Increased microbial functional diversity under long-term organic and integrated fertilization in a paddy soil.

Science.gov (United States)

Ding, Long-Jun; Su, Jian-Qiang; Sun, Guo-Xin; Wu, Jin-Shui; Wei, Wen-Xue

2018-02-01

Microbes play key roles in diverse biogeochemical processes including nutrient cycling. However, responses of soil microbial community and functional genes to long-term integrated fertilization (chemical combined with organic fertilization) remain unclear. Here, we used pyrosequencing and a microarray-based GeoChip to explore the shifts of microbial community and functional genes in a paddy soil which received over 21-year fertilization with various regimes, including control (no fertilizer), rice straw (R), rice straw plus chemical fertilizer nitrogen (NR), N and phosphorus (NPR), NP and potassium (NPKR), and reduced rice straw plus reduced NPK (L-NPKR). Significant shifts of the overall soil bacterial composition only occurred in the NPKR and L-NPKR treatments, with enrichment of certain groups including Bradyrhizobiaceae and Rhodospirillaceae families that benefit higher productivity. All fertilization treatments significantly altered the soil microbial functional structure with increased diversity and abundances of genes for carbon and nitrogen cycling, in which NPKR and L-NPKR exhibited the strongest effect, while R exhibited the least. Functional gene structure and abundance were significantly correlated with corresponding soil enzymatic activities and rice yield, respectively, suggesting that the structural shift of the microbial functional community under fertilization might promote soil nutrient turnover and thereby affect yield. Overall, this study indicates that the combined application of rice straw and balanced chemical fertilizers was more pronounced in shifting the bacterial composition and improving the functional diversity toward higher productivity, providing a microbial point of view on applying a cost-effective integrated fertilization regime with rice straw plus reduced chemical fertilizers for sustainable nutrient management.

Analysis of the functional diversity of the microbial communities in a ...

African Journals Online (AJOL)

The Biolog method was thus evaluated in a paper-mill water system. The influence of the production of various paper grades, biocide combinations and monthly maintenance shut-downs on the functional diversity of the microbial communities were determined using the Biolog technique. The communities in the planktonic ...

Elevated Atmospheric CO2 and Drought Affect Soil Microbial Community and Functional Diversity Associated with Glycine max

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Junfeng Wang

2017-12-01

Full Text Available Abstract Under the background of climate change, the increase of atmospheric CO2 and drought frequency have been considered as significant influencers on the soil microbial communities and the yield and quality of crop. In this study, impacts of increased ambient CO2 and drought on soil microbial structure and functional diversity of a Stagnic Anthrosol were investigated in phytotron growth chambers, by testing two representative CO2 levels, three soil moisture levels, and two soil cover types (with or without Glycine max. The 16S rDNA and 18S rDNA fragments were amplified to analyze the functional diversity of fungi and bacteria. Results showed that rhizosphere microbial biomass and community structure were significantly affected by drought, but effects differed between fungi and bacteria. Drought adaptation of fungi was found to be easier than that of bacteria. The diversity of fungi was less affected by drought than that of bacteria, evidenced by their higher diversity. Severe drought reduced soil microbial functional diversity and restrained the metabolic activity. Elevated CO2 alone, in the absence of crops (bare soil, did not enhance the metabolic activity of soil microorganisms. Generally, due to the co-functioning of plant and soil microorganisms in water and nutrient use, plants have major impacts on the soil microbial community, leading to atmospheric CO2 enrichment, but cannot significantly reduce the impacts of drought on soil microorganisms.

Microbial mat ecosystems: Structure types, functional diversity, and biotechnological application

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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.

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.

Shifts in taxonomic and functional microbial diversity with agriculture: How fragile is the Brazilian Cerrado?

Science.gov (United States)

Souza, Renata Carolini; Mendes, Iêda Carvalho; Reis-Junior, Fábio Bueno; Carvalho, Fabíola Marques; Nogueira, Marco Antonio; Vasconcelos, Ana Tereza Ribeiro; Vicente, Vânia Aparecida; Hungria, Mariangela

2016-03-16

The Cerrado--an edaphic type of savannah--comprises the second largest biome of the Brazilian territory and is the main area for grain production in the country, but information about the impact of land conversion to agriculture on microbial diversity is still scarce. We used a shotgun metagenomic approach to compare undisturbed (native) soil and soils cropped for 23 years with soybean/maize under conservation tillage--"no-till" (NT)--and conventional tillage (CT) systems in the Cerrado biome. Soil management and fertilizer inputs with the introduction of agriculture improved chemical properties, but decreased soil macroporosity and microbial biomass of carbon and nitrogen. Principal coordinates analyses confirmed different taxonomic and functional profiles for each treatment. There was predominance of the Bacteria domain, especially the phylum Proteobacteria, with higher numbers of sequences in the NT and CT treatments; Archaea and Viruses also had lower numbers of sequences in the undisturbed soil. Within the Alphaproteobacteria, there was dominance of Rhizobiales and of the genus Bradyrhizobium in the NT and CT systems, attributed to massive inoculation of soybean, and also of Burkholderiales. In contrast, Rhizobium, Azospirillum, Xanthomonas, Pseudomonas and Acidobacterium predominated in the native Cerrado. More Eukaryota, especially of the phylum Ascomycota were detected in the NT. The functional analysis revealed lower numbers of sequences in the five dominant categories for the CT system, whereas the undisturbed Cerrado presented higher abundance. High impact of agriculture in taxonomic and functional microbial diversity in the biome Cerrado was confirmed. Functional diversity was not necessarily associated with taxonomic diversity, as the less conservationist treatment (CT) presented increased taxonomic sequences and reduced functional profiles, indicating a strategy to try to maintain soil functioning by favoring taxa that are probably not the most

Effects of Conservation Agriculture and Fertilization on Soil Microbial Diversity and Activity

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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.

Functional soil microbial diversity across Europe estimated by EEA, MicroResp and BIOLOG

DEFF Research Database (Denmark)

Winding, Anne; Rutgers, Michiel; Creamer, Rachel

consisting of 81 soil samples covering five Biogeograhical Zones and three land-uses in order to test the sensitivity, ease and cost of performance and biological significance of the data output. The techniques vary in how close they are to in situ functions; dependency on growth during incubation......Soil microorganisms are abundant and essential for the bio-geochemical processes of soil, soil quality and soil ecosystem services. All this is dependent on the actual functions the microbial communities are performing in the soil. Measuring soil respiration has for many years been the basis...... of estimating soil microbial activity. However, today several techniques are in use for determining microbial functional diversity and assessing soil biodiversity: Methods based on CO2 development by the microbes such as substrate induced respiration (SIR) on specific substrates have lead to the development...

Analyses of the influencing factors of soil microbial functional gene diversity in tropical rainforest based on GeoChip 5.0.

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Cong, Jing; Liu, Xueduan; Lu, Hui; Xu, Han; Li, Yide; Deng, Ye; Li, Diqiang; Zhang, Yuguang

2015-09-01

To examine soil microbial functional gene diversity and causative factors in tropical rainforests, we used a microarray-based metagenomic tool named GeoChip 5.0 to profile it. We found that high microbial functional gene diversity and different soil microbial metabolic potential for biogeochemical processes were considered to exist in tropical rainforest. Soil available nitrogen was the most associated with soil microbial functional gene structure. Here, we mainly describe the experiment design, the data processing, and soil biogeochemical analyses attached to the study in details, which could be published on BMC microbiology Journal in 2015, whose raw data have been deposited in NCBI's Gene Expression Omnibus (accession number GSE69171).

Functional gene diversity of soil microbial communities from five oil-contaminated fields in China.

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Liang, Yuting; Van Nostrand, Joy D; Deng, Ye; He, Zhili; Wu, Liyou; Zhang, Xu; Li, Guanghe; Zhou, Jizhong

2011-03-01

To compare microbial functional diversity in different oil-contaminated fields and to know the effects of oil contaminant and environmental factors, soil samples were taken from typical oil-contaminated fields located in five geographic regions of China. GeoChip, a high-throughput functional gene array, was used to evaluate the microbial functional genes involved in contaminant degradation and in other major biogeochemical/metabolic processes. Our results indicated that the overall microbial community structures were distinct in each oil-contaminated field, and samples were clustered by geographic locations. The organic contaminant degradation genes were most abundant in all samples and presented a similar pattern under oil contaminant stress among the five fields. In addition, alkane and aromatic hydrocarbon degradation genes such as monooxygenase and dioxygenase were detected in high abundance in the oil-contaminated fields. Canonical correspondence analysis indicated that the microbial functional patterns were highly correlated to the local environmental variables, such as oil contaminant concentration, nitrogen and phosphorus contents, salt and pH. Finally, a total of 59% of microbial community variation from GeoChip data can be explained by oil contamination, geographic location and soil geochemical parameters. This study provided insights into the in situ microbial functional structures in oil-contaminated fields and discerned the linkages between microbial communities and environmental variables, which is important to the application of bioremediation in oil-contaminated sites.

Partitioning of functional and taxonomic diversity in surface-associated microbial communities.

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Roth-Schulze, Alexandra J; Zozaya-Valdés, Enrique; Steinberg, Peter D; Thomas, Torsten

2016-12-01

Surfaces, including those submerged in the marine environment, are subjected to constant interactions and colonisation by surrounding microorganisms. The principles that determine the assembly of those epibiotic communities are however poorly understood. In this study, we employed a hierarchical design to assess the functionality and diversity of microbial communities on different types of host surfaces (e.g. macroalgae, seagrasses). We found that taxonomic diversity was unique to each type of host, but that the majority of functions (> 95%) could be found in any given surface community, suggesting a high degree of functional redundancy. However, some community functions were enriched on certain surfaces and were related to host-specific properties (e.g. the degradation of specific polysaccharides). Together these observations support a model, whereby communities on surfaces are assembled from guilds of microorganisms with a functionality that is partitioned into general properties for a surface-associated life-style, but also specific features that mediate host-specificity. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

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...

Analyses of the influencing factors of soil microbial functional gene diversity in tropical rainforest based on GeoChip 5.0

Directory of Open Access Journals (Sweden)

Jing Cong

2015-09-01

Full Text Available To examine soil microbial functional gene diversity and causative factors in tropical rainforests, we used a microarray-based metagenomic tool named GeoChip 5.0 to profile it. We found that high microbial functional gene diversity and different soil microbial metabolic potential for biogeochemical processes were considered to exist in tropical rainforest. Soil available nitrogen was the most associated with soil microbial functional gene structure. Here, we mainly describe the experiment design, the data processing, and soil biogeochemical analyses attached to the study in details, which could be published on BMC microbiology Journal in 2015, whose raw data have been deposited in NCBI's Gene Expression Omnibus (accession number GSE69171.

Taxonomic and functional diversity provides insight into microbial pathways and stress responses in the saline Qinghai Lake, China.

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Qiuyuan Huang

Full Text Available Microbe-mediated biogeochemical cycles contribute to the global climate system and have sensitive responses and feedbacks to environmental stress caused by climate change. Yet, little is known about the effects of microbial biodiversity (i.e., taxonmic and functional diversity on biogeochemical cycles in ecosytems that are highly sensitive to climate change. One such sensitive ecosystem is Qinghai Lake, a high-elevation (3196 m saline (1.4% lake located on the Tibetan Plateau, China. This study provides baseline information on the microbial taxonomic and functional diversity as well as the associated stress response genes. Illumina metagenomic and metatranscriptomic datasets were generated from lake water samples collected at two sites (B and E. Autotrophic Cyanobacteria dominated the DNA samples, while heterotrophic Proteobacteria dominated the RNA samples at both sites. Photoheterotrophic Loktanella was also present at both sites. Photosystem II was the most active pathway at site B; while, oxidative phosphorylation was most active at site E. Organisms that expressed photosystem II or oxidative phosphorylation also expressed genes involved in photoprotection and oxidative stress, respectively. Assimilatory pathways associated with the nitrogen cycle were dominant at both sites. Results also indicate a positive relationship between functional diversity and the number of stress response genes. This study provides insight into the stress resilience of microbial metabolic pathways supported by greater taxonomic diversity, which may affect the microbial community response to climate change.

[Effects of nitrogen application rate on faba bean fusarium wilt and rhizospheric microbial metabolic functional diversity].

Science.gov (United States)

Dong, Yan; Yang, Zhi-xian; Dong, Kun; Tang, Li; Zheng, Yi; Hu, Guo-bin

2013-04-01

A field plot experiment was conducted to study the effects of different nitrogen (N) application rates on the microbial functional diversity in faba bean rhizosphere and the relationships between the microbial functional diversity and the occurrence of faba bean fusarium wilt. Four nitrogen application rates were installed, i. e. , N0(0 kg hm-2 , N1 (56. 25 kg hm-2) , N2(112. 5 kg hm-2), and N3 (168.75 kg hm-2), and Biolog microbial analysis system was applied to study the damage of faba bean fusarium wilt and the rhizospheric microbial metabolic functional diversity. Applying N (N1 N2, and N3) decreased the disease index of faba bean fusarium wilt and the quantity of Fusarium oxysporum significantly, and increased the quantities of bacteria and actinomyces and the ratios of bacteria/fungi and actinomyces/fungi significantly, with the peak values of bacteria and actinomyces, bacteria/fungi, and actinomyces/fungi, and the lowest disease index and F. oxysporum density in N2. As compared with N0, applying N increased the AWCD value significantly, but the effects of different N application rates on the ability of rhizospheric microbes in utilizing six types of carbon sources had definite differences. Under the application of N, the utilization rates of carbohydrates, carboxylic acids, and amino acids by the rhizospheric microbes were higher. Principal component analysis demonstrated that applying N changed the rhizospheric microbial community composition obviously, and the carbohydrates, carboxylic acids, and amino acids were the sensitive carbon sources differentiating the changes of the microbial community induced by N application. Applying N inhibited the utilization of carbohydrates and carboxylic acids but improved the utilization of amino acids and phenolic acids by the rhizospheric microbes, which could be one of the main reasons of applying N being able to reduce the harm of faba bean fusarium wilt. It was suggested that rationally applying N could increase the

MBGD update 2013: the microbial genome database for exploring the diversity of microbial world.

Science.gov (United States)

Uchiyama, Ikuo; Mihara, Motohiro; Nishide, Hiroyo; Chiba, Hirokazu

2013-01-01

The microbial genome database for comparative analysis (MBGD, available at http://mbgd.genome.ad.jp/) is a platform for microbial genome comparison based on orthology analysis. As its unique feature, MBGD allows users to conduct orthology analysis among any specified set of organisms; this flexibility allows MBGD to adapt to a variety of microbial genomic study. Reflecting the huge diversity of microbial world, the number of microbial genome projects now becomes several thousands. To efficiently explore the diversity of the entire microbial genomic data, MBGD now provides summary pages for pre-calculated ortholog tables among various taxonomic groups. For some closely related taxa, MBGD also provides the conserved synteny information (core genome alignment) pre-calculated using the CoreAligner program. In addition, efficient incremental updating procedure can create extended ortholog table by adding additional genomes to the default ortholog table generated from the representative set of genomes. Combining with the functionalities of the dynamic orthology calculation of any specified set of organisms, MBGD is an efficient and flexible tool for exploring the microbial genome diversity.

Microbial diversity and their roles in the vinegar fermentation process.

Science.gov (United States)

Li, Sha; Li, Pan; Feng, Feng; Luo, Li-Xin

2015-06-01

Vinegar is one of the oldest acetic acid-diluted solution products in the world. It is produced from any fermentable sugary substrate by various fermentation methods. The final vinegar products possess unique functions, which are endowed with many kinds of compounds formed in the fermentation process. The quality of vinegar is determined by many factors, especially by the raw materials and microbial diversity involved in vinegar fermentation. Given that metabolic products from the fermenting strains are directly related to the quality of the final products of vinegar, the microbial diversity and features of the dominant strains involved in different fermentation stages should be analyzed to improve the strains and stabilize fermentation. Moreover, although numerous microbiological studies have been conducted to examine the process of vinegar fermentation, knowledge about microbial diversity and their roles involved in fermentation is still fragmentary and not systematic enough. Therefore, in this review, the dominant microorganism species involved in the stages of alcoholic fermentation and acetic acid fermentation of dissimilar vinegars were summarized. We also summarized various physicochemical properties and crucial compounds in disparate types of vinegar. Furthermore, the merits and drawbacks of vital fermentation methods were generalized. Finally, we described in detail the relationships among microbial diversity, raw materials, fermentation methods, physicochemical properties, compounds, functionality, and final quality of vinegar. The integration of this information can provide us a detailed map about the microbial diversity and function involved in vinegar fermentation.

Stream microbial diversity responds to environmental changes: Review and synthesis of existing research

Directory of Open Access Journals (Sweden)

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

Deciphering Diversity Indices for a Better Understanding of Microbial Communities.

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Kim, Bo-Ra; Shin, Jiwon; Guevarra, Robin; Lee, Jun Hyung; Kim, Doo Wan; Seol, Kuk-Hwan; Lee, Ju-Hoon; Kim, Hyeun Bum; Isaacson, Richard

2017-12-28

The past decades have been a golden era during which great tasks were accomplished in the field of microbiology, including food microbiology. In the past, culture-dependent methods have been the primary choice to investigate bacterial diversity. However, using cultureindependent high-throughput sequencing of 16S rRNA genes has greatly facilitated studies exploring the microbial compositions and dynamics associated with health and diseases. These culture-independent DNA-based studies generate large-scale data sets that describe the microbial composition of a certain niche. Consequently, understanding microbial diversity becomes of greater importance when investigating the composition, function, and dynamics of the microbiota associated with health and diseases. Even though there is no general agreement on which diversity index is the best to use, diversity indices have been used to compare the diversity among samples and between treatments with controls. Tools such as the Shannon- Weaver index and Simpson index can be used to describe population diversity in samples. The purpose of this review is to explain the principles of diversity indices, such as Shannon- Weaver and Simpson, to aid general microbiologists in better understanding bacterial communities. In this review, important questions concerning microbial diversity are addressed. Information from this review should facilitate evidence-based strategies to explore microbial communities.

Farm management, not soil microbial diversity, controls nutrient loss from smallholder tropical agriculture

Directory of Open Access Journals (Sweden)

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.

Linking phylogenetic and functional diversity to nutrient spiraling in microbial mats from Lower Kane Cave (USA).

Science.gov (United States)

Engel, Annette Summers; Meisinger, Daniela B; Porter, Megan L; Payn, Robert A; Schmid, Michael; Stern, Libby A; Schleifer, K H; Lee, Natuschka M

2010-01-01

Microbial mats in sulfidic cave streams offer unique opportunities to study redox-based biogeochemical nutrient cycles. Previous work from Lower Kane Cave, Wyoming, USA, focused on the aerobic portion of microbial mats, dominated by putative chemolithoautotrophic, sulfur-oxidizing groups within the Epsilonproteobacteria and Gammaproteobacteria. To evaluate nutrient cycling and turnover within the whole mat system, a multidisciplinary strategy was used to characterize the anaerobic portion of the mats, including application of the full-cycle rRNA approach, the most probable number method, and geochemical and isotopic analyses. Seventeen major taxonomic bacterial groups and one archaeal group were retrieved from the anaerobic portions of the mats, dominated by Deltaproteobacteria and uncultured members of the Chloroflexi phylum. A nutrient spiraling model was applied to evaluate upstream to downstream changes in microbial diversity based on carbon and sulfur nutrient concentrations. Variability in dissolved sulfide concentrations was attributed to changes in the abundance of sulfide-oxidizing microbial groups and shifts in the occurrence and abundance of sulfate-reducing microbes. Gradients in carbon and sulfur isotopic composition indicated that released and recycled byproduct compounds from upstream microbial activities were incorporated by downstream communities. On the basis of the type of available chemical energy, the variability of nutrient species in a spiraling model may explain observed differences in microbial taxonomic affiliations and metabolic functions, thereby spatially linking microbial diversity to nutrient spiraling in the cave stream ecosystem.

Microbial and functional diversity of a subterrestrial high pH groundwater associated to serpentinization.

Science.gov (United States)

Tiago, Igor; Veríssimo, António

2013-06-01

Microbial and functional diversity were assessed, from a serpentinization-driven subterrestrial alkaline aquifer - Cabeço de Vide Aquifer (CVA) in Portugal. DGGE analyses revealed the presence of a stable microbial community. By 16S rRNA gene libraries and pyrosequencing analyses, a diverse bacterial composition was determined, contrasting with low archaeal diversity. Within Bacteria the majority of the populations were related to organisms or sequences affiliated to class Clostridia, but members of classes Acidobacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, Deinococci, Gammaproteobacteria and of the phyla Bacteroidetes, Chloroflexi and Nitrospira were also detected. Domain Archaea encompassed mainly sequences affiliated to Euryarchaeota. Only form I RuBisCO - cbbL was detected. Autotrophic carbon fixation via the rTCA, 3-HP and 3-HP/4H-B cycles could not be confirmed. The detected APS reductase alpha subunit - aprA sequences were phylogenetically related to sequences of sulfate-reducing bacteria belonging to Clostridia, and also to sequences of chemolithoautothrophic sulfur-oxidizing bacteria belonging to Betaproteobacteria. Sequences of methyl coenzyme M reductase - mcrA were phylogenetically affiliated to sequences belonging to Anaerobic Methanotroph group 1 (ANME-1). The populations found and the functional key markers detected in CVA suggest that metabolisms related to H2 , methane and/or sulfur may be the major driving forces in this environment. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

PHYLOGENETIC AND FUNCTIONAL DIVERSITY OF SEAGULL AND CANADIAN GEESE FECAL MICROBIAL COMMUNITIES

Science.gov (United States)

In spite of increasing public health concerns on the risks associated with swimming in waters contaminated with waterfowl feces, there is little information on the gut microbial communities of aquatic birds. To address the molecular microbial diversity of waterfowl, 16S rDNA and ...

Microbial community diversity and composition varies with habitat characteristics and biofilm function in macrophyte-rich streams

DEFF Research Database (Denmark)

Levi, Peter S.; Starnawski, Piotr; Poulsen, Britta

2017-01-01

Biofilms in streams play an integral role in ecosystem processes and function yet few studies have investigated the broad diversity of these complex prokaryotic and eukaryotic microbial communities. Physical habitat characteristics can affect the composition and abundance of microorganisms...... in these biofilms by creating microhabitats. Here we describe the prokaryotic and eukaryotic microbial diversity of biofilms in sand and macrophyte habitats (i.e. epipsammon and epiphyton, respectively) in five macrophyte-rich streams in Jutland, Denmark. The macrophyte species varied in growth morphology, C......:N stoichiometry, and preferred stream habitat, providing a range in environmental conditions for the epiphyton. Among all habitats and streams, the prokaryotic communities were dominated by common phyla, including Alphaproteobacteria, Bacteriodetes, and Gammaproteobacteria, while the eukaryotic communities were...

Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality.

Science.gov (United States)

Jiang, Yue; Xiong, Xuejian; Danska, Jayne; Parkinson, John

2016-01-12

Metatranscriptomics is emerging as a powerful technology for the functional characterization of complex microbial communities (microbiomes). Use of unbiased RNA-sequencing can reveal both the taxonomic composition and active biochemical functions of a complex microbial community. However, the lack of established reference genomes, computational tools and pipelines make analysis and interpretation of these datasets challenging. Systematic studies that compare data across microbiomes are needed to demonstrate the ability of such pipelines to deliver biologically meaningful insights on microbiome function. Here, we apply a standardized analytical pipeline to perform a comparative analysis of metatranscriptomic data from diverse microbial communities derived from mouse large intestine, cow rumen, kimchi culture, deep-sea thermal vent and permafrost. Sequence similarity searches allowed annotation of 19 to 76% of putative messenger RNA (mRNA) reads, with the highest frequency in the kimchi dataset due to its relatively low complexity and availability of closely related reference genomes. Metatranscriptomic datasets exhibited distinct taxonomic and functional signatures. From a metabolic perspective, we identified a common core of enzymes involved in amino acid, energy and nucleotide metabolism and also identified microbiome-specific pathways such as phosphonate metabolism (deep sea) and glycan degradation pathways (cow rumen). Integrating taxonomic and functional annotations within a novel visualization framework revealed the contribution of different taxa to metabolic pathways, allowing the identification of taxa that contribute unique functions. The application of a single, standard pipeline confirms that the rich taxonomic and functional diversity observed across microbiomes is not simply an artefact of different analysis pipelines but instead reflects distinct environmental influences. At the same time, our findings show how microbiome complexity and availability of

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.

[Research on functional diversity of microorganisms on jujube fruit surface in storage].

Science.gov (United States)

Sha, Yuexia

2009-10-01

Disease during storage caused by microbial infection is a serious problem of jujube fruits. The aim of the study was to characterize the microbial diversity in stored jujube fruits. I used Biolog in experiment. The types of micro-plates were Filamentous Fungi micro-plate and Economicmicro-plate. There was much difference in microbial functional diversity on the surface of stored jujube fruit. The microbial functional diversity of stored 30 days was richer than it of stored 15 days. The diversity, homogeneity and average well color development of jujube used by fruit perservatives were lower than it not used by fruit preservatives. There were six kinds of the characteristic carbon. Our study firstly showed microbial diversity on the surface of stored jujube fruit. Biolog could be applied in the research on microbial functional diversity of fruit surface.

Microbial functional diversity responses to 2 years since biochar application in silt-loam soils on the Loess Plateau.

Science.gov (United States)

Zhu, Li-Xia; Xiao, Qian; Shen, Yu-Fang; Li, Shi-Qing

2017-10-01

The structure and function of soil microbial communities have been widely used as indicators of soil quality and fertility. The effect of biochar application on carbon sequestration has been studied, but the effect on soil microbial functional diversity has received little attention. We evaluated effects of biochar application on the functional diversities of microbes in a loam soil. The effects of biochar on microbial activities and related processes in the 0-10 and 10-20cm soil layers were determined in a two-year experiment in maize field on the Loess Plateau in China. Low-pyrolysis biochar produced from maize straw was applied into soils at rates of 0 (BC0), 10 (BC10) and 30 (BC30)tha -1 . Chemical analysis indicated that the biochar did not change the pH, significantly increased the amounts of organic carbon and nitrogen, and decreased the amount of mineral nitrogen and the microbial quotient. The biochar significantly decreased average well colour development (AWCD) values in Biolog EcoPlates™ for both layers, particularly for the rate of 10tha -1 . Biochar addition significantly decreased substrate richness (S) except for BC30 in the 0-10cm layer. Effects of biochar on the Shannon-Wiener index (H) and Simpson's dominance (D) were not significant, except for a significant increase in evenness index (E) in BC10 in the 10-20cm layer. A principal component analysis clearly differentiated the treatments, and microbial use of six categories of substrates significantly decreased in both layers after biochar addition, although the use of amines and amides did not differ amongst the three treatments in the deeper layer. Maize above ground dry biomass and height did not differ significantly amongst the treatments, and biochar had no significant effect on nitrogen uptake by maize seedlings. H was positively correlated with AWCD, and negatively with pH. AWCD was positively correlated with mineral N and negatively with pH. Our results indicated that shifts in soil

Soil Microbial Functional and Fungal Diversity as Influenced by Municipal Sewage Sludge Accumulation

OpenAIRE

Frąc, Magdalena; Oszust, Karolina; Lipiec, Jerzy; Jezierska-Tys, Stefania; Nwaichi, Eucharia Oluchi

2014-01-01

Safe disposal of municipal sewage sludge is a challenging global environmental concern. The aim of this study was to assess the response of soil microbial functional diversity to the accumulation of municipal sewage sludge during landfill storage. Soil samples of a municipal sewage sludge (SS) and from a sewage sludge landfill that was 3 m from a SS landfill (SS3) were analyzed relative to an undisturbed reference soil. Biolog EcoPlatesTM were inoculated with a soil suspension, and the Avera...

Exploring spatial planning and functional program impact on microbial diversity and distribution in two South African hospital microbiomes

CSIR Research Space (South Africa)

Nice, Jaco A

2015-07-01

Full Text Available This paper presents a theoretical and experimental research approach on the impact of spatial planning and functional program on the microbial load, distribution and organism diversity in hospital environments. The investigation aims to identify...

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes.

Science.gov (United States)

Fierer, Noah; Leff, Jonathan W; Adams, Byron J; Nielsen, Uffe N; Bates, Scott Thomas; Lauber, Christian L; Owens, Sarah; Gilbert, Jack A; Wall, Diana H; Caporaso, J Gregory

2012-12-26

For centuries ecologists have studied how the diversity and functional traits of plant and animal communities vary across biomes. In contrast, we have only just begun exploring similar questions for soil microbial communities despite soil microbes being the dominant engines of biogeochemical cycles and a major pool of living biomass in terrestrial ecosystems. We used metagenomic sequencing to compare the composition and functional attributes of 16 soil microbial communities collected from cold deserts, hot deserts, forests, grasslands, and tundra. Those communities found in plant-free cold desert soils typically had the lowest levels of functional diversity (diversity of protein-coding gene categories) and the lowest levels of phylogenetic and taxonomic diversity. Across all soils, functional beta diversity was strongly correlated with taxonomic and phylogenetic beta diversity; the desert microbial communities were clearly distinct from the nondesert communities regardless of the metric used. The desert communities had higher relative abundances of genes associated with osmoregulation and dormancy, but lower relative abundances of genes associated with nutrient cycling and the catabolism of plant-derived organic compounds. Antibiotic resistance genes were consistently threefold less abundant in the desert soils than in the nondesert soils, suggesting that abiotic conditions, not competitive interactions, are more important in shaping the desert microbial communities. As the most comprehensive survey of soil taxonomic, phylogenetic, and functional diversity to date, this study demonstrates that metagenomic approaches can be used to build a predictive understanding of how microbial diversity and function vary across terrestrial biomes.

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.

Integrating microbial diversity in soil carbon dynamic models parameters

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Louis, Benjamin; Menasseri-Aubry, Safya; Leterme, Philippe; Maron, Pierre-Alain; Viaud, Valérie

2015-04-01

Faced with the numerous concerns about soil carbon dynamic, a large quantity of carbon dynamic models has been developed during the last century. These models are mainly in the form of deterministic compartment models with carbon fluxes between compartments represented by ordinary differential equations. Nowadays, lots of them consider the microbial biomass as a compartment of the soil organic matter (carbon quantity). But the amount of microbial carbon is rarely used in the differential equations of the models as a limiting factor. Additionally, microbial diversity and community composition are mostly missing, although last advances in soil microbial analytical methods during the two past decades have shown that these characteristics play also a significant role in soil carbon dynamic. As soil microorganisms are essential drivers of soil carbon dynamic, the question about explicitly integrating their role have become a key issue in soil carbon dynamic models development. Some interesting attempts can be found and are dominated by the incorporation of several compartments of different groups of microbial biomass in terms of functional traits and/or biogeochemical compositions to integrate microbial diversity. However, these models are basically heuristic models in the sense that they are used to test hypotheses through simulations. They have rarely been confronted to real data and thus cannot be used to predict realistic situations. The objective of this work was to empirically integrate microbial diversity in a simple model of carbon dynamic through statistical modelling of the model parameters. This work is based on available experimental results coming from a French National Research Agency program called DIMIMOS. Briefly, 13C-labelled wheat residue has been incorporated into soils with different pedological characteristics and land use history. Then, the soils have been incubated during 104 days and labelled and non-labelled CO2 fluxes have been measured at ten

The complicated substrates enhance the microbial diversity and zinc leaching efficiency in sphalerite bioleaching system.

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Xiao, Yunhua; Xu, YongDong; Dong, Weiling; Liang, Yili; Fan, Fenliang; Zhang, Xiaoxia; Zhang, Xian; Niu, Jiaojiao; Ma, Liyuan; She, Siyuan; He, Zhili; Liu, Xueduan; Yin, Huaqun

2015-12-01

This study used an artificial enrichment microbial consortium to examine the effects of different substrate conditions on microbial diversity, composition, and function (e.g., zinc leaching efficiency) through adding pyrite (SP group), chalcopyrite (SC group), or both (SPC group) in sphalerite bioleaching systems. 16S rRNA gene sequencing analysis showed that microbial community structures and compositions dramatically changed with additions of pyrite or chalcopyrite during the sphalerite bioleaching process. Shannon diversity index showed a significantly increase in the SP (1.460), SC (1.476), and SPC (1.341) groups compared with control (sphalerite group, 0.624) on day 30, meanwhile, zinc leaching efficiencies were enhanced by about 13.4, 2.9, and 13.2%, respectively. Also, additions of pyrite or chalcopyrite could increase electric potential (ORP) and the concentrations of Fe3+ and H+, which were the main factors shaping microbial community structures by Mantel test analysis. Linear regression analysis showed that ORP, Fe3+ concentration, and pH were significantly correlated to zinc leaching efficiency and microbial diversity. In addition, we found that leaching efficiency showed a positive and significant relationship with microbial diversity. In conclusion, our results showed that the complicated substrates could significantly enhance microbial diversity and activity of function.

Microbial diversity and metabolic networks in acid mine drainage habitats

Directory of Open Access Journals (Sweden)

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.

Microbial functional genes enriched in the Xiangjiang River sediments with heavy metal contamination.

Science.gov (United States)

Jie, Shiqi; Li, Mingming; Gan, Min; Zhu, Jianyu; Yin, Huaqun; Liu, Xueduan

2016-08-08

Xiangjiang River (Hunan, China) has been contaminated with heavy metal for several decades by surrounding factories. However, little is known about the influence of a gradient of heavy metal contamination on the diversity, structure of microbial functional gene in sediment. To deeply understand the impact of heavy metal contamination on microbial community, a comprehensive functional gene array (GeoChip 5.0) has been used to study the functional genes structure, composition, diversity and metabolic potential of microbial community from three heavy metal polluted sites of Xiangjiang River. A total of 25595 functional genes involved in different biogeochemical processes have been detected in three sites, and different diversities and structures of microbial functional genes were observed. The analysis of gene overlapping, unique genes, and various diversity indices indicated a significant correlation between the level of heavy metal contamination and the functional diversity. Plentiful resistant genes related to various metal were detected, such as copper, arsenic, chromium and mercury. The results indicated a significantly higher abundance of genes involved in metal resistance including sulfate reduction genes (dsr) in studied site with most serious heavy metal contamination, such as cueo, mer, metc, merb, tehb and terc gene. With regard to the relationship between the environmental variables and microbial functional structure, S, Cu, Cd, Hg and Cr were the dominating factor shaping the microbial distribution pattern in three sites. This study suggests that high level of heavy metal contamination resulted in higher functional diversity and the abundance of metal resistant genes. These variation therefore significantly contribute to the resistance, resilience and stability of the microbial community subjected to the gradient of heavy metals contaminant in Xiangjiang River.

The Biogeographic Pattern of Microbial Functional Genes along an Altitudinal Gradient of the Tibetan Pasture

Energy Technology Data Exchange (ETDEWEB)

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.

The effect of soil habitat connectivity on microbial interactions, community structure and diversity: a microcosm-based approach

NARCIS (Netherlands)

Wolf, A.B.

2014-01-01

Soils contain tremendous microbial phylogenetic and functional diversity. Recent advances in the application of molecular methods into microbial ecology have provided a new appreciation of the extent of soil-borne microbial diversity, but our understanding of the forces that shape and maintain this

Evaluation of microbial diversity of different soil layers at a contaminated diesel site

CSIR Research Space (South Africa)

Maila, MP

2005-01-01

Full Text Available with high TPH removal. Analysis of the microbial diversity in the different soil layers using functional diversity (community-level physiological profile, via Biolog) and genetic diversity using polymerase chain reaction-denaturing gradient gel...

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 functional diversity and enzymatic activity of soil degraded by sulphur mining reclaimed with various waste

Science.gov (United States)

Joniec, Jolanta; Frąc, Magdalena

2017-10-01

The aim of the study was to evaluate microbial functional diversity based on community level physiological profiling and β-glucosidase activity changes in soil degraded by sulphur mining and subjected to reclamation with various waste. The experiment was set up in the area of the former `Jeziórko' Sulphur Mine (Poland), on a soilless substrate with a particle size distribution of slightly loamy sand. The experimental variants included the application of post-flotation lime, sewage sludge and mineral wool. The analyses of soil samples included the assessment of the following microbiological indices: β-glucosidase activity and functional diversity average well color development and richness). The results indicate that sewage sludge did not exert a significant impact on the functional diversity of microorganisms present in the reclaimed soil. In turn, the application of other types of waste contributed to a significant increase in the parameters of total metabolic activity and functional diversity of the reclaimed soil. However, the temporal analysis of the metabolic profile of soil microorganisms demonstrated that a single application of waste did not yield a durable, stable metabolic profile in the reclaimed soil. Still, there was an increase in β-glucosidase activity, especially in objects treated with sewage sludge.

Habitat constraints on the functional significance of soil microbial communities

Science.gov (United States)

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.

Environmental conditions influence the plant functional diversity effect on potential denitrification.

Directory of Open Access Journals (Sweden)

Ariana E Sutton-Grier

2011-02-01

Full Text Available Global biodiversity loss has prompted research on the relationship between species diversity and ecosystem functioning. Few studies have examined how plant diversity impacts belowground processes; even fewer have examined how varying resource levels can influence the effect of plant diversity on microbial activity. In a field experiment in a restored wetland, we examined the role of plant trait diversity (or functional diversity, (FD and its interactions with natural levels of variability of soil properties, on a microbial process, denitrification potential (DNP. We demonstrated that FD significantly affected microbial DNP through its interactions with soil conditions; increasing FD led to increased DNP but mainly at higher levels of soil resources. Our results suggest that the effect of species diversity on ecosystem functioning may depend on environmental factors such as resource availability. Future biodiversity experiments should examine how natural levels of environmental variability impact the importance of biodiversity to ecosystem functioning.

Activity and functional diversity of microbial communities in long-term hydrocarbon and heavy metal contaminated soils

Directory of Open Access Journals (Sweden)

Markowicz Anna

2016-12-01

Full Text Available The impacts of long-term polycyclic aromatic hydrocarbons (PAHs and heavy metal pollution on soil microbial communities functioning were studied in soils taken from an old coke plant. The concentrations of PAHs in the tested soils ranged from 171 to 2137 mg kg-1. From the group of tested heavy metals, concentrations of lead were found to be the highest, ranging from 57 to 3478 mg kg-1, while zinc concentrations varied from 247 to 704 mg kg-1 and nickel from 10 to 666 mg kg-1. High dehydrogenase, acid and alkaline phosphatase activities were observed in the most contaminated soil. This may indicate bacterial adaptation to long-term heavy metal and hydrocarbon contamination. However, the Community Level Physiological Profiles (CLPPs analysis showed that the microbial functional diversity was reduced and influenced to a higher extent by some metals (Pb, Ni, moisture and conductivity than by PAHs.

Metagenomic and functional analyses of the consequences of reduction of bacterial diversity on soil functions and bioremediation in diesel-contaminated microcosms.

Science.gov (United States)

Jung, Jaejoon; Philippot, Laurent; Park, Woojun

2016-03-14

The relationship between microbial biodiversity and soil function is an important issue in ecology, yet most studies have been performed in pristine ecosystems. Here, we assess the role of microbial diversity in ecological function and remediation strategies in diesel-contaminated soils. Soil microbial diversity was manipulated using a removal by dilution approach and microbial functions were determined using both metagenomic analyses and enzymatic assays. A shift from Proteobacteria- to Actinobacteria-dominant communities was observed when species diversity was reduced. Metagenomic analysis showed that a large proportion of functional gene categories were significantly altered by the reduction in biodiversity. The abundance of genes related to the nitrogen cycle was significantly reduced in the low-diversity community, impairing denitrification. In contrast, the efficiency of diesel biodegradation was increased in the low-diversity community and was further enhanced by addition of red clay as a stimulating agent. Our results suggest that the relationship between microbial diversity and ecological function involves trade-offs among ecological processes, and should not be generalized as a positive, neutral, or negative relationship.

Modeling microbial diversity in anaerobic digestion through an extended ADM1 model.

Science.gov (United States)

Ramirez, Ivan; Volcke, Eveline I P; Rajinikanth, Rajagopal; Steyer, Jean-Philippe

2009-06-01

The anaerobic digestion process comprises a whole network of sequential and parallel reactions, of both biochemical and physicochemical nature. Mathematical models, aiming at understanding and optimization of the anaerobic digestion process, describe these reactions in a structured way, the IWA Anaerobic Digestion Model No. 1 (ADM1) being the most well established example. While these models distinguish between different microorganisms involved in different reactions, to our knowledge they all neglect species diversity between organisms with the same function, i.e. performing the same reaction. Nevertheless, available experimental evidence suggests that the structure and properties of a microbial community may be influenced by process operation and on their turn also determine the reactor functioning. In order to adequately describe these phenomena, mathematical models need to consider the underlying microbial diversity. This is demonstrated in this contribution by extending the ADM1 to describe microbial diversity between organisms of the same functional group. The resulting model has been compared with the traditional ADM1 in describing experimental data of a pilot-scale hybrid Upflow Anaerobic Sludge Filter Bed (UASFB) reactor, as well as in a more detailed simulation study. The presented model is further shown useful in assessing the relationship between reactor performance and microbial community structure in mesophilic CSTRs seeded with slaughterhouse wastewater when facing increasing levels of ammonia.

