtained from single point samples is then related to the geochemistry and physical parameters of the environment. Since most microbial life is adapted to a relatively narrow ecological niche (multiplicity of physical and chemical parameters that characterize a local habitat), these assessments provide only modest insight into the controls on community composition. Temporal variation in temperature or geochemical composition would be expected to add another dimension to the complexity of niche space available to support microbial diversity, with systems that experience greater variation supporting a greater biodiversity until a point where the variability is too extreme. . Hot springs often exhibit significant temporal variation, both in physical as well as chemical characteristics. This is a result of subsurface processes including boiling, phase separation, and differential mixing of liquid and vapor phase constituents. These characteristics of geothermal systems, which vary significantly over short periods of time, provide ideal natural laboratories for investigating how i) the extent of microbial community biodiversity and ii) the composition of those communities are shaped by temporal fluctuations in geochemistry. Geochemical and molecular samples were collected from 17 temporally variable hot springs across Yellowstone National Park, Wyoming. Temperature measurements using data-logging thermocouples, allowing accurate determination of temperature maximums, minimums, and ranges for each collection site, were collected in parallel, along with multiple geochemical characterizations as conditions varied. There were significant variations in temperature maxima (54.5 to 90.5°C), minima (12.5 to 82.5°C), and range (3.5 to 77.5°C) for
Silica ecosystem for synergistic biotransformation

Science.gov (United States)

Mutlu, Baris R.; Sakkos, Jonathan K.; Yeom, Sujin; Wackett, Lawrence P.; Aksan, Alptekin

2016-06-01

Synergistical bacterial species can perform more varied and complex transformations of chemical substances than either species alone, but this is rarely used commercially because of technical difficulties in maintaining mixed cultures. Typical problems with mixed cultures on scale are unrestrained growth of one bacterium, which leads to suboptimal population ratios, and lack of control over bacterial spatial distribution, which leads to inefficient substrate transport. To address these issues, we designed and produced a synthetic ecosystem by co-encapsulation in a silica gel matrix, which enabled precise control of the microbial populations and their microenvironment. As a case study, two greatly different microorganisms: Pseudomonas sp. NCIB 9816 and Synechococcus elongatus PCC 7942 were encapsulated. NCIB 9816 can aerobically biotransform over 100 aromatic hydrocarbons, a feat useful for synthesis of higher value commodity chemicals or environmental remediation. In our system, NCIB 9816 was used for biotransformation of naphthalene (a model substrate) into CO2 and the cyanobacterium PCC 7942 was used to provide the necessary oxygen for the biotransformation reactions via photosynthesis. A mathematical model was constructed to determine the critical cell density parameter to maximize oxygen production, and was then used to maximize the biotransformation rate of the system.
[Advances in microbial genome reduction and modification].

Science.gov (United States)

Wang, Jianli; Wang, Xiaoyuan

2013-08-01

Microbial genome reduction and modification are important strategies for constructing cellular chassis used for synthetic biology. This article summarized the essential genes and the methods to identify them in microorganisms, compared various strategies for microbial genome reduction, and analyzed the characteristics of some microorganisms with the minimized genome. This review shows the important role of genome reduction in constructing cellular chassis.
Soil microbial respiration beneath Stipa tenacissima L. and in surrounding bare soil

Directory of Open Access Journals (Sweden)

Irena Novosádová

2011-01-01

Full Text Available Open steppes dominated by Stipa tenacissima L. constitute one of the most representative ecosystems of the semi-arid zones of Eastern Mediterranean Basin (Iberian Peninsula, North of Africa. Ecosystem functioning of these steppes is strongly related to the spatial pattern of grass tussocks. Soils beneath Stipa tenacissima L. grass show different fertility and different microclimatic conditions than in surrounding bare soil. The objective of this study was to assess the effect of Stipa tenacissima L. on the key soil microbial activities under controlled incubation conditions (basal and potential respiration. Basal and potential microbial respirations in the soils beneath Stipa tenacissima L. were, in general, not significantly different from the bare soils. The differences were less than 10%. Significantly less ethylene produced by microbial activity in soils beneath Stipa tenacissima L. after the addition of glucose could indicate the dependence of rhizospheric microbial communities on available carbon compounds. It can be concluded, that the soil respiration in semi-arid Mediterranean ecosystems is not necessarily associated with the patchy plant distribution and that some microbial activities characteristics can be unexpectedly homogenous.
Coastal microbial mats: the physiology of a small-scale ecosystem

NARCIS (Netherlands)

Stal, L.J.

2001-01-01

Coastal inter-tidal sandy sediments, salt marshes and mangrove forests often support the development of microbial mats. Microbial mats are complex associations of one or several functional groups of microorganisms and their formation usually starts with the growth of a cyanobacterial population on a
Nitrogen transformations in stratified aquatic microbial ecosystems

DEFF Research Database (Denmark)

Revsbech, N. P.; Risgaard-Petersen, N.; Schramm, A.

2006-01-01

Abstract New analytical methods such as advanced molecular techniques and microsensors have resulted in new insights about how nitrogen transformations in stratified microbial systems such as sediments and biofilms are regulated at a µm-mm scale. A large and ever-expanding knowledge base about n...
Microbial ecology of artisanal italian cheese: Molecular microbial characterization by culture-independent method

International Nuclear Information System (INIS)

Colombo, E.; Scarpellini, M.; Franzatti, L.; Dioguardi, L.

2009-01-01

Present study will treat the next topics: ecology of the natural and man made environments and functional diversity of bacteria. The microbial communities in artisanal goat cheeses produced in mountain pastures (typical farms) in Piemonte mountain (North of Italy) change a lot during precessing and ripening time. Moreover cheese microbial ecosystems are different in each small dairy because adventitious microflora can come from the environment and contamination the milk before the cheese making process and the product during manufacture and ripening. (Author)
Microbial ecology of artisanal italian cheese: Molecular microbial characterization by culture-independent method

Energy Technology Data Exchange (ETDEWEB)

Colombo, E.; Scarpellini, M.; Franzatti, L.; Dioguardi, L.

2009-07-01

Present study will treat the next topics: ecology of the natural and man made environments and functional diversity of bacteria. The microbial communities in artisanal goat cheeses produced in mountain pastures (typical farms) in Piemonte mountain (North of Italy) change a lot during precessing and ripening time. Moreover cheese microbial ecosystems are different in each small dairy because adventitious microflora can come from the environment and contamination the milk before the cheese making process and the product during manufacture and ripening. (Author)
Synthetic biology: programming cells for biomedical applications.

Science.gov (United States)

Hörner, Maximilian; Reischmann, Nadine; Weber, Wilfried

2012-01-01

The emerging field of synthetic biology is a novel biological discipline at the interface between traditional biology, chemistry, and engineering sciences. Synthetic biology aims at the rational design of complex synthetic biological devices and systems with desired properties by combining compatible, modular biological parts in a systematic manner. While the first engineered systems were mainly proof-of-principle studies to demonstrate the power of the modular engineering approach of synthetic biology, subsequent systems focus on applications in the health, environmental, and energy sectors. This review describes recent approaches for biomedical applications that were developed along the synthetic biology design hierarchy, at the level of individual parts, of devices, and of complex multicellular systems. It describes how synthetic biological parts can be used for the synthesis of drug-delivery tools, how synthetic biological devices can facilitate the discovery of novel drugs, and how multicellular synthetic ecosystems can give insight into population dynamics of parasites and hosts. These examples demonstrate how this new discipline could contribute to novel solutions in the biopharmaceutical industry.
Microbial transformation of synthetic estrogen 17 alpha-ethinylestradiol

Czech Academy of Sciences Publication Activity Database

Cajthaml, Tomáš; Křesinová, Zdena; Svobodová, Kateřina; Sigler, Karel; Řezanka, Tomáš

2009-01-01

Roč. 157, č. 12 (2009), s. 3325-3335 ISSN 0269-7491 R&D Projects: GA MŠk LC06066; GA AV ČR KJB600200613 Institutional research plan: CEZ:AV0Z50200510 Keywords : 17 alpha-Ethinylestradiol * Microbial biodegradation * Ligninolytic fungi Subject RIV: EE - Microbiology, Virology Impact factor: 3.426, year: 2009
Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond.

Science.gov (United States)

Hiraoka, Satoshi; Yang, Ching-Chia; Iwasaki, Wataru

2016-09-29

Metagenomic approaches are now commonly used in microbial ecology to study microbial communities in more detail, including many strains that cannot be cultivated in the laboratory. Bioinformatic analyses make it possible to mine huge metagenomic datasets and discover general patterns that govern microbial ecosystems. However, the findings of typical metagenomic and bioinformatic analyses still do not completely describe the ecology and evolution of microbes in their environments. Most analyses still depend on straightforward sequence similarity searches against reference databases. We herein review the current state of metagenomics and bioinformatics in microbial ecology and discuss future directions for the field. New techniques will allow us to go beyond routine analyses and broaden our knowledge of microbial ecosystems. We need to enrich reference databases, promote platforms that enable meta- or comprehensive analyses of diverse metagenomic datasets, devise methods that utilize long-read sequence information, and develop more powerful bioinformatic methods to analyze data from diverse perspectives.
Impact of ecosystem management on microbial community level physiological profiles of postmining forest rehabilitation.

Science.gov (United States)

Cookson, W R; O'Donnell, A J; Grant, C D; Grierson, P F; Murphy, D V

2008-02-01

acids also tended to increase with increasing soil total C and organic C contents but decreased with increasing nitrate content, whereas the opposite was true for carboxylic acids. Only 45% of the variance in CLPP was explained using a multivariate multiple regression model, but soil C and N pools and litter mass were significant predictors of CLPP. Differences in soil textural components between treatments were also correlated with CLPP; likely causes of these differences are discussed. Our results suggest that 1 year after treatment, CLPP from this mined forest ecosystem are resilient to a spring prescribed fire but not forest thinning. We conclude that differences in CLPP are likely to result from complex interactions among soil properties that mediate substrate availability, microbial nutrient demand, and microbial community composition.
Aerobic Granular Sludge: Effect of Salt and Insights into Microbial Ecology

KAUST Repository

Wang, Zhongwei

2017-01-01

Like other artificial microbial ecosystems (e.g. CAS plant and anaerobic digester), a firm understanding of the microbial ecology of AGS system is essential for process design and optimization. The second part
Microbial Communities Are Well Adapted to Disturbances in Energy Input.

Science.gov (United States)

Fernandez-Gonzalez, Nuria; Huber, Julie A; Vallino, Joseph J

2016-01-01

Although microbial systems are well suited for studying concepts in ecological theory, little is known about how microbial communities respond to long-term periodic perturbations beyond diel oscillations. Taking advantage of an ongoing microcosm experiment, we studied how methanotrophic microbial communities adapted to disturbances in energy input over a 20-day cycle period. Sequencing of bacterial 16S rRNA genes together with quantification of microbial abundance and ecosystem function were used to explore the long-term dynamics (510 days) of methanotrophic communities under continuous versus cyclic chemical energy supply. We observed that microbial communities appeared inherently well adapted to disturbances in energy input and that changes in community structure in both treatments were more dependent on internal dynamics than on external forcing. The results also showed that the rare biosphere was critical to seeding the internal community dynamics, perhaps due to cross-feeding or other strategies. We conclude that in our experimental system, internal feedbacks were more important than external drivers in shaping the community dynamics over time, suggesting that ecosystems can maintain their function despite inherently unstable community dynamics. IMPORTANCE Within the broader ecological context, biological communities are often viewed as stable and as only experiencing succession or replacement when subject to external perturbations, such as changes in food availability or the introduction of exotic species. Our findings indicate that microbial communities can exhibit strong internal dynamics that may be more important in shaping community succession than external drivers. Dynamic "unstable" communities may be important for ecosystem functional stability, with rare organisms playing an important role in community restructuring. Understanding the mechanisms responsible for internal community dynamics will certainly be required for understanding and manipulating
Potential of Thermophilic microorganisms for the degradation of synthetic polymers

Energy Technology Data Exchange (ETDEWEB)

Dominguez, A.; Deive, F. J.; Sanroman, M. A.; Longo, M. A.

2009-07-01

Nowadays, synthetic polymers are used in all areas of human activity, mainly due to their high stability against environmental conditions and microbial attack. However, these properties are also a problem from an environmental point of view, and thus it is necessary to find biodegradable synthetic polymers that can be easily removed in nature after disposal, and decomposed into biomass, CO{sub 2} and water. (Author)
Effects of Conservation Agriculture and Fertilization on Soil Microbial Diversity and Activity

Directory of Open Access Journals (Sweden)

Johan Habig

2015-07-01

Full Text Available Soil microbial communities perform critical functions in ecosystem processes. These functions can be used to assess the impact of agricultural practices on sustainable crop production. In this five-year study, the effect of various agricultural practices on soil microbial diversity and activity was investigated in a summer rainfall area under South African dryland conditions. Microbial diversity and activity were measured in the 0–15 cm layer of a field trial consisting of two fertilizer levels, three cropping systems, and two tillage systems. Using the Shannon–Weaver and Evenness diversity indices, soil microbial species richness and abundance were measured. Microbial enzymatic activities: β-glucosidase, phosphatase and urease, were used to evaluate ecosystem functioning. Cluster analysis revealed a shift in soil microbial community diversity and activity over time. Microbial diversity and activity were higher under no-till than conventional tillage. Fertilizer levels seemed to play a minor role in determining microbial diversity and activity, whereas the cropping systems played a more important role in determining the activity of soil microbial communities. Conservation agriculture yielded the highest soil microbial diversity and activity in diversified cropping systems under no-till.
Lessons from Suiyo Seamount studies, for understanding extreme (ancient?) microbial ecosystems in the deep-sea hydrothermal fields

Science.gov (United States)

Maruyama, A.; Higashi, Y.; Sunamura, M.; Urabe, T.

2004-12-01

Deep-sea hydrothermal ecosystems are driven with various geo-thermally modified, mainly reduced, compounds delivered from extremely hot subsurface environments. To date, several unique microbes including thermophilic archaeons have been isolated from/around vent chimneys. However, there is little information about microbes in over-vent and sub-vent fields. Here, we report several new findings on microbial diversity and ecology of the Suiyo Seamount that locates on the Izu-Bonin Arc in the northwest Pacific Ocean, as a result of the Japanese Archaean Park project, with special concern to the sub-vent biosphere. At first, we succeeded to reveal a very unique microbial ecosystem in hydrothermal plume reserved within the outer rim of the seamount crater, that is, it consisted of almost all metabolically active microbes belonged to only two Bacteria phylotypes, probably of sulfur oxidizers. In the center of the caldera seafloor (ca. 1,388-m deep) consisted mainly of whitish sands and pumices, we found many small chimneys (ca. 5-10 cm) and bivalve colonies distributed looking like gray to black patches. These geo/ecological features of the seafloor were supposed to be from a complex mixing of hydrothermal venting and strong water current near the seafloor. Through quantitative FISH analysis for various environmental samples, one of the two representative groups in the plume was assessed to be from some of the bivalve colonies. Using the Benthic Multi-coring System (BMS), total 10 points were drilled and 6 boreholes were maintained with stainless or titanium casing pipes. In the following submersible surveys, newly developed catheter- and column-type in situ growth chambers were deployed in and on the boreholes, respectively, for collecting indigenous sub-vent microbes. Finally, we succeeded to detect several new phylotypes of microbes in these chamber samples, e.g., within epsilon-Proteobacteria, a photosynthetic group of alpha-Proteobacteria, and hyperthermophile
Cold adaptation and replicable microbial community development during long-term low-temperature anaerobic digestion treatment of synthetic sewage.

Science.gov (United States)

Keating, C; Hughes, D; Mahony, T; Cysneiros, D; Ijaz, U Z; Smith, C J; O'Flaherty, V

2018-07-01

The development and activity of a cold-adapting microbial community was monitored during low-temperature anaerobic digestion (LtAD) treatment of wastewater. Two replicate hybrid anaerobic sludge bed-fixed-film reactors treated a synthetic sewage wastewater at 12°C, at organic loading rates of 0.25-1.0 kg chemical oxygen demand (COD) m-3 d-1, over 889 days. The inoculum was obtained from a full-scale anaerobic digestion reactor, which was operated at 37°C. Both LtAD reactors readily degraded the influent with COD removal efficiencies regularly exceeding 78% for both the total and soluble COD fractions. The biomass from both reactors was sampled temporally and tested for activity against hydrolytic and methanogenic substrates at 12°C and 37°C. Data indicated that significantly enhanced low-temperature hydrolytic and methanogenic activity developed in both systems. For example, the hydrolysis rate constant (k) at 12°C had increased 20-30-fold by comparison to the inoculum by day 500. Substrate affinity also increased for hydrolytic substrates at low temperature. Next generation sequencing demonstrated that a shift in a community structure occurred over the trial, involving a 1-log-fold change in 25 SEQS (OTU-free approach) from the inoculum. Microbial community structure changes and process performance were replicable in the LtAD reactors.
Simulated Carbon Cycling in a Model Microbial Mat.

Science.gov (United States)

Decker, K. L.; Potter, C. S.

2006-12-01

We present here the novel addition of detailed organic carbon cycling to our model of a hypersaline microbial mat ecosystem. This ecosystem model, MBGC (Microbial BioGeoChemistry), simulates carbon fixation through oxygenic and anoxygenic photosynthesis, and the release of C and electrons for microbial heterotrophs via cyanobacterial exudates and also via a pool of dead cells. Previously in MBGC, the organic portion of the carbon cycle was simplified into a black-box rate of accumulation of simple and complex organic compounds based on photosynthesis and mortality rates. We will discuss the novel inclusion of fermentation as a source of carbon and electrons for use in methanogenesis and sulfate reduction, and the influence of photorespiration on labile carbon exudation rates in cyanobacteria. We will also discuss the modeling of decomposition of dead cells and the ultimate release of inorganic carbon. The detailed modeling of organic carbon cycling is important to the accurate representation of inorganic carbon flux through the mat, as well as to accurate representation of growth models of the heterotrophs under different environmental conditions. Because the model ecosystem is an analog of ancient microbial mats that had huge impacts on the atmosphere of early earth, this MBGC can be useful as a biological component to either early earth models or models of other planets that potentially harbor life.
Synthetic biology advances for pharmaceutical production

OpenAIRE

Breitling, Rainer; Takano, Eriko

2015-01-01

Synthetic biology enables a new generation of microbial engineering for the biotechnological production of pharmaceuticals and other high-value chemicals. This review presents an overview of recent advances in the field, describing new computational and experimental tools for the discovery, optimization and production of bioactive molecules, and outlining progress towards the application of these tools to pharmaceutical production systems.

Differences in microbial communities and performance between suspended and attached growth anaerobic membrane bioreactors treating synthetic municipal wastewater

KAUST Repository

Harb, Moustapha

2015-08-14

Two lab-scale anaerobic membrane bioreactors (AnMBRs), one up-flow attached-growth (UA) and another continuously stirred (CSTR), were operated under mesophilic conditions (35 °C) while treating synthetic municipal wastewater (800 mg L−1 COD). Each reactor was attached to both polyvinylidene fluoride (PVDF) and polyethersulfone (PES) microfiltration (MF) membranes in an external cross-flow configuration. Both reactors were started up and run under the same operating conditions for multiple steady-state experiments. Chemical oxygen demand (COD) removal rates were similar for both reactors (90–96%), but captured methane was found to be 11–18% higher for the CSTR than the UA reactor. Ion Torrent sequencing targeting 16S rRNA genes showed that several operational taxonomic units (OTUs) most closely related to fermentative bacteria (e.g., Microbacter margulisiae) were dominant in the suspended biomass of the CSTR, accounting for 30% of the microbial community. Conversely, methanogenic archaea (e.g., Methanosaeta) and syntrophic bacteria (e.g., Smithella propionica) were found in significantly higher relative abundances in the UA AnMBR as compared to the CSTR due to their affinity for surface attachment. Of the methanogens that were present in the CSTR sludge, hydrogenotrophic methanogens dominated (e.g., Methanobacterium). Measured EPS (both proteins and carbohydrates), which has been broadly linked to fouling, was determined to be consistently lower in the UA AnMBR membrane samples than in CSTR AnMBR membrane samples. Principal component analysis (PCA) based on HPLC profiles of soluble microbial products (SMPs) further demonstrated these differences between reactor types in replicate runs. The results of this study showed that reactor configuration can significantly impact the development of the microbial communities of AnMBRs that are responsible for both membrane and reactor performance.
Environmental and Microbial Features Affecting Denitrification and Anammox Hotspots in an Estuarine Ecosystem

Science.gov (United States)

Lisa, J.; Song, B.; Lefcheck, J. S.; Tobias, C. R.

2016-02-01

Biogeochemical hotspots are characterized as a few sites that exhibit extremely high reaction rates relative to surrounding area, and often account for a high percentage of the overall reaction rates in an ecosystem. Criteria for quantitatively identifying these sites have not been well established. Further, the underlying mechanisms of hotspots have been described in terms of environmental conditions, with little attention paid to the microbial community. The objectives of this study were to establish quantitative criteria to identify denitrification and anammox hotspots, and determine the underlying microbial and environmental factors responsible for elevated N2 production. We used 15N isotope pairing incubation experiments to measure denitrification and anammox rates in the New River Estuary, NC. Quantitative PCR assays of nitrous oxide reductase (nosZ Clades I and II) and hydrazine oxidoreductase (hzo) genes were conducted to estimate denitrifier and anammox abundance. Structural Equation Modeling (SEM) was used to elucidate complex causal relationships between environmental and biological variables. Denitrification hotspots, quantitatively defined as statistical outliers, accounted for 35.6% total denitrification while comprising only 7.3% of the sites. Anammox hotspots,10.6% of the sites, accounted for 60.9% of total anammox. SEM revealed increased sediment organics at lower salinities supported higher functional gene abundance, which in turn resulted in higher N2 production. Surprisingly, denitrification rates were significantly and positively correlated with nosZ Clade II gene abundance, after accounting for the non-significant contributions of the naturally more abundant nosZ Clade I, and other environmental covariates. This is the first time that a quantitative definition of biogeochemical hotspots was put forth and used to determine the importance of anammox and denitrification hotspots in estuarine nitrogen removal capacity. Despite the low area
Microbial dynamics in petroleum oilfields and their relationship with physiological properties of petroleum oil reservoirs.

Science.gov (United States)

Varjani, Sunita J; Gnansounou, Edgard

2017-12-01

Petroleum is produced by thermal decay of buried organic material over millions of years. Petroleum oilfield ecosystems represent resource of reduced carbon which favours microbial growth. Therefore, it is obvious that many microorganisms have adapted to harsh environmental conditions of these ecosystems specifically temperature, oxygen availability and pressure. Knowledge of microorganisms present in ecosystems of petroleum oil reservoirs; their physiological and biological properties help in successful exploration of petroleum. Understanding microbiology of petroleum oilfield(s) can be used to enhance oil recovery, as microorganisms in oil reservoirs produce various metabolites viz. gases, acids, solvents, biopolymers and biosurfactants. The aim of this review is to discuss characteristics of petroleum oil reservoirs. This review also provides an updated literature on microbial ecology of these extreme ecosystems including microbial origin as well as various types of microorganisms such as methanogens; iron, nitrate and sulphate reducing bacteria, and fermentative microbes present in petroleum oilfield ecosystems. Copyright © 2017 Elsevier Ltd. All rights reserved.
Microbial community functional change during vertebrate carrion decomposition.

Directory of Open Access Journals (Sweden)

Jennifer L Pechal

Full Text Available Microorganisms play a critical role in the decomposition of organic matter, which contributes to energy and nutrient transformation in every ecosystem. Yet, little is known about the functional activity of epinecrotic microbial communities associated with carrion. The objective of this study was to provide a description of the carrion associated microbial community functional activity using differential carbon source use throughout decomposition over seasons, between years and when microbial communities were isolated from eukaryotic colonizers (e.g., necrophagous insects. Additionally, microbial communities were identified at the phyletic level using high throughput sequencing during a single study. We hypothesized that carrion microbial community functional profiles would change over the duration of decomposition, and that this change would depend on season, year and presence of necrophagous insect colonization. Biolog EcoPlates™ were used to measure the variation in epinecrotic microbial community function by the differential use of 29 carbon sources throughout vertebrate carrion decomposition. Pyrosequencing was used to describe the bacterial community composition in one experiment to identify key phyla associated with community functional changes. Overall, microbial functional activity increased throughout decomposition in spring, summer and winter while it decreased in autumn. Additionally, microbial functional activity was higher in 2011 when necrophagous arthropod colonizer effects were tested. There were inconsistent trends in the microbial function of communities isolated from remains colonized by necrophagous insects between 2010 and 2011, suggesting a greater need for a mechanistic understanding of the process. These data indicate that functional analyses can be implemented in carrion studies and will be important in understanding the influence of microbial communities on an essential ecosystem process, carrion decomposition.
Deep Microbial Ecosystems in the U.S. Great Basin: A Second Home for Desulforudis audaxviator?

Science.gov (United States)

Moser, D. P.

2012-12-01

Deep subsurface microbial ecosystems have attracted scientific and public interest in recent years. Of deep habitats so far investigated, continental hard rock environments may be the least understood. Our Census of Deep Life (CoDL) project targets deep microbial ecosystems of three little explored (for microbiology), North American geological provinces: the Basin and Range, Black Hills, and Canadian Shield. Here we focus on the Basin and Range, specifically radioactive fluids from nuclear device test cavities (U12N.10 tunnel and ER-EC-11) at the Nevada National Security Site (NNSS) and non-radioactive samples from a deep dolomite aquifer associated with Death Valley, CA (BLM-1 and Nevares Deep Well 2). Six pyrotag sequencing runs were attempted at the Marine Biology Lab (MBL) (bacterial v6v4 amplification for all sites and archaeal v6v4 amplification for BLM-1 and Nevares DW2). Of these, DNA extracts from five samples (all but Nevares DW2 Arch) successfully amplified. Bacterial libraries were generally dominated by Proteobacteria, Firmicutes, and Nitrospirae (ER-EC-11: Proteobacteria (45%), Deinococcus-Thermus (35%), Firmicutes (15%); U12N.10: Proteobacteria (37%), Firmicutes (32%), Nitrospirae (15%), Bacteroidetes (11%); BLM-1 (Bact): Firmicutes (93%); and Nevares DW2: Firmicutes (51%), Proteobacteria (16%), Nitrospirae (15%)). The BLM-1 (Arch) library contained >99% Euryarchaeota, with 98% of sequences represented by a single uncharacterized species of Methanothermobacter. Alpha diversity was calculated using the MBL VAMPS (Visualization and Analysis of Microbial Population Structures) system; showing the highest richness at both the phylum and genus levels in U12N.10 (Sp = 42; Sg = 341), and the lowest (Sp = 3; Sg = 11) in the BLM-1(Arch) library. Diversity was covered well at this depth of sequencing (~20,000 reads per sample) based on rarefaction analysis. One Firmicute lineage, candidatus D. audaxviator, has been shown to dominate microbial communities from
The role of ecological theory in microbial ecology.

Science.gov (United States)

Prosser, James I; Bohannan, Brendan J M; Curtis, Tom P; Ellis, Richard J; Firestone, Mary K; Freckleton, Rob P; Green, Jessica L; Green, Laura E; Killham, Ken; Lennon, Jack J; Osborn, A Mark; Solan, Martin; van der Gast, Christopher J; Young, J Peter W

2007-05-01

Microbial ecology is currently undergoing a revolution, with repercussions spreading throughout microbiology, ecology and ecosystem science. The rapid accumulation of molecular data is uncovering vast diversity, abundant uncultivated microbial groups and novel microbial functions. This accumulation of data requires the application of theory to provide organization, structure, mechanistic insight and, ultimately, predictive power that is of practical value, but the application of theory in microbial ecology is currently very limited. Here we argue that the full potential of the ongoing revolution will not be realized if research is not directed and driven by theory, and that the generality of established ecological theory must be tested using microbial systems.
Calibration and analysis of genome-based models for microbial ecology.

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Louca, Stilianos; Doebeli, Michael

2015-10-16

Microbial ecosystem modeling is complicated by the large number of unknown parameters and the lack of appropriate calibration tools. Here we present a novel computational framework for modeling microbial ecosystems, which combines genome-based model construction with statistical analysis and calibration to experimental data. Using this framework, we examined the dynamics of a community of Escherichia coli strains that emerged in laboratory evolution experiments, during which an ancestral strain diversified into two coexisting ecotypes. We constructed a microbial community model comprising the ancestral and the evolved strains, which we calibrated using separate monoculture experiments. Simulations reproduced the successional dynamics in the evolution experiments, and pathway activation patterns observed in microarray transcript profiles. Our approach yielded detailed insights into the metabolic processes that drove bacterial diversification, involving acetate cross-feeding and competition for organic carbon and oxygen. Our framework provides a missing link towards a data-driven mechanistic microbial ecology.
Synthetic biology advances for pharmaceutical production

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Breitling, Rainer; Takano, Eriko

2015-01-01

Synthetic biology enables a new generation of microbial engineering for the biotechnological production of pharmaceuticals and other high-value chemicals. This review presents an overview of recent advances in the field, describing new computational and experimental tools for the discovery, optimization and production of bioactive molecules, and outlining progress towards the application of these tools to pharmaceutical production systems. PMID:25744872
Synthetic biology of microbes synthesizing polyhydroxyalkanoates (PHA

Directory of Open Access Journals (Sweden)

Guo-Qiang Chen

2016-12-01

Full Text Available Microbial polyhydroxyalkanoates (PHA have been produced as bioplastics for various purposes. Under the support of China National Basic Research 973 Project, we developed synthetic biology methods to diversify the PHA structures into homo-, random, block polymers with improved properties to better meet various application requirements. At the same time, various pathways were assembled to produce various PHA from glucose as a simple carbon source. At the end, Halomonas bacteria were reconstructed to produce PHA in changing morphology for low cost production under unsterile and continuous conditions. The synthetic biology will advance the PHA into a bio- and material industry.
Lipid Biomarkers for a Hypersaline Microbial Mat Community

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Jahnke, Linda L.; Embaye, Tsege; Turk, Kendra A.

2003-01-01

The use of lipid biomarkers and their carbon isotopic compositions are valuable tools for establishing links to ancient microbial ecosystems. As witnessed by the stromatolite record, benthic microbial mats grew in shallow water lagoonal environments where microorganisms had virtually no competition apart from the harsh conditions of hypersalinity, desiccation and intense light. Today, the modern counterparts of these microbial ecosystems find appropriate niches in only a few places where extremes eliminate eukaryotic grazers. Answers to many outstanding questions about the evolution of microorganisms and their environments on early Earth are best answered through study of these extant analogs. Lipids associated with various groups of bacteria can be valuable biomarkers for identification of specific groups of microorganisms both in ancient organic-rich sedimentary rocks (geolipids) and contemporary microbial communities (membrane lipids). Use of compound specific isotope analysis adds additional refinement to the identification of biomarker source, so that it is possible to take advantage of the 3C-depletions associated with various functional groups of organisms (i.e. autotrophs, heterotrophs, methanotrophs, methanogens) responsible for the cycling of carbon within a microbial community. Our recent work has focused on a set of hypersaline evaporation ponds at Guerrero Negro, Baja California Sur, Mexico which support the abundant growth of Microcoleus-dominated microbial mats. Specific biomarkers for diatoms, cyanobacteria, archaea, green nonsulfur (GNS), sulfate reducing, and methanotrophic bacteria have been identified. Analyses of the ester-bound fatty acids indicate a highly diverse microbial community, dominated by photosynthetic organisms at the surface.
Soil ecosystem functioning under climate change: plant species and community effects

Energy Technology Data Exchange (ETDEWEB)

Kardol, Paul [ORNL; Cregger, Melissa [ORNL; Campany, Courtney E [ORNL; Classen, Aimee T [ORNL

2010-01-01

Feedbacks of terrestrial ecosystems to climate change depend on soil ecosystem dynamics. Soil ecosystems can directly and indirectly respond to climate change. For example, warming directly alters microbial communities by increasing their activity. Climate change may also alter plant community composition, thus indirectly altering the microbial communities that feed on their inputs. To better understand how climate change may directly and indirectly alter soil ecosystem functioning, we investigated old-field plant community and soil ecosystem responses to single and combined effects of elevated [CO2], warming, and water availability. Specifically, we collected soils at the plot level (plant community soils), and beneath dominant plant species (plant-specific soils). We used microbial enzyme activities and soil nematodes as indicators for soil ecosystem functioning. Our study resulted in two main findings: 1) Overall, while there were some interactions, water, relative to increases in [CO2] and warming, had the largest impact on plant community composition, soil enzyme activities, and soil nematodes. Multiple climate change factors can interact to shape ecosystems, but in this case, those interactions were largely driven by changes in water availability. 2) Indirect effects of climate change, via changes in plant communities, had a significant impact on soil ecosystem functioning and this impact was not obvious when looking at plant community soils. Climate change effects on enzyme activities and soil nematode abundance and community structure strongly differed between plant community soils and plant-specific soils, but also within plant-specific soils. In sum, these results indicate that accurate assessments of climate change impacts on soil ecosystem functioning require incorporating the concurrent changes in plant function and plant community composition. Climate change-induced shifts in plant community composition will likely modify or counteract the direct
Quantifying the Importance of the Rare Biosphere for Microbial Community Response to Organic Pollutants in a Freshwater Ecosystem.

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Wang, Yuanqi; Hatt, Janet K; Tsementzi, Despina; Rodriguez-R, Luis M; Ruiz-Pérez, Carlos A; Weigand, Michael R; Kizer, Heidi; Maresca, Gina; Krishnan, Raj; Poretsky, Rachel; Spain, Jim C; Konstantinidis, Konstantinos T

2017-04-15

value of this astonishing biodiversity for ecosystem functioning remains poorly understood, primarily due to the fact that microbial community analysis frequently focuses on abundant organisms. Using a combination of culture-dependent and culture-independent (metagenomics) techniques, we showed that rare taxa and genes commonly contribute to the microbial community response to organic pollutants. Our findings should have implications for future studies that aim to study the role of rare species in environmental processes, including environmental bioremediation efforts of oil spills or other contaminants. Copyright © 2017 American Society for Microbiology.
Non-enzymatic palladium recovery on microbial and synthetic surfaces.

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Rotaru, Amelia-Elena; Jiang, Wei; Finster, Kai; Skrydstrup, Troels; Meyer, Rikke Louise

2012-08-01

The use of microorganisms as support for reduction of dissolved Pd(II) to immobilized Pd(0) nanoparticles is an environmentally friendly approach for Pd recovery from waste. To better understand and engineer Pd(0) nanoparticle synthesis, one has to consider the mechanisms by which Pd(II) is reduced on microbial surfaces. Escherichia coli, Shewanella oneidensis, and Pseudomonas putida were used as model organisms in order to elucidate the role of microbial cells in Pd(II) reduction under acidic conditions. Pd(II) was reduced by formate under acidic conditions, and the process occurred substantially faster in the presence of cells as compared to cell-free controls. We found no difference between native (untreated) and autoclaved cells, and could demonstrate that even a non-enzymatic protein (bovine serum albumin) stimulated Pd(II) reduction as efficiently as bacterial cells. Amine groups readily interact with Pd(II), and to specifically test their role in surface-assisted Pd(II) reduction by formate, we replaced bacterial cells with polystyrene microparticles functionalized with amine or carboxyl groups. Amine-functionalized microparticles had the same effect on Pd(II) reduction as bacterial cells, and the effect could be hampered if the amine groups were blocked by acetylation. The interaction with amine groups was confirmed by infrared spectroscopy on whole cells and amine-functionalized microparticles. In conclusion, bio-supported Pd(II) reduction on microbial surfaces is possibly mediated by a non-enzymatic mechanism. We therefore suggest the use of amine-rich biomaterials rather than intact cells for Pd bio-recovery from waste. Copyright © 2012 Wiley Periodicals, Inc.
BIOMASS AND MICROBIAL ACTIVITY UNDER DIFFERENT FOREST COVERS

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Rafael Malfitano Braga

2016-06-01

Full Text Available This study evaluated the soil fertility, biomass and microbial activity of the soil under forest cover of Eucalyptus grandis, Eucalyptus pilularis, Eucalyptus cloeziana and Corymbia maculata; Pinus Caribbean var. hondurensis, 40 years old, and a fragment of Semideciduous Forest, located on the campus of the Federal University of Lavras. In soil samples collected in the 0-5 cm layer were determined fertility parameters, basal respiration and microbial biomass carbon. The results showed that for the species E. grandis and E. cloeziana the carbon of biomass microbial content was higher than for any other ecosystem evaluated, and equal to those observed under native forest. In contrast, the ground under Pinus had the lowest microbiological indexes. Under C. maculata and E. pilularis the contents were intermediate for this parameter. The basal respiration of all ecosystems was equal. The fertility level was very low in all types of evaluated vegetation.
TOXICITY COMPARISON OF BIOSURFACTANTS AND SYNTHETIC SURFACTANTS USED IN OIL SPILL REMEDIATION TO TWO ESTUARINE SPECIES

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The relative environmental toxicities of synthetic and biogenic surfactants used in oil spill remediation efforts are not well understood. Acute and chronic toxicities of three synthetic surfactants and three microbially produced surfactants were determined and compared in this s...
Microbial diversity in Brazilian mangrove sediments – a mini review

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Ghizelini, Angela Michelato; Mendonça-Hagler, Leda Cristina Santana; Macrae, Andrew

2012-01-01

The importance and protection of mangrove ecosystems has been recognized in Brazilian Federal law since 1965. Being protected in law, however, has not always guaranteed their protection in practice. Mangroves are found in coastal and estuarine locations, which are prime real estate for the growth of cities, ports and other economic activities important for Brazilian development. In this mini-review we introduce what mangroves are and why they are so important. We give a brief overview of the microbial diversity found in mangrove sediments and then focus on diversity studies from Brazilian mangroves. We highlight the breadth and depth of knowledge about mangrove microbial communities gained from studying Brazilian mangroves. We report on the exciting findings of molecular microbial ecology methods that have been very successfully applied to study bacterial communities. We note that there have been fewer studies that focus on fungal communities and that fungal diversity studies deserve more attention. The review ends with a look at how a combination of new molecular biology methods and isolation studies are being developed to monitor and conserve mangrove ecosystems and their associated microbial communities. These recent studies are having a global impact and we hope they will help to protect and re-establish mangrove ecosystems. PMID:24031949
Microbial biomass carbon and enzyme activities of urban soils in Beijing.

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Wang, Meie; Markert, Bernd; Shen, Wenming; Chen, Weiping; Peng, Chi; Ouyang, Zhiyun

2011-07-01

To promote rational and sustainable use of soil resources and to maintain the urban soil quality, it is essential to assess urban ecosystem health. In this study, the microbiological properties of urban soils in Beijing and their spatial distribution patterns across the city were evaluated based on measurements of microbial biomass carbon and urease and invertase activities of the soils for the purpose of assessing the urban ecosystem health of Beijing. Grid sampling design, normal Kriging technique, and the multiple comparisons among different land use types were used in soil sampling and data treatment. The inherent chemical characteristics of urban soils in Beijing, e.g., soil pH, electronic conductivity, heavy metal contents, total N, P and K contents, and soil organic matter contents were detected. The size and diversity of microbial community and the extent of microbial activity in Beijing urban soils were measured as the microbial biomass carbon content and the ratio of microbial biomass carbon content to total soil organic carbon. The microbial community health measured in terms of microbial biomass carbon, urease, and invertase activities varied with the organic substrate and nutrient contents of the soils and were not adversely affected by the presence of heavy metals at p urban soils influenced the nature and activities of the microbial communities.
Linking genes to ecosystem trace gas fluxes in a large-scale model system

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Meredith, L. K.; Cueva, A.; Volkmann, T. H. M.; Sengupta, A.; Troch, P. A.

2017-12-01

Soil microorganisms mediate biogeochemical cycles through biosphere-atmosphere gas exchange with significant impact on atmospheric trace gas composition. Improving process-based understanding of these microbial populations and linking their genomic potential to the ecosystem-scale is a challenge, particularly in soil systems, which are heterogeneous in biodiversity, chemistry, and structure. In oligotrophic systems, such as the Landscape Evolution Observatory (LEO) at Biosphere 2, atmospheric trace gas scavenging may supply critical metabolic needs to microbial communities, thereby promoting tight linkages between microbial genomics and trace gas utilization. This large-scale model system of three initially homogenous and highly instrumented hillslopes facilitates high temporal resolution characterization of subsurface trace gas fluxes at hundreds of sampling points, making LEO an ideal location to study microbe-mediated trace gas fluxes from the gene to ecosystem scales. Specifically, we focus on the metabolism of ubiquitous atmospheric reduced trace gases hydrogen (H2), carbon monoxide (CO), and methane (CH4), which may have wide-reaching impacts on microbial community establishment, survival, and function. Additionally, microbial activity on LEO may facilitate weathering of the basalt matrix, which can be studied with trace gas measurements of carbonyl sulfide (COS/OCS) and carbon dioxide (O-isotopes in CO2), and presents an additional opportunity for gene to ecosystem study. This work will present initial measurements of this suite of trace gases to characterize soil microbial metabolic activity, as well as links between spatial and temporal variability of microbe-mediated trace gas fluxes in LEO and their relation to genomic-based characterization of microbial community structure (phylogenetic amplicons) and genetic potential (metagenomics). Results from the LEO model system will help build understanding of the importance of atmospheric inputs to
New Frontiers in Synthetic Biology for Spaceflight

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Galazka, Jonathan M.

2017-01-01

Exploration of the solar system is constrained by the cost of moving mass off Earth. Producing materials in situ will reduce the mass that must be delivered from earth. CO2 is abundant on Mars and manned spacecraft. On the ISS, NASA reacts excess CO2 with H2 to generate CH4 and H2O using the Sabatier System. The resulting water is recovered into the ISS, but the methane is vented to space. Thus, there is a capability need for systems that convert methane into valuable materials. Methanotrophic bacteria consume methane but these are poor synthetic biology platforms. Thus, there is a knowledge gap in utilizing methane in a robust and flexible synthetic biology platform. The yeast Pichia pastoris is a refined microbial factory that is used widely by industry because it efficiently secretes products. Pichia could produce a variety of useful products in space. Pichia does not consume methane but robustly consumes methanol, which is one enzymatic step removed from methane. Our goal is to engineer Pichia to consume methane thereby creating a powerful methane-consuming microbial factory.
What is microbial community ecology?

Science.gov (United States)

Konopka, Allan

2009-11-01

The activities of complex communities of microbes affect biogeochemical transformations in natural, managed and engineered ecosystems. Meaningfully defining what constitutes a community of interacting microbial populations is not trivial, but is important for rigorous progress in the field. Important elements of research in microbial community ecology include the analysis of functional pathways for nutrient resource and energy flows, mechanistic understanding of interactions between microbial populations and their environment, and the emergent properties of the complex community. Some emergent properties mirror those analyzed by community ecologists who study plants and animals: biological diversity, functional redundancy and system stability. However, because microbes possess mechanisms for the horizontal transfer of genetic information, the metagenome may also be considered as a community property.

Compartmentalized metabolic network reconstruction of microbial communities to determine the effect of agricultural intervention on soils

Science.gov (United States)

Álvarez-Yela, Astrid Catalina; Gómez-Cano, Fabio; Zambrano, María Mercedes; Husserl, Johana; Danies, Giovanna; Restrepo, Silvia; González-Barrios, Andrés Fernando

2017-01-01

Soil microbial communities are responsible for a wide range of ecological processes and have an important economic impact in agriculture. Determining the metabolic processes performed by microbial communities is crucial for understanding and managing ecosystem properties. Metagenomic approaches allow the elucidation of the main metabolic processes that determine the performance of microbial communities under different environmental conditions and perturbations. Here we present the first compartmentalized metabolic reconstruction at a metagenomics scale of a microbial ecosystem. This systematic approach conceives a meta-organism without boundaries between individual organisms and allows the in silico evaluation of the effect of agricultural intervention on soils at a metagenomics level. To characterize the microbial ecosystems, topological properties, taxonomic and metabolic profiles, as well as a Flux Balance Analysis (FBA) were considered. Furthermore, topological and optimization algorithms were implemented to carry out the curation of the models, to ensure the continuity of the fluxes between the metabolic pathways, and to confirm the metabolite exchange between subcellular compartments. The proposed models provide specific information about ecosystems that are generally overlooked in non-compartmentalized or non-curated networks, like the influence of transport reactions in the metabolic processes, especially the important effect on mitochondrial processes, as well as provide more accurate results of the fluxes used to optimize the metabolic processes within the microbial community. PMID:28767679
Compartmentalized metabolic network reconstruction of microbial communities to determine the effect of agricultural intervention on soils.

Directory of Open Access Journals (Sweden)

María Camila Alvarez-Silva

Full Text Available Soil microbial communities are responsible for a wide range of ecological processes and have an important economic impact in agriculture. Determining the metabolic processes performed by microbial communities is crucial for understanding and managing ecosystem properties. Metagenomic approaches allow the elucidation of the main metabolic processes that determine the performance of microbial communities under different environmental conditions and perturbations. Here we present the first compartmentalized metabolic reconstruction at a metagenomics scale of a microbial ecosystem. This systematic approach conceives a meta-organism without boundaries between individual organisms and allows the in silico evaluation of the effect of agricultural intervention on soils at a metagenomics level. To characterize the microbial ecosystems, topological properties, taxonomic and metabolic profiles, as well as a Flux Balance Analysis (FBA were considered. Furthermore, topological and optimization algorithms were implemented to carry out the curation of the models, to ensure the continuity of the fluxes between the metabolic pathways, and to confirm the metabolite exchange between subcellular compartments. The proposed models provide specific information about ecosystems that are generally overlooked in non-compartmentalized or non-curated networks, like the influence of transport reactions in the metabolic processes, especially the important effect on mitochondrial processes, as well as provide more accurate results of the fluxes used to optimize the metabolic processes within the microbial community.
Elevated temperature alters carbon cycling in a model microbial community

Science.gov (United States)

Mosier, A.; Li, Z.; Thomas, B. C.; Hettich, R. L.; Pan, C.; Banfield, J. F.

2013-12-01

Earth's climate is regulated by biogeochemical carbon exchanges between the land, oceans and atmosphere that are chiefly driven by microorganisms. Microbial communities are therefore indispensible to the study of carbon cycling and its impacts on the global climate system. In spite of the critical role of microbial communities in carbon cycling processes, microbial activity is currently minimally represented or altogether absent from most Earth System Models. Method development and hypothesis-driven experimentation on tractable model ecosystems of reduced complexity, as presented here, are essential for building molecularly resolved, benchmarked carbon-climate models. Here, we use chemoautotropic acid mine drainage biofilms as a model community to determine how elevated temperature, a key parameter of global climate change, regulates the flow of carbon through microbial-based ecosystems. This study represents the first community proteomics analysis using tandem mass tags (TMT), which enable accurate, precise, and reproducible quantification of proteins. We compare protein expression levels of biofilms growing over a narrow temperature range expected to occur with predicted climate changes. We show that elevated temperature leads to up-regulation of proteins involved in amino acid metabolism and protein modification, and down-regulation of proteins involved in growth and reproduction. Closely related bacterial genotypes differ in their response to temperature: Elevated temperature represses carbon fixation by two Leptospirillum genotypes, whereas carbon fixation is significantly up-regulated at higher temperature by a third closely related genotypic group. Leptospirillum group III bacteria are more susceptible to viral stress at elevated temperature, which may lead to greater carbon turnover in the microbial food web through the release of viral lysate. Overall, this proteogenomics approach revealed the effects of climate change on carbon cycling pathways and other
Board-invited review: Rumen microbiology: leading the way in microbial ecology.

Science.gov (United States)

Krause, D O; Nagaraja, T G; Wright, A D G; Callaway, T R

2013-01-01

Robert Hungate, considered the father of rumen microbiology, was the first to initiate a systematic exploration of the microbial ecosystem of the rumen, but he was not alone. The techniques he developed to isolate and identify cellulose-digesting bacteria from the rumen have had a major impact not only in delineating the complex ecosystem of the rumen but also in clinical microbiology and in the exploration of a number of other anaerobic ecosystems, including the human hindgut. Rumen microbiology has pioneered our understanding of much of microbial ecology and has broadened our knowledge of ecology in general, as well as improved the ability to feed ruminants more efficiently. The discovery of anaerobic fungi as a component of the ruminal flora disproved the central dogma in microbiology that all fungi are aerobic organisms. Further novel interactions between bacterial species such as nutrient cross feeding and interspecies H2 transfer were first described in ruminal microorganisms. The complexity and diversity present in the rumen make it an ideal testing ground for microbial theories (e.g., the effects of nutrient limitation and excess) and techniques (such as 16S rRNA), which have rewarded the investigators that have used this easily accessed ecosystem to understand larger truths. Our understanding of characteristics of the ruminal microbial population has opened new avenues of microbial ecology, such as the existence of hyperammonia-producing bacteria and how they can be used to improve N efficiency in ruminants. In this review, we examine some of the contributions to science that were first made in the rumen, which have not been recognized in a broader sense.
Scaling Soil Microbe-Water Interactions from Pores to Ecosystems

Science.gov (United States)

Manzoni, S.; Katul, G. G.

2014-12-01

The spatial scales relevant to soil microbial activity are much finer than scales relevant to whole-ecosystem function and biogeochemical cycling. On the one hand, how to link such different scales and develop scale-aware biogeochemical and ecohydrological models remains a major challenge. On the other hand, resolving these linkages is becoming necessary for testing ecological hypotheses and resolving data-theory inconsistencies. Here, the relation between microbial respiration and soil moisture expressed in water potential is explored. Such relation mediates the water availability effects on ecosystem-level heterotrophic respiration and is of paramount importance for understanding CO2 emissions under increasingly variable rainfall regimes. Respiration has been shown to decline as the soil dries in a remarkably consistent way across climates and soil types (open triangles in Figure). Empirical models based on these respiration-moisture relations are routinely used in Earth System Models to predict moisture effects on ecosystem respiration. It has been hypothesized that this consistency in microbial respiration decline is due to breakage of water film continuity causing in turn solute diffusion limitations in dry conditions. However, this hypothesis appears to be at odds with what is known about soil hydraulic properties. Water film continuity estimated from soil water retention (SWR) measurements at the 'Darcy' scale breaks at far less negative water potential (micro-level relevant to microbial activity. Such downscaling resolves the inconsistency between respiration thresholds and hydrological thresholds. This result, together with observations of residual microbial activity well below -15 MPa (dashed back curve in Figure), lends support to the hypothesis that soil microbes are substrate-limited in dry conditions.
Microbial Mechanisms Enhancing Soil C Storage

Energy Technology Data Exchange (ETDEWEB)

Zak, Donald [Univ. of Michigan, Ann Arbor, MI (United States)

2015-09-24

Human activity has globally increased the amount of nitrogen (N) entering ecosystems, which could foster higher rates of C sequestration in the N-limited forests of the Northern Hemisphere. Presently, these ecosystems are a large global sink for atmospheric CO2, the magnitude of which could be influenced by the input of human-derived N from the atmosphere. Nevertheless, empirical studies and simulation models suggest that anthropogenic N deposition could have either an important or inconsequential effect on C storage in forests of the Northern Hemisphere, a set of observations that continues to fuel scientific discourse. Although a relatively simple set of physiological processes control the C balance of terrestrial ecosystems, we still fail to understand how these processes directly and indirectly respond to greater N availability in the environment. The uptake of anthropogenic N by N-limited forest trees and a subsequent enhancement of net primary productivity have been the primary mechanisms thought to increase ecosystem C storage in Northern Hemisphere forests. However, there are reasons to expect that anthropogenic N deposition could slow microbial activity in soil, decrease litter decay, and increase soil C storage. Fungi dominate the decay of plant detritus in forests and, under laboratory conditions, high inorganic N concentrations can repress the transcription of genes coding for enzymes which depolymerize lignin in plant detritus; this observation presents the possibility that anthropogenic N deposition could elicit a similar effect under field conditions. In our 18-yr-long field experiment, we have been able to document that simulated N deposition, at a rate expected in the near future, resulted in a significant decline in cellulolytic and lignolytic microbial activity, slowed plant litter decay, and increased soil C storage (+10%); this response is not portrayed in any biogeochemical model simulating the effect of atmospheric N deposition on ecosystem C
Using community trait-distributions to assign microbial responses to pH changes and Cd in forest soils treated with wood ash

DEFF Research Database (Denmark)

Cruz Paredes, Carla; Wallander, Håkan; Kjøller, Rasmus

2017-01-01

is the current land-use. In forestry, wood ash has been proposed as a liming agent and a fertilizer, but has been questioned due to the risk associated with its Cd content. The aim of this study was to determine the effects of wood ash on the structure and function of decomposer microbial communities in forest......The identification of causal links between microbial community structure and ecosystem functions are required for a mechanistic understanding of ecosystem responses to environmental change. One of the most influential factors affecting plants and microbial communities in soil in managed ecosystems...... soils and to assign them to causal mechanisms. To do this, we assessed the responses to wood ash application of (i) the microbial community size and structure, (ii) microbial community trait-distributions, including bacterial pH relationships and Cd-tolerance, to assign the microbial responses to p...
Stay connected: Electrical conductivity of microbial aggregates.