Management with willow short rotation coppice increase the functional gene diversity and functional activity of a heavy metal polluted soil.

Science.gov (United States)

Xue, K; van Nostrand, J D; Vangronsveld, J; Witters, N; Janssen, J O; Kumpiene, J; Siebielec, G; Galazka, R; Giagnoni, L; Arenella, M; Zhou, J-Z; Renella, G

2015-11-01

We studied the microbial functional diversity, biochemical activity, heavy metals (HM) availability and soil toxicity of Cd, Pb and Zn contaminated soils, kept under grassland or short rotation coppice (SRC) to attenuate the risks associated with HM contamination and restore the soil ecological functions. Soil microbial functional diversity was analyzed by the GeoChip, a functional gene microarray containing probes for genes involved in nutrient cycling, metal resistance and stress response. Soil under SRC showed a higher abundance of microbial genes involved in C, N, P and S cycles and resistance to various HM, higher microbial biomass, respiration and enzyme activity rates, and lower HM availability than the grassland soil. The linkages between functional genes of soil microbial communities and soil chemical properties, HM availability and biochemical activity were also investigated. Soil toxicity and N, P and Pb availability were important factors in shaping the microbial functional diversity, as determined by CCA. We concluded that in HM contaminated soils the microbial functional diversity was positively influenced by SRC management through the reduction of HM availability and soil toxicity increase of nutrient cycling. The presented results can be important in predicting the long term environmental sustainability of plant-based soil remediation. Copyright © 2015 Elsevier Ltd. All rights reserved.

Microbial biomass and bacterial functional diversity in forest soils: effects of organic matter removal, compaction, and vegetation control

Science.gov (United States)

Qingchao Li; H. Lee Allen; Arthur G. Wollum

2004-01-01

The effects of organic matter removal, soil compaction, and vegetation control on soil microbial biomass carbon, nitrogen, C-to-N ratio, and functional diversity were examined in a 6-year loblolly pine plantation on a Coastal Plain site in eastern North Carolina, USA. This experimental plantation was established as part of the US Forest Service's Long Term Soil...

Estimating and comparing microbial diversity in the presence of sequencing errors

Science.gov (United States)

Chiu, Chun-Huo

2016-01-01

Estimating and comparing microbial diversity are statistically challenging due to limited sampling and possible sequencing errors for low-frequency counts, producing spurious singletons. The inflated singleton count seriously affects statistical analysis and inferences about microbial diversity. Previous statistical approaches to tackle the sequencing errors generally require different parametric assumptions about the sampling model or about the functional form of frequency counts. Different parametric assumptions may lead to drastically different diversity estimates. We focus on nonparametric methods which are universally valid for all parametric assumptions and can be used to compare diversity across communities. We develop here a nonparametric estimator of the true singleton count to replace the spurious singleton count in all methods/approaches. Our estimator of the true singleton count is in terms of the frequency counts of doubletons, tripletons and quadrupletons, provided these three frequency counts are reliable. To quantify microbial alpha diversity for an individual community, we adopt the measure of Hill numbers (effective number of taxa) under a nonparametric framework. Hill numbers, parameterized by an order q that determines the measures’ emphasis on rare or common species, include taxa richness (q = 0), Shannon diversity (q = 1, the exponential of Shannon entropy), and Simpson diversity (q = 2, the inverse of Simpson index). A diversity profile which depicts the Hill number as a function of order q conveys all information contained in a taxa abundance distribution. Based on the estimated singleton count and the original non-singleton frequency counts, two statistical approaches (non-asymptotic and asymptotic) are developed to compare microbial diversity for multiple communities. (1) A non-asymptotic approach refers to the comparison of estimated diversities of standardized samples with a common finite sample size or sample completeness. This

Metagenomic and functional analyses of the consequences of reduction of bacterial diversity on soil functions and bioremediation in diesel-contaminated microcosms

OpenAIRE

Jung, Jaejoon; Philippot, Laurent

2016-01-01

The relationship between microbial biodiversity and soil function is an important issue in ecology, yet most studies have been performed in pristine ecosystems. Here, we assess the role of microbial diversity in ecological function and remediation strategies in diesel-contaminated soils. Soil microbial diversity was manipulated using a removal by dilution approach and microbial functions were determined using both metagenomic analyses and enzymatic assays. A shift from Proteobacteria- to Acti...

Soil fertility and plant diversity enhance microbial performance in metal-polluted soils.

Science.gov (United States)

Stefanowicz, Anna M; Kapusta, Paweł; Szarek-Łukaszewska, Grażyna; Grodzińska, Krystyna; Niklińska, Maria; Vogt, Rolf D

2012-11-15

This study examined the effects of soil physicochemical properties (including heavy metal pollution) and vegetation parameters on soil basal respiration, microbial biomass, and the activity and functional richness of culturable soil bacteria and fungi. In a zinc and lead mining area (S Poland), 49 sites were selected to represent all common plant communities and comprise the area's diverse soil types. Numerous variables describing habitat properties were reduced by PCA to 7 independent factors, mainly representing subsoil type (metal-rich mining waste vs. sand), soil fertility (exchangeable Ca, Mg and K, total C and N, organic C), plant species richness, phosphorus content, water-soluble heavy metals (Zn, Cd and Pb), clay content and plant functional diversity (based on graminoids, legumes and non-leguminous forbs). Multiple regression analysis including these factors explained much of the variation in most microbial parameters; in the case of microbial respiration and biomass, it was 86% and 71%, respectively. The activity of soil microbes was positively affected mainly by soil fertility and, apparently, by the presence of mining waste in the subsoil. The mining waste contained vast amounts of trace metals (total Zn, Cd and Pb), but it promoted microbial performance due to its inherently high content of macronutrients (total Ca, Mg, K and C). Plant species richness had a relatively strong positive effect on all microbial parameters, except for the fungal component. In contrast, plant functional diversity was practically negligible in its effect on microbes. Other explanatory variables had only a minor positive effect (clay content) or no significant influence (phosphorus content) on microbial communities. The main conclusion from this study is that high nutrient availability and plant species richness positively affected the soil microbes and that this apparently counteracted the toxic effects of metal contamination. Copyright © 2012 Elsevier B.V. All rights

Gut Microbial Diversity in Rat Model Induced by Rhubarb

Science.gov (United States)

Peng, Ying; Wu, Chunfu; Yang, Jingyu; Li, Xiaobo

2014-01-01

Rhubarb is often used to establish chronic diarrhea and spleen (Pi)-deficiency syndrome animal models in China. In this study, we utilized the enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) method to detect changes in bacterial diversity in feces and the bowel mucosa associated with this model. Total microbial genomic DNA from the small bowel (duodenum, jejunum, and ileum), large bowel (proximal colon, distal colon, and rectum), cecum, and feces of normal and rhubarb-exposed rats were used as templates for the ERIC-PCR analysis. We found that the fecal microbial composition did not correspond to the bowel bacteria mix. More bacterial diversity was observed in the ileum of rhubarb-exposed rats (Panalysis with the SPSS software, the Canonical Discriminant Function Formulae for model rats was established. PMID:25048267

Taxa-area Relationship (TAR) of Microbial Functional Genes with Long-TGerm Fertilization

Energy Technology Data Exchange (ETDEWEB)

Liang, Yuting; Wu, Liyou; Clark, Ian; Xue, Kai; Van Nostrand, Joy D.; Deng, Ye; He, Zhili; Hirsch, Penny; Mcgrath, Steve; Zhou, Jizhong

2010-05-17

Diversity and spatial patterns in plant and animal communities are well documented as a positive-power law of a taxa-area relationship (TAR). At present little is known whether this also applies to soil microbial communities and whether long-term fertilization has an influence on the underlying microbial diversity. To test the effects of long-term fertilization on above-ground botanical diversity and below-ground microbial diversity, a nested sampling approach on Park Grass plots (12d& 11/2c) of Rothamsted Reseach in United Kingdom, both at ~;; pH 5 but with plant diversities of between 42 and 13 respectively were used. GeoChip 3.0, covering approximately 57, 000 gene sequences of 292 gene families involved in nitrogen, carbon, sulfur and phosphorus cycling, metal reduction and resistance, and organic contaminant degradation, was used to determine the gene area relationships for both functional and phylogenetic groups and the relationship to plant diversity. Our analysis indicated that the microbial communities were separated by different plant diversity based on DCA. The soil microbial diversity was in accord with plant diversity. Soil microbial community exhibited different z value with different plant diversity, z = 0.0449 with higher plant diversity and z = 0.0583 with lower plant diversity (P< 0.0001). These results suggest that the turnover in space of microorganisms may be higher with long-term fertilization.

PanFP: pangenome-based functional profiles for microbial communities.

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Jun, Se-Ran; Robeson, Michael S; Hauser, Loren J; Schadt, Christopher W; Gorin, Andrey A

2015-09-26

For decades there has been increasing interest in understanding the relationships between microbial communities and ecosystem functions. Current DNA sequencing technologies allows for the exploration of microbial communities in two principle ways: targeted rRNA gene surveys and shotgun metagenomics. For large study designs, it is often still prohibitively expensive to sequence metagenomes at both the breadth and depth necessary to statistically capture the true functional diversity of a community. Although rRNA gene surveys provide no direct evidence of function, they do provide a reasonable estimation of microbial diversity, while being a very cost-effective way to screen samples of interest for later shotgun metagenomic analyses. However, there is a great deal of 16S rRNA gene survey data currently available from diverse environments, and thus a need for tools to infer functional composition of environmental samples based on 16S rRNA gene survey data. We present a computational method called pangenome-based functional profiles (PanFP), which infers functional profiles of microbial communities from 16S rRNA gene survey data for Bacteria and Archaea. PanFP is based on pangenome reconstruction of a 16S rRNA gene operational taxonomic unit (OTU) from known genes and genomes pooled from the OTU's taxonomic lineage. From this lineage, we derive an OTU functional profile by weighting a pangenome's functional profile with the OTUs abundance observed in a given sample. We validated our method by comparing PanFP to the functional profiles obtained from the direct shotgun metagenomic measurement of 65 diverse communities via Spearman correlation coefficients. These correlations improved with increasing sequencing depth, within the range of 0.8-0.9 for the most deeply sequenced Human Microbiome Project mock community samples. PanFP is very similar in performance to another recently released tool, PICRUSt, for almost all of survey data analysed here. But, our method is unique

Groundwater shapes sediment biogeochemistry and microbial diversity in a submerged Great Lake sinkhole.

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Kinsman-Costello, L E; Sheik, C S; Sheldon, N D; Allen Burton, G; Costello, D M; Marcus, D; Uyl, P A Den; Dick, G J

2017-03-01

For a large part of earth's history, cyanobacterial mats thrived in low-oxygen conditions, yet our understanding of their ecological functioning is limited. Extant cyanobacterial mats provide windows into the putative functioning of ancient ecosystems, and they continue to mediate biogeochemical transformations and nutrient transport across the sediment-water interface in modern ecosystems. The structure and function of benthic mats are shaped by biogeochemical processes in underlying sediments. A modern cyanobacterial mat system in a submerged sinkhole of Lake Huron (LH) provides a unique opportunity to explore such sediment-mat interactions. In the Middle Island Sinkhole (MIS), seeping groundwater establishes a low-oxygen, sulfidic environment in which a microbial mat dominated by Phormidium and Planktothrix that is capable of both anoxygenic and oxygenic photosynthesis, as well as chemosynthesis, thrives. We explored the coupled microbial community composition and biogeochemical functioning of organic-rich, sulfidic sediments underlying the surface mat. Microbial communities were diverse and vertically stratified to 12 cm sediment depth. In contrast to previous studies, which used low-throughput or shotgun metagenomic approaches, our high-throughput 16S rRNA gene sequencing approach revealed extensive diversity. This diversity was present within microbial groups, including putative sulfate-reducing taxa of Deltaproteobacteria, some of which exhibited differential abundance patterns in the mats and with depth in the underlying sediments. The biological and geochemical conditions in the MIS were distinctly different from those in typical LH sediments of comparable depth. We found evidence for active cycling of sulfur, methane, and nutrients leading to high concentrations of sulfide, ammonium, and phosphorus in sediments underlying cyanobacterial mats. Indicators of nutrient availability were significantly related to MIS microbial community composition, while LH

A communal catalogue reveals Earth's multiscale microbial diversity.

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Thompson, Luke R; Sanders, Jon G; McDonald, Daniel; Amir, Amnon; Ladau, Joshua; Locey, Kenneth J; Prill, Robert J; Tripathi, Anupriya; Gibbons, Sean M; Ackermann, Gail; Navas-Molina, Jose A; Janssen, Stefan; Kopylova, Evguenia; Vázquez-Baeza, Yoshiki; González, Antonio; Morton, James T; Mirarab, Siavash; Zech Xu, Zhenjiang; Jiang, Lingjing; Haroon, Mohamed F; Kanbar, Jad; Zhu, Qiyun; Jin Song, Se; Kosciolek, Tomasz; Bokulich, Nicholas A; Lefler, Joshua; Brislawn, Colin J; Humphrey, Gregory; Owens, Sarah M; Hampton-Marcell, Jarrad; Berg-Lyons, Donna; McKenzie, Valerie; Fierer, Noah; Fuhrman, Jed A; Clauset, Aaron; Stevens, Rick L; Shade, Ashley; Pollard, Katherine S; Goodwin, Kelly D; Jansson, Janet K; Gilbert, Jack A; Knight, Rob

2017-11-23

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.

In Search of functionality-diversity relationships in anaerobic mixed culture fermentations

International Nuclear Information System (INIS)

Kleerebezem, R.; Temudo, M.; Muyzer Van Loosdrecht, M. C. M.

2009-01-01

Based on the work described in this paper we will postulate that in environmental ecosystems with a weak selective pressure no clear relationship exists between the ecosystem functionality and the microbial diversity and microbial composition. In the past years we have been investigating the anaerobic fermentation of glucose, xylose, and glycerol, and mixtures of these substrates in continuously stirred tank reactors (CSTR) inoculated with an activated sludge characterized by a very rich microbial diversity. (Author)

A highly diverse, desert-like microbial biocenosis on solar panels in a Mediterranean city.

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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.

Microbial diversity: a bonanza of phyla.

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Eme, Laura; Doolittle, W Ford

2015-03-16

Metagenomics and single-cell genomics are now the gold standard for exploring microbial diversity. A new study focusing on enigmatic ultra-small archaea greatly expands known genetic diversity within Archaea, and reports the first complete archaeal genomes reconstructed from metagenomic data only. Copyright © 2015 Elsevier Ltd. All rights reserved.

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.

New Dimensions in Microbial Ecology—Functional Genes in Studies to Unravel the Biodiversity and Role of Functional Microbial Groups in the Environment

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Imhoff, Johannes F.

2016-01-01

During the past decades, tremendous advances have been made in the possibilities to study the diversity of microbial communities in the environment. The development of methods to study these communities on the basis of 16S rRNA gene sequences analysis was a first step into the molecular analysis of environmental communities and the study of biodiversity in natural habitats. A new dimension in this field was reached with the introduction of functional genes of ecological importance and the establishment of genetic tools to study the diversity of functional microbial groups and their responses to environmental factors. Functional gene approaches are excellent tools to study the diversity of a particular function and to demonstrate changes in the composition of prokaryote communities contributing to this function. The phylogeny of many functional genes largely correlates with that of the 16S rRNA gene, and microbial species may be identified on the basis of functional gene sequences. Functional genes are perfectly suited to link culture-based microbiological work with environmental molecular genetic studies. In this review, the development of functional gene studies in environmental microbiology is highlighted with examples of genes relevant for important ecophysiological functions. Examples are presented for bacterial photosynthesis and two types of anoxygenic phototrophic bacteria, with genes of the Fenna-Matthews-Olson-protein (fmoA) as target for the green sulfur bacteria and of two reaction center proteins (pufLM) for the phototrophic purple bacteria, with genes of adenosine-5′phosphosulfate (APS) reductase (aprA), sulfate thioesterase (soxB) and dissimilatory sulfite reductase (dsrAB) for sulfur oxidizing and sulfate reducing bacteria, with genes of ammonia monooxygenase (amoA) for nitrifying/ammonia-oxidizing bacteria, with genes of particulate nitrate reductase and nitrite reductases (narH/G, nirS, nirK) for denitrifying bacteria and with genes of methane

New Dimensions in Microbial Ecology—Functional Genes in Studies to Unravel the Biodiversity and Role of Functional Microbial Groups in the Environment

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Johannes F. Imhoff

2016-05-01

Full Text Available During the past decades, tremendous advances have been made in the possibilities to study the diversity of microbial communities in the environment. The development of methods to study these communities on the basis of 16S rRNA gene sequences analysis was a first step into the molecular analysis of environmental communities and the study of biodiversity in natural habitats. A new dimension in this field was reached with the introduction of functional genes of ecological importance and the establishment of genetic tools to study the diversity of functional microbial groups and their responses to environmental factors. Functional gene approaches are excellent tools to study the diversity of a particular function and to demonstrate changes in the composition of prokaryote communities contributing to this function. The phylogeny of many functional genes largely correlates with that of the 16S rRNA gene, and microbial species may be identified on the basis of functional gene sequences. Functional genes are perfectly suited to link culture-based microbiological work with environmental molecular genetic studies. In this review, the development of functional gene studies in environmental microbiology is highlighted with examples of genes relevant for important ecophysiological functions. Examples are presented for bacterial photosynthesis and two types of anoxygenic phototrophic bacteria, with genes of the Fenna-Matthews-Olson-protein (fmoA as target for the green sulfur bacteria and of two reaction center proteins (pufLM for the phototrophic purple bacteria, with genes of adenosine-5′phosphosulfate (APS reductase (aprA, sulfate thioesterase (soxB and dissimilatory sulfite reductase (dsrAB for sulfur oxidizing and sulfate reducing bacteria, with genes of ammonia monooxygenase (amoA for nitrifying/ammonia-oxidizing bacteria, with genes of particulate nitrate reductase and nitrite reductases (narH/G, nirS, nirK for denitrifying bacteria and with genes

Linking the development and functioning of a carnivorous pitcher plant's microbial digestive community.

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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.

Microbial functional diversity of a shrubland soil experimentally burned and treated with two post-fire stabilization techniques (straw mulch and seeding

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M.T. Fonturbel

2013-01-01

Full Text Available The study examined the effect of two post-fire stabilization treatments (seeding and mulching on microbial diversity of a shrubland area of Galicia after an experimental fire. The soil was a Leptosol developed over granite with a slope of 38-54% and the soil microbial functional diversity was assessed using Biolog substrate utilization EcoPlates (Biolog Inc., Hayward, CA, USA. Soil samples were taken from the A horizon (0-5 cm depth at different sampling times over one year after the experimental fire. The results indicated that immediately after the fire there were significant differences in the categorized substrate utilization pattern between the microbial communities of the burnt soil treatments and the corresponding unburnt control. The burned soils exhibited significant higher values for the utilization of carboxylic acids, amino acids, carbohydrates and phenolic compounds, suggesting that the microbial community in the burned soils could be favoured by the increase in available C and nutrients following the experimental fire. These changes in the categorized substrate utilization pattern were attenuated with time; thus, one year after the fire, similar values for utilization of different C sources were observed for all unburned and burnt soils. With respect to post-fire treatments only the mulching showed an effect on the C utilization pattern.

Genetic and functional diversity of soil microbial communities associated to grapevine plants and wine quality

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Mocali, Stefano; Fabiani, Arturo; Kuramae, Eiko; de Hollander, Mattias; Kowalchuk, George A.; Vignozzi, Nadia; Valboa, Giuseppe; Costantini, Edoardo

2013-04-01

soils. The structure of soil microbial communities was assessed using 16S and 18S rRNA genes pyrosequencing and the determination of some soil microbial properties such as microbial respiration, microbial C-biomass were also determined. The role of both genetic and functional diversity of soil bacterial community on grape physiology and wine quality will be discussed.

Dormancy contributes to the maintenance of microbial diversity.

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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.

Microbial diversity of a Mediterranean soil and its changes after biotransformed dry olive residue amendment.

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José A Siles

Full Text Available The Mediterranean basin has been identified as a biodiversity hotspot, about whose soil microbial diversity little is known. Intensive land use and aggressive management practices are degrading the soil, with a consequent loss of fertility. The use of organic amendments such as dry olive residue (DOR, a waste produced by a two-phase olive-oil extraction system, has been proposed as an effective way to improve soil properties. However, before its application to soil, DOR needs a pre-treatment, such as by a ligninolytic fungal transformation, e.g. Coriolopsis floccosa. The present study aimed to describe the bacterial and fungal diversity in a Mediterranean soil and to assess the impact of raw DOR (DOR and C. floccosa-transformed DOR (CORDOR on function and phylogeny of soil microbial communities after 0, 30 and 60 days. Pyrosequencing of the 16S rRNA gene demonstrated that bacterial diversity was dominated by the phyla Proteobacteria, Acidobacteria, and Actinobacteria, while 28S-rRNA gene data revealed that Ascomycota and Basidiomycota accounted for the majority of phyla in the fungal community. A Biolog EcoPlate experiment showed that DOR and CORDOR amendments decreased functional diversity and altered microbial functional structures. These changes in soil functionality occurred in parallel with those in phylogenetic bacterial and fungal community structures. Some bacterial and fungal groups increased while others decreased depending on the relative abundance of beneficial and toxic substances incorporated with each amendment. In general, DOR was observed to be more disruptive than CORDOR.

Diet simplification selects for high gut microbial diversity and strong fermenting ability in high-altitude pikas.

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Li, Huan; Qu, Jiapeng; Li, Tongtong; Wirth, Stephan; Zhang, Yanming; Zhao, Xinquan; Li, Xiangzhen

2018-06-03

The gut microbiota in mammals plays a key role in host metabolism and adaptation. However, relatively little is known regarding to how the animals adapts to extreme environments through regulating gut microbial diversity and function. Here, we investigated the diet, gut microbiota, short-chain fatty acid (SCFA) profiles, and cellulolytic activity from two common pika (Ochotona spp.) species in China, including Plateau pika (Ochotona curzoniae) from the Qinghai-Tibet Plateau and Daurian pika (Ochotona daurica) from the Inner Mongolia Grassland. Despite a partial diet overlap, Plateau pikas harbored lower diet diversity than Daurian pikas. Some bacteria (e.g., Prevotella and Ruminococcus) associated with fiber degradation were enriched in Plateau pikas. They harbored higher gut microbial diversity, total SCFA concentration, and cellulolytic activity than Daurian pikas. Interestingly, cellulolytic activity was positively correlated with the gut microbial diversity and SCFAs. Gut microbial communities and SCFA profiles were segregated structurally between host species. PICRUSt metagenome predictions demonstrated that microbial genes involved in carbohydrate metabolism and energy metabolism were overrepresented in the gut microbiota of Plateau pikas. Our results demonstrate that Plateau pikas harbor a stronger fermenting ability for the plant-based diet than Daurian pikas via gut microbial fermentation. The enhanced ability for utilization of plant-based diets in Plateau pikas may be partly a kind of microbiota adaptation for more energy requirements in cold and hypoxic high-altitude environments.

Microbial diversity in European alpine permafrost and active layers.

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Frey, Beat; Rime, Thomas; Phillips, Marcia; Stierli, Beat; Hajdas, Irka; Widmer, Franco; Hartmann, Martin

2016-03-01

Permafrost represents a largely understudied genetic resource. Thawing of permafrost with global warming will not only promote microbial carbon turnover with direct feedback on greenhouse gases, but also unlock an unknown microbial diversity. Pioneering metagenomic efforts have shed light on the permafrost microbiome in polar regions, but temperate mountain permafrost is largely understudied. We applied a unique experimental design coupled to high-throughput sequencing of ribosomal markers to characterize the microbiota at the long-term alpine permafrost study site 'Muot-da-Barba-Peider' in eastern Switzerland with an approximate radiocarbon age of 12 000 years. Compared to the active layers, the permafrost community was more diverse and enriched with members of the superphylum Patescibacteria (OD1, TM7, GN02 and OP11). These understudied phyla with no cultured representatives proposedly feature small streamlined genomes with reduced metabolic capabilities, adaptations to anaerobic fermentative metabolisms and potential ectosymbiotic lifestyles. The permafrost microbiota was also enriched with yeasts and lichenized fungi known to harbour various structural and functional adaptation mechanisms to survive under extreme sub-zero conditions. These data yield an unprecedented view on microbial life in temperate mountain permafrost, which is increasingly important for understanding the biological dynamics of permafrost in order to anticipate potential ecological trajectories in a warming world. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Brazilian Microbiome Project: revealing the unexplored microbial diversity--challenges and prospects.

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Pylro, Victor Satler; Roesch, Luiz Fernando Wurdig; Ortega, José Miguel; do Amaral, Alexandre Morais; Tótola, Marcos Rogério; Hirsch, Penny Ruth; Rosado, Alexandre Soares; Góes-Neto, Aristóteles; da Costa da Silva, Artur Luiz; Rosa, Carlos Augusto; Morais, Daniel Kumazawa; Andreote, Fernando Dini; Duarte, Gabriela Frois; de Melo, Itamar Soares; Seldin, Lucy; Lambais, Márcio Rodrigues; Hungria, Mariangela; Peixoto, Raquel Silva; Kruger, Ricardo Henrique; Tsai, Siu Mui; Azevedo, Vasco

2014-02-01

The Brazilian Microbiome Project (BMP) aims to assemble a Brazilian Metagenomic Consortium/Database. At present, many metagenomic projects underway in Brazil are widely known. Our goal in this initiative is to co-ordinate and standardize these together with new projects to come. It is estimated that Brazil hosts approximately 20 % of the entire world's macroorganism biological diversity. It is 1 of the 17 countries that share nearly 70 % of the world's catalogued animal and plant species, and is recognized as one of the most megadiverse countries. At the end of 2012, Brazil has joined GBIF (Global Biodiversity Information Facility), as associated member, to improve the access to the Brazilian biodiversity data in a free and open way. This was an important step toward increasing international collaboration and clearly shows the commitment of the Brazilian government in directing national policies toward sustainable development. Despite its importance, the Brazilian microbial diversity is still considered to be largely unknown, and it is clear that to maintain ecosystem dynamics and to sustainably manage land use, it is crucial to understand the biological and functional diversity of the system. This is the first attempt to collect and collate information about Brazilian microbial genetic and functional diversity in a systematic and holistic manner. The success of the BMP depends on a massive collaborative effort of both the Brazilian and international scientific communities, and therefore, we invite all colleagues to participate in this project.

Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion.

Science.gov (United States)

Vanwonterghem, Inka; Jensen, Paul D; Rabaey, Korneel; Tyson, Gene W

2016-09-01

Our understanding of the complex interconnected processes performed by microbial communities is hindered by our inability to culture the vast majority of microorganisms. Metagenomics provides a way to bypass this cultivation bottleneck and recent advances in this field now allow us to recover a growing number of genomes representing previously uncultured populations from increasingly complex environments. In this study, a temporal genome-centric metagenomic analysis was performed of lab-scale anaerobic digesters that host complex microbial communities fulfilling a series of interlinked metabolic processes to enable the conversion of cellulose to methane. In total, 101 population genomes that were moderate to near-complete were recovered based primarily on differential coverage binning. These populations span 19 phyla, represent mostly novel species and expand the genomic coverage of several rare phyla. Classification into functional guilds based on their metabolic potential revealed metabolic networks with a high level of functional redundancy as well as niche specialization, and allowed us to identify potential roles such as hydrolytic specialists for several rare, uncultured populations. Genome-centric analyses of complex microbial communities across diverse environments provide the key to understanding the phylogenetic and metabolic diversity of these interactive communities. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

The pig gut microbial diversity: Understanding the pig gut microbial ecology through the next generation high throughput sequencing.

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Kim, Hyeun Bum; Isaacson, Richard E

2015-06-12

The importance of the gut microbiota of animals is widely acknowledged because of its pivotal roles in the health and well being of animals. The genetic diversity of the gut microbiota contributes to the overall development and metabolic needs of the animal, and provides the host with many beneficial functions including production of volatile fatty acids, re-cycling of bile salts, production of vitamin K, cellulose digestion, and development of immune system. Thus the intestinal microbiota of animals has been the subject of study for many decades. Although most of the older studies have used culture dependent methods, the recent advent of high throughput sequencing of 16S rRNA genes has facilitated in depth studies exploring microbial populations and their dynamics in the animal gut. These culture independent DNA based studies generate large amounts of data and as a result contribute to a more detailed understanding of the microbiota dynamics in the gut and the ecology of the microbial populations. Of equal importance, is being able to identify and quantify microbes that are difficult to grow or that have not been grown in the laboratory. Interpreting the data obtained from this type of study requires using basic principles of microbial diversity to understand importance of the composition of microbial populations. In this review, we summarize the literature on culture independent studies of the pig gut microbiota with an emphasis on its succession and alterations caused by diverse factors. Copyright © 2015 Elsevier B.V. All rights reserved.

Distinctive tropical forest variants have unique soil microbial communities, but not always low microbial diversity

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Binu M Tripathi

2016-04-01

Full Text Available There has been little study of whether different variants of tropical rainforest have distinct soil microbial communities and levels of diversity. We compared bacterial and fungal community composition and diversity between primary mixed dipterocarp, secondary mixed dipterocarp, white sand heath, inland heath, and peat swamp forests in Brunei Darussalam, northwest Borneo by analyzing Illumina Miseq sequence data of 16S rRNA gene and ITS1 region. We hypothesized that white sand heath, inland heath and peat swamp forests would show lower microbial diversity and relatively distinct microbial communities (compared to MDF primary and secondary forests due to their distinctive environments. We found that soil properties together with bacterial and fungal communities varied significantly between forest types. Alpha and beta-diversity of bacteria was highest in secondary dipterocarp and white sand heath forests. Also, bacterial alpha diversity was strongly structured by pH, adding another instance of this widespread pattern in nature. The alpha diversity of fungi was equally high in all forest types except peat swamp forest, although fungal beta-diversity was highest in primary and secondary mixed dipterocarp forests. The relative abundance of ectomycorrhizal (EcM fungi varied significantly between forest types, with highest relative abundance observed in MDF primary forest. Overall, our results suggest that the soil bacterial and fungal communities in these forest types are to a certain extent predictable and structured by soil properties, but that diversity is not determined by how distinctive the conditions are. This contrasts with the diversity patterns seen in rainforest trees, where distinctive soil conditions have consistently lower tree diversity.

Microbial Functional Diversity, Biomass and Activity as Affected by Soil Surface Mulching in a Semiarid Farmland.

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Yufang Shen

Full Text Available Mulching is widely used to increase crop yield in semiarid regions in northwestern China, but little is known about the effect of different mulching systems on the microbial properties of the soil, which play an important role in agroecosystemic functioning and nutrient cycling. Based on a 4-year spring maize (Zea mays L. field experiment at Changwu Agricultural and Ecological Experimental Station, Shaanxi, we evaluated the responses of soil microbial activity and crop to various management systems. The treatments were NMC (no mulching with inorganic N fertilizer, GMC (gravel mulching with inorganic N fertilizer, FMC (plastic-film mulching with inorganic N fertilizer and FMO (plastic-film mulching with inorganic N fertilizer and organic manure addition. The results showed that the FMO soil had the highest contents of microbial biomass carbon and nitrogen, dehydrogenase activity, microbial activity and Shannon diversity index. The relative use of carbohydrates and amino acids by microbes was highest in the FMO soil, whereas the relative use of polymers, phenolic compounds and amines was highest in the soil in the NMC soil. Compared with the NMC, an increased but no significant trend of biomass production and nitrogen accumulation was observed under the GMC treatment. The FMC and FMO led a greater increase in biomass production than GMC and NMC. Compare with the NMC treatment, FMC increased grain yield, maize biomass and nitrogen accumulation by 62.2, 62.9 and 86.2%, but no significant difference was found between the FMO and FMC treatments. Some soil biological properties, i.e. microbial biomass carbon, microbial biomass nitrogen, being sensitive to the mulching and organic fertilizer, were significant correlated with yield and nitrogen availability. Film mulching over gravel mulching can serve as an effective measure for crop production and nutrient cycling, and plus organic fertilization additions may thus have improvements in the biological

Soil microbial diversity in the vicinity of desert shrubs.

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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.

Functional gene array-based analysis of microbial community structure in groundwaters with a gradient of contaminant levels

Energy Technology Data Exchange (ETDEWEB)

Waldron, P.J.; Wu, L.; Van Nostrand, J.D.; Schadt, C.W.; Watson, D.B.; Jardine, P.M.; Palumbo, A.V.; Hazen, T.C.; Zhou, J.

2009-06-15

To understand how contaminants affect microbial community diversity, heterogeneity, and functional structure, six groundwater monitoring wells from the Field Research Center of the U.S. Department of Energy Environmental Remediation Science Program (ERSP; Oak Ridge, TN), with a wide range of pH, nitrate, and heavy metal contamination were investigated. DNA from the groundwater community was analyzed with a functional gene array containing 2006 probes to detect genes involved in metal resistance, sulfate reduction, organic contaminant degradation, and carbon and nitrogen cycling. Microbial diversity decreased in relation to the contamination levels of the wells. Highly contaminated wells had lower gene diversity but greater signal intensity than the pristine well. The microbial composition was heterogeneous, with 17-70% overlap between different wells. Metal-resistant and metal-reducing microorganisms were detected in both contaminated and pristine wells, suggesting the potential for successful bioremediation of metal-contaminated groundwaters. In addition, results of Mantel tests and canonical correspondence analysis indicate that nitrate, sulfate, pH, uranium, and technetium have a significant (p < 0.05) effect on microbial community structure. This study provides an overall picture of microbial community structure in contaminated environments with functional gene arrays by showing that diversity and heterogeneity can vary greatly in relation to contamination.

Decreases in soil microbial function and functional diversity in response to depleted uranium

International Nuclear Information System (INIS)

Meyer, M.C.; Paschke, M.W.; McLendon, T.

1998-01-01

A soil microcosm experiment was used to analyze effects of depleted uranium (DU) on soil function, and the concomitant changes in bacterial functional diversity. Uranium treatment levels were 0, 50, 500, 5000, 10,000 and 25,000 mg DU kg -1 soil. Three measures of soil function were made. Overall soil biological activity was assessed via measurement of soil respiration. Decomposition was assessed by measurement of mass loss of four different plant litter types: wood sticks, cellulose paper, high-N grass, and low-N grass. Mineral N availability in the microcosms was estimated using ion-exchange resin bags. Functional diversity of the microcosms was analyzed through the use of the Biolog-system of sole-C-utilization patterns. Soil respiration was the most sensitive measure of functional changes, with significant decreases observed starting at the 500 mg kg -1 treatment. No differences in N availability were observed across the U treatments. Litter decomposition was significantly decreased at the 25,000 mg kg -1 level relative to the control for all litter types except the high-N grass. Wood decomposition was reduced by 84% at the 25,000 mg kg - treatment, cellulose paper by 68%, and low-N grass by 15%. Decreases in the functional diversity of the bacterial community were related to the observed decrease in soil respiration, and to the greater effect on decomposition of the lower-quality litter types

Low Microbial Diversity and Abnormal Microbial Succession Is Associated with Necrotizing Enterocolitis in Preterm Infants

Science.gov (United States)

Dobbler, Priscila T.; Procianoy, Renato S.; Mai, Volker; Silveira, Rita C.; Corso, Andréa L.; Rojas, Bruna S.; Roesch, Luiz F. W.

2017-01-01

Despite increased efforts, the diverse etiologies of Necrotizing Enterocolitis (NEC) have remained largely elusive. Clinical predictors of NEC remain ill-defined and currently lack sufficient specificity. The development of a thorough understanding of initial gut microbiota colonization pattern in preterm infants might help to improve early detection or prediction of NEC and its associated morbidities. Here we compared the fecal microbiota successions, microbial diversity, abundance and structure of newborns that developed NEC with preterm controls. A 16S rRNA based microbiota analysis was conducted in a total of 132 fecal samples that included the first stool (meconium) up until the 5th week of life or NEC diagnosis from 40 preterm babies (29 controls and 11 NEC cases). A single phylotype matching closest to the Enterobacteriaceae family correlated strongly with NEC. In DNA from the sample with the greatest abundance of this phylotype additional shotgun metagenomic sequencing revealed Citrobacter koseri and Klebsiella pneumoniae as the dominating taxa. These two taxa might represent suitable microbial biomarker targets for early diagnosis of NEC. In NEC cases, we further detected lower microbial diversity and an abnormal succession of the microbial community before NEC diagnosis. Finally, we also detected a disruption in anaerobic microorganisms in the co-occurrence network of meconium samples from NEC cases. Our data suggest that a strong dominance of Citrobacter koseri and/or Klebsiella pneumoniae, low diversity, low abundance of Lactobacillus, as well as an altered microbial-network structure during the first days of life, correlate with NEC risk in preterm infants. Confirmation of these findings in other hospitals might facilitate the development of a microbiota based screening approach for early detection of NEC. PMID:29187842

Soil microbial functional and fungal diversity as influenced by municipal sewage sludge accumulation.

Science.gov (United States)

Frąc, Magdalena; Oszust, Karolina; Lipiec, Jerzy; Jezierska-Tys, Stefania; Nwaichi, Eucharia Oluchi

2014-08-28

Safe disposal of municipal sewage sludge is a challenging global environmental concern. The aim of this study was to assess the response of soil microbial functional diversity to the accumulation of municipal sewage sludge during landfill storage. Soil samples of a municipal sewage sludge (SS) and from a sewage sludge landfill that was 3 m from a SS landfill (SS3) were analyzed relative to an undisturbed reference soil. Biolog EcoPlatesTM were inoculated with a soil suspension, and the Average Well Color Development (AWCD), Richness (R) and Shannon-Weaver index (H) were calculated to interpret the results. The fungi isolated from the sewage sludge were identified using comparative rDNA sequencing of the LSU D2 region. The MicroSEQ® ID software was used to assess the raw sequence files, perform sequence matching to the MicroSEQ® ID-validated reference database and create Neighbor-Joining trees. Moreover, the genera of fungi isolated from the soil were identified using microscopic methods. Municipal sewage sludge can serve as a habitat for plant pathogens and as a source of pathogen strains for biotechnological applications.

Prebiotics Modulate the Effects of Antibiotics on Gut Microbial Diversity and Functioning in Vitro.

Science.gov (United States)

Johnson, Laura P; Walton, Gemma E; Psichas, Arianna; Frost, Gary S; Gibson, Glenn R; Barraclough, Timothy G

2015-06-04

Intestinal bacteria carry out many fundamental roles, such as the fermentation of non-digestible dietary carbohydrates to produce short chain fatty acids (SCFAs), which can affect host energy levels and gut hormone regulation. Understanding how to manage this ecosystem to improve human health is an important but challenging goal. Antibiotics are the front line of defence against pathogens, but in turn they have adverse effects on indigenous microbial diversity and function. Here, we have investigated whether dietary supplementation--another method used to modulate gut composition and function--could be used to ameliorate the side effects of antibiotics. We perturbed gut bacterial communities with gentamicin and ampicillin in anaerobic batch cultures in vitro. Cultures were supplemented with either pectin (a non-fermentable fibre), inulin (a commonly used prebiotic that promotes the growth of beneficial bacteria) or neither. Although antibiotics often negated the beneficial effects of dietary supplementation, in some treatment combinations, notably ampicillin and inulin, dietary supplementation ameliorated the effects of antibiotics. There is therefore potential for using supplements to lessen the adverse effects of antibiotics. Further knowledge of such mechanisms could lead to better therapeutic manipulation of the human gut microbiota.

Functional ecology of soil microbial communities along a glacier forefield in Tierra del Fuego (Chile).

Science.gov (United States)

Fernández-Martínez, Miguel A; Pointing, Stephen B; Pérez-Ortega, Sergio; Arróniz-Crespo, María; Green, T G Allan; Rozzi, Ricardo; Sancho, Leopoldo G; de Los Ríos, Asunción

2016-09-01

A previously established chronosequence from Pia Glacier forefield in Tierra del Fuego (Chile) containing soils of different ages (from bare soils to forest ones) is analyzed. We used this chronosequence as framework to postulate that microbial successional development would be accompanied by changes in functionality. To test this, the GeoChip functional microarray was used to identify diversity of genes involved in microbial carbon and nitrogen metabolism, as well as other genes related to microbial stress response and biotic interactions. Changes in putative functionality generally reflected succession-related taxonomic composition of soil microbiota. Major shifts in carbon fixation and catabolism were observed, as well as major changes in nitrogen metabolism. At initial microbial dominated succession stages, microorganisms could be mainly involved in pathways that help to increase nutrient availability, while more complex microbial transformations such as denitrification and methanogenesis, and later degradation of complex organic substrates, could be more prevalent at vegetated successional states. Shifts in virus populations broadly reflected changes in microbial diversity. Conversely, stress response pathways appeared relatively well conserved for communities along the entire chronosequence. We conclude that nutrient utilization is likely the major driver of microbial succession in these soils. [Int Microbiol 19(3):161-173 (2016)]. Copyright© by the Spanish Society for Microbiology and Institute for Catalan Studies.

Microbial community functional structure in response to antibiotics in pharmaceutical wastewater treatment systems.

Science.gov (United States)

Zhang, Yu; Xie, Jianping; Liu, Miaomiao; Tian, Zhe; He, Zhili; van Nostrand, Joy D; Ren, Liren; Zhou, Jizhong; Yang, Min

2013-10-15

It is widely demonstrated that antibiotics in the environment affect microbial community structure. However, direct evidence regarding the impacts of antibiotics on microbial functional structures in wastewater treatment systems is limited. Herein, a high-throughput functional gene array (GeoChip 3.0) in combination with quantitative PCR and clone libraries were used to evaluate the microbial functional structures in two biological wastewater treatment systems, which treat antibiotic production wastewater mainly containing oxytetracycline. Despite the bacteriostatic effects of antibiotics, the GeoChip detected almost all key functional gene categories, including carbon cycling, nitrogen cycling, etc., suggesting that these microbial communities were functionally diverse. Totally 749 carbon-degrading genes belonging to 40 groups (24 from bacteria and 16 from fungi) were detected. The abundance of several fungal carbon-degrading genes (e.g., glyoxal oxidase (glx), lignin peroxidase or ligninase (lip), manganese peroxidase (mnp), endochitinase, exoglucanase_genes) was significantly correlated with antibiotic concentrations (Mantel test; P functional genes have been enhanced by the presence of antibiotics. However, from the fact that the majority of carbon-degrading genes were derived from bacteria and diverse antibiotic resistance genes were detected in bacteria, it was assumed that many bacteria could survive in the environment by acquiring antibiotic resistance and may have maintained the position as a main player in nutrient removal. Variance partitioning analysis showed that antibiotics could explain 24.4% of variations in microbial functional structure of the treatment systems. This study provides insights into the impacts of antibiotics on microbial functional structure of a unique system receiving antibiotic production wastewater, and reveals the potential importance of the cooperation between fungi and bacteria with antibiotic resistance in maintaining the

Soil-borne microbial functional structure across different land uses.

Science.gov (United States)

Kuramae, Eiko E; Zhou, Jizhong Z; Kowalchuk, George A; van Veen, Johannes A

2014-01-01

Land use change alters the structure and composition of microbial communities. However, the links between environmental factors and microbial functions are not well understood. Here we interrogated the functional structure of soil microbial communities across different land uses. In a multivariate regression tree analysis of soil physicochemical properties and genes detected by functional microarrays, the main factor that explained the different microbial community functional structures was C : N ratio. C : N ratio showed a significant positive correlation with clay and soil pH. Fields with low C : N ratio had an overrepresentation of genes for carbon degradation, carbon fixation, metal reductase, and organic remediation categories, while fields with high C : N ratio had an overrepresentation of genes encoding dissimilatory sulfate reductase, methane oxidation, nitrification, and nitrogen fixation. The most abundant genes related to carbon degradation comprised bacterial and fungal cellulases; bacterial and fungal chitinases; fungal laccases; and bacterial, fungal, and oomycete polygalacturonases. The high number of genes related to organic remediation was probably driven by high phosphate content, while the high number of genes for nitrification was probably explained by high total nitrogen content. The functional gene diversity found in different soils did not group the sites accordingly to land management. Rather, the soil factors, C : N ratio, phosphate, and total N, were the main factors driving the differences in functional genes across the fields examined.

Mineralogic control on abundance and diversity of surface-adherent microbial communities

Science.gov (United States)

Mauck, Brena S.; Roberts, Jennifer A.

2007-01-01

In this study, we investigated the role of mineral-bound P and Fe in defining microbial abundance and diversity in a carbon-rich groundwater. Field colonization experiments of initially sterile mineral surfaces were combined with community structure characterization of the attached microbial population. Silicate minerals containing varying concentrations of P (∼1000 ppm P) and Fe (∼4 wt % Fe 2 O3), goethite (FeOOH), and apatite [Ca5(PO4)3(OH)] were incubated for 14 months in three biogeochemically distinct zones within a petroleum-contaminated aquifer. Phospholipid fatty acid analysis of incubated mineral surfaces and groundwater was used as a measure of microbial community structure and biomass. Microbial biomass on minerals exhibited distinct trends as a function of mineralogy depending on the environment of incubation. In the carbon-rich, aerobic groundwater attached biomass did not correlate to the P- or Fe- content of the mineral. In the methanogenic groundwater, however, biomass was most abundant on P-containing minerals. Similarly, in the Fe-reducing groundwater a correlation between Fe-content and biomass was observed. The community structure of the mineral-adherent microbial population was compared to the native groundwater community. These two populations were significantly different regardless of mineralogy, suggesting differentiation of the planktonic community through attachment, growth, and death of colonizing cells. Biomarkers specific for dissimilatory Fe-reducing bacteria native to the aquifer were identified only on Fe-containing minerals in the Fe-reducing groundwater. These results demonstrate that the trace nutrient content of minerals affects both the abundance and diversity of surface-adherent microbial communities. This behavior may be a means to access limiting nutrients from the mineral, creating a niche for a particular microbial population. These results suggest that heterogeneity of microbial populations and their associated

Fermentation Characteristics and Microbial Diversity of Tropical Grass-legumes Silages

Directory of Open Access Journals (Sweden)

Roni Ridwan

2015-04-01

Full Text Available Calliandra calothyrsus preserved in silage is an alternative method for improving the crude protein content of feeds for sustainable ruminant production. The aim of this research was to evaluate the quality of silage which contained different levels of C. calothyrsus by examining the fermentation characteristics and microbial diversity. Silage was made in a completely randomized design consisting of five treatments with three replications i.e.: R0, Pennisetum purpureum 100%; R1, P. purpureum 75%+C. calothyrsus 25%;, R2, P. purpureum 50%+C. calothyrsus 50%; R3, P. purpureum 25%+C. calothyrsus 75%; and R4, C. calothyrsus 100%. All silages were prepared using plastic jar silos (600 g and incubated at room temperature for 30 days. Silages were analyzed for fermentation characteristics and microbial diversity. Increased levels of C. calothyrsus in silage had a significant effect (p<0.01 on the fermentation characteristics. The microbial diversity index decreased and activity was inhibited with increasing levels of C. calothyrsus. The microbial community indicated that there was a population of Lactobacillus plantarum, L. casei, L. brevis, Lactococcus lactis, Chryseobacterium sp., and uncultured bacteria. The result confirmed that silage with a combination of grass and C. calothyrsus had good fermentation characteristics and microbial communities were dominated by L. plantarum.

Introduced ascidians harbor highly diverse and host-specific symbiotic microbial assemblages.

Science.gov (United States)

Evans, James S; Erwin, Patrick M; Shenkar, Noa; López-Legentil, Susanna

2017-09-08

Many ascidian species have experienced worldwide introductions, exhibiting remarkable success in crossing geographic borders and adapting to local environmental conditions. To investigate the potential role of microbial symbionts in these introductions, we examined the microbial communities of three ascidian species common in North Carolina harbors. Replicate samples of the globally introduced species Distaplia bermudensis, Polyandrocarpa anguinea, and P. zorritensis (n = 5), and ambient seawater (n = 4), were collected in Wrightsville Beach, NC. Microbial communities were characterized by next-generation (Illumina) sequencing of partial (V4) 16S rRNA gene sequences. Ascidians hosted diverse symbiont communities, consisting of 5,696 unique microbial OTUs (at 97% sequenced identity) from 47 bacterial and three archaeal phyla. Permutational multivariate analyses of variance revealed clear differentiation of ascidian symbionts compared to seawater bacterioplankton, and distinct microbial communities inhabiting each ascidian species. 103 universal core OTUs (present in all ascidian replicates) were identified, including taxa previously described in marine invertebrate microbiomes with possible links to ammonia-oxidization, denitrification, pathogenesis, and heavy-metal processing. These results suggest ascidian microbial symbionts exhibit a high degree of host-specificity, forming intimate associations that may contribute to host adaptation to new environments via expanded tolerance thresholds and enhanced holobiont function.

Environmental and Geographical Factors Structure Soil Microbial Diversity in New Caledonian Ultramafic Substrates: A Metagenomic Approach.

Directory of Open Access Journals (Sweden)

Véronique Gourmelon

Full Text Available Soil microorganisms play key roles in ecosystem functioning and are known to be influenced by biotic and abiotic factors, such as plant cover or edaphic parameters. New Caledonia, a biodiversity hotspot located in the southwest Pacific, is one-third covered by ultramafic substrates. These types of soils are notably characterised by low nutrient content and high heavy metal concentrations. Ultramafic outcrops harbour diverse vegetation types and remarkable plant diversity. In this study, we aimed to assess soil bacterial and fungal diversity in New Caledonian ultramafic substrates and to determine whether floristic composition, edaphic parameters and geographical factors affect this microbial diversity. Therefore, four plant formation types at two distinct sites were studied. These formations represent different stages in a potential chronosequence. Soil cores, according to a given sampling procedure, were collected to assess microbial diversity using a metagenomic approach, and to characterise the physico-chemical parameters. A botanical inventory was also performed. Our results indicated that microbial richness, composition and abundance were linked to the plant cover type and the dominant plant species. Furthermore, a large proportion of Ascomycota phylum (fungi, mostly in non-rainforest formations, and Planctomycetes phylum (bacteria in all formations were observed. Interestingly, such patterns could be indicators of past disturbances that occurred on different time scales. Furthermore, the bacteria and fungi were influenced by diverse edaphic parameters as well as by the interplay between these two soil communities. Another striking finding was the existence of a site effect. Differences in microbial communities between geographical locations may be explained by dispersal limitation in the context of the biogeographical island theory. In conclusion, each plant formation at each site possesses is own microbial community resulting from

Soil-Borne Microbial Functional Structure across Different Land Uses

Directory of Open Access Journals (Sweden)

Eiko E. Kuramae

2014-01-01

Full Text Available Land use change alters the structure and composition of microbial communities. However, the links between environmental factors and microbial functions are not well understood. Here we interrogated the functional structure of soil microbial communities across different land uses. In a multivariate regression tree analysis of soil physicochemical properties and genes detected by functional microarrays, the main factor that explained the different microbial community functional structures was C : N ratio. C : N ratio showed a significant positive correlation with clay and soil pH. Fields with low C : N ratio had an overrepresentation of genes for carbon degradation, carbon fixation, metal reductase, and organic remediation categories, while fields with high C : N ratio had an overrepresentation of genes encoding dissimilatory sulfate reductase, methane oxidation, nitrification, and nitrogen fixation. The most abundant genes related to carbon degradation comprised bacterial and fungal cellulases; bacterial and fungal chitinases; fungal laccases; and bacterial, fungal, and oomycete polygalacturonases. The high number of genes related to organic remediation was probably driven by high phosphate content, while the high number of genes for nitrification was probably explained by high total nitrogen content. The functional gene diversity found in different soils did not group the sites accordingly to land management. Rather, the soil factors, C : N ratio, phosphate, and total N, were the main factors driving the differences in functional genes across the fields examined.

Astrobiology and Microbial Diversity Websites at MBL

Science.gov (United States)

Bahr, M.; Bordenstein, S. R.

2006-12-01

The NASA Astrobiology Institute (NAI) mission is to study the origin, evolution and future of life in the Universe. The MBL Astrobiology team explores the evolution and interaction of genomes of diverse organisms that play significant roles in environmental biology over evolutionary time scales. Communication about our research includes the personal contact of teacher workshops, and the development of web-based resources. Microbial Life Educational Resources (MLER) provides an expanding internet resource about the ecology, diversity and evolution for students, K-12 teachers, university faculty, and the general public. MLER includes websites, PowerPoint presentations, teaching activities, data sets, and other useful materials for creating or enhancing courses related to astrobiology. Our second site, micro*scope (http://microscope.mbl.edu), has images of microbes, classification schemes, descriptions of organisms, talks and other educational resources to improve awareness of the biodiversity of our microbial partners.

Studying Microbial Mat Functioning Amidst "Unexpected Diversity": Methodological Approaches and Initial Results from Metatranscriptomes of Mats Over Diel cycles, iTags from Long Term Manipulations, and Biogeochemical Cycling in Simplified Microbial Mats Constructed from Cultures

Science.gov (United States)

Bebout, B.; Bebout, L. E.; Detweiler, A. M.; Everroad, R. C.; Lee, J.; Pett-Ridge, J.; Weber, P. K.

2014-12-01

Microbial mats are famously amongst the most diverse microbial ecosystems on Earth, inhabiting some of the most inclement environments known, including hypersaline, dry, hot, cold, nutrient poor, and high UV environments. The high microbial diversity of microbial mats makes studies of microbial ecology notably difficult. To address this challenge, we have been using a combination of metagenomics, metatranscriptomics, iTags and culture-based simplified microbial mats to study biogeochemical cycling (H2 production, N2 fixation, and fermentation) in microbial mats collected from Elkhorn Slough, Monterey Bay, California. Metatranscriptomes of microbial mats incubated over a diel cycle have revealed that a number of gene systems activate only during the day in Cyanobacteria, while the remaining appear to be constitutive. The dominant cyanobacterium in the mat (Microcoleus chthonoplastes) expresses several pathways for nitrogen scavenging undocumented in cultured strains, as well as the expression of two starch storage and utilization cycles. Community composition shifts in response to long term manipulations of mats were assessed using iTags. Changes in community diversity were observed as hydrogen fluxes increased in response to a lowering of sulfate concentrations. To produce simplified microbial mats, we have isolated members of 13 of the 15 top taxa from our iTag libraries into culture. Simplified microbial mats and simple co-cultures and consortia constructed from these isolates reproduce many of the natural patterns of biogeochemical cycling in the parent natural microbial mats, but against a background of far lower overall diversity, simplifying studies of changes in gene expression (over the short term), interactions between community members, and community composition changes (over the longer term), in response to environmental forcing.

Unique Microbial Diversity and Metabolic Pathway Features of Fermented Vegetables From Hainan, China

Science.gov (United States)

Peng, Qiannan; Jiang, Shuaiming; Chen, Jieling; Ma, Chenchen; Huo, Dongxue; Shao, Yuyu; Zhang, Jiachao

2018-01-01

Fermented vegetables are typically traditional foods made of fresh vegetables and their juices, which are fermented by beneficial microorganisms. Herein, we applied high-throughput sequencing and culture-dependent technology to describe the diversities of microbiota and identify core microbiota in fermented vegetables from different areas of Hainan Province, and abundant metabolic pathways in the fermented vegetables were simultaneously predicted. At the genus level, Lactobacillus bacteria were the most abundant. Lactobacillus plantarum was the most abundant species, followed by Lactobacillus fermentum, Lactobacillus pentosaceus, and Weissella cibaria. These species were present in each sample with average absolute content values greater than 1% and were thus defined as core microbiota. Analysis results based on the alpha and beta diversities of the microbial communities showed that the microbial profiles of the fermented vegetables differed significantly based on the regions and raw materials used, and the species of the vegetables had a greater effect on the microbial community structure than the region from where they were harvested. Regarding microbial functional metabolism, we observed an enrichment of metabolic pathways, including membrane transport, replication and repair and translation, which implied that the microbial metabolism in the fermented vegetables tended to be vigorous. In addition, Lactobacillus plantarum and Lactobacillus fermentum were calculated to be major metabolic pathway contributors. Finally, we constructed a network to better explain correlations among the core microbiota and metabolic pathways. This study facilitates an understanding of the differences in microbial profiles and fermentation pathways involved in the production of fermented vegetables, establishes a basis for optimally selecting microorganisms to manufacture high-quality fermented vegetable products, and lays the foundation for better utilizing tropical microbial

Unique Microbial Diversity and Metabolic Pathway Features of Fermented Vegetables From Hainan, China

Directory of Open Access Journals (Sweden)

Qiannan Peng

2018-03-01

Full Text Available Fermented vegetables are typically traditional foods made of fresh vegetables and their juices, which are fermented by beneficial microorganisms. Herein, we applied high-throughput sequencing and culture-dependent technology to describe the diversities of microbiota and identify core microbiota in fermented vegetables from different areas of Hainan Province, and abundant metabolic pathways in the fermented vegetables were simultaneously predicted. At the genus level, Lactobacillus bacteria were the most abundant. Lactobacillus plantarum was the most abundant species, followed by Lactobacillus fermentum, Lactobacillus pentosaceus, and Weissella cibaria. These species were present in each sample with average absolute content values greater than 1% and were thus defined as core microbiota. Analysis results based on the alpha and beta diversities of the microbial communities showed that the microbial profiles of the fermented vegetables differed significantly based on the regions and raw materials used, and the species of the vegetables had a greater effect on the microbial community structure than the region from where they were harvested. Regarding microbial functional metabolism, we observed an enrichment of metabolic pathways, including membrane transport, replication and repair and translation, which implied that the microbial metabolism in the fermented vegetables tended to be vigorous. In addition, Lactobacillus plantarum and Lactobacillus fermentum were calculated to be major metabolic pathway contributors. Finally, we constructed a network to better explain correlations among the core microbiota and metabolic pathways. This study facilitates an understanding of the differences in microbial profiles and fermentation pathways involved in the production of fermented vegetables, establishes a basis for optimally selecting microorganisms to manufacture high-quality fermented vegetable products, and lays the foundation for better utilizing

Soil Microbial Functional and Fungal Diversity as Influenced by Municipal Sewage Sludge Accumulation

Directory of Open Access Journals (Sweden)

Magdalena Frąc

2014-08-01

Full Text Available Safe disposal of municipal sewage sludge is a challenging global environmental concern. The aim of this study was to assess the response of soil microbial functional diversity to the accumulation of municipal sewage sludge during landfill storage. Soil samples of a municipal sewage sludge (SS and from a sewage sludge landfill that was 3 m from a SS landfill (SS3 were analyzed relative to an undisturbed reference soil. Biolog EcoPlatesTM were inoculated with a soil suspension, and the Average Well Color Development (AWCD, Richness (R and Shannon-Weaver index (H were calculated to interpret the results. The fungi isolated from the sewage sludge were identified using comparative rDNA sequencing of the LSU D2 region. The MicroSEQ® ID software was used to assess the raw sequence files, perform sequence matching to the MicroSEQ® ID-validated reference database and create Neighbor-Joining trees. Moreover, the genera of fungi isolated from the soil were identified using microscopic methods. Municipal sewage sludge can serve as a habitat for plant pathogens and as a source of pathogen strains for biotechnological applications.

Soil Microbial Functional and Fungal Diversity as Influenced by Municipal Sewage Sludge Accumulation

Science.gov (United States)

Frąc, Magdalena; Oszust, Karolina; Lipiec, Jerzy; Jezierska-Tys, Stefania; Nwaichi, Eucharia Oluchi

2014-01-01

Safe disposal of municipal sewage sludge is a challenging global environmental concern. The aim of this study was to assess the response of soil microbial functional diversity to the accumulation of municipal sewage sludge during landfill storage. Soil samples of a municipal sewage sludge (SS) and from a sewage sludge landfill that was 3 m from a SS landfill (SS3) were analyzed relative to an undisturbed reference soil. Biolog EcoPlatesTM were inoculated with a soil suspension, and the Average Well Color Development (AWCD), Richness (R) and Shannon-Weaver index (H) were calculated to interpret the results. The fungi isolated from the sewage sludge were identified using comparative rDNA sequencing of the LSU D2 region. The MicroSEQ® ID software was used to assess the raw sequence files, perform sequence matching to the MicroSEQ® ID-validated reference database and create Neighbor-Joining trees. Moreover, the genera of fungi isolated from the soil were identified using microscopic methods. Municipal sewage sludge can serve as a habitat for plant pathogens and as a source of pathogen strains for biotechnological applications. PMID:25170681

Detection of Metabolism Function of Microbial Community of Corpses by Biolog-Eco Method.

Science.gov (United States)

Jiang, X Y; Wang, J F; Zhu, G H; Ma, M Y; Lai, Y; Zhou, H

2016-06-01

To detect the changes of microbial community functional diversity of corpses with different postmortem interval （PMI） and to evaluate forensic application value for estimating PMI. The cultivation of microbial community from the anal swabs of a Sus scrofa and a human corpse placed in field environment from 0 to 240 h after death was performed using the Biolog-Eco Microplate and the variations of the absorbance values were also monitored. Combined with the technology of forensic pathology and flies succession, the metabolic characteristics and changes of microbial community on the decomposed corpse under natural environment were also observed. The diversity of microbial metabolism function was found to be negatively correlated with the number of maggots in the corpses. The freezing processing had the greatest impact on average well color development value at 0 h and the impact almost disappeared after 48 h. The diversity of microbial metabolism of the samples became relatively unstable after 192 h. The principal component analysis showed that 31 carbon sources could be consolidated for 5 principal components （accumulative contribution ratio >90%）.The carbon source tsquare-analysis showed that N -acetyl- D -glucosamine and L -serine were the dominant carbon sources for estimating the PMI （0=240 h） of the Sus scrofa and human corpse. The Biolog-Eco method can be used to reveal the metabolic differences of the carbon resources utilization of the microbial community on the corpses during 0-240 h after death, which could provide a new basis for estimating the PMI. Copyright© by the Editorial Department of Journal of Forensic Medicine

Humboldt's spa: microbial diversity is controlled by temperature in geothermal environments.

Science.gov (United States)

Sharp, Christine E; Brady, Allyson L; Sharp, Glen H; Grasby, Stephen E; Stott, Matthew B; Dunfield, Peter F

2014-06-01

Over 200 years ago Alexander von Humboldt (1808) observed that plant and animal diversity peaks at tropical latitudes and decreases toward the poles, a trend he attributed to more favorable temperatures in the tropics. Studies to date suggest that this temperature-diversity gradient is weak or nonexistent for Bacteria and Archaea. To test the impacts of temperature as well as pH on bacterial and archaeal diversity, we performed pyrotag sequencing of 16S rRNA genes retrieved from 165 soil, sediment and biomat samples of 36 geothermal areas in Canada and New Zealand, covering a temperature range of 7.5-99 °C and a pH range of 1.8-9.0. This represents the widest ranges of temperature and pH yet examined in a single microbial diversity study. Species richness and diversity indices were strongly correlated to temperature, with R(2) values up to 0.62 for neutral-alkaline springs. The distributions were unimodal, with peak diversity at 24 °C and decreasing diversity at higher and lower temperature extremes. There was also a significant pH effect on diversity; however, in contrast to previous studies of soil microbial diversity, pH explained less of the variability (13-20%) than temperature in the geothermal samples. No correlation was observed between diversity values and latitude from the equator, and we therefore infer a direct temperature effect in our data set. These results demonstrate that temperature exerts a strong control on microbial diversity when considered over most of the temperature range within which life is possible.

Comparison of multivariate microbial datasets with the Shannon index: An example using enzyme activity from diverse marine environments

DEFF Research Database (Denmark)

Steen, Andrew; Ziervogel, K.; Arnosti, C.

2010-01-01

Heterotrophic microbial communities contain substantial functional diversity, so studies of community function often generate multivariate data sets. Techniques for data reduction and analysis can help elucidate qualitative differences among sites from multivariate data sets that may be difficult...... of four cases, surface water communities accessed substrates at a more even rate than in deeper waters. The technique could usefully be applied to other types of data obtained in studies of microbial activity and the geochemical effects....

Microbial diversity in Brazilian mangrove sediments – a mini review

Science.gov (United States)

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 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.

Predicting taxonomic and functional structure of microbial communities in acid mine drainage.

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Kuang, Jialiang; Huang, Linan; He, Zhili; Chen, Linxing; Hua, Zhengshuang; Jia, Pu; Li, Shengjin; Liu, Jun; Li, Jintian; Zhou, Jizhong; Shu, Wensheng

2016-06-01

Predicting the dynamics of community composition and functional attributes responding to environmental changes is an essential goal in community ecology but remains a major challenge, particularly in microbial ecology. Here, by targeting a model system with low species richness, we explore the spatial distribution of taxonomic and functional structure of 40 acid mine drainage (AMD) microbial communities across Southeast China profiled by 16S ribosomal RNA pyrosequencing and a comprehensive microarray (GeoChip). Similar environmentally dependent patterns of dominant microbial lineages and key functional genes were observed regardless of the large-scale geographical isolation. Functional and phylogenetic β-diversities were significantly correlated, whereas functional metabolic potentials were strongly influenced by environmental conditions and community taxonomic structure. Using advanced modeling approaches based on artificial neural networks, we successfully predicted the taxonomic and functional dynamics with significantly higher prediction accuracies of metabolic potentials (average Bray-Curtis similarity 87.8) as compared with relative microbial abundances (similarity 66.8), implying that natural AMD microbial assemblages may be better predicted at the functional genes level rather than at taxonomic level. Furthermore, relative metabolic potentials of genes involved in many key ecological functions (for example, nitrogen and phosphate utilization, metals resistance and stress response) were extrapolated to increase under more acidic and metal-rich conditions, indicating a critical strategy of stress adaptation in these extraordinary communities. Collectively, our findings indicate that natural selection rather than geographic distance has a more crucial role in shaping the taxonomic and functional patterns of AMD microbial community that readily predicted by modeling methods and suggest that the model-based approach is essential to better understand natural

Status of microbial diversity in agroforestry systems in Tamil Nadu, India.

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Radhakrishnan, Srinivasan; Varadharajan, Mohan

2016-06-01

Soil is a complex and dynamic biological system. Agroforestry systems are considered to be an alternative land use option to help and prevent soil degradation, improve soil fertility, microbial diversity, and organic matter status. An increasing interest has emerged with respect to the importance of microbial diversity in soil habitats. The present study deals with the status of microbial diversity in agroforestry systems in Tamil Nadu. Eight soil samples were collected from different fields in agroforestry systems in Cuddalore, Villupuram, Tiruvanamalai, and Erode districts, Tamil Nadu. The number of microorganisms and physico-chemical parameters of soils were quantified. Among different microbial population, the bacterial population was recorded maximum (64%), followed by actinomycetes (23%) and fungi (13%) in different samples screened. It is interesting to note that the microbial population was positively correlated with the physico-chemical properties of different soil samples screened. Total bacterial count had positive correlation with soil organic carbon (C), moisture content, pH, nitrogen (N), and micronutrients such as Iron (Fe), copper (Cu), and zinc (Zn). Similarly, the total actinomycete count also showed positive correlations with bulk density, moisture content, pH, C, N, phosphorus (P), potassium (K), calcium (Ca), copper (Cu), magnesium (Mg), manganese (Mn), and zinc (Zn). It was also noticed that the soil organic matter, vegetation, and soil nutrients altered the microbial community under agroforestry systems. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Microbial community functional structures in wastewater treatment plants as characterized by GeoChip.

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Wang, Xiaohui; Xia, Yu; Wen, Xianghua; Yang, Yunfeng; Zhou, Jizhong

2014-01-01

Biological WWTPs must be functionally stable to continuously and steadily remove contaminants which rely upon the activity of complex microbial communities. However, knowledge is still lacking in regard to microbial community functional structures and their linkages to environmental variables. To investigate microbial community functional structures of activated sludge in wastewater treatment plants (WWTPs) and to understand the effects of environmental factors on their structure. 12 activated sludge samples were collected from four WWTPs in Beijing. A comprehensive functional gene array named GeoChip 4.2 was used to determine the microbial functional genes involved in a variety of biogeochemical processes such as carbon, nitrogen, phosphorous and sulfur cycles, metal resistance, antibiotic resistance and organic contaminant degradation. High similarities of the microbial community functional structures were found among activated sludge samples from the four WWTPs, as shown by both diversity indices and the overlapped genes. For individual gene category, such as egl, amyA, lip, nirS, nirK, nosZ, ureC, ppx, ppk, aprA, dsrA, sox and benAB, there were a number of microorganisms shared by all 12 samples. Canonical correspondence analysis (CCA) showed that the microbial functional patterns were highly correlated with water temperature, dissolved oxygen (DO), ammonia concentrations and loading rate of chemical oxygen demand (COD). Based on the variance partitioning analyses (VPA), a total of 53% of microbial community variation from GeoChip data can be explained by wastewater characteristics (25%) and operational parameters (23%), respectively. This study provided an overall picture of microbial community functional structures of activated sludge in WWTPs and discerned the linkages between microbial communities and environmental variables in WWTPs.

Microbial community functional structures in wastewater treatment plants as characterized by GeoChip.

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Xiaohui Wang

Full Text Available BACKGROUND: Biological WWTPs must be functionally stable to continuously and steadily remove contaminants which rely upon the activity of complex microbial communities. However, knowledge is still lacking in regard to microbial community functional structures and their linkages to environmental variables. AIMS: To investigate microbial community functional structures of activated sludge in wastewater treatment plants (WWTPs and to understand the effects of environmental factors on their structure. METHODS: 12 activated sludge samples were collected from four WWTPs in Beijing. A comprehensive functional gene array named GeoChip 4.2 was used to determine the microbial functional genes involved in a variety of biogeochemical processes such as carbon, nitrogen, phosphorous and sulfur cycles, metal resistance, antibiotic resistance and organic contaminant degradation. RESULTS: High similarities of the microbial community functional structures were found among activated sludge samples from the four WWTPs, as shown by both diversity indices and the overlapped genes. For individual gene category, such as egl, amyA, lip, nirS, nirK, nosZ, ureC, ppx, ppk, aprA, dsrA, sox and benAB, there were a number of microorganisms shared by all 12 samples. Canonical correspondence analysis (CCA showed that the microbial functional patterns were highly correlated with water temperature, dissolved oxygen (DO, ammonia concentrations and loading rate of chemical oxygen demand (COD. Based on the variance partitioning analyses (VPA, a total of 53% of microbial community variation from GeoChip data can be explained by wastewater characteristics (25% and operational parameters (23%, respectively. CONCLUSIONS: This study provided an overall picture of microbial community functional structures of activated sludge in WWTPs and discerned the linkages between microbial communities and environmental variables in WWTPs.

The microbial diversity of a storm cloud as assessed by hailstones.

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Temkiv, Tina Šantl; Finster, Kai; Hansen, Bjarne Munk; Nielsen, Niels Woetmann; Karlson, Ulrich Gosewinkel

2012-09-01

Being an extreme environment, the atmosphere may act as a selective barrier for bacterial dispersal, where only most robust organisms survive. By remaining viable during atmospheric transport, these cells affect the patterns of microbial distribution and modify the chemical composition of the atmosphere. The species evenness and richness, and the community composition of a storm cloud were studied applying cultivation-dependent and cultivation-independent techniques to a collection of hailstones. In toto 231 OTUs were identified, and the total species richness was estimated to be about 1800 OTUs. The diversity indices - species richness and evenness - suggest a functionally stable community, capable of resisting environmental stress. A broad substrate spectrum of the isolates with epiphytic origin (genus Methylobacterium) implied opportunistic ecologic strategy with high growth rates and fast growth responses. These may grow in situ despite their short residence times in cloud droplets. In addition, epiphytic isolates utilized many atmospheric organic compounds, including a variety of carboxylic acids. In summary, the highly diverse bacterial community, within which the opportunistic bacteria may be particularly important in terms of atmospheric chemistry, is likely to remain functional under stressful conditions. Overall our study adds important details to the growing evidence of active microbial life in clouds. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Metagenomic approach reveals microbial diversity and predictive microbial metabolic pathways in Yucha, a traditional Li fermented food.

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Zhang, Jiachao; Wang, Xiaoru; Huo, Dongxue; Li, Wu; Hu, Qisong; Xu, Chuanbiao; Liu, Sixin; Li, Congfa

2016-08-31

Yucha is a typical traditional fermented food of the Li population in the Hainan province of China, and it is made up of cooked rice and fresh fish. In the present study, metagenomic approach and culture-dependent technology were applied to describe the diversity of microbiota and identify beneficial microbes in the Yucha. At the genus level, Lactobacillus was the most abundant genus (43.82% of the total reads), followed by Lactococcus, Enterococcus, Vibrio, Weissella, Pediococcus, Enterobacter, Salinivibrio, Acinetobacter, Macrococcus, Kluyvera and Clostridium; this result was confirmed by q-PCR. PCoA based on Weighted UniFrac distances showed an apparent clustering pattern for Yucha samples from different locations, and Lactobacillus sakei, Lactobacillus saniviri and Staphylococcus sciuri represented OTUs according to the major identified markers. At the microbial functional level, it was observed that there was an enrichment of metabolic functional features, including amino acid and carbohydrate metabolism, which implied that the microbial metabolism in the Yucha samples tended to be vigorous. Accordingly, we further investigated the correlation between the predominant microbes and metabolic functional features. Thirteen species of Lactobacillus (147 strains) were isolated, and Lactobacillus plantarum (60 isolates) and Lactobacillus pentosus (34 isolates) were isolated from every sample.

Patterns in wetland microbial community composition and functional gene repertoire associated with methane emissions.

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He, Shaomei; Malfatti, Stephanie A; McFarland, Jack W; Anderson, Frank E; Pati, Amrita; Huntemann, Marcel; Tremblay, Julien; Glavina del Rio, Tijana; Waldrop, Mark P; Windham-Myers, Lisamarie; Tringe, Susannah G

2015-05-19

Wetland restoration on peat islands previously drained for agriculture has potential to reverse land subsidence and sequester atmospheric carbon dioxide as peat accretes. However, the emission of methane could potentially offset the greenhouse gas benefits of captured carbon. As microbial communities play a key role in governing wetland greenhouse gas fluxes, we are interested in how microbial community composition and functions are associated with wetland hydrology, biogeochemistry, and methane emission, which is critical to modeling the microbial component in wetland methane fluxes and to managing restoration projects for maximal carbon sequestration. Here, we couple sequence-based methods with biogeochemical and greenhouse gas measurements to interrogate microbial communities from a pilot-scale restored wetland in the Sacramento-San Joaquin Delta of California, revealing considerable spatial heterogeneity even within this relatively small site. A number of microbial populations and functions showed strong correlations with electron acceptor availability and methane production; some also showed a preference for association with plant roots. Marker gene phylogenies revealed a diversity of major methane-producing and -consuming populations and suggested novel diversity within methanotrophs. Methanogenic archaea were observed in all samples, as were nitrate-, sulfate-, and metal-reducing bacteria, indicating that no single terminal electron acceptor was preferred despite differences in energetic favorability and suggesting spatial microheterogeneity and microniches. Notably, methanogens were negatively correlated with nitrate-, sulfate-, and metal-reducing bacteria and were most abundant at sampling sites with high peat accretion and low electron acceptor availability, where methane production was highest. Wetlands are the largest nonanthropogenic source of atmospheric methane but also a key global carbon reservoir. Characterizing belowground microbial communities

Exploring Biogeochemistry and Microbial Diversity of Extant Microbialites in Mexico and Cuba

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Valdespino-Castillo, Patricia M.; Hu, Ping; Merino-Ibarra, Martín; López-Gómez, Luz M.; Cerqueda-García, Daniel; González-De Zayas, Roberto; Pi-Puig, Teresa; Lestayo, Julio A.; Holman, Hoi-Ying; Falcón, Luisa I.

2018-01-01

Microbialites are modern analogs of ancient microbial consortia that date as far back as the Archaean Eon. Microbialites have contributed to the geochemical history of our planet through their diverse metabolic capacities that mediate mineral precipitation. These mineral-forming microbial assemblages accumulate major ions, trace elements and biomass from their ambient aquatic environments; their role in the resulting chemical structure of these lithifications needs clarification. We studied the biogeochemistry and microbial structure of microbialites collected from diverse locations in Mexico and in a previously undescribed microbialite in Cuba. We examined their structure, chemistry and mineralogy at different scales using an array of nested methods including 16S rRNA gene high-throughput sequencing, elemental analysis, X-Ray fluorescence (XRF), X-Ray diffraction (XRD), Scanning Electron Microscopy-Energy Dispersive Spectroscopy (SEM-EDS), Fourier Transformed Infrared (FTIR) spectroscopy and Synchrotron Radiation-based Fourier Transformed Infrared (SR-FTIR) spectromicroscopy. The resulting data revealed high biological and chemical diversity among microbialites and specific microbe to chemical correlations. Regardless of the sampling site, Proteobacteria had the most significant correlations with biogeochemical parameters such as organic carbon (Corg), nitrogen and Corg:Ca ratio. Biogeochemically relevant bacterial groups (dominant phototrophs and heterotrophs) showed significant correlations with major ion composition, mineral type and transition element content, such as cadmium, cobalt, chromium, copper and nickel. Microbial-chemical relationships were discussed in reference to microbialite formation, microbial metabolic capacities and the role of transition elements as enzyme cofactors. This paper provides an analytical baseline to drive our understanding of the links between microbial diversity with the chemistry of their lithified precipitations. PMID

Phylogenetic and Functional Diversity of Total (DNA) and Expressed (RNA) Bacterial Communities in Urban Green Infrastructure Bioswale Soils.

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Gill, Aman S; Lee, Angela; McGuire, Krista L

2017-08-15

New York City (NYC) is pioneering green infrastructure with the use of bioswales and other engineered soil-based habitats to provide stormwater infiltration and other ecosystem functions. In addition to avoiding the environmental and financial costs of expanding traditional built infrastructure, green infrastructure is thought to generate cobenefits in the form of diverse ecological processes performed by its plant and microbial communities. Yet, although plant communities in these habitats are closely managed, we lack basic knowledge about how engineered ecosystems impact the distribution and functioning of soil bacteria. We sequenced amplicons of the 16S ribosomal subunit, as well as seven genes associated with functional pathways, generated from both total (DNA-based) and expressed (RNA) soil communities in the Bronx, NYC, NY, in order to test whether bioswale soils host characteristic bacterial communities with evidence for enriched microbial functioning, compared to nonengineered soils in park lawns and tree pits. Bioswales had distinct, phylogenetically diverse bacterial communities, including taxa associated with nutrient cycling and metabolism of hydrocarbons and other pollutants. Bioswale soils also had a significantly greater diversity of genes involved in several functional pathways, including carbon fixation ( cbbL-R [ cbbL gene, red-like subunit] and apsA ), nitrogen cycling ( noxZ and amoA ), and contaminant degradation ( bphA ); conversely, no functional genes were significantly more abundant in nonengineered soils. These results provide preliminary evidence that urban land management can shape the diversity and activity of soil communities, with positive consequences for genetic resources underlying valuable ecological functions, including biogeochemical cycling and degradation of common urban pollutants. IMPORTANCE Management of urban soil biodiversity by favoring taxa associated with decontamination or other microbial metabolic processes is a

Analyses of soil microbial community compositions and functional genes reveal potential consequences of natural forest succession.

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Cong, Jing; Yang, Yunfeng; Liu, Xueduan; Lu, Hui; Liu, Xiao; Zhou, Jizhong; Li, Diqiang; Yin, Huaqun; Ding, Junjun; Zhang, Yuguang

2015-05-06

The succession of microbial community structure and function is a central ecological topic, as microbes drive the Earth's biogeochemical cycles. To elucidate the response and mechanistic underpinnings of soil microbial community structure and metabolic potential relevant to natural forest succession, we compared soil microbial communities from three adjacent natural forests: a coniferous forest (CF), a mixed broadleaf forest (MBF) and a deciduous broadleaf forest (DBF) on Shennongjia Mountain in central China. In contrary to plant communities, the microbial taxonomic diversity of the DBF was significantly (P the DBF. Furthermore, a network analysis of microbial carbon and nitrogen cycling genes showed the network for the DBF samples was relatively large and tight, revealing strong couplings between microbes. Soil temperature, reflective of climate regimes, was important in shaping microbial communities at both taxonomic and functional gene levels. As a first glimpse of both the taxonomic and functional compositions of soil microbial communities, our results suggest that microbial community structure and function potentials will be altered by future environmental changes, which have implications for forest succession.

Diversity and function of the microbial community on anodes of sediment microbial fuel cells fueled by root exudates

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Cabezas da Rosa, Angela

2010-11-26

our study on identifying the bacteria capable of rice root exudate assimilation on anodes of planted SMFCs. Using stable isotope probing (SIP) with {sup 13}C-CO{sub 2} combined with high throughput sequencing, we detected that labeled bacteria belonged to {beta}-proteobacteria and Anaerolineae indicating their relevance in root exudate degradation. The main current producing bacteria, belonging to {delta}-proteobacteria were not able to assimilate root exudates. A microbial ''food chain'' combining activities of anode reducing bacteria with root exudate degrading bacteria is necessary for current production. However, we cannot dismiss the possibility that some bacteria might be able to directly use root exudates for current production. In the last part, we found that by submerging an anode into rice field soil up to 50% methane emission was reduced compared with open circuit controls. This mitigation could not only be explained by competition for common electron donors like acetate. We suggest that the anode, even in non-current controls, can be used as electron acceptor capturing electrons and transferring them from one part of the sediment to a spatially distant one, communicating biogeochemical processes occurring in different parts of the sediment. Our work is a first approach in understanding the microbial diversity on anodes of SMFCs fueled by rice root exudation and their potential as methane emission mitigation strategy. (orig.)