Science.gov (United States)

Li, Cheng; Lesnik, Keaton Larson; Liu, Hong

2017-11-01

The discovery of direct extracellular electron transfer offers an alternative to the traditional understanding of diffusional electron exchange via small molecules. The establishment of electronic connections between electron donors and acceptors in microbial communities is critical to electron transfer via electrical currents. These connections are facilitated through conductivity associated with various microbial aggregates. However, examination of conductivity in microbial samples is still in its relative infancy and conceptual models in terms of conductive mechanisms are still being developed and debated. The present review summarizes the fundamental understanding of electrical conductivity in microbial aggregates (e.g. biofilms, granules, consortia, and multicellular filaments) highlighting recent findings and key discoveries. A greater understanding of electrical conductivity in microbial aggregates could facilitate the survey for additional microbial communities that rely on direct extracellular electron transfer for survival, inform rational design towards the aggregates-based production of bioenergy/bioproducts, and inspire the construction of new synthetic conductive polymers. Copyright © 2017 Elsevier Inc. All rights reserved.
Microbial mutualism at a distance: The role of geometry in diffusive exchanges

Science.gov (United States)

Peaudecerf, François J.; Bunbury, Freddy; Bhardwaj, Vaibhav; Bees, Martin A.; Smith, Alison G.; Goldstein, Raymond E.; Croze, Ottavio A.

2018-02-01

The exchange of diffusive metabolites is known to control the spatial patterns formed by microbial populations, as revealed by recent studies in the laboratory. However, the matrices used, such as agarose pads, lack the structured geometry of many natural microbial habitats, including in the soil or on the surfaces of plants or animals. Here we address the important question of how such geometry may control diffusive exchanges and microbial interaction. We model mathematically mutualistic interactions within a minimal unit of structure: two growing reservoirs linked by a diffusive channel through which metabolites are exchanged. The model is applied to study a synthetic mutualism, experimentally parametrized on a model algal-bacterial co-culture. Analytical and numerical solutions of the model predict conditions for the successful establishment of remote mutualisms, and how this depends, often counterintuitively, on diffusion geometry. We connect our findings to understanding complex behavior in synthetic and naturally occurring microbial communities.
Soil biochemical properties of grassland ecosystems under anthropogenic emission of nitrogen compounds

Science.gov (United States)

Kudrevatykh, Irina; Ivashchenko, Kristina; Ananyeva, Nadezhda

2016-04-01

Inflow of pollutants in terrestrial ecosystems nowadays increases dramatically, that might be led to disturbance of natural biogeochemical cycles and landscapes structure. Production of nitrogen fertilizers is one of the air pollution sources, namely by nitrogen compounds (NH4+, NO3-, NO2-). Air pollution by nitrogen compounds of terrestrial ecosystems might be affected on soil biochemical properties, which results increasing mineral nitrogen content in soil, changing soil P/N and Al/Ca ratios, and, finally, the deterioration of soil microbial community functioning. The research is focused on the assessment of anthropogenic emission of nitrogen compounds on soil properties of grassland ecosystems in European Russia. Soil samples (Voronic Chernozem Pachic, upper 10 cm mineral layer, totally 10) were taken from grassland ecosystem: near (5-10 m) nitrogen fertilizer factory (NFF), and far from it (20-30 km, served as a control) in Tula region. In soil samples the NH4+ and NO3- (Kudeyarov's photocolorimetric method), P, Ca, Al (X-ray fluorescence method) contents were measured. Soil microbial biomass carbon (Cmic) was analyzed by substrate-induced respiration method. Soil microbial respiration (MR) was assessed by CO2 rate production. Soil microbial metabolic quotient (qCO2) was calculated as MR/Cmic ratio. Near NFF the soil ammonium and nitrate nitrogen contents were a strongly varied, variation coefficient (CV) was 42 and 86This study was supported by Russian Foundation of Basic Research Grant No. 14-04-00098, 15-44-03220, 15-04-00915.
Microbial ecology to manage processes in environmental biotechnology.

Science.gov (United States)

Rittmann, Bruce E

2006-06-01

Microbial ecology and environmental biotechnology are inherently tied to each other. The concepts and tools of microbial ecology are the basis for managing processes in environmental biotechnology; and these processes provide interesting ecosystems to advance the concepts and tools of microbial ecology. Revolutionary advancements in molecular tools to understand the structure and function of microbial communities are bolstering the power of microbial ecology. A push from advances in modern materials along with a pull from a societal need to become more sustainable is enabling environmental biotechnology to create novel processes. How do these two fields work together? Five principles illuminate the way: (i) aim for big benefits; (ii) develop and apply more powerful tools to understand microbial communities; (iii) follow the electrons; (iv) retain slow-growing biomass; and (v) integrate, integrate, integrate.
Yeast synthetic biology for high-value metabolites.

Science.gov (United States)

Dai, Zhubo; Liu, Yi; Guo, Juan; Huang, Luqi; Zhang, Xueli

2015-02-01

Traditionally, high-value metabolites have been produced through direct extraction from natural biological sources which are inefficient, given the low abundance of these compounds. On the other hand, these high-value metabolites are usually difficult to be synthesized chemically, due to their complex structures. In the last few years, the discovery of genes involved in the synthetic pathways of these metabolites, combined with advances in synthetic biology tools, has allowed the construction of increasing numbers of yeast cell factories for production of these metabolites from renewable biomass. This review summarizes recent advances in synthetic biology in terms of the use of yeasts as microbial hosts for the identification of the pathways involved in the synthesis, as well as for the production of high-value metabolites. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permission@oup.com.
Microbial biotechnology addressing the plastic waste disaster

OpenAIRE

Narancic, Tanja; O'Connor, Kevin E.

2017-01-01

Oceans are a major source of biodiversity, they provide livelihood, and regulate the global ecosystem by absorbing heat and CO 2. However, they are highly polluted with plastic waste. We are discussing here microbial biotechnology advances with the view to improve the start and the end of life of biodegradable polymers, which could contribute to the sustainable use of marine and coastal ecosystems (UN Sustainability development goal 14).
Microbial diversity and metabolic networks in acid mine drainage habitats

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Celia eMendez-Garcia

2015-05-01

Full Text Available Acid mine drainage (AMD emplacements are low-complexity natural systems. Low-pH conditions appear to be the main factor underlying the limited diversity of the microbial populations thriving in these environments, although temperature, ionic composition, total organic carbon and dissolved oxygen are also considered to significantly influence their microbial life. This natural reduction in diversity driven by extreme conditions was reflected in several studies on the microbial populations inhabiting the various micro-environments present in such ecosystems. Early studies based on the physiology of the autochthonous microbiota and the growing success of omics technologies have enabled a better understanding of microbial ecology and function in low-pH mine outflows; however, complementary omics-derived data should be included to completely describe their microbial ecology. Furthermore, recent updates on the distribution of eukaryotes and ultra-micro-archaea demand their inclusion in the microbial characterisation of AMD systems. In this review, we present a complete overview of the bacterial, archaeal (including ultra-micro-archaeal and eukaryotic diversity in these ecosystems and include a thorough depiction of the metabolism and element cycling in AMD habitats. We also review different metabolic network structures at the organismal level, which is necessary to disentangle the role of each member of the AMD communities described thus far.
Recovery of microbial community structure and functioning after wildfire in semi-arid environments: optimising methods for monitoring and assessment

Science.gov (United States)

Muñoz-Rojas, Miriam; Martini, Dylan; Erickson, Todd; Merritt, David; Dixon, Kingsley

2015-04-01

Introduction In semi-arid areas such as northern Western Australia, wildfires are a natural part of the environment and many ecosystems in these landscapes have evolved and developed a strong relationship with fire. Soil microbial communities play a crucial role in ecosystem processes by regulating the cycling of nutrients via decomposition, mineralization, and immobilization processes. Thus, the structure (e.g. soil microbial biomass) and functioning (e.g. soil microbial activity) of microbial communities, as well as their changes after ecosystem disturbance, can be useful indicators of soil quality and health recovery. In this research, we assess the impacts of fire on soil microbial communities and their recovery in a biodiverse semi-arid environment of Western Australia (Pilbara region). New methods for determining soil microbial respiration as an indicator of microbial activity and soil health are also tested. Methodology Soil samples were collected from 10 similar ecosystems in the Pilbara with analogous native vegetation, but differing levels of post-fire disturbance (i.e. 3 months, 1 year, 5, 7 and 14 years after wildfire). Soil microbial activity was measured with the Solvita test which determines soil microbial respiration rate based on the measurement of the CO2 burst of a dry soil after it is moistened. Soils were dried and re-wetted and a CO2 probe was inserted before incubation at constant conditions of 25°C during 24 h. Measurements were taken with a digital mini spectrometer. Microbial (bacteria and fungi) biomass and community composition were measured by phospholipid fatty acid analysis (PLFA). Results Immediately after the fire (i.e. 3 months), soil microbial activity and microbial biomass are similar to 14 years 'undisturbed' levels (53.18±3.68 ppm CO2-CO and 14.07±0.65 mg kg-1, respectively). However, after the first year post-fire, with larger plant productivity, microbial biomass and microbial activity increase rapidly, peaking after 5
Bentonite. Geotechnical barrier and source for microbial life

International Nuclear Information System (INIS)

Matschiavelli, Nicole; Kluge, Sindy; Cherkouk, Andrea; Steglich, Jennifer

2017-01-01

Due to their properties, namely a high swelling capacity and a low hydraulic conductivity, Bentonites fulfil as geotechnical barrier a sealing and buffering function in the nuclear waste repository. Depending on the mineral composition Bentonites contain many suitable electron-donors and -acceptors, enabling potential microbial life. For the potential repository of highly radioactive waste the microbial mediated transformation of Bentonite could influence its properties as a barrier material. Microcosms were set up containing Bentonite and anaerobic synthetic Opalinus-clay-pore water solution under an N_2/CO_2-atmosphere to elucidate the microbial potential within selected Bentonites. Substrates like acetate and lactate were supplemented to stimulate potential microbial activity. First results show that bentonites represent a source for microbial life, demonstrated by the consumption of lactate and the formation of pyruvate. Furthermore, microbial iron-reduction was determined, which plays a crucial role in Betonite-transformation.
Bentonite. Geotechnical barrier and source for microbial life

Energy Technology Data Exchange (ETDEWEB)

Matschiavelli, Nicole; Kluge, Sindy; Cherkouk, Andrea [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). HZDR Young Investigator Group; Steglich, Jennifer

2017-06-01

Due to their properties, namely a high swelling capacity and a low hydraulic conductivity, Bentonites fulfil as geotechnical barrier a sealing and buffering function in the nuclear waste repository. Depending on the mineral composition Bentonites contain many suitable electron-donors and -acceptors, enabling potential microbial life. For the potential repository of highly radioactive waste the microbial mediated transformation of Bentonite could influence its properties as a barrier material. Microcosms were set up containing Bentonite and anaerobic synthetic Opalinus-clay-pore water solution under an N{sub 2}/CO{sub 2}-atmosphere to elucidate the microbial potential within selected Bentonites. Substrates like acetate and lactate were supplemented to stimulate potential microbial activity. First results show that bentonites represent a source for microbial life, demonstrated by the consumption of lactate and the formation of pyruvate. Furthermore, microbial iron-reduction was determined, which plays a crucial role in Betonite-transformation.
Cell-free synthetic biology for in vitro prototype engineering.

Science.gov (United States)

Moore, Simon J; MacDonald, James T; Freemont, Paul S

2017-06-15

Cell-free transcription-translation is an expanding field in synthetic biology as a rapid prototyping platform for blueprinting the design of synthetic biological devices. Exemplar efforts include translation of prototype designs into medical test kits for on-site identification of viruses (Zika and Ebola), while gene circuit cascades can be tested, debugged and re-designed within rapid turnover times. Coupled with mathematical modelling, this discipline lends itself towards the precision engineering of new synthetic life. The next stages of cell-free look set to unlock new microbial hosts that remain slow to engineer and unsuited to rapid iterative design cycles. It is hoped that the development of such systems will provide new tools to aid the transition from cell-free prototype designs to functioning synthetic genetic circuits and engineered natural product pathways in living cells. © 2017 The Author(s).
Modeling adaptation of carbon use efficiency in microbial communities

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Steven D Allison

2014-10-01

Full Text Available In new microbial-biogeochemical models, microbial carbon use efficiency (CUE is often assumed to decline with increasing temperature. Under this assumption, soil carbon losses under warming are small because microbial biomass declines. Yet there is also empirical evidence that CUE may adapt (i.e. become less sensitive to warming, thereby mitigating negative effects on microbial biomass. To analyze potential mechanisms of CUE adaptation, I used two theoretical models to implement a tradeoff between microbial uptake rate and CUE. This rate-yield tradeoff is based on thermodynamic principles and suggests that microbes with greater investment in resource acquisition should have lower CUE. Microbial communities or individuals could adapt to warming by reducing investment in enzymes and uptake machinery. Consistent with this idea, a simple analytical model predicted that adaptation can offset 50% of the warming-induced decline in CUE. To assess the ecosystem implications of the rate-yield tradeoff, I quantified CUE adaptation in a spatially-structured simulation model with 100 microbial taxa and 12 soil carbon substrates. This model predicted much lower CUE adaptation, likely due to additional physiological and ecological constraints on microbes. In particular, specific resource acquisition traits are needed to maintain stoichiometric balance, and taxa with high CUE and low enzyme investment rely on low-yield, high-enzyme neighbors to catalyze substrate degradation. In contrast to published microbial models, simulations with greater CUE adaptation also showed greater carbon storage under warming. This pattern occurred because microbial communities with stronger CUE adaptation produced fewer degradative enzymes, despite increases in biomass. Thus the rate-yield tradeoff prevents CUE adaptation from driving ecosystem carbon loss under climate warming.
Homogeneous versus heterogeneous probes for microbial ecological microarrays.

Science.gov (United States)

Bae, Jin-Woo; Park, Yong-Ha

2006-07-01

Microbial ecological microarrays have been developed for investigating the composition and functions of microorganism communities in environmental niches. These arrays include microbial identification microarrays, which use oligonucleotides, gene fragments or microbial genomes as probes. In this article, the advantages and disadvantages of each type of probe are reviewed. Oligonucleotide probes are currently useful for probing uncultivated bacteria that are not amenable to gene fragment probing, whereas the functional gene fragments amplified randomly from microbial genomes require phylogenetic and hierarchical categorization before use as microbial identification probes, despite their high resolution for both specificity and sensitivity. Until more bacteria are sequenced and gene fragment probes are thoroughly validated, heterogeneous bacterial genome probes will provide a simple, sensitive and quantitative tool for exploring the ecosystem structure.

Microbial Indicators of Soil Quality under Different Land Use Systems in Subtropical Soils

Science.gov (United States)

Maharjan, M.

2016-12-01

Land-use change from native forest to intensive agricultural systems can negatively impact numerous soil parameters. Understanding the effects of forest ecosystem transformations on markers of long-term soil health is particularly important in rapidly developing regions such as Nepal, where unprecedented levels of agriculturally-driven deforestation have occurred in recent decades. However, the effects of widespread land use changes on soil quality in this region have yet to be properly characterized. Microbial indicators (soil microbial biomass, metabolic quotient and enzymes activities) are particularly suited to assessing the consequences of such ecosystem disturbances, as microbial communities are especially sensitive to environmental change. Thus, the aim of this study was to assess the effect of land use system; i.e. forest, organic and conventional farming, on soil quality in Chitwan, Nepal using markers of microbial community size and activity. Total organic C and N contents were higher in organic farming compared with conventional farming and forest, suggesting higher nutrient retention and soil preservation with organic farming practices compared to conventional. These differences in soil composition were reflected in the health of the soil microbial communities: Organic farm soil exhibited higher microbial biomass C, elevated β-glucosidase and chitinase activities, and a lower metabolic quotient relative to other soils, indicating a larger, more active, and less stressed microbial community, respectively. These results collectively demonstrate that application of organic fertilizers and organic residues positively influence nutrient availability, with subsequent improvements in soil quality and productivity. Furthermore, the sensitivity of microbial indicators to different management practices demonstrated in this study supports their use as effective markers of ecosystem disturbance in subtropical soils.
Farm management, not soil microbial diversity, controls nutrient loss from smallholder tropical agriculture

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Stephen A Wood

2015-03-01

Full Text Available Tropical smallholder agriculture supports the livelihoods of over 900 million of the world’s poorest people. This form of agriculture is undergoing rapid transformation in nutrient cycling pathways as international development efforts strongly promote greater use of mineral fertilizers to increase crop yields. These changes in nutrient availability may alter the composition of microbial communities with consequences for rates of biogeochemical processes that control nutrient losses to the environment. Ecological theory suggests that altered microbial diversity will strongly influence processes performed by relatively few microbial taxa, such as denitrification and hence nitrogen losses as nitrous oxide, a powerful greenhouse gas. Whether this theory helps predict nutrient losses from agriculture depends on the relative effects of microbial community change and increased nutrient availability on ecosystem processes. We find that mineral and organic nutrient addition to smallholder farms in Kenya alters the taxonomic and functional diversity of soil microbes. However, we find that the direct effects of farm management on both denitrification and carbon mineralization are greater than indirect effects through changes in the taxonomic and functional diversity of microbial communities. Changes in functional diversity are strongly coupled to changes in specific functional genes involved in denitrification, suggesting that it is the expression, rather than abundance, of key functional genes that can serve as an indicator of ecosystem process rates. Our results thus suggest that widely used broad summary statistics of microbial diversity based on DNA may be inappropriate for linking microbial communities to ecosystem processes in certain applied settings. Our results also raise doubts about the relative control of microbial composition compared to direct effects of management on nutrient losses in applied settings such as tropical agriculture.
Microbial diversity arising from thermodynamic constraints

Science.gov (United States)

Großkopf, Tobias; Soyer, Orkun S

2016-01-01

The microbial world displays an immense taxonomic diversity. This diversity is manifested also in a multitude of metabolic pathways that can utilise different substrates and produce different products. Here, we propose that these observations directly link to thermodynamic constraints that inherently arise from the metabolic basis of microbial growth. We show that thermodynamic constraints can enable coexistence of microbes that utilise the same substrate but produce different end products. We find that this thermodynamics-driven emergence of diversity is most relevant for metabolic conversions with low free energy as seen for example under anaerobic conditions, where population dynamics is governed by thermodynamic effects rather than kinetic factors such as substrate uptake rates. These findings provide a general understanding of the microbial diversity based on the first principles of thermodynamics. As such they provide a thermodynamics-based framework for explaining the observed microbial diversity in different natural and synthetic environments. PMID:27035705
Microbial diversity arising from thermodynamic constraints.

Science.gov (United States)

Großkopf, Tobias; Soyer, Orkun S

2016-11-01

The microbial world displays an immense taxonomic diversity. This diversity is manifested also in a multitude of metabolic pathways that can utilise different substrates and produce different products. Here, we propose that these observations directly link to thermodynamic constraints that inherently arise from the metabolic basis of microbial growth. We show that thermodynamic constraints can enable coexistence of microbes that utilise the same substrate but produce different end products. We find that this thermodynamics-driven emergence of diversity is most relevant for metabolic conversions with low free energy as seen for example under anaerobic conditions, where population dynamics is governed by thermodynamic effects rather than kinetic factors such as substrate uptake rates. These findings provide a general understanding of the microbial diversity based on the first principles of thermodynamics. As such they provide a thermodynamics-based framework for explaining the observed microbial diversity in different natural and synthetic environments.
Deciphering the microbial ecology in bio- gas reactors for optimizing the anaerobic digestion process

DEFF Research Database (Denmark)

Zhu, Xinyu

of the basic microbial metabolism and ecology, methanogenic microbial communities were enriched in a lab-scale continuous stirred-tank reactor (CSTR) fed with synthetic feedstocks. In the experiment, the substrates used were stepwise simplified (i.e. polysaccharide, monosaccharide, short chain fatty acids...
Global microbialization of coral reefs.

Science.gov (United States)

Haas, Andreas F; Fairoz, Mohamed F M; Kelly, Linda W; Nelson, Craig E; Dinsdale, Elizabeth A; Edwards, Robert A; Giles, Steve; Hatay, Mark; Hisakawa, Nao; Knowles, Ben; Lim, Yan Wei; Maughan, Heather; Pantos, Olga; Roach, Ty N F; Sanchez, Savannah E; Silveira, Cynthia B; Sandin, Stuart; Smith, Jennifer E; Rohwer, Forest

2016-04-25

Microbialization refers to the observed shift in ecosystem trophic structure towards higher microbial biomass and energy use. On coral reefs, the proximal causes of microbialization are overfishing and eutrophication, both of which facilitate enhanced growth of fleshy algae, conferring a competitive advantage over calcifying corals and coralline algae. The proposed mechanism for this competitive advantage is the DDAM positive feedback loop (dissolved organic carbon (DOC), disease, algae, microorganism), where DOC released by ungrazed fleshy algae supports copiotrophic, potentially pathogenic bacterial communities, ultimately harming corals and maintaining algal competitive dominance. Using an unprecedented data set of >400 samples from 60 coral reef sites, we show that the central DDAM predictions are consistent across three ocean basins. Reef algal cover is positively correlated with lower concentrations of DOC and higher microbial abundances. On turf and fleshy macroalgal-rich reefs, higher relative abundances of copiotrophic microbial taxa were identified. These microbial communities shift their metabolic potential for carbohydrate degradation from the more energy efficient Embden-Meyerhof-Parnas pathway on coral-dominated reefs to the less efficient Entner-Doudoroff and pentose phosphate pathways on algal-dominated reefs. This 'yield-to-power' switch by microorganism directly threatens reefs via increased hypoxia and greater CO2 release from the microbial respiration of DOC.
Microbial synthesis of alka(enes

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Weihua eWang

2013-10-01

Full Text Available Alka(enes are the predominant constituents of gasoline, diesel, and jet fuels. They can be produced naturally by a wide range of microorganisms. Bio- alka(enes can be used as drop-in biofuels. To date, five microbial pathways that convert free fatty acids or fatty acid derivatives into alka(enes have been identified or reconstituted. The discoveries open a door to achieve microbial production of alka(enes with high efficiency. The modules derived from these alka(ene biosynthetic pathways can be assembled as biological parts and synthetic biology strategies can be employed to optimize the metabolic pathways and improve alka(ene production.
Comparison of the active and resident community of a coastal microbial mat

OpenAIRE

Cardoso, Daniela Clara; Sandionigi, Anna; Cretoiu, Mariana Silvia; Casiraghi, Maurizio; Stal, Lucas; Bolhuis, Henk

2017-01-01

Coastal microbial mats form a nearly closed micro-scale ecosystem harboring a complex microbial community. Previous DNA based analysis did not necessarily provide information about the active fraction of the microbial community because it includes dormant, inactive cells as well as a potential stable pool of extracellular DNA. Here we focused on the active microbial community by comparing 16S rRNA sequences obtained from the ribosomal RNA pool with gene sequences obtained from the DNA fractio...
Soil Microbial Community Structure Evolution along Halophyte Succession in Bohai Bay Wetland

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Mingyang Cong

2014-01-01

Full Text Available It is urgent to recover Bohai Bay costal wetland ecosystem because of covering a large area of severe saline-alkali soil. To explore the relationship between halophyte herbaceous succession and microbial community structure, we chose four local communities which played an important role in improving soil microenvironment. We performed phospholipid fatty acid analysis, measured soil parameters, and evaluated shifts of microbial community structure. Results showed that microbial community structure changed significantly along succession and bacteria community was dominant. Total phospholipid fatty acid content increased in different successional stages but decreased with depth, with similar variations in bacterial and fungal biomass. Soil organic carbon and especially total nitrogen were positively correlated with microbial biomass. Colonization of pioneering salt-tolerant plants Suaeda glauca in saline-alkali bare land changed total soil microorganism content and composition. These results showed that belowground processes were strongly related with aboveground halophyte succession. Fungal/bacterial ratio, Gram-negative/Gram-positive bacteria ratio, total microbial biomass, and fungi and bacteria content could indicate the degree of succession stages in Bohai Bay wetland ecosystem. And also these findings demonstrated that microbial community biomass and composition evolved along with vegetation succession environmental variables.
Soil Carbon Inputs and Ecosystem Respiration: a Field Priming Experiment in Arctic Coastal Tundra

Science.gov (United States)

Vaughn, L. S.; Zhu, B.; Bimueller, C.; Curtis, J. B.; Chafe, O.; Bill, M.; Abramoff, R. Z.; Torn, M. S.

2016-12-01

In Arctic ecosystems, climate change is expected to influence soil carbon stocks through changes in both plant carbon inputs and organic matter decomposition. This study addresses the potential for a priming effect, an interaction between these changes in which root-derived carbon inputs alter SOM decomposition rates via microbial biomass increases, co-metabolism of substrates, induced nitrogen limitation, or other possible mechanisms. The priming effect has been observed in numerous laboratory and greenhouse experiments, and is increasingly included in ecosystem models. Few studies, however, have evaluated the priming effect with in situ field manipulations. In a two-year field experiment in Barrow, Alaska, we tested for a priming effect under natural environmental variability. In September 2014 and August 2015, we added 6.1g of 13C-labeled glucose to 25cm diameter mesocosms, 15cm below the soil surface in the mineral soil layer. Over the following month, we quantified effects on the rate and temperature sensitivity of native (non-glucose) ecosystem respiration and GPP. Following the 2014 treatment, soil samples were collected at 1 and 3 weeks for microbial biomass carbon and 13C/12C analysis, and ion exchange membranes were buried for one week to assess nitrate and ammonium availability. In contrast with many laboratory incubation studies using soils from a broad range of ecosystems, we observed no significant priming effect. In spite of a clear signal of 13C-glucose decomposition in respired CO2 and microbial biomass, we detected no treatment effect on background ecosystem respiration or total microbial biomass carbon. Our findings suggest that glucose taken up by microbes was not used for production of additional SOM-decomposing enzymes, possibly due to stoichiometric limitations on enzyme production. To best inform models representing complex and dynamic ecosystems, this study calls for further research relating theory, laboratory findings, and field
Detrital microbial community development and phosphorus dynamics in a stream ecosystem

International Nuclear Information System (INIS)

Perkins, R.E.; Elwood, J.W.; Sayler, G.S.

1986-06-01

Detrital microbial community development and phosphorus dynamics in a lotic system were investigated in non-recirculating laboratory streams contains leaf detritus. Temporal patterns of microbial colonization, as determined by scanning electron microscopy, indicate leaf species dependency and that bacteria were the first colonizers followed by fungi. An extensive glycocalyx layer developed. Phosphorus incorporation rates of both the whole community and intracellular components were determined by time-course measurements of 33 PO 4 or 32 PO 4 . Phosphorus turnover rates were determined by a sequential double-labeling procedure using 33 PO 4 and 32 PO 4 , in which the microbiota were labeled with 33 P until in isotopic equilibrium, then 32 P was added. The turnover rate was determined by time-course measurements of the ratio 32 P to 33 P. Snail grazing resulted in an increase in phosphorus metabolism per unit microbial biomass; however, per unit area of leaf surface no increase was observed. Grazing also caused a two-fold reduction in microbial biomass. The results indicate that microbiota associated with decomposing leaves slowly recycle phosphorus, are slowly growing, and have a low metabolic activity. The spiraling length is shortened by microbiota on a short-term basis; however, it may increase on a long-term basis due to hydrological transport of detritus downstream
Linking diagnostic features to soil microbial biomass and respiration in agricultural grassland soil

NARCIS (Netherlands)

Richter, A.; Huallacháin, D.O.; Doyle, E.; Clipson, N.; Leeuwen, Van J.P.; Heuvelink, G.B.; Creamer, R.E.

2018-01-01

The functional potential of soil ecosystems can be predicted from the activity and abundance of the microbial community in relation to key soil properties. When describing microbial community dynamics, soil physicochemical properties have traditionally been used. The extent of correlations between
Microbial ecology of deep-sea hypersaline anoxic basins

KAUST Repository

Merlino, Giuseppe; Barozzi, Alan; Michoud, Gregoire; Ngugi, David; Daffonchio, Daniele

2018-01-01

of mixing and by extreme conditions of salinity, anoxia, and relatively high hydrostatic pressure and temperatures. Due to these combined selection factors, unique microbial assemblages thrive in these polyextreme ecosystems. The topological localization
Modes of Action of Microbially-Produced Phytotoxins

Science.gov (United States)

Duke, Stephen O.; Dayan, Franck E.

2011-01-01

Some of the most potent phytotoxins are synthesized by microbes. A few of these share molecular target sites with some synthetic herbicides, but many microbial toxins have unique target sites with potential for exploitation by the herbicide industry. Compounds from both non-pathogenic and pathogenic microbes are discussed. Microbial phytotoxins with modes of action the same as those of commercial herbicides and those with novel modes of action of action are covered. Examples of the compounds discussed are tentoxin, AAL-toxin, auscaulitoxin aglycone, hydantocidin, thaxtomin, and tabtoxin. PMID:22069756
Microbial ecology and nematode control in natural ecosystems

NARCIS (Netherlands)

Costa, S.R.; Van der Putten, W.H.; Kerry, B.R.

2011-01-01

Plant-parasitic nematodes have traditionally been studied in agricultural systems, where they can be pests of importance on a wide range of crops. Nevertheless, nematode ecology in natural ecosystems is receiving increasing interest because of the role of nematodes in soil food webs, nutrient
Increased resiliency and activity of microbial mediated carbon cycling enzymes in diversified bioenergy cropping systems

Science.gov (United States)

Upton, R.; Bach, E.; Hofmockel, K. S.

2017-12-01

Microbes are mediators of soil carbon (C) and are influenced in membership and activity by nitrogen (N) fertilization and inter-annual abiotic factors. Microbial communities and their extracellular enzyme activities (EEA) are important parameters that influence ecosystem C cycling properties and are often included in microbial explicit C cycling models. In an effort to generate model relevant, empirical findings, we investigated how both microbial community structure and C degrading enzyme activity are influenced by inter-annual variability and N inputs in bioenergy crops. Our study was performed at the Comparison of Biofuel Systems field-site from 2011 to 2014, in three bioenergy cropping systems, continuous corn (CC) and two restored prairies, both fertilized (FP) and unfertilized (P). We hypothesized microbial community structure would diverge during the prairie restoration, leading to changes in C cycling enzymes over time. Using a sequencing approach (16S and ITS) we determined the bacterial and fungal community structure response to the cropping system, fertilization, and inter-annual variability. Additionally, we used EEA of β-glucosidase, cellobiohydrolase, and β-xylosidase to determine inter-annual and ecosystem impacts on microbial activity. Our results show cropping system was a main effect for microbial community structure, with corn diverging from both prairies to be less diverse. Inter-annual changes showed that a drought occurring in 2012 significantly impacted microbial community structure in both the P and CC, decreasing microbial richness. However, FP increased in microbial richness, suggesting the application of N increased resiliency to drought. Similarly, the only year in which C cycling enzymes were impacted by ecosystem was 2012, with FP supporting higher potential enzymatic activity then CC and P. The highest EEA across all ecosystems occurred in 2014, suggesting the continued root biomass and litter build-up in this no till system
Microbial enzymes for the recycling of recalcitrant petroleum-based plastics: how far are we?

Science.gov (United States)

Wei, Ren; Zimmermann, Wolfgang

2017-11-01

Petroleum-based plastics have replaced many natural materials in their former applications. With their excellent properties, they have found widespread uses in almost every area of human life. However, the high recalcitrance of many synthetic plastics results in their long persistence in the environment, and the growing amount of plastic waste ending up in landfills and in the oceans has become a global concern. In recent years, a number of microbial enzymes capable of modifying or degrading recalcitrant synthetic polymers have been identified. They are emerging as candidates for the development of biocatalytic plastic recycling processes, by which valuable raw materials can be recovered in an environmentally sustainable way. This review is focused on microbial biocatalysts involved in the degradation of the synthetic plastics polyethylene, polystyrene, polyurethane and polyethylene terephthalate (PET). Recent progress in the application of polyester hydrolases for the recovery of PET building blocks and challenges for the application of these enzymes in alternative plastic waste recycling processes will be discussed. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.
Iron-based microbial ecosystem on and below the seafloor: a case study of hydrothermal fields of the southern mariana trough.

Science.gov (United States)

Kato, Shingo; Nakamura, Kentaro; Toki, Tomohiro; Ishibashi, Jun-Ichiro; Tsunogai, Urumu; Hirota, Akinori; Ohkuma, Moriya; Yamagishi, Akihiko

2012-01-01

Microbial community structures in deep-sea hydrothermal vents fields are constrained by available energy yields provided by inorganic redox reactions, which are in turn controlled by chemical composition of hydrothermal fluids. In the past two decades, geochemical and microbiological studies have been conducted in deep-sea hydrothermal vents at three geographically different areas of the Southern Mariana Trough (SMT). A variety of geochemical data of hydrothermal fluids and an unparalleled microbiological dataset of various samples (i.e., sulfide structures of active vents, iron-rich mats, borehole fluids, and ambient seawater) are available for comparative analyses. Here, we summarize the geochemical and microbiological characteristics in the SMT and assess the relationship between the microbial community structures and the fluid geochemistry in the SMT by thermodynamic modeling. In the high temperature vent fluids, aerobic sulfide-oxidation has the potential to yield large amounts of bioavailable energy in the vent fluids, which is consistent with the detection of species related to sulfide-oxidizing bacteria (such as Thiomicrospira in the Gammaproteobacteria and Sulfurimonas in the Epsilonproteobacteria). Conversely, the bioavailable energy yield from aerobic iron-oxidation reactions in the low-temperature fluids collected from man-made boreholes and several natural vents were comparable to or higher than those from sulfide-oxidation. This is also consistent with the detection of species related to iron-oxidizing bacteria (Mariprofundus in the Zetaproteobacteria) in such low-temperature samples. The results of combination of microbiological, geochemical, and thermodynamic analyses in the SMT provide novel insights into the presence and significance of iron-based microbial ecosystems in deep-sea hydrothermal fields.
Microbial food web dynamics along a soil chronosequence of a glacier forefield

Directory of Open Access Journals (Sweden)

J. Esperschütz

2011-11-01

Full Text Available Microbial food webs are critical for efficient nutrient turnover providing the basis for functional and stable ecosystems. However, the successional development of such microbial food webs and their role in "young" ecosystems is unclear. Due to a continuous glacier retreat since the middle of the 19th century, glacier forefields have expanded offering an excellent opportunity to study food web dynamics in soils at different developmental stages. In the present study, litter degradation and the corresponding C fluxes into microbial communities were investigated along the forefield of the Damma glacier (Switzerland. ¹³C-enriched litter of the pioneering plant Leucanthemopsis alpina (L. Heywood was incorporated into the soil at sites that have been free from ice for approximately 10, 60, 100 and more than 700 years. The structure and function of microbial communities were identified by ¹³C analysis of phospholipid fatty acids (PLFA and phospholipid ether lipids (PLEL. Results showed increasing microbial diversity and biomass, and enhanced proliferation of bacterial groups as ecosystem development progressed. Initially, litter decomposition proceeded faster at the more developed sites, but at the end of the experiment loss of litter mass was similar at all sites, once the more easily-degradable litter fraction was processed. As a result incorporation of ¹³C into microbial biomass was more evident during the first weeks of litter decomposition. ¹³C enrichments of both PLEL and PLFA biomarkers following litter incorporation were observed at all sites, suggesting similar microbial foodwebs at all stages of soil development. Nonetheless, the contribution of bacteria, especially actinomycetes to litter turnover became more pronounced as soil age increased in detriment of archaea, fungi and protozoa, more prominent in recently deglaciated terrain.
Nutrient limitation of soil microbial activity during the earliest stages of ecosystem development.

Science.gov (United States)

Castle, Sarah C; Sullivan, Benjamin W; Knelman, Joseph; Hood, Eran; Nemergut, Diana R; Schmidt, Steven K; Cleveland, Cory C

2017-11-01

A dominant paradigm in ecology is that plants are limited by nitrogen (N) during primary succession. Whether generalizable patterns of nutrient limitation are also applicable to metabolically and phylogenetically diverse soil microbial communities, however, is not well understood. We investigated if measures of N and phosphorus (P) pools inform our understanding of the nutrient(s) most limiting to soil microbial community activities during primary succession. We evaluated soil biogeochemical properties and microbial processes using two complementary methodological approaches-a nutrient addition microcosm experiment and extracellular enzyme assays-to assess microbial nutrient limitation across three actively retreating glacial chronosequences. Microbial respiratory responses in the microcosm experiment provided evidence for N, P and N/P co-limitation at Easton Glacier, Washington, USA, Puca Glacier, Peru, and Mendenhall Glacier, Alaska, USA, respectively, and patterns of nutrient limitation generally reflected site-level differences in soil nutrient availability. The activities of three key extracellular enzymes known to vary with soil N and P availability developed in broadly similar ways among sites, increasing with succession and consistently correlating with changes in soil total N pools. Together, our findings demonstrate that during the earliest stages of soil development, microbial nutrient limitation and activity generally reflect soil nutrient supply, a result that is broadly consistent with biogeochemical theory.

Coupling Spatiotemporal Community Assembly Processes to Changes in Microbial Metabolism

Energy Technology Data Exchange (ETDEWEB)

Graham, Emily B.; Crump, Alex R.; Resch, Charles T.; Fansler, Sarah; Arntzen, Evan; Kennedy, David W.; Fredrickson, Jim K.; Stegen, James C.

2016-12-16

Community assembly processes govern shifts in species abundances in response to environmental change, yet our understanding of assembly remains largely decoupled from ecosystem function. Here, we test hypotheses regarding assembly and function across space and time using hyporheic microbial communities as a model system. We pair sampling of two habitat types through hydrologic fluctuation with null modeling and multivariate statistics. We demonstrate that dual selective pressures assimilate to generate compositional changes at distinct timescales among habitat types, resulting in contrasting associations of Betaproteobacteria and Thaumarchaeota with selection and with seasonal changes in aerobic metabolism. Our results culminate in a conceptual model in which selection from contrasting environments regulates taxon abundance and ecosystem function through time, with increases in function when oscillating selection opposes stable selective pressures. Our model is applicable within both macrobial and microbial ecology and presents an avenue for assimilating community assembly processes into predictions of ecosystem function.
Cloud shading and fog drip influence the metabolism of a coastal pine ecosystem.

Science.gov (United States)

Carbone, Mariah S; Park Williams, A; Ambrose, Anthony R; Boot, Claudia M; Bradley, Eliza S; Dawson, Todd E; Schaeffer, Sean M; Schimel, Joshua P; Still, Christopher J

2013-02-01

Assessing the ecological importance of clouds has substantial implications for our basic understanding of ecosystems and for predicting how they will respond to a changing climate. This study was conducted in a coastal Bishop pine forest ecosystem that experiences regular cycles of stratus cloud cover and inundation in summer. Our objective was to understand how these clouds impact ecosystem metabolism by contrasting two sites along a gradient of summer stratus cover. The site that was under cloud cover ~15% more of the summer daytime hours had lower air temperatures and evaporation rates, higher soil moisture content, and received more frequent fog drip inputs than the site with less cloud cover. These cloud-driven differences in environmental conditions translated into large differences in plant and microbial activity. Pine trees at the site with greater cloud cover exhibited less water stress in summer, larger basal area growth, and greater rates of sap velocity. The difference in basal area growth between the two sites was largely due to summer growth. Microbial metabolism was highly responsive to fog drip, illustrated by an observed ~3-fold increase in microbial biomass C with increasing summer fog drip. In addition, the site with more cloud cover had greater total soil respiration and a larger fractional contribution from heterotrophic sources. We conclude that clouds are important to the ecological functioning of these coastal forests, providing summer shading and cooling that relieve pine and microbial drought stress as well as regular moisture inputs that elevate plant and microbial metabolism. These findings are important for understanding how these and other seasonally dry coastal ecosystems will respond to predicted changes in stratus cover, rainfall, and temperature. © 2012 Blackwell Publishing Ltd.
How ecosystems change following invasion by Robinia pseudoacacia: Insights from soil chemical properties and soil microbial, nematode, microarthropod and plant communities.

Science.gov (United States)

Lazzaro, Lorenzo; Mazza, Giuseppe; d'Errico, Giada; Fabiani, Arturo; Giuliani, Claudia; Inghilesi, Alberto F; Lagomarsino, Alessandra; Landi, Silvia; Lastrucci, Lorenzo; Pastorelli, Roberta; Roversi, Pio Federico; Torrini, Giulia; Tricarico, Elena; Foggi, Bruno

2018-05-01

Biological invasions are a global threat to biodiversity. Since the spread of invasive alien plants may have many impacts, an integrated approach, assessing effects across various ecosystem components, is needed for a correct understanding of the invasion process and its consequences. The nitrogen-fixing tree Robinia pseudoacacia (black locust) is a major invasive species worldwide and is used in forestry production. While its effects on plant communities and soils are well known, there have been few studies on soil fauna and microbes. We investigated the impacts of the tree on several ecosystem components, using a multi-trophic approach to combine evidence of soil chemical properties and soil microbial, nematode, microarthropod and plant communities. We sampled soil and vegetation in managed forests, comparing those dominated by black locust with native deciduous oak stands. We found qualitative and quantitative changes in all components analysed, such as the well-known soil nitrification and acidification in stands invaded by black locust. Bacterial richness was the only component favoured by the invasion. On the contrary, abundance and richness of microarthropods, richness of nematodes, and richness and diversity of plant communities decreased significantly in invaded stands. The invasion process caused a compositional shift in all studied biotic communities and in relationships between the different ecosystem components. We obtained clear insights into the effects of invasion of managed native forests by black locust. Our data confirms that the alien species transforms several ecosystem components, modifying the plant-soil community and affecting biodiversity at different levels. Correct management of this aggressive invader in temperate forests is urgently required. Copyright © 2017 Elsevier B.V. All rights reserved.
Characterizing microbial communities and processes in a modern stromatolite (Shark Bay) using lipid biomarkers and two-dimensional distributions of porewater solutes

DEFF Research Database (Denmark)

Pagès, Anais; Grice, Kliti; Vacher, Michael

2014-01-01

Summary: Modern microbial mats are highly complex and dynamic ecosystems. Diffusive equilibration in thin films (DET) and diffusive gradients in thin films (DGT) samplers were deployed in a modern smooth microbial mat from Shark Bay in order to observe, for the first time, two-dimensional distrib......Summary: Modern microbial mats are highly complex and dynamic ecosystems. Diffusive equilibration in thin films (DET) and diffusive gradients in thin films (DGT) samplers were deployed in a modern smooth microbial mat from Shark Bay in order to observe, for the first time, two...
Detrital microbial community development and phosphorus dynamics in a stream ecosystem

Energy Technology Data Exchange (ETDEWEB)

Perkins, R.E.; Elwood, J.W.; Sayler, G.S.

1986-06-01

Detrital microbial community development and phosphorus dynamics in a lotic system were investigated in non-recirculating laboratory streams contains leaf detritus. Temporal patterns of microbial colonization, as determined by scanning electron microscopy, indicate leaf species dependency and that bacteria were the first colonizers followed by fungi. An extensive glycocalyx layer developed. Phosphorus incorporation rates of both the whole community and intracellular components were determined by time-course measurements of /sup 33/PO/sub 4/ or /sup 32/PO/sub 4/. Phosphorus turnover rates were determined by a sequential double-labeling procedure using /sup 33/PO/sub 4/ and /sup 32/PO/sub 4/, in which the microbiota were labeled with /sup 33/P until in isotopic equilibrium, then /sup 32/P was added. The turnover rate was determined by time-course measurements of the ratio /sup 32/P to /sup 33/P. Snail grazing resulted in an increase in phosphorus metabolism per unit microbial biomass; however, per unit area of leaf surface no increase was observed. Grazing also caused a two-fold reduction in microbial biomass. The results indicate that microbiota associated with decomposing leaves slowly recycle phosphorus, are slowly growing, and have a low metabolic activity. The spiraling length is shortened by microbiota on a short-term basis; however, it may increase on a long-term basis due to hydrological transport of detritus downstream.
Methodological approaches for studying the microbial ecology of drinking water distribution systems

OpenAIRE

Douterelo, Isabel; Boxall, Joby B.; Deines, Peter; Sekar, Raju; Fish, Katherine E.; Biggs, Catherine A.

2014-01-01

The study of the microbial ecology of drinking water distribution systems (DWDS) has traditionally been based on culturing organisms from bulk water samples. The development and application of molecular methods has supplied new tools for examining the microbial diversity and activity of environmental samples, yielding new insights into the microbial community and its diversity within these engineered ecosystems. In this review, the currently available methods and emerging approaches for chara...
From Genes to Ecosystems in Microbiology: Modeling Approaches and the Importance of Individuality

Directory of Open Access Journals (Sweden)

Jan-Ulrich Kreft

2017-11-01

Full Text Available Models are important tools in microbial ecology. They can be used to advance understanding by helping to interpret observations and test hypotheses, and to predict the effects of ecosystem management actions or a different climate. Over the past decades, biological knowledge and ecosystem observations have advanced to the molecular and in particular gene level. However, microbial ecology models have changed less and a current challenge is to make them utilize the knowledge and observations at the genetic level. We review published models that explicitly consider genes and make predictions at the population or ecosystem level. The models can be grouped into three general approaches, i.e., metabolic flux, gene-centric and agent-based. We describe and contrast these approaches by applying them to a hypothetical ecosystem and discuss their strengths and weaknesses. An important distinguishing feature is how variation between individual cells (individuality is handled. In microbial ecosystems, individual heterogeneity is generated by a number of mechanisms including stochastic interactions of molecules (e.g., gene expression, stochastic and deterministic cell division asymmetry, small-scale environmental heterogeneity, and differential transport in a heterogeneous environment. This heterogeneity can then be amplified and transferred to other cell properties by several mechanisms, including nutrient uptake, metabolism and growth, cell cycle asynchronicity and the effects of age and damage. For example, stochastic gene expression may lead to heterogeneity in nutrient uptake enzyme levels, which in turn results in heterogeneity in intracellular nutrient levels. Individuality can have important ecological consequences, including division of labor, bet hedging, aging and sub-optimality. Understanding the importance of individuality and the mechanism(s underlying it for the specific microbial system and question investigated is essential for selecting the
Resistance and Resilience of Soil Microbial Communities Exposed to Petroleum-Derived Compounds

DEFF Research Database (Denmark)

Modrzynski, Jakub Jan

Functioning of soil microbial communities is generally considered resilient to disturbance, including chemical stress. Activities of soil microbial communities are often sustained in polluted environments due to exceptional plasticity of microbial communities and functional redundancy. Pollution......-induced community tolerance (PICT) often develops following chemical stress. Nonetheless, environmental pollution may severely disturb functioning of soil microbial communities, thereby threatening provision of important ecosystem services provided by microorganisms. Pollution with petroleum and petroleum......-derived compounds (PDCs) is a significant environmental problem on a global scale. Research addressing interactions between microorganisms and PDC pollution is dominated by studies of biodegradation, with less emphasis on microbial ecotoxicology. Soil microbial communities are generally considered highly resilient...
Microbial response of an acid forest soil to experimental soil warming

Science.gov (United States)

S.S. Arnold; I.J. Fernandez; L.E. Rustad; L.M. Zibilske

1999-01-01

Effects of increased soil temperature on soil microbial biomass and dehydrogenase activity were examined on organic (O) horizon material in a low-elevation spruce-fir ecosystem. Soil temperature was maintained at 5 Â°C above ambient during the growing season in the experimental plots, and soil temperature, moisture, microbial biomass, and dehydrogenase activity were...
Forest soil microbial communities: Using metagenomic approaches to survey permanent plots

Science.gov (United States)

Amy L. Ross-Davis; Jane E. Stewart; John W. Hanna; John D. Shaw; Andrew T. Hudak; Theresa B. Jain; Robert J. Denner; Russell T. Graham; Deborah S. Page-Dumroese; Joanne M. Tirocke; Mee-Sook Kim; Ned B. Klopfenstein

2014-01-01

Forest soil ecosystems include some of the most complex microbial communities on Earth (Fierer et al. 2012). These assemblages of archaea, bacteria, fungi, and protists play essential roles in biogeochemical cycles (van der Heijden et al. 2008) and account for considerable terrestrial biomass (Nielsen et al. 2011). Yet, determining the microbial composition of forest...
The contribution of microbial biotechnology to mitigating coral reef degradation.

Science.gov (United States)

Damjanovic, Katarina; Blackall, Linda L; Webster, Nicole S; van Oppen, Madeleine J H

2017-09-01

The decline of coral reefs due to anthropogenic disturbances is having devastating impacts on biodiversity and ecosystem services. Here we highlight the potential and challenges of microbial manipulation strategies to enhance coral tolerance to stress and contribute to coral reef restoration and protection. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.
Interactions between Cryptosporidium parvum and the Intestinal Ecosystem

KAUST Repository

Douvropoulou, Olga

2017-04-01

Cryptosporidium parvum is an apicomplexan protozoan parasite commonly causing diarrhea, particularly in infants in developing countries. The research challenges faced in the development of therapies against Cryptosporidium slow down the process of drug discovery. However, advancement of knowledge towards the interactions of the intestinal ecosystem and the parasite could provide alternative approaches to tackle the disease. Under this perspective, the primary focus of this work was to study interactions between Cryptosporidium parvum and the intestinal ecosystem in a mouse model. Mice were treated with antibiotics with different activity spectra and the resulted perturbation of the native gut microbiota was identified by microbiome studies. In particular, 16S amplicon sequencing and Whole Genome Sequencing (WGS) were used to determine the bacterial composition and the genetic repertoire of the fecal microbial communities in the mouse gut. Following alteration of the microbial communities of mice by application of antibiotic treatment, Cryptosporidium parasites were propagated in mice with perturbed microbiota and the severity of the infection was quantified. This approach enabled the prediction of the functional capacity of the microbial communities in the mouse gut and led to the identification of bacterial taxa that positively or negatively correlate in abundance with Cryptosporidium proliferation.
The Green Roof Microbiome: Improving Plant Survival for Ecosystem Service Delivery

Directory of Open Access Journals (Sweden)

Roberta Fulthorpe

2018-02-01

Full Text Available Plants are key contributors to ecosystem services delivered by green roofs in cities including stormwater capture, temperature regulation, and wildlife habitat. As a result, current research has primarily focused on their growth in relationship to extensive green roof (e.g., substrates <15 cm depth ecosystem services. Green roofs are exposed to a variety of harsh abiotic factors such as intense solar radiation, wind, and isolation from ground-level habitats, making survival exceedingly difficult. Plants in natural habitats benefit from a variety of interactions with fungi and bacteria. These plant-microbial interactions improve mechanisms of survival and productivity; however, many green roof substrates are sterilized prior to installation and lack microbial communities with unstudied consequences for green roof plant health and subsequent survival and performance. In this paper, we present six hypotheses on the positive role of microbes in green roof applications. In natural and experimental systems, microbial interactions have been linked to plant (1 drought tolerance, (2 pathogen protection, (3 nutrient availability, (4 salt tolerance, (5 phytohormone production, and (6 substrate stabilization, all of which are desirable properties of green roof ecosystems. As few studies exist that directly examine these relationships on green roofs, we explore the existing ecological literature on these topics to unravel the mechanisms that could support more complex green roof ecosystem and lead to new insight into the design, performance, and broader applications in green infrastructure.
Microbial interactions involving sulfur bacteria : implications for the ecology and evolution of bacterial communities

NARCIS (Netherlands)

Overmann, J; van Gemerden, H

2000-01-01

A major goal of microbial ecology is the identification and characterization of those microorganisms which govern transformations in natural ecosystems. This review summarizes our present knowledge of microbial interactions in the natural sulfur cycle. Central to the discussion is the recent
The potential for retreating alpine glaciers to alter alpine ecosystems in the Colorado Front Range

Science.gov (United States)

Hall, E.; Baron, J.