Contributions of understory and/or overstory vegetations to soil microbial PLFA and nematode diversities in Eucalyptus monocultures.

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Jie Zhao

Full Text Available Ecological interactions between aboveground and belowground biodiversity have received many attentions in the recent decades. Although soil biodiversity declined with the decrease of plant diversity, many previous studies found plant species identities were more important than plant diversity in controlling soil biodiversity. This study focused on the responses of soil biodiversity to the altering of plant functional groups, namely overstory and understory vegetations, rather than plant diversity gradient. We conducted an experiment by removing overstory and/or understory vegetation to compare their effects on soil microbial phospholipid fatty acid (PLFA and nematode diversities in eucalyptus monocultures. Our results indicated that both overstory and understory vegetations could affect soil microbial PLFA and nematode diversities, which manifested as the decrease in Shannon-Wiener diversity index (H' and Pielou evenness index (J and the increase in Simpson dominance index (λ after vegetation removal. Soil microclimate change explained part of variance of soil biodiversity indices. Both overstory and understory vegetations positively correlated with soil microbial PLFA and nematode diversities. In addition, the alteration of soil biodiversity might be due to a mixing effect of bottom-up control and soil microclimate change after vegetation removal in the studied plantations. Given the studied ecosystem is common in humid subtropical and tropical region of the world, our findings might have great potential to extrapolate to large scales and could be conducive to ecosystem management and service.

Long-term oil contamination alters the molecular ecological networks of soil microbial functional genes

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Yuting eLiang

2016-02-01

Full Text Available With knowledge on microbial composition and diversity, investigation of within-community interactions is a further step to elucidate microbial ecological functions, such as the biodegradation of hazardous contaminants. In this work, microbial functional molecular ecological networks were studied in both contaminated and uncontaminated soils to determine the possible influences of oil contamination on microbial interactions and potential functions. Soil samples were obtained from an oil-exploring site located in South China, and the microbial functional genes were analyzed with GeoChip, a high-throughput functional microarray. By building random networks based on null model, we demonstrated that overall network structures and properties were significantly different between contaminated and uncontaminated soils (P < 0.001. Network connectivity, module numbers, and modularity were all reduced with contamination. Moreover, the topological roles of the genes (module hub and connectors were altered with oil contamination. Subnetworks of genes involved in alkane and polycyclic aromatic hydrocarbon degradation were also constructed. Negative co-occurrence patterns prevailed among functional genes, thereby indicating probable competition relationships. The potential keystone genes, defined as either hubs or genes with highest connectivities in the network, were further identified. The network constructed in this study predicted the potential effects of anthropogenic contamination on microbial community co-occurrence interactions.

Microbial Fingerprints of Community Structure Correlate with Changes in Ecosystem Function Induced by Perturbing the Redox Environment

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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.

Nitrogen deposition and management practices increase soil microbial biomass carbon but decrease diversity in Moso bamboo plantations

Science.gov (United States)

Li, Quan; Song, Xinzhang; Gu, Honghao; Gao, Fei

2016-06-01

Because microbial communities play a key role in carbon (C) and nitrogen (N) cycling, changes in the soil microbial community may directly affect ecosystem functioning. However, the effects of N deposition and management practices on soil microbes are still poorly understood. We studied the effects of these two factors on soil microbial biomass carbon (MBC) and community composition in Moso bamboo plantations using high-throughput sequencing of the 16S rRNA gene. Plantations under conventional (CM) or intensive management (IM) were subjected to one of four N treatments for 30 months. IM and N addition, both separately and in combination, significantly increased soil MBC while decreasing bacterial diversity. However, increases in soil MBC were inhibited when N addition exceeded 60 kg N•ha-1•yr-1. IM increased the relative abundances of Actinobacteria and Crenarchaeota but decreased that of Acidobacteria. N addition increased the relative abundances of Acidobacteria, Crenarchaeota, and Actinobacteria but decreased that of Proteobacteria. Soil bacterial diversity was significantly related to soil pH, C/N ratio, and nitrogen and available phosphorus content. Management practices exerted a greater influence over regulation of the soil MBC and microbial diversity compared to that of N deposition in Moso bamboo plantations.

16S/18S ribosomal DNA clone library analysis of rumen microbial diversity

International Nuclear Information System (INIS)

Wright, A.G.; Kiyoshi Tajima; Aminov, R.I.

2005-01-01

The rumen contains a complex ecosystem where billions of bacteria, archaea, protozoa and fungi reside. This diverse microbiota is well adapted to live in the rumen and play an important role in the digestion of feed and nutrient supply to the host in the form of microbial protein and volatile fatty acids. It is estimated that the rumen microbial population consists of about 10 6 protozoa/ml, 10 3 -10 7 fungi/ml, 10 10 bacteria/ml, and 10 9 methanogens/ml. To better understand the complex relationships in the rumen, it is necessary to gain an insight into the diversity of the rumen microbes and how the quantity and composition of rumen micro-organisms are altered by a number of different host factors such as age, genetics and diet. In the past, the diversity of micro-organisms from the digestive tracts of domesticated ruminants has been identified by classical microbiological techniques. However, given the fastidious growth requirements of rumen micro-organisms, it is reasonable to concede that the culture-dependent methods may select against some species, or taxonomic groups, leading researchers to underestimate the microbial diversity that is actually present in the rumen. In fact, it has been speculated that 90% of micro-organisms in nature have escaped traditional cultivation methods. Therefore, a major challenge in microbial ecology has been to assess the diversity and structure of natural microbial communities. The field of molecular biology has advanced with many innovative technological breakthroughs. The ability to extract and to isolate high-molecular weight DNA from rumen digesta, PCR amplify genes from specific microbial groups and obtain gene sequence data is now a routine event. The small subunit ribosomal RNA (SSU-rRNA) gene, called 16S in prokaryotes and 18S in eukaryotes, is the most widely used molecular marker to presumptively identify morphologically indistinguishable species, to infer their phylogenetic relationships, and to elucidate microbial

Fungal Genetics and Functional Diversity of Microbial Communities in the Soil under Long-Term Monoculture of Maize Using Different Cultivation Techniques

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Anna Gałązka

2018-01-01

Full Text Available Fungal diversity in the soil may be limited under natural conditions by inappropriate environmental factors such as: nutrient resources, biotic and abiotic factors, tillage system and microbial interactions that prevent the occurrence or survival of the species in the environment. The aim of this paper was to determine fungal genetic diversity and community level physiological profiling of microbial communities in the soil under long-term maize monoculture. The experimental scheme involved four cultivation techniques: direct sowing (DS, reduced tillage (RT, full tillage (FT, and crop rotation (CR. Soil samples were taken in two stages: before sowing of maize (DSBS-direct sowing, RTBS-reduced tillage, FTBS-full tillage, CRBS-crop rotation and the flowering stage of maize growth (DSF-direct sowing, RTF-reduced tillage, FTF-full tillage, CRF-crop rotation. The following plants were used in the crop rotation: spring barley, winter wheat and maize. The study included fungal genetic diversity assessment by ITS-1 next generation sequencing (NGS analyses as well as the characterization of the catabolic potential of microbial communities (Biolog EcoPlates in the soil under long-term monoculture of maize using different cultivation techniques. The results obtained from the ITS-1 NGS technique enabled to classify and correlate the fungi species or genus to the soil metabolome. The research methods used in this paper have contributed to a better understanding of genetic diversity and composition of the population of fungi in the soil under the influence of the changes that have occurred in the soil under long-term maize cultivation. In all cultivation techniques, the season had a great influence on the fungal genetic structure in the soil. Significant differences were found on the family level (P = 0.032, F = 3.895, genus level (P = 0.026, F = 3.313 and on the species level (P = 0.033, F = 2.718. This study has shown that: (1 fungal diversity was changed

Influence of organic and inorganic sources of nutrients on the functional diversity of microbial communities in the vegetable cropping system of the Indo-Gangetic plains.

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Manjunath, Mallappa; Kumar, Upendra; Yadava, Raj Bahadur; Rai, Awadhesh Bahadur; Singh, Bijendra

2018-05-31

The aim of the present study was to assess the effects of different organic and inorganic fertilizers on the functional diversity of soil microbial community under a vegetable production system. The Biolog ® Eco-plate technique and indices, such as average well-colour development (AWCD), McIntosh and Shannon diversity were employed to study the diversity of soil microorganisms. The AWCD, i.e. overall utilization of carbon sources, suggested that different organic treatments had a significant impact on the metabolic activity of soil microorganisms. After 120h, the highest AWCD values were observed in poultry manure (2.5 t·ha -1 )+vermicompost (3.5 t·ha -1 ) (0.63) and farm yard manure (FYM) (10 t·ha -1 )+vermicompost (3.5 t·ha -1 ) (0.61). After 72h, the highest value of the McIntosh diversity index was recorded in poultry manure (2.5 t·ha -1 )+vermicompost (3.5 t·ha -1 ) (3.87), followed by poultry manure (2.5 t·ha -1 )+vermicompost (3.5 t·ha -1 )+biofertilizers (Azotobacter 500 g·ha -1 applied as seed treatment) (3.12). In the case of the Shannon diversity index, the highest values were noticed in organic treatments; however, there was no significant differences between organic and inorganic treatments. Biplot analysis showed a clear differentiation of organic treatments from the inorganic control. The amino acids, phenolics and polymer utilizing microorganisms were dominant in organic treatments. Inorganic control recorded the lowest values of the microbial diversity indices. Through this study, we have identified the best combination of organic nutrients, i.e. poultry manure (2.5 t·ha -1 )+vermicompost (3.5 t·ha -1 ) for the stimulation of metabolically active soil microbial communities. Copyright © 2018 Académie des sciences. Published by Elsevier Masson SAS. All rights reserved.

Microbial diversity and structure are drivers of the biological barrier effect against Listeria monocytogenes in soil.

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Vivant, Anne-Laure; Garmyn, Dominique; Maron, Pierre-Alain; Nowak, Virginie; Piveteau, Pascal

2013-01-01

Understanding the ecology of pathogenic organisms is important in order to monitor their transmission in the environment and the related health hazards. We investigated the relationship between soil microbial diversity and the barrier effect against Listeria monocytogenes invasion. By using a dilution-to-extinction approach, we analysed the consequence of eroding microbial diversity on L. monocytogenes population dynamics under standardised conditions of abiotic parameters and microbial abundance in soil microcosms. We demonstrated that highly diverse soil microbial communities act as a biological barrier against L. monocytogenes invasion and that phylogenetic composition of the community also has to be considered. This suggests that erosion of diversity may have damaging effects regarding circulation of pathogenic microorganisms in the environment.

Prebiotics Modulate the Effects of Antibiotics on Gut Microbial Diversity and Functioning in Vitro

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Laura P. Johnson

2015-06-01

Full Text Available Intestinal bacteria carry out many fundamental roles, such as the fermentation of non-digestible dietary carbohydrates to produce short chain fatty acids (SCFAs, which can affect host energy levels and gut hormone regulation. Understanding how to manage this ecosystem to improve human health is an important but challenging goal. Antibiotics are the front line of defence against pathogens, but in turn they have adverse effects on indigenous microbial diversity and function. Here, we have investigated whether dietary supplementation—another method used to modulate gut composition and function—could be used to ameliorate the side effects of antibiotics. We perturbed gut bacterial communities with gentamicin and ampicillin in anaerobic batch cultures in vitro. Cultures were supplemented with either pectin (a non-fermentable fibre, inulin (a commonly used prebiotic that promotes the growth of beneficial bacteria or neither. Although antibiotics often negated the beneficial effects of dietary supplementation, in some treatment combinations, notably ampicillin and inulin, dietary supplementation ameliorated the effects of antibiotics. There is therefore potential for using supplements to lessen the adverse effects of antibiotics. Further knowledge of such mechanisms could lead to better therapeutic manipulation of the human gut microbiota.

Gasification biochar has limited effects on functional and structural diversity of soil microbial communities in a temperate agroecosystem

DEFF Research Database (Denmark)

Imparato, Valentina; Hansen, Veronika; Santos, Susana

2016-01-01

caused an increase in the relative abundance of the rare members in the microbial communities thus increasing the diversity of soil microorganisms. A comparable effect was observed with the addition of fresh straw. Overall, our results indicated that GBC as soil amendment had a limited effect...

Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach.

Directory of Open Access Journals (Sweden)

Erin A Gontang

Full Text Available Investigations of gut microbiomes have shed light on the diversity and genetic content of these communities, and helped shape our understanding of how host-associated microorganisms influence host physiology, behavior, and health. Despite the importance of gut microbes to metazoans, our understanding of the changes in diversity and composition across the alimentary tract, and the source of the resident community are limited. Here, using community metagenomics and 16S rRNA gene sequencing, we assess microbial community diversity and coding potential in the foregut, midgut, and hindgut of a juvenile Panchlora cockroach, which resides in the refuse piles of the leaf-cutter ant species Atta colombica. We found a significant shift in the microbial community structure and coding potential throughout the three gut sections of Panchlora sp., and through comparison with previously generated metagenomes of the cockroach's food source and niche, we reveal that this shift in microbial community composition is influenced by the ecosystems in which Panchlora sp. occurs. While the foregut is composed of microbes that likely originate from the symbiotic fungus gardens of the ants, the midgut and hindgut are composed of a microbial community that is likely cockroach-specific. Analogous to mammalian systems, the midgut and hindgut appear to be dominated by Firmicutes and Bacteroidetes with the capacity for polysaccharide degradation, suggesting they may assist in the degradation of dietary plant material. Our work underscores the prominence of community changes throughout gut microbiomes and highlights ecological factors that underpin the structure and function of the symbiotic microbial communities of metazoans.

Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach.

Science.gov (United States)

Gontang, Erin A; Aylward, Frank O; Carlos, Camila; Glavina Del Rio, Tijana; Chovatia, Mansi; Fern, Alison; Lo, Chien-Chi; Malfatti, Stephanie A; Tringe, Susannah G; Currie, Cameron R; Kolter, Roberto

2017-01-01

Investigations of gut microbiomes have shed light on the diversity and genetic content of these communities, and helped shape our understanding of how host-associated microorganisms influence host physiology, behavior, and health. Despite the importance of gut microbes to metazoans, our understanding of the changes in diversity and composition across the alimentary tract, and the source of the resident community are limited. Here, using community metagenomics and 16S rRNA gene sequencing, we assess microbial community diversity and coding potential in the foregut, midgut, and hindgut of a juvenile Panchlora cockroach, which resides in the refuse piles of the leaf-cutter ant species Atta colombica. We found a significant shift in the microbial community structure and coding potential throughout the three gut sections of Panchlora sp., and through comparison with previously generated metagenomes of the cockroach's food source and niche, we reveal that this shift in microbial community composition is influenced by the ecosystems in which Panchlora sp. occurs. While the foregut is composed of microbes that likely originate from the symbiotic fungus gardens of the ants, the midgut and hindgut are composed of a microbial community that is likely cockroach-specific. Analogous to mammalian systems, the midgut and hindgut appear to be dominated by Firmicutes and Bacteroidetes with the capacity for polysaccharide degradation, suggesting they may assist in the degradation of dietary plant material. Our work underscores the prominence of community changes throughout gut microbiomes and highlights ecological factors that underpin the structure and function of the symbiotic microbial communities of metazoans.

Reduced Oral Microbial Diversity in Individuals Harbor Periodontal Diseases

Directory of Open Access Journals (Sweden)

Jinghua Sun

2012-02-01

Full Text Available Introduction: Bacteria colonize a variety of surfaces of the hu-man body. The bacterial diversity in the oral cavity is estimated to be more than 700 different species. The oral cavity is home to microbial communities, with important implications for human health and disease. Oral microbial flora is responsible for two major human infectious diseases of the oral cavity, dental caries and periodontal diseases. From the clinical samples, previously, using polymerase chain reaction-based denaturing gradient gel electrophoresis (PCR-DGGE technique, we found a significantly greater diversity of oral microbes in caries-free individuals compared with caries-active individuals. The hypothesis: We hypothesize that a greater diversity of indigenous bacteria inhabits a healthy oral environment, and that a sig-nificant proportion of oral biota may be absent, suppressed, or replaced in a periodontal diseases environment. Evaluation of the hypothesis: The microbiota undergoes a transition from a commensal to a pathogenic relationship with the host due to factors that trigger a shift in the proportions of resident microorganisms. If our hypothesis is true, many techniques which were used to detect the oral bacterial diversity can be used in diagnosis and prognosis of periodontal diseases.

Influence of microbial community diversity and function on pollutant removal in ecological wastewater treatment.

Science.gov (United States)

Bai, Yaohui; Huo, Yang; Liao, Kailingli; Qu, Jiuhui

2017-10-01

Traditional wastewater treatments based on activated sludge often encounter the problems of bulking and foaming, as well as malodor. To solve these problems, new treatment technologies have emerged in recent decades, including the ecological wastewater treatment process, which introduces selected local plants into the treatment system. With a focus on the underlying mechanisms of the ecological treatment process, we explored the microbial community biomass, composition, and function in the treatment system to understand the microbial growth in this system and its role in pollutant removal. Flow cytometry analysis revealed that ecological treatment significantly decreased influent bacterial quantity, with around 80% removal. 16S rRNA gene sequencing showed that the ecological treatment also altered the bacterial community structure of the wastewater, leading to a significant change in Comamonadaceae in the effluent. In the internal ecological system, because most of microbes aggregate in the plant rhizosphere and the sludge under plant roots, we selected two plant species (Nerium oleander and Arundo donax) to study the characteristics of rhizosphere and sludge microbes. Metagenomic results showed that the microbial community composition and function differed between the two species, and the microbial communities of A. donax were more sensitive to seasonal effects. Combined with their greater biomass and abundance of metabolic genes, microbes associated with N. oleander showed a greater contribution to pollutant removal. Further, the biodegradation pathways of some micropollutants, e.g., atrazine, were estimated.

Analyses of the microbial diversity across the human microbiome.

Directory of Open Access Journals (Sweden)

Kelvin Li

Full Text Available Analysis of human body microbial diversity is fundamental to understanding community structure, biology and ecology. The National Institutes of Health Human Microbiome Project (HMP has provided an unprecedented opportunity to examine microbial diversity within and across body habitats and individuals through pyrosequencing-based profiling of 16 S rRNA gene sequences (16 S from habits of the oral, skin, distal gut, and vaginal body regions from over 200 healthy individuals enabling the application of statistical techniques. In this study, two approaches were applied to elucidate the nature and extent of human microbiome diversity. First, bootstrap and parametric curve fitting techniques were evaluated to estimate the maximum number of unique taxa, S(max, and taxa discovery rate for habitats across individuals. Next, our results demonstrated that the variation of diversity within low abundant taxa across habitats and individuals was not sufficiently quantified with standard ecological diversity indices. This impact from low abundant taxa motivated us to introduce a novel rank-based diversity measure, the Tail statistic, ("τ", based on the standard deviation of the rank abundance curve if made symmetric by reflection around the most abundant taxon. Due to τ's greater sensitivity to low abundant taxa, its application to diversity estimation of taxonomic units using taxonomic dependent and independent methods revealed a greater range of values recovered between individuals versus body habitats, and different patterns of diversity within habitats. The greatest range of τ values within and across individuals was found in stool, which also exhibited the most undiscovered taxa. Oral and skin habitats revealed variable diversity patterns, while vaginal habitats were consistently the least diverse. Collectively, these results demonstrate the importance, and motivate the introduction, of several visualization and analysis methods tuned specifically for

Dissolved Organic Carbon Influences Microbial Community Composition and Diversity in Managed Aquifer Recharge Systems

KAUST Repository

Li, D.; Sharp, J. O.; Saikaly, Pascal; Ali, Shahjahan; Alidina, M.; Alarawi, M. S.; Keller, S.; Hoppe-Jones, C.; Drewes, J. E.

2012-01-01

This study explores microbial community structure in managed aquifer recharge (MAR) systems across both laboratory and field scales. Two field sites, the Taif River (Taif, Saudi Arabia) and South Platte River (Colorado), were selected as geographically distinct MAR systems. Samples derived from unsaturated riverbed, saturated-shallow-infiltration (depth, 1 to 2 cm), and intermediate-infiltration (depth, 10 to 50 cm) zones were collected. Complementary laboratory-scale sediment columns representing low (0.6 mg/liter) and moderate (5 mg/liter) dissolved organic carbon (DOC) concentrations were used to further query the influence of DOC and depth on microbial assemblages. Microbial density was positively correlated with the DOC concentration, while diversity was negatively correlated at both the laboratory and field scales. Microbial communities derived from analogous sampling zones in each river were not phylogenetically significantly different on phylum, class, genus, and species levels, as determined by 16S rRNA gene pyrosequencing, suggesting that geography and season exerted less sway than aqueous geochemical properties. When field-scale communities derived from the Taif and South Platte River sediments were grouped together, principal coordinate analysis revealed distinct clusters with regard to the three sample zones (unsaturated, shallow, and intermediate saturated) and, further, with respect to DOC concentration. An analogous trend as a function of depth and corresponding DOC loss was observed in column studies. Canonical correspondence analysis suggests that microbial classes Betaproteobacteria and Gammaproteobacteria are positively correlated with DOC concentration. Our combined analyses at both the laboratory and field scales suggest that DOC may exert a strong influence on microbial community composition and diversity in MAR saturated zones.

Dissolved Organic Carbon Influences Microbial Community Composition and Diversity in Managed Aquifer Recharge Systems

KAUST Repository

Li, D.

2012-07-13

This study explores microbial community structure in managed aquifer recharge (MAR) systems across both laboratory and field scales. Two field sites, the Taif River (Taif, Saudi Arabia) and South Platte River (Colorado), were selected as geographically distinct MAR systems. Samples derived from unsaturated riverbed, saturated-shallow-infiltration (depth, 1 to 2 cm), and intermediate-infiltration (depth, 10 to 50 cm) zones were collected. Complementary laboratory-scale sediment columns representing low (0.6 mg/liter) and moderate (5 mg/liter) dissolved organic carbon (DOC) concentrations were used to further query the influence of DOC and depth on microbial assemblages. Microbial density was positively correlated with the DOC concentration, while diversity was negatively correlated at both the laboratory and field scales. Microbial communities derived from analogous sampling zones in each river were not phylogenetically significantly different on phylum, class, genus, and species levels, as determined by 16S rRNA gene pyrosequencing, suggesting that geography and season exerted less sway than aqueous geochemical properties. When field-scale communities derived from the Taif and South Platte River sediments were grouped together, principal coordinate analysis revealed distinct clusters with regard to the three sample zones (unsaturated, shallow, and intermediate saturated) and, further, with respect to DOC concentration. An analogous trend as a function of depth and corresponding DOC loss was observed in column studies. Canonical correspondence analysis suggests that microbial classes Betaproteobacteria and Gammaproteobacteria are positively correlated with DOC concentration. Our combined analyses at both the laboratory and field scales suggest that DOC may exert a strong influence on microbial community composition and diversity in MAR saturated zones.

Dissolved organic carbon influences microbial community composition and diversity in managed aquifer recharge systems.

Science.gov (United States)

Li, Dong; Sharp, Jonathan O; Saikaly, Pascal E; Ali, Shahjahan; Alidina, Mazahirali; Alarawi, Mohammed S; Keller, Stephanie; Hoppe-Jones, Christiane; Drewes, Jörg E

2012-10-01

This study explores microbial community structure in managed aquifer recharge (MAR) systems across both laboratory and field scales. Two field sites, the Taif River (Taif, Saudi Arabia) and South Platte River (Colorado), were selected as geographically distinct MAR systems. Samples derived from unsaturated riverbed, saturated-shallow-infiltration (depth, 1 to 2 cm), and intermediate-infiltration (depth, 10 to 50 cm) zones were collected. Complementary laboratory-scale sediment columns representing low (0.6 mg/liter) and moderate (5 mg/liter) dissolved organic carbon (DOC) concentrations were used to further query the influence of DOC and depth on microbial assemblages. Microbial density was positively correlated with the DOC concentration, while diversity was negatively correlated at both the laboratory and field scales. Microbial communities derived from analogous sampling zones in each river were not phylogenetically significantly different on phylum, class, genus, and species levels, as determined by 16S rRNA gene pyrosequencing, suggesting that geography and season exerted less sway than aqueous geochemical properties. When field-scale communities derived from the Taif and South Platte River sediments were grouped together, principal coordinate analysis revealed distinct clusters with regard to the three sample zones (unsaturated, shallow, and intermediate saturated) and, further, with respect to DOC concentration. An analogous trend as a function of depth and corresponding DOC loss was observed in column studies. Canonical correspondence analysis suggests that microbial classes Betaproteobacteria and Gammaproteobacteria are positively correlated with DOC concentration. Our combined analyses at both the laboratory and field scales suggest that DOC may exert a strong influence on microbial community composition and diversity in MAR saturated zones.

Natural Microbial Assemblages Reflect Distinct Organismal and Functional Partitioning

Science.gov (United States)

Wilmes, P.; Andersson, A.; Kalnejais, L. H.; Verberkmoes, N. C.; Lefsrud, M. G.; Wexler, M.; Singer, S. W.; Shah, M.; Bond, P. L.; Thelen, M. P.; Hettich, R. L.; Banfield, J. F.

2007-12-01

also highlights the importance of strain heterogeneity for the maintenance of community structure and function. These findings explain the importance of genetic diversity in facilitating the stable performance of complex microbial processes. Furthermore, although very different in terms of habitat, both microbial communities exhibit distinct functional compartmentalization and demonstrate its role in sustaining microbial community structure.

Analysis of Microbial Communities in the Oil Reservoir Subjected to CO2-Flooding by Using Functional Genes as Molecular Biomarkers for Microbial CO2 Sequestration

Directory of Open Access Journals (Sweden)

Jin-Feng eLiu

2015-03-01

Full Text Available Sequestration of CO2 in oil reservoirs is considered to be one of the feasible options for mitigating atmospheric CO2 building up and also for the in situ potential bioconversion of stored CO2 to methane. However, the information on these functional microbial communities and the impact of CO2 storage on them is hardly available. In this paper a comprehensive molecular survey was performed on microbial communities in production water samples from oil reservoirs experienced CO2-flooding by analysis of functional genes involved in the process, including cbbM, cbbL, fthfs, [FeFe]-hydrogenase and mcrA. As a comparison, these functional genes in the production water samples from oil reservoir only experienced water-flooding in areas of the same oil bearing bed were also analyzed. It showed that these functional genes were all of rich diversity in these samples, and the functional microbial communities and their diversity were strongly affected by a long-term exposure to injected CO2. More interestingly, microorganisms affiliated with members of the genera Methanothemobacter, Acetobacterium and Halothiobacillus as well as hydrogen producers in CO2 injected area either increased or remained unchanged in relative abundance compared to that in water-flooded area, which implied that these microorganisms could adapt to CO2 injection and, if so, demonstrated the potential for microbial fixation and conversion of CO2 into methane in subsurface oil reservoirs.

Effects of uranium on soil microbial biomass carbon, enzymes, plant biomass and microbial diversity in yellow soils

International Nuclear Information System (INIS)

Yan, X.; Zhang, Y.; Luo, X.; Yu, L.

2016-01-01

We conducted an experiment to investigate the effects of uranium (U) on soil microbial biomass carbon (MBC), enzymes, plant biomass and microbial diversity in yellow soils under three concentrations: 0 mg kg"-"1 (T1, control), 30 mg kg"-"1 (T2) and 60 mg kg"-"1 (T3). Under each treatment, elevated U did not reduce soil MBC or plant biomass, but inhibited the activity of the soil enzymes urease (UR), dehydrogenase (DH) and phosphatase (PHO). The microbial diversity was different, with eight dominant phyla in T1 and six in T2 and T3. Furthermore, Proteobacteria and material X were both detected in each treatment site (T1, T2 and T3). Pseudomonas sp. was the dominant strain, followed by Acidiphilium sp. This initial study provided valuable data for further research toward a better understanding of U contamination in yellow soils in China. (authors)

Structure, function and diversity of the healthy human microbiome.

Science.gov (United States)

2012-06-13

Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics and early microbial exposure have all been implicated. Accordingly, to characterize the ecology of human-associated microbial communities, the Human Microbiome Project has analysed the largest cohort and set of distinct, clinically relevant body habitats so far. We found the diversity and abundance of each habitat's signature microbes to vary widely even among healthy subjects, with strong niche specialization both within and among individuals. The project encountered an estimated 81-99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome. Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure, and ethnic/racial background proved to be one of the strongest associations of both pathways and microbes with clinical metadata. These results thus delineate the range of structural and functional configurations normal in the microbial communities of a healthy population, enabling future characterization of the epidemiology, ecology and translational applications of the human microbiome.

Microbial community structure and diversity in a municipal solid waste landfill.

Science.gov (United States)

Wang, Xiaolin; Cao, Aixin; Zhao, Guozhu; Zhou, Chuanbin; Xu, Rui

2017-08-01

Municipal solid waste (MSW) landfills are the most prevalent waste disposal method and constitute one of the largest sources of anthropogenic methane emissions in the world. Microbial activities in disposed waste play a crucial role in greenhouse gas emissions; however, only a few studies have examined metagenomic microbial profiles in landfills. Here, the MiSeq high-throughput sequencing method was applied for the first time to examine microbial diversity of the cover soil and stored waste located at different depths (0-150cm) in a typical MSW landfill in Yangzhou City, East China. The abundance of microorganisms in the cover soil (0-30cm) was the lowest among all samples, whereas that in stored waste decreased from the top to the middle layer (30-90cm) and then increased from the middle to the bottom layer (90-150cm). In total, 14 phyla and 18 genera were found in the landfill. A microbial diversity analysis showed that Firmicutes, Proteobacteria, and Bacteroidetes were the dominant phyla, whereas Halanaerobium, Methylohalobius, Syntrophomonas, Fastidiosipila, and Spirochaeta were the dominant genera. Methylohalobius (methanotrophs) was more abundant in the cover layers of soil than in stored waste, whereas Syntrophomonas and Fastidiosipila, which affect methane production, were more abundant in the middle to bottom layers (90-150cm) in stored waste. A canonical correlation analysis showed that microbial diversity in the landfill was most strongly correlated with the conductivity, organic matter, and moisture content of the stored waste. Copyright © 2017 Elsevier Ltd. All rights reserved.

Functional patterns of microbial communities of rhizospheric soils across the development stages of a young mangrove in French Guiana.

Science.gov (United States)

Luglia, Mathieu; Criquet, Stéven; Sarrazin, Max; Ziarelli, Fabio; Guiral, Daniel

2014-02-01

The functional patterns of microbial communities (microbial respiration, enzyme activities, functional diversity) and the relevant physico-chemical characteristics of rhizospheric soils were studied during the process of mudflat colonization by mangrove. The study site is a fringe mangrove stand located in Montabo Bay at Cayenne (French Guiana). It is characterized by different vegetation development stages dominated by an assemblage of Avicennia germinans and Laguncularia racemosa. Rhizospheric and surface soils were collected from three stations based on successional stages of mangrove colonization: pioneer (P), coppice (C), and young forest (F). The microbial functional patterns showed significant progressive shifts along the mangrove vegetation profile. The P stages, those most influenced by tide currents, were macroscopically characterized by hydro-sedimentary instability and micro-phytobenthic colonization of mudflat. This stage, characterized by low total organic carbon (TOC) content and quality, showed the lowest extracellular enzymatic activities and the highest functional metabolic diversities. TOC quality analyses by (13)C CPMAS NMR provided evidence of progressive TOC enrichment and an increasing imprint of aboveground vegetation on C quality as succession occurs. These differences in the origin, amount, and quality of soil organic matter (SOM) of older stages exerted both a quantitative and qualitative control over microbial functional responses. This indicated the enhancement of aboveground-belowground functional linkages, leading to the expression of high decomposition activities and a functional loss and specialization of rhizospheric microbial communities.

Microbial diversity in European and South American spacecraft assembly clean rooms

Science.gov (United States)

Moissl-Eichinger, Christine; Stieglmeier, Michaela; Schwendner, Petra

Spacecraft assembly clean rooms are unique environments for microbes: Due to low nutri-ent levels, desiccated, clean conditions, constant control of humidity and temperature, these environments are quite inhospitable to microbial life and even considered "extreme". Many procedures keep the contamination as low as possible, but these conditions are also highly se-lective for indigenous microbial communities. For space missions under planetary protection requirements, it is crucial to control the contaminating bioburden as much as possible; but for the development of novel cleaning/sterilization methods it is also important to identify and characterize (understand) the present microbial community of spacecraft clean rooms. In prepa-ration for the recently approved ESA ExoMars mission, two European and one South American spacecraft assembly clean rooms were analyzed with respect to their microbial diversity, using standard procedures, new cultivation approaches and molecular methods, that should shed light onto the presence of planetary protection relevant microorganisms. For this study, the Her-schel Space Observatory (launched in May 2009) and its housing clean rooms in Friedrichshafen (Germany), at ESTEC (The Netherlands) and CSG, Kourou (French Guyana) were sampled during assembly, test and launch operations. Although Herschel does not demand planetary protection requirements, all clean rooms were in a fully operating state during sampling. This gave us the opportunity to sample the microbial diversity under strict particulate and molecular contamination-control. Samples were collected from spacecraft and selected clean room surface areas and were subjected to cultivation assays (32 different media), molecular studies (based on 16S rRNA gene sequence analysis) and quantitative PCR. The results from different strategies will be compared and critically discussed, showing the advantages and limits of the selected methodologies. This talk will sum up the lessons

Soil microbial diversity, site conditions, shelter forest land, saline water drip-irrigation, drift desert.

Science.gov (United States)

Jin, Zhengzhong; Lei, Jiaqiang; Li, Shengyu; Xu, Xinwen

2013-10-01

Soil microbes in forest land are crucial to soil development in extreme areas. In this study, methods of conventional culture, PLFA and PCR-DGGE were utilized to analyze soil microbial quantity, fatty acids and microbial DNA segments of soils subjected to different site conditions in the Tarim Desert Highway forest land. The main results were as follows: the soil microbial amount, diversity indexes of fatty acid and DNA segment differed significantly among sites with different conditions (F 84%), followed by actinomycetes and then fungi (<0.05%). Vertical differences in the soil microbial diversity were insignificant at 0-35 cm. Correlation analysis indicated that the forest trees grew better as the soil microbial diversity index increased. Therefore, construction of the Tarim Desert Highway shelter-forest promoted soil biological development; however, for enhancing sand control efficiency and promoting sand development, we should consider the effects of site condition in the construction and regeneration of shelter-forest ecological projects. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Linking microbial diversity and functionality of arctic glacial surface habitats.

Science.gov (United States)

Lutz, Stefanie; Anesio, Alexandre M; Edwards, Arwyn; Benning, Liane G

2017-02-01

Distinct microbial habitats on glacial surfaces are dominated by snow and ice algae, which are the critical players and the dominant primary colonisers and net producers during the melt season. Here for the first time we have evaluated the role of these algae in association with the full microbial community composition (i.e., algae, bacteria, archaea) in distinct surface habitats and on 12 glaciers and permanent snow fields in Svalbard and Arctic Sweden. We cross-correlated these data with the analyses of specific metabolites such as fatty acids and pigments, and a full suite of potential critical physico-chemical parameters including major and minor nutrients, and trace metals. It has been shown that correlations between single algal species, metabolites, and specific geochemical parameters can be used to unravel mixed metabolic signals in complex communities, further assign them to single species and infer their functionality. The data also clearly show that the production of metabolites in snow and ice algae is driven mainly by nitrogen and less so by phosphorus limitation. This is especially important for the synthesis of secondary carotenoids, which cause a darkening of glacial surfaces leading to a decrease in surface albedo and eventually higher melting rates. © 2016 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

A phylogenetic perspective on species diversity, β-diversity and biogeography for the microbial world.

Science.gov (United States)

Barberán, Albert; Casamayor, Emilio O

2014-12-01

There is an increasing interest to combine phylogenetic data with distributional and ecological records to assess how natural communities arrange under an evolutionary perspective. In the microbial world, there is also a need to go beyond the problematic species definition to deeply explore ecological patterns using genetic data. We explored links between evolution/phylogeny and community ecology using bacterial 16S rRNA gene information from a high-altitude lakes district data set. We described phylogenetic community composition, spatial distribution, and β-diversity and biogeographical patterns applying evolutionary relatedness without relying on any particular operational taxonomic unit definition. High-altitude lakes districts usually contain a large mosaic of highly diverse small water bodies and conform a fine biogeographical model of spatially close but environmentally heterogeneous ecosystems. We sampled 18 lakes in the Pyrenees with a selection criteria focused on capturing the maximum environmental variation within the smallest geographical area. The results showed highly diverse communities nonrandomly distributed with phylogenetic β-diversity patterns mainly shaped by the environment and not by the spatial distance. Community similarity based on both bacterial taxonomic composition and phylogenetic β-diversity shared similar patterns and was primarily structured by similar environmental drivers. We observed a positive relationship between lake area and phylogenetic diversity with a slope consistent with highly dispersive planktonic organisms. The phylogenetic approach incorporated patterns of common ancestry into bacterial community analysis and emerged as a very convenient analytical tool for direct inter- and intrabiome biodiversity comparisons and sorting out microbial habitats with potential application in conservation studies. © 2014 John Wiley & Sons Ltd.

Responses of Soil Microbial Community Structure and Diversity to Agricultural Deintensification

Institute of Scientific and Technical Information of China (English)

ZHANG Wei-Jian; S.HU; RUI Wen-Yi; C.TU; H.G.DIAB; F.J.LOUWS; J.P.MUELLER; N.CREAMER; M.BELL; M.G.WAGGER

2005-01-01

Using a scheme of agricultural fields with progressively less intensive management (deintensification), different management practices in six agroecosystems located near Goldsboro, NC, USA were tested in a large-scale experiment, including two cash-grain cropping systems employing either tillage (CT) or no-tillage (NT), an organic farming system (OR), an integrated cropping system with animals (IN), a successional field (SU), and a plantation woodlot (WO). Microbial phospholipid fatty acid (PLFA) profiles and substrate utilization patterns (BIOLOG ECO plates) were measured to examine the effects of deintensification on the structure and diversity of soil microbial communities. Principle component analyses of PLFA and BIOLOG data showed that the microbial community structure diverged among the soils of the six systems.Lower microbial diversity was found in lowly managed ecosystem than that in intensive and moderately managed agroecosystems, and both fungal contribution to the total identified PLFAs and the ratio of microbial biomass C/N increased along with agricultural deintensification. Significantly higher ratios of C/N (P ＜ 0.05) were found in the WO and SU systems, and for fungal/bacterial PLFAs in the WO system (P ＜ 0.05). There were also significant decreases (P ＜ 0.05)along with agricultural deintensification for contributions of total bacterial and gram positive (G+) bacterial PLFAs.Agricultural deintensification could facilitate the development of microbial communities that favor soil fungi over bacteria.

Soil functional diversity analysis of a bauxite-mined restoration chronosequence.

Science.gov (United States)

Lewis, Dawn E; White, John R; Wafula, Denis; Athar, Rana; Dickerson, Tamar; Williams, Henry N; Chauhan, Ashvini

2010-05-01

Soil microorganisms are sensitive to environmental perturbations such that changes in microbial community structure and function can provide early signs of anthropogenic disturbances and even predict restoration success. We evaluated the bacterial functional diversity of un-mined and three chronosequence sites at various stages of rehabilitation (0, 10, and 20 years old) located in the Mocho Mountains of Jamaica. Samples were collected during the dry and wet seasons and analyzed for metal concentrations, microbial biomass carbon, bacterial numbers, and functional responses of soil microbiota using community-level physiological profile (CLPP) assays. Regardless of the season, un-mined soils consisted of higher microbial biomass and numbers than any of the rehabilitated sites. Additionally, the number and rate of substrates utilized and substrate evenness (the distribution of color development between the substrates) were significantly greater in the un-mined soils with carbohydrates being preferentially utilized than amino acids, polymers, carboxylic acids, and esters. To some extent, functional responses varied with the seasons but the least physiological activity was shown by the site rehabilitated in 1987 indicating long-term perturbation to this ecosystem. Small subunit ribosomal DNA (SSUrDNA)-denaturing gradient-gel electrophoresis analyses on the microbiota collected from the most preferred CLPP substrates followed by taxonomic analyses showed Proteobacteria, specifically the gamma-proteobacteria, as the most functionally active phyla, indicating a propensity of this phyla to out-compete other groups under the prevailing conditions. Additionally, multivariate statistical analyses, Shannon's diversity, and evenness indices, principal component analysis, biplot and un-weighted-pair-group method with arithmetic averages dendrograms further confirmed that un-mined sites were distinctly different from the rehabilitated soils.

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.