2013-12-01

Glaciers are retreating at an unprecedented rate. In mid-latitude alpine ecosystems the presence of glaciers and rock glaciers govern rates and ecology of alpine and sub-alpine ecosystems. Changes in the thermal environment due to the loss of isothermal habitat and inputs from glacier melt chemistry are altering alpine ecosystems in unpredictable ways. In particular, glacier may be a source of nitrogen that is altering alpine ecosystem dynamics. Loch Vale Watershed (LVWS) located within Rocky Mountain National Park. LVWS contains a surface glacier (Andrew's glacier) and a rock glacier (Taylor's glacier) at the headwater of each of the two drainages within the watershed. We collected precipitation from a National Atmospheric Deposition Site and surface water from multiple alpine lakes and streams during a particularly high and low snow year in the Colorado Front Range. We also sampled stream and lake sediments at each site to analyze the associated microbial community. Concentrations of nitrate and ammonium, relative abundance of amoA (the gene responsible for a key step in the microbial nitrification pathway), and the dual isotope signal to nitrate all point to snow melt as a key deliverer of nitrogen to ecosystems along the Colorado Front Range. However, late summer surface water chemistry is isotopically similar to the chemistry of glacial ice. This suggests that retreating glacier may be an additional source of N to alpine ecosystems and have the potential to alter microbial community composition, biogeochemical rate processes, and ecosystem function. These dynamics are most likely not unique to the Colorado Front Range and should be globally distributed as glaciers continue to retreat in high altitude ecosystems around the world.
A global analysis of soil microbial biomass carbon, nitrogen and phosphorus in terrestrial ecosystems

Energy Technology Data Exchange (ETDEWEB)

Xu, Xiaofeng [ORNL; Thornton, Peter E [ORNL; Post, Wilfred M [ORNL

2013-01-01

Soil microbes play a pivotal role in regulating land-atmosphere interactions; the soil microbial biomass carbon (C), nitrogen (N), phosphorus (P) and C:N:P stoichiometry are important regulators for soil biogeochemical processes; however, the current knowledge on magnitude, stoichiometry, storage, and spatial distribution of global soil microbial biomass C, N, and P is limited. In this study, 3087 pairs of data points were retrieved from 281 published papers and further used to summarize the magnitudes and stoichiometries of C, N, and P in soils and soil microbial biomass at global- and biome-levels. Finally, global stock and spatial distribution of microbial biomass C and N in 0-30 cm and 0-100 cm soil profiles were estimated. The results show that C, N, and P in soils and soil microbial biomass vary substantially across biomes; the fractions of soil nutrient C, N, and P in soil microbial biomass are 1.6% in a 95% confidence interval of (1.5%-1.6%), 2.9% in a 95% confidence interval of (2.8%-3.0%), and 4.4% in a 95% confidence interval of (3.9%-5.0%), respectively. The best estimates of C:N:P stoichiometries for soil nutrients and soil microbial biomass are 153:11:1, and 47:6:1, respectively, at global scale, and they vary in a wide range among biomes. Vertical distribution of soil microbial biomass follows the distribution of roots up to 1 m depth. The global stock of soil microbial biomass C and N were estimated to be 15.2 Pg C and 2.3 Pg N in the 0-30 cm soil profiles, and 21.2 Pg C and 3.2 Pg N in the 0-100 cm soil profiles. We did not estimate P in soil microbial biomass due to data shortage and insignificant correlation with soil total P and climate variables. The spatial patterns of soil microbial biomass C and N were consistent with those of soil organic C and total N, i.e. high density in northern high latitude, and low density in low latitudes and southern hemisphere.
Short-term Effect of Nitrogen Addition on Microbial and Root Respiration in an Alpine Spruce Ecosystem

Directory of Open Access Journals (Sweden)

Jian Wang1

2017-03-01

Full Text Available Soil respiration plays an important role in the carbon (C flux of the global C cycle and is greatly affected by nitrogen (N additions in the form of deposition or fertilization. The aim of this study was to investigate the response of total soil respiration (Rs, microbial respiration (Rm, and root respiration (Rr to short-term N addition and the potential mechanisms of short-term N deposition influencing soil respiration in an alpine spruce ecosystem. Four N treatment levels (0, 50, 100, 150 kg N ha-1 year-1 were applied monthly in a Picea balfouriana (commonly known as "alpine spruce" plantation beginning in November 2013 and Rs, Rm, and Rr were measured from May to November 2014. The results show that simulated N depositions stimulate Rs, Rm, and Rr and the beneficial effects decreased along N gradients from hourly to seasonal scales. The seasonal temperature coefficients (Q10 of Rs, Rm, and Rr ranged from 2.50 to 3.8, 2.99 to 4.63, and 1.86 to 2.96, while the diurnal Q10 ranged from 1.71 to 2.04, 1.89 to 2.32, 1.42 to 1.75, and there was a similar trend with soil respiration along N gradients. In addition, Rr showed significant positive correlation with fine root biomass, and Rm was likely driven by soil enzyme related to the microbial C cycle in the growing season. Our results indicate that short-term N addition stimulated fine root biomass and soil enzymatic activity to bring about a potential increase in soil respiration rates under low-N addition, while the opposite occurred under high-N addition.
Synthetic Biology of Polyhydroxyalkanoates (PHA).

Science.gov (United States)

Meng, De-Chuan; Chen, Guo-Qiang

Microbial polyhydroxyalkanoates (PHA) are a family of biodegradable and biocompatible polyesters which have been extensively studied using synthetic biology and metabolic engineering methods for improving production and for widening its diversity. Synthetic biology has allowed PHA to become composition controllable random copolymers, homopolymers, and block copolymers. Recent developments showed that it is possible to establish a microbial platform for producing not only random copolymers with controllable monomers and their ratios but also structurally defined homopolymers and block copolymers. This was achieved by engineering the genome of Pseudomonas putida or Pseudomonas entomophiles to weaken the β-oxidation and in situ fatty acid synthesis pathways, so that a fatty acid fed to the bacteria maintains its original chain length and structures when incorporated into the PHA chains. The engineered bacterium allows functional groups in a fatty acid to be introduced into PHA, forming functional PHA, which, upon grafting, generates endless PHA variety. Recombinant Escherichia coli also succeeded in producing efficiently poly(3-hydroxypropionate) or P3HP, the strongest member of PHA. Synthesis pathways of P3HP and its copolymer P3HB3HP of 3-hydroxybutyrate and 3-hydroxypropionate were assembled respectively to allow their synthesis from glucose. CRISPRi was also successfully used to manipulate simultaneously multiple genes and control metabolic flux in E. coli to obtain a series of copolymer P3HB4HB of 3-hydroxybutyrate (3HB) and 4-hydroxybutyrate (4HB). The bacterial shapes were successfully engineered for enhanced PHA accumulation.
Predicting Disturbance-driven Impacts on Ecosystem Services in Coastal Wetlands

Science.gov (United States)

Rajan, S.; Crawford, P.; Kleinhuizen, A.; Mortazavi, B.; Sobecky, P.

2017-12-01

Natural and human-induced disturbances pose significant threats to the health and long-term productivity of Alabama coastal wetlands. As wetlands are a vital state resource, decisions on management, restoration, and remediation require actionable data if socio-economic demands are to be balanced with efforts to sustain these habitats. In 2010, the BP oil spill was a large and severe disturbance that threatened coastal Gulf ecosystem services. The largest marine oil spill to date served to highlight fundamental gaps in our knowledge of oil-induced disturbances and the resiliency and restoration of coastal Alabama wetland functions. To address these gaps, a year-long mesocosm study was conducted to investigate oil-induced effects on (i) plant-microbial interactions, (ii) microbial and plant biodiversity, and, (iii) the contributions of microbial genetic biodiversity to ecosystems services. In this study, Avicennia germinans (black mangrove), a C3 plant that grows from the tropics to warm temperate latitudes, were grown with or without mono- and polyculture mixtures of Spartina alterniflora, a C4 plant. At an interval of 3-months, oil was introduced as a pulse disturbance to achieve a concentration of 4000 ppm. Molecular-based analyses of microbial community biodiversity, genetic diversity, and functional metabolic genes were compared to controls (i.e., no oil disturbance). To assess the oil-induced effects on the nitrogen (N) cycle, measurements of denitrification and N fixation processes were conducted. Our results showed that community diversity and phylogenetic diversity significantly changed and that the oil disturbance contributed to the creation of niches for distinct microbial types. The abundance of N-fixing microbial types increased as the abundance of denitrifying microbial types decreased as a result of the oil disturbance. As denitrification is an ecosystem service that directly contributes to removing nitrate (NO3-) loading to coastal zones, impairment
Microbial-Catalyzed Biotransformation of Multifunctional Triterpenoids Derived from Phytonutrients

Science.gov (United States)

Shah, Syed Adnan Ali; Tan, Huey Ling; Sultan, Sadia; Mohd Faridz, Muhammad Afifi Bin; Mohd Shah, Mohamad Azlan Bin; Nurfazilah, Sharifah; Hussain, Munawar

2014-01-01

Microbial-catalyzed biotransformations have considerable potential for the generation of an enormous variety of structurally diversified organic compounds, especially natural products with complex structures like triterpenoids. They offer efficient and economical ways to produce semi-synthetic analogues and novel lead molecules. Microorganisms such as bacteria and fungi could catalyze chemo-, regio- and stereospecific hydroxylations of diverse triterpenoid substrates that are extremely difficult to produce by chemical routes. During recent years, considerable research has been performed on the microbial transformation of bioactive triterpenoids, in order to obtain biologically active molecules with diverse structures features. This article reviews the microbial modifications of tetranortriterpenoids, tetracyclic triterpenoids and pentacyclic triterpenoids. PMID:25003642

Microbial eukaryotic diversity and distribution in a river plume and cyclonic eddy-influenced ecosystem in the South China Sea.

Science.gov (United States)

Wu, Wenxue; Wang, Lei; Liao, Yu; Huang, Bangqin

2015-10-01

To evaluate microbial eukaryotic diversity and distribution in mesoscale processes, we investigated 18S rDNA diversity in a river plume and cyclonic eddy-influenced ecosystem in the southwestern South China Sea (SCS). Restriction fragment length polymorphism analysis was carried out using multiple primer sets. Relative to a wide range of previous similar studies, we observed a significantly higher proportion of sequences of pigmented taxa. Among the photosynthetic groups, Haptophyta accounted for 27.7% of the sequenced clones, which belonged primarily to Prymnesiophyceae. Unexpectedly, five operational taxonomic units of Cryptophyta were closely related to freshwater species. The Chlorophyta mostly fell within the Prasinophyceae, which was comprised of six clades, including Clade III, which is detected in the SCS for the first time in this study. Among the photosynthetic stramenopiles, Chrysophyceae was the most diverse taxon, which included seven clades. The majority of 18S rDNA sequences affiliated with the Dictyochophyceae, Eustigmatophyceae, and Pelagophyceae were closely related to those of pure cultures. The results of redundancy analysis and the permutation Mantel test based on unweighted UniFrac distances, conducted for spatial analyses of the Haptophyta subclades suggested that the Mekong River plume and cyclonic eddy play important roles in regulating microbial eukaryotic diversity and distribution in the southwestern SCS. © 2015 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.
Abundance and genetic diversity of microbial polygalacturonase and pectate lyase in the sheep rumen ecosystem.

Directory of Open Access Journals (Sweden)

Peng Yuan

Full Text Available Efficient degradation of pectin in the rumen is necessary for plant-based feed utilization. The objective of this study was to characterize the diversity, abundance, and functions of pectinases from microorganisms in the sheep rumen.A total of 103 unique fragments of polygalacturonase (PF00295 and pectate lyase (PF00544 and PF09492 genes were retrieved from microbial DNA in the rumen of a Small Tail Han sheep, and 66% of the sequences of these fragments had low identities (<65% with known sequences. Phylogenetic tree building separated the PF00295, PF00544, and PF09492 sequences into five, three, and three clades, respectively. Cellulolytic and noncellulolytic Butyrivibrio, Prevotella, and Fibrobacter species were the major sources of the pectinases. The two most abundant pectate lyase genes were cloned, and their protein products, expressed in Escherichia coli, were characterized. Both enzymes probably act extracellularly as their nucleotide sequences contained signal sequences, and they had optimal activities at the ruminal physiological temperature and complementary pH-dependent activity profiles.This study reveals the specificity, diversity, and abundance of pectinases in the rumen ecosystem and provides two additional ruminal pectinases for potential industrial use under physiological conditions.
Invasion in microbial communities: Role of community composition and assembly processes

DEFF Research Database (Denmark)

Kinnunen, Marta

of microbial community assembly. Biotic factors include interactions between different microbial groups as well as the community response to alien species – invaders. Microbial invasions can have significant effects on the composition and functioning of resident communities. There is, however, lack......Microbes contribute to all biogeochemical cycles on earth and are responsible for key biological processes that support the survival of plants and animals. There is increased interest in controlling and managing microbial communities in different ecosystems in order to make targeted microbiological...... processes more effective. In order to manage microbial communities, it is essential to understand the factors that shape and influence microbial community composition. In addition to abiotic factors, such as environmental conditions and resource availability, biotic factors also shape the dynamics...
METABOLIC MODELLING IN THE DEVELOPMENT OF CELL FACTORIES BY SYNTHETIC BIOLOGY

Directory of Open Access Journals (Sweden)

Paula Jouhten

2012-10-01

Full Text Available Cell factories are commonly microbial organisms utilized for bioconversion of renewable resources to bulk or high value chemicals. Introduction of novel production pathways in chassis strains is the core of the development of cell factories by synthetic biology. Synthetic biology aims to create novel biological functions and systems not found in nature by combining biology with engineering. The workflow of the development of novel cell factories with synthetic biology is ideally linear which will be attainable with the quantitative engineering approach, high-quality predictive models, and libraries of well-characterized parts. Different types of metabolic models, mathematical representations of metabolism and its components, enzymes and metabolites, are useful in particular phases of the synthetic biology workflow. In this minireview, the role of metabolic modelling in synthetic biology will be discussed with a review of current status of compatible methods and models for the in silico design and quantitative evaluation of a cell factory.
Cellulolytic potential under environmental changes in microbial communities from grassland litter

Directory of Open Access Journals (Sweden)

Renaud eBerlemont

2014-11-01

Full Text Available In many ecosystems, global changes are likely to profoundly affect microorganisms. In Southern California, changes in precipitation and nitrogen deposition may influence the composition and functional potential of microbial communities and their resulting ability to degrade plant material. To test whether environmental changes impact the distribution of functional groups involved in leaf litter degradation, we determined how the genomic diversity of microbial communities in a semi-arid grassland ecosystem changed under reduced precipitation or increased N deposition. We monitored communities seasonally over a period of two years to place environmental change responses into the context of natural variation. Fungal and bacterial communities displayed strong seasonal patterns, Fungi being mostly detected during the dry season whereas Bacteria were common during wet periods. Most putative cellulose degraders were associated with 33 bacterial genera and constituted ~18.2% of the microbial community. Precipitation reduction reduced bacterial abundance and cellulolytic potential whereas nitrogen addition did not affect the cellulolytic potential of the microbial community. Finally, we detected a strong correlation between the frequencies of genera putative cellulose degraders and cellulase genes. Thus, microbial taxonomic composition was predictive of cellulolytic potential. This work provides a framework for how environmental changes affect microorganisms responsible for plant litter deconstruction.
The information science of microbial ecology.

Science.gov (United States)

Hahn, Aria S; Konwar, Kishori M; Louca, Stilianos; Hanson, Niels W; Hallam, Steven J

2016-06-01

A revolution is unfolding in microbial ecology where petabytes of 'multi-omics' data are produced using next generation sequencing and mass spectrometry platforms. This cornucopia of biological information has enormous potential to reveal the hidden metabolic powers of microbial communities in natural and engineered ecosystems. However, to realize this potential, the development of new technologies and interpretative frameworks grounded in ecological design principles are needed to overcome computational and analytical bottlenecks. Here we explore the relationship between microbial ecology and information science in the era of cloud-based computation. We consider microorganisms as individual information processing units implementing a distributed metabolic algorithm and describe developments in ecoinformatics and ubiquitous computing with the potential to eliminate bottlenecks and empower knowledge creation and translation. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.
Groundwater Ecosystems Vary with Land Use across a Mixed Agricultural Landscape.

Science.gov (United States)

Korbel, K L; Hancock, P J; Serov, P; Lim, R P; Hose, G C

2013-01-01

Changes in surface land use may threaten groundwater quality and ecosystem integrity, particularly in shallow aquifers where links between groundwater and surface activities are most intimate. In this study we examine the response of groundwater ecosystem to agricultural land uses in the shallow alluvial aquifer of the Gwydir River valley, New South Wales, Australia. We compared groundwater quality and microbial and stygofauna assemblages among sites under irrigated cropping, non-irrigated cropping and grazing land uses. Stygofauna abundance and richness was greatest at irrigated sites, with the composition of the assemblage suggestive of disturbance. Microbial assemblages and water quality also varied with land use. Our study demonstrates significant differences in the composition of groundwater ecosystems in areas with different surface land use, and highlights the utility of groundwater biota for biomonitoring, particularly in agricultural landscapes. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.
Inclusion of caraway in the ryegrass-red clover mixture modifies soil microbial community composition

DEFF Research Database (Denmark)

Cong, Wenfeng; Jing, Jingying; Søegaard, Karen

-containing grass-clover mixtures may potentially affect soil microbial community structure, biomass and associated ecosystem functions, but it is yet to be elucidated. We hypothesized that inclusion of plantain in the grass-clover mixture would enhance soil microbial biomas and functions through its high biomass...
Microbial activity and community structure in two drained fen soils in the Ljubljana Marsh

NARCIS (Netherlands)

Kraigher, Barbara; Stres, Blaz; Hacin, Janez; Ausec, Luka; Mahne, Ivan; van Elsas, Jan D.; Mandic-Mulec, Ines

Fen peatlands are specific wetland ecosystems containing high soil organic carbon (SOC). There is a general lack of knowledge about the microbial communities that abound in these systems. We examined the microbial activity and community structure in two fen soils differing in SOC content sampled
Switchgrass ecotypes alter microbial contribution to deep-soil C

Science.gov (United States)

Roosendaal, Damaris; Stewart, Catherine E.; Denef, Karolien; Follett, Ronald F.; Pruessner, Elizabeth; Comas, Louise H.; Varvel, Gary E.; Saathoff, Aaron; Palmer, Nathan; Sarath, Gautam; Jin, Virginia L.; Schmer, Marty; Soundararajan, Madhavan

2016-05-01

Switchgrass (Panicum virgatum L.) is a C4, perennial grass that is being developed as a bioenergy crop for the United States. While aboveground biomass production is well documented for switchgrass ecotypes (lowland, upland), little is known about the impact of plant belowground productivity on microbial communities down deep in the soil profiles. Microbial dynamics in deeper soils are likely to exert considerable control on ecosystem services, including C and nutrient cycles, due to their involvement in such processes as soil formation and ecosystem biogeochemistry. Differences in root biomass and rooting characteristics of switchgrass ecotypes could lead to distinct differences in belowground microbial biomass and microbial community composition. We quantified root abundance and root architecture and the associated microbial abundance, composition, and rhizodeposit C uptake for two switchgrass ecotypes using stable-isotope probing of microbial phospholipid fatty acids (PLFAs) after 13CO2 pulse-chase labeling. Kanlow, a lowland ecotype with thicker roots, had greater plant biomass above- and belowground (g m-2), greater root mass density (mg cm-3), and lower specific root length (m g-1) compared to Summer, an upland ecotype with finer root architecture. The relative abundance of bacterial biomarkers dominated microbial PLFA profiles for soils under both Kanlow and Summer (55.4 and 53.5 %, respectively; P = 0.0367), with differences attributable to a greater relative abundance of Gram-negative bacteria in soils under Kanlow (18.1 %) compared to soils under Summer (16.3 %; P = 0.0455). The two ecotypes also had distinctly different microbial communities process rhizodeposit C: greater relative atom % 13C excess in Gram-negative bacteria (44.1 ± 2.3 %) under the thicker roots of Kanlow and greater relative atom % 13C excess in saprotrophic fungi under the thinner roots of Summer (48.5 ± 2.2 %). For bioenergy production systems, variation between switchgrass
Soil microbial biomass, activity and community composition along altitudinal gradients in the High Arctic (Billefjorden, Svalbard)

Science.gov (United States)

Kotas, Petr; Šantrůčková, Hana; Elster, Josef; Kaštovská, Eva

2018-03-01

The unique and fragile High Arctic ecosystems are vulnerable to global climate warming. The elucidation of factors driving microbial distribution and activity in arctic soils is essential for a comprehensive understanding of ecosystem functioning and its response to environmental change. The goals of this study were to investigate microbial biomass and activity, microbial community structure (MCS), and their environmental controls in soils along three elevational transects in the coastal mountains of Billefjorden, central Svalbard. Soils from four different altitudes (25, 275, 525 and 765 m above sea level) were analyzed for a suite of characteristics including temperature regimes, organic matter content, base cation availability, moisture, pH, potential respiration, and microbial biomass and community structure using phospholipid fatty acids (PLFAs). We observed significant spatial heterogeneity of edaphic properties among transects, resulting in transect-specific effects of altitude on most soil parameters. We did not observe any clear elevation pattern in microbial biomass, and microbial activity revealed contrasting elevational patterns between transects. We found relatively large horizontal variability in MCS (i.e., between sites of corresponding elevation in different transects), mainly due to differences in the composition of bacterial PLFAs, but also a systematic altitudinal shift in MCS related to different habitat preferences of fungi and bacteria, which resulted in high fungi-to-bacteria ratios at the most elevated sites. The biological soil crusts on these most elevated, unvegetated sites can host microbial assemblages of a size and activity comparable to those of the arctic tundra ecosystem. The key environmental factors determining horizontal and vertical changes in soil microbial properties were soil pH, organic carbon content, soil moisture and Mg2+ availability.
Soil microbial biomass, activity and community composition along altitudinal gradients in the High Arctic (Billefjorden, Svalbard

Directory of Open Access Journals (Sweden)

P. Kotas

2018-03-01

Full Text Available The unique and fragile High Arctic ecosystems are vulnerable to global climate warming. The elucidation of factors driving microbial distribution and activity in arctic soils is essential for a comprehensive understanding of ecosystem functioning and its response to environmental change. The goals of this study were to investigate microbial biomass and activity, microbial community structure (MCS, and their environmental controls in soils along three elevational transects in the coastal mountains of Billefjorden, central Svalbard. Soils from four different altitudes (25, 275, 525 and 765 m above sea level were analyzed for a suite of characteristics including temperature regimes, organic matter content, base cation availability, moisture, pH, potential respiration, and microbial biomass and community structure using phospholipid fatty acids (PLFAs. We observed significant spatial heterogeneity of edaphic properties among transects, resulting in transect-specific effects of altitude on most soil parameters. We did not observe any clear elevation pattern in microbial biomass, and microbial activity revealed contrasting elevational patterns between transects. We found relatively large horizontal variability in MCS (i.e., between sites of corresponding elevation in different transects, mainly due to differences in the composition of bacterial PLFAs, but also a systematic altitudinal shift in MCS related to different habitat preferences of fungi and bacteria, which resulted in high fungi-to-bacteria ratios at the most elevated sites. The biological soil crusts on these most elevated, unvegetated sites can host microbial assemblages of a size and activity comparable to those of the arctic tundra ecosystem. The key environmental factors determining horizontal and vertical changes in soil microbial properties were soil pH, organic carbon content, soil moisture and Mg2+ availability.
An integrated study to analyze soil microbial community structure and metabolic potential in two forest types.

Science.gov (United States)

Zhang, Yuguang; Cong, Jing; Lu, Hui; Yang, Caiyun; Yang, Yunfeng; Zhou, Jizhong; Li, Diqiang

2014-01-01

Soil microbial metabolic potential and ecosystem function have received little attention owing to difficulties in methodology. In this study, we selected natural mature forest and natural secondary forest and analyzed the soil microbial community and metabolic potential combing the high-throughput sequencing and GeoChip technologies. Phylogenetic analysis based on 16S rRNA sequencing showed that one known archaeal phylum and 15 known bacterial phyla as well as unclassified phylotypes were presented in these forest soils, and Acidobacteria, Protecobacteria, and Actinobacteria were three of most abundant phyla. The detected microbial functional gene groups were related to different biogeochemical processes, including carbon degradation, carbon fixation, methane metabolism, nitrogen cycling, phosphorus utilization, sulfur cycling, etc. The Shannon index for detected functional gene probes was significantly higher (PThe regression analysis showed that a strong positive (Pthe soil microbial functional gene diversity and phylogenetic diversity. Mantel test showed that soil oxidizable organic carbon, soil total nitrogen and cellulose, glucanase, and amylase activities were significantly linked (Pthe relative abundance of corresponded functional gene groups. Variance partitioning analysis showed that a total of 81.58% of the variation in community structure was explained by soil chemical factors, soil temperature, and plant diversity. Therefore, the positive link of soil microbial structure and composition to functional activity related to ecosystem functioning was existed, and the natural secondary forest soil may occur the high microbial metabolic potential. Although the results can't directly reflect the actual microbial populations and functional activities, this study provides insight into the potential activity of the microbial community and associated feedback responses of the terrestrial ecosystem to environmental changes.
Ecosystem development in roadside grasslands: biotic control, plant–soil interactions and dispersal limitations

Science.gov (United States)

García-Palacios, Pablo; Bowker, Matthew A.; Maestre, Fernando T.; Soliveres, Santiago; Valladares, Fernando; Papadopoulos, Jorge; Escudero, Adrián

2015-01-01

Roadside grasslands undergoing secondary succession are abundant, and represent ecologically meaningful examples of novel, human-created ecosystems. Interactions between plant and soil communities (hereafter plant–soil interactions) are of major importance in understanding the role of biotic control in ecosystem functioning, but little is known about these links in the context of ecosystem restoration and succession. The assessment of the key biotic communities and interactions driving ecosystem development will help practitioners to better allocate the limited resources devoted to roadside grassland restoration. We surveyed roadside grasslands from three successional stages (0–2, 7–9 and > 20 years) in two Mediterranean regions of Spain. Structural equation modeling was used to evaluate how interactions between plants, biological soil crusts [BSCs], and soil microbial functional diversity [soil microorganisms] affect indicators of ecosystem development and restoration: plant similarity to the reference ecosystem, erosion control and soil C storage and N accumulation. Changes in plant community composition along the successional gradient exerted the strongest influence on these indicators. High BSC cover was associated with high soil stability, and high soil microbial functional diversity from late-successional stages was associated with high soil fertility. Contrary to our expectations, the indirect effects of plants, mediated by either BSCs or soil microorganisms, were very weak in both regions, suggesting a minor role for plant–soil interactions upon ecosystem development indicators over long periods. Our results suggest that natural vegetation dynamics effectively improved ecosystem development within a time frame of 20 years in the grasslands evaluated. They also indicate that this time could be shortened if management actions focus on: 1) maintain well-conserved natural areas close to roadsides to enhance plant compositional changes towards late
Ecosystem development in roadside grasslands: Biotic control, plant-soil interactions, and dispersal limitations

Science.gov (United States)

Garcia-Palacios, P.; Bowker, M.A.; Maestre, F.T.; Soliveres, S.; Valladares, F.; Papadopoulos, J.; Escudero, A.

2011-01-01

Roadside grasslands undergoing secondary succession are abundant, and represent ecologically meaningful examples of novel, human-created ecosystems. Interactions between plant and soil communities (hereafter plant-soil interactions) are of major importance in understanding the role of biotic control in ecosystem functioning, but little is known about these links in the context of ecosystem restoration and succession. The assessment of the key biotic communities and interactions driving ecosystem development will help practitioners to better allocate the limited resources devoted to roadside grassland restoration. We surveyed roadside grasslands from three successional stages (0-2, 7-9, and > 20 years) in two Mediterranean regions of Spain. Structural equation modeling was used to evaluate how interactions between plants, biological soil crusts (BSCs), and soil microbial functional diversity (soil microorganisms) affect indicators of ecosystem development and restoration: plant similarity to the reference ecosystem, erosion control, and soil C storage and N accumulation. Changes in plant community composition along the successional gradient exerted the strongest influence on these indicators. High BSC cover was associated with high soil stability, and high soil microbial functional diversity from late-successional stages was associated with high soil fertility. Contrary to our expectations, the indirect effects of plants, mediated by either BSCs or soil microorganisms, were very weak in both regions, suggesting a minor role for plant-soil interactions upon ecosystem development indicators over long periods. Our results suggest that natural vegetation dynamics effectively improved ecosystem development within a time frame of 20 years in the grasslands evaluated. They also indicate that this time could be shortened if management actions focus on: (1) maintaining wellconserved natural areas close to roadsides to enhance plant compositional changes towards late
Soil microbial community composition is correlated to soil carbon processing along a boreal wetland formation gradient

Science.gov (United States)

Chapman, Eric; Cadillo-Quiroz, Hinsby; Childers, Daniel L.; Turetsky, Merritt R.; Waldrop, Mark P.

2017-01-01

Climate change is modifying global biogeochemical cycles. Microbial communities play an integral role in soil biogeochemical cycles; knowledge about microbial composition helps provide a mechanistic understanding of these ecosystem-level phenomena. Next generation sequencing approaches were used to investigate changes in microbial functional groups during ecosystem development, in response to climate change, in northern boreal wetlands. A gradient of wetlands that developed following permafrost degradation was used to characterize changes in the soil microbial communities that mediate C cycling: a bog representing an “undisturbed” system with intact permafrost, and a younger bog and an older bog that formed following the disturbance of permafrost thaw. Reference 16S rRNA databases and several diversity indices were used to assess structural differences among these communities, to assess relationships between soil microbial community composition and various environmental variables including redox potential and pH. Rates of potential CO2 and CH4 gas production were quantified to correlate sequence data with gas flux. The abundance of organic C degraders was highest in the youngest bog, suggesting higher rates of microbial processes, including potential CH4 production. In addition, alpha diversity was also highest in the youngest bog, which seemed to be related to a more neutral pH and a lower redox potential. These results could potentially be driven by increased niche differentiation in anaerobic soils. These results suggest that ecosystem structure, which was largely driven by changes in edaphic and plant community characteristics between the “undisturbed” permafrost bog and the two bogs formed following permafrost thaw, strongly influenced microbial function.
Divergent Responses of Forest Soil Microbial Communities under Elevated CO2 in Different Depths of Upper Soil Layers.

Science.gov (United States)

Yu, Hao; He, Zhili; Wang, Aijie; Xie, Jianping; Wu, Liyou; Van Nostrand, Joy D; Jin, Decai; Shao, Zhimin; Schadt, Christopher W; Zhou, Jizhong; Deng, Ye

2018-01-01

Numerous studies have shown that the continuous increase of atmosphere CO 2 concentrations may have profound effects on the forest ecosystem and its functions. However, little is known about the response of belowground soil microbial communities under elevated atmospheric CO 2 (eCO 2 ) at different soil depth profiles in forest ecosystems. Here, we examined soil microbial communities at two soil depths (0 to 5 cm and 5 to 15 cm) after a 10-year eCO 2 exposure using a high-throughput functional gene microarray (GeoChip). The results showed that eCO 2 significantly shifted the compositions, including phylogenetic and functional gene structures, of soil microbial communities at both soil depths. Key functional genes, including those involved in carbon degradation and fixation, methane metabolism, denitrification, ammonification, and nitrogen fixation, were stimulated under eCO 2 at both soil depths, although the stimulation effect of eCO 2 on these functional markers was greater at the soil depth of 0 to 5 cm than of 5 to 15 cm. Moreover, a canonical correspondence analysis suggested that NO 3 -N, total nitrogen (TN), total carbon (TC), and leaf litter were significantly correlated with the composition of the whole microbial community. This study revealed a positive feedback of eCO 2 in forest soil microbial communities, which may provide new insight for a further understanding of forest ecosystem responses to global CO 2 increases. IMPORTANCE The concentration of atmospheric carbon dioxide (CO 2 ) has continuously been increasing since the industrial revolution. Understanding the response of soil microbial communities to elevated atmospheric CO 2 (eCO 2 ) is important for predicting the contribution of the forest ecosystem to global atmospheric change. This study analyzed the effect of eCO 2 on microbial communities at two soil depths (0 to 5 cm and 5 to 15 cm) in a forest ecosystem. Our findings suggest that the compositional and functional structures of microbial
Interactions between plant and rhizosphere microbial communities in a metalliferous soil

International Nuclear Information System (INIS)

Epelde, Lur; Becerril, Jose M.; Barrutia, Oihana; Gonzalez-Oreja, Jose A.; Garbisu, Carlos

2010-01-01

In the present work, the relationships between plant consortia, consisting of 1-4 metallicolous pseudometallophytes with different metal-tolerance strategies (Thlaspi caerulescens: hyperaccumulator; Jasione montana: accumulator; Rumex acetosa: indicator; Festuca rubra: excluder), and their rhizosphere microbial communities were studied in a mine soil polluted with high levels of Cd, Pb and Zn. Physiological response and phytoremediation potential of the studied pseudometallophytes were also investigated. The studied metallicolous populations are tolerant to metal pollution and offer potential for the development of phytoextraction and phytostabilization technologies. T. caerulescens appears very tolerant to metal stress and most suitable for metal phytoextraction; the other three species enhance soil functionality. Soil microbial properties had a stronger effect on plant biomass rather than the other way around (35.2% versus 14.9%). An ecological understanding of how contaminants, ecosystem functions and biological communities interact in the long-term is needed for proper management of these fragile metalliferous ecosystems. - Rhizosphere microbial communities in highly polluted mine soils are determinant for the growth of pseudometallophytes.
Interactions between plant and rhizosphere microbial communities in a metalliferous soil

Energy Technology Data Exchange (ETDEWEB)

Epelde, Lur [NEIKER-Tecnalia, Department of Ecosystems, c/Berreaga 1, E-48160 Derio (Spain); Becerril, Jose M.; Barrutia, Oihana [Department of Plant Biology and Ecology, University of the Basque Country, UPV/EHU, P.O. Box 644, E-48080 Bilbao (Spain); Gonzalez-Oreja, Jose A. [NEIKER-Tecnalia, Department of Ecosystems, c/Berreaga 1, E-48160 Derio (Spain); Garbisu, Carlos, E-mail: cgarbisu@neiker.ne [NEIKER-Tecnalia, Department of Ecosystems, c/Berreaga 1, E-48160 Derio (Spain)

2010-05-15

In the present work, the relationships between plant consortia, consisting of 1-4 metallicolous pseudometallophytes with different metal-tolerance strategies (Thlaspi caerulescens: hyperaccumulator; Jasione montana: accumulator; Rumex acetosa: indicator; Festuca rubra: excluder), and their rhizosphere microbial communities were studied in a mine soil polluted with high levels of Cd, Pb and Zn. Physiological response and phytoremediation potential of the studied pseudometallophytes were also investigated. The studied metallicolous populations are tolerant to metal pollution and offer potential for the development of phytoextraction and phytostabilization technologies. T. caerulescens appears very tolerant to metal stress and most suitable for metal phytoextraction; the other three species enhance soil functionality. Soil microbial properties had a stronger effect on plant biomass rather than the other way around (35.2% versus 14.9%). An ecological understanding of how contaminants, ecosystem functions and biological communities interact in the long-term is needed for proper management of these fragile metalliferous ecosystems. - Rhizosphere microbial communities in highly polluted mine soils are determinant for the growth of pseudometallophytes.
Soil microbial community profiles and functional diversity in limestone cedar glades

Science.gov (United States)

Cartwright, Jennifer M.; Dzantor, E. Kudjo; Momen, Bahram

2016-01-01

Rock outcrop ecosystems, such as limestone cedar glades (LCGs), are known for their rare and endemic plant species adapted to high levels of abiotic stress. Soils in LCGs are thin (< 25 cm), soil-moisture conditions fluctuate seasonally between xeric and saturated, and summer soil temperatures commonly exceed 48 °C. The effects of these stressors on soil microbial communities (SMC) remain largely unstudied, despite the importance of SMC-plant interactions in regulating the structure and function of terrestrial ecosystems. SMC profiles and functional diversity were characterized in LCGs using community level physiological profiling (CLPP) and plate-dilution frequency assays (PDFA). Most-probable number (MPN) estimates and microbial substrate-utilization diversity (H) were positively related to soil thickness, soil organic matter (OM), soil water content, and vegetation density, and were diminished in alkaline soil relative to circumneutral soil. Soil nitrate showed no relationship to SMCs, suggesting lack of N-limitation. Canonical correlation analysis indicated strong correlations between microbial CLPP patterns and several physical and chemical properties of soil, primarily temperature at the ground surface and at 4-cm depth, and secondarily soil-water content, enabling differentiation by season. Thus, it was demonstrated that several well-described abiotic determinants of plant community structure in this ecosystem are also reflected in SMC profiles.

Synthetic biology approaches: Towards sustainable exploitation of marine bioactive molecules.

Science.gov (United States)

Seghal Kiran, G; Ramasamy, Pasiyappazham; Sekar, Sivasankari; Ramu, Meenatchi; Hassan, Saqib; Ninawe, A S; Selvin, Joseph

2018-06-01

The discovery of genes responsible for the production of bioactive metabolites via metabolic pathways combined with the advances in synthetic biology tools, has allowed the establishment of numerous microbial cell factories, for instance the yeast cell factories, for the manufacture of highly useful metabolites from renewable biomass. Genome mining and metagenomics are two platforms provide base-line data for reconstruction of genomes and metabolomes which is based in the development of synthetic/semi-synthetic genomes for marine natural products discovery. Engineered biofilms are being innovated on synthetic biology platform using genetic circuits and cell signalling systems as represillators controlling biofilm formation. Recombineering is a process of homologous recombination mediated genetic engineering, includes insertion, deletion or modification of any sequence specifically. Although this discipline considered new to the scientific domain, this field has now developed as promising endeavor on the accomplishment of sustainable exploitation of marine natural products. Copyright © 2018 Elsevier B.V. All rights reserved.
Response of soil microbial activities and microbial community structure to vanadium stress.

Science.gov (United States)

Xiao, Xi-Yuan; Wang, Ming-Wei; Zhu, Hui-Wen; Guo, Zhao-Hui; Han, Xiao-Qing; Zeng, Peng

2017-08-01

High levels of vanadium (V) have long-term, hazardous impacts on soil ecosystems and biological processes. In the present study, the effects of V on soil enzymatic activities, basal respiration (BR), microbial biomass carbon (MBC), and the microbial community structure were investigated through 12-week greenhouse incubation experiments. The results showed that V content affected soil dehydrogenase activity (DHA), BR, and MBC, while urease activity (UA) was less sensitive to V stress. The average median effective concentration (EC 50 ) thresholds of V were predicted using a log-logistic dose-response model, and they were 362mgV/kg soil for BR and 417mgV/kg soil for DHA. BR and DHA were more sensitive to V addition and could be used as biological indicators for soil V pollution. According to a polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analysis, the structural diversity of the microbial community decreased for soil V contents ranged between 254 and 1104mg/kg after 1 week of incubation. As the incubation time increased, the diversity of the soil microbial community structure increased for V contents ranged between 354 and 1104mg/kg, indicating that some new V-tolerant bacterial species might have replicated under these conditions. Copyright © 2017 Elsevier Inc. All rights reserved.
Fast microbial reduction of ferrihydrite colloids from a soil effluent

Science.gov (United States)

Fritzsche, Andreas; Bosch, Julian; Rennert, Thilo; Heister, Katja; Braunschweig, Juliane; Meckenstock, Rainer U.; Totsche, Kai U.

2012-01-01

Recent studies on the microbial reduction of synthetic iron oxide colloids showed their superior electron accepting property in comparison to bulk iron oxides. However, natural colloidal iron oxides differ in composition from their synthetic counterparts. Besides a potential effect of colloid size, microbial iron reduction may be accelerated by electron-shuttling dissolved organic matter (DOM) as well as slowed down by inhibitors such as arsenic. We examined the microbial reduction of OM- and arsenic-containing ferrihydrite colloids. Four effluent fractions were collected from a soil column experiment run under water-saturated conditions. Ferrihydrite colloids precipitated from the soil effluent and exhibited stable hydrodynamic diameters ranging from 281 (±146) nm in the effluent fraction that was collected first and 100 (±43) nm in a subsequently obtained effluent fraction. Aliquots of these oxic effluent fractions were added to anoxic low salt medium containing diluted suspensions of Geobacter sulfurreducens. Independent of the initial colloid size, the soil effluent ferrihydrite colloids were quickly and completely reduced. The rates of Fe2+ formation ranged between 1.9 and 3.3 fmol h-1 cell-1, and are in the range of or slightly exceeding previously reported rates of synthetic ferrihydrite colloids (1.3 fmol h-1 cell-1), but greatly exceeding previously known rates of macroaggregate-ferrihydrite reduction (0.07 fmol h-1 cell-1). The inhibition of microbial Fe(III) reduction by arsenic is unlikely or overridden by the concurrent enhancement induced by soil effluent DOM. These organic species may have increased the already high intrinsic reducibility of colloidal ferrihydrite owing to quinone-mediated electron shuttling. Additionally, OM, which is structurally associated with the soil effluent ferrihydrite colloids, may also contribute to the higher reactivity due to increasing solubility and specific surface area of ferrihydrite. In conclusion, ferrihydrite
Microconchids from microbialite ecosystem immediately after end-Permian mass extinction: ecologic selectivity and implications for microbialite ecosystem structure

Science.gov (United States)

Yang, H.; Chen, Z.; Wang, Y. B.; Ou, W.; Liao, W.; Mei, X.

2013-12-01

The Permian-Triassic (P-Tr) carbonate successions are often characterized by the presence of microbialite buildups worldwide. The widespread microbialites are believed as indication of microbial proliferation immediately after the P-Tr mass extinction. The death of animals representing the primary consumer trophic structure of marine ecosystem in the P-Tr crisis allows the bloom of microbes as an important primary producer in marine trophic food web structure. Thus, the PTB microbialite builders have been regarded as disaster taxa of the P-Tr ecologic crisis. Microbialite ecosystems were suitable for most organisms to inhabit. However, increasing evidence show that microbialite dwellers are also considerably abundant and diverse, including mainly foraminifers Earlandia sp. and Rectocornuspira sp., lingulid brachiopods, ostrocods, gastropods, and microconchids. In particular, ostracods are extremely abundant in this special ecosystem. Microconchid-like calcareous tubes are also considerably abundant. Here, we have sampled systematically a PTB microbialite deposit from the Dajiang section, southern Guizhou Province, southwest China and have extracted abundant isolated specimens of calcareous worm tubes. Quantitative analysis enables to investigate stratigraphic and facies preferences of microconchids in the PTB microbialites. Our preliminary result indicates that three microconchid species Microconchus sp., Helicoconchus elongates and Microconchus aberrans inhabited in microbialite ecosystem. Most microconchilds occurred in the upper part of the microbialite buildup and the grainstone-packstone microfacies. Very few microconchilds were found in the rocks bearing well-developed microbialite structures. Their stratigraphic and environmental preferences indicate proliferation of those metazoan organisms is coupled with ebb of the microbialite development. They also proliferated in some local niches in which microbial activities were not very active even if those
Changes in microbial community structure in the wake of Hurricanes Katrina and Rita.

Science.gov (United States)

Amaral-Zettler, Linda A; Rocca, Jennifer D; Lamontagne, Michael G; Dennett, Mark R; Gast, Rebecca J

2008-12-15

Hurricanes have the potential to alter the structures of coastal ecosystems and generate pathogen-laden floodwaters thatthreaten public health. To examine the impact of hurricanes on urban systems, we compared microbial community structures in samples collected after Hurricane Katrina and before and after Hurricane Rita. We extracted environmental DNA and sequenced small-subunit rRNA (SSU rRNA) gene clone libraries to survey microbial communities in floodwater, water, and sediment samples collected from Lake Charles, Lake Pontchartrain, the 17th Street and Industrial Canals in New Orleans, and raw sewage. Correspondence analysis showed that microbial communities associated with sediments formed one cluster while communities associated with lake and Industrial Canal water formed a second. Communities associated with water from the 17th Street Canal and floodwaters collected in New Orleans showed similarity to communities in raw sewage and contained a number of sequences associated with possible pathogenic microbes. This suggests that a distinct microbial community developed in floodwaters following Hurricane Katrina and that microbial community structures as a whole might be sensitive indicators of ecosystem health and serve as "sentinels" of water quality in the environment.
Coupling of the spatial dynamic of picoplankton and nanoflagellate grazing pressure and carbon flow of the microbial food web in the subtropical pelagic continental shelf ecosystem

Science.gov (United States)

Chiang, K.-P.; Tsai, A.-Y.; Tsai, P.-J.; Gong, G.-C.; Tsai, S.-F.

2013-01-01

In order to investigate the mechanism of spatial dynamics of picoplankton community (bacteria and Synechococcus spp.) and estimate the carbon flux of the microbial food web in the oligotrophic Taiwan Warm Current Water of subtropical marine pelagic ecosystem, we conducted size-fractionation experiments in five cruises by the R/V Ocean Research II during the summers of 2010 and 2011 in the southern East China Sea. We carried out culture experiments using surface water which, according to a temperature-salinity (T-S) diagram, is characterized as oligotrophic Taiwan Current Warm Water. We found a negative correlation bettween bacteria growth rate and temperature, indicating that the active growth of heterotrophic bacteria might be induced by nutrients lifted from deep layer by cold upwelling water. This finding suggests that the area we studied was a bottom-up control pelagic ecosystem. We suggest that the microbial food web of an oligotrophic ecosystem may be changed from top-down control to resource supply (bottom-up control) when a physical force brings nutrient into the oligotrophic ecosystem. Upwelling brings nutrient-rich water to euphotic zone and promotes bacteria growth, increasing the picoplankton biomass which increased the consumption rate of nanoflagellate. The net growth rate (growth rate-grazing rate) becomes negative when the densities of bacteria and Synechococcus spp. are lower than the threshold values. The interaction between growth and grazing will limit the abundances of bacteria (105-106 cells mL-1 and Synechococcus spp. (104-105 cells mL-1) within a narrow range, forming a predator-prey eddy. Meanwhile, 62% of bacteria production and 55% of Synechococcus spp. production are transported to higher trophic level (nanoflagellate), though the cascade effect might cause an underestimation of both percentages of transported carbon. Based on the increasing number of sizes we found in the size-fractionation experiments, we estimated that the predation
Seasonal and episodic moisture controls on plant and microbial contributions to soil respiration.

Science.gov (United States)

Carbone, Mariah S; Still, Christopher J; Ambrose, Anthony R; Dawson, Todd E; Williams, A Park; Boot, Claudia M; Schaeffer, Sean M; Schimel, Joshua P

2011-09-01

Moisture inputs drive soil respiration (SR) dynamics in semi-arid and arid ecosystems. However, determining the contributions of root and microbial respiration to SR, and their separate temporal responses to periodic drought and water pulses, remains poorly understood. This study was conducted in a pine forest ecosystem with a Mediterranean-type climate that receives seasonally varying precipitation inputs from both rainfall (in the winter) and fog-drip (primarily in the summer). We used automated SR measurements, radiocarbon SR source partitioning, and a water addition experiment to understand how SR, and its separate root and microbial sources, respond to seasonal and episodic changes in moisture. Seasonal changes in SR were driven by surface soil water content and large changes in root respiration contributions. Superimposed on these seasonal patterns were episodic pulses of precipitation that determined the short-term SR patterns. Warm season precipitation pulses derived from fog-drip, and rainfall following extended dry periods, stimulated the largest SR responses. Microbial respiration dominated these SR responses, increasing within hours, whereas root respiration responded more slowly over days. We conclude that root and microbial respiration sources respond differently in timing and magnitude to both seasonal and episodic moisture inputs. These findings have important implications for the mechanistic representation of SR in models and the response of dry ecosystems to changes in precipitation patterns.
A model ecosystem experiment and its computational simulation studies

International Nuclear Information System (INIS)

Doi, M.

2002-01-01

Simplified microbial model ecosystem and its computer simulation model are introduced as eco-toxicity test for the assessment of environmental responses from the effects of environmental impacts. To take the effects on the interactions between species and environment into account, one option is to select the keystone species on the basis of ecological knowledge, and to put it in the single-species toxicity test. Another option proposed is to put the eco-toxicity tests as experimental micro ecosystem study and a theoretical model ecosystem analysis. With these tests, the stressors which are more harmful to the ecosystems should be replace with less harmful ones on the basis of unified measures. Management of radioactive materials, chemicals, hyper-eutrophic, and other artificial disturbances of ecosystem should be discussed consistently from the unified view point of environmental protection. (N.C.)
Microbial ecology of corals, sponges, and algae in mesophotic coral environments

Science.gov (United States)

Olson, Julie B.; Kellogg, Christina A.

2010-01-01

Mesophotic coral ecosystems that occur at depths from 30 to 200 m have historically been understudied and yet appear to support a diverse biological community. The microbiology of these systems is particularly poorly understood, especially with regard to the communities associated with corals, sponges, and algae. This lack of information is partly due to the problems associated with gaining access to these environments and poor reproducibility across sampling methods. To summarize what is known about the microbiology of these ecosystems and to highlight areas where research is urgently needed, an overview of the current state of knowledge is presented. Emphasis is placed on the characterization of microbial populations, both prokaryotic and eukaryotic, associated with corals, sponges, and algae and the factors that influence microbial community structure. In topic areas where virtually nothing is known from mesophotic environments, the knowledge pertaining to shallow-water ecosystems is summarized to provide a starting point for a discussion on what might be expected in the mesophotic zone.
Effects of heavy metals on soil microbial community

Science.gov (United States)

Chu, Dian

2018-02-01

Soil is one of the most important environmental natural resources for human beings living, which is of great significance to the quality of ecological environment and human health. The study of the function of arable soil microbes exposed to heavy metal pollution for a long time has a very important significance for the usage of farmland soil. In this paper, the effects of heavy metals on soil microbial community were reviewed. The main contents were as follows: the effects of soil microbes on soil ecosystems; the effects of heavy metals on soil microbial activity, soil enzyme activities and the composition of soil microbial community. In addition, a brief description of main methods of heavy metal detection for soil pollution is given, and the means of researching soil microbial community composition are introduced as well. Finally, it is concluded that the study of soil microbial community can well reflect the degree of soil heavy metal pollution and the impact of heavy metal pollution on soil ecology.
Microbial Extremophiles for Earth and Beyond: Pushing the Boundaries with Synthetic Biology

Science.gov (United States)

Rothschild, Lynn J.

2017-01-01

All organisms live in a multi-dimensional physical and chemical niche space. Discoveries in the 20th century enormously expanded the range of what was considered "habitable." However, the current diversity of life on Earth begs the question of what terrestrial life - or indeed, another life form - would be capable of. With the needs of both modern laboratory science and the burgeoning field of biotechnology, as well as our deeply held desire to answer the question "are we alone in the universe?, we are exploiting the tools of synthetic biology to probe the question of whether we can create "synthetic extremophiles" or, as our lab has dubbed them, "Hell Cells."
Ability of industrial anaerobic ecosystems to produce methane from ethanol in psychrophilic, mesophilic and thermophilic conditions

International Nuclear Information System (INIS)

Mabala, Jojo Charlie

2012-01-01

The process of anaerobic degradation of organic matter is a natural phenomenon widespread in many ecosystems (eg, marshes, lakes, rice fields, digestive systems of animals and humans). A high microbial diversity is maintained during this process, reflecting a diversity of metabolic pathways involved. When complete, the anaerobic digestion results in the formation of biogas (mixture of methane and carbon dioxide). In terms of biotechnology, anaerobic treatment of organic pollution reduces the volume of waste and generates energy as methane recoverable in several forms (electricity, heat, natural gas, biofuels). Industrial digesters are mostly operated at 35 deg. C or 55 deg. C which requires exogenous energy. The objective of the thesis is to study the adaptability of ecosystems sourced from anaerobic industrial scale reactors treating different range of wastes from different processes to convert ethanol into biogas at various temperatures. The first phase of the study was to adapt, in laboratory reactors ecosystems to their original temperature with a readily biodegradable substrate (ethanol). Then, the performances of microbial communities (the maximum methanogenic potential and degradation kinetics) were estimated on a temperature gradient from 5 deg. C to 55 deg. C in batch reactors. The adaptation phase of the ecosystems in lab-scale reactors showed that the biogas averaged theoretical production and this production was followed by a decrease in reaction time with successive addition of the substrate. In addition, the kinetics of the biogas obtained varied greatly from one ecosystem to another. Molecular fingerprinting profiles (CE-SSCP) of bacterial and archaeal communities were performed at the beginning and at the end of conditioning. These community profiles were compared with each other by principal component analysis (PCA). Bacterial populations that ensured efficient performance were different from those that ensured a good adaptability. In addition, the
Above- and belowground linkages in Sphagnum peatland: climate warming affects plant-microbial interactions.