Altitudinal patterns of diversity and functional traits of metabolically active microorganisms in stream biofilms

Science.gov (United States)

Wilhelm, Linda; Besemer, Katharina; Fragner, Lena; Peter, Hannes; Weckwerth, Wolfram; Battin, Tom J

2015-01-01

Resources structure ecological communities and potentially link biodiversity to energy flow. It is commonly believed that functional traits (generalists versus specialists) involved in the exploitation of resources depend on resource availability and environmental fluctuations. The longitudinal nature of stream ecosystems provides changing resources to stream biota with yet unknown effects on microbial functional traits and community structure. We investigated the impact of autochthonous (algal extract) and allochthonous (spruce extract) resources, as they change along alpine streams from above to below the treeline, on microbial diversity, community composition and functions of benthic biofilms. Combining bromodeoxyuridine labelling and 454 pyrosequencing, we showed that diversity was lower upstream than downstream of the treeline and that community composition changed along the altitudinal gradient. We also found that, especially for allochthonous resources, specialisation by biofilm bacteria increased along that same gradient. Our results suggest that in streams below the treeline biofilm diversity, specialisation and functioning are associated with increasing niche differentiation as potentially modulated by divers allochthonous and autochthonous constituents contributing to resources. These findings expand our current understanding on biofilm structure and function in alpine streams. PMID:25978543

Characterizing microbial diversity and damage in mural paintings.

Science.gov (United States)

Rosado, Tânia; Mirão, José; Candeias, António; Caldeira, Ana Teresa

2015-02-01

Mural paintings are some of the oldest and most important cultural expressions of mankind and play an important role for the understanding of societies and civilizations. These cultural assets have high economic and cultural value and therefore their degradation has social and economic impact. The present work presents a novel microanalytical approach to understand the damages caused by microbial communities in mural paintings. This comprises the characterization and identification of microbial diversity and evaluation of damage promoted by their biological activity. Culture-dependent methods and DNA-based approaches like denaturing gradient gel electrophoresis (DGGE) and pyrosequencing are important tools in the isolation and identification of the microbial communities allowing characterization of the biota involved in the biodeterioration phenomena. Raman microspectrometry, infrared spectrometry, and variable pressure scanning electron microscopy coupled with energy-dispersive X-ray spectrometry are also useful tools for evaluation of the presence of microbial contamination and detection of the alteration products resulting from metabolic activity of the microorganisms. This study shows that the degradation status of mural paintings can be correlated to the presence of metabolically active microorganisms.

Mineralogical Control on Microbial Diversity in a Weathered Granite?

Science.gov (United States)

Gleeson, D.; Clipson, N.; McDermott, F.

2003-12-01

Mineral transformation reactions and the behaviour of metals in rock and soils are affected not only by physicochemical parameters but also by biological factors, particularly by microbial activity. Microbes inhabit a wide range of niches in surface and subsurface environments, with mineral-microbe interactions being generally poorly understood. The focus of this study is to elucidate the role of microbial activity in the weathering of common silicate minerals in granitic rocks. A site in the Wicklow Mountains (Ireland) has been identified that consists of an outcrop surface of Caledonian (ca. 400 million years old) pegmatitic granite from which large intact crystals of variably weathered muscovite, plagioclase, K-feldspar and quartz were sampled, together with whole-rock granite. Culture-based microbial approaches have been widely used to profile microbial communities, particularly from copiotrophic environments, but it is now well established that for oligotrophic environments such as those that would be expected on weathering faces, perhaps less than 1% of microbial diversity can be profiled by cultural means. A number of culture-independent molecular based approaches have been developed to profile microbial diversity and community structure. These rely on successfully isolating environmental DNA from a given environment, followed by the use of the polymerase chain reaction (PCR) to amplify the typically small quantities of extracted DNA. Amplified DNA can then be analysed using cloning based approaches as well as community fingerprinting systems such as denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (TRFLP) and ribosomal intergenic spacer analysis (RISA). Community DNA was extracted and the intergenic spacer region (ITS) between small (16S) and large (23S) bacterial subunit rRNA genes was amplified. RISA fragments were then electrophoresed on a non-denaturing polyacrylamide gel. Banding patterns suggest that

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.

Microbial diversity in sediment ecosystems (evaporites domes, microbial mats and crusts of hypersaline Laguna Tebenquiche, Salar de Atacama, Chile

Directory of Open Access Journals (Sweden)

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.

Boom clay pore water, home of a diverse microbial community

International Nuclear Information System (INIS)

Wouters, Katinka; Moors, Hugo; Leys, Natalie

2012-01-01

Document available in extended abstract form only. Boom Clay pore water (BCPW) has been studied in the framework of geological disposal of nuclear waste for over two decades, thereby mainly addressing its geochemical properties. A reference composition for synthetic clay water has been derived earlier by modelling and spatial calibration efforts, mainly based on interstitial water sampled from different layers within the Boom clay. However, since microbial activity is found in a range of extreme circumstances, the possibility of microbes interacting with future radioactive waste in a host formation like Boom Clay, cannot be ignored. In this respect, BCPW was sampled from different Boom Clay layers using the Morpheus piezometer and subsequently analysed by a complementary set of microbiological and molecular techniques, in search for overall shared and abundant microorganisms. Similar to the previous characterization of the 'average' BCPW chemical composition, the primary aim of this microbiological study is to determine a representative BCPW microbial community which can be used in laboratory studies. Secondly, the in situ activity and the metabolic properties of members of this community were addressed, aiming to assess their survival and proliferation chances in repository conditions. In a first approach, total microbial DNA of the community was extracted from the BCPW samples. This molecular approach allows a broad insight in the total microbial ecology of the BCPW samples. By polymerase chain reaction (PCR) on the highly conserved 16S rRNA genes in this DNA pool and subsequent sequencing and bio-informatics analysis, operational taxonomic units (OTUs) could be assigned to the microbial community. The bacterial community was found to be quite diverse, with OTUs belonging to 8 different phyla (Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Chlorobi, Spirochetes, Chloroflexi and Deinococcus-Thermus). These results provide an overall view of the

Boom clay pore water, home of a diverse microbial community

Energy Technology Data Exchange (ETDEWEB)

Wouters, Katinka; Moors, Hugo; Leys, Natalie [SCK.CEN, Environment, Health and Safety Institute, B-2400 Mol (Belgium)

2012-10-15

Document available in extended abstract form only. Boom Clay pore water (BCPW) has been studied in the framework of geological disposal of nuclear waste for over two decades, thereby mainly addressing its geochemical properties. A reference composition for synthetic clay water has been derived earlier by modelling and spatial calibration efforts, mainly based on interstitial water sampled from different layers within the Boom clay. However, since microbial activity is found in a range of extreme circumstances, the possibility of microbes interacting with future radioactive waste in a host formation like Boom Clay, cannot be ignored. In this respect, BCPW was sampled from different Boom Clay layers using the Morpheus piezometer and subsequently analysed by a complementary set of microbiological and molecular techniques, in search for overall shared and abundant microorganisms. Similar to the previous characterization of the 'average' BCPW chemical composition, the primary aim of this microbiological study is to determine a representative BCPW microbial community which can be used in laboratory studies. Secondly, the in situ activity and the metabolic properties of members of this community were addressed, aiming to assess their survival and proliferation chances in repository conditions. In a first approach, total microbial DNA of the community was extracted from the BCPW samples. This molecular approach allows a broad insight in the total microbial ecology of the BCPW samples. By polymerase chain reaction (PCR) on the highly conserved 16S rRNA genes in this DNA pool and subsequent sequencing and bio-informatics analysis, operational taxonomic units (OTUs) could be assigned to the microbial community. The bacterial community was found to be quite diverse, with OTUs belonging to 8 different phyla (Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Chlorobi, Spirochetes, Chloroflexi and Deinococcus-Thermus). These results provide an overall view of the

Microbial diversity in different compartments of an aquaponics system.

Science.gov (United States)

Schmautz, Zala; Graber, Andreas; Jaenicke, Sebastian; Goesmann, Alexander; Junge, Ranka; Smits, Theo H M

2017-05-01

Aquaponics is a solution for sustainable production of fish and plants in a single semi-closed system, where nutrient-rich water from the aquaculture provides nutrients for plant growth. We examined the microbial communities within an experimental aquaponics system. Whereas the fish feces contained a separate community dominated by bacteria of the genus Cetobacterium, the samples from plant roots, biofilter, and periphyton were more similar to each other, while the communities were more diverse. Detailed examination of the data gave the first indications to functional groups of organisms in the different compartments of the aquaponic system. As other nitrifiers other than members of the genus Nitrospira were only present at low numbers, it was anticipated that Nitrospirae may perform the nitrification process in the biofilm.

Effects of different soil management practices on soil properties and microbial diversity

Science.gov (United States)

Gajda, Anna M.; Czyż, Ewa A.; Dexter, Anthony R.; Furtak, Karolina M.; Grządziel, Jarosław; Stanek-Tarkowska, Jadwiga

2018-01-01

The effects of different tillage systems on the properties and microbial diversity of an agricultural soil was investigated. In doing so, soil physical, chemical and biological properties were analysed in 2013-2015, on a long-term field experiment on a loamy sand at the IUNG-PIB Experimental Station in Grabów, Poland. Winter wheat was grown under two tillage treatments: conventional tillage using a mouldboard plough and traditional soil tillage equipment, and reduced tillage based on soil crushing-loosening equipment and a rigid-tine cultivator. Chopped wheat straw was used as a mulch on both treatments. Reduced tillage resulted in increased water content throughout the whole soil profile, in comparison with conventional tillage. Under reduced tillage, the content of readily dispersible clay was also reduced, and, therefore, soil stability was increased in the toplayers, compared with conventional tillage. In addition, the beneficial effects of reduced tillage were reflected in higher soil microbial activity as measured with dehydrogenases and hydrolysis of fluorescein diacetate, compared with conventional tillage. Moreover, the polimerase chain reaction - denaturing gradient gel electrophoresis analysis showed that soil under reduced till-age had greater diversity of microbial communities, compared with conventionally-tilled soil. Finally, reduced tillage increased organic matter content, stability in water and microbial diversity in the top layer of the soil.

Microbial diversity in cold seep sediments from the northern South China Sea

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Yong Zhang

2012-05-01

Full Text Available South China Sea (SCS is the largest Western Pacific marginal sea. However, microbial studies have never been performed in the cold seep sediments in the SCS. In 2004, “SONNE” 177 cruise found two cold seep areas with different water depth in the northern SCS. Haiyang 4 area, where the water depth is around 3000 m, has already been confirmed for active seeping on the seafloor, such as microbial mats, authigenic carbonate crusts and bivalves. We investigated microbial abundance and diversity in a 5.55-m sediment core collected from this cold seep area. An integrated approach was employed including geochemistry and 16S rRNA gene phylogenetic analyses. Here, we show that microbial abundance and diversity along with geochemistry profiles of the sediment core revealed a coupled reaction between sulphate reduction and methane oxidation. Acridine orange direct count results showed that microbial abundance ranges from 105 to 106 cells/g sediment (wet weight. The depth-related variation of the abundance showed the same trend as the methane concentration profile. Phylogenetic analysis indicated the presence of sulphate-reducing bacteria and anaerobic methane-oxidizing archaea. The diversity was much higher at the surface, but decreased sharply with depth in response to changes in the geochemical conditions of the sediments, such as methane, sulphate concentration and total organic carbon. Marine Benthic Group B, Chloroflexi and JS1 were predominant phylotypes of the archaeal and bacterial libraries, respectively.

Response of Microbial Community Function to Fluctuating Geochemical Conditions within a Legacy Radioactive Waste Trench Environment.

Science.gov (United States)

Vázquez-Campos, Xabier; Kinsela, Andrew S; Bligh, Mark W; Harrison, Jennifer J; Payne, Timothy E; Waite, T David

2017-09-01

During the 1960s, small quantities of radioactive materials were codisposed with chemical waste at the Little Forest Legacy Site (Sydney, Australia) in 3-meter-deep, unlined trenches. Chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a 6-week period immediately after a prolonged rainfall event to assess the impact of changing water levels upon the microbial ecology and contaminant mobility. Collectively, results demonstrated that oxygen-laden rainwater rapidly altered the redox balance in the trench water, strongly impacting microbial functioning as well as the radiochemistry. Two contaminants of concern, plutonium and americium, were shown to transition from solid-iron-associated species immediately after the initial rainwater pulse to progressively more soluble moieties as reducing conditions were enhanced. Functional metagenomics revealed the potentially important role that the taxonomically diverse microbial community played in this transition. In particular, aerobes dominated in the first day, followed by an increase of facultative anaerobes/denitrifiers at day 4. Toward the mid-end of the sampling period, the functional and taxonomic profiles depicted an anaerobic community distinguished by a higher representation of dissimilatory sulfate reduction and methanogenesis pathways. Our results have important implications to similar near-surface environmental systems in which redox cycling occurs. IMPORTANCE The role of chemical and microbiological factors in mediating the biogeochemistry of groundwaters from trenches used to dispose of radioactive materials during the 1960s is examined in this study. Specifically, chemical and microbial analyses, including functional and taxonomic information derived from shotgun metagenomics, were collected across a 6-week period immediately after a prolonged rainfall event to assess how changing water levels influence microbial ecology and

Microbial diversity and carbon cycling in San Francisco Bay wetlands

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.

2014-03-21

Wetland restoration efforts in San Francisco Bay aim to rebuild habitat for endangered species and provide an effective carbon storage solution, reversing land subsidence caused by a century of industrial and agricultural development. However, the benefits of carbon sequestration may be negated by increased methane production in newly constructed wetlands, making these wetlands net greenhouse gas (GHG) sources to the atmosphere. We investigated the effects of wetland restoration on below-ground microbial communities responsible for GHG cycling in a suite of historic and restored wetlands in SF Bay. Using DNA and RNA sequencing, coupled with real-time GHG monitoring, we profiled the diversity and metabolic potential of wetland soil microbial communities. The wetland soils harbor diverse communities of bacteria and archaea whose membership varies with sampling location, proximity to plant roots and sampling depth. Our results also highlight the dramatic differences in GHG production between historic and restored wetlands and allow us to link microbial community composition and GHG cycling with key environmental variables including salinity, soil carbon and plant species.

Microbial diversity in soil : Selection of microbial populations by plant and soil type and implications for disease suppressiveness

NARCIS (Netherlands)

Garbeva, P; van Veen, JA; van Elsas, JD

2004-01-01

An increasing interest has emerged with respect to the importance of microbial diversity in soil habitats. The extent of the diversity of microorganisms in soil is seen to be critical to the maintenance of soil health and quality, as a wide range of microorganisms is involved in important soil

Structural and functional diversity of microbial communities from a lake sediment contaminated with trenbolone, an endocrine-disrupting chemical

International Nuclear Information System (INIS)

Radl, Viviane; Pritsch, Karin; Munch, Jean Charles; Schloter, Michael

2005-01-01

Effects of trenbolone (TBOH), a hormone used in cattle production, on the structure and function of microbial communities in a fresh water sediment from a lake in Southern Germany were studied in a microcosm experiment. The microbial community structure and the total gene pool of the sediment, assessed by 16S rRNA/rDNA and RAPD fingerprint analysis, respectively, were not significantly affected by TBOH. In contrast, the N-acetyl-glucosaminidase activity was almost 50% lower in TBOH treated samples (P<0.05). Also, the substrate utilization potential, measured using the BIOLOG[reg] system, was reduced after TBOH treatment. Interestingly, this potential did not recover at the end of the experiment, i.e. 19 days after the addition of the chemical. Repeated application of TBOH did not lead to an additional reduction in the substrate utilization potential. Overall results indicate that microbial community function was more sensitive to TBOH treatment than the community structure and the total gene pool. - The steroid hormone trenbolone affects microbial community function in a lake sediment

Structural and functional diversity of microbial communities from a lake sediment contaminated with trenbolone, an endocrine-disrupting chemical

Energy Technology Data Exchange (ETDEWEB)

Radl, Viviane [GSF National Research Center for Environment and Health, Institute of Soil Ecology, PO Box 1129, D-85764, Neuherberg (Germany)]. E-mail: barbosa@gsf.de; Pritsch, Karin [GSF National Research Center for Environment and Health, Institute of Soil Ecology, PO Box 1129, D-85764, Neuherberg (Germany); Munch, Jean Charles [GSF National Research Center for Environment and Health, Institute of Soil Ecology, PO Box 1129, D-85764, Neuherberg (Germany); Schloter, Michael [GSF National Research Center for Environment and Health, Institute of Soil Ecology, PO Box 1129, D-85764, Neuherberg (Germany)

2005-09-15

Effects of trenbolone (TBOH), a hormone used in cattle production, on the structure and function of microbial communities in a fresh water sediment from a lake in Southern Germany were studied in a microcosm experiment. The microbial community structure and the total gene pool of the sediment, assessed by 16S rRNA/rDNA and RAPD fingerprint analysis, respectively, were not significantly affected by TBOH. In contrast, the N-acetyl-glucosaminidase activity was almost 50% lower in TBOH treated samples (P<0.05). Also, the substrate utilization potential, measured using the BIOLOG[reg] system, was reduced after TBOH treatment. Interestingly, this potential did not recover at the end of the experiment, i.e. 19 days after the addition of the chemical. Repeated application of TBOH did not lead to an additional reduction in the substrate utilization potential. Overall results indicate that microbial community function was more sensitive to TBOH treatment than the community structure and the total gene pool. - The steroid hormone trenbolone affects microbial community function in a lake sediment.

Microbial diversity and community structure across environmental gradients in Bransfield Strait, Western Antarctic Peninsula

Directory of Open Access Journals (Sweden)

Camila Negrão Signori

2014-12-01

Full Text Available The Southern Ocean is currently subject to intense investigations, mainly related to its importance for global biogeochemical cycles and its alarming rate of warming in response to climate change. Microbes play an essential role in the functioning of this ecosystem and are the main drivers of the biogeochemical cycling of elements. Yet, the diversity and abundance of microorganisms in this system remains poorly studied, in particular with regards to changes along environmental gradients. Here, we used amplicon sequencing of 16S rRNA gene tags using primers covering both Bacteria and Archaea to assess the composition and diversity of the microbial communities from four sampling depths (surface, the maximum and minimum of the oxygen concentration, and near the seafloor at ten oceanographic stations located in Bransfield Strait (northwest of the Antarctic Peninsula (AP and near the sea ice edge (north of the AP. Samples collected near the seafloor and at the oxygen minimum exhibited a higher diversity than those from the surface and oxygen maximum for both bacterial and archaeal communities. The main taxonomic groups identified below 100 m were Thaumarchaeota, Euryarchaeota and Proteobacteria (Gamma-, Delta-, Beta- and Alphaproteobacteria, whereas in the mixed layer above 100 m Bacteroidetes and Proteobacteria (mainly Alpha- and Gammaproteobacteria were found to be dominant. A combination of environmental factors seems to influence the microbial community composition. Our results help to understand how the dynamic seascape of the Southern Ocean shapes the microbial community composition and set a baseline for upcoming studies to evaluate the response of this ecosystem to future changes.

Responses of microbial community functional structures to pilot-scale uranium in situ bioremediation

Energy Technology Data Exchange (ETDEWEB)

Xu, M.; Wu, W.-M.; Wu, L.; He, Z.; Van Nostrand, J.D.; Deng, Y.; Luo, J.; Carley, J.; Ginder-Vogel, M.; Gentry, T.J.; Gu, B.; Watson, D.; Jardine, P.M.; Marsh, T.L.; Tiedje, J.M.; Hazen, T.C.; Criddle, C.S.; Zhou, J.

2010-02-15

A pilot-scale field test system with an inner loop nested within an outer loop was constructed for in situ U(VI) bioremediation at a US Department of Energy site, Oak Ridge, TN. The outer loop was used for hydrological protection of the inner loop where ethanol was injected for biostimulation of microorganisms for U(VI) reduction/immobilization. After 2 years of biostimulation with ethanol, U(VI) levels were reduced to below drinking water standard (<30 {micro}gl{sup -1}) in the inner loop monitoring wells. To elucidate the microbial community structure and functions under in situ uranium bioremediation conditions, we used a comprehensive functional gene array (GeoChip) to examine the microbial functional gene composition of the sediment samples collected from both inner and outer loop wells. Our study results showed that distinct microbial communities were established in the inner loop wells. Also, higher microbial functional gene number, diversity and abundance were observed in the inner loop wells than the outer loop wells. In addition, metal-reducing bacteria, such as Desulfovibrio, Geobacter, Anaeromyxobacter and Shewanella, and other bacteria, for example, Rhodopseudomonas and Pseudomonas, are highly abundant in the inner loop wells. Finally, the richness and abundance of microbial functional genes were highly correlated with the mean travel time of groundwater from the inner loop injection well, pH and sulfate concentration in groundwater. These results suggest that the indigenous microbial communities can be successfully stimulated for U bioremediation in the groundwater ecosystem, and their structure and performance can be manipulated or optimized by adjusting geochemical and hydrological conditions.

Wind and sunlight shape microbial diversity in surface waters of the North Pacific Subtropical Gyre.

Science.gov (United States)

Bryant, Jessica A; Aylward, Frank O; Eppley, John M; Karl, David M; Church, Matthew J; DeLong, Edward F

2016-06-01

Few microbial time-series studies have been conducted in open ocean habitats having low seasonal variability such as the North Pacific Subtropical Gyre (NPSG), where surface waters experience comparatively mild seasonal variation. To better describe microbial seasonal variability in this habitat, we analyzed rRNA amplicon and shotgun metagenomic data over two years at the Hawaii Ocean Time-series Station ALOHA. We postulated that this relatively stable habitat might reveal different environmental factors that influence planktonic microbial community diversity than those previously observed in more seasonally dynamic habitats. Unexpectedly, the data showed that microbial diversity at 25 m was positively correlated with average wind speed 3 to 10 days prior to sampling. In addition, microbial community composition at 25 m exhibited significant correlations with solar irradiance. Many bacterial groups whose relative abundances varied with solar radiation corresponded to taxa known to exhibit strong seasonality in other oceanic regions. Network co-correlation analysis of 25 m communities showed seasonal transitions in composition, and distinct successional cohorts of co-occurring phylogenetic groups. Similar network analyses of metagenomic data also indicated distinct seasonality in genes originating from cyanophage, and several bacterial clades including SAR116 and SAR324. At 500 m, microbial community diversity and composition did not vary significantly with any measured environmental parameters. The minimal seasonal variability in the NPSG facilitated detection of more subtle environmental influences, such as episodic wind variation, on surface water microbial diversity. Community composition in NPSG surface waters varied in response to solar irradiance, but less dramatically than reported in other ocean provinces.

Effects of sodium hypochlorite and high pH buffer solution in electrokinetic soil treatment on soil chromium removal and the functional diversity of soil microbial community

International Nuclear Information System (INIS)

Cang Long; Zhou Dongmei; Alshawabkeh, Akram N.; Chen Haifeng

2007-01-01

Effects of sodium hypochlorite (NaClO), applied as an oxidant in catholyte, and high pH buffer solution on soil Cr removal and the functional diversity of soil microbial community during enhanced electrokinetic treatments of a chromium (Cr) contaminated red soil are evaluated. Using pH control system to maintain high alkalinity of soil together with the use of NaClO increased the electrical conductivities of soil pore liquid and electroosmotic flux compared with the control (Exp-01). The pH control and NaClO improved the removal of Cr(VI) and total Cr from the soil. The highest removal percentages of soil Cr(VI) and total Cr were 96 and 72%, respectively, in Exp-04 when the pH value of the anolyte was controlled at 10 and NaClO was added in the catholyte. The alkaline soil environment and introduction of NaClO in the soil enhanced the desorption of Cr(VI) from the soil and promoted Cr(III) oxidation to mobile Cr(VI), respectively. However, the elevated pH and introduction of NaClO in the soil, which are necessary for improving the removal efficiency of soil Cr, resulted in a significantly adverse impact on the functional diversity of soil microbial community. It suggests that to assess the negative impact of extreme conditions for enhancing the extraction efficiencies of Cr on the soil properties and function is necessary

Genome Surfing As Driver of Microbial Genomic Diversity.

Science.gov (United States)

Choudoir, Mallory J; Panke-Buisse, Kevin; Andam, Cheryl P; Buckley, Daniel H

2017-08-01

Historical changes in population size, such as those caused by demographic range expansions, can produce nonadaptive changes in genomic diversity through mechanisms such as gene surfing. We propose that demographic range expansion of a microbial population capable of horizontal gene exchange can result in genome surfing, a mechanism that can cause widespread increase in the pan-genome frequency of genes acquired by horizontal gene exchange. We explain that patterns of genetic diversity within Streptomyces are consistent with genome surfing, and we describe several predictions for testing this hypothesis both in Streptomyces and in other microorganisms. Copyright © 2017 Elsevier Ltd. All rights reserved.

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.

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.

Assessment of the impact of textile effluents on microbial diversity in Tirupur district, Tamil Nadu

Science.gov (United States)

Prabha, Shashi; Gogoi, Anindita; Mazumder, Payal; Ramanathan, AL.; Kumar, Manish

2017-09-01

The expedited advent of urbanization and industrialization for economic growth has adversely affected the biological diversity, which is one of the major concerns of the developing countries. Microbes play a crucial role in decontaminating polluted sites and degrades pollution load of textile effluent. The present study was based on identification of microbial diversity along the Noyaal river of Tirupur area. River water samples from industrial and non-industrial sites and effluent samples of before and after treatment were tested and it was found that microbial diversity was higher in the river water at the industrial site (Kasipalayam) as compared to the non-industrial site (Perur). Similarly, the microbial populations were found to be high in the untreated effluent as compared to the treated one by conventional treatment systems. Similar trends were observed for MBR treatment systems as well. Pseudomonas sp ., Achromobacter sp. (bacterial species) and Aspergillus fumigates (fungal species), found exclusively at the industrial site have been reported to possess decolorization potential of dye effluent, thus can be used for treatment of dye effluent. The comparison of different microbial communities from different dye wastewater sources and textile effluents was done, which showed that the microbes degrade dyestuffs, reduce toxicity of wastewaters, etc. From the study, it can be concluded that the microbial community helps to check on the pollutants and minimize their affect. Therefore, there is a need to understand the systematic variation in microbial diversity with the accumulation of pollution load through monitoring.

Microbial diversity of septic tank effluent and a soil biomat.

Science.gov (United States)

Tomaras, Jill; Sahl, Jason W; Siegrist, Robert L; Spear, John R

2009-05-01

Microbial diversity of septic tank effluent (STE) and the biomat that is formed as a result of STE infiltration on soil were characterized by 16S rRNA gene sequence analysis. Results indicate that microbial communities are different within control soil, STE, and the biomat and that microbes found in STE are not found in the biomat. The development of a stable soil biomat appears to provide the best on-site water treatment or protection for subsequent groundwater interactions of STE.

Microbial diversity of a high salinity oil field

International Nuclear Information System (INIS)

Neria, I.; Gales, G.; Alazard, D.; Ollivier, B.; Borgomano, J.; Joulian, C.

2009-01-01

This work is a preliminary study to investigate the microbial diversity of an onshore oil field. It aim to compare results obtained from molecular methods, physicochemical analyses and cultivation. A core of 1150 m depth sediments ( in situ T=45 degree centigrade) was collected and immediately frozen with liquid nitrogen prior to further investigation. Macroscopic and Scanning Electron Microscopy analyses were performed. (Author)

Plant diversity predicts beta but not alpha diversity of soil microbes across grasslands worldwide

Science.gov (United States)

Prober, Suzanne M.; Leff, Jonathan W.; Bates, Scott T.; Borer, Elizabeth T.; Firn, Jennifer; Harpole, W. Stanley; Lind, Eric M.; Seabloom, Eric W.; Adler, Peter B.; Bakker, Jonathan D.; Cleland, Elsa E.; DeCrappeo, Nicole; DeLorenze, Elizabeth; Hagenah, Nicole; Hautier, Yann; Hofmockel, Kirsten S.; Kirkman, Kevin P.; Knops, Johannes M. H.; La Pierre, Kimberly J.; MacDougall, Andrew S.; McCulley, Rebecca L.; Mitchell, Charles E.; Risch, Anita C.; Schuetz, Martin; Stevens, Carly J.; Williams, Ryan J.; Fierer, Noah

2015-01-01

Aboveground–belowground interactions exert critical controls on the composition and function of terrestrial ecosystems, yet the fundamental relationships between plant diversity and soil microbial diversity remain elusive. Theory predicts predominantly positive associations but tests within single sites have shown variable relationships, and associations between plant and microbial diversity across broad spatial scales remain largely unexplored. We compared the diversity of plant, bacterial, archaeal and fungal communities in one hundred and forty-five 1 m2 plots across 25 temperate grassland sites from four continents. Across sites, the plant alpha diversity patterns were poorly related to those observed for any soil microbial group. However, plant beta diversity (compositional dissimilarity between sites) was significantly correlated with the beta diversity of bacterial and fungal communities, even after controlling for environmental factors. Thus, across a global range of temperate grasslands, plant diversity can predict patterns in the composition of soil microbial communities, but not patterns in alpha diversity.

Evaluating the use of diversity indices to distinguish between microbial communities with different traits.

Science.gov (United States)

Feranchuk, Sergey; Belkova, Natalia; Potapova, Ulyana; Kuzmin, Dmitry; Belikov, Sergei

2018-05-23

Several measures of biodiversity are commonly used to describe microbial communities, analyzed using 16S gene sequencing. A wide range of available experiments on 16S gene sequencing allows us to present a framework for a comparison of various diversity indices. The criterion for the comparison is the statistical significance of the difference in index values for microbial communities with different traits, within the same experiment. The results of the evaluation indicate that Shannon diversity is the most effective measure among the commonly used diversity indices. The results also indicate that, within the present framework, the Gini coefficient as a diversity index is comparable to Shannon diversity, despite the fact that the Gini coefficient, as a diversity estimator, is far less popular in microbiology than several other measures. Copyright © 2018 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Illumina-based analysis the microbial diversity associated with Thalassia hemprichii in Xincun Bay, South China Sea.

Science.gov (United States)

Jiang, Yu-Feng; Ling, Juan; Dong, Jun-De; Chen, Biao; Zhang, Yan-Ying; Zhang, Yuan-Zhou; Wang, You-Shao

2015-10-01

In order to increase our understanding of the microbial diversity associated with seagrass Thalassia hemprichii in Xincun Bay, South China Sea, 16S rRNA gene was identified by highthrough sequencing method. Bacteria associated with seagrass T. hemprichii belonged to 37 phyla, 99 classes. The diversity of bacteria associated with seagrass was similar among the geographically linked coastal locations of Xincun Bay. Proteobacteria was the dominant bacteria and the α-proteobacteria had adapted to the seagrass ecological niche. As well, α-proteobacteria and Pseudomonadales were associated microflora in seagrass meadows, but the interaction between the bacteria and plant is needed to further research. Burkholderiales and Verrucomicrobiae indicated the influence of the bay from anthropogenic activities. Further, Cyanobacteria could imply the difference of the nutrient conditions in the sites. γ-proteobacteria, Desulfobacterales and Pirellulales played a role in the cycle of sulfur, organic mineralization and meadow ecosystem, respectively. In addition, the less abundance bacteria species have key functions in the seagrass meadows, but there is lack knowledge of the interaction of the seagrass and less abundance bacteria species. Microbial communities can response to surroundings and play key functions in the biochemical cycle.

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.

Magnetic Separation for the Direct Observation of Mineral-Associated Microbial Diversity

Science.gov (United States)

Harrison, B. K.; Orphan, V.

2006-12-01

Previous studies have demonstrated that microorganisms may selectively colonize mineral surfaces in diverse environments. Mineral substrates may serve as an important source of limiting nutrients or provide electron acceptors and donors for dissimilatory reactions. This work presents a new method for characterizing the microbial diversity associated with specific components in environmental samples. Minerals are concentrated from the bulk sample according to magnetic susceptibility, resulting in compositionally distinct partitions. The microbial communities associated with these partitions are subsequently characterized using molecular techniques. Initial testing of samples from active and dormant hydrothermal chimney structures from the Lau and Fiji Basins show that mineral components may be concentrated from bulk samples without concealing pre-existing patterns of selective colonization. 16S gene surveys from environmental clone libraries reveal distinct colonization patterns for thermophilic archaea and bacteria between sulfide mineral partitions. This method offers a unique tool discerning the role of mineral composition in surface-associated diversity.

GeoChip-based analysis of the microbial community functional structures in simultaneous desulfurization and denitrification process.

Science.gov (United States)

Yu, Hao; Chen, Chuan; Ma, Jincai; Liu, Wenzong; Zhou, Jizhong; Lee, Duu-Jong; Ren, Nanqi; Wang, Aijie

2014-07-01

The elemental sulfur (S°) recovery was evaluated in the presence of nitrate in two development models of simultaneous desulfurization and denitrification (SDD) process. At the loading rates of 0.9 kg S/(m³·day) for sulfide and 0.4 kg N/(m³·day) for nitrate, S° conversion rate was 91.1% in denitrifying sulfide removal (DSR) model which was higher than in integrated simultaneous desulfurization and denitrification (ISDD) model (25.6%). A comprehensive analysis of functional diversity, structure and metabolic potential of microbial communities was examined in two models by using functional gene array (GeoChip 2.0). GeoChip data indicated that diversity indices, community structure, and abundance of functional genes were distinct between two models. Diversity indices (Simpson's diversity index (1/D) and Shannon-Weaver index (H')) of all detected genes showed that with elevated influent loading rate, the functional diversity decreased in ISDD model but increased in DSR model. In contrast to ISDD model, the overall abundance of dsr genes was lower in DSR model, while some functional genes targeting from nitrate-reducing sulfide-oxidizing bacteria (NR-SOB), such as Thiobacillus denitrificans, Sulfurimonas denitrificans, and Paracoccus pantotrophus were more abundant in DSR model which were highly associated with the change of S(0) conversion rate obtained in two models. The results obtained in this study provide additional insights into the microbial metabolic mechanisms involved in ISDD and DSR models, which in turn will improve the overall performance of SDD process. Copyright © 2014. Published by Elsevier B.V.

Applications of the rep-PCR DNA fingerprinting technique to study microbial diversity, ecology and evolution.

Science.gov (United States)

Ishii, Satoshi; Sadowsky, Michael J

2009-04-01

A large number of repetitive DNA sequences are found in multiple sites in the genomes of numerous bacteria, archaea and eukarya. While the functions of many of these repetitive sequence elements are unknown, they have proven to be useful as the basis of several powerful tools for use in molecular diagnostics, medical microbiology, epidemiological analyses and environmental microbiology. The repetitive sequence-based PCR or rep-PCR DNA fingerprint technique uses primers targeting several of these repetitive elements and PCR to generate unique DNA profiles or 'fingerprints' of individual microbial strains. Although this technique has been extensively used to examine diversity among variety of prokaryotic microorganisms, rep-PCR DNA fingerprinting can also be applied to microbial ecology and microbial evolution studies since it has the power to distinguish microbes at the strain or isolate level. Recent advancement in rep-PCR methodology has resulted in increased accuracy, reproducibility and throughput. In this minireview, we summarize recent improvements in rep-PCR DNA fingerprinting methodology, and discuss its applications to address fundamentally important questions in microbial ecology and evolution.

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.

Functional assays and metagenomic analyses reveals differences between the microbial communities inhabiting the soil horizons of a Norway spruce plantation.

Directory of Open Access Journals (Sweden)

Stéphane Uroz

Full Text Available In temperate ecosystems, acidic forest soils are among the most nutrient-poor terrestrial environments. In this context, the long-term differentiation of the forest soils into horizons may impact the assembly and the functions of the soil microbial communities. To gain a more comprehensive understanding of the ecology and functional potentials of these microbial communities, a suite of analyses including comparative metagenomics was applied on independent soil samples from a spruce plantation (Breuil-Chenue, France. The objectives were to assess whether the decreasing nutrient bioavailability and pH variations that naturally occurs between the organic and mineral horizons affects the soil microbial functional biodiversity. The 14 Gbp of pyrosequencing and Illumina sequences generated in this study revealed complex microbial communities dominated by bacteria. Detailed analyses showed that the organic soil horizon was significantly enriched in sequences related to Bacteria, Chordata, Arthropoda and Ascomycota. On the contrary the mineral horizon was significantly enriched in sequences related to Archaea. Our analyses also highlighted that the microbial communities inhabiting the two soil horizons differed significantly in their functional potentials according to functional assays and MG-RAST analyses, suggesting a functional specialisation of these microbial communities. Consistent with this specialisation, our shotgun metagenomic approach revealed a significant increase in the relative abundance of sequences related glycoside hydrolases in the organic horizon compared to the mineral horizon that was significantly enriched in glycoside transferases. This functional stratification according to the soil horizon was also confirmed by a significant correlation between the functional assays performed in this study and the functional metagenomic analyses. Together, our results suggest that the soil stratification and particularly the soil resource

Investigations into the metabolic diversity of microorganisms as part of microbial diversity

Energy Technology Data Exchange (ETDEWEB)

Leadbetter, Jared [California Inst. of Technology (CalTech), Pasadena, CA (United States)

2016-07-25

DOE funds supported a key portion of the MBL Microbial Diversity (Woods Hole) program across 6 complete summers. The initial 4 years of the funded period were overseen by two co-Directors, Daniel Buckley (Cornell) and Steve Zinder (Cornell), who then completed their term. The final 2 summers were overseen by 2 new co-Directors, Jared R. Leadbetter (Caltech) and Dianne Newman (Caltech). The 6 funded summer iterations of the course included the incorporation of new themes such as single cell approaches applied to natural microbial communities (cell separation and sorting, genome amplification from single cells, and the use of Nano-SIMS to examine assimilation of carbon and nitrogen from isotopically labeled substrates into single cells), genetics and genomics on bacteria freshly isolated during the course of the programs, quantitative systems biology, and modern quantitative light microscopy.

In Silico Gene-Level Evolution Explains Microbial Population Diversity through Differential Gene Mobility

NARCIS (Netherlands)

van Dijk, Bram; Hogeweg, P.

2016-01-01

Microbial communities can show astonishing ecological and phylogenetic diversity. What is the role of pervasive horizontal gene transfer (HGT) in shaping this diversity in the presence of clonally expanding "killer strains"? Does HGT of antibiotic production and resistance genes erase phylogenetic

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.

Diversity and stability of coral endolithic microbial communities at a naturally high pCO2 reef.

Science.gov (United States)

Marcelino, Vanessa Rossetto; Morrow, Kathleen M; van Oppen, Madeleine J H; Bourne, David G; Verbruggen, Heroen

2017-10-01

The health and functioning of reef-building corals is dependent on a balanced association with prokaryotic and eukaryotic microbes. The coral skeleton harbours numerous endolithic microbes, but their diversity, ecological roles and responses to environmental stress, including ocean acidification (OA), are not well characterized. This study tests whether pH affects the diversity and structure of prokaryotic and eukaryotic algal communities associated with skeletons of Porites spp. using targeted amplicon (16S rRNA gene, UPA and tufA) sequencing. We found that the composition of endolithic communities in the massive coral Porites spp. inhabiting a naturally high pCO 2 reef (avg. pCO 2 811 μatm) is not significantly different from corals inhabiting reference sites (avg. pCO 2 357 μatm), suggesting that these microbiomes are less disturbed by OA than previously thought. Possible explanations may be that the endolithic microhabitat is highly homeostatic or that the endolithic micro-organisms are well adapted to a wide pH range. Some of the microbial taxa identified include nitrogen-fixing bacteria (Rhizobiales and cyanobacteria), algicidal bacteria in the phylum Bacteroidetes, symbiotic bacteria in the family Endozoicomoniaceae, and endolithic green algae, considered the major microbial agent of reef bioerosion. Additionally, we test whether host species has an effect on the endolithic community structure. We show that the endolithic community of massive Porites spp. is substantially different and more diverse than that found in skeletons of the branching species Seriatopora hystrix and Pocillopora damicornis. This study reveals highly diverse and structured microbial communities in Porites spp. skeletons that are possibly resilient to OA. © 2017 John Wiley & Sons Ltd.

Response of Functional Structure of Soil Microbial Community to Multi-level Nitrogen Additions on the Central Tibetan Plateau

Science.gov (United States)

Zhang, G.; Yuan, Y.

2015-12-01

The use of fossil fuels and fertilizers has increased the amount of biologically reactive nitrogen in the atmosphere over the past century. Tibet is the one of the most threatened regions by nitrogen deposition, thus understanding how its microbial communities function maybe of high importance to predicting microbial responses to nitrogen deposition. Here we describe a short-time nitrogen addition conducted in an alpine steppe ecosystem to investigate the response of functional structure of soil microbial community to multi-level nitrogen addition. Using a GeoChip 4.0, we showed that functional diversities and richness of functional genes were unchanged at low level of nitrogen fertilizer inputs (=40 kg N ha-1 yr-1). Detrended correspondence analysis indicated that the functional structure of microbial communities was markedly different across the nitrogen gradients. Most C degradation genes whose abundances significantly increased under elevated N fertilizer were those involved in the degradation of relatively labile C (starch, hemicellulose, cellulose), whereas the abundance of certain genes involved in the degradation of recalcitrant C (i.e. lignin) was largely decreased (such as manganese peroxidase, mnp). The results suggest that the elevated N fertilization rates might significantly accelerate the labile C degradation, but might not spur recalcitrant C degradation. The combined effect of gdh and ureC genes involved in N cycling appeared to shift the balance between ammonia and organic N toward organic N ammonification and hence increased the N mineralization potential. Moreover, Urease directly involved in urea mineralization significantly increased. Lastly, Canonical correspondence analysis showed that soil (TOC+NH4++NO3-+NO2-+pH) and plant (Aboveground plant productivity + Shannon Diversity) variables could explain 38.9% of the variation of soil microbial community composition. On the basis of above observations, we predict that increasing of nitrogen

Tree species diversity promotes aboveground carbon storage through functional diversity and functional dominance.

Science.gov (United States)

Mensah, Sylvanus; Veldtman, Ruan; Assogbadjo, Achille E; Glèlè Kakaï, Romain; Seifert, Thomas

2016-10-01

The relationship between biodiversity and ecosystem function has increasingly been debated as the cornerstone of the processes behind ecosystem services delivery. Experimental and natural field-based studies have come up with nonconsistent patterns of biodiversity-ecosystem function, supporting either niche complementarity or selection effects hypothesis. Here, we used aboveground carbon (AGC) storage as proxy for ecosystem function in a South African mistbelt forest, and analyzed its relationship with species diversity, through functional diversity and functional dominance. We hypothesized that (1) diversity influences AGC through functional diversity and functional dominance effects; and (2) effects of diversity on AGC would be greater for functional dominance than for functional diversity. Community weight mean (CWM) of functional traits (wood density, specific leaf area, and maximum plant height) were calculated to assess functional dominance (selection effects). As for functional diversity (complementarity effects), multitrait functional diversity indices were computed. The first hypothesis was tested using structural equation modeling. For the second hypothesis, effects of environmental variables such as slope and altitude were tested first, and separate linear mixed-effects models were fitted afterward for functional diversity, functional dominance, and both. Results showed that AGC varied significantly along the slope gradient, with lower values at steeper sites. Species diversity (richness) had positive relationship with AGC, even when slope effects were considered. As predicted, diversity effects on AGC were mediated through functional diversity and functional dominance, suggesting that both the niche complementarity and the selection effects are not exclusively affecting carbon storage. However, the effects were greater for functional diversity than for functional dominance. Furthermore, functional dominance effects were strongly transmitted by CWM of

Support vector regression model of wastewater bioreactor performance using microbial community diversity indices: effect of stress and bioaugmentation.

Science.gov (United States)

Seshan, Hari; Goyal, Manish K; Falk, Michael W; Wuertz, Stefan

2014-04-15

The relationship between microbial community structure and function has been examined in detail in natural and engineered environments, but little work has been done on using microbial community information to predict function. We processed microbial community and operational data from controlled experiments with bench-scale bioreactor systems to predict reactor process performance. Four membrane-operated sequencing batch reactors treating synthetic wastewater were operated in two experiments to test the effects of (i) the toxic compound 3-chloroaniline (3-CA) and (ii) bioaugmentation targeting 3-CA degradation, on the sludge microbial community in the reactors. In the first experiment, two reactors were treated with 3-CA and two reactors were operated as controls without 3-CA input. In the second experiment, all four reactors were additionally bioaugmented with a Pseudomonas putida strain carrying a plasmid with a portion of the pathway for 3-CA degradation. Molecular data were generated from terminal restriction fragment length polymorphism (T-RFLP) analysis targeting the 16S rRNA and amoA genes from the sludge community. The electropherograms resulting from these T-RFs were used to calculate diversity indices - community richness, dynamics and evenness - for the domain Bacteria as well as for ammonia-oxidizing bacteria in each reactor over time. These diversity indices were then used to train and test a support vector regression (SVR) model to predict reactor performance based on input microbial community indices and operational data. Considering the diversity indices over time and across replicate reactors as discrete values, it was found that, although bioaugmentation with a bacterial strain harboring a subset of genes involved in the degradation of 3-CA did not bring about 3-CA degradation, it significantly affected the community as measured through all three diversity indices in both the general bacterial community and the ammonia-oxidizer community (�

Molecular Technique to Understand Deep Microbial Diversity

Science.gov (United States)

Vaishampayan, Parag A.; Venkateswaran, Kasthuri J.

2012-01-01

Current sequencing-based and DNA microarray techniques to study microbial diversity are based on an initial PCR (polymerase chain reaction) amplification step. However, a number of factors are known to bias PCR amplification and jeopardize the true representation of bacterial diversity. PCR amplification of the minor template appears to be suppressed by the exponential amplification of the more abundant template. It is widely acknowledged among environmental molecular microbiologists that genetic biosignatures identified from an environment only represent the most dominant populations. The technological bottleneck has overlooked the presence of the less abundant minority population, and underestimated their role in the ecosystem maintenance. To generate PCR amplicons for subsequent diversity analysis, bacterial l6S rRNA genes are amplified by PCR using universal primers. Two distinct PCR regimes are employed in parallel: one using normal and the other using biotinlabeled universal primers. PCR products obtained with biotin-labeled primers are mixed with streptavidin-labeled magnetic beads and selectively captured in the presence of a magnetic field. Less-abundant DNA templates that fail to amplify in this first round of PCR amplification are subjected to a second round of PCR using normal universal primers. These PCR products are then subjected to downstream diversity analyses such as conventional cloning and sequencing. A second round of PCR amplified the minority population and completed the deep diversity picture of the environmental sample.

Salinity shapes microbial diversity and community structure in surface sediments of the Qinghai-Tibetan Lakes.

Science.gov (United States)

Yang, Jian; Ma, Li'an; Jiang, Hongchen; Wu, Geng; Dong, Hailiang

2016-04-26

Investigating microbial response to environmental variables is of great importance for understanding of microbial acclimatization and evolution in natural environments. However, little is known about how microbial communities responded to environmental factors (e.g. salinity, geographic distance) in lake surface sediments of the Qinghai-Tibetan Plateau (QTP). In this study, microbial diversity and community structure in the surface sediments of nine lakes on the QTP were investigated by using the Illumina Miseq sequencing technique and the resulting microbial data were statistically analyzed in combination with environmental variables. The results showed total microbial community of the studied lakes was significantly correlated (r = 0.631, P diversity and community structure in the studied samples. In addition, the abundant and rare taxa (OTUs with relative abundance higher than 1% and lower than 0.01% within one sample, respectively) were significantly (P < 0.05) correlated (r = 0.427 and 0.783, respectively) with salinity, suggesting rare taxa might be more sensitive to salinity than their abundant counterparts, thus cautions should be taken in future when evaluating microbial response (abundant vs. rare sub-communities) to environmental conditions.

Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea

KAUST Repository

Lee, Onon

2010-11-18

Marine sponges are associated with a remarkable array of microorganisms. Using a tag pyrosequencing technology, this study was the first to investigate in depth the microbial communities associated with three Red Sea sponges, Hyrtios erectus, Stylissa carteri and Xestospongia testudinaria. We revealed highly diverse sponge-associated bacterial communities with up to 1000 microbial operational taxonomic units (OTUs) and richness estimates of up to 2000 species. Altogether, 26 bacterial phyla were detected from the Red Sea sponges, 11 of which were absent from the surrounding sea water and 4 were recorded in sponges for the first time. Up to 100 OTUs with richness estimates of up to 300 archaeal species were revealed from a single sponge species. This is by far the highest archaeal diversity ever recorded for sponges. A non-negligible proportion of unclassified reads was observed in sponges. Our results demonstrated that the sponge-associated microbial communities remained highly consistent in the same sponge species from different locations, although they varied at different degrees among different sponge species. A significant proportion of the tag sequences from the sponges could be assigned to one of the sponge-specific clusters previously defined. In addition, the sponge-associated microbial communities were consistently divergent from those present in the surrounding sea water. Our results suggest that the Red Sea sponges possess highly sponge-specific or even sponge-species-specific microbial communities that are resistant to environmental disturbance, and much of their microbial diversity remains to be explored. © 2011 International Society for Microbial Ecology All rights reserved.

Microbial Diversity of Septic Tank Effluent and a Soil Biomat▿ †

Science.gov (United States)

Tomaras, Jill; Sahl, Jason W.; Siegrist, Robert L.; Spear, John R.

2009-01-01

Microbial diversity of septic tank effluent (STE) and the biomat that is formed as a result of STE infiltration on soil were characterized by 16S rRNA gene sequence analysis. Results indicate that microbial communities are different within control soil, STE, and the biomat and that microbes found in STE are not found in the biomat. The development of a stable soil biomat appears to provide the best on-site water treatment or protection for subsequent groundwater interactions of STE. PMID:19304840

Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input.

Science.gov (United States)

Armstrong, Alacia; Valverde, Angel; Ramond, Jean-Baptiste; Makhalanyane, Thulani P; Jansson, Janet K; Hopkins, David W; Aspray, Thomas J; Seely, Mary; Trindade, Marla I; Cowan, Don A

2016-09-29

The temporal dynamics of desert soil microbial communities are poorly understood. Given the implications for ecosystem functioning under a global change scenario, a better understanding of desert microbial community stability is crucial. Here, we sampled soils in the central Namib Desert on sixteen different occasions over a one-year period. Using Illumina-based amplicon sequencing of the 16S rRNA gene, we found that α-diversity (richness) was more variable at a given sampling date (spatial variability) than over the course of one year (temporal variability). Community composition remained essentially unchanged across the first 10 months, indicating that spatial sampling might be more important than temporal sampling when assessing β-diversity patterns in desert soils. However, a major shift in microbial community composition was found following a single precipitation event. This shift in composition was associated with a rapid increase in CO 2 respiration and productivity, supporting the view that desert soil microbial communities respond rapidly to re-wetting and that this response may be the result of both taxon-specific selection and changes in the availability or accessibility of organic substrates. Recovery to quasi pre-disturbance community composition was achieved within one month after rainfall.

Temporal dynamics of hot desert microbial communities reveal structural and functional responses to water input

Energy Technology Data Exchange (ETDEWEB)

Armstrong, Alacia; Valverde, Angel; Ramond, Jean-Baptiste; Makhalanyane, Thulani P.; Jansson, Janet K.; Hopkins, David W.; Aspray, Thomas J.; Seely, Mary; Trindade, Marla I.; Cowan, Don A.

2016-09-29

The temporal dynamics of desert soil microbial communities are poorly understood. Given the implications for ecosystem functioning under a global change scenario, a better understanding of desert microbial community stability is crucial. Here, we sampled soils in the central Namib Desert on sixteen different occasions over a one-year period. Using Illumina-based amplicon sequencing of the 16S rRNA gene, we found that α-diversity (richness) was more variable at a given sampling date (spatial variability) than over the course of one year (temporal variability). Community composition remained essentially unchanged across the first 10 months, indicating that spatial sampling might be more important than temporal sampling when assessing β-diversity patterns in desert soils. However, a major shift in microbial community composition was found following a single precipitation event. This shift in composition was associated with a rapid increase in CO2 respiration and productivity, supporting the view that desert soil microbial communities respond rapidly to re-wetting and that this response may be the result of both taxon-specific selection and changes in the availability or accessibility of organic substrates. Recovery to quasi pre-disturbance community composition was achieved within one month after rainfall.

MICROBIAL DIVERSITY IN SURFACE SEDIMENTS: A COMPARISON OF TWO ESTUARINE CONTINUUMS

Science.gov (United States)

The microbial diversity in estuarine sediments of the Altamaha and Savannah Rivers in Georgia were compared temporally and spatially using phospholipid fatty acid (PLFA) analysis. Surface sediment samples collected along a salinity gradient were also analyzed for ATP, TOC, and C ...

Effect of Pulp mill sludge on soil characteristics, microbial diversity and vegetal production of Lollium perene

Energy Technology Data Exchange (ETDEWEB)

Gallardo, F.; Cea, M.; Diez, M. C.

2009-07-01

The Chemical properties of the sludge (High organic matter content, pH, buffer capacity, nitrogen and phosphorous level, and low concentration of trace heavy metals and organic pollutants) suggest that this material may represent a valuable resource as soil amendment, improving soil characteristics, microbial diversity and vegetal production of mill sludge addition to volcanic soil (Andisol) on soil characteristics, microbial diversity and vegetal production of Lollium perenne, in field assays. (Author)

Recovery of microbial diversity and activity during bioremediation following chemical oxidation of diesel contaminated soils.

Science.gov (United States)

Sutton, Nora B; Langenhoff, Alette A M; Lasso, Daniel Hidalgo; van der Zaan, Bas; van Gaans, Pauline; Maphosa, Farai; Smidt, Hauke; Grotenhuis, Tim; Rijnaarts, Huub H M

2014-03-01

To improve the coupling of in situ chemical oxidation and in situ bioremediation, a systematic analysis was performed of the effect of chemical oxidation with Fenton's reagent, modified Fenton's reagent, permanganate, or persulfate, on microbial diversity and activity during 8 weeks of incubation in two diesel-contaminated soils (peat and fill). Chemical oxidant and soil type affected the microbial community diversity and biodegradation activity; however, this was only observed following treatment with Fenton's reagent and modified Fenton's reagent, and in the biotic control without oxidation. Differences in the highest overall removal efficiencies of 69 % for peat (biotic control) and 59 % for fill (Fenton's reagent) were partially explained by changes in contaminant soil properties upon oxidation. Molecular analysis of 16S rRNA and alkane monooxygenase (alkB) gene abundances indicated that oxidation with Fenton's reagent and modified Fenton's reagent negatively affected microbial abundance. However, regeneration occurred, and final relative alkB abundances were 1-2 orders of magnitude higher in chemically treated microcosms than in the biotic control. 16S rRNA gene fragment fingerprinting with DGGE and prominent band sequencing illuminated microbial community composition and diversity differences between treatments and identified a variety of phylotypes within Alpha-, Beta-, and Gammaproteobacteria. Understanding microbial community dynamics during coupled chemical oxidation and bioremediation is integral to improved biphasic field application.

Microbial diversity and component variation in Xiaguan Tuo Tea during pile fermentation.

Science.gov (United States)

Li, Haizhou; Li, Min; Yang, Xinrui; Gui, Xin; Chen, Guofeng; Chu, Jiuyun; He, Xingwang; Wang, Weitao; Han, Feng; Li, Ping

2018-01-01

Xiaguan Tuo Tea is largely consumed by the Chinese, but there is little research into the microbial diversity and component changes during the fermentation of this tea. In this study, we first used fluorescence in situ hybridization (FISH), next-generation sequencing (NGS) and chemical analysis methods to determine the microbial abundance and diversity and the chemical composition during fermentation. The FISH results showed that the total number of microorganisms ranges from 2.3×102 to 4.0×108 cells per gram of sample during fermentation and is mainly dominated by fungi. In the early fermentation stages, molds are dominant (0.6×102~2.8×106 cells/g, 0~35 d). However, in the late stages of fermentation, yeasts are dominant (3.6×104~9.6×106 cells/g, 35~56 d). The bacteria have little effect during the fermentation of tea (102~103 cells/g, fermentation (Shannon-Weaver index: 1.195857), and lower diversity was observed on days 6 and 56 of fermentation (Shannon-Weaver index 0.860589 and 1.119106, respectively). During the microbial fermentation, compared to the unfermented tea, the tea polyphenol content decreased by 54%, and the caffeine content increased by 59%. Theanine and free amino acid contents were reduced during fermentation by 81.1 and 92.85%, respectively.

Effects of bamboo charcoal on fouling and microbial diversity in a flat-sheet ceramic membrane bioreactor.

Science.gov (United States)

Zhang, Wenjie; Liu, Xiaoning; Wang, Dunqiu; Jin, Yue

2017-11-01

Membrane fouling is a problem in full-scale membrane bioreactors. In this study, bamboo charcoal (BC) was evaluated for its efficacy in alleviating membrane fouling in flat-sheet membrane bioreactors treating municipal wastewater. The results showed that BC addition markedly improved treatment performance based on COD, NH 4 + -N, total nitrogen, and total phosphorus levels. Adding BC slowed the increase in the trans-membrane pressure rate and resulted in lower levels of soluble microbial products and extracellular polymeric substances detected in the flat-sheet membrane bioreactor. BC has a porous structure, and a large quantity of biomass was detected using scanning electron microscopy. The microbial community analysis results indicated that BC increased the microbial diversity and Aminomonas, Anaerofustis, uncultured Anaerolineaceae, Anaerolinea, and Anaerotruncus were found in higher abundances in the reactor with BC. BC addition is an effective method for reducing membrane fouling, and can be applied to full-scale flat-sheet membrane bioreactors to improve their function. Copyright © 2017 Elsevier Ltd. All rights reserved.

Microbial Species Diversity, Community Dynamics, and Metabolite Kinetics of Water Kefir Fermentation

Science.gov (United States)

Laureys, David

2014-01-01

Water kefir is a sour, alcoholic, and fruity fermented beverage of which the fermentation is started with water kefir grains. These water kefir grains consist of polysaccharide and contain the microorganisms responsible for the water kefir fermentation. In this work, a water kefir fermentation process was followed as a function of time during 192 h to unravel the community dynamics, the species diversity, and the kinetics of substrate consumption and metabolite production. The majority of the water kefir ecosystem was found to be present on the water kefir grains. The most important microbial species present were Lactobacillus casei/paracasei, Lactobacillus harbinensis, Lactobacillus hilgardii, Bifidobacterium psychraerophilum/crudilactis, Saccharomyces cerevisiae, and Dekkera bruxellensis. The microbial species diversities in the water kefir liquor and on the water kefir grains were similar and remained stable during the whole fermentation process. The major substrate, sucrose, was completely converted after 24 h of fermentation, which coincided with the production of the major part of the water kefir grain polysaccharide. The main metabolites of the fermentation were ethanol and lactic acid. Glycerol, acetic acid, and mannitol were produced in low concentrations. The major part of these metabolites was produced during the first 72 h of fermentation, during which the pH decreased from 4.26 to 3.45. The most prevalent volatile aroma compounds were ethyl acetate, isoamyl acetate, ethyl hexanoate, ethyl octanoate, and ethyl decanoate, which might be of significance with respect to the aroma of the end product. PMID:24532061

Microbial species diversity, community dynamics, and metabolite kinetics of water kefir fermentation.

Science.gov (United States)

Laureys, David; De Vuyst, Luc

2014-04-01

Water kefir is a sour, alcoholic, and fruity fermented beverage of which the fermentation is started with water kefir grains. These water kefir grains consist of polysaccharide and contain the microorganisms responsible for the water kefir fermentation. In this work, a water kefir fermentation process was followed as a function of time during 192 h to unravel the community dynamics, the species diversity, and the kinetics of substrate consumption and metabolite production. The majority of the water kefir ecosystem was found to be present on the water kefir grains. The most important microbial species present were Lactobacillus casei/paracasei, Lactobacillus harbinensis, Lactobacillus hilgardii, Bifidobacterium psychraerophilum/crudilactis, Saccharomyces cerevisiae, and Dekkera bruxellensis. The microbial species diversities in the water kefir liquor and on the water kefir grains were similar and remained stable during the whole fermentation process. The major substrate, sucrose, was completely converted after 24 h of fermentation, which coincided with the production of the major part of the water kefir grain polysaccharide. The main metabolites of the fermentation were ethanol and lactic acid. Glycerol, acetic acid, and mannitol were produced in low concentrations. The major part of these metabolites was produced during the first 72 h of fermentation, during which the pH decreased from 4.26 to 3.45. The most prevalent volatile aroma compounds were ethyl acetate, isoamyl acetate, ethyl hexanoate, ethyl octanoate, and ethyl decanoate, which might be of significance with respect to the aroma of the end product.

Exploration of microbial diversity and community structure of Lonar Lake: the only hypersaline meteorite crater lake within basalt rock

Directory of Open Access Journals (Sweden)

Dhiraj ePaul

2016-01-01

Full Text Available Lonar Lake is a hypersaline and hyperalkaline soda lake and the only meteorite impact crater in the world created in the basalt rocks. Although culture-dependent studies have been reported, the comprehensive understanding of microbial community composition and structure of Lonar Lake remain obscure. In the present study, microbial community structure associated with Lonar Lake sediment and water samples was investigated using high throughput sequencing. Microbial diversity analysis revealed the existence of diverse, yet near consistent community composition. The predominance of bacterial phyla Proteobacteria (30% followed by Actinobacteria (24%, Firmicutes (11% and Cyanobacteria (5% was observed. Bacterial phylum Bacteroidetes (1.12%, BD1-5 (0.5%, Nitrospirae (0.41% and Verrucomicrobia (0.28% were detected as relatively minor populations in Lonar Lake ecosystem. Within Proteobacteria, Gammaproteobacteria represented the most abundant population (21-47% among all the sediments and as a minor population in water samples. Bacterial members Proteobacteria and Firmicutes were present significantly higher (p≥0.05 in sediment samples, whereas members of Actinobacteria, Candidate_division_TM7 and Cyanobacteria (p≥0.05 were significantly abundant in water samples. It was noted that compared to other hypersaline soda lakes, Lonar Lake samples formed one distinct cluster, suggesting a different microbial community composition and structure. The present study reports for the first time the different composition of indigenous microbial communities between the sediment and water samples of Lonar Lake. Having better insight of community structure of this Lake ecosystem could be useful in understanding the microbial role in the geochemical cycle for future functional exploration of the unique hypersaline Lonar Lake.

[Influence of PCR cycle number on microbial diversity analysis through next generation sequencing].

Science.gov (United States)

An, Yunhe; Gao, Lijuan; Li, Junbo; Tian, Yanjie; Wang, Jinlong; Zheng, Xuejuan; Wu, Huijuan

2016-08-25

Using of high throughput sequencing technology to study the microbial diversity in complex samples has become one of the hottest issues in the field of microbial diversity research. In this study, the soil and sheep rumen chyme samples were used to extract DNA, respectively. Then the 25 ng total DNA was used to amplify the 16S rRNA V3 region with 20, 25, 30 PCR cycles, and the final sequencing library was constructed by mixing equal amounts of purified PCR products. Finally, the operational taxonomic unit (OUT) amount, rarefaction curve, microbial number and species were compared through data analysis. It was found that at the same amount of DNA template, the proportion of the community composition was not the best with more numbers of PCR cycle, although the species number was much more. In all, when the PCR cycle number is 25, the number of species and proportion of the community composition were the most optimal both in soil or chyme samples.

Microbial Profiling Of Cyanobacteria From VIT Lake

Directory of Open Access Journals (Sweden)

Swati Singh

2015-08-01

Full Text Available The application of molecular biological methods to study the diversity and ecology of micro-organisms in natural environments has been practice in mid-1980. The aim of our research is to access the diversity composition and functioning of complex microbial community found in VIT Lake. Molecular ecology is a new field in which microbes can be recognized and their function can be understood at the DNA or RNA level which is useful for constructing genetically modified microbes by recombinant DNA technology for reputed use in the environment. In this research first we will isolate cyanobacteria in lab using conventional methods like broth culture and spread plate method then we will analyze their morphology using various staining methods and DNA and protein composition using electrophoresis method. The applications of community profiling approaches will advance our understanding of the functional role of microbial diversity in VIT Lake controls on microbial community composition.

Species Diversity and Functional Prediction of Surface Bacterial Communities on Aging Flue-Cured Tobaccos.

Science.gov (United States)

Wang, Fan; Zhao, Hongwei; Xiang, Haiying; Wu, Lijun; Men, Xiao; Qi, Chang; Chen, Guoqiang; Zhang, Haibo; Wang, Yi; Xian, Mo

2018-06-05

Microbes on aging flue-cured tobaccos (ATFs) improve the aroma and other qualities desirable in products. Understanding the relevant organisms would picture microbial community diversity, metabolic potential, and their applications. However, limited efforts have been made on characterizing the microbial quality and functional profiling. Herein, we present our investigation of the bacterial diversity and predicted potential genetic capability of the bacteria from two AFTs using 16S rRNA gene sequences and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) software. The results show that dominant bacteria from AFT surfaces were classified into 48 genera, 36 families, and 7 phyla. In addition, Bacillus spp. was found prevalent on both ATFs. Furthermore, PICRUSt predictions of bacterial community functions revealed many attractive metabolic capacities in the AFT microbiota, including several involved in the biosynthesis of flavors and fragrances and the degradation of harmful compounds, such as nicotine and nitrite. These results provide insights into the importance of AFT bacteria in determining product qualities and indicate specific microbial species with predicted enzymatic capabilities for the production of high-efficiency flavors, the degradation of undesirable compounds, and the provision of nicotine and nitrite tolerance which suggest fruitful areas of investigation into the manipulation of AFT microbiota for AFT and other product improvements.

A metagenomic snapshot of taxonomic and functional diversity in an alpine glacier cryoconite ecosystem

International Nuclear Information System (INIS)

Edwards, Arwyn; Pachebat, Justin A; Swain, Martin; Hegarty, Matt; Rassner, Sara M E; Hodson, Andrew J; Irvine-Fynn, Tristram D L; Sattler, Birgit

2013-01-01

Cryoconite is a microbe–mineral aggregate which darkens the ice surface of glaciers. Microbial process and marker gene PCR-dependent measurements reveal active and diverse cryoconite microbial communities on polar glaciers. Here, we provide the first report of a cryoconite metagenome and culture-independent study of alpine cryoconite microbial diversity. We assembled 1.2 Gbp of metagenomic DNA sequenced using an Illumina HiScanSQ from cryoconite holes across the ablation zone of Rotmoosferner in the Austrian Alps. The metagenome revealed a bacterially-dominated community, with Proteobacteria (62% of bacterial-assigned contigs) and Bacteroidetes (14%) considerably more abundant than Cyanobacteria (2.5%). Streptophyte DNA dominated the eukaryotic metagenome. Functional genes linked to N, Fe, S and P cycling illustrated an acquisitive trend and a nitrogen cycle based upon efficient ammonia recycling. A comparison of 32 metagenome datasets revealed a similarity in functional profiles between the cryoconite and metagenomes characterized from other cold microbe–mineral aggregates. Overall, the metagenomic snapshot reveals the cryoconite ecosystem of this alpine glacier as dependent on scavenging carbon and nutrients from allochthonous sources, in particular mosses transported by wind from ice-marginal habitats, consistent with net heterotrophy indicated by productivity measurements. A transition from singular snapshots of cryoconite metagenomes to comparative analyses is advocated. (letter)

Heavy metal pollution decreases microbial abundance, diversity and activity within particle-size fractions of a paddy soil.

Science.gov (United States)

Chen, Junhui; He, Feng; Zhang, Xuhui; Sun, Xuan; Zheng, Jufeng; Zheng, Jinwei

2014-01-01

Chemical and microbial characterisations of particle-size fractions (PSFs) from a rice paddy soil subjected to long-term heavy metal pollution (P) and nonpolluted (NP) soil were performed to investigate whether the distribution of heavy metals (Cd, Cu, Pb and Zn) regulates microbial community activity, abundance and diversity at the microenvironment scale. The soils were physically fractionated into coarse sand, fine sand, silt and clay fractions. Long-term heavy metal pollution notably decreased soil basal respiration (a measurement of the total activity of the soil microbial community) and microbial biomass carbon (MBC) across the fractions by 3-45% and 21-53%, respectively. The coarse sand fraction was more affected by pollution than the clay fraction and displayed a significantly lower MBC content and respiration and dehydrogenase activity compared with the nonpolluted soils. The abundances and diversities of bacteria were less affected within the PSFs under pollution. However, significant decreases in the abundances and diversities of fungi were noted, which may have strongly contributed to the decrease in MBC. Sequencing of denaturing gradient gel electrophoresis bands revealed that the groups Acidobacteria, Ascomycota and Chytridiomycota were clearly inhibited under pollution. Our findings suggest that long-term heavy metal pollution decreased the microbial biomass, activity and diversity in PSFs, particularly in the large-size fractions. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Seasonal and spatial patterns of microbial diversity along a trophic gradient in the interconnected lakes of the Osterseen Lake District, Bavaria

Science.gov (United States)

Zwirglmaier, Katrin; Keiz, Katharina; Engel, Marion; Geist, Juergen; Raeder, Uta

2015-01-01

The Osterseen Lake District in Bavaria consists of 19 small interconnected lakes that exhibit a pronounced trophic gradient from eutrophic to oligotrophic. It therefore presents a unique model system to address ecological questions regarding niche adaptation and Baas Becking's long standing hypothesis of “everything is everywhere, but the environment selects.” Here, we present the first assessment of the microbial diversity in these lakes. We sampled the lakes in August and December and used 454 pyrosequencing of 16S rRNA amplicons to analyze the microbial diversity. The diversity patterns between lakes and seasons were compared and the bacterial community composition was correlated with key chemical and physical parameters. Distinct patterns of bacterial diversity only emerged at the level of individual OTUs (operational taxonomic units), but not at the level of the major bacterial phyla. This emphasizes the high functional and physiological diversity among bacterial species within a phylum and calls for analysis of biodiversity at the level of OTUs in order to understand fine-scale biogeography. We were able to identify a number of cosmopolitan OTUs as well as specialist OTUs that were restricted to certain lakes or seasons, suggesting adaptation to specific ecological niches. PMID:26579082

Soil microbial community structure in diverse land use systems:A comparative study using Biolog,DGGE,and PLFA analyses

Institute of Scientific and Technical Information of China (English)

XUE Dong; YAO Huai-Ying; GE De-Yong; HUANG Chang-Yong

2008-01-01

Biolog,16S rRNA gene denaturing gradient gel electrophoresis (DGGE),and phospholipid fatty acid (PLFA) analyses were used to assess soil microbial community characteristics in a chronosequence of tea garden systems (8-,50-,and 90year-old tea gardens),an adjacent wasteland,and a 90-year-old forest.Biolog analysis showed that the average well color development (AWCD) of all carbon sources and the functional diversity based on the Shannon index decreased (P＜0.05)in the following order:wasteland＞forest＞tea garden.For the DGGE analysis,the genetic diversity based on the Shannon index was significantly lower in the tea garden soils than in the wasteland.However,compared to the 90-year-old forest,the tea garden soils showed significantly higher genetic diversity.PLFA analysis showed that the ratio of Gram positive bacteria to Gram negative bacteria was significantly higher in the tea garden soils than in the wasteland,and the highest value was found in the 90-year-old forest.Both the fungal PLFA and the ratio of fungi to bacteria were significantly higher in the three tea garden soils than in the wasteland and forest,indicating that fungal PLFA was significantly affected by land-use change.Based on cluster analysis of the soil microbial community structure,all three analytical methods showed that land-use change had a greater effect on soil microbial community structure than tea garden age.

Microbial community composition and functions are resilient to metal pollution along two forest soil gradients.

Science.gov (United States)

Azarbad, Hamed; Niklińska, Maria; Laskowski, Ryszard; van Straalen, Nico M; van Gestel, Cornelis A M; Zhou, Jizhong; He, Zhili; Wen, Chongqing; Röling, Wilfred F M

2015-01-01

Despite the global importance of forests, it is virtually unknown how their soil microbial communities adapt at the phylogenetic and functional level to long-term metal pollution. Studying 12 sites located along two distinct gradients of metal pollution in Southern Poland revealed that functional potential and diversity (assessed using GeoChip 4.2) were highly similar across the gradients despite drastically diverging metal contamination levels. Metal pollution level did, however, significantly impact bacterial community structure (as shown by MiSeq Illumina sequencing of 16S rRNA genes), but not bacterial taxon richness and community composition. Metal pollution caused changes in the relative abundance of specific bacterial taxa, including Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Planctomycetes and Proteobacteria. Also, a group of metal-resistance genes showed significant correlations with metal concentrations in soil. Our study showed that microbial communities are resilient to metal pollution; despite differences in community structure, no clear impact of metal pollution levels on overall functional diversity was observed. While screens of phylogenetic marker genes, such as 16S rRNA genes, provide only limited insight into resilience mechanisms, analysis of specific functional genes, e.g. involved in metal resistance, appears to be a more promising strategy. © FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Microbial diversity and biomarker analysis of modern freshwater microbialites from Laguna Bacalar, Mexico.

Science.gov (United States)

Johnson, D B; Beddows, P A; Flynn, T M; Osburn, M R

2018-05-01

Laguna Bacalar is a sulfate-rich freshwater lake on the Yucatan Peninsula that hosts large microbialites. High sulfate concentrations distinguish Laguna Bacalar from other freshwater microbialite sites such as Pavilion Lake and Alchichica, Mexico, as well as from other aqueous features on the Yucatan Peninsula. While cyanobacterial populations have been described here previously, this study offers a more complete characterization of the microbial populations and corresponding biogeochemical cycling using a three-pronged geobiological approach of microscopy, high-throughput DNA sequencing, and lipid biomarker analyses. We identify and compare diverse microbial communities of Alphaproteobacteria, Deltaproteobacteria, and Gammaproteobacteria that vary with location along a bank-to-bank transect across the lake, within microbialites, and within a neighboring mangrove root agglomeration. In particular, sulfate-reducing bacteria are extremely common and diverse, constituting 7%-19% of phylogenetic diversity within the microbialites, and are hypothesized to significantly influence carbonate precipitation. In contrast, Cyanobacteria account for less than 1% of phylogenetic diversity. The distribution of lipid biomarkers reflects these changes in microbial ecology, providing meaningful biosignatures for the microbes in this system. Polysaturated short-chain fatty acids characteristic of cyanobacteria account for Bacalar microbialites. By contrast, even short-chain and monounsaturated short-chain fatty acids attributable to both Cyanobacteria and many other organisms including types of Alphaproteobacteria and Gammaproteobacteria constitute 43%-69% and 17%-25%, respectively, of total abundance in microbialites. While cyanobacteria are the largest and most visible microbes within these microbialites and dominate the mangrove root agglomeration, it is clear that their smaller, metabolically diverse associates are responsible for significant biogeochemical cycling in this

Soil-Borne Microbial Functional Structure across Different Land Uses

NARCIS (Netherlands)

Kuramae, E.E.; Zhou, J.Z.; Kowalchuk, G.A.; van Veen, J.A..

2014-01-01

Land use change alters the structure and composition of microbial communities. However, the links between environmental factors and microbial functions are not well understood. Here we interrogated the functional structure of soil microbial communities across different land uses. In a multivariate

Soil-borne microbial functional structure across different land uses

NARCIS (Netherlands)

Kuramae, Eiko E; Zhou, Jizhong Z; Kowalchuk, George A; van Veen, Johannes A

2014-01-01

Land use change alters the structure and composition of microbial communities. However, the links between environmental factors and microbial functions are not well understood. Here we interrogated the functional structure of soil microbial communities across different land uses. In a multivariate

[Study on Microbial Diversity of Peri-implantitis Subgingival by High-throughput Sequencing].

Science.gov (United States)

Li, Zhi-jie; Wang, Shao-guo; Li, Yue-hong; Tu, Dong-xiang; Liu, Shi-yun; Nie, Hong-bing; Li, Zhi-qiang; Zhang, Ju-mei

2015-07-01

To study microbial diversity of peri-implantitis subgingival with high-throughput sequencing, and investigate microbiological etiology of peri-implantitis. Subgingival plaques were sampled from the patients with peri-implantitis (D group) and non-peri-implantitis subjects (N group). The microbiological diversity of the subgingival plaques was detected by sequencing V4 region of 16S rRNA with Illumina Miseq platform. The diversity of the community structure was analyzed using Mothur software. A total of 156 507 gene sequences were detected in nine samples and 4 402 operational taxonomic units (OTUs) were found. Selenomonas, Pseudomonas, and Fusobacterium were dominant bacteria in D group, while Fusobacterium, Veillonella and Streptococcus were dominant bacteria in N group. Differences between peri-implantitis and non-peri-implantitis bacterial communities were observed at all phylogenetic levels by LEfSe, which was also found in PcoA test. The occurrence of peri-implantitis is not only related to periodontitis pathogenic microbe, but also related with the changes of oral microbial community structure. Treponema, Herbaspirillum, Butyricimonas and Phaeobacte may be closely related to the occurrence and development of peri-implantitis.

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.

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)

Distribution and Diversity of Microbial Eukaryotes in Bathypelagic Waters of the South China Sea.

Science.gov (United States)

Xu, Dapeng; Jiao, Nianzhi; Ren, Rui; Warren, Alan

2017-05-01

Little is known about the biodiversity of microbial eukaryotes in the South China Sea, especially in waters at bathyal depths. Here, we employed SSU rDNA gene sequencing to reveal the diversity and community structure across depth and distance gradients in the South China Sea. Vertically, the highest alpha diversity was found at 75-m depth. The communities of microbial eukaryotes were clustered into shallow-, middle-, and deep-water groups according to the depth from which they were collected, indicating a depth-related diversity and distribution pattern. Rhizaria sequences dominated the microeukaryote community and occurred in all samples except those from less than 50-m deep, being most abundant near the sea floor where they contributed ca. 64-97% and 40-74% of the total sequences and OTUs recovered, respectively. A large portion of rhizarian OTUs has neither a nearest named neighbor nor a nearest neighbor in the GenBank database which indicated the presence of new phylotypes in the South China Sea. Given their overwhelming abundance and richness, further phylogenetic analysis of rhizarians were performed and three new genetic clusters were revealed containing sequences retrieved from the deep waters of the South China Sea. Our results shed light on the diversity and community structure of microbial eukaryotes in this not yet fully explored area. © 2016 The Author(s) Journal of Eukaryotic Microbiology © 2016 International Society of Protistologists.

Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH.

Science.gov (United States)

Twing, Katrina I; Brazelton, William J; Kubo, Michael D Y; Hyer, Alex J; Cardace, Dawn; Hoehler, Tori M; McCollom, Tom M; Schrenk, Matthew O

2017-01-01

Serpentinization is a widespread geochemical process associated with aqueous alteration of ultramafic rocks that produces abundant reductants (H 2 and CH 4 ) for life to exploit, but also potentially challenging conditions, including high pH, limited availability of terminal electron acceptors, and low concentrations of inorganic carbon. As a consequence, past studies of serpentinites have reported low cellular abundances and limited microbial diversity. Establishment of the Coast Range Ophiolite Microbial Observatory (California, U.S.A.) allowed a comparison of microbial communities and physicochemical parameters directly within serpentinization-influenced subsurface aquifers. Samples collected from seven wells were subjected to a range of analyses, including solute and gas chemistry, microbial diversity by 16S rRNA gene sequencing, and metabolic potential by shotgun metagenomics, in an attempt to elucidate what factors drive microbial activities in serpentinite habitats. This study describes the first comprehensive interdisciplinary analysis of microbial communities in hyperalkaline groundwater directly accessed by boreholes into serpentinite rocks. Several environmental factors, including pH, methane, and carbon monoxide, were strongly associated with the predominant subsurface microbial communities. A single operational taxonomic unit (OTU) of Betaproteobacteria and a few OTUs of Clostridia were the almost exclusive inhabitants of fluids exhibiting the most serpentinized character. Metagenomes from these extreme samples contained abundant sequences encoding proteins associated with hydrogen metabolism, carbon monoxide oxidation, carbon fixation, and acetogenesis. Metabolic pathways encoded by Clostridia and Betaproteobacteria, in particular, are likely to play important roles in the ecosystems of serpentinizing groundwater. These data provide a basis for further biogeochemical studies of key processes in serpentinite subsurface environments.

Microbial Dark Matter Investigations: How Microbial Studies Transform Biological Knowledge and Empirically Sketch a Logic of Scientific Discovery

Science.gov (United States)

Bernard, Guillaume; Pathmanathan, Jananan S; Lannes, Romain; Lopez, Philippe; Bapteste, Eric

2018-01-01

Abstract Microbes are the oldest and most widespread, phylogenetically and metabolically diverse life forms on Earth. However, they have been discovered only 334 years ago, and their diversity started to become seriously investigated even later. For these reasons, microbial studies that unveil novel microbial lineages and processes affecting or involving microbes deeply (and repeatedly) transform knowledge in biology. Considering the quantitative prevalence of taxonomically and functionally unassigned sequences in environmental genomics data sets, and that of uncultured microbes on the planet, we propose that unraveling the microbial dark matter should be identified as a central priority for biologists. Based on former empirical findings of microbial studies, we sketch a logic of discovery with the potential to further highlight the microbial unknowns. PMID:29420719

Performance assessment and microbial diversity of two pilot scale multi-stage sub-surface flow constructed wetland systems.

Science.gov (United States)

Babatunde, A O; Miranda-CasoLuengo, Raul; Imtiaz, Mehreen; Zhao, Y Q; Meijer, Wim G

2016-08-01

This study assessed the performance and diversity of microbial communities in multi-stage sub-surface flow constructed wetland systems (CWs). Our aim was to assess the impact of configuration on treatment performance and microbial diversity in the systems. Results indicate that at loading rates up to 100gBOD5/(m(2)·day), similar treatment performances can be achieved using either a 3 or 4 stage configuration. In the case of phosphorus (P), the impact of configuration was less obvious and a minimum of 80% P removal can be expected for loadings up to 10gP/(m(2)·day) based on the performance results obtained within the first 16months of operation. Microbial analysis showed an increased bacterial diversity in stage four compared to the first stage. These results indicate that the design and configuration of multi-stage constructed wetland systems may have an impact on the treatment performance and the composition of the microbial community in the systems, and such knowledge can be used to improve their design and performance. Copyright © 2016. Published by Elsevier B.V.