Science.gov (United States)

Jassey, Vincent E J; Chiapusio, Geneviève; Binet, Philippe; Buttler, Alexandre; Laggoun-Défarge, Fatima; Delarue, Frédéric; Bernard, Nadine; Mitchell, Edward A D; Toussaint, Marie-Laure; Francez, André-Jean; Gilbert, Daniel

2013-03-01

Peatlands contain approximately one third of all soil organic carbon (SOC). Warming can alter above- and belowground linkages that regulate soil organic carbon dynamics and C-balance in peatlands. Here we examine the multiyear impact of in situ experimental warming on the microbial food web, vegetation, and their feedbacks with soil chemistry. We provide evidence of both positive and negative impacts of warming on specific microbial functional groups, leading to destabilization of the microbial food web. We observed a strong reduction (70%) in the biomass of top-predators (testate amoebae) in warmed plots. Such a loss caused a shortening of microbial food chains, which in turn stimulated microbial activity, leading to slight increases in levels of nutrients and labile C in water. We further show that warming altered the regulatory role of Sphagnum-polyphenols on microbial community structure with a potential inhibition of top predators. In addition, warming caused a decrease in Sphagnum cover and an increase in vascular plant cover. Using structural equation modelling, we show that changes in the microbial food web affected the relationships between plants, soil water chemistry, and microbial communities. These results suggest that warming will destabilize C and nutrient recycling of peatlands via changes in above- and belowground linkages, and therefore, the microbial food web associated with mosses will feedback positively to global warming by destabilizing the carbon cycle. This study confirms that microbial food webs thus constitute a key element in the functioning of peatland ecosystems. Their study can help understand how mosses, as ecosystem engineers, tightly regulate biogeochemical cycling and climate feedback in peatlands. © 2012 Blackwell Publishing Ltd.
RESPONSE OF SOIL MICROBIAL BIOMASS AND COMMUNITY COMPOSITION TO CHRONIC NITROGEN ADDITIONS AT HARVARD FOREST

Science.gov (United States)

Soil microbial communities may respond to anthropogenic increases in ecosystem nitrogen (N) availability, and their response may ultimately feedback on ecosystem carbon and N dynamics. We examined the long-term effects of chronic N additions on soil microbes by measuring soil mi...
Exometabolomics Assisted Design and Validation of Synthetic Obligate Mutualism.

Science.gov (United States)

Kosina, Suzanne M; Danielewicz, Megan A; Mohammed, Mujahid; Ray, Jayashree; Suh, Yumi; Yilmaz, Suzan; Singh, Anup K; Arkin, Adam P; Deutschbauer, Adam M; Northen, Trent R

2016-07-15

Synthetic microbial ecology has the potential to enhance the productivity and resiliency of biotechnology processes compared to approaches using single isolates. Engineering microbial consortia is challenging; however, one approach that has attracted significant attention is the creation of synthetic obligate mutualism using auxotrophic mutants that depend on each other for exchange or cross-feeding of metabolites. Here, we describe the integration of mutant library fitness profiling with mass spectrometry based exometabolomics as a method for constructing synthetic mutualism based on cross-feeding. Two industrially important species lacking known ecological interactions, Zymomonas mobilis and Escherichia coli, were selected as the test species. Amino acid exometabolites identified in the spent medium of Z. mobilis were used to select three corresponding E. coli auxotrophs (proA, pheA and IlvA), as potential E. coli counterparts for the coculture. A pooled mutant fitness assay with a Z. mobilis transposon mutant library was used to identify mutants with improved growth in the presence of E. coli. An auxotroph mutant in a gene (ZMO0748) with sequence similarity to cysteine synthase A (cysK), was selected as the Z. mobilis counterpart for the coculture. Exometabolomic analysis of spent E. coli medium identified glutathione related metabolites as potentially available for rescue of the Z. mobilis cysteine synthase mutant. Three sets of cocultures between the Z. mobilis auxotroph and each of the three E. coli auxotrophs were monitored by optical density for growth and analyzed by flow cytometry to confirm high cell counts for each species. Taken together, our methods provide a technological framework for creating synthetic mutualisms combining existing screening based methods and exometabolomics for both the selection of obligate mutualism partners and elucidation of metabolites involved in auxotroph rescue.
Fifty important research questions in microbial ecology.

Science.gov (United States)

Antwis, Rachael E; Griffiths, Sarah M; Harrison, Xavier A; Aranega-Bou, Paz; Arce, Andres; Bettridge, Aimee S; Brailsford, Francesca L; de Menezes, Alexandre; Devaynes, Andrew; Forbes, Kristian M; Fry, Ellen L; Goodhead, Ian; Haskell, Erin; Heys, Chloe; James, Chloe; Johnston, Sarah R; Lewis, Gillian R; Lewis, Zenobia; Macey, Michael C; McCarthy, Alan; McDonald, James E; Mejia-Florez, Nasmille L; O'Brien, David; Orland, Chloé; Pautasso, Marco; Reid, William D K; Robinson, Heather A; Wilson, Kenneth; Sutherland, William J

2017-05-01

Microbial ecology provides insights into the ecological and evolutionary dynamics of microbial communities underpinning every ecosystem on Earth. Microbial communities can now be investigated in unprecedented detail, although there is still a wealth of open questions to be tackled. Here we identify 50 research questions of fundamental importance to the science or application of microbial ecology, with the intention of summarising the field and bringing focus to new research avenues. Questions are categorised into seven themes: host-microbiome interactions; health and infectious diseases; human health and food security; microbial ecology in a changing world; environmental processes; functional diversity; and evolutionary processes. Many questions recognise that microbes provide an extraordinary array of functional diversity that can be harnessed to solve real-world problems. Our limited knowledge of spatial and temporal variation in microbial diversity and function is also reflected, as is the need to integrate micro- and macro-ecological concepts, and knowledge derived from studies with humans and other diverse organisms. Although not exhaustive, the questions presented are intended to stimulate discussion and provide focus for researchers, funders and policy makers, informing the future research agenda in microbial ecology. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
Environmental bacteriophages : viruses of microbes in aquatic ecosystems

Directory of Open Access Journals (Sweden)

Télesphore eSIME - NGANDO

2014-07-01

Full Text Available Since the discovery 2-3 decades ago that viruses of microbes are abundant in marine ecosystems, viral ecology has grown increasingly to reach the status of a full scientific discipline in environmental sciences. A dedicated ISVM society, the International Society for Viruses of Microorganisms (http://www.isvm.org/, was recently launched. Increasing studies in viral ecology are sources of novel knowledge related to the biodiversity of living things, the functioning of ecosystems, and the evolution of the cellular world. This is because viruses are perhaps the most diverse, abundant, and ubiquitous biological entities in the biosphere, although local environmental conditions enrich for certain viral types through selective pressure. They exhibit various lifestyles that intimately depend on the deep-cellular mechanisms, and are ultimately replicated by members of all three domains of cellular life (Bacteria, Eukarya, Archaea, as well as by giant viruses of some eukaryotic cells. This establishes viral parasites as microbial killers but also as cell partners or metabolic manipulators in microbial ecology. The present chapter sought to review the literature on the diversity and functional roles of viruses of microbes in environmental microbiology, focusing primarily on prokaryotic viruses (i.e. phages in aquatic ecosystems, which form the bulk of our knowledge in modern environmental viral ecology.
Ecosystem microbiology of coral reefs: linking genomic, metabolomic, and biogeochemical dynamics from animal symbioses to reefscape processes

NARCIS (Netherlands)

Wegley Kelly, L.; Haas, A.F.; Nelson, C.E.

2018-01-01

Over the past 2 decades, molecular techniques have established the critical role of both free-living and host-associated microbial partnerships in the environment. Advancing research to link microbial community dynamics simultaneously to host physiology and ecosystem biogeochemistry is required to
Final technical report. Can microbial functional traits predict the response and resilience of decomposition to global change?

Energy Technology Data Exchange (ETDEWEB)

Allison, Steven D. [Univ. of California, Irvine, CA (United States)

2015-09-24

The role of specific micro-organisms in the carbon cycle, and their responses to environmental change, are unknown in most ecosystems. This knowledge gap limits scientists’ ability to predict how important ecosystem processes, like soil carbon storage and loss, will change with climate and other environmental factors. The investigators addressed this knowledge gap by transplanting microbial communities from different environments into new environments and measuring the response of community composition and carbon cycling over time. Using state-of-the-art sequencing techniques, computational tools, and nanotechnology, the investigators showed that microbial communities on decomposing plant material shift dramatically with natural and experimentally-imposed drought. Microbial communities also shifted in response to added nitrogen, but the effects were smaller. These changes had implications for carbon cycling, with lower rates of carbon loss under drought conditions, and changes in the efficiency of decomposition with nitrogen addition. Even when transplanted into the same conditions, microbial communities from different environments remained distinct in composition and functioning for up to one year. Changes in functioning were related to differences in enzyme gene content across different microbial groups. Computational approaches developed for this project allowed the conclusions to be tested more broadly in other ecosystems, and new computer models will facilitate the prediction of microbial traits and functioning across environments. The data and models resulting from this project benefit the public by improving the ability to predict how microbial communities and carbon cycling functions respond to climate change, nutrient enrichment, and other large-scale environmental changes.
Synthetic Biology Guides Biofuel Production

Directory of Open Access Journals (Sweden)

Michael R. Connor

2010-01-01

Full Text Available The advancement of microbial processes for the production of renewable liquid fuels has increased with concerns about the current fuel economy. The development of advanced biofuels in particular has risen to address some of the shortcomings of ethanol. These advanced fuels have chemical properties similar to petroleum-based liquid fuels, thus removing the need for engine modification or infrastructure redesign. While the productivity and titers of each of these processes remains to be improved, progress in synthetic biology has provided tools to guide the engineering of these processes through present and future challenges.

Initial shifts in nitrogen impact on ecosystem carbon fluxes in an alpine meadow: patterns and causes

Science.gov (United States)

Song, Bing; Sun, Jian; Zhou, Qingping; Zong, Ning; Li, Linghao; Niu, Shuli

2017-09-01

Increases in nitrogen (N) deposition can greatly stimulate ecosystem net carbon (C) sequestration through positive N-induced effects on plant productivity. However, how net ecosystem CO2 exchange (NEE) and its components respond to different N addition rates remains unclear. Using an N addition gradient experiment (six levels: 0, 2, 4, 8, 16, 32 gN m-2 yr-1) in an alpine meadow on the Qinghai-Tibetan Plateau, we explored the responses of different ecosystem C fluxes to an N addition gradient and revealed mechanisms underlying the dynamic responses. Results showed that NEE, ecosystem respiration (ER), and gross ecosystem production (GEP) all increased linearly with N addition rates in the first year of treatment but shifted to N saturation responses in the second year with the highest NEE (-7.77 ± 0.48 µmol m-2 s-1) occurring under an N addition rate of 8 gN m-2 yr-1. The saturation responses of NEE and GEP were caused by N-induced accumulation of standing litter, which limited light availability for plant growth under high N addition. The saturation response of ER was mainly due to an N-induced saturation response of aboveground plant respiration and decreasing soil microbial respiration along the N addition gradient, while decreases in soil microbial respiration under high N addition were caused by N-induced reductions in soil pH. We also found that various components of ER, including aboveground plant respiration, soil respiration, root respiration, and microbial respiration, responded differentially to the N addition gradient. These results reveal temporal dynamics of N impacts and the rapid shift in ecosystem C fluxes from N limitation to N saturation. Our findings bring evidence of short-term initial shifts in responses of ecosystem C fluxes to increases in N deposition, which should be considered when predicting long-term changes in ecosystem net C sequestration.
Emergent biosynthetic capacity in simple microbial communities.

Directory of Open Access Journals (Sweden)

Hsuan-Chao Chiu

2014-07-01

Full Text Available Microbes have an astonishing capacity to transform their environments. Yet, the metabolic capacity of a single species is limited and the vast majority of microorganisms form complex communities and join forces to exhibit capabilities far exceeding those achieved by any single species. Such enhanced metabolic capacities represent a promising route to many medical, environmental, and industrial applications and call for the development of a predictive, systems-level understanding of synergistic microbial capacity. Here we present a comprehensive computational framework, integrating high-quality metabolic models of multiple species, temporal dynamics, and flux variability analysis, to study the metabolic capacity and dynamics of simple two-species microbial ecosystems. We specifically focus on detecting emergent biosynthetic capacity--instances in which a community growing on some medium produces and secretes metabolites that are not secreted by any member species when growing in isolation on that same medium. Using this framework to model a large collection of two-species communities on multiple media, we demonstrate that emergent biosynthetic capacity is highly prevalent. We identify commonly observed emergent metabolites and metabolic reprogramming patterns, characterizing typical mechanisms of emergent capacity. We further find that emergent secretion tends to occur in two waves, the first as soon as the two organisms are introduced, and the second when the medium is depleted and nutrients become limited. Finally, aiming to identify global community determinants of emergent capacity, we find a marked association between the level of emergent biosynthetic capacity and the functional/phylogenetic distance between community members. Specifically, we demonstrate a "Goldilocks" principle, where high levels of emergent capacity are observed when the species comprising the community are functionally neither too close, nor too distant. Taken together
Streamlining genomes: toward the generation of simplified and stabilized microbial systems

NARCIS (Netherlands)

Leprince, A.; Passel, van M.W.J.; Martins Dos Santos, V.A.P.

2012-01-01

At the junction between systems and synthetic biology, genome streamlining provides a solid foundation both for increased understanding of cellular circuitry, and for the tailoring of microbial chassis towards innovative biotechnological applications. Iterative genomic deletions (targeted and
Assessment of soil microbial diversity with functional multi-endpoint methods

DEFF Research Database (Denmark)

Winding, Anne; Creamer, R. E.; Rutgers, M.

on CO2 development by the microbes such as substrate induced respiration (SIR) on specific substrates have lead to the development of MicroResp™ and Community Level Physiological Profile (CLPP) with Biolog™ plates, and soil enzymatic activity assayed by Extracellular Enzyme Activity (EEA) based on MUF......Soil microbial diversity provides the cornerstone for support of soil ecosystem services by key roles in soil organic matter turnover, carbon sequestration and water infiltration. However, standardized methods to quantify the multitude of microbial functions in soils are lacking. Methods based...... to the lack of principle methods, the data obtained from these substitute methods are currently not used in classification and assessment schemes, making quantification of natural capital and ecosystems services of the soil a difficult venture. In this contribution, we compare and contrast the three...
Synthetic Biology and Microbial Fuel Cells: Towards Self-Sustaining Life Support Systems

Data.gov (United States)

National Aeronautics and Space Administration — NASA ARC and the J. Craig Venter Institute (JCVI) collaborated to investigate the development of advanced microbial fuels cells (MFCs) for biological wastewater...
mcaGUI: microbial community analysis R-Graphical User Interface (GUI)

OpenAIRE

Copeland, Wade K.; Krishnan, Vandhana; Beck, Daniel; Settles, Matt; Foster, James A.; Cho, Kyu-Chul; Day, Mitch; Hickey, Roxana; Schütte, Ursel M.E.; Zhou, Xia; Williams, Christopher J.; Forney, Larry J.; Abdo, Zaid

2012-01-01

Summary: Microbial communities have an important role in natural ecosystems and have an impact on animal and human health. Intuitive graphic and analytical tools that can facilitate the study of these communities are in short supply. This article introduces Microbial Community Analysis GUI, a graphical user interface (GUI) for the R-programming language (R Development Core Team, 2010). With this application, researchers can input aligned and clustered sequence data to create custom abundance ...
Patterns of Early-Life Gut Microbial Colonization during Human Immune Development: An Ecological Perspective

Directory of Open Access Journals (Sweden)

Isabelle Laforest-Lapointe

2017-07-01

Full Text Available Alterations in gut microbial colonization during early life have been reported in infants that later developed asthma, allergies, type 1 diabetes, as well as in inflammatory bowel disease patients, previous to disease flares. Mechanistic studies in animal models have established that microbial alterations influence disease pathogenesis via changes in immune system maturation. Strong evidence points to the presence of a window of opportunity in early life, during which changes in gut microbial colonization can result in immune dysregulation that predisposes susceptible hosts to disease. Although the ecological patterns of microbial succession in the first year of life have been partly defined in specific human cohorts, the taxonomic and functional features, and diversity thresholds that characterize these microbial alterations are, for the most part, unknown. In this review, we summarize the most important links between the temporal mosaics of gut microbial colonization and the age-dependent immune functions that rely on them. We also highlight the importance of applying ecology theory to design studies that explore the interactions between this complex ecosystem and the host immune system. Focusing research efforts on understanding the importance of temporally structured patterns of diversity, keystone groups, and inter-kingdom microbial interactions for ecosystem functions has great potential to enable the development of biologically sound interventions aimed at maintaining and/or improving immune system development and preventing disease.
Nutrient controls on biocomplexity of mangrove ecosystems

Science.gov (United States)

McKee, Karen L.

2004-01-01

Mangrove forests are important coastal ecosystems that provide a variety of ecological and societal services. These intertidal, tree-dominated communities along tropical coastlines are often described as “simple systems,” compared to other tropical forests with larger numbers of plant species and multiple understory strata; however, mangrove ecosystems have complex trophic structures, and organisms exhibit unique physiological, morphological, and behavioral adaptations to environmental conditions characteristic of the land-sea interface. Biogeochemical functioning of mangrove forests is also controlled by interactions among the microbial, plant, and animal communities and feedback linkages mediated by hydrology and other forcing functions. Scientists with the U.S. Geological Survey (USGS) at the National Wetlands Research Center are working to understand more fully the impact of nutrient variability on these delicate and important ecosystems.
The complete nitrogen cycle of an N-saturated spruce forest ecosystem.

Science.gov (United States)

Kreutzer, K; Butterbach-Bahl, K; Rennenberg, H; Papen, H

2009-09-01

Long-term nitrogen deposition into forest ecosystems has turned many forests in Central Europe and North America from N-limited to N-saturated systems, with consequences for climate as well as air and groundwater quality. However, complete quantification of processes that convert the N deposited and contributed to ecosystem N cycling is scarce. In this study, we provide the first complete quantification of external and internal N fluxes in an old-growth spruce forest, the Höglwald, Bavaria, Germany, exposed to high chronic N deposition. In this forest, N cycling is dominated by high rates of mineralisation of soil organic matter, nitrification and immobilisation of ammonium and nitrate into microbial biomass. The amount of ammonium available is sufficient to cover the entire N demand of the spruce trees. The data demonstrate the existence of a highly dynamic internal N cycle within the soil, driven by growth and death of the microbial biomass, which turns over approximately seven times each year. Although input and output fluxes are of high environmental significance, they are low compared to the internal fluxes mediated by microbial activity.
Solar radiation uncorks the lignin bottleneck on plant litter decomposition in terrestrial ecosystems

Science.gov (United States)

Austin, A.; Ballare, C. L.; Méndez, M. S.

2015-12-01

Plant litter decomposition is an essential process in the first stages of carbon and nutrient turnover in terrestrial ecosystems, and together with soil microbial biomass, provide the principal inputs of carbon for the formation of soil organic matter. Photodegradation, the photochemical mineralization of organic matter, has been recently identified as a mechanism for previously unexplained high rates of litter mass loss in low rainfall ecosystems; however, the generality of this process as a control on carbon cycling in terrestrial ecosystems is not known, and the indirect effects of photodegradation on biotic stimulation of carbon turnover have been debated in recent studies. We demonstrate that in a wide range of plant species, previous exposure to solar radiation, and visible light in particular, enhanced subsequent biotic degradation of leaf litter. Moreover, we demonstrate that the mechanism for this enhancement involves increased accessibility for microbial enzymes to plant litter carbohydrates due to a reduction in lignin content. Photodegradation of plant litter reduces the structural and chemical bottleneck imposed by lignin in secondary cell walls. In litter from woody plant species, specific interactions with ultraviolet radiation obscured facilitative effects of solar radiation on biotic decomposition. The generalized positive effect of solar radiation exposure on subsequent microbial activity is mediated by increased accessibility to cell wall polysaccharides, which suggests that photodegradation is quantitatively important in determining rates of mass loss, nutrient release and the carbon balance in a broad range of terrestrial ecosystems.
Limits on carbon sequestration in arid blue carbon ecosystems.

Science.gov (United States)

Schile, Lisa M; Kauffman, J Boone; Crooks, Stephen; Fourqurean, James W; Glavan, Jane; Megonigal, J Patrick

2017-04-01

Coastal ecosystems produce and sequester significant amounts of carbon ("blue carbon"), which has been well documented in humid and semi-humid regions of temperate and tropical climates but less so in arid regions where mangroves, marshes, and seagrasses exist near the limit of their tolerance for extreme temperature and salinity. To better understand these unique systems, we measured whole-ecosystem carbon stocks in 58 sites across the United Arab Emirates (UAE) in natural and planted mangroves, salt marshes, seagrass beds, microbial mats, and coastal sabkha (inter- and supratidal unvegetated salt flats). Natural mangroves held significantly more carbon in above- and belowground biomass than other vegetated ecosystems. Planted mangrove carbon stocks increased with age, but there were large differences for sites of similar age. Soil carbon varied widely across sites (2-367 Mg C/ha), with ecosystem averages that ranged from 49 to 156 Mg C/ha. For the first time, microbial mats were documented to contain soil carbon pools comparable to vascular plant-dominated ecosystems, and could arguably be recognized as a unique blue carbon ecosystem. Total ecosystem carbon stocks ranged widely from 2 to 515 Mg C/ha (seagrass bed and mangrove, respectively). Seagrass beds had the lowest carbon stock per unit area, but the largest stock per total area due to their large spatial coverage. Compared to similar ecosystems globally, mangroves and marshes in the UAE have lower plant and soil carbon stocks; however, the difference in soil stocks is far larger than with plant stocks. This incongruent difference between stocks is likely due to poor carbon preservation under conditions of weakly reduced soils (200-350 mV), coarse-grained sediments, and active shoreline migration. This work represents the first attempt to produce a country-wide coastal ecosystem carbon accounting using a uniform sampling protocol, and was motivated by specific policy goals identified by the Abu Dhabi Global
Bioinformatic approaches reveal metagenomic characterization of soil microbial community.

Directory of Open Access Journals (Sweden)

Zhuofei Xu

Full Text Available As is well known, soil is a complex ecosystem harboring the most prokaryotic biodiversity on the Earth. In recent years, the advent of high-throughput sequencing techniques has greatly facilitated the progress of soil ecological studies. However, how to effectively understand the underlying biological features of large-scale sequencing data is a new challenge. In the present study, we used 33 publicly available metagenomes from diverse soil sites (i.e. grassland, forest soil, desert, Arctic soil, and mangrove sediment and integrated some state-of-the-art computational tools to explore the phylogenetic and functional characterizations of the microbial communities in soil. Microbial composition and metabolic potential in soils were comprehensively illustrated at the metagenomic level. A spectrum of metagenomic biomarkers containing 46 taxa and 33 metabolic modules were detected to be significantly differential that could be used as indicators to distinguish at least one of five soil communities. The co-occurrence associations between complex microbial compositions and functions were inferred by network-based approaches. Our results together with the established bioinformatic pipelines should provide a foundation for future research into the relation between soil biodiversity and ecosystem function.
Combining Microbial Enzyme Kinetics Models with Light Use Efficiency Models to Predict CO2 and CH4 Ecosystem Exchange from Flooded and Drained Peatland Systems

Science.gov (United States)

Oikawa, P. Y.; Jenerette, D.; Knox, S. H.; Sturtevant, C. S.; Verfaillie, J. G.; Baldocchi, D. D.

2014-12-01

Under California's Cap-and-Trade program, companies are looking to invest in land-use practices that will reduce greenhouse gas (GHG) emissions. The Sacramento-San Joaquin River Delta is a drained cultivated peatland system and a large source of CO2. To slow soil subsidence and reduce CO2 emissions, there is growing interest in converting drained peatlands to wetlands. However, wetlands are large sources of CH4 that could offset CO2-based GHG reductions. The goal of our research is to provide accurate measurements and model predictions of the changes in GHG budgets that occur when drained peatlands are restored to wetland conditions. We have installed a network of eddy covariance towers across multiple land use types in the Delta and have been measuring CO2 and CH4 ecosystem exchange for multiple years. In order to upscale these measurements through space and time we are using these data to parameterize and validate a process-based biogeochemical model. To predict gross primary productivity (GPP), we are using a simple light use efficiency (LUE) model which requires estimates of light, leaf area index and air temperature and can explain 90% of the observed variation in GPP in a mature wetland. To predict ecosystem respiration we have adapted the Dual Arrhenius Michaelis-Menten (DAMM) model. The LUE-DAMM model allows accurate simulation of half-hourly net ecosystem exchange (NEE) in a mature wetland (r2=0.85). We are working to expand the model to pasture, rice and alfalfa systems in the Delta. To predict methanogenesis, we again apply a modified DAMM model, using simple enzyme kinetics. However CH4 exchange is complex and we have thus expanded the model to predict not only microbial CH4 production, but also CH4 oxidation, CH4 storage and the physical processes regulating the release of CH4 to the atmosphere. The CH4-DAMM model allows accurate simulation of daily CH4 ecosystem exchange in a mature wetland (r2=0.55) and robust estimates of annual CH4 budgets. The LUE
Information transmission in microbial and fungal communication: from classical to quantum.

Science.gov (United States)

Majumdar, Sarangam; Pal, Sukla

2018-06-01

Microbes have their own communication systems. Secretion and reception of chemical signaling molecules and ion-channels mediated electrical signaling mechanism are yet observed two special ways of information transmission in microbial community. In this article, we address the aspects of various crucial machineries which set the backbone of microbial cell-to-cell communication process such as quorum sensing mechanism (bacterial and fungal), quorum sensing regulated biofilm formation, gene expression, virulence, swarming, quorum quenching, role of noise in quorum sensing, mathematical models (therapy model, evolutionary model, molecular mechanism model and many more), synthetic bacterial communication, bacterial ion-channels, bacterial nanowires and electrical communication. In particular, we highlight bacterial collective behavior with classical and quantum mechanical approaches (including quantum information). Moreover, we shed a new light to introduce the concept of quantum synthetic biology and possible cellular quantum Turing test.
Microbial ecology of four coral atolls in the Northern Line Islands.

Directory of Open Access Journals (Sweden)

Elizabeth A Dinsdale

Full Text Available Microbes are key players in both healthy and degraded coral reefs. A combination of metagenomics, microscopy, culturing, and water chemistry were used to characterize microbial communities on four coral atolls in the Northern Line Islands, central Pacific. Kingman, a small uninhabited atoll which lies most northerly in the chain, had microbial and water chemistry characteristic of an open ocean ecosystem. On this atoll the microbial community was equally divided between autotrophs (mostly Prochlorococcus spp. and heterotrophs. In contrast, Kiritimati, a large and populated ( approximately 5500 people atoll, which is most southerly in the chain, had microbial and water chemistry characteristic of a near-shore environment. On Kiritimati, there were 10 times more microbial cells and virus-like particles in the water column and these microbes were dominated by heterotrophs, including a large percentage of potential pathogens. Culturable Vibrios were common only on Kiritimati. The benthic community on Kiritimati had the highest prevalence of coral disease and lowest coral cover. The middle atolls, Palmyra and Tabuaeran, had intermediate densities of microbes and viruses and higher percentages of autotrophic microbes than either Kingman or Kiritimati. The differences in microbial communities across atolls could reflect variation in 1 oceaonographic and/or hydrographic conditions or 2 human impacts associated with land-use and fishing. The fact that historically Kingman and Kiritimati did not differ strongly in their fish or benthic communities (both had large numbers of sharks and high coral cover suggest an anthropogenic component in the differences in the microbial communities. Kingman is one of the world's most pristine coral reefs, and this dataset should serve as a baseline for future studies of coral reef microbes. Obtaining the microbial data set, from atolls is particularly important given the association of microbes in the ongoing degradation
Microbial Ecology of Four Coral Atolls in the Northern Line Islands

Science.gov (United States)

Smriga, Steven; Edwards, Robert A.; Angly, Florent; Wegley, Linda; Hatay, Mark; Hall, Dana; Brown, Elysa; Haynes, Matthew; Krause, Lutz; Sala, Enric; Sandin, Stuart A.; Thurber, Rebecca Vega; Willis, Bette L.; Azam, Farooq; Knowlton, Nancy; Rohwer, Forest

2008-01-01

Microbes are key players in both healthy and degraded coral reefs. A combination of metagenomics, microscopy, culturing, and water chemistry were used to characterize microbial communities on four coral atolls in the Northern Line Islands, central Pacific. Kingman, a small uninhabited atoll which lies most northerly in the chain, had microbial and water chemistry characteristic of an open ocean ecosystem. On this atoll the microbial community was equally divided between autotrophs (mostly Prochlorococcus spp.) and heterotrophs. In contrast, Kiritimati, a large and populated (∼5500 people) atoll, which is most southerly in the chain, had microbial and water chemistry characteristic of a near-shore environment. On Kiritimati, there were 10 times more microbial cells and virus-like particles in the water column and these microbes were dominated by heterotrophs, including a large percentage of potential pathogens. Culturable Vibrios were common only on Kiritimati. The benthic community on Kiritimati had the highest prevalence of coral disease and lowest coral cover. The middle atolls, Palmyra and Tabuaeran, had intermediate densities of microbes and viruses and higher percentages of autotrophic microbes than either Kingman or Kiritimati. The differences in microbial communities across atolls could reflect variation in 1) oceaonographic and/or hydrographic conditions or 2) human impacts associated with land-use and fishing. The fact that historically Kingman and Kiritimati did not differ strongly in their fish or benthic communities (both had large numbers of sharks and high coral cover) suggest an anthropogenic component in the differences in the microbial communities. Kingman is one of the world's most pristine coral reefs, and this dataset should serve as a baseline for future studies of coral reef microbes. Obtaining the microbial data set, from atolls is particularly important given the association of microbes in the ongoing degradation of coral reef ecosystems
Rational synthetic pathway refactoring of natural products biosynthesis in actinobacteria.

Science.gov (United States)

Tan, Gao-Yi; Liu, Tiangang

2017-01-01

Natural products (NPs) and their derivatives are widely used as frontline treatments for many diseases. Actinobacteria spp. are used to produce most of NP antibiotics and have also been intensively investigated for NP production, derivatization, and discovery. However, due to the complicated transcriptional and metabolic regulation of NP biosynthesis in Actinobacteria, especially in the cases of genome mining and heterologous expression, it is often difficult to rationally and systematically engineer synthetic pathways to maximize biosynthetic efficiency. With the emergence of new tools and methods in metabolic engineering, the synthetic pathways of many chemicals, such as fatty acids and biofuels, in model organisms (e.g. Escherichia coli ), have been refactored to realize precise and flexible control of production. These studies also offer a promising approach for synthetic pathway refactoring in Actinobacteria. In this review, the great potential of Actinobacteria as a microbial cell factory for biosynthesis of NPs is discussed. To this end, recent progress in metabolic engineering of NP synthetic pathways in Actinobacteria are summarized and strategies and perspectives to rationally and systematically refactor synthetic pathways in Actinobacteria are highlighted. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.
Chernozems microbial community under anthropogenic impact (Russia)

Science.gov (United States)

Ivashchenko, Kristina; Ananyeva, Nadezhda; Sushko, Sofia; Vasenev, Viacheslav

2017-04-01

Chernozems is important natural resource, which in the last decade under intense influence as a result of plowing and urbanization. The parameters of soil microbial community functioning might be identify some soil deterioration under the impacts. Our research was focused on assessment of microbial community status in different soil layers of virgin steppe, bare fallow and urban ecosystems (Kursk region). In each ecosystem, we chose randomly 3-5 spatially distributed sites, where soil samples were collected by auguring up to 0.5 m depth (each layer 10 cm thickness) and up to 1.5 m depth (0-10, 10-50, 50-100, 100-150 cm layers), totally 127 samples. The bulk density was measured for these soil layers. In all soil samples the microbial biomass carbon content (Cmic) was analyzed by substrate-induced respiration (SIR) method and basal respiration (BR) was assessed by CO2 rate production. The fungi-to-bacteria ratio (selective inhibition technique with antibiotics) was determined and portion of Cmic in soil organic carbon (Corg) content was calculated in topsoil (0-10 cm). The Corg (dichromate oxidation) and pHw (potentiometry) values were measured. The Cmic and BR profile pools were calculated using bulk density and thickness of studied layers. The Cmic (0-10 cm) was varied from 84 to 1954 µg C g-1 soil, in steppe it was on average 3-4 times higher than those in bare fallow and urban. The BR rate was amounted from 0.20 to 1.57 µg CO2-C g-1 soil h-1, however no significant difference between studied ecosystems was found. It was shown the relationship between Cmic, BR and Corg (the linear regression, R2=0.92 and 0.75, respectively, pecosystems row: virgin steppe>bare fallow>urban, and it was on average 6.0, 5.2 and 1.8, respectively. The Cmic profile pool (0.5 m) of steppe was reached up on average 206 g C m-2, and it was 2.0 and 2.5 times higher those bare fallow and urban, respectively. The BR profile pool (0.5 m) in steppe and bare fallow was reached up 5.9 and 5
Ecosystem productivity is associated with bacterial phylogenetic distance in surface marine waters.

Science.gov (United States)

Galand, Pierre E; Salter, Ian; Kalenitchenko, Dimitri

2015-12-01

Understanding the link between community diversity and ecosystem function is a fundamental aspect of ecology. Systematic losses in biodiversity are widely acknowledged but the impact this may exert on ecosystem functioning remains ambiguous. There is growing evidence of a positive relationship between species richness and ecosystem productivity for terrestrial macro-organisms, but similar links for marine micro-organisms, which help drive global climate, are unclear. Community manipulation experiments show both positive and negative relationships for microbes. These previous studies rely, however, on artificial communities and any links between the full diversity of active bacterial communities in the environment, their phylogenetic relatedness and ecosystem function remain hitherto unexplored. Here, we test the hypothesis that productivity is associated with diversity in the metabolically active fraction of microbial communities. We show in natural assemblages of active bacteria that communities containing more distantly related members were associated with higher bacterial production. The positive phylogenetic diversity-productivity relationship was independent of community diversity calculated as the Shannon index. From our long-term (7-year) survey of surface marine bacterial communities, we also found that similarly, productive communities had greater phylogenetic similarity to each other, further suggesting that the traits of active bacteria are an important predictor of ecosystem productivity. Our findings demonstrate that the evolutionary history of the active fraction of a microbial community is critical for understanding their role in ecosystem functioning. © 2015 John Wiley & Sons Ltd.
Electrochemical evaluation of Ti/TiO{sub 2}-polyaniline anodes for microbial fuel cells using hypersaline microbial consortia for synthetic-wastewater treatment

Energy Technology Data Exchange (ETDEWEB)

Benetton, X.D.; Navarro-Avila, S.G. [Univ. Autonoma de Yucatan, Yucatan (Mexico). Biotecnologia y Bioingenieria; Carrera-Figueiras, C. [Univ. Autonoma de Yucatan, Yucatan (Mexico). Quimica Fundamental y Aplicada

2010-07-01

This paper described the development of a titanium (Ti/TiO{sub 2}) polyaniline composite electrode. The electrode was designed for use with a microbial fuel cell (MFC) that generated electricity through the microbial biodegradation of organic compounds. A modified NBAF medium was used with a 20 mM acetate as an electron donor and 53 mM fumarate as an electron acceptor for a period of 96 hours at 37 degrees C. Strains were cultured under strict anaerobic conditions. Two microbial cultures were used: (1) pure cultures of Geobacter sulfur-reducens; and (2) an uncharacterized stable microbial consortia isolated from hypersaline swamp sediments. The anodes were made with an emeraldine form of PANI deposited over Ti/TiO{sub 2} electrodes. Electrochemical impedance spectroscopy (EIS) monitoring was used to determine the open circuit potential of the MFC. Negative real impedances were obtained and reproduced in all systems studied with the Ti/TiO{sub 2}-PANI anodes. The highest power density was obtained using the Geobacter sulfur-reducens culture. Further research is needed to study the mechanisms that contribute to the occurrence of negative real impedances. 23 refs., 1 tab., 5 figs.

Microbial community dynamics in the forefield of glaciers.

Science.gov (United States)

Bradley, James A; Singarayer, Joy S; Anesio, Alexandre M

2014-11-22

Retreating ice fronts (as a result of a warming climate) expose large expanses of deglaciated forefield, which become colonized by microbes and plants. There has been increasing interest in characterizing the biogeochemical development of these ecosystems using a chronosequence approach. Prior to the establishment of plants, microbes use autochthonously produced and allochthonously delivered nutrients for growth. The microbial community composition is largely made up of heterotrophic microbes (both bacteria and fungi), autotrophic microbes and nitrogen-fixing diazotrophs. Microbial activity is thought to be responsible for the initial build-up of labile nutrient pools, facilitating the growth of higher order plant life in developed soils. However, it is unclear to what extent these ecosystems rely on external sources of nutrients such as ancient carbon pools and periodic nitrogen deposition. Furthermore, the seasonal variation of chronosequence dynamics and the effect of winter are largely unexplored. Modelling this ecosystem will provide a quantitative evaluation of the key processes and could guide the focus of future research. Year-round datasets combined with novel metagenomic techniques will help answer some of the pressing questions in this relatively new but rapidly expanding field, which is of growing interest in the context of future large-scale ice retreat.
Leaf bacterial diversity mediates plant diversity and ecosystem function relationships.

Science.gov (United States)

Laforest-Lapointe, Isabelle; Paquette, Alain; Messier, Christian; Kembel, Steven W

2017-06-01

Research on biodiversity and ecosystem functioning has demonstrated links between plant diversity and ecosystem functions such as productivity. At other trophic levels, the plant microbiome has been shown to influence host plant fitness and function, and host-associated microbes have been proposed to influence ecosystem function through their role in defining the extended phenotype of host organisms However, the importance of the plant microbiome for ecosystem function has not been quantified in the context of the known importance of plant diversity and traits. Here, using a tree biodiversity-ecosystem functioning experiment, we provide strong support for the hypothesis that leaf bacterial diversity is positively linked to ecosystem productivity, even after accounting for the role of plant diversity. Our results also show that host species identity, functional identity and functional diversity are the main determinants of leaf bacterial community structure and diversity. Our study provides evidence of a positive correlation between plant-associated microbial diversity and terrestrial ecosystem productivity, and a new mechanism by which models of biodiversity-ecosystem functioning relationships can be improved.
Microbial conversion of synthetic and food waste-derived volatile fatty acids to lipids.

Science.gov (United States)

Vajpeyi, Shashwat; Chandran, Kartik

2015-01-01

Lipid accumulation in the oleaginous yeast Cryptococcus albidus was evaluated using mixtures of volatile fatty acids (VFA) as substrates. In general, batch growth under nitrogen limitation led to higher lipid accumulation using synthetic VFA. During batch growth, an initial COD:N ratio of 25:1mg COD:mg N led to maximum intracellular lipid accumulation (28.3 ± 0.7% g/g dry cell weight), which is the maximum reported for C. albidus using VFA as the carbon source, without compromising growth kinetics. At this feed COD:N ratio, chemostat cultures fed with synthetic VFA yielded statistically similar intracellular lipid content as batch cultures (29.9 ± 1.9%, g/g). However, batch cultures fed with VFA produced from the fermentation of food waste, yielded a lower lipid content (14.9 ± 0.1%, g/g). The lipid composition obtained with synthetic and food-waste-derived VFA was similar to commercial biodiesel feedstock. We therefore demonstrate the feasibility of linking biochemical waste treatment and biofuel production using VFA as key intermediates. Copyright © 2015 Elsevier Ltd. All rights reserved.
Microbes in the Anthropocene: spillover of agriculturally selected bacteria and their impact on natural ecosystems.

Science.gov (United States)

Bell, Thomas; Tylianakis, Jason M

2016-12-14

Soil microbial communities are enormously diverse, with at least millions of species and trillions of genes unknown to science or poorly described. Soil microbial communities are key components of agriculture, for example, in provisioning nitrogen and protecting crops from pathogens, providing overall ecosystem services in excess of $1000bn per year. It is important to know how humans are affecting this hidden diversity. Much is known about the negative consequences of agricultural intensification on higher organisms, but almost nothing is known about how alterations to landscapes affect microbial diversity, distributions and processes. We review what is known about spatial flows of microbes and their response to land-use change, and outline nine hypotheses to advance research of microbiomes across landscapes. We hypothesize that intensified agriculture selects for certain taxa and genes, which then 'spill over' into adjacent unmodified areas and generate a halo of genetic differentiation around agricultural fields. Consequently, the spatial configuration and management intensity of different habitats combines with the dispersal ability of individual taxa to determine the extent of spillover, which can impact the functioning of adjacent unmodified habitats. When landscapes are heterogeneous and dispersal rates are high, this will select for large genomes that allow exploitation of multiple habitats, a process that may be accelerated through horizontal gene transfer. Continued expansion of agriculture will increase genotypic similarity, making microbial community functioning increasingly variable in human-dominated landscapes, potentially also impacting the consistent provisioning of ecosystem services. While the resulting economic costs have not been calculated, it is clear that dispersal dynamics of microbes should be taken into consideration to ensure that ecosystem functioning and services are maintained in agri-ecosystem mosaics. © 2016 The Authors.
Microbes in the Anthropocene: spillover of agriculturally selected bacteria and their impact on natural ecosystems

Science.gov (United States)

2016-01-01

Soil microbial communities are enormously diverse, with at least millions of species and trillions of genes unknown to science or poorly described. Soil microbial communities are key components of agriculture, for example, in provisioning nitrogen and protecting crops from pathogens, providing overall ecosystem services in excess of $1000bn per year. It is important to know how humans are affecting this hidden diversity. Much is known about the negative consequences of agricultural intensification on higher organisms, but almost nothing is known about how alterations to landscapes affect microbial diversity, distributions and processes. We review what is known about spatial flows of microbes and their response to land-use change, and outline nine hypotheses to advance research of microbiomes across landscapes. We hypothesize that intensified agriculture selects for certain taxa and genes, which then ‘spill over’ into adjacent unmodified areas and generate a halo of genetic differentiation around agricultural fields. Consequently, the spatial configuration and management intensity of different habitats combines with the dispersal ability of individual taxa to determine the extent of spillover, which can impact the functioning of adjacent unmodified habitats. When landscapes are heterogeneous and dispersal rates are high, this will select for large genomes that allow exploitation of multiple habitats, a process that may be accelerated through horizontal gene transfer. Continued expansion of agriculture will increase genotypic similarity, making microbial community functioning increasingly variable in human-dominated landscapes, potentially also impacting the consistent provisioning of ecosystem services. While the resulting economic costs have not been calculated, it is clear that dispersal dynamics of microbes should be taken into consideration to ensure that ecosystem functioning and services are maintained in agri-ecosystem mosaics. PMID:27928044
Tracking heavy water (D₂O) incorporation for identifying and sorting active microbial cells

DEFF Research Database (Denmark)

Berry, David; Mader, Esther; Lee, Tae Kwon

2015-01-01

Microbial communities are essential to the function of virtually all ecosystems and eukaryotes, including humans. However, it is still a major challenge to identify microbial cells active under natural conditions in complex systems. In this study, we developed a new method to identify and sort ac...
Theoretical microbial ecology without species

Science.gov (United States)

Tikhonov, Mikhail

2017-09-01

Ecosystems are commonly conceptualized as networks of interacting species. However, partitioning natural diversity of organisms into discrete units is notoriously problematic and mounting experimental evidence raises the intriguing question whether this perspective is appropriate for the microbial world. Here an alternative formalism is proposed that does not require postulating the existence of species as fundamental ecological variables and provides a naturally hierarchical description of community dynamics. This formalism allows approaching the species problem from the opposite direction. While the classical models treat a world of imperfectly clustered organism types as a perturbation around well-clustered species, the presented approach allows gradually adding structure to a fully disordered background. The relevance of this theoretical construct for describing highly diverse natural ecosystems is discussed.
Microbial ecology of hot desert edaphic systems.

Science.gov (United States)

Makhalanyane, Thulani P; Valverde, Angel; Gunnigle, Eoin; Frossard, Aline; Ramond, Jean-Baptiste; Cowan, Don A

2015-03-01

A significant proportion of the Earth's surface is desert or in the process of desertification. The extreme environmental conditions that characterize these areas result in a surface that is essentially barren, with a limited range of higher plants and animals. Microbial communities are probably the dominant drivers of these systems, mediating key ecosystem processes. In this review, we examine the microbial communities of hot desert terrestrial biotopes (including soils, cryptic and refuge niches and plant-root-associated microbes) and the processes that govern their assembly. We also assess the possible effects of global climate change on hot desert microbial communities and the resulting feedback mechanisms. We conclude by discussing current gaps in our understanding of the microbiology of hot deserts and suggest fruitful avenues for future research. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
THE WIDESPREAD OF Fe(III)-REDUCING BACTERIA IN NATURAL ECOSYSTEMS OF ECUADOR.

Science.gov (United States)

Tashyrev, O B; Govorukha, V M

2015-01-01

The widespread of Fe(III)-reducing microorganisms in natural ecosystems of Ecuador of La Favorita, Tungurahua volcano and Papallacta areas was experimentally proved. High efficiency of microbial precipitation of soluble iron compounds was also demonstrated. Obtained results indicate the potential ability of Fe(III)-reducing microorganisms to influence the formation of carbon and iron vector fluxes in ecosystems, as well as development of effective biotechnologies of water purification from iron compounds.
Towards evolution-guided microbial engineering - tools development and applications

DEFF Research Database (Denmark)

Genee, Hans Jasper

is thedevelopment of highly robust biosensor-based synthetic selection systemsthat enable high-throughput functional interrogation of complexphenotypic libraries. Using the model organism Escherichia coli as a host, Ideploy these systems to i) perform metagenome wide sequenceindependentidentification of novel...... for microbial engineering anddemonstrates direct applications to gene discovery, protein engineering andcell factory development....
Exploring the Impacts of Anthropogenic Disturbance on Seawater and Sediment Microbial Communities in Korean Coastal Waters Using Metagenomics Analysis

Directory of Open Access Journals (Sweden)

Nam-Il Won

2017-01-01

Full Text Available The coastal ecosystems are considered as one of the most dynamic and vulnerable environments under various anthropogenic developments and the effects of climate change. Variations in the composition and diversity of microbial communities may be a good indicator for determining whether the marine ecosystems are affected by complex forcing stressors. DNA sequence-based metagenomics has recently emerged as a promising tool for analyzing the structure and diversity of microbial communities based on environmental DNA (eDNA. However, few studies have so far been performed using this approach to assess the impacts of human activities on the microbial communities in marine systems. In this study, using metagenomic DNA sequencing (16S ribosomal RNA gene, we analyzed and compared seawater and sediment communities between sand mining and control (natural sites in southern coastal waters of Korea to assess whether anthropogenic activities have significantly affected the microbial communities. The sand mining sites harbored considerably lower levels of microbial diversities in the surface seawater community during spring compared with control sites. Moreover, the sand mining areas had distinct microbial taxonomic group compositions, particularly during spring season. The microbial groups detected solely in the sediment load/dredging areas (e.g., Marinobacter, Alcanivorax, Novosphingobium are known to be involved in degradation of toxic chemicals such as hydrocarbon, oil, and aromatic compounds, and they also contain potential pathogens. This study highlights the versatility of metagenomics in monitoring and diagnosing the impacts of human disturbance on the environmental health of marine ecosystems from eDNA.
Molecular and Microbial Mechanisms Increasing Soil C Storage Under Future Rates of Anthropogenic N Deposition

Energy Technology Data Exchange (ETDEWEB)

Zak, Donald R. [Univ. of Michigan, Ann Arbor, MI (United States)

2017-11-17

A growing body of evidence reveals that anthropogenic N deposition can reduce the microbial decay of plant detritus and increase soil C storage across a wide range of terrestrial ecosystems. This aspect of global change has the potential to constrain the accumulation of anthropogenic CO₂ in the Earth’s atmosphere, and hence slow the pace of climate warming. The molecular and microbial mechanisms underlying this biogeochemical response are not understood, and they are not a component of any coupled climate-biogeochemical model estimating ecosystem C storage, and hence, the future climate of an N-enriched Earth. Here, we report the use of genomic-enabled approaches to identify the molecular underpinnings of the microbial mechanisms leading to greater soil C storage in response to anthropogenic N deposition, thereby enabling us to better anticipate changes in soil C storage.
Extensive Management Promotes Plant and Microbial Nitrogen Retention in Temperate Grassland

Science.gov (United States)

de Vries, Franciska T.; Bloem, Jaap; Quirk, Helen; Stevens, Carly J.; Bol, Roland; Bardgett, Richard D.

2012-01-01

Leaching losses of nitrogen (N) from soil and atmospheric N deposition have led to widespread changes in plant community and microbial community composition, but our knowledge of the factors that determine ecosystem N retention is limited. A common feature of extensively managed, species-rich grasslands is that they have fungal-dominated microbial communities, which might reduce soil N losses and increase ecosystem N retention, which is pivotal for pollution mitigation and sustainable food production. However, the mechanisms that underpin improved N retention in extensively managed, species-rich grasslands are unclear. We combined a landscape-scale field study and glasshouse experiment to test how grassland management affects plant and soil N retention. Specifically, we hypothesised that extensively managed, species-rich grasslands of high conservation value would have lower N loss and greater N retention than intensively managed, species-poor grasslands, and that this would be due to a greater immobilisation of N by a more fungal-dominated microbial community. In the field study, we found that extensively managed, species-rich grasslands had lower N leaching losses. Soil inorganic N availability decreased with increasing abundance of fungi relative to bacteria, although the best predictor of soil N leaching was the C/N ratio of aboveground plant biomass. In the associated glasshouse experiment we found that retention of added 15N was greater in extensively than in intensively managed grasslands, which was attributed to a combination of greater root uptake and microbial immobilisation of 15N in the former, and that microbial immobilisation increased with increasing biomass and abundance of fungi. These findings show that grassland management affects mechanisms of N retention in soil through changes in root and microbial uptake of N. Moreover, they support the notion that microbial communities might be the key to improved N retention through tightening linkages
Adverse effects of lindane in a maize agro-ecosystem in Uganda

International Nuclear Information System (INIS)

Tukarhirwa, E.M.; Tinzaara, W.; Kiremire, B.T.

1997-01-01

The impact of lindane, at commercial rates of application, on invertebrate fauna, soil microbial activity, earthworm populations, crop damage and yields in a maize agro-ecosystem was studied and compared with unsprayed control plots of maize using a pitfall trap, D-Vac suction, litter bag, the earthworm formalin expulsion and crop assessment methods. The findings of the study generally portrayed lindane as having very few effects on the maize agro-ecosystem. (author). 5 refs, 9 tabs
Changing composition of microbial communities indicates seepage fluid difference of the Thuwal Seeps in the Red Sea

KAUST Repository

Yang, Bo

2015-06-10

© Springer International Publishing Switzerland 2015. Cold seeps are unique ecosystems that are generally characterized by high salinity and reducing solutions. Seepage fluid, the major water influx of this system, contains hypersaline water, sediment pore water, and other components. The Thuwal cold seeps were recently discovered on the continental margin of the Red Sea. Using 16S rRNA gene pyro-sequencing technology, microbial communities were investigated by comparing samples collected in 2011 and 2013. The results revealed differences in the microbial communities between the two sampling times. In particular, a significantly higher abundance of Marine Group I (MGI) Thaumarchaeota was coupled with lower salinity in 2013. In the brine pool, the dominance of Desulfobacterales in 2011 was supplanted byMGI Thaumarchaeota in 2013, perhaps due to a reduced supply of hydrogen sulfide from the seepage fluid. Collectively, this study revealed a difference in water components in this ecosystem between two sampling times. The results indicated that the seawater in this cold seep displayed a greater number of characteristics of normal seawater in 2013 than in 2011, which might represent the dominant driving force for changes in microbial community structures. This is the first study to provide a temporal comparison of the microbial biodiversity of a cold seep ecosystem in the Red Sea.
Changing composition of microbial communities indicates seepage fluid difference of the Thuwal Seeps in the Red Sea

KAUST Repository

Yang, Bo; Zhang, Weipeng; Tian, Renmao; Wang, Yong; Qian, Pei-Yuan

2015-01-01

© Springer International Publishing Switzerland 2015. Cold seeps are unique ecosystems that are generally characterized by high salinity and reducing solutions. Seepage fluid, the major water influx of this system, contains hypersaline water, sediment pore water, and other components. The Thuwal cold seeps were recently discovered on the continental margin of the Red Sea. Using 16S rRNA gene pyro-sequencing technology, microbial communities were investigated by comparing samples collected in 2011 and 2013. The results revealed differences in the microbial communities between the two sampling times. In particular, a significantly higher abundance of Marine Group I (MGI) Thaumarchaeota was coupled with lower salinity in 2013. In the brine pool, the dominance of Desulfobacterales in 2011 was supplanted byMGI Thaumarchaeota in 2013, perhaps due to a reduced supply of hydrogen sulfide from the seepage fluid. Collectively, this study revealed a difference in water components in this ecosystem between two sampling times. The results indicated that the seawater in this cold seep displayed a greater number of characteristics of normal seawater in 2013 than in 2011, which might represent the dominant driving force for changes in microbial community structures. This is the first study to provide a temporal comparison of the microbial biodiversity of a cold seep ecosystem in the Red Sea.
Exposure to dairy manure leads to greater antibiotic resistance and increased mass-specific respiration in soil microbial communities

Science.gov (United States)

Avera, Bethany; Badgley, Brian; Barrett, John E.; Franklin, Josh; Knowlton, Katharine F.; Ray, Partha P.; Smitherman, Crystal

2017-01-01

Intensifying livestock production to meet the demands of a growing global population coincides with increases in both the administration of veterinary antibiotics and manure inputs to soils. These trends have the potential to increase antibiotic resistance in soil microbial communities. The effect of maintaining increased antibiotic resistance on soil microbial communities and the ecosystem processes they regulate is unknown. We compare soil microbial communities from paired reference and dairy manure-exposed sites across the USA. Given that manure exposure has been shown to elicit increased antibiotic resistance in soil microbial communities, we expect that manure-exposed sites will exhibit (i) compositionally different soil microbial communities, with shifts toward taxa known to exhibit resistance; (ii) greater abundance of antibiotic resistance genes; and (iii) corresponding maintenance of antibiotic resistance would lead to decreased microbial efficiency. We found that bacterial and fungal communities differed between reference and manure-exposed sites. Additionally, the β-lactam resistance gene ampC was 5.2-fold greater under manure exposure, potentially due to the use of cephalosporin antibiotics in dairy herds. Finally, ampC abundance was positively correlated with indicators of microbial stress, and microbial mass-specific respiration, which increased 2.1-fold under manure exposure. These findings demonstrate that the maintenance of antibiotic resistance associated with manure inputs alters soil microbial communities and ecosystem function. PMID:28356447
Exposure to dairy manure leads to greater antibiotic resistance and increased mass-specific respiration in soil microbial communities.

Science.gov (United States)

Wepking, Carl; Avera, Bethany; Badgley, Brian; Barrett, John E; Franklin, Josh; Knowlton, Katharine F; Ray, Partha P; Smitherman, Crystal; Strickland, Michael S

2017-03-29

Intensifying livestock production to meet the demands of a growing global population coincides with increases in both the administration of veterinary antibiotics and manure inputs to soils. These trends have the potential to increase antibiotic resistance in soil microbial communities. The effect of maintaining increased antibiotic resistance on soil microbial communities and the ecosystem processes they regulate is unknown. We compare soil microbial communities from paired reference and dairy manure-exposed sites across the USA. Given that manure exposure has been shown to elicit increased antibiotic resistance in soil microbial communities, we expect that manure-exposed sites will exhibit (i) compositionally different soil microbial communities, with shifts toward taxa known to exhibit resistance; (ii) greater abundance of antibiotic resistance genes; and (iii) corresponding maintenance of antibiotic resistance would lead to decreased microbial efficiency. We found that bacterial and fungal communities differed between reference and manure-exposed sites. Additionally, the β-lactam resistance gene ampC was 5.2-fold greater under manure exposure, potentially due to the use of cephalosporin antibiotics in dairy herds. Finally, ampC abundance was positively correlated with indicators of microbial stress, and microbial mass-specific respiration, which increased 2.1-fold under manure exposure. These findings demonstrate that the maintenance of antibiotic resistance associated with manure inputs alters soil microbial communities and ecosystem function. © 2017 The Author(s).
Subsurface microbial habitats on Mars

Science.gov (United States)

Boston, P. J.; Mckay, C. P.

1991-01-01

We developed scenarios for shallow and deep subsurface cryptic niches for microbial life on Mars. Such habitats could have considerably prolonged the persistence of life on Mars as surface conditions became increasingly inhospitable. The scenarios rely on geothermal hot spots existing below the near or deep subsurface of Mars. Recent advances in the comparatively new field of deep subsurface microbiology have revealed previously unsuspected rich aerobic and anaerobic microbal communities far below the surface of the Earth. Such habitats, protected from the grim surface conditions on Mars, could receive warmth from below and maintain water in its liquid state. In addition, geothermally or volcanically reduced gases percolating from below through a microbiologically active zone could provide the reducing power needed for a closed or semi-closed microbial ecosystem to thrive.
Impacts of chemical gradients on microbial community structure

DEFF Research Database (Denmark)

Chen, Jianwei; Hanke, Anna; Tegetmeyer, Halina E

2017-01-01

Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the 'redox ...... Journal advance online publication, 17 January 2017; doi:10.1038/ismej.2016.175....

Mangrove microbial diversity and the impact of trophic contamination.

Science.gov (United States)

Bouchez, Agnès; Pascault, Noémie; Chardon, Cècile; Bouvy, Marc; Cecchi, Philippe; Lambs, Luc; Herteman, Mélanie; Fromard, François; Got, Patrice; Leboulanger, Christophe

2013-01-15

Mangroves are threatened ecosystems that provide numerous ecosystem services, especially through their wide biodiversity, and their bioremediation capacity is a challenging question in tropical areas. In a mangrove in Mayotte, we studied the potential role of microbial biofilm communities in removing nutrient loads from pre-treated wastewater. Microbial community samples were collected from tree roots, sediments, water, and from a colonization device, and their structure and dynamics were compared in two areas: one exposed to sewage and the other not. The samples from the colonization devices accurately reflected the natural communities in terms of diversity. Communities in the zone exposed to sewage were characterized by more green algae and diatoms, higher bacteria densities, as well as different compositions. In the area exposed to sewage, the higher cell densities associated with specific diversity patterns highlighted adapted communities that may play a significant role in the fate of nutrients. Copyright © 2012 Elsevier Ltd. All rights reserved.
Cell-free protein synthesis enabled rapid prototyping for metabolic engineering and synthetic biology

Directory of Open Access Journals (Sweden)

Lihong Jiang

2018-06-01

Full Text Available Advances in metabolic engineering and synthetic biology have facilitated the manufacturing of many valuable-added compounds and commodity chemicals using microbial cell factories in the past decade. However, due to complexity of cellular metabolism, the optimization of metabolic pathways for maximal production represents a grand challenge and an unavoidable barrier for metabolic engineering. Recently, cell-free protein synthesis system (CFPS has been emerging as an enabling alternative to address challenges in biomanufacturing. This review summarizes the recent progresses of CFPS in rapid prototyping of biosynthetic pathways and genetic circuits (biosensors to speed up design-build-test (DBT cycles of metabolic engineering and synthetic biology. Keywords: Cell-free protein synthesis, Metabolic pathway optimization, Genetic circuits, Metabolic engineering, Synthetic biology
Ecological effects of ionizing radiation on population and ecosystem: a computational model ecosystem study

International Nuclear Information System (INIS)

Doi, Masahiro; Fuma, Shoichi; Ishii, Nobuyuki; Sakashita, Tetsuya; Miyamoto, Kiriko; Takeda, Hiroshi; Kawabata, Zenichiro

2003-01-01

Ecosystem is a self-sustaining system of complexity, and their responses to the impacts are synergistic and subjected to the demographic stochasticity of the species, environmental stochasticity and randomness. Environmental fate and effects of radiation has ranged from observable DNA damage of the cell to the fare on tissues, individual, population, community and ecosystems. The quantitative, systematic individual-based model, SIM-COSM was developed to simulate impacts of radiation exposure and other toxicants on an aquatic microbial ecosystem (microcosm). The microcosm consists of heterotroph ciliate protozoa (Tetrahymena thermophila B) as a consumer, autotroph flagellate algae (Euglena gracilis Z) as a producer and saprotroph bacteria (Escherichia coli DH5) as a decomposer. The symbiosis among microbes is self-organized by realizing material cycle and sustained for more than 2 years after inoculation. The system can not afford to lose any one of the microbes to maintain its sustainability. Experimental ecotoxicological tests for (a) gamma radiation, (b) Manganese ions and (c) Gadolinium are summarized. Population dynamics of microbes in Microcosm and its computer simulations by SIM-COSM are shown together in a figure. Population dynamics in Microcosm and SIM-COSM exposed to 500 Gy of gamma-radiation at 50 days after inoculation are shown also in a figure. To take the effects on the interactions between species and environment into account, one option is to put the ecotoxicity tests as experimental micro ecosystem study and theoretical model ecosystem analysis. (M. Suetake)
Earth's Earliest Ecosystems in the Classroom: The Use of Microbial Mats to Teach General Principles in Microbial Ecology, and Scientific Inquiry

Science.gov (United States)

Beboutl, Brad M.; Bucaria, Robin

2004-01-01

Microbial mats are living examples of the most ancient biological communities on earth, and may also be useful models for the search for life elsewhere. They are centrally important to Astrobiology. In this lecture, we will present an introduction to microbial mats, as well as an introduction to our web-based educational module on the subject of microbial ecology, featuring living mats maintained in a mini "Web Lab" complete with remotely-operable instrumentation. We have partnered with a number of outreach specialists in order to produce an informative and educational web-based presentation, aspects of which will be exported to museum exhibits reaching a wide audience. On our web site, we will conduct regularly scheduled experimental manipulations, linking the experiments to our research activities, and demonstrating fundamental principles of scientific research.
Effects of Plant Functional Group Loss on Soil Microbial Community and Litter Decomposition in a Steppe Vegetation.

Science.gov (United States)

Xiao, Chunwang; Zhou, Yong; Su, Jiaqi; Yang, Fan

2017-01-01

Globally, many terrestrial ecosystems are experiencing a rapid loss of biodiversity. Continued improvements in our understanding of interrelationships between plant diversity and soil microbes are critical to address the concern over the consequences of the decline in biodiversity on ecosystem functioning and services. By removing forbs, or grasses, or, to an extreme scenario, both forbs and grasses in a steppe vegetation in Inner Mongolia, we studied how plant functional group (PFG) loss affects soil microbial community composition using phospholipid fatty acid analysis (PLFA) and litter decomposition using a litter-bag method. PFG loss significantly decreased above- and below-ground plant biomass, soil microbial biomass carbon (SMBC) and nitrogen (SMBN), but had no effect on the ratio of SMBC to SMBN. Although the ratio of fungal to bacterial PLFAs remained unaffected, PFG loss significantly reduced the amount of bacterial, fungal, and total PLFAs. PFG loss decreased litter monthly mass loss and decay constant, and such decrease was significant when both forbs and grasses were removed. Our results provide robust evidence that PFG loss in grassland ecosystem can lead to a rapid response of soil microbial activity which may affect litter decomposition and soil nutrient cycling, suggesting that the assessment of plant-microbe interactions in soils is an integral component of ecosystem response to biodiversity loss.
Initial shifts in nitrogen impact on ecosystem carbon fluxes in an alpine meadow: patterns and causes

Directory of Open Access Journals (Sweden)

B. Song

2017-09-01

Full Text Available Increases in nitrogen (N deposition can greatly stimulate ecosystem net carbon (C sequestration through positive N-induced effects on plant productivity. However, how net ecosystem CO2 exchange (NEE and its components respond to different N addition rates remains unclear. Using an N addition gradient experiment (six levels: 0, 2, 4, 8, 16, 32 gN m−2 yr−1 in an alpine meadow on the Qinghai–Tibetan Plateau, we explored the responses of different ecosystem C fluxes to an N addition gradient and revealed mechanisms underlying the dynamic responses. Results showed that NEE, ecosystem respiration (ER, and gross ecosystem production (GEP all increased linearly with N addition rates in the first year of treatment but shifted to N saturation responses in the second year with the highest NEE (−7.77 ± 0.48 µmol m−2 s−1 occurring under an N addition rate of 8 gN m−2 yr−1. The saturation responses of NEE and GEP were caused by N-induced accumulation of standing litter, which limited light availability for plant growth under high N addition. The saturation response of ER was mainly due to an N-induced saturation response of aboveground plant respiration and decreasing soil microbial respiration along the N addition gradient, while decreases in soil microbial respiration under high N addition were caused by N-induced reductions in soil pH. We also found that various components of ER, including aboveground plant respiration, soil respiration, root respiration, and microbial respiration, responded differentially to the N addition gradient. These results reveal temporal dynamics of N impacts and the rapid shift in ecosystem C fluxes from N limitation to N saturation. Our findings bring evidence of short-term initial shifts in responses of ecosystem C fluxes to increases in N deposition, which should be considered when predicting long-term changes in ecosystem net C sequestration.
Spatial heterogeneity of physicochemical properties explains differences in microbial composition in arid soils from Cuatro Cienegas, Mexico

Directory of Open Access Journals (Sweden)

Silvia Pajares

2016-09-01

Full Text Available Arid ecosystems are characterized by high spatial heterogeneity, and the variation among vegetation patches is a clear example. Soil biotic and abiotic factors associated with these patches have also been well documented as highly heterogeneous in space. Given the low vegetation cover and little precipitation in arid ecosystems, soil microorganisms are the main drivers of nutrient cycling. Nonetheless, little is known about the spatial distribution of microorganisms and the relationship that their diversity holds with nutrients and other physicochemical gradients in arid soils. In this study, we evaluated the spatial variability of soil microbial diversity and chemical parameters (nutrients and ion content at local scale (meters occurring in a gypsum-based desert soil, to gain knowledge on what soil abiotic factors control the distribution of microbes in arid ecosystems. We analyzed 32 soil samples within a 64 m2 plot and: (a characterized microbial diversity using T-RFLPs of the bacterial 16S rRNA gene, (b determined soil chemical parameters, and (c identified relationships between microbial diversity and chemical properties. Overall, we found a strong correlation between microbial composition heterogeneity and spatial variation of cations (Ca2, K+ and anions (HCO ${}_{3}^{-}$ 3 − , Cl−, SO ${}_{4}^{2-}$ 4 2 − content in this small plot. Our results could be attributable to spatial differences of soil saline content, favoring the patchy emergence of salt and soil microbial communities.
Metagenomes from two microbial consortia associated with Santa Barbara seep oil.

Science.gov (United States)

Hawley, Erik R; Malfatti, Stephanie A; Pagani, Ioanna; Huntemann, Marcel; Chen, Amy; Foster, Brian; Copeland, Alexander; del Rio, Tijana Glavina; Pati, Amrita; Jansson, Janet R; Gilbert, Jack A; Tringe, Susannah Green; Lorenson, Thomas D; Hess, Matthias

2014-12-01

The metagenomes from two microbial consortia associated with natural oils seeping into the Pacific Ocean offshore the coast of Santa Barbara (California, USA) were determined to complement already existing metagenomes generated from microbial communities associated with hydrocarbons that pollute the marine ecosystem. This genomics resource article is the first of two publications reporting a total of four new metagenomes from oils that seep into the Santa Barbara Channel. Copyright © 2014 Elsevier B.V. All rights reserved.
Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere.

Science.gov (United States)

Berg, Gabriele; Smalla, Kornelia

2009-04-01

The rhizosphere is of central importance not only for plant nutrition, health and quality but also for microorganism-driven carbon sequestration, ecosystem functioning and nutrient cycling in terrestrial ecosystems. A multitude of biotic and abiotic factors are assumed to influence the structural and functional diversity of microbial communities in the rhizosphere. In this review, recent studies on the influence of the two factors, plant species and soil type, on rhizosphere-associated microbial communities are discussed. Root exudates and the response of microorganisms to the latter as well as to root morphology were shown to shape rhizosphere microbial communities. All studies revealed that soil is the main reservoir for rhizosphere microorganisms. Many secrets of microbial life in the rhizosphere were recently uncovered due to the enormous progress in molecular and microscopic tools. Physiological and molecular data on the factors that drive selection processes in the rhizosphere are presented here. Furthermore, implications for agriculture, nature conservation and biotechnology will also be discussed.
Investigations of the microbial transformation of cortisol to prednisolone in urine samples.

Science.gov (United States)

Bredehöft, Michael; Baginski, Rainer; Parr, Maria-Kristina; Thevis, Mario; Schänzer, Wilhelm

2012-03-01

Doping control samples are normally collected under non-sterile conditions and sometimes, storage and transportation are influenced by parameters such as the temperature. Therefore, microbial contamination and subsequent alteration of a sample's composition are possible. Studies regarding sample collection in cattle breeding have already shown enzymatic transformation of endogenous testosterone to boldenone causing false-positive findings. The aim of the present study was to investigate whether positive doping cases with the synthetic corticosteroids prednisolone and prednisone may result from microbial transformation of the endogenous corticosteroids cortisol and cortisone, respectively. A method comprising parameters such as pH values and screening results for synthetic glucocorticosteroids as well as incubation experiments followed by liquid chromatographic and mass spectrometric analysis was employed to test for contaminating germs with Δ(1)-dehydrogenase activity. Over 700 urine samples comprising inpatient and doping control specimens were investigated. In none of them, 1,2-dehydrogenating activity was confirmed. These findings are in accordance with other studies. However, the problem of microbial alteration of doping control specimens with special respect to 1,2-dehydrogenation must not be underestimated. Article from a special issue on steroids and microorganisms. Copyright Â© 2010 Elsevier Ltd. All rights reserved.
Ecosystem Warming Affects CO2 Flux in an Agricultural Soil

Science.gov (United States)

Global warming seems likely based on present-day climate predictions. Our objective was to characterize and quantify the interactive effects of ecosystem warming (i.e., canopy temperature, TS), soil moisture content ('S) and microbial biomass (BM: bacteria, fungi) on the intra-row soil CO2 flux (FS)...
Impact of Wildfire on Microbial Biomass in Critical Zone Observatory

Science.gov (United States)

Murphy, M. A.; Fairbanks, D.; Chorover, J.; Gallery, R. E.; Rich, V. I.

2014-12-01

The recovery of the critical zone following disturbances such as wildfire is not fully understood. Wildfires have increased in size and intensity in western US forests in recent years and these fires influence soil microbial communities, both in composition and overall biomass. Studies have typically shown a 50% post-fire decline in overall microbial biomass (µg per g soil) that can persist for years. There is however, some variability in the severity of biomass decline, and its relationship with burn severity and landscape position have not yet been studied. Since microbial biomass has a cascade of impacts in soil systems, from helping control the rate and diversity the biogeochemical processes occurring, to promoting soil fertility, to impacting the nature and structure of soil carbon (C), fire's lasting impact on it is one mechanistic determinant of the overall post-fire recovery of impacted ecosystems. Additionally, microbial biomass measurements hold potential for testing and incorporation into land surface models (NoahMP, CLM, etc.) in order to improve estimates of long-term effects of climate change and disturbances such as fire on the C cycle. In order to refine our understanding of the impact of fire on microbial biomass and then relate that to biogeochemical processes and ecosystem recovery, we used chloroform fumigation extraction to quantify total microbial biomass C (Cmic ). One year after the June 2013 Thompson Ridge fire in the Jemez River Basin Critical Zone Observatory, we are measuring the Cmic of 22 sites across a gradient of burn severities and 4 control unburned sites, from six depth intervals at each site (0-2, 2-5, 5-10, 10-20, 20-30, and 30-40 cm). We hypothesize that the decrease in microbial biomass in burned sites relative to control sites will correlate with changes in soil biogeochemistry related to burn severity; and that the extent of the impact on biomass will be inversely related to depth in the soil column. Additionally, as the
Termite hindguts and the ecology of microbial communities in the sequencing age.

Science.gov (United States)

Tai, Vera; Keeling, Patrick J

2013-01-01

Advances in high-throughput nucleic acid sequencing have improved our understanding of microbial communities in a number of ways. Deeper sequence coverage provides the means to assess diversity at the resolution necessary to recover ecological and biogeographic patterns, and at the same time single-cell genomics provides detailed information about the interactions between members of a microbial community. Given the vastness and complexity of microbial ecosystems, such analyses remain challenging for most environments, so greater insight can also be drawn from analysing less dynamic ecosystems. Here, we outline the advantages of one such environment, the wood-digesting hindgut communities of termites and cockroaches, and how it is a model to examine and compare both protist and bacterial communities. Beyond the analysis of diversity, our understanding of protist community ecology will depend on using statistically sound sampling regimes at biologically relevant scales, transitioning from discovery-based to experimental ecology, incorporating single-cell microbiology and other data sources, and continued development of analytical tools. © 2013 The Author(s) Journal of Eukaryotic Microbiology © 2013 International Society of Protistologists.
Nutrients and temperature additively increase stream microbial respiration

Science.gov (United States)

David W. P. Manning; Amy D. Rosemond; Vladislav Gulis; Jonathan P. Benstead; John S. Kominoski

2017-01-01

Rising temperatures and nutrient enrichment are coâoccurring globalâchange drivers that stimulate microbial respiration of detrital carbon, but nutrient effects on the temperature dependence of respiration in aquatic ecosystems remain uncertain. We measured respiration rates associated with leaf litter, wood, and fine benthic organic matter (FBOM) across...
Microbial fuel cell: A green technology

International Nuclear Information System (INIS)

Jong Bor Chyan; Liew Pauline Woan Ying; Muhamad Lebai Juri; Ahmad Zainuri Mohd Dzomir; Leo Kwee Wah; Mat Rasol Awang

2010-01-01

Microbial Fuel Cell (MFC) was developed which was able to generate bio energy continuously while consuming wastewater containing organic matters. Even though the bio energy generated is not as high as hydrogen fuel cell, the MFC demonstrated great potential in bio-treating wastewater while using it as fuel source. Thus far, the dual-ability of the MFC to generate bio energy and bio-treating organic wastewater has been examined successfully using synthetic acetate and POME wastewaters. (author)
The life sulfuric: microbial ecology of sulfur cycling in marine sediments.

Science.gov (United States)

Wasmund, Kenneth; Mußmann, Marc; Loy, Alexander

2017-08-01

Almost the entire seafloor is covered with sediments that can be more than 10 000 m thick and represent a vast microbial ecosystem that is a major component of Earth's element and energy cycles. Notably, a significant proportion of microbial life in marine sediments can exploit energy conserved during transformations of sulfur compounds among different redox states. Sulfur cycling, which is primarily driven by sulfate reduction, is tightly interwoven with other important element cycles (carbon, nitrogen, iron, manganese) and therefore has profound implications for both cellular- and ecosystem-level processes. Sulfur-transforming microorganisms have evolved diverse genetic, metabolic, and in some cases, peculiar phenotypic features to fill an array of ecological niches in marine sediments. Here, we review recent and selected findings on the microbial guilds that are involved in the transformation of different sulfur compounds in marine sediments and emphasise how these are interlinked and have a major influence on ecology and biogeochemistry in the seafloor. Extraordinary discoveries have increased our knowledge on microbial sulfur cycling, mainly in sulfate-rich surface sediments, yet many questions remain regarding how sulfur redox processes may sustain the deep-subsurface biosphere and the impact of organic sulfur compounds on the marine sulfur cycle. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.
Effects of uranium concentration on microbial community structure and functional potential.

Science.gov (United States)

Sutcliffe, Brodie; Chariton, Anthony A; Harford, Andrew J; Hose, Grant C; Greenfield, Paul; Elbourne, Liam D H; Oytam, Yalchin; Stephenson, Sarah; Midgley, David J; Paulsen, Ian T

2017-08-01

Located in the Northern Territory of Australia, Ranger uranium mine is directly adjacent to the UNESCO World Heritage listed Kakadu National Park, with rehabilitation targets needed to ensure the site can be incorporated into the park following the mine's closure in 2026. This study aimed to understand the impact of uranium concentration on microbial communities, in order to identify and describe potential breakpoints in microbial ecosystem services. This is the first study to report in situ deployment of uranium-spiked sediments along a concentration gradient (0-4000 mg U kg -1 ), with the study design maximising the advantages of both field surveys and laboratory manipulative studies. Changes to microbial communities were characterised through the use of amplicon and shotgun metagenomic next-generation sequencing. Significant changes to taxonomic and functional community assembly occurred at a concentration of 1500 mg U kg -1 sediment and above. At uranium concentrations of ≥ 1500 mg U kg -1 , genes associated with methanogenic consortia and processes increased in relative abundance, while numerous significant changes were also seen in the relative abundances of genes involved in nitrogen cycling. Such alterations in carbon and nitrogen cycling pathways suggest that taxonomic and functional changes to microbial communities may result in changes in ecosystem processes and resilience. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.
Metabolic engineering for the microbial production of isoprenoids: Carotenoids and isoprenoid-based biofuels

Directory of Open Access Journals (Sweden)

Fu-Xing Niu

2017-09-01

Full Text Available Isoprenoids are the most abundant and highly diverse group of natural products. Many isoprenoids have been used for pharmaceuticals, nutraceuticals, flavors, cosmetics, food additives and biofuels. Carotenoids and isoprenoid-based biofuels are two classes of important isoprenoids. These isoprenoids have been produced microbially through metabolic engineering and synthetic biology efforts. Herein, we briefly review the engineered biosynthetic pathways in well-characterized microbial systems for the production of carotenoids and several isoprenoid-based biofuels.
Microbial diversity in restored wetlands of San Francisco Bay

Energy Technology Data Exchange (ETDEWEB)

Theroux, Susanna [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; Hartman, Wyatt [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; He, Shaomei [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.; Univ. of Wisconsin, Madison, WI (United States); Tringe, Susannah [Lawrence Berkeley National Lab. (LBNL), Walnut Creek, CA (United States). Dept. of Energy Joint Genome Inst.

2013-12-09

Wetland ecosystems may serve as either a source or a sink for atmospheric carbon and greenhouse gases. This delicate carbon balance is influenced by the activity of belowground microbial communities that return carbon dioxide and methane to the atmosphere. Wetland restoration efforts in the San Francisco Bay-Delta region may help to reverse land subsidence and possibly increase carbon storage in soils. However, the effects of wetland restoration on microbial communities, which mediate soil metabolic activity and carbon cycling, are poorly studied. In an effort to better understand the underlying factors which shape the balance of carbon flux in wetland soils, we targeted the microbial communities in a suite of restored and historic wetlands in the San Francisco Bay-Delta region. Using DNA and RNA sequencing, coupled with greenhouse gas monitoring, we profiled the diversity and metabolic potential of the wetland soil microbial communities along biogeochemical and wetland age gradients. Our results show relationships among geochemical gradients, availability of electron acceptors, and microbial community composition. Our study provides the first genomic glimpse into microbial populations in natural and restored wetlands of the San Francisco Bay-Delta region and provides a valuable benchmark for future studies.
2007 Microbial Population Biology (July 22-26, 2007)

Energy Technology Data Exchange (ETDEWEB)

Anthony M. Dean

2008-04-01

Microbial Population Biology covers a diverse range of cutting edge issues in the microbial sciences and beyond. Firmly founded in evolutionary biology and with a strongly integrative approach, past meetings have covered topics ranging from the dynamics and genetics of adaptation to the evolution of mutation rate, community ecology, evolutionary genomics, altruism, and epidemiology. This meeting is never dull: some of the most significant and contentious issues in biology have been thrashed out here. We anticipate the 2007 meeting being no exception. The final form of the 2007 meeting is yet to be decided, but the following topics are likely to be included: evolutionary emergence of infectious disease and antibiotic resistance, genetic architecture and implications for the evolution of microbial populations, ageing in bacteria, biogeography, evolution of symbioses, the role of microbes in ecosystem function, and ecological genomics.

Changes in microbial community characteristics and soil organic matter with nitrogen additions in two tropical forests

Science.gov (United States)

Daniela F. Cusack; Whendee L. Silver; Margaret S. Torn; Sarah D. Burton; Mary K. Firestone

2011-01-01

Microbial communities and their associated enzyme activities affect the amount and chemical quality of carbon (C) in soils. Increasing nitrogen (N) deposition, particularly in N-rich tropical forests, is likely to change the composition and behavior of microbial communities and feed back on ecosystem structure and function. This study presents a novel assessment of...
The limnic ecosystems at Forsmark and Laxemar-Simpevarp

Energy Technology Data Exchange (ETDEWEB)

Andersson, Eva

2010-12-15

The overall objective of this report is to describe the limnic ecosystems at Forsmark and Laxemar- Simpevarp, identify important processes in a radionuclide perspective and provide a description of the radionuclide model for the biosphere used in SR-Site. The report includes a thorough description of the lakes and streams in Forsmark and Laxemar- Simpevarp and covers the following areas: catchment area characteristics, hydrology, climate, sediment characteristics, physical characteristics of streams, habitat distribution in lakes, biotic components (biomass as well as production), water chemistry, and comparison with other lakes and streams in the region, and a historical description. Ecosystem models for carbon and mass balances for a number of elements have been calculated to further improve the understanding of the lake ecosystems. Important processes for the safety assessment are described and evaluated in the report. A separate chapter is included to specifically describe how and where these processes are included in the radionuclide model. The radionuclide model is described and parameterisation and guidance to parameter calculation is provided. The last chapter of the report provides a summary of the knowledge of the limnic systems at the two areas. The Forsmark regional model area contains more than 25 permanent lakes and pools. All lakes are small and shallow, and are characterized as oligotrophic hardwater lakes. Calcareous soils in the area give rise to high calcium concentrations in the surface water, which in turn leads to high pH and low nutrient concentrations in water as phosphorus often co-precipitates with calcium. The shallow depths and moderate water colour permit photosynthesis in the entire benthic habitat of the lakes, and the bottoms are covered by dense stands of the macroalgae Chara sp. Moreover, many of the lakes also have a thick microbial mat (>10 cm), consisting of cyanobacteria and diatoms, in the benthic habitat. Fish in the lakes
The limnic ecosystems at Forsmark and Laxemar-Simpevarp

International Nuclear Information System (INIS)

Andersson, Eva

2010-12-01

The overall objective of this report is to describe the limnic ecosystems at Forsmark and Laxemar- Simpevarp, identify important processes in a radionuclide perspective and provide a description of the radionuclide model for the biosphere used in SR-Site. The report includes a thorough description of the lakes and streams in Forsmark and Laxemar- Simpevarp and covers the following areas: catchment area characteristics, hydrology, climate, sediment characteristics, physical characteristics of streams, habitat distribution in lakes, biotic components (biomass as well as production), water chemistry, and comparison with other lakes and streams in the region, and a historical description. Ecosystem models for carbon and mass balances for a number of elements have been calculated to further improve the understanding of the lake ecosystems. Important processes for the safety assessment are described and evaluated in the report. A separate chapter is included to specifically describe how and where these processes are included in the radionuclide model. The radionuclide model is described and parameterisation and guidance to parameter calculation is provided. The last chapter of the report provides a summary of the knowledge of the limnic systems at the two areas. The Forsmark regional model area contains more than 25 permanent lakes and pools. All lakes are small and shallow, and are characterized as oligotrophic hardwater lakes. Calcareous soils in the area give rise to high calcium concentrations in the surface water, which in turn leads to high pH and low nutrient concentrations in water as phosphorus often co-precipitates with calcium. The shallow depths and moderate water colour permit photosynthesis in the entire benthic habitat of the lakes, and the bottoms are covered by dense stands of the macroalgae Chara sp. Moreover, many of the lakes also have a thick microbial mat (>10 cm), consisting of cyanobacteria and diatoms, in the benthic habitat. Fish in the lakes
'One physical system': Tansley's ecosystem as Earth's critical zone.

Science.gov (United States)

Richter, Daniel deB; Billings, Sharon A

2015-05-01

Integrative concepts of the biosphere, ecosystem, biogeocenosis and, recently, Earth's critical zone embrace scientific disciplines that link matter, energy and organisms in a systems-level understanding of our remarkable planet. Here, we assert the congruence of Tansley's (1935) venerable ecosystem concept of 'one physical system' with Earth science's critical zone. Ecosystems and critical zones are congruent across spatial-temporal scales from vegetation-clad weathering profiles and hillslopes, small catchments, landscapes, river basins, continents, to Earth's whole terrestrial surface. What may be less obvious is congruence in the vertical dimension. We use ecosystem metabolism to argue that full accounting of photosynthetically fixed carbon includes respiratory CO₂ and carbonic acid that propagate to the base of the critical zone itself. Although a small fraction of respiration, the downward diffusion of CO₂ helps determine rates of soil formation and, ultimately, ecosystem evolution and resilience. Because life in the upper portions of terrestrial ecosystems significantly affects biogeochemistry throughout weathering profiles, the lower boundaries of most terrestrial ecosystems have been demarcated at depths too shallow to permit a complete understanding of ecosystem structure and function. Opportunities abound to explore connections between upper and lower components of critical-zone ecosystems, between soils and streams in watersheds, and between plant-derived CO₂ and deep microbial communities and mineral weathering. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.
Function of Wildfire-Deposited Pyrogenic Carbon in Terrestrial Ecosystems

Directory of Open Access Journals (Sweden)

Melissa R. A. Pingree

2017-08-01

Full Text Available Fire is an important driver of change in most forest, savannah, and prairie ecosystems and fire-altered organic matter, or pyrogenic carbon (PyC, conveys numerous functions in soils of fire-maintained terrestrial ecosystems. Although an exceptional number of recent review articles and books have addressed agricultural soil application of charcoal or biochar, few reviews have addressed the functional role of naturally formed PyC in fire-maintained ecosystems. Recent advances in molecular spectroscopic techniques have helped strengthen our understanding of PyC as a ubiquitous, complex material that is capable of altering soil chemical, physical, and biological properties and processes. The uniquely recalcitrant nature of PyC in soils is partly a result of its stable C = C double-bonded, graphene-like structure and C-rich, N-poor composition. This attribute allows it to persist in soils for hundreds to thousands of years and represent net ecosystem C sequestration in fire-maintained ecosystems. The rapid formation of PyC during wildfire or anthropogenic fire events short-circuits the normally tortuous pathway of recalcitrant soil C formation. Existing literature also suggests that PyC provides an essential role in the cycling of certain nutrients, greatly extending the timeframe by which fires influence soil processes and facilitating recovery in ecosystems where organic matter inputs are low and post-fire surface soil bacterial and fungal activity is reduced. The high surface area of PyC allows for the adsorption a broad spectrum of organic compounds that directly or indirectly influence microbial processes after fire events. Adsorption capacity and microsite conditions created by PyC yields a “charosphere” effect in soil with heightened microbial activity in the vicinity of PyC. In this mini-review, we explore the function of PyC in natural and semi-natural settings, provide a mechanistic approach to understanding these functions, and examine
Resilience of Soil Microbial Communities to Metals and Additional Stressors: DNA-Based Approaches for Assessing “Stress-on-Stress” Responses

NARCIS (Netherlands)

Azarbad, H.; van Gestel, C.A.M.; Niklińska, M.; Laskowski, R.; Röling, W.F.M.; van Straalen, N.M.

2016-01-01

Many microbial ecology studies have demonstrated profound changes in community composition caused by environmental pollution, as well as adaptation processes allowing survival of microbes in polluted ecosystems. Soil microbial communities in polluted areas with a long-term history of contamination
Diversity of total and functional microbiome of anammox reactors fed with complex and synthetic nitrogen-rich wastewaters

DEFF Research Database (Denmark)

Gülay, Arda; Pellicer i Nàcher, Carles; Mutlu, Ayten Gizem

diversity than the bioreactors treating synthetic wastewaters inferred from observed OTUs0.03, Chao1, Shannon index and Phylogenetic distance calculations. Differences in total microbial diversity agreed with the ecological theory concerning the positive correlation between substrate complexity...
Changes in soil microbial community structure influenced by agricultural management practices in a mediterranean agro-ecosystem.

Science.gov (United States)

García-Orenes, Fuensanta; Morugán-Coronado, Alicia; Zornoza, Raul; Cerdà, Artemi; Scow, Kate

2013-01-01

Agricultural practices have proven to be unsuitable in many cases, causing considerable reductions in soil quality. Land management practices can provide solutions to this problem and contribute to get a sustainable agriculture model. The main objective of this work was to assess the effect of different agricultural management practices on soil microbial community structure (evaluated as abundance of phospholipid fatty acids, PLFA). Five different treatments were selected, based on the most common practices used by farmers in the study area (eastern Spain): residual herbicides, tillage, tillage with oats and oats straw mulching; these agricultural practices were evaluated against an abandoned land after farming and an adjacent long term wild forest coverage. The results showed a substantial level of differentiation in the microbial community structure, in terms of management practices, which was highly associated with soil organic matter content. Addition of oats straw led to a microbial community structure closer to wild forest coverage soil, associated with increases in organic carbon, microbial biomass and fungal abundances. The microbial community composition of the abandoned agricultural soil was characterised by increases in both fungal abundances and the metabolic quotient (soil respiration per unit of microbial biomass), suggesting an increase in the stability of organic carbon. The ratio of bacteria:fungi was higher in wild forest coverage and land abandoned systems, as well as in the soil treated with oat straw. The most intensively managed soils showed higher abundances of bacteria and actinobacteria. Thus, the application of organic matter, such as oats straw, appears to be a sustainable management practice that enhances organic carbon, microbial biomass and activity and fungal abundances, thereby changing the microbial community structure to one more similar to those observed in soils under wild forest coverage.
Effects of long-term radionuclide and heavy metal contamination on the activity of microbial communities, inhabiting uranium mining impacted soils.

Science.gov (United States)

Boteva, Silvena; Radeva, Galina; Traykov, Ivan; Kenarova, Anelia

2016-03-01

Ore mining and processing have greatly altered ecosystems, often limiting their capacity to provide ecosystem services critical to our survival. The soil environments of two abandoned uranium mines were chosen to analyze the effects of long-term uranium and heavy metal contamination on soil microbial communities using dehydrogenase and phosphatase activities as indicators of metal stress. The levels of soil contamination were low, ranging from 'precaution' to 'moderate', calculated as Nemerow index. Multivariate analyses of enzyme activities revealed the following: (i) spatial pattern of microbial endpoints where the more contaminated soils had higher dehydrogenase and phosphatase activities, (ii) biological grouping of soils depended on both the level of soil contamination and management practice, (iii) significant correlations between both dehydrogenase and alkaline phosphatase activities and soil organic matter and metals (Cd, Co, Cr, and Zn, but not U), and (iv) multiple relationships between the alkaline than the acid phosphatase and the environmental factors. The results showed an evidence of microbial tolerance and adaptation to the soil contamination established during the long-term metal exposure and the key role of soil organic matter in maintaining high microbial enzyme activities and mitigating the metal toxicity. Additionally, the results suggested that the soil microbial communities are able to reduce the metal stress by intensive phosphatase synthesis, benefiting a passive environmental remediation and provision of vital ecosystem services.
Coupled cryoconite ecosystem structure-function relationships are revealed by comparing bacterial communities in alpine and Arctic glaciers

DEFF Research Database (Denmark)

Edwards, Arwyn; Mur, Luis A. J.; Girdwood, Susan E.

2014-01-01

Cryoconite holes are known as foci of microbial diversity and activity on polar glacier surfaces, but are virtually unexplored microbial habitats in alpine regions. In addition, whether cryoconite community structure reflects ecosystem functionality is poorly understood. Terminal restriction...... revealed Proteobacteria were particularly abundant, with Cyanobacteria likely acting as ecosystem engineers in both alpine and Arctic cryoconite communities. However, despite these generalities, significant differences in bacterial community structures, compositions and metabolomes are found between alpine...... fragment length polymorphism and Fourier transform infrared metabolite fingerprinting of cryoconite from glaciers in Austria, Greenland and Svalbard demonstrated cryoconite bacterial communities are closely correlated with cognate metabolite fingerprints. The influence of bacterial-associated fatty acids...
Microbial Communities: Tracing Growth Processes from Antarctic Lakes to Early Earth to Other Planets

Science.gov (United States)

Sumner, D. Y.

2014-12-01

Life in the Universe is dominated by microbes: they are numerically the most abundant cells in our bodies and in Earth's biosphere, and they are the only life that might be present elsewhere in our solar system. Life beyond our solar system could include macroscopic organisms, but everything we understand about the origin of life suggests it must start with microbes. Thus, understanding microbial ecosystems, in the absence of macroscopic organisms, is critical to understanding early life on Earth and life elsewhere in the Universe - if it exists. But what are the general principles of microbial ecology in the absence of predation? What happens when each cell is a chemical factory that can swap among metabolic processes in response to environmental and emergent cues? Geobiologists and astrobiologists are addressing these questions in diverse ways using both Earth's modern biosphere and its fossil record. Modern microbial communities in shallow, ice-covered lakes, Antarctica (Fig.), provide a model for high productivity microbial ecosystems with no to low predation. In these lakes, photosynthetic communities create macroscopic pinnacles and domes, sometime lithified into stromatolites. They provide an ecological, geochemical and morphological model for Precambrian microbial communities in low sedimentation, low current environments. Insights from these communities include new growth processes for ancient mats, especially some that grew prior to the oxidation of Earth's atmosphere. The diversity of biosignatures created in these communities also provides context for models of life under ice elsewhere in our solar system such as paleolakes on Mars and on icy moons. Results from the Mars Science Laboratory (MSL) team document formerly habitable fluvial and lacustrine environments. Lacustrine environments, in particular, are favorable for preserving biosignatures, and continued investigations by MSL will provide a deeper understanding of the duration of habitable
Microbial community responses to soil tillage and crop rotation in a corn/soybean agroecosystem.

Science.gov (United States)

Smith, Chris R; Blair, Peter L; Boyd, Charlie; Cody, Brianne; Hazel, Alexander; Hedrick, Ashley; Kathuria, Hitesh; Khurana, Parul; Kramer, Brent; Muterspaw, Kristin; Peck, Charles; Sells, Emily; Skinner, Jessica; Tegeler, Cara; Wolfe, Zoe

2016-11-01

The acreage planted in corn and soybean crops is vast, and these crops contribute substantially to the world economy. The agricultural practices employed for farming these crops have major effects on ecosystem health at a worldwide scale. The microbial communities living in agricultural soils significantly contribute to nutrient uptake and cycling and can have both positive and negative impacts on the crops growing with them. In this study, we examined the impact of the crop planted and soil tillage on nutrient levels, microbial communities, and the biochemical pathways present in the soil. We found that farming practice, that is conventional tillage versus no-till, had a much greater impact on nearly everything measured compared to the crop planted. No-till fields tended to have higher nutrient levels and distinct microbial communities. Moreover, no-till fields had more DNA sequences associated with key nitrogen cycle processes, suggesting that the microbial communities were more active in cycling nitrogen. Our results indicate that tilling of agricultural soil may magnify the degree of nutrient waste and runoff by altering nutrient cycles through changes to microbial communities. Currently, a minority of acreage is maintained without tillage despite clear benefits to soil nutrient levels, and a decrease in nutrient runoff-both of which have ecosystem-level effects and both direct and indirect effects on humans and other organisms.
mcaGUI: microbial community analysis R-Graphical User Interface (GUI).

Science.gov (United States)

Copeland, Wade K; Krishnan, Vandhana; Beck, Daniel; Settles, Matt; Foster, James A; Cho, Kyu-Chul; Day, Mitch; Hickey, Roxana; Schütte, Ursel M E; Zhou, Xia; Williams, Christopher J; Forney, Larry J; Abdo, Zaid

2012-08-15

Microbial communities have an important role in natural ecosystems and have an impact on animal and human health. Intuitive graphic and analytical tools that can facilitate the study of these communities are in short supply. This article introduces Microbial Community Analysis GUI, a graphical user interface (GUI) for the R-programming language (R Development Core Team, 2010). With this application, researchers can input aligned and clustered sequence data to create custom abundance tables and perform analyses specific to their needs. This GUI provides a flexible modular platform, expandable to include other statistical tools for microbial community analysis in the future. The mcaGUI package and source are freely available as part of Bionconductor at http://www.bioconductor.org/packages/release/bioc/html/mcaGUI.html
Metal-macrofauna interactions determine microbial community structure and function in copper contaminated sediments.

Science.gov (United States)

Mayor, Daniel J; Gray, Nia B; Elver-Evans, Joanna; Midwood, Andrew J; Thornton, Barry

2013-01-01

Copper is essential for healthy cellular functioning, but this heavy metal quickly becomes toxic when supply exceeds demand. Marine sediments receive widespread and increasing levels of copper contamination from antifouling paints owing to the 2008 global ban of organotin-based products. The toxicity of copper will increase in the coming years as seawater pH decreases and temperature increases. We used a factorial mesocosm experiment to investigate how increasing sediment copper concentrations and the presence of a cosmopolitan bioturbating amphipod, Corophium volutator, affected a range of ecosystem functions in a soft sediment microbial community. The effects of copper on benthic nutrient release, bacterial biomass, microbial community structure and the isotopic composition of individual microbial membrane [phospholipid] fatty acids (PLFAs) all differed in the presence of C. volutator. Our data consistently demonstrate that copper contamination of global waterways will have pervasive effects on the metabolic functioning of benthic communities that cannot be predicted from copper concentrations alone; impacts will depend upon the resident macrofauna and their capacity for bioturbation. This finding poses a major challenge for those attempting to manage the impacts of copper contamination on ecosystem services, e.g. carbon and nutrient cycling, across different habitats. Our work also highlights the paucity of information on the processes that result in isotopic fractionation in natural marine microbial communities. We conclude that the assimilative capacity of benthic microbes will become progressively impaired as copper concentrations increase. These effects will, to an extent, be mitigated by the presence of bioturbating animals and possibly other processes that increase the influx of oxygenated seawater into the sediments. Our findings support the move towards an ecosystem approach for environmental management.
Metal-macrofauna interactions determine microbial community structure and function in copper contaminated sediments.

Directory of Open Access Journals (Sweden)

Daniel J Mayor

Full Text Available Copper is essential for healthy cellular functioning, but this heavy metal quickly becomes toxic when supply exceeds demand. Marine sediments receive widespread and increasing levels of copper contamination from antifouling paints owing to the 2008 global ban of organotin-based products. The toxicity of copper will increase in the coming years as seawater pH decreases and temperature increases. We used a factorial mesocosm experiment to investigate how increasing sediment copper concentrations and the presence of a cosmopolitan bioturbating amphipod, Corophium volutator, affected a range of ecosystem functions in a soft sediment microbial community. The effects of copper on benthic nutrient release, bacterial biomass, microbial community structure and the isotopic composition of individual microbial membrane [phospholipid] fatty acids (PLFAs all differed in the presence of C. volutator. Our data consistently demonstrate that copper contamination of global waterways will have pervasive effects on the metabolic functioning of benthic communities that cannot be predicted from copper concentrations alone; impacts will depend upon the resident macrofauna and their capacity for bioturbation. This finding poses a major challenge for those attempting to manage the impacts of copper contamination on ecosystem services, e.g. carbon and nutrient cycling, across different habitats. Our work also highlights the paucity of information on the processes that result in isotopic fractionation in natural marine microbial communities. We conclude that the assimilative capacity of benthic microbes will become progressively impaired as copper concentrations increase. These effects will, to an extent, be mitigated by the presence of bioturbating animals and possibly other processes that increase the influx of oxygenated seawater into the sediments. Our findings support the move towards an ecosystem approach for environmental management.
Synthetic alienation of microbial organisms by using genetic code engineering: Why and how?

Science.gov (United States)

Kubyshkin, Vladimir; Budisa, Nediljko

2017-08-01

The main goal of synthetic biology (SB) is the creation of biodiversity applicable for biotechnological needs, while xenobiology (XB) aims to expand the framework of natural chemistries with the non-natural building blocks in living cells to accomplish artificial biodiversity. Protein and proteome engineering, which overcome limitation of the canonical amino acid repertoire of 20 (+2) prescribed by the genetic code by using non-canonic amino acids (ncAAs), is one of the main focuses of XB research. Ideally, estranging the genetic code from its current form via systematic introduction of ncAAs should enable the development of bio-containment mechanisms in synthetic cells potentially endowing them with a "genetic firewall" i.e. orthogonality which prevents genetic information transfer to natural systems. Despite rapid progress over the past two decades, it is not yet possible to completely alienate an organism that would use and maintain different genetic code associations permanently. In order to engineer robust bio-contained life forms, the chemical logic behind the amino acid repertoire establishment should be considered. Starting from recent proposal of Hartman and Smith about the genetic code establishment in the RNA world, here the authors mapped possible biotechnological invasion points for engineering of bio-contained synthetic cells equipped with non-canonical functionalities. Copyright © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Resolution of habitat-associated ecogenomic signatures in bacteriophage genomes and application to microbial source tracking.

Science.gov (United States)

Ogilvie, Lesley A; Nzakizwanayo, Jonathan; Guppy, Fergus M; Dedi, Cinzia; Diston, David; Taylor, Huw; Ebdon, James; Jones, Brian V

2018-04-01

Just as the expansion in genome sequencing has revealed and permitted the exploitation of phylogenetic signals embedded in bacterial genomes, the application of metagenomics has begun to provide similar insights at the ecosystem level for microbial communities. However, little is known regarding this aspect of bacteriophage associated with microbial ecosystems, and if phage encode discernible habitat-associated signals diagnostic of underlying microbiomes. Here we demonstrate that individual phage can encode clear habitat-related 'ecogenomic signatures', based on relative representation of phage-encoded gene homologues in metagenomic data sets. Furthermore, we show the ecogenomic signature encoded by the gut-associated ɸB124-14 can be used to segregate metagenomes according to environmental origin, and distinguish 'contaminated' environmental metagenomes (subject to simulated in silico human faecal pollution) from uncontaminated data sets. This indicates phage-encoded ecological signals likely possess sufficient discriminatory power for use in biotechnological applications, such as development of microbial source tracking tools for monitoring water quality.
Cyanobacteria in Coral Reef Ecosystems: A Review

Directory of Open Access Journals (Sweden)

L. Charpy

2012-01-01

Full Text Available Cyanobacteria have dominated marine environments and have been reef builders on Earth for more than three million years (myr. Cyanobacteria still play an essential role in modern coral reef ecosystems by forming a major component of epiphytic, epilithic, and endolithic communities as well as of microbial mats. Cyanobacteria are grazed by reef organisms and also provide nitrogen to the coral reef ecosystems through nitrogen fixation. Recently, new unicellular cyanobacteria that express nitrogenase were found in the open ocean and in coral reef lagoons. Furthermore, cyanobacteria are important in calcification and decalcification. All limestone surfaces have a layer of boring algae in which cyanobacteria often play a dominant role. Cyanobacterial symbioses are abundant in coral reefs; the most common hosts are sponges and ascidians. Cyanobacteria use tactics beyond space occupation to inhibit coral recruitment. Cyanobacteria can also form pathogenic microbial consortia in association with other microbes on living coral tissues, causing coral tissue lysis and death, and considerable declines in coral reefs. In deep lagoons, coccoid cyanobacteria are abundant and are grazed by ciliates, heteroflagellates, and the benthic coral reef community. Cyanobacteria produce metabolites that act as attractants for some species and deterrents for some grazers of the reef communities.
Evaluation of soil microbial communities as influenced by crude oil ...

African Journals Online (AJOL)

Impact of petroleum pollution in a vulnerable Niger Delta ecosystem was investigated to assess interactions in a first-generation phytoremediation site of a crude oil freshly-spilled agricultural soil. Community-level approach for assessing patterns of sole carbon-source utilization by mixed microbial samples was employed to ...
Microbial liquefaction of peat for the production of synthetic fuels

Energy Technology Data Exchange (ETDEWEB)

Gunasekaran, M.