NEMiD: a web-based curated microbial diversity database with geo-based plotting.

Science.gov (United States)

Bhattacharjee, Kaushik; Joshi, Santa Ram

2014-01-01

The majority of the Earth's microbes remain unknown, and that their potential utility cannot be exploited until they are discovered and characterized. They provide wide scope for the development of new strains as well as biotechnological uses. The documentation and bioprospection of microorganisms carry enormous significance considering their relevance to human welfare. This calls for an urgent need to develop a database with emphasis on the microbial diversity of the largest untapped reservoirs in the biosphere. The data annotated in the North-East India Microbial database (NEMiD) were obtained by the isolation and characterization of microbes from different parts of the Eastern Himalayan region. The database was constructed as a relational database management system (RDBMS) for data storage in MySQL in the back-end on a Linux server and implemented in an Apache/PHP environment. This database provides a base for understanding the soil microbial diversity pattern in this megabiodiversity hotspot and indicates the distribution patterns of various organisms along with identification. The NEMiD database is freely available at www.mblabnehu.info/nemid/.

NEMiD: A Web-Based Curated Microbial Diversity Database with Geo-Based Plotting

Science.gov (United States)

Bhattacharjee, Kaushik; Joshi, Santa Ram

2014-01-01

The majority of the Earth's microbes remain unknown, and that their potential utility cannot be exploited until they are discovered and characterized. They provide wide scope for the development of new strains as well as biotechnological uses. The documentation and bioprospection of microorganisms carry enormous significance considering their relevance to human welfare. This calls for an urgent need to develop a database with emphasis on the microbial diversity of the largest untapped reservoirs in the biosphere. The data annotated in the North-East India Microbial database (NEMiD) were obtained by the isolation and characterization of microbes from different parts of the Eastern Himalayan region. The database was constructed as a relational database management system (RDBMS) for data storage in MySQL in the back-end on a Linux server and implemented in an Apache/PHP environment. This database provides a base for understanding the soil microbial diversity pattern in this megabiodiversity hotspot and indicates the distribution patterns of various organisms along with identification. The NEMiD database is freely available at www.mblabnehu.info/nemid/. PMID:24714636

The Link between Microbial Diversity and Nitrogen Cycling in Marine Sediments Is Modulated by Macrofaunal Bioturbation.

Science.gov (United States)

Yazdani Foshtomi, Maryam; Braeckman, Ulrike; Derycke, Sofie; Sapp, Melanie; Van Gansbeke, Dirk; Sabbe, Koen; Willems, Anne; Vincx, Magda; Vanaverbeke, Jan

2015-01-01

The marine benthic nitrogen cycle is affected by both the presence and activity of macrofauna and the diversity of N-cycling microbes. However, integrated research simultaneously investigating macrofauna, microbes and N-cycling is lacking. We investigated spatio-temporal patterns in microbial community composition and diversity, macrofaunal abundance and their sediment reworking activity, and N-cycling in seven subtidal stations in the Southern North Sea. Our results indicated that bacteria (total and β-AOB) showed more spatio-temporal variation than archaea (total and AOA) as sedimentation of organic matter and the subsequent changes in the environment had a stronger impact on their community composition and diversity indices in our study area. However, spatio-temporal patterns of total bacterial and β-AOB communities were different and related to the availability of ammonium for the autotrophic β-AOB. Highest bacterial richness and diversity were observed in June at the timing of the phytoplankton bloom deposition, while richness of β-AOB as well as AOA peaked in September. Total archaeal community showed no temporal variation in diversity indices. Distance based linear models revealed that, independent from the effect of grain size and the quality and quantity of sediment organic matter, nitrification and N-mineralization were affected by respectively the diversity of metabolically active β-AOB and AOA, and the total bacteria, near the sediment-water interface. Separate models demonstrated a significant and independent effect of macrofaunal activities on community composition and richness of total bacteria, and diversity indices of metabolically active AOA. Diversity of β-AOB was significantly affected by macrofaunal abundance. Our results support the link between microbial biodiversity and ecosystem functioning in marine sediments, and provided broad correlative support for the hypothesis that this relationship is modulated by macrofaunal activity. We

The Link between Microbial Diversity and Nitrogen Cycling in Marine Sediments Is Modulated by Macrofaunal Bioturbation.

Directory of Open Access Journals (Sweden)

Maryam Yazdani Foshtomi

Full Text Available The marine benthic nitrogen cycle is affected by both the presence and activity of macrofauna and the diversity of N-cycling microbes. However, integrated research simultaneously investigating macrofauna, microbes and N-cycling is lacking. We investigated spatio-temporal patterns in microbial community composition and diversity, macrofaunal abundance and their sediment reworking activity, and N-cycling in seven subtidal stations in the Southern North Sea.Our results indicated that bacteria (total and β-AOB showed more spatio-temporal variation than archaea (total and AOA as sedimentation of organic matter and the subsequent changes in the environment had a stronger impact on their community composition and diversity indices in our study area. However, spatio-temporal patterns of total bacterial and β-AOB communities were different and related to the availability of ammonium for the autotrophic β-AOB. Highest bacterial richness and diversity were observed in June at the timing of the phytoplankton bloom deposition, while richness of β-AOB as well as AOA peaked in September. Total archaeal community showed no temporal variation in diversity indices.Distance based linear models revealed that, independent from the effect of grain size and the quality and quantity of sediment organic matter, nitrification and N-mineralization were affected by respectively the diversity of metabolically active β-AOB and AOA, and the total bacteria, near the sediment-water interface. Separate models demonstrated a significant and independent effect of macrofaunal activities on community composition and richness of total bacteria, and diversity indices of metabolically active AOA. Diversity of β-AOB was significantly affected by macrofaunal abundance. Our results support the link between microbial biodiversity and ecosystem functioning in marine sediments, and provided broad correlative support for the hypothesis that this relationship is modulated by macrofaunal

Metagenomic insights into effects of spent engine oil perturbation on the microbial community composition and function in a tropical agricultural soil.

Science.gov (United States)

Salam, Lateef B; Obayori, Sunday O; Nwaokorie, Francisca O; Suleiman, Aisha; Mustapha, Raheemat

2017-03-01

Analyzing the microbial community structure and functions become imperative for ecological processes. To understand the impact of spent engine oil (SEO) contamination on microbial community structure of an agricultural soil, soil microcosms designated 1S (agricultural soil) and AB1 (agricultural soil polluted with SEO) were set up. Metagenomic DNA extracted from the soil microcosms and sequenced using Miseq Illumina sequencing were analyzed for their taxonomic and functional properties. Taxonomic profiling of the two microcosms by MG-RAST revealed the dominance of Actinobacteria (23.36%) and Proteobacteria (52.46%) phyla in 1S and AB1 with preponderance of Streptomyces (12.83%) and Gemmatimonas (10.20%) in 1S and Geodermatophilus (26.24%), Burkholderia (15.40%), and Pseudomonas (12.72%) in AB1, respectively. Our results showed that soil microbial diversity significantly decreased in AB1. Further assignment of the metagenomic reads to MG-RAST, Cluster of Orthologous Groups (COG) of proteins, Kyoto Encyclopedia of Genes and Genomes (KEGG), GhostKOALA, and NCBI's CDD hits revealed diverse metabolic potentials of the autochthonous microbial community. It also revealed the adaptation of the community to various environmental stressors such as hydrocarbon hydrophobicity, heavy metal toxicity, oxidative stress, nutrient starvation, and C/N/P imbalance. To the best of our knowledge, this is the first study that investigates the effect of SEO perturbation on soil microbial communities through Illumina sequencing. The results indicated that SEO contamination significantly affects soil microbial community structure and functions leading to massive loss of nonhydrocarbon degrading indigenous microbiota and enrichment of hydrocarbonoclastic organisms such as members of Proteobacteria and Actinobacteria.

Microbial biosensors

International Nuclear Information System (INIS)

Le Yu; Chen, Wilfred; Mulchandani, Ashok

2006-01-01

A microbial biosensor is an analytical device that couples microorganisms with a transducer to enable rapid, accurate and sensitive detection of target analytes in fields as diverse as medicine, environmental monitoring, defense, food processing and safety. The earlier microbial biosensors used the respiratory and metabolic functions of the microorganisms to detect a substance that is either a substrate or an inhibitor of these processes. Recently, genetically engineered microorganisms based on fusing of the lux, gfp or lacZ gene reporters to an inducible gene promoter have been widely applied to assay toxicity and bioavailability. This paper reviews the recent trends in the development and application of microbial biosensors. Current advances and prospective future direction in developing microbial biosensor have also been discussed

Diversity and stratification of archaea in a hypersaline microbial mat.

Science.gov (United States)

Robertson, Charles E; Spear, John R; Harris, J Kirk; Pace, Norman R

2009-04-01

The Guerrero Negro (GN) hypersaline microbial mats have become one focus for biogeochemical studies of stratified ecosystems. The GN mats are found beneath several of a series of ponds of increasing salinity that make up a solar saltern fed from Pacific Ocean water pumped from the Laguna Ojo de Liebre near GN, Baja California Sur, Mexico. Molecular surveys of the laminated photosynthetic microbial mat below the fourth pond in the series identified an enormous diversity of bacteria in the mat, but archaea have received little attention. To determine the bulk contribution of archaeal phylotypes to the pond 4 study site, we determined the phylogenetic distribution of archaeal rRNA gene sequences in PCR libraries based on nominally universal primers. The ratios of bacterial/archaeal/eukaryotic rRNA genes, 90%/9%/1%, suggest that the archaeal contribution to the metabolic activities of the mat may be significant. To explore the distribution of archaea in the mat, sequences derived using archaeon-specific PCR primers were surveyed in 10 strata of the 6-cm-thick mat. The diversity of archaea overall was substantial albeit less than the diversity observed previously for bacteria. Archaeal diversity, mainly euryarchaeotes, was highest in the uppermost 2 to 3 mm of the mat and decreased rapidly with depth, where crenarchaeotes dominated. Only 3% of the sequences were specifically related to known organisms including methanogens. While some mat archaeal clades corresponded with known chemical gradients, others did not, which is likely explained by heretofore-unrecognized gradients. Some clades did not segregate by depth in the mat, indicating broad metabolic repertoires, undersampling, or both.

Microbial Diversity and Lipid Abundance in Microbial Mats from a Sulfidic, Saline, Warm Spring in Utah, USA

Science.gov (United States)

Gong, J.; Edwardson, C.; Mackey, T. J.; Dzaugis, M.; Ibarra, Y.; Course 2012, G.; Frantz, C. M.; Osburn, M. R.; Hirst, M.; Williamson, C.; Hanselmann, K.; Caporaso, J.; Sessions, A. L.; Spear, J. R.

2012-12-01

The microbial diversity of Stinking Springs, a sulfidic, saline, warm spring northeast of the Great Salt Lake was investigated. The measured pH, temperature, salinity, and sulfide concentration along the flow path ranged from 6.64-7.77, 40-28° C, 2.9-2.2%, and 250 μM to negligible, respectively. Five sites were selected along the flow path and within each site microbial mats were dissected into depth profiles based on the color and texture of the mat layers. Genomic DNA was extracted from each layer, and the 16S rRNA gene was amplified and sequenced on the Roche 454 Titanium platform. Fatty acids were also extracted from the mat layers and analyzed by liquid chromatography and mass spectrometry. The mats at Stinking Springs were classified into roughly two morphologies with respect to their spatial distribution: loose, sometimes floating mats proximal to the spring source; and thicker, well-laminated mats distal to the spring source. Loosely-laminated mats were found in turbulent stream flow environments, whereas well-laminated mats were common in less turbulent sheet flows. Phototrophs, sulfur oxidizers, sulfate reducers, methanogens, other bacteria and archaea were identified by 16S rRNA gene sequences. Diatoms, identified by microscopy and lipid analysis were found to increase in abundance with distance from the source. Methanogens were generally more abundant in deeper mat laminae. Photoheterotrophs were found in all mat layers. Microbial diversity increased significantly with depth at most sites. In addition, two distinct microbial streamers were identified and characterized at the two fast flowing sites. These two streamer varieties were dominated by either cyanobacteria or flavobacteria. Overall, our genomic and lipid analysis suggest that the physical and chemical environment is more predictive of the community composition than mat morphology. Site Map

Changes in microbial diversity in industrial wastewater evaporation ponds following artificial salination.

Science.gov (United States)

Ben-Dov, Eitan; Shapiro, Orr H; Gruber, Ronen; Brenner, Asher; Kushmaro, Ariel

2008-11-01

The salinity of industrial wastewater evaporation ponds was artificially increased from 3-7% to 12-16% (w/v), in an attempt to reduce the activity of sulfate-reducing bacteria (SRB) and subsequent emission of H2S. To investigate the changes in bacterial diversity in general, and SRB in particular, following this salination, two sets of universal primers targeting the 16S rRNA gene and the functional apsA [adenosine-5'-phosphosulfate (APS) reductase alpha-subunit] gene of SRB were used. Phylogenetic analysis indicated that Proteobacteria was the most dominant phylum both before and after salination (with 52% and 68%, respectively), whereas Firmicutes was the second most dominant phylum before (39%) and after (19%) salination. Sequences belonging to Bacteroidetes, Spirochaetes and Actinobacteria were also found. Several groups of SRB from Proteobacteria and Firmicutes were also found to inhabit this saline environment. Comparison of bacterial diversity before and after salination of the ponds revealed both a shift in community composition and an increase in microbial diversity following salination. The share of SRB in the 16S rRNA gene was reduced following salination, consistent with the reduction of H2S emissions. However, the community composition, as shown by apsA gene analysis, was not markedly affected.

Culture-Dependent and Independent Studies of Microbial Diversity in Highly Copper-Contaminated Chilean Marine Sediments

NARCIS (Netherlands)

Besaury, L.; Marty, F.; Buquet, S.; Mesnage, V.; Muijzer, G.; Quillet, L.

2013-01-01

Cultivation and molecular-based approaches were used to study microbial diversity in two Chilean marine sediments contaminated with high (835 ppm) and very high concentrations of copper (1,533 ppm). The diversity of cultivable bacteria resistant to copper was studied at oxic and anoxic conditions,

The microbial diversity, distribution, and ecology of permafrost in China: a review.

Science.gov (United States)

Hu, Weigang; Zhang, Qi; Tian, Tian; Cheng, Guodong; An, Lizhe; Feng, Huyuan

2015-07-01

Permafrost in China mainly located in high-altitude areas. It represents a unique and suitable ecological niche that can be colonized by abundant microbes. Permafrost microbial community varies across geographically separated locations in China, and some lineages are novel and possible endemic. Besides, Chinese permafrost is a reservoir of functional microbial groups involved in key biogeochemical cycling processes. In future, more work is necessary to determine if these phylogenetic groups detected by DNA-based methods are part of the viable microbial community, and their functional roles and how they potentially respond to climate change. This review summaries recent studies describing microbial biodiversity found in permafrost and associated environments in China, and provides a framework for better understanding the microbial ecology of permafrost.

Microbial Diversity of Browning Peninsula, Eastern Antarctica Revealed Using Molecular and Cultivation Methods.

Science.gov (United States)

Pudasaini, Sarita; Wilson, John; Ji, Mukan; van Dorst, Josie; Snape, Ian; Palmer, Anne S; Burns, Brendan P; Ferrari, Belinda C

2017-01-01

Browning Peninsula is an ice-free polar desert situated in the Windmill Islands, Eastern Antarctica. The entire site is described as a barren landscape, comprised of frost boils with soils dominated by microbial life. In this study, we explored the microbial diversity and edaphic drivers of community structure across this site using traditional cultivation methods, a novel approach the soil substrate membrane system (SSMS), and culture-independent 454-tag pyrosequencing. The measured soil environmental and microphysical factors of chlorine, phosphate, aspect and elevation were found to be significant drivers of the bacterial community, while none of the soil parameters analyzed were significantly correlated to the fungal community. Overall, Browning Peninsula soil harbored a distinctive microbial community in comparison to other Antarctic soils comprised of a unique bacterial diversity and extremely limited fungal diversity. Tag pyrosequencing data revealed the bacterial community to be dominated by Actinobacteria (36%), followed by Chloroflexi (18%), Cyanobacteria (14%), and Proteobacteria (10%). For fungi, Ascomycota (97%) dominated the soil microbiome, followed by Basidiomycota. As expected the diversity recovered from culture-based techniques was lower than that detected using tag sequencing. However, in the SSMS enrichments, that mimic the natural conditions for cultivating oligophilic "k-selected" bacteria, a larger proportion of rare bacterial taxa (15%), such as Blastococcus, Devosia, Herbaspirillum, Propionibacterium and Methylocella and fungal (11%) taxa, such as Nigrospora, Exophiala, Hortaea , and Penidiella were recovered at the genus level. At phylum level, a comparison of OTU's showed that the SSMS shared 21% of Acidobacteria, 11% of Actinobacteria and 10% of Proteobacteria OTU's with soil. For fungi, the shared OTUs was 4% (Basidiomycota) and <0.5% (Ascomycota). This was the first known attempt to culture microfungi using the SSMS which resulted in

Microbial Community Profiles in Wastewaters from Onsite Wastewater Treatment Systems Technology.

Directory of Open Access Journals (Sweden)

Łukasz Jałowiecki

Full Text Available The aim of the study was to determine the potential of community-level physiological profiles (CLPPs methodology as an assay for characterization of the metabolic diversity of wastewater samples and to link the metabolic diversity patterns to efficiency of select onsite biological wastewater facilities. Metabolic fingerprints obtained from the selected samples were used to understand functional diversity implied by the carbon substrate shifts. Three different biological facilities of onsite wastewater treatment were evaluated: fixed bed reactor (technology A, trickling filter/biofilter system (technology B, and aerated filter system (the fluidized bed reactor, technology C. High similarities of the microbial community functional structures were found among the samples from the three onsite wastewater treatment plants (WWTPs, as shown by the diversity indices. Principal components analysis (PCA showed that the diversity and CLPPs of microbial communities depended on the working efficiency of the wastewater treatment technologies. This study provided an overall picture of microbial community functional structures of investigated samples in WWTPs and discerned the linkages between microbial communities and technologies of onsite WWTPs used. The results obtained confirmed that metabolic profiles could be used to monitor treatment processes as valuable biological indicators of onsite wastewater treatment technologies efficiency. This is the first step toward understanding relations of technology types with microbial community patterns in raw and treated wastewaters.

Impact of simulated acid rain on soil microbial community function in Masson pine seedlings

Directory of Open Access Journals (Sweden)

Lin Wang

2014-09-01

Conclusion: The results obtained indicated that the higher acid load decreased the soil microbial activity and no effects on soil microbial diversity assessed by Biolog of potted Masson pine seedlings. Simulated acid rain also changed the metabolic capability of the soil microbial community.

Multitrophic microbial interactions for eco- and agro-biotechnological processes: theory and practice.

Science.gov (United States)

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.

Disturbance Regimes Predictably Alter Diversity in an Ecologically Complex Bacterial System

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Sean M. Gibbons

2016-12-01

Full Text Available Diversity is often associated with the functional stability of ecological communities from microbes to macroorganisms. Understanding how diversity responds to environmental perturbations and the consequences of this relationship for ecosystem function are thus central challenges in microbial ecology. Unimodal diversity-disturbance relationships, in which maximum diversity occurs at intermediate levels of disturbance, have been predicted for ecosystems where life history tradeoffs separate organisms along a disturbance gradient. However, empirical support for such peaked relationships in macrosystems is mixed, and few studies have explored these relationships in microbial systems. Here we use complex microbial microcosm communities to systematically determine diversity-disturbance relationships over a range of disturbance regimes. We observed a reproducible switch between community states, which gave rise to transient diversity maxima when community states were forced to mix. Communities showed reduced compositional stability when diversity was highest. To further explore these dynamics, we formulated a simple model that reveals specific regimes under which diversity maxima are stable. Together, our results show how both unimodal and non-unimodal diversity-disturbance relationships can be observed as a system switches between two distinct microbial community states; this process likely occurs across a wide range of spatially and temporally heterogeneous microbial ecosystems.

Microbial network, phylogenetic diversity and community membership in the active layer across a permafrost thaw gradient.

Science.gov (United States)

Mondav, Rhiannon; McCalley, Carmody K; Hodgkins, Suzanne B; Frolking, Steve; Saleska, Scott R; Rich, Virginia I; Chanton, Jeff P; Crill, Patrick M

2017-08-01

Biogenic production and release of methane (CH 4 ) from thawing permafrost has the potential to be a strong source of radiative forcing. We investigated changes in the active layer microbial community of three sites representative of distinct permafrost thaw stages at a palsa mire in northern Sweden. The palsa site (intact permafrost and low radiative forcing signature) had a phylogenetically clustered community dominated by Acidobacteria and Proteobacteria. The bog (thawing permafrost and low radiative forcing signature) had lower alpha diversity and midrange phylogenetic clustering, characteristic of ecosystem disturbance affecting habitat filtering. Hydrogenotrophic methanogens and Acidobacteria dominated the bog shifting from palsa-like to fen-like at the waterline. The fen (no underlying permafrost, high radiative forcing signature) had the highest alpha, beta and phylogenetic diversity, was dominated by Proteobacteria and Euryarchaeota and was significantly enriched in methanogens. The Mire microbial network was modular with module cores consisting of clusters of Acidobacteria, Euryarchaeota or Xanthomonodales. Loss of underlying permafrost with associated hydrological shifts correlated to changes in microbial composition, alpha, beta and phylogenetic diversity associated with a higher radiative forcing signature. These results support the complex role of microbial interactions in mediating carbon budget changes and climate feedback in response to climate forcing. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Microbial diversity and impact on carbonate geochemistry across a changing geochemical gradient in a karst aquifer.

Science.gov (United States)

Gray, Cassie J; Engel, Annette S

2013-02-01

Although microbes are known to influence karst (carbonate) aquifer ecosystem-level processes, comparatively little information is available regarding the diversity of microbial activities that could influence water quality and geological modification. To assess microbial diversity in the context of aquifer geochemistry, we coupled 16S rRNA Sanger sequencing and 454 tag pyrosequencing to in situ microcosm experiments from wells that cross the transition from fresh to saline and sulfidic water in the Edwards Aquifer of central Texas, one of the largest karst aquifers in the United States. The distribution of microbial groups across the transition zone correlated with dissolved oxygen and sulfide concentration, and significant variations in community composition were explained by local carbonate geochemistry, specifically calcium concentration and alkalinity. The waters were supersaturated with respect to prevalent aquifer minerals, calcite and dolomite, but in situ microcosm experiments containing these minerals revealed significant mass loss from dissolution when colonized by microbes. Despite differences in cell density on the experimental surfaces, carbonate loss was greater from freshwater wells than saline, sulfidic wells. However, as cell density increased, which was correlated to and controlled by local geochemistry, dissolution rates decreased. Surface colonization by metabolically active cells promotes dissolution by creating local disequilibria between bulk aquifer fluids and mineral surfaces, but this also controls rates of karst aquifer modification. These results expand our understanding of microbial diversity in karst aquifers and emphasize the importance of evaluating active microbial processes that could affect carbonate weathering in the subsurface.

Metagenomes reveal microbial structures, functional potentials, and biofouling-related genes in a membrane bioreactor.

Science.gov (United States)

Ma, Jinxing; Wang, Zhiwei; Li, Huan; Park, Hee-Deung; Wu, Zhichao

2016-06-01

Metagenomic sequencing was used to investigate the microbial structures, functional potentials, and biofouling-related genes in a membrane bioreactor (MBR). The results showed that the microbial community in the MBR was highly diverse. Notably, function analysis of the dominant genera indicated that common genes from different phylotypes were identified for important functional potentials with the observation of variation of abundances of genes in a certain taxon (e.g., Dechloromonas). Despite maintaining similar metabolic functional potentials with a parallel full-scale conventional activated sludge (CAS) system due to treating the identical wastewater, the MBR had more abundant nitrification-related bacteria and coding genes of ammonia monooxygenase, which could well explain its excellent ammonia removal in the low-temperature period. Furthermore, according to quantification of the genes involved in exopolysaccharide and extracellular polymeric substance (EPS) protein metabolism, the MBR did not show a much different potential in producing EPS compared to the CAS system, and bacteria from the membrane biofilm had lower abundances of genes associated with EPS biosynthesis and transport compared to the activated sludge in the MBR.

Microbial diversity from chlorophyll maximum, oxygen minimum and bottom zones in the southwestern Atlantic Ocean

Science.gov (United States)

Medina-Silva, Renata; de Oliveira, Rafael R.; Pivel, Maria A. G.; Borges, Luiz G. A.; Simão, Taiz L. L.; Pereira, Leandro M.; Trindade, Fernanda J.; Augustin, Adolpho H.; Valdez, Fernanda P.; Eizirik, Eduardo; Utz, Laura R. P.; Groposo, Claudia; Miller, Dennis J.; Viana, Adriano R.; Ketzer, João M. M.; Giongo, Adriana

2018-02-01

Conspicuous physicochemical vertical stratification in the deep sea is one of the main forces driving microbial diversity in the oceans. Oxygen and sunlight availability are key factors promoting microbial diversity throughout the water column. Ocean currents also play a major role in the physicochemical stratification, carrying oxygen down to deeper zones as well as moving deeper water masses up towards shallower depths. Water samples within a 50-km radius in a pockmark location of the southwestern Atlantic Ocean were collected and the prokaryotic communities from different water depths - chlorophyll maximum, oxygen minimum and deep-sea bottom (down to 1355 m) - were described. At phylum level, Proteobacteria were the most frequent in all water depths, Cyanobacteria were statistically more frequent in chlorophyll maximum zone, while Thaumarchaeota were significantly more abundant in both oxygen minimum and bottom waters. The most frequent microorganism in the chlorophyll maximum and oxygen minimum zones was a Pelagibacteraceae operational taxonomic unit (OTU). At the bottom, the most abundant genus was the archaeon Nitrosopumilus. Beta diversity analysis of the 16S rRNA gene sequencing data uncovered in this study shows high spatial heterogeneity among water zones communities. Our data brings important contribution for the characterisation of oceanic microbial diversity, as it consists of the first description of prokaryotic communities occurring in different oceanic water zones in the southwestern Atlantic Ocean.

Microbial Diversity in KURT Groundwater and Biomineralization Characteristics

International Nuclear Information System (INIS)

Roh, Yul; Rhee, Sung Keun; Oh, Jong Min; Park, Byung Jun

2009-03-01

The Underground Research Tunnel (URT) located in Korea Atomic Energy Research Institute (KAERI), Daejeon, South Korea was recently constructed as an experimental site to study radionuclide transport, biogeochemistry, radionuclide-mineral interactions for the geological disposal of high level nuclear waste. Groundwater sampled from URT was used to examine microbial diversity and to enrich metal reducing bacteria for studying microbe-metal interactions. Genomic analysis indicated that the groundwater contained diverse microorganisms such as metal reducers, metal oxidizers, anaerobic denitrifying bacteria, and bacteria for reductive dechlorination. Metal-reducing bacteria enriched from the groundwater was used to study metal reduction and biomineralization. The metal-reducing bacteria enriched with acetate or lactate as the electron donors showed the bacteria reduced Fe(III)-citrate, Fe(III) oxyhydroxides, Mn(IV) oxide, and Cr(VI) as the electron acceptors. Preliminary study indicated that the enriched bacteria were able to use glucose, lactate, acetate, and hydrogen as electron donors while reducing Fe(III)-citrate or Fe(III) oxyhydroxide as the electron acceptor. The bacteria exhibited diverse mineral precipitation capabilities including the formation of magnetite, siderite, and rhodochrosite. The results indicated that Fe(III)- and metal-reducing communities are present in URT at the KAERI

Effects of above-ground plant species composition and diversity on the diversity of soil-borne microorganisms

NARCIS (Netherlands)

Kowalchuk, G.A.; Buma, D.S; De Boer, W.; Klinkhamer, P.G.L.; Van Veen, J.A.

2002-01-01

A coupling of above-ground plant diversity and below-ground microbial diversity has been implied in studies dedicated to assessing the role of macrophyte diversity on the stability, resilience, and functioning of ecosystems. Indeed, above-ground plant communities have long been assumed to drive

Functional Stability and Community Dynamics during Spring and Autumn Seasons Over 3 Years in Camargue Microbial Mats

Directory of Open Access Journals (Sweden)

Mercedes Berlanga

2017-12-01

Full Text Available Microbial mats are complex biofilms in which the major element cycles are represented at a millimeter scale. In this study, community variability within microbial mats from the Camargue wetlands (Rhone Delta, southern France were analyzed over 3 years during two different seasons (spring and autumn and at different layers of the mat (0–2, 2–4, and 4–6 mm. To assess bacterial diversity in the mats, amplicons of the V1–V2 region of the 16S rRNA gene were sequenced. The community’s functionality was characterized using two approaches: (i inferred functionality through 16S rRNA amplicons genes according to PICRUSt, and (ii a shotgun metagenomic analysis. Based on the reads distinguished, microbial communities were dominated by Bacteria (∼94%, followed by Archaea (∼4% and Eukarya (∼1%. The major phyla of Bacteria were Proteobacteria, Bacteroidetes, Spirochaetes, Actinobacteria, Firmicutes, and Cyanobacteria, which together represented 70–80% of the total population detected. The phylum Euryarchaeota represented ∼80% of the Archaea identified. These results showed that the total bacterial diversity from the Camargue microbial mats was not significantly affected by seasonal changes at the studied location; however, there were differences among layers, especially between the 0–2 mm layer and the other two layers. PICRUSt and shotgun metagenomic analyses revealed similar general biological processes in all samples analyzed, by season and depth, indicating that different layers were functionally stable, although some taxa changed during the spring and autumn seasons over the 3 years. Several gene families and pathways were tracked with the oxic-anoxic gradient of the layers. Genes directly involved in photosynthesis (KO, KEGG Orthology were significantly more abundant in the top layer (0–2 mm than in the lower layers (2–4 and 4–6 mm. In the anoxic layers, the presence of ferredoxins likely reflected the variation of redox

Application of Sequence-based Methods in Human MicrobialEcology

Energy Technology Data Exchange (ETDEWEB)

Weng, Li; Rubin, Edward M.; Bristow, James

2005-08-29

Ecologists studying microbial life in the environment have recognized the enormous complexity of microbial diversity for many years, and the development of a variety of culture-independent methods, many of them coupled with high-throughput DNA sequencing, has allowed this diversity to be explored in ever greater detail. Despite the widespread application of these new techniques to the characterization of uncultivated microbes and microbial communities in the environment, their application to human health and disease has lagged behind. Because DNA based-techniques for defining uncultured microbes allow not only cataloging of microbial diversity, but also insight into microbial functions, investigators are beginning to apply these tools to the microbial communities that abound on and within us, in what has aptly been called the second Human Genome Project. In this review we discuss the sequence-based methods for microbial analysis that are currently available and their application to identify novel human pathogens, improve diagnosis of known infectious diseases, and to advance understanding of our relationship with microbial communities that normally reside in and on the human body.

Microbial diversity of the 180 million-year-old Toarcian argillite from Tournemire, France

International Nuclear Information System (INIS)

Urios, Laurent; Marsal, François; Pellegrini, Delphine; Magot, Michel

2012-01-01

Even though the microbiology of various subsurface environments has been investigated for more than 30 a, the microbial diversity of deep argillaceous media is still poorly known. In the context of radioactive waste disposal in clayey formations, the consequence of microbial activity is of concern regarding e.g. the corrosion of metallic components. The purpose of the present work was to characterise the cultivable microbial diversity of different zones of the Toarcian argillite of Tournemire (France) as a preliminary indication regarding the potential of development of microbes in such subterrestrial environments. Cores were drilled in the Excavation Damaged Zone (EDZ) and in the deeper undisturbed zone of the argillite layer, as well as in a zone intersected by a geological fault. Samples from the wall of the drift were also collected. Microorganisms were cultivated from all samples, but the biodiversity differed depending mainly on the O 2 and moisture content. Aerobic bacteria were identified on the wall, in the EDZ and in the wet faulted area, whereas SO 4 -reducing bacteria were isolated from the wet faulted area only. Anaerobic heterotrophs were cultivated from all zones. One hundred and twelve isolates were identified. Small ribosomal subunit gene sequences showed that bacteria of the undisturbed zone were affiliated to three genera only, whereas the three other sampled zones harbour more diverse microflora, including isolates closely related to taxons characterized from subsurface, deep marine and polar environments.

Biogeographical diversity of leaf-associated microbial communities from salt-secreting Tamarix trees of the Dead Sea region.

Science.gov (United States)

Qvit-Raz, Noga; Finkel, Omri M; Al-Deeb, Taghleb M; Malkawi, Hanan I; Hindiyeh, Muna Y; Jurkevitch, Edouard; Belkin, Shimshon

2012-02-01

The leaves of Tamarix, a salt-secreting desert tree, form an extreme niche that harbors a unique microbial community. In view of the global distribution of this tree, its island-like phyllosphere is highly suitable for studying microbial diversity along geographical gradients. Here we present an analysis of microbial community diversity using leaf surface samples collected at six different sites, on both sides of the Dead Sea, over a period of one year. Biodiversity analysis of denaturing gradient gel electrophoresis (DGGE) patterns of the bacterial 16S rRNA gene revealed a significant degree of bacterial community similarity within trees sampled at the same site, much higher than the similarity between trees from different geographical locations. Statistical analysis indicated that the degree of similarity was negatively correlated with the distance between sampling sites, and that a weak correlation existed between diversity and leaf pH. Copyright © 2011 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Ecological effects of soil properties and metal concentrations on the composition and diversity of microbial communities associated with land use patterns in an electronic waste recycling region.

Science.gov (United States)

Wu, Wencheng; Dong, Changxun; Wu, Jiahui; Liu, Xiaowen; Wu, Yingxin; Chen, Xianbin; Yu, Shixiao

2017-12-01

Soil microbes play vital roles in ecosystem functions, and soil microbial communities may be strongly structured by land use patterns associated with electronic waste (e-waste) recycling activities, which can increase the heavy metal concentration in soils. In this study, a suite of soils from five land use types (paddy field, vegetable field, dry field, forest field, and e-waste recycling site) were collected in Longtang Town, Guangdong Province, South China. Soil physicochemical properties and heavy metal concentrations were measured, and the indigenous microbial assemblages were profiled using 16S rRNA high-throughput sequencing and clone library analyses. The results showed that mercury concentration was positively correlated with both Faith's PD and Chao1 estimates, suggesting that the soil microbial alpha diversity was predominantly regulated by mercury. In addition, redundancy analysis indicated that available phosphorus, soil moisture, and mercury were the three major drivers affecting the microbial assemblages. Overall, the microbial composition was determined primarily by land use patterns, and this study provides a novel insight on the composition and diversity of microbial communities in soils associated with e-waste recycling activities. Copyright © 2017 Elsevier B.V. All rights reserved.

Microbial diversity and metabolite composition of Belgian red-brown acidic ales.

Science.gov (United States)

Snauwaert, Isabel; Roels, Sanne P; Van Nieuwerburg, Filip; Van Landschoot, Anita; De Vuyst, Luc; Vandamme, Peter

2016-03-16

Belgian red-brown acidic ales are sour and alcoholic fermented beers, which are produced by mixed-culture fermentation and blending. The brews are aged in oak barrels for about two years, after which mature beer is blended with young, non-aged beer to obtain the end-products. The present study evaluated the microbial community diversity of Belgian red-brown acidic ales at the end of the maturation phase of three subsequent brews of three different breweries. The microbial diversity was compared with the metabolite composition of the brews at the end of the maturation phase. Therefore, mature brew samples were subjected to 454 pyrosequencing of the 16S rRNA gene (bacteria) and the internal transcribed spacer region (yeasts) and a broad range of metabolites was quantified. The most important microbial species present in the Belgian red-brown acidic ales investigated were Pediococcus damnosus, Dekkera bruxellensis, and Acetobacter pasteurianus. In addition, this culture-independent analysis revealed operational taxonomic units that were assigned to an unclassified fungal community member, Candida, and Lactobacillus. The main metabolites present in the brew samples were L-lactic acid, D-lactic acid, and ethanol, whereas acetic acid was produced in lower quantities. The most prevailing aroma compounds were ethyl acetate, isoamyl acetate, ethyl hexanoate, and ethyl octanoate, which might be of impact on the aroma of the end-products. Copyright © 2016 Elsevier B.V. All rights reserved.

GeoChip-based insights into the microbial functional gene repertoire of marine sponges (high microbial abundance, low microbial abundance) and seawater

KAUST Repository

Bayer, Kristina

2015-01-08

The GeoChip 4.2 gene array was employed to interrogate the microbial functional gene repertoire of sponges and seawater collected from the Red Sea and the Mediterranean. Complementary amplicon sequencing confirmed the microbial community composition characteristic of high microbial abundance (HMA) and low microbial abundance (LMA) sponges. By use of GeoChip, altogether 20 273 probes encoding for 627 functional genes and representing 16 gene categories were identified. Minimum curvilinear embedding analyses revealed a clear separation between the samples. The HMA/LMA dichotomy was stronger than any possible geographic pattern, which is shown here for the first time on the level of functional genes. However, upon inspection of individual genes, very few specific differences were discernible. Differences were related to microbial ammonia oxidation, ammonification, and archaeal autotrophic carbon fixation (higher gene abundance in sponges over seawater) as well as denitrification and radiation-stress-related genes (lower gene abundance in sponges over seawater). Except for few documented specific differences the functional gene repertoire between the different sources appeared largely similar. This study expands previous reports in that functional gene convergence is not only reported between HMA and LMA sponges but also between sponges and seawater.

GeoChip-based insights into the microbial functional gene repertoire of marine sponges (high microbial abundance, low microbial abundance) and seawater

KAUST Repository

Bayer, Kristina; Moitinho-Silva, Lucas; Brü mmer, Franz; Cannistraci, Carlo V.; Ravasi, Timothy; Hentschel, Ute

2015-01-01

The GeoChip 4.2 gene array was employed to interrogate the microbial functional gene repertoire of sponges and seawater collected from the Red Sea and the Mediterranean. Complementary amplicon sequencing confirmed the microbial community composition characteristic of high microbial abundance (HMA) and low microbial abundance (LMA) sponges. By use of GeoChip, altogether 20 273 probes encoding for 627 functional genes and representing 16 gene categories were identified. Minimum curvilinear embedding analyses revealed a clear separation between the samples. The HMA/LMA dichotomy was stronger than any possible geographic pattern, which is shown here for the first time on the level of functional genes. However, upon inspection of individual genes, very few specific differences were discernible. Differences were related to microbial ammonia oxidation, ammonification, and archaeal autotrophic carbon fixation (higher gene abundance in sponges over seawater) as well as denitrification and radiation-stress-related genes (lower gene abundance in sponges over seawater). Except for few documented specific differences the functional gene repertoire between the different sources appeared largely similar. This study expands previous reports in that functional gene convergence is not only reported between HMA and LMA sponges but also between sponges and seawater.

Survey of Microbial Diversity in Flood Areas during Thailand 2011 Flood Crisis Using High-Throughput Tagged Amplicon Pyrosequencing.

Science.gov (United States)

Mhuantong, Wuttichai; Wongwilaiwalin, Sarunyou; Laothanachareon, Thanaporn; Eurwilaichitr, Lily; Tangphatsornruang, Sithichoke; Boonchayaanant, Benjaporn; Limpiyakorn, Tawan; Pattaragulwanit, Kobchai; Punmatharith, Thantip; McEvoy, John; Khan, Eakalak; Rachakornkij, Manaskorn; Champreda, Verawat

2015-01-01

The Thailand flood crisis in 2011 was one of the largest recorded floods in modern history, causing enormous damage to the economy and ecological habitats of the country. In this study, bacterial and fungal diversity in sediments and waters collected from ten flood areas in Bangkok and its suburbs, covering residential and agricultural areas, were analyzed using high-throughput 454 pyrosequencing of 16S rRNA gene and internal transcribed spacer sequences. Analysis of microbial community showed differences in taxa distribution in water and sediment with variations in the diversity of saprophytic microbes and sulfate/nitrate reducers among sampling locations, suggesting differences in microbial activity in the habitats. Overall, Proteobacteria represented a major bacterial group in waters, while this group co-existed with Firmicutes, Bacteroidetes, and Actinobacteria in sediments. Anaeromyxobacter, Steroidobacter, and Geobacter were the dominant bacterial genera in sediments, while Sulfuricurvum, Thiovirga, and Hydrogenophaga predominated in waters. For fungi in sediments, Ascomycota, Glomeromycota, and Basidiomycota, particularly in genera Philipsia, Rozella, and Acaulospora, were most frequently detected. Chytridiomycota and Ascomycota were the major fungal phyla, and Rhizophlyctis and Mortierella were the most frequently detected fungal genera in water. Diversity of sulfate-reducing bacteria, related to odor problems, was further investigated using analysis of the dsrB gene which indicated the presence of sulfate-reducing bacteria of families Desulfobacteraceae, Desulfobulbaceae, Syntrobacteraceae, and Desulfoarculaceae in the flood sediments. The work provides an insight into the diversity and function of microbes related to biological processes in flood areas.