1988-01-01

Objectives of this study were: to evaluate the potential of using various microorganisms to hydrolyse and liquify peat; to determine the optimal conditions for peat hydrolysis and liquefaction; to study the co-metabolizable substances; to separate the compounds present in liquified peat by alumina and silica acid chromatography and capillary gas chromatography; and to identify the compounds in liquified peat by capillary GC-Mass spectrometry. Organisms used in the study include: Coprinus comatus, Coriolus hirsutus, Ganoderma lucidum, Lentinus edodes, Lenzites trabea, Phanerochaete chrysosporium, Pleurotus ostreatus, P. sapidus, Polyporus adjustus, Neurospora sitophila, Rhizophus arrhizus, Bacillus subtilis, Acinetobacter sp. and Alcaligenes sp. The fungi were maintained and cultivated in potato dextrose agar at 30 C. The bacteria were maintained in nutrient agar at 30 C. We have also initiated work on coal solubilization in addition to the studies on peat liquefaction. A relatively new substratum or semi-solid base for culture media called Pluronic F-127, or Polyol (BASF, New Jersey). Objectives of this study were: (1) to study the growth patterns of Candida ML 13 on pluronic as substratum; (2) to determine the rate of microbial coal solubilization on pluronic F-127 amended in different growth media; (3) to separate the mycelial mat of Candida ML 13 from unsolubilized coal particles and solubilized coal products from pluronic F-127; (4) to determine the effects of pH on microbial coal solubilization in pluronic F-127 media; (5) the effect of concentration of pluronic F-127 in media on coal solubilization; and, (6) to study the role of extracellular factors secreted by Candida ML 13 on coal solubilization in pluronic F-127 media. Results are discussed. 4 refs.

Diversity and distribution of autotrophic microbial community along environmental gradients in grassland soils on the Tibetan Plateau.

Science.gov (United States)

Guo, Guangxia; Kong, Weidong; Liu, Jinbo; Zhao, Jingxue; Du, Haodong; Zhang, Xianzhou; Xia, Pinhua

2015-10-01

Soil microbial autotrophs play a significant role in CO2 fixation in terrestrial ecosystem, particularly in vegetation-constrained ecosystems with environmental stresses, such as the Tibetan Plateau characterized by low temperature and high UV. However, soil microbial autotrophic communities and their driving factors remain less appreciated. We investigated the structure and shift of microbial autotrophic communities and their driving factors along an elevation gradient (4400-5100 m above sea level) in alpine grassland soils on the Tibetan Plateau. The autotrophic microbial communities were characterized by quantitative PCR, terminal restriction fragment length polymorphism (T-RFLP), and cloning/sequencing of cbbL genes, encoding the large subunit for the CO2 fixation protein ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO). High cbbL gene abundance and high RubisCO enzyme activity were observed and both significantly increased with increasing elevations. Path analysis identified that soil RubisCO enzyme causally originated from microbial autotrophs, and its activity was indirectly driven by soil water content, temperature, and NH4 (+) content. Soil autotrophic microbial community structure dramatically shifted along the elevation and was jointly driven by soil temperature, water content, nutrients, and plant types. The autotrophic microbial communities were dominated by bacterial autotrophs, which were affiliated with Rhizobiales, Burkholderiales, and Actinomycetales. These autotrophs have been well documented to degrade organic matters; thus, metabolic versatility could be a key strategy for microbial autotrophs to survive in the harsh environments. Our results demonstrated high abundance of microbial autotrophs and high CO2 fixation potential in alpine grassland soils and provided a novel model to identify dominant drivers of soil microbial communities and their ecological functions.
Microbial nitrogen cycling in Arctic snowpacks

International Nuclear Information System (INIS)

Larose, Catherine; Vogel, Timothy M; Dommergue, Aurélien

2013-01-01

Arctic snowpacks are often considered as chemical reactors for a variety of chemicals deposited through wet and dry events, but are overlooked as potential sites for microbial metabolism of reactive nitrogen species. The fate of deposited species is critical since warming leads to the transfer of contaminants to snowmelt-fed ecosystems. Here, we examined the role of microorganisms and the potential pathways involved in nitrogen cycling in the snow. Next generation sequencing data were used to follow functional gene abundances and a 16S rRNA (ribosomal ribonucleic acid) gene microarray was used to follow shifts in microbial community structure during a two-month spring-time field study at a high Arctic site, Svalbard, Norway (79° N). We showed that despite the low temperatures and limited water supply, microbial communities inhabiting the snow cover demonstrated dynamic shifts in their functional potential to follow several different pathways of the nitrogen cycle. In addition, microbial specific phylogenetic probes tracked different nitrogen species over time. For example, probes for Roseomonas tracked nitrate concentrations closely and probes for Caulobacter tracked ammonium concentrations after a delay of one week. Nitrogen cycling was also shown to be a dominant process at the base of the snowpack. (letter)
The effects of high dose of two manganese supplements (organic and inorganic) on the rumen microbial ecosystem.

Science.gov (United States)

Kišidayová, Svetlana; Pristaš, Peter; Zimovčáková, Michaela; Blanár Wencelová, Monika; Homol'ová, Lucia; Mihaliková, Katarína; Čobanová, Klaudia; Grešáková, Ľubomíra; Váradyová, Zora

2018-01-01

Little is known about the effects of the high dose and types of manganese supplements on rumen environment at manganese intake level close above the limit of 150 mg/kg of dry feed matter. The effects of high dose of two manganese supplements (organic and inorganic) on rumen microbial ecosystem after four months of treatment of 18 lambs divided into three treatment groups were studied. We examined the enzyme activities (α-amylase, xylanase, and carboxymethyl cellulase), total and differential microscopic counts of rumen ciliates, total microscopic counts of bacteria, and fingerprinting pattern of the eubacterial and ciliates population analyzed by PCR-DGGE. Lambs were fed a basal diet with a basal Mn content (34.3 mg/kg dry matter; control) and supplemented either with inorganic manganous sulfate or organic Mn-chelate hydrate (daily 182.7, 184 mg/kg dry matter of feed, respectively). Basal diet, offered twice daily, consisted of ground barley and hay (268 and 732 g/kg dry matter per animal and day). The rumens of the lambs harbored ciliates of the genera of Entodinium, Epidinium, Diplodinium, Eudiplodinium, Dasytricha, and Isotricha. No significant differences between treatment groups were observed in the total ciliate number, the number of ciliates at the genus level, as well as the total number of bacteria. Organic Mn did decrease the species richness and diversity of the eubacterial population examined by PCR-DGGE. No effects of type of Mn supplement on the enzyme activities were observed. In comparison to the control, α-amylase specific activities were decreased and carboxymethyl-cellulase specific activities were increased by the Mn supplements. Xylanase activities were not influenced. In conclusion, our results suggested that the intake of tested inorganic and organic manganese supplements in excess may affect the specific groups of eubacteria. More studies on intake of Mn supplements at a level close to the limit can reveal if the changes in microbial
Non-enzymatic palladium recovery on microbial and synthetic surfaces

DEFF Research Database (Denmark)

Rotaru, Amelia-Elena; Jiang, Wei; Finster, Kai

2012-01-01

in the presence of cells as compared to cell-free controls. We found no difference between native (untreated) and autoclaved cells, and could demonstrate that even a non-enzymatic protein (bovine serum albumin) stimulated Pd(II) reduction as efficiently as bacterial cells. Amine groups readily interact with Pd......(II), and to specifically test their role in surface-assisted Pd(II) reduction by formate, we replaced bacterial cells with polystyrene microparticles functionalized with amine or carboxyl groups. Amine-functionalized microparticles had the same effect on Pd(II) reduction as bacterial cells, and the effect could...... be hampered if the amine groups were blocked by acetylation. The interaction with amine groups was confirmed by infrared spectroscopy on whole cells and amine-functionalized microparticles. In conclusion, bio-supported Pd(II) reduction on microbial surfaces is possibly mediated by a non-enzymatic mechanism...
Gammarus-Microbial Interactions: A Review

Directory of Open Access Journals (Sweden)

Daniel Nelson

2011-01-01

Full Text Available Gammarus spp. are typically classified as shredders under the functional feeding group classification. In the wild and in the laboratory, Gammarus spp. will often shred leaves, breaking them down into finer organic matter fractions. However, leaf litter is a poor quality food source (i.e., high C : N and C : P ratios and very little leaf material is assimilated by shredders. In freshwater habitats leaf litter is colonized rapidly (within ∼1-2 weeks by aquatic fungi and bacteria, making the leaves more palatable and nutritious to consumers. Several studies have shown that Gammarus spp. show preference for conditioned leaves over nonconditioned leaves and certain fungal species to others. Furthermore, Gammarus spp. show increased survival and growth rates when fed conditioned leaves compared to non-conditioned leaves. Thus, Gammarus spp. appear to rely on the microbial biofilm associated with leaf detritus as a source of carbon and/or essential nutrients. Also, Gammarus spp. can have both positive and negative effects on the microbial communities on which they fed, making them an important component of the microbial loop in aquatic ecosystems.
Evolution of microbial activity in a mediterranean ecosystem submitted to chronic gamma irradiation. Investigation of nitrogen transfer with isotopic tracers

International Nuclear Information System (INIS)

Castet, R.

1987-07-01

A mediterranean ecosystem located on the site of Cadarache (France) has been experimentally by irradiated over the past fifteen years. The potential effects of ionizing radiations for different doses of its ecological system has been studied. The objective of the work was to demonstrate the level of soil microbial population and its activity. Chronic exposures reduced the biomass and the dehydrogenase activity by a factor of 50% and increased the amount of nitrate in the soil. To measure the direct impact of irradiations on soil microorganisms, we have irradiated soil sample in laboratory at 0.1; 0.5; 1 kGy, and observed its evolution during a period of six weeks thereafter. We have a reduction of the dehydrogenase activity and an increase of nitrate being proportionaly to the dose delivered. Using nitrogen labelled, we state that this high rate of nitrate production is due to an inhibition of the organization of this form of nitrogen. Conversely, the ammonification and the nitrification are not affected. Also, for anaerobic conditions created by glucose, the nitrate labelled (15N) permitted us to show that in untreated soil, 45% of nitrate was reduced to nitrogen gas by denitrification and 24% of nitrate was reduced to ammonium by dissimilation in the irradiated soil. These experiments show that gamma irradiations are of great interest for studying soil microorganisms. As of now, very little is known on the effects of this kind of stress for attention and need to be pursued on such ecosystems. Further investigations call [fr
The responses of microbial temperature relationships to seasonal change and winter warming in a temperate grassland.

Science.gov (United States)

Birgander, Johanna; Olsson, Pål Axel; Rousk, Johannes

2018-01-18

Microorganisms dominate the decomposition of organic matter and their activities are strongly influenced by temperature. As the carbon (C) flux from soil to the atmosphere due to microbial activity is substantial, understanding temperature relationships of microbial processes is critical. It has been shown that microbial temperature relationships in soil correlate with the climate, and microorganisms in field experiments become more warm-tolerant in response to chronic warming. It is also known that microbial temperature relationships reflect the seasons in aquatic ecosystems, but to date this has not been investigated in soil. Although climate change predictions suggest that temperatures will be mostly affected during winter in temperate ecosystems, no assessments exist of the responses of microbial temperature relationships to winter warming. We investigated the responses of the temperature relationships of bacterial growth, fungal growth, and respiration in a temperate grassland to seasonal change, and to 2 years' winter warming. The warming treatments increased winter soil temperatures by 5-6°C, corresponding to 3°C warming of the mean annual temperature. Microbial temperature relationships and temperature sensitivities (Q 10 ) could be accurately established, but did not respond to winter warming or to seasonal temperature change, despite significant shifts in the microbial community structure. The lack of response to winter warming that we demonstrate, and the strong response to chronic warming treatments previously shown, together suggest that it is the peak annual soil temperature that influences the microbial temperature relationships, and that temperatures during colder seasons will have little impact. Thus, mean annual temperatures are poor predictors for microbial temperature relationships. Instead, the intensity of summer heat-spells in temperate systems is likely to shape the microbial temperature relationships that govern the soil-atmosphere C
Integrating biological redesign: where synthetic biology came from and where it needs to go.

Science.gov (United States)

Way, Jeffrey C; Collins, James J; Keasling, Jay D; Silver, Pamela A

2014-03-27

Synthetic biology seeks to extend approaches from engineering and computation to redesign of biology, with goals such as generating new chemicals, improving human health, and addressing environmental issues. Early on, several guiding principles of synthetic biology were articulated, including design according to specification, separation of design from fabrication, use of standardized biological parts and organisms, and abstraction. We review the utility of these principles over the past decade in light of the field's accomplishments in building complex systems based on microbial transcription and metabolism and describe the progress in mammalian cell engineering. Copyright © 2014 Elsevier Inc. All rights reserved.
Multimodeling Framework for Predicting Water Quality in Fragmented Agriculture-Forest Ecosystems

Science.gov (United States)

Rose, J. B.; Guber, A.; Porter, W. F.; Williams, D.; Tamrakar, S.; Dechen Quinn, A.

2012-12-01

Both livestock and wildlife are major contributors of nonpoint pollution of surface water bodies. The interactions among them can substantially increase the chance of contamination especially in fragmented agriculture-forest landscapes, where wildlife (e.g. white tailed deer) can transmit diseases between remote farms. Unfortunately, models currently available for predicting fate and transport of microorganisms in these ecosystems do not account for such interactions. The objectives of this study are to develop and test a multimodeling framework that assesses the risk of microbial contamination of surface water caused by wildlife-livestock interactions in fragmented agriculture-forest ecosystems. The framework consists of a modified Soil Water Assessment Tool (SWAT), KINematic Runoff and EROSion model (KINEROS2) with the add-on module STWIR (Microorganism Transport with Infiltration and Runoff), RAMAS GIS, SIR compartmental model and Quantitative Microbial Risk Assessment model (QMRA). The watershed-scale model SWAT simulates plant biomass growth, wash-off of microorganisms from foliage and soil, overland and in-stream microbial transport, microbial growth, and die-off in foliage and soil. RAMAS GIS model predicts the most probable habitat and subsequent population of white-tailed deer based on land use and crop biomass. KINEROS-STWIR simulates overland transport of microorganisms released from soil, surface applied manure, and fecal deposits during runoff events at high temporal and special resolutions. KINEROS-STWIR and RAMAS GIS provide input for an SIR compartmental model which simulates disease transmission within and between deer groups. This information is used in SWAT model to account for transmission and deposition of pathogens by white tailed deer in stream water, foliage and soil. The QMRA approach extends to microorganisms inactivated in forage and water consumed by deer. Probabilities of deer infections and numbers of infected animals are computed
Introducing BASE: the Biomes of Australian Soil Environments soil microbial diversity database.

Science.gov (United States)

Bissett, Andrew; Fitzgerald, Anna; Meintjes, Thys; Mele, Pauline M; Reith, Frank; Dennis, Paul G; Breed, Martin F; Brown, Belinda; Brown, Mark V; Brugger, Joel; Byrne, Margaret; Caddy-Retalic, Stefan; Carmody, Bernie; Coates, David J; Correa, Carolina; Ferrari, Belinda C; Gupta, Vadakattu V S R; Hamonts, Kelly; Haslem, Asha; Hugenholtz, Philip; Karan, Mirko; Koval, Jason; Lowe, Andrew J; Macdonald, Stuart; McGrath, Leanne; Martin, David; Morgan, Matt; North, Kristin I; Paungfoo-Lonhienne, Chanyarat; Pendall, Elise; Phillips, Lori; Pirzl, Rebecca; Powell, Jeff R; Ragan, Mark A; Schmidt, Susanne; Seymour, Nicole; Snape, Ian; Stephen, John R; Stevens, Matthew; Tinning, Matt; Williams, Kristen; Yeoh, Yun Kit; Zammit, Carla M; Young, Andrew

2016-01-01

Microbial inhabitants of soils are important to ecosystem and planetary functions, yet there are large gaps in our knowledge of their diversity and ecology. The 'Biomes of Australian Soil Environments' (BASE) project has generated a database of microbial diversity with associated metadata across extensive environmental gradients at continental scale. As the characterisation of microbes rapidly expands, the BASE database provides an evolving platform for interrogating and integrating microbial diversity and function. BASE currently provides amplicon sequences and associated contextual data for over 900 sites encompassing all Australian states and territories, a wide variety of bioregions, vegetation and land-use types. Amplicons target bacteria, archaea and general and fungal-specific eukaryotes. The growing database will soon include metagenomics data. Data are provided in both raw sequence (FASTQ) and analysed OTU table formats and are accessed via the project's data portal, which provides a user-friendly search tool to quickly identify samples of interest. Processed data can be visually interrogated and intersected with other Australian diversity and environmental data using tools developed by the 'Atlas of Living Australia'. Developed within an open data framework, the BASE project is the first Australian soil microbial diversity database. The database will grow and link to other global efforts to explore microbial, plant, animal, and marine biodiversity. Its design and open access nature ensures that BASE will evolve as a valuable tool for documenting an often overlooked component of biodiversity and the many microbe-driven processes that are essential to sustain soil function and ecosystem services.
Data-directed modelling of Daphnia dynamics in a long-term micro-ecosystem experiment

NARCIS (Netherlands)

Grasman, J.; Nes, van E.H.; Kersting, K.

2009-01-01

The micro-ecosystem under consideration consists of three compartments forming a closed chain in which water circulates. Three trophic levels are represented in different compartments: autotrophs (algae, mainly Chlorella vulgaris), herbivores (Daphnia magna) and microbial decomposers. From a 20
Diffuse flow environments within basalt- and sediment-based hydrothermal vent ecosystems harbor specialized microbial communities.

Science.gov (United States)

Campbell, Barbara J; Polson, Shawn W; Zeigler Allen, Lisa; Williamson, Shannon J; Lee, Charles K; Wommack, K Eric; Cary, S Craig

2013-01-01

Hydrothermal vents differ both in surface input and subsurface geochemistry. The effects of these differences on their microbial communities are not clear. Here, we investigated both alpha and beta diversity of diffuse flow-associated microbial communities emanating from vents at a basalt-based hydrothermal system along the East Pacific Rise (EPR) and a sediment-based hydrothermal system, Guaymas Basin. Both Bacteria and Archaea were targeted using high throughput 16S rRNA gene pyrosequencing analyses. A unique aspect of this study was the use of a universal set of 16S rRNA gene primers to characterize total and diffuse flow-specific microbial communities from varied deep-sea hydrothermal environments. Both surrounding seawater and diffuse flow water samples contained large numbers of Marine Group I (MGI) Thaumarchaea and Gammaproteobacteria taxa previously observed in deep-sea systems. However, these taxa were geographically distinct and segregated according to type of spreading center. Diffuse flow microbial community profiles were highly differentiated. In particular, EPR dominant diffuse flow taxa were most closely associated with chemolithoautotrophs, and off axis water was dominated by heterotrophic-related taxa, whereas the opposite was true for Guaymas Basin. The diversity and richness of diffuse flow-specific microbial communities were strongly correlated to the relative abundance of Epsilonproteobacteria, proximity to macrofauna, and hydrothermal system type. Archaeal diversity was higher than or equivalent to bacterial diversity in about one third of the samples. Most diffuse flow-specific communities were dominated by OTUs associated with Epsilonproteobacteria, but many of the Guaymas Basin diffuse flow samples were dominated by either OTUs within the Planctomycetes or hyperthermophilic Archaea. This study emphasizes the unique microbial communities associated with geochemically and geographically distinct hydrothermal diffuse flow environments.
Mangrove succession enriches the sediment microbial community in South China.

Science.gov (United States)

Chen, Quan; Zhao, Qian; Li, Jing; Jian, Shuguang; Ren, Hai

2016-06-06

Sediment microorganisms help create and maintain mangrove ecosystems. Although the changes in vegetation during mangrove forest succession have been well studied, the changes in the sediment microbial community during mangrove succession are poorly understood. To investigate the changes in the sediment microbial community during succession of mangroves at Zhanjiang, South China, we used phospholipid fatty acid (PLFA) analysis and the following chronosequence from primary to climax community: unvegetated shoal; Avicennia marina community; Aegiceras corniculatum community; and Bruguiera gymnorrhiza + Rhizophora stylosa community. The PLFA concentrations of all sediment microbial groups (total microorganisms, fungi, gram-positive bacteria, gram-negative bacteria, and actinomycetes) increased significantly with each stage of mangrove succession. Microbial PLFA concentrations in the sediment were significantly lower in the wet season than in the dry season. Regression and ordination analyses indicated that the changes in the microbial community with mangrove succession were mainly associated with properties of the aboveground vegetation (mainly plant height) and the sediment (mainly sediment organic matter and total nitrogen). The changes in the sediment microbial community can probably be explained by increases in nutrients and microhabitat heterogeneity during mangrove succession.
Prescreening of microbial populations for the assessment of sequencing potential.

Science.gov (United States)

Hanning, Irene B; Ricke, Steven C

2011-01-01

Next-generation sequencing (NGS) is a powerful tool that can be utilized to profile and compare microbial populations. By amplifying a target gene present in all bacteria and subsequently sequencing amplicons, the bacteria genera present in the populations can be identified and compared. In some scenarios, little to no difference may exist among microbial populations being compared in which case a prescreening method would be practical to determine which microbial populations would be suitable for further analysis by NGS. Denaturing density-gradient electrophoresis (DGGE) is relatively cheaper than NGS and the data comparing microbial populations are ready to be viewed immediately after electrophoresis. DGGE follows essentially the same initial methodology as NGS by targeting and amplifying the 16S rRNA gene. However, as opposed to sequencing amplicons, DGGE amplicons are analyzed by electrophoresis. By prescreening microbial populations with DGGE, more efficient use of NGS methods can be accomplished. In this chapter, we outline the protocol for DGGE targeting the same gene (16S rRNA) that would be targeted for NGS to compare and determine differences in microbial populations from a wide range of ecosystems.
Engineering microbial electrocatalysis for chemical and fuel production.

Science.gov (United States)

Rosenbaum, Miriam A; Henrich, Alexander W

2014-10-01

In many biotechnological areas, metabolic engineering and synthetic biology have become core technologies for biocatalyst development. Microbial electrocatalysis for biochemical and fuel production is still in its infancy and reactions rates and the product spectrum are currently very low. Therefore, molecular engineering strategies will be crucial for the advancement and realization of many new bioproduction routes using electroactive microorganisms. The complex and unresolved biochemistry and physiology of extracellular electron transfer and the lack of molecular tools for these new non-model hosts for genetic engineering constitute the major challenges for this effort. This review is providing an insight into the current status, challenges and promising approaches of pathway engineering for microbial electrocatalysis. Copyright © 2014 Elsevier Ltd. All rights reserved.
Soil bacterial and fungal diversity differently correlated with soil biochemistry in alpine grassland ecosystems in response to environmental changes

Science.gov (United States)

Zhang, Yong; Dong, Shikui; Gao, Qingzhu; Liu, Shiliang; Ganjurjav, Hasbagan; Wang, Xuexia; Su, Xukun; Wu, Xiaoyu

2017-03-01

To understand effects of soil microbes on soil biochemistry in alpine grassland ecosystems under environmental changes, we explored relationships between soil microbial diversity and soil total nitrogen, organic carbon, available nitrogen and phosphorus, soil microbial biomass and soil enzyme activities in alpine meadow, alpine steppe and cultivated grassland on the Qinghai-Tibetan plateau under three-year warming, enhanced precipitation and yak overgrazing. Soil total nitrogen, organic carbon and NH4-N were little affected by overgrazing, warming or enhanced precipitation in three types of alpine grasslands. Soil microbial biomass carbon and phosphorus along with the sucrase and phosphatase activities were generally stable under different treatments. Soil NO3-N, available phosphorus, urease activity and microbial biomass nitrogen were increased by overgrazing in the cultivated grassland. Soil bacterial diversity was positively correlated with, while soil fungal diversity negatively with soil microbial biomass and enzyme activities. Soil bacterial diversity was negatively correlated with, while soil fungal diversity positively with soil available nutrients. Our findings indicated soil bacteria and fungi played different roles in affecting soil nutrients and microbiological activities that might provide an important implication to understand why soil biochemistry was generally stable under environmental changes in alpine grassland ecosystems.
The path to next generation biofuels: successes and challenges in the era of synthetic biology

Science.gov (United States)

2010-01-01

Volatility of oil prices along with major concerns about climate change, oil supply security and depleting reserves have sparked renewed interest in the production of fuels from renewable resources. Recent advances in synthetic biology provide new tools for metabolic engineers to direct their strategies and construct optimal biocatalysts for the sustainable production of biofuels. Metabolic engineering and synthetic biology efforts entailing the engineering of native and de novo pathways for conversion of biomass constituents to short-chain alcohols and advanced biofuels are herewith reviewed. In the foreseeable future, formal integration of functional genomics and systems biology with synthetic biology and metabolic engineering will undoubtedly support the discovery, characterization, and engineering of new metabolic routes and more efficient microbial systems for the production of biofuels. PMID:20089184
Engineering microbial consortia for controllable outputs

Energy Technology Data Exchange (ETDEWEB)

Lindemann, Stephen R.; Bernstein, Hans C.; Song, Hyun-Seob; Fredrickson, Jim K.; Fields, Matthew W.; Shou, Wenying; Johnson, David R.; Beliaev, Alexander S.

2016-03-11

Much research has been invested into engineering microorganisms to perform desired biotransformations; nonetheless, these efforts frequently fall short of expected results due to the unforeseen effects of biofeedback regulation and functional incompatibility. In nature, metabolic function is compartmentalized into diverse organisms assembled into resilient consortia, in which the division of labor is thought to lead to increased community efficiency and productivity. Here, we consider whether and how consortia can be designed to perform bioprocesses of interest beyond the metabolic flexibility limitations of a single organism. Advances in post-genomic analysis of microbial consortia and application of high-resolution global measurements now offer the promise of systems-level understanding of how microbial consortia adapt to changes in environmental variables and inputs of carbon and energy. We argue that when combined with appropriate modeling framework that predictive knowledge generates testable hypotheses and orthogonal synthetic biology tools, such understanding can dramatically improve our ability to control the fate and functioning of consortia. In this article, we articulate our collective perspective on the current and future state of microbial community engineering and control while placing specific emphasis on ecological principles that promote control over community function and emergent properties.
Shallow freshwater ecosystems of the circumpolar Arctic

DEFF Research Database (Denmark)

Rautio, Milla; Dufresne, France; Laurion, Isabelle

2011-01-01

to large annual temperature fluctuations, a short growing season, and freeze-up and desiccation stress in winter, these ecosystems are strongly regulated by the supply of organic matter and its optical and biogeochemical properties. Dissolved organic carbon affects bacterial diversity and production......This review provides a synthesis of limnological data and conclusions from studies on ponds and small lakes at our research sites in Subarctic and Arctic Canada, Alaska, northern Scandinavia, and Greenland. Many of these water bodies contain large standing stocks of benthic microbial mats that grow...... in relatively nutrient-rich conditions, while the overlying water column is nutrient-poor and supports only low concentrations of phytoplankton. Zooplankton biomass can, however, be substantial and is supported by grazing on the microbial mats as well as detrital inputs, algae, and other plankton. In addition...
Stable, geochemically mediated biospheres in the Deep Mine Microbial Observatory, SD, USA

Science.gov (United States)

Osburn, M. R.; Casar, C. P.; Kruger, B.; Flynn, T. M.

2017-12-01

The terrestrial subsurface is a vast reservoir of life, hosting diverse microbial ecosystems with varying levels of connectivity to surface inputs. Understanding long term ecosystem dynamics within the subsurface biosphere is very challenging due to limitations in accessibility, sample availability, and slow microbial growth rates. The establishment of the Deep Mine Microbial Observatory (DeMMO) at the Sanford Underground Research Facility, SD, USA has allowed for bimonthly sampling for nearly two years at six sites spanning 250 to 1500 m below the surface. Here we present a time-resolved analysis of the geomicrobiology of the six DeMMO sites, which have been created from legacy mine boreholes modified to allow for controlled sampling. Our interdisciplinary approach includes analysis of passively draining fracture fluid for aqueous and gas geochemistry, DNA sequencing, microscopy, and isotopic measurements of organic and inorganic substrates. Fluid geochemistry varies significantly between sites, but is relatively stable over time for a given site, even through significant external perturbations such as drilling and installation of permanent sampling devices into the boreholes. The fluid-hosted microbial diversity follows these trends, with consistent populations present at each site through time, even through drilling events. For instance, the shallowest site (DeMMO 1) consistently hosts >30% uncharacterized phyla and >25% Omnitrophica whereas the deepest site (DeMMO 6) is dominated by Firmicutes and Bacterioidetes. Microbial diversity appears to respond to the availability of energy sources such as organic carbon, sulfate, sulfide, hydrogen, and iron. Carbon isotopic measurements reveal closed system behavior with significant recycling of organic carbon into the DIC pool. Together these observations suggest DeMMO hosts isolated subsurface microbial populations adapted to local geochemistry that are stable on yearlong timescales.

A meta-analysis of soil microbial biomass responses to forest disturbances

Directory of Open Access Journals (Sweden)

Sandra Robin Holden

2013-06-01

Full Text Available Climate warming is likely to increase the frequency and severity of forest disturbances, with uncertain consequences for soil microbial communities and their contribution to ecosystem C dynamics. To address this uncertainty, we conducted a meta-analysis of 139 published soil microbial responses to forest disturbances. These disturbances included abiotic (fire, harvesting, storm and biotic (insect, pathogen disturbances. We hypothesized that soil microbial biomass would decline following forest disturbances, but that abiotic disturbances would elicit greater reductions in microbial biomass than biotic disturbances. In support of this hypothesis, across all published studies, disturbances reduced soil microbial biomass by an average of 29.4%. However, microbial responses differed between abiotic and biotic disturbances. Microbial responses were significantly negative following fires, harvest, and storms (48.7%, 19.1%, and 41.7% reductions in microbial biomass, respectively. In contrast, changes in soil microbial biomass following insect infestation and pathogen-induced tree mortality were non-significant, although biotic disturbances were poorly represented in the literature. When measured separately, fungal and bacterial responses to disturbances mirrored the response of the microbial community as a whole. Changes in microbial abundance following disturbance were significantly positively correlated with changes in microbial respiration. We propose that the differential effect of abiotic and biotic disturbances on microbial biomass may be attributable to differences in soil disruption and organic C removal from forests among disturbance types. Altogether, these results suggest that abiotic forest disturbances may significantly decrease soil microbial abundance, with corresponding consequences for microbial respiration. Further studies are needed on the effect of biotic disturbances on forest soil microbial communities and soil C dynamics.
Microbial Eco-Physiology of the human intestinal tract: a flow cytometric approach

NARCIS (Netherlands)

Amor, Ben K.

2004-01-01

This thesis describes a multifaceted approach to further enhance our view of the complex human intestinal microbial ecosystem. This approach combines me advantages of flow cyrometry (FCM), a single cell and high-throughput technology, and molecular techniques that have proven themselves to be
Effects of Misgurnus anguillicaudatus and Cipangopaludina cathayensis on Pollutant Removal and Microbial Community in Constructed Wetlands

Directory of Open Access Journals (Sweden)

Pengfei Li

2015-05-01

Full Text Available Aquatic animals play an important role in the energy flow and matter cycling in the wetland ecosystem. However, little is known about their effects on pollutant removal performance and microbial community in constructed wetlands. This work presents an initial attempt to investigate the effects of Misgurnus anguillicaudatus (loach and Cipangopaludina cathayensis (snail on nutrient removal performance and microbial community of constructed wetlands (CWs. Compared with a control group, CW microcosms with aquatic animals exhibited better pollutant removal performance. The removal efficiencies of total phosphorus (TP in the loach group were 13.1% higher than in the control group, and snails increased the ammonium removal most effectively. Moreover, the concentration of total organic carbon (TOC and TP in sediment significantly reduced with the addition of loaches and snails (p < 0.05, whereas the concentration of total nitrogen (TN showed an obvious increase with the addition of loaches. High-throughput sequencing showed a microbial community structure change. Loaches and snails in wetlands changed the microbial diversity, especially in the Proteobacteria and denitrifying community. Results suggested that benthic aquatic animals might play an important role in CW ecosystems.
Comparative assessment of the effect of synthetic and natural fungicides on soil respiration.

Science.gov (United States)

Stefani, Angelo; Felício, Joanna D'Arc; de Andréa, Mara M

2012-01-01

As toxic pesticide residues may persist in agricultural soils and cause environmental pollution, research on natural fungicides to replace the synthetic compounds is currently increasing. The effect of the synthetic fungicide chlorothalonil and a natural potential fungicide on the soil microbial activity was evaluated here by the substrate-induced respiration by addition of glucose (SIR), as bioindicator in two soils (Eutrophic Humic Gley-GHE and Typic Eutroferric Chernosol-AVEC). The induced soil respiration parameter was followed during 28 days after soil treatment either with chlorathalonil (11 μg·g(-1)), or the methanolic fraction from Polymnia sonchifolia extraction (300 μg·g(-1)), and (14)C-glucose (4.0 mg and 5.18 Bq of (14)C-glucose g(-1)). The (14)C-CO(2) produced by the microbial respiration was trapped in NaOH (0.1 M) which was changed each two hours during the first 10 h, and 1, 3, 5, 7, 14 and 28 days after the treatments. The methanolic fraction of the plant extract inhibited (2.2%) and stimulated (1.8%) the respiration of GHE and AVEC, respectively, but the synthetic chlorothalonil caused 16.4% and 2.6% inhibition of the respiration, respectively of the GHE and AVEC soils. As the effects of the natural product were statistically small, this bioindicator indicates that the methanolic fraction of the Polymnia sonchifolia extract, which has fungicide properties, has no environmental effects.
Poorly known microbial taxa dominate the microbiome of permafrost thaw ponds.

Science.gov (United States)

Wurzbacher, Christian; Nilsson, R Henrik; Rautio, Milla; Peura, Sari

2017-08-01

In the transition zone of the shifting permafrost border, thaw ponds emerge as hotspots of microbial activity, processing the ancient carbon freed from the permafrost. We analyzed the microbial succession across a gradient of recently emerged to older ponds using three molecular markers: one universal, one bacterial and one fungal. Age was a major modulator of the microbial community of the thaw ponds. Surprisingly, typical freshwater taxa comprised only a small fraction of the community. Instead, thaw ponds of all age classes were dominated by enigmatic bacterial and fungal phyla. Our results on permafrost thaw ponds lead to a revised perception of the thaw pond ecosystem and their microbes, with potential implications for carbon and nutrient cycling in this increasingly important class of freshwaters.
A Novel Method for Analyzing Microbially Affiliated Volatile Organic Compounds in Soil Environments

Science.gov (United States)

Ruhs, C. V.; McNeal, K. S.

2010-12-01

A concerted, international effort by citizens, governments, industries and educational systems is necessary to address the myriad environmental issues that face us today. The authors of this paper concentrate on soil environments and, specifically, the methods currently used to characterize them. The ability to efficiently and effectively monitor and characterize various soils is desired, allows for the study, supervision, and protection of natural and cultivated ecosystems, and may assist stakeholders in meeting governmentally-imposed environmental standards. This research addresses soil characterization by a comparison of four methods that emphasize a combination of microbial community and metabolic measures: BIOLOG, fatty acid methyl-ester analysis (FAME), descriptive physical and chemical analysis (moisture content, pH, carbon content, nutrient content, and grain size), and the novel soil-microbe volatile organic compound analysis (SMVOC) presented in this work. In order to achieve the method comparison, soils were collected from three climatic regions (Bahamas, Michigan, and Mississippi), with three samples taken from niche ecosystems found at each climatic region (a total of nine sites). Of interest to the authors is whether or not an investigation of microbial communities and the volatile organic compounds (VOCs) produced by microbial communities from nine separate soil ecosystems provides useful information about soil dynamics. In essence, is analysis of soil-derived VOCs using gas chromatography-mass spectrometry (GC-MS) an effective method for characterizing microbial communities and their metabolic activity of soils rapidly and accurately compared with the other three traditional characterization methods? Preliminary results suggest that VOCs in each of these locales differ with changes in soil types, soil moisture, and bacterial community. Each niche site shows distinct patterns in both VOCs and BIOLOG readings. Results will be presented to show the
Shift in soil microbial communities with shrub encroachment in Inner Mongolia grasslands, China

Science.gov (United States)

Shen, H.; Li, H.; Zhang, J.; Hu, H.; Chen, L.; Zhu, Y.; Fang, J.

2017-12-01

The ongoing expansion of shrub encroachment into grasslands represents a unique form of land cover change. How this process affects soil microbial communities is poorly understood. In this study, we aim to assess the effects of shrub encroachment on soil microbial biomass, abundance and composition by comparing data between shrub patches and neighboring herb patches in shrub-encroached grasslands (SEGs) in Inner Mongolia, China. Fourteen SEG sites from two ecosystem types (typical and desert grasslands) were investigated. The phospholipid fatty acid (PLFA) method was used to analyze the composition and biomass of the soil microbial community. Our results showed that the top-soil microbial biomass and abundances of gram-negative bacteria, arbuscular mycorrhizal fungi, and actinomycetes were significantly higher in shrub patches than in herb patches in both typical and desert grasslands (P fungi to bacteria ratio was significantly higher in shrub patches than in herb patches in desert grassland (P soil microbial communities, which makes the microbial communities toward a fresh organic carbon-based structure. This study highlights the importance of edaphic and climate factors in microbial community shifts in SEGs.
Flow of light energy in benthic photosynthetic microbial mats

Energy Technology Data Exchange (ETDEWEB)

Al-Najjar, Mohammad Ahmad A.

2010-12-15

The work in this thesis demonstrates the assessment of the energy budget inside microbial mat ecosystems, and the factors affecting light utilization efficiency. It presents the first balanced light energy budget for benthic microbial mat ecosystems, and shows how the budget and the spatial distribution of the local photosynthetic efficiencies within the euphotic zone depend on the absorbed irradiance (Jabs). The energy budget was dominated by heat dissipation on the expense of photosynthesis. The maximum efficiency of photosynthesis was at light limiting conditions When comparing three different marine benthic photosynthetic ecosystems (originated from Abu-Dhabi, Arctic, and Exmouth Gulf in Western Australia), differences in the efficiencies were calculated. The results demonstrated that the maximum efficiency depended on mat characteristics affecting light absorption and scattering; such as, photopigments ratio and distribution, and the structural organization of the photosynthetic organisms relative to other absorbing components of the ecosystem (i.e., EPS, mineral particles, detritus, etc.). The maximum efficiency decreased with increasing light penetration depth, and increased with increasing the accessory pigments (phycocyanin and fucoxanthin)/chlorophyll ratio. Spatial heterogeneity in photosynthetic efficiency, pigment distribution, as well as light acclimation in microbial mats originating from different geographical locations was investigated. We used a combined pigment imaging approach (variable chlorophyll fluorescence and hyperspectral imaging), and fingerprinting approach. For each mat, the photosynthetic activity was proportional to the local pigment concentration in the photic zone, but not for the deeper layers and between different mats. In each mat, yield of PSII and E1/2 (light acclimation) generally decreased in parallel with depth, but the gradients in both parameters varied greatly between samples. This mismatch between pigments concentration
Stimulation of microbial nitrogen cycling in aquatic ecosystems by benthic macrofauna: mechanisms and environmental implications

DEFF Research Database (Denmark)

Stief, P.

2013-01-01

(mainly nitrate and ammonium) and the emission of the greenhouse gas nitrous oxide are evaluated. Published data indicate that ecosystem engineering by sediment-burrowing macrofauna stimulates benthic nitrification and denitrification, which together allows fixed nitrogen removal. However, the release...... enhance nitrous oxide emission from shallow aquatic ecosystems. The beneficial effect of benthic macrofauna on fixed nitrogen removal through coupled nitrification-denitrification can thus be offset by the concurrent release of (i) ammonium that stimulates aquatic primary production and (ii) nitrous oxide...... of ammonium from sediments is enhanced more strongly than the sedimentary uptake of nitrate. Ecosystem engineering by reef-building macrofauna increases nitrogen retention and ammonium concentrations in shallow aquatic ecosystems, but allows organic nitrogen removal through harvesting. Grazing by macrofauna...
Synthetic Biology and Metabolic Engineering Approaches and Its Impact on Non-Conventional Yeast and Biofuel Production

Energy Technology Data Exchange (ETDEWEB)

Madhavan, Aravind [Biotechnology Division, National Institute for Interdisciplinary Science and Technology, Council of Scientific and Industrial Research, Trivandrum (India); Rajiv Gandhi Centre for Biotechnology, Trivandrum (India); Jose, Anju Alphonsa; Binod, Parameswaran; Sindhu, Raveendran, E-mail: sindhurgcb@gmail.com; Sukumaran, Rajeev K. [Biotechnology Division, National Institute for Interdisciplinary Science and Technology, Council of Scientific and Industrial Research, Trivandrum (India); Pandey, Ashok [Biotechnology Division, National Institute for Interdisciplinary Science and Technology, Council of Scientific and Industrial Research, Trivandrum (India); Center for Innovative and Applied Bioprocessing, Mohali, Punjab (India); Castro, Galliano Eulogio [Dpt. Ingeniería Química, Ambiental y de los Materiales Edificio, Universidad de Jaén, Jaén (Spain)

2017-04-25

The increasing fossil fuel scarcity has led to an urgent need to develop alternative fuels. Currently microorganisms have been extensively used for the production of first-generation biofuels from lignocellulosic biomass. Yeast is the efficient producer of bioethanol among all existing biofuels option. Tools of synthetic biology have revolutionized the field of microbial cell factories especially in the case of ethanol and fatty acid production. Most of the synthetic biology tools have been developed for the industrial workhorse Saccharomyces cerevisiae. The non-conventional yeast systems have several beneficial traits like ethanol tolerance, thermotolerance, inhibitor tolerance, genetic diversity, etc., and synthetic biology have the power to expand these traits. Currently, synthetic biology is slowly widening to the non-conventional yeasts like Hansenula polymorpha, Kluyveromyces lactis, Pichia pastoris, and Yarrowia lipolytica. Herein, we review the basic synthetic biology tools that can apply to non-conventional yeasts. Furthermore, we discuss the recent advances employed to develop efficient biofuel-producing non-conventional yeast strains by metabolic engineering and synthetic biology with recent examples. Looking forward, future synthetic engineering tools’ development and application should focus on unexplored non-conventional yeast species.
Synthetic Biology and Metabolic Engineering Approaches and Its Impact on Non-Conventional Yeast and Biofuel Production

Directory of Open Access Journals (Sweden)

Raveendran Sindhu

2017-04-01

Full Text Available The increasing fossil fuel scarcity has led to an urgent need to develop alternative fuels. Currently microorganisms have been extensively used for the production of first-generation biofuels from lignocellulosic biomass. Yeast is the efficient producer of bioethanol among all existing biofuels option. Tools of synthetic biology have revolutionized the field of microbial cell factories especially in the case of ethanol and fatty acid production. Most of the synthetic biology tools have been developed for the industrial workhorse Saccharomyces cerevisiae. The non-conventional yeast systems have several beneficial traits like ethanol tolerance, thermotolerance, inhibitor tolerance, genetic diversity, etc., and synthetic biology have the power to expand these traits. Currently, synthetic biology is slowly widening to the non-conventional yeasts like Hansenula polymorpha, Kluyveromyces lactis, Pichia pastoris, and Yarrowia lipolytica. Herein, we review the basic synthetic biology tools that can apply to non-conventional yeasts. Furthermore, we discuss the recent advances employed to develop efficient biofuel-producing non-conventional yeast strains by metabolic engineering and synthetic biology with recent examples. Looking forward, future synthetic engineering tools’ development and application should focus on unexplored non-conventional yeast species.
Synthetic Biology and Metabolic Engineering Approaches and Its Impact on Non-Conventional Yeast and Biofuel Production

International Nuclear Information System (INIS)

Madhavan, Aravind; Jose, Anju Alphonsa; Binod, Parameswaran; Sindhu, Raveendran; Sukumaran, Rajeev K.; Pandey, Ashok; Castro, Galliano Eulogio

2017-01-01

The increasing fossil fuel scarcity has led to an urgent need to develop alternative fuels. Currently microorganisms have been extensively used for the production of first-generation biofuels from lignocellulosic biomass. Yeast is the efficient producer of bioethanol among all existing biofuels option. Tools of synthetic biology have revolutionized the field of microbial cell factories especially in the case of ethanol and fatty acid production. Most of the synthetic biology tools have been developed for the industrial workhorse Saccharomyces cerevisiae. The non-conventional yeast systems have several beneficial traits like ethanol tolerance, thermotolerance, inhibitor tolerance, genetic diversity, etc., and synthetic biology have the power to expand these traits. Currently, synthetic biology is slowly widening to the non-conventional yeasts like Hansenula polymorpha, Kluyveromyces lactis, Pichia pastoris, and Yarrowia lipolytica. Herein, we review the basic synthetic biology tools that can apply to non-conventional yeasts. Furthermore, we discuss the recent advances employed to develop efficient biofuel-producing non-conventional yeast strains by metabolic engineering and synthetic biology with recent examples. Looking forward, future synthetic engineering tools’ development and application should focus on unexplored non-conventional yeast species.
Molecular analysis of the biomass of a fluidized bed reactor treating synthetic vinasse at anaerobic and micro-aerobic conditions

NARCIS (Netherlands)

Rodriguez, E.; Lopes, A.; Fdz-Polanco, M.; Stams, A.J.M.; Garcia Encina, P.A.

2012-01-01

The microbial communities (Bacteria and Archaea) established in an anaerobic fluidized bed reactor used to treat synthetic vinasse (betaine, glucose, acetate, propionate, and butyrate) were characterized by denaturing gradient gel electrophoresis (DGGE) and phylogenetic analysis. This study was
Developing Model Benchtop Systems for Microbial Experimental Evolution

Science.gov (United States)

Gentry, D.; Wang, J.; Arismendi, D.; Alvarez, J.; Ouandji, C.; Blaich, J.

2017-12-01

Understanding how microbes impact an ecosystem has improved through advances of molecular and genetic tools, but creating complex systems that emulate natural biology goes beyond current technology. In fact, many chemical, biological, and metabolic pathways of even model organisms are still poorly characterized. Even then, standard laboratory techniques for testing microbial impact on environmental change can have many drawbacks; they are time-consuming, labor intensive, and are at risk of contamination. By having an automated process, many of these problems can be reduced or even eliminated. We are developing a benchtop system that can run for long periods of time without the need for human intervention, involve multiple environmental stressors at once, perform real-time adjustments of stressor exposure based on current state of the population, and minimize contamination risks. Our prototype device allows operators to generate an analogue of real world micro-scale ecosystems that can be used to model the effects of disruptive environmental change on microbial ecosystems. It comprises of electronics, mechatronics, and fluidics based systems to control, measure, and evaluate the before and after state of microbial cultures from exposure to environmental stressors. Currently, it uses four parallel growth chambers to perform tests on liquid cultures. To measure the population state, optical sensors (LED/photodiode) are used. Its primary selection pressure is UV-C radiation, a well-studied stressor known for its cell- and DNA- damaging effects and as a mutagen. Future work will involve improving the current growth chambers, as well as implementing additional sensors and environmental stressors into the system. Full integration of multiple culture testing will allow inter-culture comparisons. Besides the temperature and OD sensors, other types of sensors can be integrated such as conductivity, biomass, pH, and dissolved gasses such as CO2 and O2. Additional
Methodological approaches for studying the microbial ecology of drinking water distribution systems.

Science.gov (United States)

Douterelo, Isabel; Boxall, Joby B; Deines, Peter; Sekar, Raju; Fish, Katherine E; Biggs, Catherine A

2014-11-15

The study of the microbial ecology of drinking water distribution systems (DWDS) has traditionally been based on culturing organisms from bulk water samples. The development and application of molecular methods has supplied new tools for examining the microbial diversity and activity of environmental samples, yielding new insights into the microbial community and its diversity within these engineered ecosystems. In this review, the currently available methods and emerging approaches for characterising microbial communities, including both planktonic and biofilm ways of life, are critically evaluated. The study of biofilms is considered particularly important as it plays a critical role in the processes and interactions occurring at the pipe wall and bulk water interface. The advantages, limitations and usefulness of methods that can be used to detect and assess microbial abundance, community composition and function are discussed in a DWDS context. This review will assist hydraulic engineers and microbial ecologists in choosing the most appropriate tools to assess drinking water microbiology and related aspects. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.
Board-invited review: Rumen microbiology: Leading the way in microbial ecology

Science.gov (United States)

Robert Hungate, considered the father of rumen microbiology, was the first to initiate a systematic exploration of the microbial ecosystem of the rumen, but he was not alone. The techniques he developed to isolate and identify cellulose-digesting bacteria from the rumen have had a major impact not ...
Phosphate solubilization as a microbial strategy for promoting plant growth

Directory of Open Access Journals (Sweden)

Mayra Eleonora Beltrán Pineda

2014-01-01

Full Text Available Because of the constant application of chemical inputs in Agroecosystem, the cost of crop production and environmental quality of soil and water have been affected. Microorganisms carry out most biogeochemical cycles; therefore, their role is essential for agro ecosystem balance. One such functional group is the phosphate solubilizing microorganisms, which are recognized plant growth promoters. These microbial populations perform an important activity, since in many soils there are large reserves of insoluble phosphorus, as a result of fixing much of the phosphorus fertilizer applied, which cannot be assimilated by the plant. The phosphate solubilizing microorganisms use different solubilization mechanisms such as the production of organic acids, which solubilize theses insoluble phosphates in the rhizosphere region. Soluble phosphates are absorbed by the plant, which enhances their growth and productivity. By using these phosphate reserves in soils, application of chemical fertilizers is decreased, on the one hand, can again be fixed by ions Ca, Al or Fe making them insoluble and, by the other hand, increase the costs of crop production. Microbial populations have been widely studied in different types of ecosystems, both natural and Agroecosystem. Thanks to its effectiveness, in laboratory and field studies, the phosphate solubilizing phenotype is of great interest to microbial ecologists who have begun to establish the molecular basis of the traitr.
Electronic Nose Technology to Measure Soil Microbial Activity and Classify Soil Metabolic Status

OpenAIRE

Fabrizio De Cesare; Elena Di Mattia; Simone Pantalei; Emiliano Zampetti; Vittorio Vinciguerra; Antonella Macagnano

2011-01-01

The electronic nose (E-nose) is a sensing technology that has been widely used to monitor environments in the last decade. In the present study, the capability of an E-nose, in combination with biochemical and microbiological techniques, of both detecting the microbial activity and estimating the metabolic status of soil ecosystems, was tested by measuring on one side respiration, enzyme activities and growth of bacteria in natural but simplified soil ecosystems over 23 days of incubation thr...
Anthropogenic pollutants affect ecosystem services of freshwater sediments. The need for a 'triad plus x' approach

Energy Technology Data Exchange (ETDEWEB)

Gerbersdorf, Sabine Ulrike; Wieprecht, Silke [Stuttgart Univ. (Germany). Dept. of Hydraulic Engineering and Water Resources Management; Hollert, Henner; Brinkmann, Markus [RWTH Aachen Univ. (Germany). Dept. of Ecosystem Analysis; Schuettrumpf, Holger [RWTH Aachen Univ. (Germany). Inst. of Hydraulic Engineering and Water Resources Management; Manz, Werner [Koblenz-Landau Univ., Koblenz (Germany). Inst. for Integrated Natural Sciences

2011-09-15

Purpose: Freshwater sediments and their attached microbial communities (biofilms) are essential features of rivers and lakes, providing valuable ecosystem services such as nutrient recycling or self-purification which extend beyond the aquatic environment. Anthropogenic pollutants, whether from the industrial era or as a result of our contemporary lifestyles, can negatively affect these functions with hitherto unknown consequences on ecology, the economy and human health. Thus far, the singular view of the involved disciplines such as ecotoxicology, environmental microbiology, hydrology and geomorphology has prevented a deeper understanding of this emerging issue. Main features: This paper discusses briefly the progressions and the state-of-the-art methods within the disciplines of concern related to contaminated sediments, ranging from ecotoxicological test systems, microbiological/molecular approaches to unravel changes of microbial ecosystems, up to the modelling of sediment transport and sorption/desorption of associated pollutants. The first bilateral research efforts on contaminated sediments include efforts to assess ecotoxicological sediment risk including sediment mobility (i.e. ecotoxicology and engineering), enhance bioremediation potential (i.e. microbiology and ecotoxicology) or to understand biostabilisation processes of sediments by microbial assemblages (i.e. microbiology and engineering). Conclusions and perspectives: In freshwater habitats, acute, chronic and mechanism-specific toxic effects on organisms, shifts in composition, structure and functionality of benthic microbial communities, as well as the obstruction of important ecosystem services by continuously discharged and long-deposited pollutants, should be related to the in situ sediment dynamics. To achieve an improved understanding of the ecology of freshwater sediments and the impairment of their important ecosystem functions by human-derived pollutants, we suggest a 'triad plus x
Incorporating microbial dormancy dynamics into soil decomposition models to improve quantification of soil carbon dynamics of northern temperate forests

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He, Yujie; Yang, Jinyan; Zhuang, Qianlai; Harden, Jennifer W.; McGuire, A. David; Liu, Yaling; Wang, Gangsheng; Gu, Lianhong

2015-01-01

Soil carbon dynamics of terrestrial ecosystems play a significant role in the global carbon cycle. Microbial-based decomposition models have seen much growth recently for quantifying this role, yet dormancy as a common strategy used by microorganisms has not usually been represented and tested in these models against field observations. Here we developed an explicit microbial-enzyme decomposition model and examined model performance with and without representation of microbial dormancy at six temperate forest sites of different forest types. We then extrapolated the model to global temperate forest ecosystems to investigate biogeochemical controls on soil heterotrophic respiration and microbial dormancy dynamics at different temporal-spatial scales. The dormancy model consistently produced better match with field-observed heterotrophic soil CO2 efflux (RH) than the no dormancy model. Our regional modeling results further indicated that models with dormancy were able to produce more realistic magnitude of microbial biomass (analysis showed that soil organic carbon content was the dominating factor (correlation coefficient = 0.4–0.6) in the simulated spatial pattern of soil RHwith both models. In contrast to strong temporal and local controls of soil temperature and moisture on microbial dormancy, our modeling results showed that soil carbon-to-nitrogen ratio (C:N) was a major regulating factor at regional scales (correlation coefficient = −0.43 to −0.58), indicating scale-dependent biogeochemical controls on microbial dynamics. Our findings suggest that incorporating microbial dormancy could improve the realism of microbial-based decomposition models and enhance the integration of soil experiments and mechanistically based modeling.

FATTY ACID STABLE ISOTOPE INDICATORS OF MICROBIAL CARBON SOURCE IN TROPICAL SOILS

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The soil microbial community plays an important role in tropical ecosystem functioning because of its importance in the soil organic matter (SOM) cycle. We have measured the stable carbon isotopic ratio (delta13C) of individual phospholipid fatty acids (PLFAs) in a variety of tr...
Relating microbial community structure to functioning in forest soil organic carbon transformation and turnover.

Science.gov (United States)

You, Yeming; Wang, Juan; Huang, Xueman; Tang, Zuoxin; Liu, Shirong; Sun, Osbert J

2014-03-01

Forest soils store vast amounts of terrestrial carbon, but we are still limited in mechanistic understanding on how soil organic carbon (SOC) stabilization or turnover is controlled by biotic and abiotic factors in forest ecosystems. We used phospholipid fatty acids (PLFAs) as biomarker to study soil microbial community structure and measured activities of five extracellular enzymes involved in the degradation of cellulose (i.e., β-1,4-glucosidase and cellobiohydrolase), chitin (i.e., β-1,4-N-acetylglucosaminidase), and lignin (i.e., phenol oxidase and peroxidase) as indicators of soil microbial functioning in carbon transformation or turnover across varying biotic and abiotic conditions in a typical temperate forest ecosystem in central China. Redundancy analysis (RDA) was performed to determine the interrelationship between individual PFLAs and biotic and abiotic site factors as well as the linkage between soil microbial structure and function. Path analysis was further conducted to examine the controls of site factors on soil microbial community structure and the regulatory pathway of changes in SOC relating to microbial community structure and function. We found that soil microbial community structure is strongly influenced by water, temperature, SOC, fine root mass, clay content, and C/N ratio in soils and that the relative abundance of Gram-negative bacteria, saprophytic fungi, and actinomycetes explained most of the variations in the specific activities of soil enzymes involved in SOC transformation or turnover. The abundance of soil bacterial communities is strongly linked with the extracellular enzymes involved in carbon transformation, whereas the abundance of saprophytic fungi is associated with activities of extracellular enzymes driving carbon oxidation. Findings in this study demonstrate the complex interactions and linkage among plant traits, microenvironment, and soil physiochemical properties in affecting SOC via microbial regulations.
A meta-analysis of soil salinization effects on nitrogen pools, cycles and fluxes in coastal ecosystems.

Science.gov (United States)

Zhou, Minghua; Butterbach-Bahl, Klaus; Vereecken, Harry; Brüggemann, Nicolas

2017-03-01

Salinity intrusion caused by land subsidence resulting from increasing groundwater abstraction, decreasing river sediment loads and increasing sea level because of climate change has caused widespread soil salinization in coastal ecosystems. Soil salinization may greatly alter nitrogen (N) cycling in coastal ecosystems. However, a comprehensive understanding of the effects of soil salinization on ecosystem N pools, cycling processes and fluxes is not available for coastal ecosystems. Therefore, we compiled data from 551 observations from 21 peer-reviewed papers and conducted a meta-analysis of experimental soil salinization effects on 19 variables related to N pools, cycling processes and fluxes in coastal ecosystems. Our results showed that the effects of soil salinization varied across different ecosystem types and salinity levels. Soil salinization increased plant N content (18%), soil NH 4 + (12%) and soil total N (210%), although it decreased soil NO 3 - (2%) and soil microbial biomass N (74%). Increasing soil salinity stimulated soil N 2 O fluxes as well as hydrological NH 4 + and NO 2 - fluxes more than threefold, although it decreased the hydrological dissolved organic nitrogen (DON) flux (59%). Soil salinization also increased the net N mineralization by 70%, although salinization effects were not observed on the net nitrification, denitrification and dissimilatory nitrate reduction to ammonium in this meta-analysis. Overall, this meta-analysis improves our understanding of the responses of ecosystem N cycling to soil salinization, identifies knowledge gaps and highlights the urgent need for studies on the effects of soil salinization on coastal agro-ecosystem and microbial N immobilization. Additional increases in knowledge are critical for designing sustainable adaptation measures to the predicted intrusion of salinity intrusion so that the productivity of coastal agro-ecosystems can be maintained or improved and the N losses and pollution of the natural
Microbial community changes in heathland soil communities along a geographical gradient: Interaction with climate change manipulations

DEFF Research Database (Denmark)

Sowerby, A.; Emmett, B.; Beier, C.

2005-01-01

. Microbial extra-cellular enzyme production is linked to microbial activity as well as soil physico-chemical properties, making soil enzymes one of the more reactive components of terrestrial ecosystems and potentially excellent indicators of soil microbial functional status and diversity. Across all sites...... and over all the substrates, organic matter content was exponentially, inversely related to enzyme activity. Although the increase in temperature produced by the CLIMOOR roofs was small (on average 0.9 degrees C), this was sufficient to increase enzyme activity in all sites (on average by 45...
Comparative metagenomic, phylogenetic and physiological analyses of soil microbial communities across nitrogen gradients.

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Fierer, Noah; Lauber, Christian L; Ramirez, Kelly S; Zaneveld, Jesse; Bradford, Mark A; Knight, Rob

2012-05-01

Terrestrial ecosystems are receiving elevated inputs of nitrogen (N) from anthropogenic sources and understanding how these increases in N availability affect soil microbial communities is critical for predicting the associated effects on belowground ecosystems. We used a suite of approaches to analyze the structure and functional characteristics of soil microbial communities from replicated plots in two long-term N fertilization experiments located in contrasting systems. Pyrosequencing-based analyses of 16S rRNA genes revealed no significant effects of N fertilization on bacterial diversity, but significant effects on community composition at both sites; copiotrophic taxa (including members of the Proteobacteria and Bacteroidetes phyla) typically increased in relative abundance in the high N plots, with oligotrophic taxa (mainly Acidobacteria) exhibiting the opposite pattern. Consistent with the phylogenetic shifts under N fertilization, shotgun metagenomic sequencing revealed increases in the relative abundances of genes associated with DNA/RNA replication, electron transport and protein metabolism, increases that could be resolved even with the shallow shotgun metagenomic sequencing conducted here (average of 75 000 reads per sample). We also observed shifts in the catabolic capabilities of the communities across the N gradients that were significantly correlated with the phylogenetic and metagenomic responses, indicating possible linkages between the structure and functioning of soil microbial communities. Overall, our results suggest that N fertilization may, directly or indirectly, induce a shift in the predominant microbial life-history strategies, favoring a more active, copiotrophic microbial community, a pattern that parallels the often observed replacement of K-selected with r-selected plant species with elevated N.
Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0.

Directory of Open Access Journals (Sweden)

Brian R Granger

2016-04-01

Full Text Available The complexity of metabolic networks in microbial communities poses an unresolved visualization and interpretation challenge. We address this challenge in the newly expanded version of a software tool for the analysis of biological networks, VisANT 5.0. We focus in particular on facilitating the visual exploration of metabolic interaction between microbes in a community, e.g. as predicted by COMETS (Computation of Microbial Ecosystems in Time and Space, a dynamic stoichiometric modeling framework. Using VisANT's unique metagraph implementation, we show how one can use VisANT 5.0 to explore different time-dependent ecosystem-level metabolic networks. In particular, we analyze the metabolic interaction network between two bacteria previously shown to display an obligate cross-feeding interdependency. In addition, we illustrate how a putative minimal gut microbiome community could be represented in our framework, making it possible to highlight interactions across multiple coexisting species. We envisage that the "symbiotic layout" of VisANT can be employed as a general tool for the analysis of metabolism in complex microbial communities as well as heterogeneous human tissues. VisANT is freely available at: http://visant.bu.edu and COMETS at http://comets.bu.edu.
Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0.

Science.gov (United States)

Granger, Brian R; Chang, Yi-Chien; Wang, Yan; DeLisi, Charles; Segrè, Daniel; Hu, Zhenjun

2016-04-01

The complexity of metabolic networks in microbial communities poses an unresolved visualization and interpretation challenge. We address this challenge in the newly expanded version of a software tool for the analysis of biological networks, VisANT 5.0. We focus in particular on facilitating the visual exploration of metabolic interaction between microbes in a community, e.g. as predicted by COMETS (Computation of Microbial Ecosystems in Time and Space), a dynamic stoichiometric modeling framework. Using VisANT's unique metagraph implementation, we show how one can use VisANT 5.0 to explore different time-dependent ecosystem-level metabolic networks. In particular, we analyze the metabolic interaction network between two bacteria previously shown to display an obligate cross-feeding interdependency. In addition, we illustrate how a putative minimal gut microbiome community could be represented in our framework, making it possible to highlight interactions across multiple coexisting species. We envisage that the "symbiotic layout" of VisANT can be employed as a general tool for the analysis of metabolism in complex microbial communities as well as heterogeneous human tissues. VisANT is freely available at: http://visant.bu.edu and COMETS at http://comets.bu.edu.
The fate of mercury in Arctic terrestrial and aquatic ecosystems, a review

DEFF Research Database (Denmark)

Douglas, Thomas A.; Loseto, Lisa L.; MacDonald, Robie W.

2012-01-01

the fate of Hg in most ecosystems, and the role of trophic processes in controlling Hg in higher order animals are also included. Case studies on Eastern Beaufort Sea beluga (Delphinapterus leucas) and landlocked Arctic char (Salvelinus alpinus) are presented as examples of the relationship between...... into non-biological archives is also addressed. The review concludes by identifying major knowledge gaps in our understanding, including: (1) the rates of Hg entry into marine and terrestrial ecosystems and the rates of inorganic and MeHg uptake by Arctic microbial and algal communities; (2...
Taxonomic and Functional Responses of Soil Microbial Communities to Annual Removal of Aboveground Plant Biomass

Science.gov (United States)

Guo, Xue; Zhou, Xishu; Hale, Lauren; Yuan, Mengting; Feng, Jiajie; Ning, Daliang; Shi, Zhou; Qin, Yujia; Liu, Feifei; Wu, Liyou; He, Zhili; Van Nostrand, Joy D.; Liu, Xueduan; Luo, Yiqi; Tiedje, James M.; Zhou, Jizhong

2018-01-01

Clipping, removal of aboveground plant biomass, is an important issue in grassland ecology. However, few studies have focused on the effect of clipping on belowground microbial communities. Using integrated metagenomic technologies, we examined the taxonomic and functional responses of soil microbial communities to annual clipping (2010–2014) in a grassland ecosystem of the Great Plains of North America. Our results indicated that clipping significantly (P microbial respiration rates. Annual temporal variation within the microbial communities was much greater than the significant changes introduced by clipping, but cumulative effects of clipping were still observed in the long-term scale. The abundances of some bacterial and fungal lineages including Actinobacteria and Bacteroidetes were significantly (P microbial communities were significantly correlated with soil respiration and plant productivity. Intriguingly, clipping effects on microbial function may be highly regulated by precipitation at the interannual scale. Altogether, our results illustrated the potential of soil microbial communities for increased soil organic matter decomposition under clipping land-use practices. PMID:29904372
Response of soil microbial communities and microbial interactions to long-term heavy metal contamination.

Science.gov (United States)

Li, Xiaoqi; Meng, Delong; Li, Juan; Yin, Huaqun; Liu, Hongwei; Liu, Xueduan; Cheng, Cheng; Xiao, Yunhua; Liu, Zhenghua; Yan, Mingli

2017-12-01

Due to the persistence of metals in the ecosystem and their threat to all living organisms, effects of heavy metal on soil microbial communities were widely studied. However, little was known about the interactions among microorganisms in heavy metal-contaminated soils. In the present study, microbial communities in Non (CON), moderately (CL) and severely (CH) contaminated soils were investigated through high-throughput Illumina sequencing of 16s rRNA gene amplicons, and networks were constructed to show the interactions among microbes. Results showed that the microbial community composition was significantly, while the microbial diversity was not significantly affected by heavy metal contamination. Bacteria showed various response to heavy metals. Bacteria that positively correlated with Cd, e.g. Acidobacteria_Gp and Proteobacteria_thiobacillus, had more links between nodes and more positive interactions among microbes in CL- and CH-networks, while bacteria that negatively correlated with Cd, e.g. Longilinea, Gp2 and Gp4 had fewer network links and more negative interactions in CL and CH-networks. Unlike bacteria, members of the archaeal domain, i.e. phyla Crenarchaeota and Euryarchaeota, class Thermoprotei and order Thermoplasmatales showed only positive correlation with Cd and had more network interactions in CH-networks. The present study indicated that (i) the microbial community composition, as well as network interactions was shift to strengthen adaptability of microorganisms to heavy metal contamination, (ii) archaea were resistant to heavy metal contamination and may contribute to the adaption to heavy metals. It was proposed that the contribution might be achieved either by improving environment conditions or by cooperative interactions. Copyright © 2017 Elsevier Ltd. All rights reserved.
Microbial transformation of sesquitepenoid ketone, (+) Nootkatone by Macrophomia phaseolina

OpenAIRE

Vajira P. Bulugahapitiya; Syed Ghulam Musharaff

2009-01-01

Microbial transformation is an effective tool for the structural modification of bioactive natural and synthetic compounds leading to synthesis of more potent derivatives. Its application in asymmetric synthesis is increasing due to its versatility and ease. This article presents biotransformation of sesquiterpenoid ketone, (+)-Nootkatone (1) by M. phaseolina, a plant pathogenic fungus. The transformation afforded four main compounds. They were determined to be 1:6 stereoisomeric mixture of 1...
Large Plankton Enhance Heterotrophy Under Experimental Warming in a Temperate Coastal Ecosystem

KAUST Repository

Huete-Stauffer, Tamara Megan

2017-12-15

Microbes are key players in oceanic carbon fluxes. Temperate ecosystems are seasonally variable and thus suitable for testing the effect of warming on microbial carbon fluxes at contrasting oceanographic conditions. In four experiments conducted in February, April, August and October 2013 in coastal NE Atlantic waters, we monitored microbial plankton stocks and daily rates of primary production, bacterial heterotrophic production and respiration at in situ temperature and at 2 and 4°C over ambient values during 4-day incubations. Ambient total primary production (TPP) exceeded total community respiration (< 200 µm, TR) in winter and fall but not in spring and summer. The bacterial contribution to ecosystem carbon fluxes was low, with bacterial production representing on average 6.9 ± 3.2% of TPP and bacterial respiration (between 0.8 and 0.2 µm) contributing on average 35 ± 7% to TR. Warming did not result in a uniform increase in the variables considered, and most significant effects were found only for the 4°C increase. In the summer and fall experiments, under warm and nutrient-deficient conditions, the net TPP/TR ratio decreased by 39 and 34% in the 4°C treatment, mainly due to the increase in respiration of large organisms rather than bacteria. Our results indicate that the interaction of temperature and substrate availability in determining microbial carbon fluxes has a strong seasonal component in temperate planktonic ecosystems, with temperature having a more pronounced effect and generating a shift toward net heterotrophy under more oligotrophic conditions as found in summer and early fall.
A highly diverse, desert-like microbial biocenosis on solar panels in a Mediterranean city.

Science.gov (United States)

Dorado-Morales, Pedro; Vilanova, Cristina; Peretó, Juli; Codoñer, Francisco M; Ramón, Daniel; Porcar, Manuel

2016-07-05

Microorganisms colonize a wide range of natural and artificial environments although there are hardly any data on the microbial ecology of one the most widespread man-made extreme structures: solar panels. Here we show that solar panels in a Mediterranean city (Valencia, Spain) harbor a highly diverse microbial community with more than 500 different species per panel, most of which belong to drought-, heat- and radiation-adapted bacterial genera, and sun-irradiation adapted epiphytic fungi. The taxonomic and functional profiles of this microbial community and the characterization of selected culturable bacteria reveal the existence of a diverse mesophilic microbial community on the panels' surface. This biocenosis proved to be more similar to the ones inhabiting deserts than to any human or urban microbial ecosystem. This unique microbial community shows different day/night proteomic profiles; it is dominated by reddish pigment- and sphingolipid-producers, and is adapted to withstand circadian cycles of high temperatures, desiccation and solar radiation.
GENOME-BASED MODELING AND DESIGN OF METABOLIC INTERACTIONS IN MICROBIAL COMMUNITIES

Directory of Open Access Journals (Sweden)

Radhakrishnan Mahadevan

2012-10-01

With the advent of genome sequencing, omics technologies, bioinformatics and genome-scale modeling, researchers now have unprecedented capabilities to analyze and engineer the metabolism of microbial communities. The goal of this review is to summarize recent applications of genome-scale metabolic modeling to microbial communities. A brief introduction to lumped community models is used to motivate the need for genome-level descriptions of individual species and their metabolic interactions. The review of genome-scale models begins with static modeling approaches, which are appropriate for communities where the extracellular environment can be assumed to be time invariant or slowly varying. Dynamic extensions of the static modeling approach are described, and then applications of genome-scale models for design of synthetic microbial communities are reviewed. The review concludes with a summary of metagenomic tools for analyzing community metabolism and an outlook for future research.
Synthetic biology, inspired by synthetic chemistry.

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Malinova, V; Nallani, M; Meier, W P; Sinner, E K

2012-07-16

The topic synthetic biology appears still as an 'empty basket to be filled'. However, there is already plenty of claims and visions, as well as convincing research strategies about the theme of synthetic biology. First of all, synthetic biology seems to be about the engineering of biology - about bottom-up and top-down approaches, compromising complexity versus stability of artificial architectures, relevant in biology. Synthetic biology accounts for heterogeneous approaches towards minimal and even artificial life, the engineering of biochemical pathways on the organismic level, the modelling of molecular processes and finally, the combination of synthetic with nature-derived materials and architectural concepts, such as a cellular membrane. Still, synthetic biology is a discipline, which embraces interdisciplinary attempts in order to have a profound, scientific base to enable the re-design of nature and to compose architectures and processes with man-made matter. We like to give an overview about the developments in the field of synthetic biology, regarding polymer-based analogs of cellular membranes and what questions can be answered by applying synthetic polymer science towards the smallest unit in life, namely a cell. Copyright © 2012 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.
Improving Marine Ecosystem Models with Biochemical Tracers

Science.gov (United States)

Pethybridge, Heidi R.; Choy, C. Anela; Polovina, Jeffrey J.; Fulton, Elizabeth A.

2018-01-01

Empirical data on food web dynamics and predator-prey interactions underpin ecosystem models, which are increasingly used to support strategic management of marine resources. These data have traditionally derived from stomach content analysis, but new and complementary forms of ecological data are increasingly available from biochemical tracer techniques. Extensive opportunities exist to improve the empirical robustness of ecosystem models through the incorporation of biochemical tracer data and derived indices, an area that is rapidly expanding because of advances in analytical developments and sophisticated statistical techniques. Here, we explore the trophic information required by ecosystem model frameworks (species, individual, and size based) and match them to the most commonly used biochemical tracers (bulk tissue and compound-specific stable isotopes, fatty acids, and trace elements). Key quantitative parameters derived from biochemical tracers include estimates of diet composition, niche width, and trophic position. Biochemical tracers also provide powerful insight into the spatial and temporal variability of food web structure and the characterization of dominant basal and microbial food web groups. A major challenge in incorporating biochemical tracer data into ecosystem models is scale and data type mismatches, which can be overcome with greater knowledge exchange and numerical approaches that transform, integrate, and visualize data.
A Community-Based Culture Collection for Targeting Novel Plant Growth-Promoting Bacteria from the Sugarcane Microbiome

Directory of Open Access Journals (Sweden)

Jaderson Silveira Leite Armanhi

2018-01-01

Full Text Available The soil-plant ecosystem harbors an immense microbial diversity that challenges investigative approaches to study traits underlying plant-microbe association. Studies solely based on culture-dependent techniques have overlooked most microbial diversity. Here we describe the concomitant use of culture-dependent and -independent techniques to target plant-beneficial microbial groups from the sugarcane microbiome. The community-based culture collection (CBC approach was used to access microbes from roots and stalks. The CBC recovered 399 unique bacteria representing 15.9% of the rhizosphere core microbiome and 61.6–65.3% of the endophytic core microbiomes of stalks. By cross-referencing the CBC (culture-dependent with the sugarcane microbiome profile (culture-independent, we designed a synthetic community comprised of naturally occurring highly abundant bacterial groups from roots and stalks, most of which has been poorly explored so far. We then used maize as a model to probe the abundance-based synthetic inoculant. We show that when inoculated in maize plants, members of the synthetic community efficiently colonize plant organs, displace the natural microbiota and dominate at 53.9% of the rhizosphere microbial abundance. As a result, inoculated plants increased biomass by 3.4-fold as compared to uninoculated plants. The results demonstrate that abundance-based synthetic inoculants can be successfully applied to recover beneficial plant microbes from plant microbiota.
Influences of Different Halophyte Vegetation on Soil Microbial Community at Temperate Salt Marsh.

Science.gov (United States)

Chaudhary, Doongar R; Kim, Jinhyun; Kang, Hojeong

2018-04-01

Salt marshes are transitional zone between terrestrial and aquatic ecosystems, occupied mainly by halophytic vegetation which provides numerous ecological services to coastal ecosystem. Halophyte-associated microbial community plays an important role in the adaptation of plants to adverse condition and also affected habitat characteristics. To explore the relationship between halophytes and soil microbial community, we studied the soil enzyme activities, soil microbial community structure, and functional gene abundance in halophytes- (Carex scabrifolia, Phragmites australis, and Suaeda japonica) covered and un-vegetated (mud flat) soils at Suncheon Bay, South Korea. Higher concentrations of total, Gram-positive, Gram-negative, total bacterial, and actinomycetes PLFAs (phospholipid fatty acids) were observed in the soil underneath the halophytes compared with mud flat soil and were highest in Carex soil. Halophyte-covered soils had different microbial community composition due to higher abundance of Gram-negative bacteria than mud flat soil. Similar to PLFA concentrations, the increased activities of β-glucosidase, cellulase, phosphatase, and sulfatase enzymes were observed under halophyte soil compared to mud flat soil and Carex exhibited highest activities. The abundance of archaeal 16S rRNA, fungal ITS, and denitrifying genes (nirK, nirS, and nosZ) were not influenced by the halophytes. Abundance bacterial 16S rRNA and dissimilatory (bi)sulfite (dsrA) genes were highest in Carex-covered soil. The abundance of functional genes involved in methane cycle (mcrA and pmoA) was not affected by the halophytes. However, the ratios of mcrA/pmoA and mcrA/dsrA increased in halophyte-covered soils which indicate higher methanogenesis activities. The finding of the study also suggests that halophytes had increased the microbial and enzyme activities, and played a pivotal role in shaping microbial community structure.
Microbial metabolomics in open microscale platforms

Science.gov (United States)

Barkal, Layla J.; Theberge, Ashleigh B.; Guo, Chun-Jun; Spraker, Joe; Rappert, Lucas; Berthier, Jean; Brakke, Kenneth A.; Wang, Clay C. C.; Beebe, David J.; Keller, Nancy P.; Berthier, Erwin

2016-01-01

The microbial secondary metabolome encompasses great synthetic diversity, empowering microbes to tune their chemical responses to changing microenvironments. Traditional metabolomics methods are ill-equipped to probe a wide variety of environments or environmental dynamics. Here we introduce a class of microscale culture platforms to analyse chemical diversity of fungal and bacterial secondary metabolomes. By leveraging stable biphasic interfaces to integrate microculture with small molecule isolation via liquid–liquid extraction, we enable metabolomics-scale analysis using mass spectrometry. This platform facilitates exploration of culture microenvironments (including rare media typically inaccessible using established methods), unusual organic solvents for metabolite isolation and microbial mutants. Utilizing Aspergillus, a fungal genus known for its rich secondary metabolism, we characterize the effects of culture geometry and growth matrix on secondary metabolism, highlighting the potential use of microscale systems to unlock unknown or cryptic secondary metabolites for natural products discovery. Finally, we demonstrate the potential for this class of microfluidic systems to study interkingdom communication between fungi and bacteria. PMID:26842393
Microbial ecology of artisanal Italian Cheese: environment and working conditions

International Nuclear Information System (INIS)

Dioguardi, L.; Colombo, E.; Franzetti, L.

2009-01-01

In agro-food sector the structural features of working environments and consequently their hygienic conditions are of primary importance for a safe and quality food production and to ensure comfortable and ergonomic working conditions. In particular, as regards high-mountain dairy production, the environment is important because it can affect the development of typical microbial ecosystem. (Author)

Microbial ecology of artisanal Italian Cheese: environment and working conditions

Energy Technology Data Exchange (ETDEWEB)

Dioguardi, L.; Colombo, E.; Franzetti, L.

2009-07-01

In agro-food sector the structural features of working environments and consequently their hygienic conditions are of primary importance for a safe and quality food production and to ensure comfortable and ergonomic working conditions. In particular, as regards high-mountain dairy production, the environment is important because it can affect the development of typical microbial ecosystem. (Author)
Cultivable microscopic fungi from an underground chemosynthesis-based ecosystem: a preliminary study

Czech Academy of Sciences Publication Activity Database

Nováková, Alena; Hubka, Vít; Valinová, Š.; Kolařík, Miroslav; Hillebrand-Voiculescu, A.M.

2018-01-01

Roč. 63, č. 1 (2018), s. 43-55 ISSN 0015-5632 R&D Projects: GA MŠk(CZ) ED1.1.00/02.0109 Institutional support: RVO:61388971 Keywords : MOVILE CAVE * GROUNDWATER ECOSYSTEM * MICROBIAL COMMUNITIES Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 1.521, year: 2016
Hydraulic fracturing offers view of microbial life in the deep terrestrial subsurface.

Science.gov (United States)

Mouser, Paula J; Borton, Mikayla; Darrah, Thomas H; Hartsock, Angela; Wrighton, Kelly C

2016-11-01

Horizontal drilling and hydraulic fracturing are increasingly used for recovering energy resources in black shales across the globe. Although newly drilled wells are providing access to rocks and fluids from kilometer depths to study the deep biosphere, we have much to learn about microbial ecology of shales before and after 'fracking'. Recent studies provide a framework for considering how engineering activities alter this rock-hosted ecosystem. We first provide data on the geochemical environment and microbial habitability in pristine shales. Next, we summarize data showing the same pattern across fractured shales: diverse assemblages of microbes are introduced into the subsurface, eventually converging to a low diversity, halotolerant, bacterial and archaeal community. Data we synthesized show that the shale microbial community predictably shifts in response to temporal changes in geochemistry, favoring conservation of key microorganisms regardless of inputs, shale location or operators. We identified factors that constrain diversity in the shale and inhibit biodegradation at the surface, including salinity, biocides, substrates and redox. Continued research in this engineered ecosystem is required to assess additive biodegradability, quantify infrastructure biocorrosion, treat wastewaters that return to the surface and potentially enhance energy production through in situ methanogenesis. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
BSocial: Deciphering Social Behaviors within Mixed Microbial Populations

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Jessica Purswani

2017-05-01

Full Text Available Ecosystem functionality depends on interactions among populations, of the same or different taxa, and these are not just the sum of pairwise interactions. Thus, know-how of the social interactions occurring in mixed-populations are of high interest, however they are commonly unknown due to the limitations posed in tagging each population. The limitations include costs/time in tediously fluorescent tagging, and the number of different fluorescent tags. Tag-free strategies exist, such as high-throughput sequencing, but ultimately both strategies require the use of expensive machinery. Our work appoints social behaviors on individual strains in mixed-populations, offering a web-tool (BSocialhttp://m4m.ugr.es/BSocial.html for analyzing the community framework. Our quick and cheap approach includes the periodic monitoring of optical density (OD from a full combinatorial testing of individual strains, where number of generations and growth rate are determined. The BSocial analyses then enable us to determine how the addition/absence of a particular species affects the net productivity of a microbial community and use this to select productive combinations, i.e., designate their social effect on a general community. Positive, neutral, or negative assignations are applied to describe the social behavior within the community by comparing fitness effects of the community against the individual strain. The usefulness of this tool for selection of optimal inoculum in biofilm-based methyl tert-butyl ether (MTBE bioremediation was demonstrated. The studied model uses seven bacterial strains with diverse MTBE degradation/growth capacities. Full combinatorial testing of seven individual strains (triplicate tests of 127 combinations were implemented, along with MTBE degradation as the desired function. Sole observation of highest species fitness did not render the best functional outcome, and only when strains with positive and neutral social assignations were
Soil microbial activity in Aleppo pine stands naturally regenerated after fire: silvicultural management and induced drought

Directory of Open Access Journals (Sweden)

D. Moya

2013-01-01

Full Text Available In post-fire restoration, early monitoring is mandatory to check impacts and ecosystem responses to apply proper management according to social standards and ecological conditions. In areas where the natural regeneration was successful, excessive tree density can be found which induces to high intraspecific competence and assisted restoration management could be adequate. In addition, climatic changes will have large impacts on vegetation productivity and resilience since the regional models for south-eastern Spain predicts a rainfall decrease of about 20% and temperature increase of 4.5 ºC. The microbial biomass could be used as indicator of ecosystem recovery, since it is negatively affected by wildfires and depends on fire characteristics, vegetation and soil properties. Our aim is to determine how forest management may affect the ecosystem recovery in different climatic scenarios, included drought scenarios with and without forest management (thinning.We compared soil physicochemical properties and microbial activity in four scenarios: unmanaged and thinned stands in two rainfall scenarios (under induced drought. The study areas were set close to Yeste (Albacete where Aleppo pine forest were burned in summer 1994 (nearly 14000 ha. We set sixteen rectangular plots (150 m2; 15 m ×10 m implementing experimental silvicultural treatments: thinning eight plots in 2004, reducing the naturally recovered tree density from about 12000 to 1600 pine trees ha-1. In addition, in half the plots, we induced drought conditions from about 500 to 400 mm (20% from March 2009. In every plot, we monitored temperature at ground level (Ts, 10 cm depth (T10d and soil relative humidity (RH. Taking into account season of the year and canopy coverage, we collected soil samples in mid-winter (ending January 2011 and mid-spring (ending May 2011 under pine trees and in bare soil. The soil samples were used to evaluate soil physicochemical properties and soil microbial
Diversity and seasonal fluctuation of predominant microbial communities in Bhitarkanika, a tropical mangrove ecosystem in India

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Rashmi Ranjan Mishra

2012-06-01

Full Text Available Different groups of microorganisms are present in mangrove areas, and they perform complex interactions for nutrient and ecological balances. Since little is known about microbial populations in mangroves, this study analyzed the microbial community structure and function in relation to soil physico-chemical properties in Bhitarkanika, a tropical mangrove ecosystem in India. Spatial and seasonal fluctuations of thirteen important groups of microorganisms were evaluated from the mangrove forest sediments during different seasons, along with soil physico-chemical parameters. The overall microbial load (x10(5cfu/g soil in soil declined in the order of heterotrophic, free living N2 fixing, Gram-negative nitrifying, sulphur oxidizing, Gram-positive, spore forming, denitrifying, anaerobic, phosphate solubilizing, cellulose degrading bacteria, fungi and actinomycetes. Populations of the heterotrophic, phosphate solubilizing, sulphur oxidizing bacteria and fungi were more represented in the rainy season, while, Gram-negative, Gram-positive, nitrifying, denitrifying, cellulose decomposing bacteria and actinomycetes in the winter season. The pool size of most of other microbes either declined or maintained throughout the season. Soil nutrients such as N, P, K (Kg/ha and total C (% contents were higher in the rainy season and they did not follow any common trend of changes throughout the study period. Soil pH and salinity (mS/cm varied from 6-8 and 6.4-19.5, respectively, and they normally affected the microbial population dynamics. Determination of bacterial diversity in Bhitarkanika mangrove soil by culture method showed the predominance of bacterial genera such as Bacillus, Pseudomonas, Desulfotomaculum, Desulfovibrio, Desulfomonas, Methylococcus, Vibrio, Micrococcus, Klebsiella and Azotobacter. Principal component analysis (PCA revealed a correlation among local environmental variables with the sampling locations on the microbial community in the
Microbial habitability of Europa sustained by radioactive sources.

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Altair, Thiago; de Avellar, Marcio G B; Rodrigues, Fabio; Galante, Douglas

2018-01-10

There is an increasing interest in the icy moons of the Solar System due to their potential habitability and as targets for future exploratory missions, which include astrobiological goals. Several studies have reported new results describing the details of these moons' geological settings; however, there is still a lack of information regarding the deep subsurface environment of the moons. The purpose of this article is to evaluate the microbial habitability of Europa constrained by terrestrial analogue environments and sustained by radioactive energy provided by natural unstable isotopes. The geological scenarios are based on known deep environments on Earth, and the bacterial ecosystem is based on a sulfate-reducing bacterial ecosystem found 2.8 km below the surface in a basin in South Africa. The results show the possibility of maintaining the modeled ecosystem based on the proposed scenarios and provides directions for future models and exploration missions for a more complete evaluation of the habitability of Europa and of icy moons in general.
Changes in Soil Organic Matter Abundance, Molecular Composition, and Diversity in an Arid Ecosystem in Response to Long-term Elevated CO2 Manipulation.

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Hess, N. J.; Tfaily, M.; Evans, R. D.; Koyama, A.

2017-12-01

Little is known about how soils in arid ecosystems will respond to rising atmospheric CO2 concentration yet arid and semi-arid ecosystems cover more than 40% of Earth's land surface. Previous work in the Mojave Desert (Evans et al., 2014 Nature Climate Change) reported higher soil organic carbon (SOC) and total nitrogen (N) concentrations following 10 years exposure to elevated atmospheric CO2 at the Nevada Desert Free-Air-Carbon dioxide-Enrichment (FACE) Facility (NDFF). In this study, we investigated potential mechanisms that resulted in increased SOC and total N accumulation and stabilization using high resolution mass spectrometry at the NDFF site. Samples were collected from soil profiles to 1 m in depth with a 0.2 m a increment under the dominant evergreen shrub Larrea tridentata. The differences in the molecular composition and diversity of soil organic matter (SOM) were more evident in surface soils and declined with depth, and were consistent with higher SOC and total N concentrations under elevated than ambient CO2. Our molecular analysis also suggested increased root exudation and/or microbial necromass from stabilization of labile C and N contributed to SOM and N stocks. Increased microbial activity and metabolism under elevated CO2 compared to ambient plots suggested that elevated CO2 altered microbial carbon (C) use patterns, reflecting changes in the quality and quantity of SOC inputs. We found that plant-derived compounds were primary substrates for microbial activity under elevated CO2 and microbial products were the main constituents of stabilized SOM. Our results suggest that arid ecosystems are a potential large C sink under elevated CO2, give the extensive coverage of the land surface, and that labile compounds are transformed to stable SOM via microbial processes. Arid systems are limited by water, and thus may have a different C storage potential under changing climates than other ecosystems that are limited by nitrogen or phosphorus.
Protection of Antarctic microbial communities – ‘out of sight, out of mind’

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Hughes, Kevin A.; Cowan, Don A.; Wilmotte, Annick

2015-01-01

Recent advances in molecular biology techniques have shown the presence of diverse microbial communities and endemic species in Antarctica. Endemic microbes may be a potential source of novel biotechnologically important compounds, including, for example, new antibiotics. Thus, the scientific and biotechnological value of Antarctic terrestrial microbial habitats can be compromised by human visitation to a greater extent than previously realized. The ever-increasing human footprint in Antarctica makes consideration of this topic more pressing, as the number of locations known to be pristine habitats, where increasingly sophisticated cutting-edge research techniques may be used to their full potential, declines. Examination of the Protected Areas system of the Antarctic Treaty shows that microbial habitats are generally poorly protected. No other continent on Earth is dominated to the same degree by microbial species, and real opportunities exist to develop new ways of conceptualizing and implementing conservation of microbial biogeography on a continental scale. Here we highlight potential threats both to the conservation of terrestrial microbial ecosystems, and to future scientific research requiring their study. PMID:25762992
Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales

Energy Technology Data Exchange (ETDEWEB)

Daly, Rebecca A.; Borton, Mikayla A.; Wilkins, Michael J.; Hoyt, David W.; Kountz, Duncan J.; Wolfe, Richard A.; Welch, Susan A.; Marcus, Daniel N.; Trexler, Ryan V.; MacRae, Jean D.; Krzycki, Joseph A.; Cole, David R.; Mouser, Paula J.; Wrighton, Kelly C.

2016-09-05

Hydraulic fracturing is the industry standard for extracting hydrocarbons from shale formations. Attention has been paid to the economic benefits and environmental impacts of this process, yet the biogeochemical changes induced in the deep subsurface are poorly understood. Recent single-gene investigations revealed that halotolerant microbial communities were enriched after hydraulic fracturing. Here the reconstruction of 31 unique genomes coupled to metabolite data from the Marcellus and Utica shales revealed that methylamine cycling supports methanogenesis in the deep biosphere. Fermentation of injected chemical additives also sustains long-term microbial persistence, while sulfide generation from thiosulfate represents a poorly recognized corrosion mechanism in shales. Extensive links between viruses and microbial hosts demonstrate active viral predation, which may contribute to the release of labile cellular constituents into the extracellular environment. Our analyses show that hydraulic fracturing provides the organismal and chemical inputs for colonization and persistence in the deep terrestrial subsurface.
Cumulative response of ecosystem carbon and nitrogen stocks to chronic CO₂ exposure in a subtropical oak woodland.

Science.gov (United States)

Hungate, Bruce A; Dijkstra, Paul; Wu, Zhuoting; Duval, Benjamin D; Day, Frank P; Johnson, Dale W; Megonigal, J Patrick; Brown, Alisha L P; Garland, Jay L

2013-11-01

Rising atmospheric carbon dioxide (CO₂) could alter the carbon (C) and nitrogen (N) content of ecosystems, yet the magnitude of these effects are not well known. We examined C and N budgets of a subtropical woodland after 11 yr of exposure to elevated CO₂. We used open-top chambers to manipulate CO₂ during regrowth after fire, and measured C, N and tracer (15) N in ecosystem components throughout the experiment. Elevated CO₂ increased plant C and tended to increase plant N but did not significantly increase whole-system C or N. Elevated CO₂ increased soil microbial activity and labile soil C, but more slowly cycling soil C pools tended to decline. Recovery of a long-term (15) N tracer indicated that CO₂ exposure increased N losses and altered N distribution, with no effect on N inputs. Increased plant C accrual was accompanied by higher soil microbial activity and increased C losses from soil, yielding no statistically detectable effect of elevated CO₂ on net ecosystem C uptake. These findings challenge the treatment of terrestrial ecosystems responses to elevated CO₂ in current biogeochemical models, where the effect of elevated CO₂ on ecosystem C balance is described as enhanced photosynthesis and plant growth with decomposition as a first-order response. © 2013 The Authors. New Phytologist © 2013 New Phytologist Trust.
Biocontainment of genetically modified organisms by synthetic protein design

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Mandell, Daniel J.; Lajoie, Marc J.; Mee, Michael T.; Takeuchi, Ryo; Kuznetsov, Gleb; Norville, Julie E.; Gregg, Christopher J.; Stoddard, Barry L.; Church, George M.

2015-02-01

Genetically modified organisms (GMOs) are increasingly deployed at large scales and in open environments. Genetic biocontainment strategies are needed to prevent unintended proliferation of GMOs in natural ecosystems. Existing biocontainment methods are insufficient because they impose evolutionary pressure on the organism to eject the safeguard by spontaneous mutagenesis or horizontal gene transfer, or because they can be circumvented by environmentally available compounds. Here we computationally redesign essential enzymes in the first organism possessing an altered genetic code (Escherichia coli strain C321.ΔA) to confer metabolic dependence on non-standard amino acids for survival. The resulting GMOs cannot metabolically bypass their biocontainment mechanisms using known environmental compounds, and they exhibit unprecedented resistance to evolutionary escape through mutagenesis and horizontal gene transfer. This work provides a foundation for safer GMOs that are isolated from natural ecosystems by a reliance on synthetic metabolites.
Understanding Microbial Contributions to Planetary Atmosphere

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DesMarais, David J.

2000-01-01

signatures of life. Remarkably little is known about the composition of our own earlier atmosphere, particularly prior to the rise of oxygen levels some 2.0 to 2.2 billion years ago. Thus, field and laboratory observations and theoretical simulations should be conducted to examine the relationships between the structure and function of microbial ecosystems and their gaseous products. Ecosystems that are analogs of our ancient biosphere (e.g., based upon chemosynthesis or non-oxygenic photosynthesis, thermophilic and subsurface communities, etc.) should be included. Because key environmental parameters such as temperature and levels of hydrogen, carbon dioxide and oxygen varied during planetary evolution, their consequences for microbial ecosystems should be explored.
Stoichiometric imbalances between terrestrial decomposer communities and their resources: mechanisms and implications of microbial adaptations to their resources

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Maria eMooshammer

2014-02-01

Full Text Available Terrestrial microbial decomposer communities thrive on a wide range of organic matter types that rarely ever meet their elemental demands. In this review we synthesize the current state-of-the-art of microbial adaptations to resource stoichiometry, in order to gain a deeper understanding of the interactions between heterotrophic microbial communities and their chemical environment. The stoichiometric imbalance between microbial communities and their organic substrates generally decreases from wood to leaf litter and further to topsoil and subsoil organic matter. Microbial communities can respond to these imbalances in four ways: first, they adapt their biomass composition towards their resource in a non-homeostatic behaviour. Such changes are, however, only moderate, and occur mainly because of changes in microbial community structure and less so due to cellular storage of elements in excess. Second, microbial communities can mobilize resources that meet their elemental demand by producing specific extracellular enzymes, which, in turn, is restricted by the C and N requirement for enzyme production itself. Third, microbes can regulate their element use efficiencies (ratio of element invested in growth over total element uptake, such that they release elements in excess depending on their demand (e.g., respiration and N mineralization. Fourth, diazotrophic bacteria and saprotrophic fungi may trigger the input of external N and P to decomposer communities. Theoretical considerations show that adjustments in element use efficiencies may be the most important mechanism by which microbes regulate their biomass stoichiometry. This review summarizes different views on how microbes cope with imbalanced supply of C, N and P, thereby providing a framework for integrating and linking microbial adaptation to resource imbalances to ecosystem scale fluxes across scales and ecosystems.
Applying Fingerprint Fourier Transformed Infrared Spectroscopy and Chemometrics to Assess Soil Ecosystem Disturbance and Recovery

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The assessment and monitoring of soil ecosystem function has been hindered due to the shortcomings of many traditional analytical techniques (e.g., soil enzyme activities, microbial incubations), including: high cost, long time investment and difficulties with data interpretation. Consequently, ther...
Integration of microbial biopesticides in greenhouse floriculture: The Canadian experience.

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Brownbridge, Michael; Buitenhuis, Rose

2017-11-28

Historically, greenhouse floriculture has relied on synthetic insecticides to meet its pest control needs. But, growers are increasingly faced with the loss or failure of synthetic chemical pesticides, declining access to new chemistries, stricter environmental/health and safety regulations, and the need to produce plants in a manner that meets the 'sustainability' demands of a consumer driven market. In Canada, reports of thrips resistance to spinosad (Success™) within 6-12 months of its registration prompted a radical change in pest management philosophy and approach. Faced with a lack of registered chemical alternatives, growers turned to biological control out of necessity. Biological control now forms the foundation for pest management programs in Canadian floriculture greenhouses. Success in a biocontrol program is rarely achieved through the use of a single agent, though. Rather, it is realized through the concurrent use of biological, cultural and other strategies within an integrated plant production system. Microbial insecticides can play a critical supporting role in biologically-based integrated pest management (IPM) programs. They have unique modes of action and are active against a range of challenging pests. As commercial microbial insecticides have come to market, research to generate efficacy data has assisted their registration in Canada, and the development and adaptation of integrated programs has promoted uptake by floriculture growers. This review documents some of the work done to integrate microbial insecticides into chrysanthemum and poinsettia production systems, outlines current use practices, and identifies opportunities to improve efficacy in Canadian floriculture crops. Copyright © 2017 Elsevier Inc. All rights reserved.
Biogeochemistry of a submerged groundwater seep ecosystem in Lake Huron near karst region of Alpena, MI

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Kinsman-Costello, L. E.; Dick, G.; Sheik, C.; Burton, G. A.; Sheldon, N. D.

2015-12-01

Submerged groundwater seeps in Lake Huron establish ecosystems with distinctive geochemical conditions. In the Middle Island Sinkhole (MIS), a 23-m deep seep, groundwater seepage establishes low O2 (< 4 mg L-1), high sulfate (6 mM) conditions, in which a purple cyanobacteria-dominated mat thrives. The mat is capable of anoxygenic photosynthesis, oxygenic photosynthesis, and chemosynthesis. Within the top 3 cm of the mat-water interface, hydrogen sulfide concentrations increase to 1-7 mM. Little is known about the structure and function of microbes within organic-rich, high-sulfide sediments beneath the mat. Using pore water and sediment geochemical characterization along with microbial community analysis, we elucidated relationships between microbial community structure and ecosystem function along vertical gradients. In sediment pore waters, biologically reactive solutes (SO42-, NH4+, PO43-, and CH4) displayed steep vertical gradients, reflecting biological and geochemical functioning. In contrast, more conservative ions (Ca+2, Mg+2, Na+, and Cl-), did not change significantly with depth in MIS sediments, indicating groundwater influence in the sediment profile. MIS sediments contained more organic matter than typical Lake Huron sediments, and were generally higher in nutrients, metals, and sulfur (acid volatile sulfide). Using the Illumina MiSeq platform we detected 14,127 unique operational taxonomic units across sediment and surface mat samples. Microbial community composition in the MIS was distinctly different from non-groundwater affected areas at similar depth nearby in Lake Huron (ANOSIM, R= 0.74, p=0.002). MIS sediment communities were more diverse that MIS surface mat communities and changed with depth into sediments. MIS sediment community composition was related to several geochemical variables, including organic matter and multiple indicators of phosphorus availability. Elucidating the structure and function of microbial consortia in MIS, a highly
The limnic ecosystems at Forsmark and Laxemar-Simpevarp. Site descriptive modelling SDM-Site

Energy Technology Data Exchange (ETDEWEB)

Norden, Sara; Soederbaeck, Bjoern [Swedish Nuclear Fuel and Waste Management Co., Stockholm (Sweden); Andersson, Eva [SWECO, Stockholm (Sweden)

2008-11-15

The overall objective of this report is to provide a thorough description of the limnic ecosystems at both Forsmark and Laxemar-Simpevarp. This information may be used in the Safety Assessment and as a basis for the Environmental Impact Assessment. Three aims were set up for the report: 1) to characterize and describe the limnic ecosystems today and in the past in the Forsmark and Laxemar-Simpevarp areas and compare these ecosystems with limnic ecosystems in other areas; 2) to evaluate and visualize major pools, fluxes and sinks of elements within the limnic ecosystems; and finally 3) to describe human impact on the limnic ecosystems. The report includes a thorough description of the lakes and streams in Forsmark and Laxemar-Simpevarp and covers the following areas: catchment area characteristics, hydrology, climate, sediment characteristics, physical characteristics of streams, habitat distribution in lakes, biotic components, water chemistry, comparisons with other lakes and streams in the region, and a historical description. Ecosystem models for carbon and mass balances for a number of elements have been calculated to further improve the understanding of the lake ecosystems. Important processes for the safety assessment are described and evaluated in the report. The Forsmark regional model area contains more than 20 permanent lakes and pools. All lakes are small and shallow, and are characterized as oligotrophic hardwater lakes. Calcareous soils in the area give rise to high calcium concentrations in the surface water, which in turn leads to high pH and low nutrient concentrations in water as phosphorus often co-precipitates with calcium. The shallow depths and moderate water colour permit photosynthesis in the entire benthic habitat of the lakes, and the bottoms are covered by dense stands of the macroalgae Chara sp. Moreover, many of the lakes also have a thick microbial mat (>10 cm), consisting of cyanobacteria and diatoms, in the benthic habitat. Fish in
Performance of Microbial Fuel Cell for Wastewater Treatment and Electricity Generation

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Z Yavari

2013-06-01

Full Text Available Renewable energy will have an important role as a resource of energy in the future. Microbial fuel cell (MFC is a promising method to obtain electricity from organic matter andwastewater treatment simultaneously. In a pilot study, use of microbial fuel cell for wastewater treatment and electricity generation investigated. The bacteria of ruminant used as inoculums. Synthetic wastewater used at different organic loading rate. Hydraulic retention time was aneffective factor in removal of soluble COD and more than 49% removed. Optimized HRT to achieve the maximum removal efficiency and sustainable operation could be regarded 1.5 and 2.5 hours. Columbic efficiency (CE affected by organic loading rate (OLR and by increasing OLR, CE reduced from 71% to 8%. Maximum voltage was 700mV. Since the microbial fuel cell reactor considered as an anaerobic process, it may be an appropriate alternative for wastewater treatment
Environmental microbiology as a mosaic of explored ecosystems and issues.

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Faure, Denis; Bonin, Patricia; Duran, Robert

2015-09-01

Microbes are phylogenetically (Archaea, Bacteria, Eukarya, and viruses) and functionally diverse. They colonize highly varied environments and rapidly respond to and evolve as a response to local and global environmental changes, including those induced by pollutants resulting from human activities. This review exemplifies the Microbial Ecology EC2CO consortium's efforts to explore the biology, ecology, diversity, and roles of microbes in aquatic and continental ecosystems.

Microbial functional diversity associated with plant litter decomposition along a climatic gradient.

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Sherman, Chen; Steinberger, Yosef

2012-08-01

Predicted changes in climate associated with increased greenhouse gas emissions can cause increases in global mean temperature and changes in precipitation regimes. These changes may affect key soil processes, e.g., microbial CO(2) evolution and biomass, mineralization rates, primary productivity, biodiversity, and litter decomposition, which play an important role in carbon and nutrient cycling in terrestrial ecosystems. Our study examined the changes in litter microbial communities and decomposition along a climatic gradient, ranging from arid desert to humid Mediterranean regions in Israel. Wheat straw litter bags were placed in arid, semi-arid, Mediterranean, and humid Mediterranean sites. Samples were collected seasonally over a 2-year period in order to evaluate mass loss, litter moisture, C/N ratio, bacterial colony-forming units (CFUs), microbial CO(2) evolution and biomass, microbial functional diversity, and catabolic profile. Decomposition rate was the highest during the first year of the study at the Mediterranean and arid sites. Community-level physiological profile and microbial biomass were the highest in summer, while bacterial CFUs were the highest in winter. Microbial functional diversity was found to be highest at the humid Mediterranean site, whereas substrate utilization increased at the arid site. Our results support the assumption that climatic factors control litter degradation and regulate microbial activity.
[Recent advances of synthetic biology for production of functional ingredients in Chinese materia medica].

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Su, Xin-Yao; Xue, Jian-Ping; Wang, Cai-Xia

2016-11-01

The functional ingredients in Chinese materia medica are the main active substance for traditional Chinese medicine and most of them are secondary metabolites derivatives. Until now,the main method to obtain those functional ingredients is through direct extraction from the Chinese materia medica. However, the income is very low because of the high extraction costs and the decreased medicinal plants. Synthetic biology technology, as a new and microbial approach, can be able to carry out large-scale production of functional ingredients and greatly ease the shortage of traditional Chinese medicine ingredients. This review mainly focused on the recent advances in synthetic biology for the functional ingredients production. Copyright© by the Chinese Pharmaceutical Association.
Sediment microbial fuel cells for wastewater treatment: challenges and opportunities

OpenAIRE

Xu, Bojun; Ge, Zheng; He, Zhen

2015-01-01

Sediment microbial fuel cells (SMFCs) have been intensively investigated for the harvest of energy from natural sediment, but studies of their application for wastewater treatment mainly occurred in the past 2-3 years. SMFCs with simple structures can generate electrical energy while decontaminating wastewater. Most SMFCs used for wastewater treatment contain plants to mimic constructed wetlands. Both synthetic and real wastewaters have been used as substrates in SMFCs that achieved satisfact...
Responses of redwood soil microbial community structure and N transformations to climate change

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Damon C. Bradbury; Mary K. Firestone

2012-01-01

Soil microorganisms perform critical ecosystem functions, including decomposition, nitrogen (N) mineralization and nitrification. Soil temperature and water availability can be critical determinants of the rates of these processes as well as microbial community composition and structure. This research examined how changes in climate affect bacterial and fungal...
Ecosystem stability in space: α, β and γ variability.

Science.gov (United States)

Wang, Shaopeng; Loreau, Michel

2014-08-01

The past two decades have seen great progress in understanding the mechanisms of ecosystem stability in local ecological systems. There is, however, an urgent need to extend existing knowledge to larger spatial scales to match the scale of management and conservation. Here, we develop a general theoretical framework to study the stability and variability of ecosystems at multiple scales. Analogously to the partitioning of biodiversity, we propose the concepts of alpha, beta and gamma variability. Gamma variability at regional (metacommunity) scale can be partitioned into local alpha variability and spatial beta variability, either multiplicatively or additively. On average, variability decreases from local to regional scales, which creates a negative variability-area relationship. Our partitioning framework suggests that mechanisms of regional ecosystem stability can be understood by investigating the influence of ecological factors on alpha and beta variability. Diversity can provide insurance effects at the various levels of variability, thus generating alpha, beta and gamma diversity-stability relationships. As a consequence, the loss of biodiversity and habitat impairs ecosystem stability at the regional scale. Overall, our framework enables a synthetic understanding of ecosystem stability at multiple scales and has practical implications for landscape management. © 2014 John Wiley & Sons Ltd/CNRS.
Soil microbial diversity in the vicinity of desert shrubs.

Science.gov (United States)

Saul-Tcherkas, Vered; Unc, Adrian; Steinberger, Yosef

2013-04-01

Water and nutrient availability are the major limiting factors of biological activity in arid and semiarid ecosystems. Therefore, perennial plants have developed different ecophysiological adaptations to cope with harsh conditions. The chemical profile of the root exudates varies among plant species and this can induce variability in associated microbial populations. We examined the influence of two shrubs species, Artemisia sieberi and Noaea mucronata, on soil microbial diversity. Soil samples were collected monthly, from December 2006 to November 2007, near canopies of both shrubs (0-10-cm depth). Samples were used for abiotic tests and determination of soil bacterial diversity. No significant differences were found in the abiotic variables (soil moisture, total organic matter, and total soluble nitrogen (TSN)) between soil samples collected from under the two shrubs during the study period. No obvious differences in the Shannon-Weaver index, evenness values, or total phylogenetic distances were found for the soil microbial communities. However, detailed denaturing gradient gel electrophoresis (DGGE) clustering as well as taxonomic diversity analyses indicated clear shifts in the soil microbial community composition. These shifts were governed by seasonal variability in water availability and, significantly, by plant species type.
Build your own soil: exploring microfluidics to create microbial habitat structures

Science.gov (United States)

Aleklett, Kristin; Kiers, E Toby; Ohlsson, Pelle; Shimizu, Thomas S; Caldas, Victor EA; Hammer, Edith C

2018-01-01

Soil is likely the most complex ecosystem on earth. Despite the global importance and extraordinary diversity of soils, they have been notoriously challenging to study. We show how pioneering microfluidic techniques provide new ways of studying soil microbial ecology by allowing simulation and manipulation of chemical conditions and physical structures at the microscale in soil model habitats. PMID:29135971
Microbial ecology of Thailand tsunami and non-tsunami affected terrestrials.

Science.gov (United States)

Somboonna, Naraporn; Wilantho, Alisa; Jankaew, Kruawun; Assawamakin, Anunchai; Sangsrakru, Duangjai; Tangphatsornruang, Sithichoke; Tongsima, Sissades

2014-01-01

The effects of tsunamis on microbial ecologies have been ill-defined, especially in Phang Nga province, Thailand. This ecosystem was catastrophically impacted by the 2004 Indian Ocean tsunami as well as the 600 year-old tsunami in Phra Thong island, Phang Nga province. No study has been conducted to elucidate their effects on microbial ecology. This study represents the first to elucidate their effects on microbial ecology. We utilized metagenomics with 16S and 18S rDNA-barcoded pyrosequencing to obtain prokaryotic and eukaryotic profiles for this terrestrial site, tsunami affected (S1), as well as a parallel unaffected terrestrial site, non-tsunami affected (S2). S1 demonstrated unique microbial community patterns than S2. The dendrogram constructed using the prokaryotic profiles supported the unique S1 microbial communities. S1 contained more proportions of archaea and bacteria domains, specifically species belonging to Bacteroidetes became more frequent, in replacing of the other typical floras like Proteobacteria, Acidobacteria and Basidiomycota. Pathogenic microbes, including Acinetobacter haemolyticus, Flavobacterium spp. and Photobacterium spp., were also found frequently in S1. Furthermore, different metabolic potentials highlighted this microbial community change could impact the functional ecology of the site. Moreover, the habitat prediction based on percent of species indicators for marine, brackish, freshwater and terrestrial niches pointed the S1 to largely comprise marine habitat indicating-species.
Influences of organic carbon speciation on hyporheic corridor biogeochemistry and microbial ecology.

Science.gov (United States)

Stegen, James C; Johnson, Tim; Fredrickson, James K; Wilkins, Michael J; Konopka, Allan E; Nelson, William C; Arntzen, Evan V; Chrisler, William B; Chu, Rosalie K; Fansler, Sarah J; Graham, Emily B; Kennedy, David W; Resch, Charles T; Tfaily, Malak; Zachara, John

2018-02-08

The hyporheic corridor (HC) encompasses the river-groundwater continuum, where the mixing of groundwater (GW) with river water (RW) in the HC can stimulate biogeochemical activity. Here we propose a novel thermodynamic mechanism underlying this phenomenon and reveal broader impacts on dissolved organic carbon (DOC) and microbial ecology. We show that thermodynamically favorable DOC accumulates in GW despite lower DOC concentration, and that RW contains thermodynamically less-favorable DOC, but at higher concentrations. This indicates that GW DOC is protected from microbial oxidation by low total energy within the DOC pool, whereas RW DOC is protected by lower thermodynamic favorability of carbon species. We propose that GW-RW mixing overcomes these protections and stimulates respiration. Mixing models coupled with geophysical and molecular analyses further reveal tipping points in spatiotemporal dynamics of DOC and indicate important hydrology-biochemistry-microbial feedbacks. Previously unrecognized thermodynamic mechanisms regulated by GW-RW mixing may therefore strongly influence biogeochemical and microbial dynamics in riverine ecosystems.
Cumulative response of ecosystem carbon and nitrogen stocks to chronic CO2 exposure in a subtropical oak woodland

Science.gov (United States)

Hungate, Bruce A; Dijkstra, Paul; Wu, Zhuoting; Duval, Benjamin D; Day, Frank P; Johnson, Dale W; Megonigal, J Patrick; Brown, Alisha L P; Garland, Jay L

2013-01-01

Summary Rising atmospheric carbon dioxide (CO2) could alter the carbon (C) and nitrogen (N) content of ecosystems, yet the magnitude of these effects are not well known. We examined C and N budgets of a subtropical woodland after 11 yr of exposure to elevated CO2. We used open-top chambers to manipulate CO2 during regrowth after fire, and measured C, N and tracer 15N in ecosystem components throughout the experiment. Elevated CO2 increased plant C and tended to increase plant N but did not significantly increase whole-system C or N. Elevated CO2 increased soil microbial activity and labile soil C, but more slowly cycling soil C pools tended to decline. Recovery of a long-term 15N tracer indicated that CO2 exposure increased N losses and altered N distribution, with no effect on N inputs. Increased plant C accrual was accompanied by higher soil microbial activity and increased C losses from soil, yielding no statistically detectable effect of elevated CO2 on net ecosystem C uptake. These findings challenge the treatment of terrestrial ecosystems responses to elevated CO2 in current biogeochemical models, where the effect of elevated CO2 on ecosystem C balance is described as enhanced photosynthesis and plant growth with decomposition as a first-order response. PMID:23718224
The use of controlled microbial cenoses in producers' link to increase steady functioning of artificial ecosystems

Science.gov (United States)

Somova, Lydia; Mikheeva, Galina; Somova, Lydia

The life support systems (LSS) for long-term missions are to use cycling-recycling systems, including biological recycling. Simple ecosystems include 3 links: producers (plants), consumers (man, animals) and reducers (microorganisms). Microorganisms are substantial component of every link of LSS. Higher plants are the traditional regenerator of air and producer of food. They should be used in many successive generations of their reproduction in LSS. Controlled microbiocenoses can increase productivity of producer's link and protect plants from infections. The goal of this work was development of methodological bases of formation of stable, controlled microbiocenoses, intended for increase of productivity of plants and for obtaining ecologically pure production of plants. Main results of our investigations: 1. Experimental microbiocenoses, has been produced in view of the developed methodology on the basis of natural association of microorganisms by long cultivation on specially developed medium. Dominating groups are bacteria of genera: Lactobacillus, Streptococcus, Leuconostoc, Bifidobacterium, Rhodopseudomonas and yeast of genera: Kluyveromyces, Saccharomyces, Torulopsis. 2. Optimal parameters of microbiocenosis cultivation (t, pH, light exposure, biogenic elements concentrations) were experimentally established. Conditions of cultivation on which domination of different groups of microbiocenosis have been found. 3. It was shown, that processing of seeds of wheat, oats, bulbs and plants Allium cepa L. (an onions) with microbial association raised energy of germination of seeds and bulbs and promoted the increase (on 20-30 %) of growth green biomass and root system of plants in comparison with the control. This work is supported by grant, Yenissey , 07-04-96806
Soil microbial community structure is unaltered by plant invasion, vegetation clipping, and nitrogen fertilization in experimental semi-arid grasslands

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Chelsea J Carey

2015-05-01

Full Text Available Global and regional environmental changes often co-occur, creating complex gradients of disturbance on the landscape. Soil microbial communities are an important component of ecosystem response to environmental change, yet little is known about how microbial structure and function respond to multiple disturbances, or whether multiple environmental changes lead to unanticipated interactive effects. Our study used experimental semi-arid grassland plots in a Mediterranean-climate to determine how soil microbial communities in a seasonally variable ecosystem respond to one, two, or three simultaneous environmental changes: exotic plant invasion, plant invasion + vegetation clipping (to simulate common management practices like mowing or livestock grazing, plant invasion + nitrogen (N fertilization, and plant invasion + clipping + N fertilization. We examined microbial community structure 5-6 years after plot establishment via sequencing of >1 million 16S rRNA genes. Abiotic soil properties (soil moisture, temperature, pH, and inorganic N and microbial functioning (nitrification and denitrification potentials were also measured and showed treatment-induced shifts, including altered NO3- availability, temperature, and nitrification potential. Despite these changes, bacterial and archaeal communities showed little variation in composition and diversity across treatments. Even communities in plots exposed to three interacting environmental changes were similar to those in restored native grassland plots. Historical exposure to large seasonal and inter-annual variations in key soil properties, in addition to prior site cultivation, may select for a functionally plastic or largely dormant microbial community, resulting in a microbial community that is structurally robust to single and multiple environmental changes.
Photodegradation alleviates the lignin bottleneck for carbon turnover in terrestrial ecosystems.

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Austin, Amy T; Méndez, M Soledad; Ballaré, Carlos L

2016-04-19

A mechanistic understanding of the controls on carbon storage and losses is essential for our capacity to predict and mitigate human impacts on the global carbon cycle. Plant litter decomposition is an important first step for carbon and nutrient turnover, and litter inputs and losses are essential in determining soil organic matter pools and the carbon balance in terrestrial ecosystems. Photodegradation, the photochemical mineralization of organic matter, has been recently identified as a mechanism for previously unexplained high rates of litter mass loss in arid lands; however, the global significance of this process as a control on carbon cycling in terrestrial ecosystems is not known. Here we show that, across a wide range of plant species, photodegradation enhanced subsequent biotic degradation of leaf litter. Moreover, we demonstrate that the mechanism for this enhancement involves increased accessibility to plant litter carbohydrates for microbial enzymes. Photodegradation of plant litter, driven by UV radiation, and especially visible (blue-green) light, reduced the structural and chemical bottleneck imposed by lignin in secondary cell walls. In leaf litter from woody species, specific interactions with UV radiation obscured facilitative effects of solar radiation on biotic decomposition. The generalized effect of sunlight exposure on subsequent microbial activity, mediated by increased accessibility to cell wall polysaccharides, suggests that photodegradation is quantitatively important in determining rates of mass loss, nutrient release, and the carbon balance in a broad range of terrestrial ecosystems.
Incorporating microbial dormancy dynamics into soil decomposition models to improve quantification of soil carbon dynamics of northern temperate forests

Energy Technology Data Exchange (ETDEWEB)

He, Yujie [Purdue Univ., West Lafayette, IN (United States). Dept. of Earth, Atmospheric, and Planetary Sciences; Yang, Jinyan [Univ. of Georgia, Athens, GA (United States). Warnell School of Forestry and Natural Resources; Northeast Forestry Univ., Harbin (China). Center for Ecological Research; Zhuang, Qianlai [Purdue Univ., West Lafayette, IN (United States). Dept. of Earth, Atmospheric, and Planetary Sciences; Purdue Univ., West Lafayette, IN (United States). Dept. of Agronomy; Harden, Jennifer W. [U.S. Geological Survey, Menlo Park, CA (United States); McGuire, Anthony D. [Alaska Cooperative Fish and Wildlife Research Unit, U.S. Geological Survey, Univ. of Alaska, Fairbanks, AK (United States). U.S. Geological Survey, Alaska Cooperative Fish and Wildlife Research Unit; Liu, Yaling [Purdue Univ., West Lafayette, IN (United States). Dept. of Earth, Atmospheric, and Planetary Sciences; Wang, Gangsheng [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Climate Change Science Inst. and Environmental Sciences Division; Gu, Lianhong [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Environmental Sciences Division

2015-11-20

Soil carbon dynamics of terrestrial ecosystems play a significant role in the global carbon cycle. Microbial-based decomposition models have seen much growth recently for quantifying this role, yet dormancy as a common strategy used by microorganisms has not usually been represented and tested in these models against field observations. Here in this study we developed an explicit microbial-enzyme decomposition model and examined model performance with and without representation of microbial dormancy at six temperate forest sites of different forest types. We then extrapolated the model to global temperate forest ecosystems to investigate biogeochemical controls on soil heterotrophic respiration and microbial dormancy dynamics at different temporal-spatial scales. The dormancy model consistently produced better match with field-observed heterotrophic soil CO₂ efflux (R_H) than the no dormancy model. Our regional modeling results further indicated that models with dormancy were able to produce more realistic magnitude of microbial biomass (<2% of soil organic carbon) and soil R_H (7.5 ± 2.4 PgCyr^-1). Spatial correlation analysis showed that soil organic carbon content was the dominating factor (correlation coefficient = 0.4-0.6) in the simulated spatial pattern of soil R_H with both models. In contrast to strong temporal and local controls of soil temperature and moisture on microbial dormancy, our modeling results showed that soil carbon-to-nitrogen ratio (C:N) was a major regulating factor at regional scales (correlation coefficient = -0.43 to -0.58), indicating scale-dependent biogeochemical controls on microbial dynamics. Our findings suggest that incorporating microbial dormancy could improve the realism of microbial-based decomposition models and enhance the integration of soil experiments and mechanistically based modeling.
Microbial Endocrinology in the Pathogenesis of Infectious Disease.

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Lyte, Mark

2016-04-01

Microbial endocrinology represents the intersection of two seemingly disparate fields, microbiology and neurobiology, and is based on the shared presence of neurochemicals that are exactly the same in host as well as in the microorganism. The ability of microorganisms to not only respond to, but also produce, many of the same neurochemicals that are produced by the host, such as during periods of stress, has led to the introduction of this evolutionary-based mechanism which has a role in the pathogenesis of infectious disease. The consideration of microbial endocrinology-based mechanisms has demonstrated, for example, that the prevalent use of catecholamine-based synthetic drugs in the clinical setting contributes to the formation of biofilms in indwelling medical devices. Production of neurochemicals by microorganisms most often employs the same biosynthetic pathways as those utilized by the host, indicating that acquisition of host neurochemical-based signaling system in the host may have been acquired due to lateral gene transfer from microorganisms. That both host and microorganism produce and respond to the very same neurochemicals means that there is bidirectionality contained with the theoretical underpinnings of microbial endocrinology. This can be seen in the role of microbial endocrinology in the microbiota-gut-brain axis and its relevance to infectious disease. Such shared pathways argue for a role of microorganism-neurochemical interactions in infectious disease.
Dissolved nitrogen transformations and microbial community structure in the organic layer of forest soils in Olkiluoto in 2006

International Nuclear Information System (INIS)

Potila, H.; Sarjala, T.; Aro, L.

2007-02-01

Carbon (C) and nitrogen (N) cycles in the ecosystem are strongly coupled. Biomass, structure and activity of the bacterial and fungal community are the key factors influencing C and N cycles. Changes in the function of soil microbial community can be a signal of plant responses to environmental changes. Dissolved N compounds, microbial biomass, microbial activity, fungal community structure and functional diversity of microbial communities were measured in September 2006 from five monitoring plots on Olkiluoto to assess information about soil microbial community structure and activity. High within and between variation in the studied plots were detected. However, in this study the values and their variation in the level of N mineralisation, dissolved N compounds, fungal biomass and microbial community structure in the studied plots were within a normal range in comparison with other published data of similar forest types in Finland. (orig.)
Ecosystem Fabrication (EcoFAB) Protocols for The Construction of Laboratory Ecosystems Designed to Study Plant-microbe Interactions.

Science.gov (United States)

Gao, Jian; Sasse, Joelle; Lewald, Kyle M; Zhalnina, Kateryna; Cornmesser, Lloyd T; Duncombe, Todd A; Yoshikuni, Yasuo; Vogel, John P; Firestone, Mary K; Northen, Trent R

2018-04-10

Beneficial plant-microbe interactions offer a sustainable biological solution with the potential to boost low-input food and bioenergy production. A better mechanistic understanding of these complex plant-microbe interactions will be crucial to improving plant production as well as performing basic ecological studies investigating plant-soil-microbe interactions. Here, a detailed description for ecosystem fabrication is presented, using widely available 3D printing technologies, to create controlled laboratory habitats (EcoFABs) for mechanistic studies of plant-microbe interactions within specific environmental conditions. Two sizes of EcoFABs are described that are suited for the investigation of microbial interactions with various plant species, including Arabidopsis thaliana, Brachypodium distachyon, and Panicum virgatum. These flow-through devices allow for controlled manipulation and sampling of root microbiomes, root chemistry as well as imaging of root morphology and microbial localization. This protocol includes the details for maintaining sterile conditions inside EcoFABs and mounting independent LED light systems onto EcoFABs. Detailed methods for addition of different forms of media, including soils, sand, and liquid growth media coupled to the characterization of these systems using imaging and metabolomics are described. Together, these systems enable dynamic and detailed investigation of plant and plant-microbial consortia including the manipulation of microbiome composition (including mutants), the monitoring of plant growth, root morphology, exudate composition, and microbial localization under controlled environmental conditions. We anticipate that these detailed protocols will serve as an important starting point for other researchers, ideally helping create standardized experimental systems for investigating plant-microbe interactions.
Water regime history drives responses of soil Namib Desert microbial communities to wetting events

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Frossard, Aline; Ramond, Jean-Baptiste; Seely, Mary; Cowan, Don A.

2015-07-01

Despite the dominance of microorganisms in arid soils, the structures and functional dynamics of microbial communities in hot deserts remain largely unresolved. The effects of wetting event frequency and intensity on Namib Desert microbial communities from two soils with different water-regime histories were tested over 36 days. A total of 168 soil microcosms received wetting events mimicking fog, light rain and heavy rainfall, with a parallel “dry condition” control. T-RFLP data showed that the different wetting events affected desert microbial community structures, but these effects were attenuated by the effects related to the long-term adaptation of both fungal and bacterial communities to soil origins (i.e. soil water regime histories). The intensity of the water pulses (i.e. the amount of water added) rather than the frequency of wetting events had greatest effect in shaping bacterial and fungal community structures. In contrast to microbial diversity, microbial activities (enzyme activities) showed very little response to the wetting events and were mainly driven by soil origin. This experiment clearly demonstrates the complexity of microbial community responses to wetting events in hyperarid hot desert soil ecosystems and underlines the dynamism of their indigenous microbial communities.
VirSorter: mining viral signal from microbial genomic data

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Simon Roux

2015-05-01

Full Text Available Viruses of microbes impact all ecosystems where microbes drive key energy and substrate transformations including the oceans, humans and industrial fermenters. However, despite this recognized importance, our understanding of viral diversity and impacts remains limited by too few model systems and reference genomes. One way to fill these gaps in our knowledge of viral diversity is through the detection of viral signal in microbial genomic data. While multiple approaches have been developed and applied for the detection of prophages (viral genomes integrated in a microbial genome, new types of microbial genomic data are emerging that are more fragmented and larger scale, such as Single-cell Amplified Genomes (SAGs of uncultivated organisms or genomic fragments assembled from metagenomic sequencing. Here, we present VirSorter, a tool designed to detect viral signal in these different types of microbial sequence data in both a reference-dependent and reference-independent manner, leveraging probabilistic models and extensive virome data to maximize detection of novel viruses. Performance testing shows that VirSorter’s prophage prediction capability compares to that of available prophage predictors for complete genomes, but is superior in predicting viral sequences outside of a host genome (i.e., from extrachromosomal prophages, lytic infections, or partially assembled prophages. Furthermore, VirSorter outperforms existing tools for fragmented genomic and metagenomic datasets, and can identify viral signal in assembled sequence (contigs as short as 3kb, while providing near-perfect identification (>95% Recall and 100% Precision on contigs of at least 10kb. Because VirSorter scales to large datasets, it can also be used in “reverse” to more confidently identify viral sequence in viral metagenomes by sorting away cellular DNA whether derived from gene transfer agents, generalized transduction or contamination. Finally, VirSorter is made
VirSorter: mining viral signal from microbial genomic data

Science.gov (United States)

Roux, Simon; Enault, Francois; Hurwitz, Bonnie L.

2015-01-01

Viruses of microbes impact all ecosystems where microbes drive key energy and substrate transformations including the oceans, humans and industrial fermenters. However, despite this recognized importance, our understanding of viral diversity and impacts remains limited by too few model systems and reference genomes. One way to fill these gaps in our knowledge of viral diversity is through the detection of viral signal in microbial genomic data. While multiple approaches have been developed and applied for the detection of prophages (viral genomes integrated in a microbial genome), new types of microbial genomic data are emerging that are more fragmented and larger scale, such as Single-cell Amplified Genomes (SAGs) of uncultivated organisms or genomic fragments assembled from metagenomic sequencing. Here, we present VirSorter, a tool designed to detect viral signal in these different types of microbial sequence data in both a reference-dependent and reference-independent manner, leveraging probabilistic models and extensive virome data to maximize detection of novel viruses. Performance testing shows that VirSorter’s prophage prediction capability compares to that of available prophage predictors for complete genomes, but is superior in predicting viral sequences outside of a host genome (i.e., from extrachromosomal prophages, lytic infections, or partially assembled prophages). Furthermore, VirSorter outperforms existing tools for fragmented genomic and metagenomic datasets, and can identify viral signal in assembled sequence (contigs) as short as 3kb, while providing near-perfect identification (>95% Recall and 100% Precision) on contigs of at least 10kb. Because VirSorter scales to large datasets, it can also be used in “reverse” to more confidently identify viral sequence in viral metagenomes by sorting away cellular DNA whether derived from gene transfer agents, generalized transduction or contamination. Finally, VirSorter is made available through the i

Methane production potential and microbial community structure for different forest soils

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Matsumoto, Y.; Ueyama, M.; Kominami, Y.; Endo, R.; Tokumoto, H.; Hirano, T.; Takagi, K.; Takahashi, Y.; Iwata, H.; Harazono, Y.

2017-12-01

Forest soils are often considered as a methane (CH4) sink, but anaerobic microsites potentially decrease the sink at the ecosystem scale. In this study, we measured biological CH4 production potential of soils at various ecosystems, including upland forests, a lowland forest, and a bog, and analyzed microbial community structure using 16S ribosomal RNA (rRNA) genes. Three different types of soil samples (upland, bank of the stream, and center of the stream) were collected from Yamashiro forest meteorology research site (YMS) at Kyoto, Japan, on 11 May 2017. The soils were incubated at dark and anaerobic conditions under three different temperatures (37°C, 25°C, and 10°C) from 9 June 2017. The upland soils emitted CH4 with largest yields among the three soils at 37°C and 25°C, although no CH4 emission was observed at 10°C. For all temperature ranges, the emission started to increase with a 14- to 20-days lag after the start of the incubation. The lag indicates a slow transition to anaerobic conditions; as dissolved oxygen in water decreased, the number and/or activity of anaerobic bacteria like methanogens increased. The soils at the bank and center of the stream emitted CH4 with smaller yields than the upland soils in the three temperature ranges. The microbial community analyses indicate that methanogenic archaea presented at the three soils including the aerobic upland soil, but compositions of methanogenic archaea were different among the soils. In upland soils, hydrogenotrophic methanogens, such as Methanobacterium and Methanothermobacter, consisted almost all of the total methanogen detected. In the bank and center of the stream, soils contained approximately 10-25% of acetoclastic methanogens, such as Methanosarcina and Methanosaeta, among the total methanogen detected. Methanotrophs, a genus of Methanobacteriaceae, was appeared in the all types of soils. We will present results from same incubation and 16S rRNA analyses for other ecosystems, including
Synthetic circuit designs for earth terraformation.

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Solé, Ricard V; Montañez, Raúl; Duran-Nebreda, Salva

2015-07-18

Mounting evidence indicates that our planet might experience runaway effects associated to rising temperatures and ecosystem overexploitation, leading to catastrophic shifts on short time scales. Remediation scenarios capable of counterbalancing these effects involve geoengineering, sustainable practices and carbon sequestration, among others. None of these scenarios seems powerful enough to achieve the desired restoration of safe boundaries. We hypothesize that synthetic organisms with the appropriate engineering design could be used to safely prevent declines in some stressed ecosystems and help improving carbon sequestration. Such schemes would include engineering mutualistic dependencies preventing undesired evolutionary processes. We hypothesize that some particular design principles introduce unescapable constraints to the engineered organisms that act as effective firewalls. Testing this designed organisms can be achieved by using controlled bioreactor models, with single and heterogeneous populations, and accurate computational models including different scales (from genetic constructs and metabolic pathways to population dynamics). Our hypothesis heads towards a future anthropogenic action that should effectively act as Terraforming processes. It also implies a major challenge in the existing biosafety policies, since we suggest release of modified organisms as potentially necessary strategy for success.
Threatened corals provide underexplored microbial habitats.

Directory of Open Access Journals (Sweden)

Shinichi Sunagawa

2010-03-01

Full Text Available Contemporary in-depth sequencing of environmental samples has provided novel insights into microbial community structures, revealing that their diversity had been previously underestimated. Communities in marine environments are commonly composed of a few dominant taxa and a high number of taxonomically diverse, low-abundance organisms. However, studying the roles and genomic information of these "rare" organisms remains challenging, because little is known about their ecological niches and the environmental conditions to which they respond. Given the current threat to coral reef ecosystems, we investigated the potential of corals to provide highly specialized habitats for bacterial taxa including those that are rarely detected or absent in surrounding reef waters. The analysis of more than 350,000 small subunit ribosomal RNA (16S rRNA sequence tags and almost 2,000 nearly full-length 16S rRNA gene sequences revealed that rare seawater biosphere members are highly abundant or even dominant in diverse Caribbean corals. Closely related corals (in the same genus/family harbored similar bacterial communities. At higher taxonomic levels, however, the similarities of these communities did not correlate with the phylogenetic relationships among corals, opening novel questions about the evolutionary stability of coral-microbial associations. Large proportions of OTUs (28.7-49.1% were unique to the coral species of origin. Analysis of the most dominant ribotypes suggests that many uncovered bacterial taxa exist in coral habitats and await future exploration. Our results indicate that coral species, and by extension other animal hosts, act as specialized habitats of otherwise rare microbes in marine ecosystems. Here, deep sequencing provided insights into coral microbiota at an unparalleled resolution and revealed that corals harbor many bacterial taxa previously not known. Given that two of the coral species investigated are listed as threatened under
Microbial transformations of natural organic compounds and radionuclides in subsurface environments

International Nuclear Information System (INIS)

Francis, A.J.

1985-10-01

A major national concern in the subsurface disposal of energy wastes is the contamination of ground and surface waters by waste leachates containing radionuclides, toxic metals, and organic compounds. Microorganisms play an important role in the transformation of organic compounds, radionuclides, and toxic metals present in the waste and affect their mobility in subsurface environments. Microbial processes involved in dissolution, mobilization, and immobilization of toxic metals under aerobic and anaerobic conditions are briefly reviewed. Metal complexing agents and several organic acids produced by microbial action affect mobilization of radionuclides and toxic metals in subsurface environments. Information on the persistence of and biodegradation rates of synthetic as well as microbiologically produced complexing agents is scarce but important in determining the mobility of metal organic complexes in subsoils. Several gaps in knowledge in the area of microbial transformation of naturally occurring organics, radionuclides, and toxic metals have been identified, and further basic research has been suggested. 31 refs., 1 fig., 3 tabs
Are there links between responses of soil microbes and ecosystem functioning to elevated CO2, N deposition and warming? A global perspective.

Science.gov (United States)

García-Palacios, Pablo; Vandegehuchte, Martijn L; Shaw, E Ashley; Dam, Marie; Post, Keith H; Ramirez, Kelly S; Sylvain, Zachary A; de Tomasel, Cecilia Milano; Wall, Diana H

2015-04-01

In recent years, there has been an increase in research to understand how global changes' impacts on soil biota translate into altered ecosystem functioning. However, results vary between global change effects, soil taxa, and ecosystem processes studied, and a synthesis of relationships is lacking. Therefore, here we initiate such a synthesis to assess whether the effect size of global change drivers (elevated CO2, N deposition, and warming) on soil microbial abundance is related with the effect size of these drivers on ecosystem functioning (plant biomass, soil C cycle, and soil N cycle) using meta-analysis and structural equation modeling. For N deposition and warming, the global change effect size on soil microbes was positively associated with the global change effect size on ecosystem functioning, and these relationships were consistent across taxa and ecosystem processes. However, for elevated CO2, such links were more taxon and ecosystem process specific. For example, fungal abundance responses to elevated CO2 were positively correlated with those of plant biomass but negatively with those of the N cycle. Our results go beyond previous assessments of the sensitivity of soil microbes and ecosystem processes to global change, and demonstrate the existence of general links between the responses of soil microbial abundance and ecosystem functioning. Further we identify critical areas for future research, specifically altered precipitation, soil fauna, soil community composition, and litter decomposition, that are need to better quantify the ecosystem consequences of global change impacts on soil biodiversity. © 2014 John Wiley & Sons Ltd.
Deciphering microbial interactions and detecting keystone species with co-occurrence networks

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David eBerry

2014-05-01

Full Text Available Co-occurrence networks produced from microbial survey sequencing data are frequently used to identify interactions between community members. While this approach has potential to reveal ecological processes, it has been insufficiently validated due to the technical limitations inherent in studying complex microbial ecosystems. Here, we simulate multi-species microbial communities with known interaction patterns using generalized Lotka-Volterra dynamics, construct co-occurrence networks, and evaluate how well networks reveal the underlying interactions, and how experimental and ecological parameters can affect network inference and interpretation. We find that co-occurrence networks can recapitulate interaction networks under certain conditions, but that they lose interpretability when the effects of habitat filtering become significant. We demonstrate that networks suffer from local hot spots of spurious correlation in the neighborhood of hub species that engage in many interactions. We also identify topological features associated with keystone species in co-occurrence networks. This study provides a substantiated framework to guide environmental microbiologists in the construction and interpretation of co-occurrence networks from microbial survey datasets.
Deciphering microbial interactions and detecting keystone species with co-occurrence networks.

Science.gov (United States)

Berry, David; Widder, Stefanie

2014-01-01

Co-occurrence networks produced from microbial survey sequencing data are frequently used to identify interactions between community members. While this approach has potential to reveal ecological processes, it has been insufficiently validated due to the technical limitations inherent in studying complex microbial ecosystems. Here, we simulate multi-species microbial communities with known interaction patterns using generalized Lotka-Volterra dynamics. We then construct co-occurrence networks and evaluate how well networks reveal the underlying interactions and how experimental and ecological parameters can affect network inference and interpretation. We find that co-occurrence networks can recapitulate interaction networks under certain conditions, but that they lose interpretability when the effects of habitat filtering become significant. We demonstrate that networks suffer from local hot spots of spurious correlation in the neighborhood of hub species that engage in many interactions. We also identify topological features associated with keystone species in co-occurrence networks. This study provides a substantiated framework to guide environmental microbiologists in the construction and interpretation of co-occurrence networks from microbial survey datasets.
Shifts in microbial community structure and diversity in a MBR combined with worm reactors treating synthetic wastewater.

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Liu, Jia; Zuo, Wei; Zhang, Jun; Li, Hui; Li, Lipin; Tian, Yu

2017-04-01

The chemical oxygen demand (COD) and NH 3 -N removal, membrane fouling, sludge characteristics and microbial community structure in a membrane bioreactor (MBR) coupled with worm reactors (SSBWR) were evaluated for 210days. The obtained results were compared to those from a conventional MBR (C-MBR) operated in parallel. The results indicated that the combined MBR (S-MBR) achieved higher COD and NH 3 -N removal efficiency, slower increase in membrane fouling, better sludge settleability and higher activities of the related enzymes in the activated sludge. Denaturing gradient gel electrophoresis was used to analyze the microbial community structures in the C-MBR and the S-MBR. The microbial community structure in the S-MBR was more diverse than that in the C-MBR. Additionally, the slow-growing microbes such as Saprospiraceae, Actinomyces, Frankia, Clostridium, Comamonas, Pseudomonas, Dechloromonas and Flavobacterium were enriched in the S-MBR, further accounting for the sludge reduction, membrane fouling alleviation and wastewater treatment. Copyright © 2016. Published by Elsevier B.V.
Effects of vegetation type on microbial biomass carbon and nitrogen in subalpine mountain forest soils.

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Ravindran, Anita; Yang, Shang-Shyng

2015-08-01

Microbial biomass plays an important role in nutrient transformation and conservation of forest and grassland ecosystems. The objective of this study was to determine the microbial biomass among three vegetation types in subalpine mountain forest soils of Taiwan. Tatachia is a typical high-altitude subalpine temperate forest ecosystem in Taiwan with an elevation of 1800-3952 m and consists of three vegetation types: spruce, hemlock, and grassland. Three plots were selected in each vegetation type. Soil samples were collected from the organic layer, topsoil, and subsoil. Microbial biomass carbon (Cmic) was determined by the chloroform fumigation-extraction method, and microbial biomass nitrogen (Nmic) was determined from the total nitrogen (Ntot) released during fumigation-extraction. Bacteria, actinomycetes, fungi, cellulolytic microbes, phosphate-solubilizing microbes, and nitrogen-fixing microbes were also counted. The Cmic and Nmic were highest in the surface soil and declined with the soil depth. These were also highest in spruce soils, followed by in hemlock soils, and were lowest in grassland soils. Cmic and Nmic had the highest values in the spring season and the lowest values in the winter season. Cmic and Nmic had significantly positive correlations with total organic carbon (Corg) and Ntot. Contributions of Cmic and Nmic, respectively, to Corg and Ntot indicated that the microbial biomass was immobilized more in spruce and hemlock soils than in grassland soils. Microbial populations of the tested vegetation types decreased with increasing soil depth. Cmic and Nmic were high in the organic layer and decreased with the depth of layers. These values were higher for spruce and hemlock soils than for grassland soils. Positive correlations were observed between Cmic and Nmic and between Corg and Ntot. Copyright © 2014. Published by Elsevier B.V.
Desert Perennial Shrubs Shape the Microbial-Community Miscellany in Laimosphere and Phyllosphere Space.

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Martirosyan, Varsik; Unc, Adrian; Miller, Gad; Doniger, Tirza; Wachtel, Chaim; Steinberger, Yosef

2016-10-01

Microbial function, composition, and distribution play a fundamental role in ecosystem ecology. The interaction between desert plants and their associated microbes is expected to greatly affect their response to changes in this harsh environment. Using comparative analyses, we studied the impact of three desert shrubs, Atriplex halimus (A), Artemisia herba-alba (AHA), and Hammada scoparia (HS), on soil- and leaf-associated microbial communities. DNA extracted from the leaf surface and soil samples collected beneath the shrubs were used to study associated microbial diversity using a sequencing survey of variable regions of bacterial 16S rRNA and fungal ribosomal internal transcribed spacer (ITS1). We found that the composition of bacterial and fungal orders is plant-type-specific, indicating that each plant type provides a suitable and unique microenvironment. The different adaptive ecophysiological properties of the three plant species and the differential effect on their associated microbial composition point to the role of adaptation in the shaping of microbial diversity. Overall, our findings suggest a link between plant ecophysiological adaptation as a "temporary host" and the biotic-community parameters in extreme xeric environments.
Microbial Metabolism in Soil at Subzero Temperatures: Adaptation Mechanisms Revealed by Position-Specific 13C Labeling

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Ezekiel K. Bore

2017-05-01

Full Text Available Although biogeochemical models designed to simulate carbon (C and nitrogen (N dynamics in high-latitude ecosystems incorporate extracellular parameters, molecular and biochemical adaptations of microorganisms to freezing remain unclear. This knowledge gap hampers estimations of the C balance and ecosystem feedback in high-latitude regions. To analyze microbial metabolism at subzero temperatures, soils were incubated with isotopomers of position-specifically 13C-labeled glucose at three temperatures: +5 (control, -5, and -20°C. 13C was quantified in CO2, bulk soil, microbial biomass, and dissolved organic carbon (DOC after 1, 3, and 10 days and also after 30 days for samples at -20°C. Compared to +5°C, CO2 decreased 3- and 10-fold at -5 and -20°C, respectively. High 13C recovery in CO2 from the C-1 position indicates dominance of the pentose phosphate pathway at +5°C. In contrast, increased oxidation of the C-4 position at subzero temperatures implies a switch to glycolysis. A threefold higher 13C recovery in microbial biomass at -5 than +5°C points to synthesis of intracellular compounds such as glycerol and ethanol in response to freezing. Less than 0.4% of 13C was recovered in DOC after 1 day, demonstrating complete glucose uptake by microorganisms even at -20°C. Consequently, we attribute the fivefold higher extracellular 13C in soil than in microbial biomass to secreted antifreeze compounds. This suggests that with decreasing temperature, intracellular antifreeze protection is complemented by extracellular mechanisms to avoid cellular damage by crystallizing water. The knowledge of sustained metabolism at subzero temperatures will not only be useful for modeling global C dynamics in ecosystems with periodically or permanently frozen soils, but will also be important in understanding and controlling the adaptive mechanisms of food spoilage organisms.
"Bugs on Bugs": An Inquiry-Based, Collaborative Activity to Learn Arthropod & Microbial Biodiversity

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Lampert, Evan C.; Morgan, Jeanelle M.

2015-01-01

Diverse communities of arthropods and microbes provide humans with essential ecosystem goods and services. Arthropods are the most diverse and abundant macroscopic animals on the planet, and many remain to be discovered. Much less is known about microbial diversity, despite their importance as free-living species and as symbionts. We created…
Manipulating soil microbial communities in extensive green roof substrates.

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Molineux, Chloe J; Connop, Stuart P; Gange, Alan C

2014-09-15

There has been very little investigation into the soil microbial community on green roofs, yet this below ground habitat is vital for ecosystem functioning. Green roofs are often harsh environments that would greatly benefit from having a healthy microbial system, allowing efficient nutrient cycling and a degree of drought tolerance in dry summer months. To test if green roof microbial communities could be manipulated, we added mycorrhizal fungi and a microbial mixture ('compost tea') to green roof rootzones, composed mainly of crushed brick or crushed concrete. The study revealed that growing media type and depth play a vital role in the microbial ecology of green roofs. There are complex relationships between depth and type of substrate and the biomass of different microbial groups, with no clear pattern being observed. Following the addition of inoculants, bacterial groups tended to increase in biomass in shallower substrates, whereas fungal biomass change was dependent on depth and type of substrate. Increased fungal biomass was found in shallow plots containing more crushed concrete and deeper plots containing more crushed brick where compost tea (a live mixture of beneficial bacteria) was added, perhaps due to the presence of helper bacteria for arbuscular mycorrhizal fungi (AMF). Often there was not an additive affect of the microbial inoculations but instead an antagonistic interaction between the added AM fungi and the compost tea. This suggests that some species of microbes may not be compatible with others, as competition for limited resources occurs within the various substrates. The overall results suggest that microbial inoculations of green roof habitats are sustainable. They need only be done once for increased biomass to be found in subsequent years, indicating that this is a novel and viable method of enhancing roof community composition. Copyright © 2014 Elsevier B.V. All rights reserved.
Initial evaluations of the use of microbial measures to quantify impact of acid rock drainage on the Finniss River (east branch)

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Holden, P.J.; Wilde, K.L.; Stone, D.J.; Ben-David, E.A.; Foster, L.J.

2002-01-01

Biological measures assessing the impact of pollution on aquatic ecosystems have been increasingly used over the last ten years to examine ecosystem health. The focus, however, has been on diversity and abundance of higher organisms, such as fish, frogs and macroinvertebrates, and it is desirable that such measures be made across all trophic levels of the ecosystem. In this study, phospholipid-fatty acid analysis and microbial carbon substrate utilisation assays (BIOLOG) of sediment and water samples were conducted to evaluate their usefulness as a measure of the effect of acid rock drainage (ARD) on the East Branch of the Finniss River. Both PLFA, and BIOLOG assays, generate data well suited to multivariate analysis and previous studies of the impact of ARD from the Brukunga mine (South Australia) have demonstrated the ability to distinguish between the effect of ARD, nutrients and dry-land salinity on microbial populations
Biocrust-forming mosses mitigate the impact of aridity on soil microbial communities in drylands: observational evidence from three continents.

Science.gov (United States)

Delgado-Baquerizo, Manuel; Maestre, Fernando T; Eldridge, David J; Bowker, Matthew A; Jeffries, Thomas C; Singh, Brajesh K

2018-04-02

Recent research indicates that increased aridity linked to climate change will reduce the diversity of soil microbial communities and shift their community composition in drylands, Earth's largest biome. However, we lack both a theoretical framework and solid empirical evidence of how important biotic components from drylands, such as biocrust-forming mosses, will regulate the responses of microbial communities to expected increases in aridity with climate change. Here we report results from a cross-continental (North America, Europe and Australia) survey of 39 locations from arid to humid ecosystems, where we evaluated how biocrust-forming mosses regulate the relationship between aridity and the community composition and diversity of soil bacteria and fungi in dryland ecosystems. Increasing aridity was negatively related to the richness of fungi, and either positively or negatively related to the relative abundance of selected microbial phyla, when biocrust-forming mosses were absent. Conversely, we found an overall lack of relationship between aridity and the relative abundance and richness of microbial communities under biocrust-forming mosses. Our results suggest that biocrust-forming mosses mitigate the impact of aridity on the community composition of globally distributed microbial taxa, and the diversity of fungi. They emphasize the importance of maintaining biocrusts as a sanctuary for soil microbes in drylands. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.
Assessing coral reefs on a Pacific-wide scale using the microbialization score.

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Tracey McDole

Full Text Available The majority of the world's coral reefs are in various stages of decline. While a suite of disturbances (overfishing, eutrophication, and global climate change have been identified, the mechanism(s of reef system decline remain elusive. Increased microbial and viral loading with higher percentages of opportunistic and specific microbial pathogens have been identified as potentially unifying features of coral reefs in decline. Due to their relative size and high per cell activity, a small change in microbial biomass may signal a large reallocation of available energy in an ecosystem; that is the microbialization of the coral reef. Our hypothesis was that human activities alter the energy budget of the reef system, specifically by altering the allocation of metabolic energy between microbes and macrobes. To determine if this is occurring on a regional scale, we calculated the basal metabolic rates for the fish and microbial communities at 99 sites on twenty-nine coral islands throughout the Pacific Ocean using previously established scaling relationships. From these metabolic rate predictions, we derived a new metric for assessing and comparing reef health called the microbialization score. The microbialization score represents the percentage of the combined fish and microbial predicted metabolic rate that is microbial. Our results demonstrate a strong positive correlation between reef microbialization scores and human impact. In contrast, microbialization scores did not significantly correlate with ocean net primary production, local chla concentrations, or the combined metabolic rate of the fish and microbial communities. These findings support the hypothesis that human activities are shifting energy to the microbes, at the expense of the macrobes. Regardless of oceanographic context, the microbialization score is a powerful metric for assessing the level of human impact a reef system is experiencing.
Assessing coral reefs on a Pacific-wide scale using the microbialization score.

Science.gov (United States)

McDole, Tracey; Nulton, James; Barott, Katie L; Felts, Ben; Hand, Carol; Hatay, Mark; Lee, Hochul; Nadon, Marc O; Nosrat, Bahador; Salamon, Peter; Bailey, Barbara; Sandin, Stuart A; Vargas-Angel, Bernardo; Youle, Merry; Zgliczynski, Brian J; Brainard, Russell E; Rohwer, Forest

2012-01-01

The majority of the world's coral reefs are in various stages of decline. While a suite of disturbances (overfishing, eutrophication, and global climate change) have been identified, the mechanism(s) of reef system decline remain elusive. Increased microbial and viral loading with higher percentages of opportunistic and specific microbial pathogens have been identified as potentially unifying features of coral reefs in decline. Due to their relative size and high per cell activity, a small change in microbial biomass may signal a large reallocation of available energy in an ecosystem; that is the microbialization of the coral reef. Our hypothesis was that human activities alter the energy budget of the reef system, specifically by altering the allocation of metabolic energy between microbes and macrobes. To determine if this is occurring on a regional scale, we calculated the basal metabolic rates for the fish and microbial communities at 99 sites on twenty-nine coral islands throughout the Pacific Ocean using previously established scaling relationships. From these metabolic rate predictions, we derived a new metric for assessing and comparing reef health called the microbialization score. The microbialization score represents the percentage of the combined fish and microbial predicted metabolic rate that is microbial. Our results demonstrate a strong positive correlation between reef microbialization scores and human impact. In contrast, microbialization scores did not significantly correlate with ocean net primary production, local chla concentrations, or the combined metabolic rate of the fish and microbial communities. These findings support the hypothesis that human activities are shifting energy to the microbes, at the expense of the macrobes. Regardless of oceanographic context, the microbialization score is a powerful metric for assessing the level of human impact a reef system is experiencing.
Biochar increases plant growth and alters microbial communities via regulating the moisture and temperature of green roof substrates.

Science.gov (United States)

Chen, Haoming; Ma, Jinyi; Wei, Jiaxing; Gong, Xin; Yu, Xichen; Guo, Hui; Zhao, Yanwen

2018-09-01

Green roofs have increasingly been designed and applied to relieve environmental problems, such as water loss, air pollution as well as heat island effect. Substrate and vegetation are important components of green roofs providing ecosystem services and benefiting the urban development. Biochar made from sewage sludge could be potentially used as the substrate amendment for green roofs, however, the effects of biochar on substrate quality and plant performance in green roofs are still unclear. We evaluated the effects of adding sludge biochar (0, 5, 10, 15 and 20%, v/v) to natural soil planted with three types of plant species (ryegrass, Sedum lineare and cucumber) on soil properties, plant growth and microbial communities in both green roof and ground ecosystems. Our results showed that sludge biochar addition significantly increased substrate moisture, adjusted substrate temperature, altered microbial community structure and increased plant growth. The application rate of 10-15% sludge biochar on the green roof exerted the most significant effects on both microbial and plant biomass by 63.9-89.6% and 54.0-54.2% respectively. Path analysis showed that biochar addition had a strong effect on microbial biomass via changing the soil air-filled porosity, soil moisture and temperature, and promoted plant growth through the positive effects on microbial biomass. These results suggest that the applications of biochar at an appropriate rate can significantly alter plant growth and microbial community structure, and increase the ecological benefits of green roofs via exerting effects on the moisture, temperature and nutrients of roof substrates. Copyright © 2018 Elsevier B.V. All rights reserved.
The Biogeographic Pattern of Microbial Functional Genes along an Altitudinal Gradient of the Tibetan Pasture

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Qi, Qi; Zhao, Mengxin; Wang, Shiping; Ma, Xingyu; Wang, Yuxuan; Gao, Ying; Lin, Qiaoyan; Li, Xiangzhen; Gu, Baohua; Li, Guoxue; Zhou, Jizhong; Yang, Yunfeng

2017-06-13

As the highest place of the world, the Tibetan plateau is a fragile ecosystem. Given the importance of microbial communities in driving soil nutrient cycling, it is of interest to document the microbial biogeographic pattern here. We adopted a microarray-based tool named GeoChip 4.0 to investigate grassland microbial functional genes along an elevation gradient from 3200 to 3800 m above sea level open to free grazing by local herdsmen and wild animals. Interestingly, microbial functional diversities increase with elevation, so does the relative abundances of genes associated with carbon degradation, nitrogen cycling, methane production, cold shock and oxygen limitation. The range of Shannon diversities (10.27–10.58) showed considerably smaller variation than what was previously observed at ungrazed sites nearby (9.95–10.65), suggesting the important role of livestock grazing on microbial diversities. Closer examination showed that the dissimilarity of microbial community at our study sites increased with elevations, revealing an elevation-decay relationship of microbial functional genes. Both microbial functional diversity and the number of unique genes increased with elevations. Furthermore, we detected a tight linkage of greenhouse gas (CO2) and relative abundances of carbon cycling genes. Our biogeographic study provides insights on microbial functional diversity and soil biogeochemical cycling in Tibetan pastures.
The Biogeographic Pattern of Microbial Functional Genes along an Altitudinal Gradient of the Tibetan Pasture

Directory of Open Access Journals (Sweden)

Qi Qi

2017-06-01

Full Text Available As the highest place of the world, the Tibetan plateau is a fragile ecosystem. Given the importance of microbial communities in driving soil nutrient cycling, it is of interest to document the microbial biogeographic pattern here. We adopted a microarray-based tool named GeoChip 4.0 to investigate grassland microbial functional genes along an elevation gradient from 3200 to 3800 m above sea level open to free grazing by local herdsmen and wild animals. Interestingly, microbial functional diversities increase with elevation, so does the relative abundances of genes associated with carbon degradation, nitrogen cycling, methane production, cold shock and oxygen limitation. The range of Shannon diversities (10.27–10.58 showed considerably smaller variation than what was previously observed at ungrazed sites nearby (9.95–10.65, suggesting the important role of livestock grazing on microbial diversities. Closer examination showed that the dissimilarity of microbial community at our study sites increased with elevations, revealing an elevation-decay relationship of microbial functional genes. Both microbial functional diversity and the number of unique genes increased with elevations. Furthermore, we detected a tight linkage of greenhouse gas (CO2 and relative abundances of carbon cycling genes. Our biogeographic study provides insights on microbial functional diversity and soil biogeochemical cycling in Tibetan pastures.

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