Soil environmental conditions and microbial build-up mediate the effect of plant diversity on soil nitrifying and denitrifying enzyme activities in temperate grasslands.

Directory of Open Access Journals (Sweden)

Xavier Le Roux

Full Text Available Random reductions in plant diversity can affect ecosystem functioning, but it is still unclear which components of plant diversity (species number - namely richness, presence of particular plant functional groups, or particular combinations of these and associated biotic and abiotic drivers explain the observed relationships, particularly for soil processes. We assembled grassland communities including 1 to 16 plant species with a factorial separation of the effects of richness and functional group composition to analyze how plant diversity components influence soil nitrifying and denitrifying enzyme activities (NEA and DEA, respectively, the abundance of nitrifiers (bacterial and archaeal amoA gene number and denitrifiers (nirK, nirS and nosZ gene number, and key soil environmental conditions. Plant diversity effects were largely due to differences in functional group composition between communities of identical richness (number of sown species, though richness also had an effect per se. NEA was positively related to the percentage of legumes in terms of sown species number, the additional effect of richness at any given legume percentage being negative. DEA was higher in plots with legumes, decreased with increasing percentage of grasses, and increased with richness. No correlation was observed between DEA and denitrifier abundance. NEA increased with the abundance of ammonia oxidizing bacteria. The effect of richness on NEA was entirely due to the build-up of nitrifying organisms, while legume effect was partly linked to modified ammonium availability and nitrifier abundance. Richness effect on DEA was entirely due to changes in soil moisture, while the effects of legumes and grasses were partly due to modified nitrate availability, which influenced the specific activity of denitrifiers. These results suggest that plant diversity-induced changes in microbial specific activity are important for facultative activities such as denitrification

Mammalian engineers drive soil microbial communities and ecosystem functions across a disturbance gradient.

Science.gov (United States)

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

The microbial ecology of permafrost

DEFF Research Database (Denmark)

Jansson, Janet; Tas, Neslihan

2014-01-01

Permafrost constitutes a major portion of the terrestrial cryosphere of the Earth and is a unique ecological niche for cold-adapted microorganisms. There is a relatively high microbial diversity in permafrost, although there is some variation in community composition across different permafrost......-gas emissions. This Review describes new data on the microbial ecology of permafrost and provides a platform for understanding microbial life strategies in frozen soil as well as the impact of climate change on permafrost microorganisms and their functional roles....

Electron acceptors for anaerobic oxidation of methane drive microbial community structure and diversity in mud volcanoes.

Science.gov (United States)

Ren, Ge; Ma, Anzhou; Zhang, Yanfen; Deng, Ye; Zheng, Guodong; Zhuang, Xuliang; Zhuang, Guoqiang; Fortin, Danielle

2018-04-06

Mud volcanoes (MVs) emit globally significant quantities of methane into the atmosphere, however, methane cycling in such environments is not yet fully understood, as the roles of microbes and their associated biogeochemical processes have been largely overlooked. Here, we used data from high-throughput sequencing of microbial 16S rRNA gene amplicons from six MVs in the Junggar Basin in northwest China to quantify patterns of diversity and characterize the community structure of archaea and bacteria. We found anaerobic methanotrophs and diverse sulfate- and iron-reducing microbes in all of the samples, and the diversity of both archaeal and bacterial communities was strongly linked to the concentrations of sulfate, iron and nitrate, which could act as electron acceptors in anaerobic oxidation of methane (AOM). The impacts of sulfate/iron/nitrate on AOM in the MVs were verified by microcosm experiments. Further, two representative MVs were selected to explore the microbial interactions based on phylogenetic molecular ecological networks. The sites showed distinct network structures, key species and microbial interactions, with more complex and numerous linkages between methane-cycling microbes and their partners being observed in the iron/sulfate-rich MV. These findings suggest that electron acceptors are important factors driving the structure of microbial communities in these methane-rich environments. © 2018 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Population cycles and species diversity in dynamic Kill-the-Winner model of microbial ecosystems

Science.gov (United States)

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

Correlating Microbial Diversity Patterns with Geochemistry in an Extreme and Heterogeneous Environment of Mine Tailings

Science.gov (United States)

Liu, Jun; Hua, Zheng-Shuang; Chen, Lin-Xing; Kuang, Jia-Liang; Li, Sheng-Jin; Shu, Wen-Sheng

2014-01-01

Recent molecular surveys have advanced our understanding of the forces shaping the large-scale ecological distribution of microbes in Earth's extreme habitats, such as hot springs and acid mine drainage. However, few investigations have attempted dense spatial analyses of specific sites to resolve the local diversity of these extraordinary organisms and how communities are shaped by the harsh environmental conditions found there. We have applied a 16S rRNA gene-targeted 454 pyrosequencing approach to explore the phylogenetic differentiation among 90 microbial communities from a massive copper tailing impoundment generating acidic drainage and coupled these variations in community composition with geochemical parameters to reveal ecological interactions in this extreme environment. Our data showed that the overall microbial diversity estimates and relative abundances of most of the dominant lineages were significantly correlated with pH, with the simplest assemblages occurring under extremely acidic conditions and more diverse assemblages associated with neutral pHs. The consistent shifts in community composition along the pH gradient indicated that different taxa were involved in the different acidification stages of the mine tailings. Moreover, the effect of pH in shaping phylogenetic structure within specific lineages was also clearly evident, although the phylogenetic differentiations within the Alphaproteobacteria, Deltaproteobacteria, and Firmicutes were attributed to variations in ferric and ferrous iron concentrations. Application of the microbial assemblage prediction model further supported pH as the major factor driving community structure and demonstrated that several of the major lineages are readily predictable. Together, these results suggest that pH is primarily responsible for structuring whole communities in the extreme and heterogeneous mine tailings, although the diverse microbial taxa may respond differently to various environmental conditions

Chronic polyaromatic hydrocarbon (PAH contamination is a marginal driver for community diversity and prokaryotic predicted functioning in coastal sediments

Directory of Open Access Journals (Sweden)

Mathilde Jeanbille

2016-08-01

Full Text Available Benthic microorganisms are key players in the recycling of organic matter and recalcitrant compounds such as polyaromatic hydrocarbons (PAHs in coastal sediments. Despite their ecological importance, the response of microbial communities to chronic PAH pollution, one of the major threats to coastal ecosystems, has received very little attention. In one of the largest surveys performed so far on coastal sediments, the diversity and composition of microbial communities inhabiting both chronically contaminated and non-contaminated coastal sediments were investigated using high-throughput sequencing on the 18S and 16S rRNA genes. Prokaryotic alpha-diversity showed significant association with salinity, temperature, and organic carbon content. The effect of particle size distribution was strong on eukaryotic diversity. Similarly to alpha-diversity, beta-diversity patterns were strongly influenced by the environmental filter, while PAHs had no influence on the prokaryotic community structure and a weak impact on the eukaryotic community structure at the continental scale. However, at the regional scale, PAHs became the main driver shaping the structure of bacterial and eukaryotic communities. These patterns were not found for PICRUSt predicted prokaryotic functions, thus indicating some degree of functional redundancy. Eukaryotes presented a greater potential for their use as PAH contamination biomarkers, owing to their stronger response at both regional and continental scales.

GeoChip 3.0 as a high-thoughput tool for analyzing microbial community composition, structure, and functional activity

Energy Technology Data Exchange (ETDEWEB)

He, Z.; Deng, Y.; Van Nostrand, J.D.; Tu, Q.; Xu, M.; Hemme, C.L.; Li, X.; Wu, L.; Gentry, T.J.; Yin, Y.; Liebich, J.; Hazen, T.C.; Zhou, J.

2010-04-01

A new generation of functional gene arrays (FGAs; GeoChip 3.0) has been developed, with {approx}28,000 probes covering approximately 57,000 gene variants from 292 functional gene families involved in carbon, nitrogen, phosphorus and sulfur cycles, energy metabolism, antibiotic resistance, metal resistance and organic contaminant degradation. GeoChip 3.0 also has several other distinct features, such as a common oligo reference standard (CORS) for data normalization and comparison, a software package for data management and future updating and the gyrB gene for phylogenetic analysis. Computational evaluation of probe specificity indicated that all designed probes would have a high specificity to their corresponding targets. Experimental analysis with synthesized oligonucleotides and genomic DNAs showed that only 0.0036-0.025% false-positive rates were observed, suggesting that the designed probes are highly specific under the experimental conditions examined. In addition, GeoChip 3.0 was applied to analyze soil microbial communities in a multifactor grassland ecosystem in Minnesota, USA, which showed that the structure, composition and potential activity of soil microbial communities significantly changed with the plant species diversity. As expected, GeoChip 3.0 is a high-throughput powerful tool for studying microbial community functional structure, and linking microbial communities to ecosystem processes and functioning.

Links between plant litter chemistry, species diversity, and below-ground ecosystem function.

Science.gov (United States)

Meier, Courtney L; Bowman, William D

2008-12-16

Decomposition is a critical source of plant nutrients, and drives the largest flux of terrestrial C to the atmosphere. Decomposing soil organic matter typically contains litter from multiple plant species, yet we lack a mechanistic understanding of how species diversity influences decomposition processes. Here, we show that soil C and N cycling during decomposition are controlled by the composition and diversity of chemical compounds within plant litter mixtures, rather than by simple metrics of plant species diversity. We amended native soils with litter mixtures containing up to 4 alpine plant species, and we used 9 litter chemical traits to evaluate the chemical composition (i.e., the identity and quantity of compounds) and chemical diversity of the litter mixtures. The chemical composition of the litter mixtures was the strongest predictor of soil respiration, net N mineralization, and microbial biomass N. Soil respiration and net N mineralization rates were also significantly correlated with the chemical diversity of the litter mixtures. In contrast, soil C and N cycling rates were poorly correlated with plant species richness, and there was no relationship between species richness and the chemical diversity of the litter mixtures. These results indicate that the composition and diversity of chemical compounds in litter are potentially important functional traits affecting decomposition, and simple metrics like plant species richness may fail to capture variation in these traits. Litter chemical traits therefore provide a mechanistic link between organisms, species diversity, and key components of below-ground ecosystem function.

Continuous exposure of pesticides in an aquifer changes microbial biomass, diversity and degradation potential

DEFF Research Database (Denmark)

de Lipthay, J. R.; Johnsen, K.; Aamand, J.

2000-01-01

We studied in situ effects of pesticide exposure on microbial degradation potential and community structure of aquifer sediments. Sediment samples pre-exposed to pesticides were significantly different to non-exposed control samples. Pre-exposed sediment showed an increased degradation potential ...... towards phenoxyalcanoic acid herbicides as well as impact on microbial diversity was observed. Furthermore, bacterial biomass was changed, e.g. increased numbers of phenoxyalcanoic acid degraders in pesticide exposed sediment.......We studied in situ effects of pesticide exposure on microbial degradation potential and community structure of aquifer sediments. Sediment samples pre-exposed to pesticides were significantly different to non-exposed control samples. Pre-exposed sediment showed an increased degradation potential...

Contribution of above- and below-ground plant traits to the structure and function of grassland soil microbial communities.

Science.gov (United States)

Legay, N; Baxendale, C; Grigulis, K; Krainer, U; Kastl, E; Schloter, M; Bardgett, R D; Arnoldi, C; Bahn, M; Dumont, M; Poly, F; Pommier, T; Clément, J C; Lavorel, S

2014-10-01

Abiotic properties of soil are known to be major drivers of the microbial community within it. Our understanding of how soil microbial properties are related to the functional structure and diversity of plant communities, however, is limited and largely restricted to above-ground plant traits, with the role of below-ground traits being poorly understood. This study investigated the relative contributions of soil abiotic properties and plant traits, both above-ground and below-ground, to variations in microbial processes involved in grassland nitrogen turnover. In mountain grasslands distributed across three European sites, a correlative approach was used to examine the role of a large range of plant functional traits and soil abiotic factors on microbial variables, including gene abundance of nitrifiers and denitrifiers and their potential activities. Direct effects of soil abiotic parameters were found to have the most significant influence on the microbial groups investigated. Indirect pathways via plant functional traits contributed substantially to explaining the relative abundance of fungi and bacteria and gene abundances of the investigated microbial communities, while they explained little of the variance in microbial activities. Gene abundances of nitrifiers and denitrifiers were most strongly related to below-ground plant traits, suggesting that they were the most relevant traits for explaining variation in community structure and abundances of soil microbes involved in nitrification and denitrification. The results suggest that consideration of plant traits, and especially below-ground traits, increases our ability to describe variation in the abundances and the functional characteristics of microbial communities in grassland soils. © The Author 2014. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

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.

Analysis of microbial diversity in Shenqu with different fermentation times by PCR-DGGE

Directory of Open Access Journals (Sweden)

Tengfei Liu

Full Text Available Abstract Shenqu is a fermented product that is widely used in traditional Chinese medicine (TCM to treat indigestion; however, the microbial strains in the fermentation process are still unknown. The aim of this study was to investigate microbial diversity in Shenqu using different fermentation time periods. DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis profiles indicated that a strain of Pediococcus acidilactici (band 9 is the predominant bacteria during fermentation and that the predominant fungi were uncultured Rhizopus, Aspergillus oryzae, and Rhizopus oryzae. In addition, pathogenic bacteria, such as Enterobacter cloacae, Klebsiella oxytoca, Erwinia billingiae, and Pantoea vagan were detected in Shenqu. DGGE analysis showed that bacterial and fungal diversity declined over the course of fermentation. This determination of the predominant bacterial and fungal strains responsible for fermentation may contribute to further Shenqu research, such as optimization of the fermentation process.

Plants Rather than Mineral Fertilization Shape Microbial Community Structure and Functional Potential in Legacy Contaminated Soil.

Science.gov (United States)

Ridl, Jakub; Kolar, Michal; Strejcek, Michal; Strnad, Hynek; Stursa, Petr; Paces, Jan; Macek, Tomas; Uhlik, Ondrej

2016-01-01

Plant-microbe interactions are of particular importance in polluted soils. This study sought to determine how selected plants (horseradish, black nightshade and tobacco) and NPK mineral fertilization shape the structure of soil microbial communities in legacy contaminated soil and the resultant impact of treatment on the soil microbial community functional potential. To explore these objectives, we combined shotgun metagenomics and 16S rRNA gene amplicon high throughput sequencing with data analysis approaches developed for RNA-seq. We observed that the presence of any of the selected plants rather than fertilization shaped the microbial community structure, and the microbial populations of the root zone of each plant significantly differed from one another and/or from the bulk soil, whereas the effect of the fertilizer proved to be insignificant. When we compared microbial diversity in root zones versus bulk soil, we observed an increase in the relative abundance of Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria or Bacteroidetes, taxa which are commonly considered copiotrophic. Our results thus align with the theory that fast-growing, copiotrophic, microorganisms which are adapted to ephemeral carbon inputs are enriched in the vegetated soil. Microbial functional potential indicated that some genetic determinants associated with signal transduction mechanisms, defense mechanisms or amino acid transport and metabolism differed significantly among treatments. Genetic determinants of these categories tend to be overrepresented in copiotrophic organisms. The results of our study further elucidate plant-microbe relationships in a contaminated environment with possible implications for the phyto/rhizoremediation of contaminated areas.

Microbial Ecology and Evolution in the Acid Mine Drainage Model System.

Science.gov (United States)

Huang, Li-Nan; Kuang, Jia-Liang; Shu, Wen-Sheng

2016-07-01

Acid mine drainage (AMD) is a unique ecological niche for acid- and toxic-metals-adapted microorganisms. These low-complexity systems offer a special opportunity for the ecological and evolutionary analyses of natural microbial assemblages. The last decade has witnessed an unprecedented interest in the study of AMD communities using 16S rRNA high-throughput sequencing and community genomic and postgenomic methodologies, significantly advancing our understanding of microbial diversity, community function, and evolution in acidic environments. This review describes new data on AMD microbial ecology and evolution, especially dynamics of microbial diversity, community functions, and population genomes, and further identifies gaps in our current knowledge that future research, with integrated applications of meta-omics technologies, will fill. Copyright © 2016 Elsevier Ltd. All rights reserved.

Interconnection of Key Microbial Functional Genes for Enhanced Benzo[a]pyrene Biodegradation in Sediments by Microbial Electrochemistry.

Science.gov (United States)

Yan, Zaisheng; He, Yuhong; Cai, Haiyuan; Van Nostrand, Joy D; He, Zhili; Zhou, Jizhong; Krumholz, Lee R; Jiang, He-Long

2017-08-01

Sediment microbial fuel cells (SMFCs) can stimulate the degradation of polycyclic aromatic hydrocarbons in sediments, but the mechanism of this process is poorly understood at the microbial functional gene level. Here, the use of SMFC resulted in 92% benzo[a]pyrene (BaP) removal over 970 days relative to 54% in the controls. Sediment functions, microbial community structure, and network interactions were dramatically altered by the SMFC employment. Functional gene analysis showed that c-type cytochrome genes for electron transfer, aromatic degradation genes, and extracellular ligninolytic enzymes involved in lignin degradation were significantly enriched in bulk sediments during SMFC operation. Correspondingly, chemical analysis of the system showed that these genetic changes resulted in increases in the levels of easily oxidizable organic carbon and humic acids which may have resulted in increased BaP bioavailability and increased degradation rates. Tracking microbial functional genes and corresponding organic matter responses should aid mechanistic understanding of BaP enhanced biodegradation by microbial electrochemistry and development of sustainable bioremediation strategies.

Clinical impact of pre-transplant gut microbial diversity on outcomes of allogeneic hematopoietic stem cell transplantation.

Science.gov (United States)

Doki, Noriko; Suyama, Masahiro; Sasajima, Satoshi; Ota, Junko; Igarashi, Aiko; Mimura, Iyo; Morita, Hidetoshi; Fujioka, Yuki; Sugiyama, Daisuke; Nishikawa, Hiroyoshi; Shimazu, Yutaka; Suda, Wataru; Takeshita, Kozue; Atarashi, Koji; Hattori, Masahira; Sato, Eiichi; Watakabe-Inamoto, Kyoko; Yoshioka, Kosuke; Najima, Yuho; Kobayashi, Takeshi; Kakihana, Kazuhiko; Takahashi, Naoto; Sakamaki, Hisashi; Honda, Kenya; Ohashi, Kazuteru

2017-09-01

Post-transplant microbial diversity in the gastrointestinal tract is closely associated with clinical outcomes following allogeneic hematopoietic stem cell transplantation (allo-HSCT). However, little is known about the impact of the fecal microbiota before allo-HSCT. We analyzed fecal samples approximately 2 weeks before conditioning among 107 allo-HSCT recipients between 2013 and 2015. Microbial analysis was performed using 16S rRNA gene sequencing. Operational taxonomic unit-based microbial diversity was estimated by calculating the Shannon index. Patients were classified into three groups based on the diversity index: low (3) diversity (18 (16.8%), 48 (44.9%), and 41 (38.3%) patients, respectively). There were no significant differences in the 20-month overall survival, cumulative incidence of relapse, and non-relapse mortality among three groups. The cumulative incidence of grade II to IV acute graft-versus-host disease (aGVHD) was similar among the three groups (low 55.6%; intermediate 35.4%; high 48.8%, p = 0.339, at day 100). Furthermore, we found no differences in the cumulative incidence of grade II to IV acute gastrointestinal GVHD among the three groups (low 38.9%; intermediate 21.3%; high 24.4%, p = 0.778, at day 100). Regarding the composition of microbiota before allo-HSCT, aGVHD patients showed a significantly higher abundance of phylum Firmicutes (p strategy to prevent aGVHD.

Geochip-based analysis of microbial communities in alpine meadow soils in the Qinghai-Tibetan plateau.

Science.gov (United States)

Zhang, Yuguang; Lu, Zhenmei; Liu, Shanshan; Yang, Yunfeng; He, Zhili; Ren, Zuohua; Zhou, Jizhong; Li, Diqiang

2013-03-29

GeoChip 3.0, a microbial functional gene array, containing ~28,000 oligonucleotide probes and targeting ~57,000 sequences from 292 functional gene families, provided a powerful tool for researching microbial community structure in natural environments. The alpine meadow is a dominant plant community in the Qinghai-Tibetan plateau, hence it is important to profile the unique geographical flora and assess the response of the microbial communities to environmental variables. In this study, Geochip 3.0 was employed to understand the microbial functional gene diversity and structure, and metabolic potential and the major environmental factors in shaping microbial communities structure of alpine meadow soil in Qinghai-Tibetan Plateau. A total of 6143 microbial functional genes involved in carbon degradation, carbon fixation, methane oxidation and production, nitrogen cycling, phosphorus utilization, sulphur cycling, organic remediation, metal resistance, energy process and other category were detected in six soil samples and high diversity was observed. Interestingly, most of the detected genes associated with carbon degradation were derived from cultivated organisms. To identify major environmental factors in shaping microbial communities, Mantel test and CCA Statistical analyses were performed. The results indicated that altitude, C/N, pH and soil organic carbon were significantly (P the microbial functional structure and a total of 80.97% of the variation was significantly explained by altitude, C/N and pH. The C/N contributed 38.2% to microbial functional gene variation, which is in accordance with the hierarchical clustering of overall microbial functional genes. High overall functional genes and phylogenetic diversity of the alpine meadow soil microbial communities existed in the Qinghai-Tibetan Plateau. Most of the genes involved in carbon degradation were derived from characterized microbial groups. Microbial composition and structures variation were

Microbial diversity in oiled and un-oiled shoreline sediments in the Norwegian Arctic

International Nuclear Information System (INIS)

Grossman, M.J.; Prince, R.C.; Garrett, R.M.; Garrett, K.K.; Bare, R.E.; O'Neil, K.R.; Sowlay, M.R.; Hinton, S.M.; Lee, K.; Sergy, G.A.; Guenette, C.C.

2000-01-01

Field trials were conducted at an oiled shoreline on the island of Spitsbergen to examine the effect of nutrient addition on the metabolic status, potential for aromatic hydrocarbon degradation, and the phylogenetic diversity of the microbial community in oiled Arctic shoreline sediments. IF-30 intermediate fuel grade oil was applied to the shoreline which was then divided into four plots. One was left untreated and two were tilled. Four applications of fertilizer were applied over a two-month period. Phospholipid fatty acid (PLFA), gene probe and 16S microbial community analysis suggested that bioremediation stimulated the metabolic activity, increased microbial biomass and genetic potential for aromatic hydrocarbon degradation, and increased the population of hydrocarbon degradation of an oiled Arctic shoreline microbial community. The results of this study are in agreement with the results from stimulation of oil biodegradation in temperate marine environments. It was concluded that biodegradation and fertilizer addition are feasible treatment methods for oil spills in Arctic regions. 31 refs., 3 tabs., 3 figs

Relating belowground microbial composition to the taxonomic, phylogenetic, and functional trait distributions of trees in a tropical forest.

Science.gov (United States)

Barberán, Albert; McGuire, Krista L; Wolf, Jeffrey A; Jones, F Andrew; Wright, Stuart Joseph; Turner, Benjamin L; Essene, Adam; Hubbell, Stephen P; Faircloth, Brant C; Fierer, Noah

2015-12-01

The complexities of the relationships between plant and soil microbial communities remain unresolved. We determined the associations between plant aboveground and belowground (root) distributions and the communities of soil fungi and bacteria found across a diverse tropical forest plot. Soil microbial community composition was correlated with the taxonomic and phylogenetic structure of the aboveground plant assemblages even after controlling for differences in soil characteristics, but these relationships were stronger for fungi than for bacteria. In contrast to expectations, the species composition of roots in our soil core samples was a poor predictor of microbial community composition perhaps due to the patchy, ephemeral, and highly overlapping nature of fine root distributions. Our ability to predict soil microbial composition was not improved by incorporating information on plant functional traits suggesting that the most commonly measured plant traits are not particularly useful for predicting the plot-level variability in belowground microbial communities. © 2015 John Wiley & Sons Ltd/CNRS.

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.

Functional diversity of soil invertebrates: a potential tool to explain N2O emission?

Science.gov (United States)

Lubbers, Ingrid; De Deyn, Gerlinde; Drake, Harold; Hunger, Sindy; Oppermann, Timo; van Groenigen, Jan Willem

2017-04-01

Soil biota play a crucial role in the mineralization of nutrients from organic material. However, they can thereby increase emissions of the potent greenhouse gas nitrous oxide (N2O). Our current lack of understanding of the factors controlling N2O production and emission is impeding the development of effective mitigation strategies. It is the challenge to control N2O emissions from production systems without reducing crop yield, and diversity of soil fauna may play a key role. A high functional diversity of soil invertebrates is known to stimulate nitrogen mineralization and thereby plant growth, however, it is unknown whether a high functional diversity of soil invertebrates can concurrently diminish N2O emissions. We hypothesized that increased functional diversity of soil invertebrates reduces faunal-induced N2O emissions by facilitating more complete denitrification through (i) stimulating the activity of denitrifying microbes, and (ii) affecting the distribution of micro and macro pores, creating more anaerobic reaction sites. Using state-of-the-art X-ray tomography and next-generation sequencing, we studied effects of functional diversity on soil structural properties and the diversity of the microbial community (16S rRNA genes and 16S rRNA), and linked these to soil N2O emissions. In a 120-day study we found that the functional composition of the soil invertebrate community determined N2O emissions: earthworm activity was key to faunal-induced N2O emissions (a 32-fold increase after 120 days, Pstructural properties (mean pore size, pore size distribution) were found to be radically altered by earthworm activity. We conclude that the presence of a few functional groups (ecosystem engineers) is more important than overall increased functional diversity in explaining faunal-affected N2O emissions.

Functional & phylogenetic diversity of copepod communities

Science.gov (United States)

Benedetti, F.; Ayata, S. D.; Blanco-Bercial, L.; Cornils, A.; Guilhaumon, F.

2016-02-01

The diversity of natural communities is classically estimated through species identification (taxonomic diversity) but can also be estimated from the ecological functions performed by the species (functional diversity), or from the phylogenetic relationships among them (phylogenetic diversity). Estimating functional diversity requires the definition of specific functional traits, i.e., phenotypic characteristics that impact fitness and are relevant to ecosystem functioning. Estimating phylogenetic diversity requires the description of phylogenetic relationships, for instance by using molecular tools. In the present study, we focused on the functional and phylogenetic diversity of copepod surface communities in the Mediterranean Sea. First, we implemented a specific trait database for the most commonly-sampled and abundant copepod species of the Mediterranean Sea. Our database includes 191 species, described by seven traits encompassing diverse ecological functions: minimal and maximal body length, trophic group, feeding type, spawning strategy, diel vertical migration and vertical habitat. Clustering analysis in the functional trait space revealed that Mediterranean copepods can be gathered into groups that have different ecological roles. Second, we reconstructed a phylogenetic tree using the available sequences of 18S rRNA. Our tree included 154 of the analyzed Mediterranean copepod species. We used these two datasets to describe the functional and phylogenetic diversity of copepod surface communities in the Mediterranean Sea. The replacement component (turn-over) and the species richness difference component (nestedness) of the beta diversity indices were identified. Finally, by comparing various and complementary aspects of plankton diversity (taxonomic, functional, and phylogenetic diversity) we were able to gain a better understanding of the relationships among the zooplankton community, biodiversity, ecosystem function, and environmental forcing.

Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity.

Science.gov (United States)

He, Yan; Caporaso, J Gregory; Jiang, Xiao-Tao; Sheng, Hua-Fang; Huse, Susan M; Rideout, Jai Ram; Edgar, Robert C; Kopylova, Evguenia; Walters, William A; Knight, Rob; Zhou, Hong-Wei

2015-01-01

The operational taxonomic unit (OTU) is widely used in microbial ecology. Reproducibility in microbial ecology research depends on the reliability of OTU-based 16S ribosomal subunit RNA (rRNA) analyses. Here, we report that many hierarchical and greedy clustering methods produce unstable OTUs, with membership that depends on the number of sequences clustered. If OTUs are regenerated with additional sequences or samples, sequences originally assigned to a given OTU can be split into different OTUs. Alternatively, sequences assigned to different OTUs can be merged into a single OTU. This OTU instability affects alpha-diversity analyses such as rarefaction curves, beta-diversity analyses such as distance-based ordination (for example, Principal Coordinate Analysis (PCoA)), and the identification of differentially represented OTUs. Our results show that the proportion of unstable OTUs varies for different clustering methods. We found that the closed-reference method is the only one that produces completely stable OTUs, with the caveat that sequences that do not match a pre-existing reference sequence collection are discarded. As a compromise to the factors listed above, we propose using an open-reference method to enhance OTU stability. This type of method clusters sequences against a database and includes unmatched sequences by clustering them via a relatively stable de novo clustering method. OTU stability is an important consideration when analyzing microbial diversity and is a feature that should be taken into account during the development of novel OTU clustering methods.

Sustaining Rare Marine Microorganisms: Macroorganisms As Repositories and Dispersal Agents of Microbial Diversity.

Science.gov (United States)

Troussellier, Marc; Escalas, Arthur; Bouvier, Thierry; Mouillot, David

2017-01-01

Recent analyses revealed that most of the biodiversity observed in marine microbial communities is represented by organisms with low abundance but, nonetheless essential for ecosystem dynamics and processes across both temporal and spatial scales. Surprisingly, few studies have considered the effect of macroorganism-microbe interactions on the ecology and distribution dynamics of rare microbial taxa. In this review, we synthesize several lines of evidence that these relationships cannot be neglected any longer. First, we provide empirical support that the microbiota of macroorganisms represents a significant part of marine bacterial biodiversity and that host-microbe interactions benefit to certain microbial populations which are part of the rare biosphere (i.e., opportunistic copiotrophic organisms). Second, we reveal the major role that macroorganisms may have on the dispersal and the geographic distribution of microbes. Third, we introduce an innovative and integrated view of the interactions between microbes and macroorganisms, namely sustaining the rares , which suggests that macroorganisms favor the maintenance of marine microbial diversity and are involved in the regulation of its richness and dynamics. Finally, we show how this hypothesis complements existing theories in microbial ecology and offers new perspectives about the importance of macroorganisms for the microbial biosphere, particularly the rare members.

Dynamics and diversity of microbial community succession in traditional fermentation of Shanxi aged vinegar.

Science.gov (United States)

Nie, Zhiqiang; Zheng, Yu; Du, Hongfu; Xie, Sankuan; Wang, Min

2015-05-01

The traditional fermentation of Shanxi aged vinegar (SAV), a well-known traditional Chinese vinegar, generally involves the preparation of starter daqu, starch saccharification, alcoholic fermentation (AF) and acetic acid fermentation (AAF). Dynamics and diversity of microbial community succession in daqu and other fermentation stages were investigated by denaturing gradient gel electrophoresis (DGGE). Results showed that eight bacterial genera and four fungal genera were found in daqu. However, Staphylococcus, Saccharopolyspora, Bacillus, Oceanobacillus, Enterobacter, Streptomyces, Eurotium, Monascus and Pichia in daqu were eradicated during AF. Four bacterial genera and three fungal genera were found in this stage. Weissella, Lactobacillus, Streptococcus, Saccharomyces, and Saccharomycopsis were the dominant microorganisms in the late stage of AF. During AAF, four bacterial genera and four fungal genera were found. Weissella, Streptococcus, Klebsiella, Escherichia, and Cladosporium gradually disappeared; the dominant microorganisms were Acetobacter, Lactobacillus, Saccharomycopsis, and Alternaria in the late stage of AAF. Alpha diversity metrics showed that fungal diversity in daqu was greater than that in AF and AAF. By contrast, bacterial diversity decreased from daqu to AF and increased in the first three days of AAF and then decreased. Hence, these results could help understand dynamics of microbial community succession in continuous fermentation of traditional Chinese vinegars. Copyright © 2014 Elsevier Ltd. All rights reserved.

The taxonomic and functional diversity of microbes at a temperate coastal site: a 'multi-omic' study of seasonal and diel temporal variation.

Directory of Open Access Journals (Sweden)

Jack A Gilbert

Full Text Available How microbial communities change over time in response to the environment is poorly understood. Previously a six-year time series of 16S rRNA V6 data from the Western English Channel demonstrated robust seasonal structure within the bacterial community, with diversity negatively correlated with day-length. Here we determine whether metagenomes and metatranscriptomes follow similar patterns. We generated 16S rRNA datasets, metagenomes (1.2 GB and metatranscriptomes (157 MB for eight additional time points sampled in 2008, representing three seasons (Winter, Spring, Summer and including day and night samples. This is the first microbial 'multi-omic' study to combine 16S rRNA amplicon sequencing with metagenomic and metatranscriptomic profiling. Five main conclusions can be drawn from analysis of these data: 1 Archaea follow the same seasonal patterns as Bacteria, but show lower relative diversity; 2 Higher 16S rRNA diversity also reflects a higher diversity of transcripts; 3 Diversity is highest in winter and at night; 4 Community-level changes in 16S-based diversity and metagenomic profiles are better explained by seasonal patterns (with samples closest in time being most similar, while metatranscriptomic profiles are better explained by diel patterns and shifts in particular categories (i.e., functional groups of genes; 5 Changes in key genes occur among seasons and between day and night (i.e., photosynthesis; but these samples contain large numbers of orphan genes without known homologues and it is these unknown gene sets that appear to contribute most towards defining the differences observed between times. Despite the huge diversity of these microbial communities, there are clear signs of predictable patterns and detectable stability over time. Renewed and intensified efforts are required to reveal fundamental deterministic patterns in the most complex microbial communities. Further, the presence of a substantial proportion of orphan

Microbial diversity and dynamicity of biogas reactors due to radical changes of feedstock composition

DEFF Research Database (Denmark)

De Francisci, Davide; Kougias, Panagiotis; Treu, Laura

2015-01-01

substrate change. The greatest increase in diversity was observed in the reactor supplemented with carbohydrates and the microbial community became dominated by lactobacilli, while the lowest corresponded to the reactor overfed with proteins, where only Desulfotomaculum showed significant increase...

Microbial community variation and functions to excess sludge reduction in a novel gravel contact oxidation reactor

Energy Technology Data Exchange (ETDEWEB)

Lin Shanshan; Jin, Y.; Fu, L. [School of Urban and Environmental Science, Northeast Normal University, Changchun (China); Quan, C. [Jilin University, College of medicine, Changchun (China); Yang, Y.S., E-mail: yangy6@cf.ac.uk [Cardiff University, School of Earth and Ocean Sciences, Cardiff CF10 3YE (United Kingdom)

2009-06-15

Excess biomass produced within the degradation processes of organic pollutants is creating environmental challenges. The gravel contact oxidation reactor (GCOR) filled with crushed stone globular aggregates as carriers, has been demonstrated capable of reducing the excess sludge effectively in some pilot and small-scale engineering studies. In order to evaluate the variation and structure of the microbial community and their functions to excess sludge reduction in GCOR, a conventional activated sludge reactor (ASR) was studied as a comparison. The 16S rDNA library of the universal bacteria was constructed, Shannon's diversity index (H) and Species evenness (E) were calculated with distance-based operational taxonomic unit and richness (DOTUR) for microbial diversity. Real-time quantity PCR and optical microscope were used for absolute bacterial DNA concentration and eukarya identification, respectively. Meanwhile, the suspended solid index in GCOR and ASR was detected for assessing the excess sludge production. The results indicated that the most abundant bacteria in GCOR were those related to the {beta}-Proteobacteria group, then {gamma}-Proteobacteria and to Cytophaga-Flexibacter-Bacteriode (CFB). In the ASR samples major bacteria were in the closest match with {gamma}-Proteobacteria, then {beta}-Proteobacteria and CFB. Shannon's index (H) was higher (3.41) for diversity of bacteria extracted from the carrier samples in GCOR than that (2.71) from the sludge sample in ASR. Species evenness (E) for the isolates from GCOR and ASR samples was 0.97 and 0.96, respectively. Comparison of the universal bacteria population in GCOR and ASR shows that the total bacterial DNA concentration on the GCOR carriers were 8.98 x 10{sup 5} {mu}g/{mu}l, twice that in ASR of 4.67 x 10{sup 5} {mu}g/{mu}l under normal operation of two reactors. But the MLSS in GCOR was only 4.5 mg/L, 25 times less than that in ASR of 115.4 mg/L. The most representative eukarya were protozoa

Microbial community variation and functions to excess sludge reduction in a novel gravel contact oxidation reactor

International Nuclear Information System (INIS)

Lin Shanshan; Jin, Y.; Fu, L.; Quan, C.; Yang, Y.S.

2009-01-01

Excess biomass produced within the degradation processes of organic pollutants is creating environmental challenges. The gravel contact oxidation reactor (GCOR) filled with crushed stone globular aggregates as carriers, has been demonstrated capable of reducing the excess sludge effectively in some pilot and small-scale engineering studies. In order to evaluate the variation and structure of the microbial community and their functions to excess sludge reduction in GCOR, a conventional activated sludge reactor (ASR) was studied as a comparison. The 16S rDNA library of the universal bacteria was constructed, Shannon's diversity index (H) and Species evenness (E) were calculated with distance-based operational taxonomic unit and richness (DOTUR) for microbial diversity. Real-time quantity PCR and optical microscope were used for absolute bacterial DNA concentration and eukarya identification, respectively. Meanwhile, the suspended solid index in GCOR and ASR was detected for assessing the excess sludge production. The results indicated that the most abundant bacteria in GCOR were those related to the β-Proteobacteria group, then γ-Proteobacteria and to Cytophaga-Flexibacter-Bacteriode (CFB). In the ASR samples major bacteria were in the closest match with γ-Proteobacteria, then β-Proteobacteria and CFB. Shannon's index (H) was higher (3.41) for diversity of bacteria extracted from the carrier samples in GCOR than that (2.71) from the sludge sample in ASR. Species evenness (E) for the isolates from GCOR and ASR samples was 0.97 and 0.96, respectively. Comparison of the universal bacteria population in GCOR and ASR shows that the total bacterial DNA concentration on the GCOR carriers were 8.98 x 10 5 μg/μl, twice that in ASR of 4.67 x 10 5 μg/μl under normal operation of two reactors. But the MLSS in GCOR was only 4.5 mg/L, 25 times less than that in ASR of 115.4 mg/L. The most representative eukarya were protozoa both in GCOR (15 no. per 20 ml) and in ASR (15

Characterizing Microbial Diversity and Function in Natural Subsurface CO2 Reservoir Systems for Applied Use in Geologic Carbon Sequestration Environments

Science.gov (United States)

Freedman, A.; Thompson, J. R.

2013-12-01

The injection of CO2 into geological formations at quantities necessary to significantly reduce CO2 emissions will represent an environmental perturbation on a continental scale. The extent to which biological processes may play a role in the fate and transport of CO2 injected into geological formations has remained an open question due to the fact that at temperatures and pressures associated with reservoirs targeted for sequestration CO2 exists as a supercritical fluid (scCO2), which has generally been regarded as a sterilizing agent. Natural subsurface accumulations of CO2 serve as an excellent analogue for studying the long-term effects, implications and benefits of CO2 capture and storage (CCS). While several geologic formations bearing significant volumes of nearly pure scCO2 phases have been identified in the western United States, no study has attempted to characterize the microbial community present in these systems. Because the CO2 in the region is thought to have first accumulated millions of years ago, it is reasonable to assume that native microbial populations have undergone extensive and unique physiological and behavioral adaptations to adjust to the exceedingly high scCO2 content. Our study focuses on the microbial communities associated with the dolomite limestone McElmo Dome scCO2 Field in the Colorado Plateau region, approximately 1,000 m below the surface. Fluid samples were collected from 10 wells at an industrial CO2 production facility outside Cortez, CO. Subsamples preserved on site in 3.7% formaldehyde were treated in the lab with Syto 9 green-fluorescent nucleic acid stain, revealing 3.2E6 to 1.4E8 microbial cells per liter of produced fluid and 8.0E9 cells per liter of local pond water used in well drilling fluids. Extracted DNAs from sterivex 0.22 um filters containing 20 L of sample biomass were used as templates for PCR targeting the 16S rRNA gene. 16S rRNA amplicons from these samples were cloned, sequenced and subjected to microbial

Application of Ion Torrent Sequencing to the Assessment of the Effect of Alkali Ballast Water Treatment on Microbial Community Diversity

Science.gov (United States)

Fujimoto, Masanori; Moyerbrailean, Gregory A.; Noman, Sifat; Gizicki, Jason P.; Ram, Michal L.; Green, Phyllis A.; Ram, Jeffrey L.

2014-01-01

The impact of NaOH as a ballast water treatment (BWT) on microbial community diversity was assessed using the 16S rRNA gene based Ion Torrent sequencing with its new 400 base chemistry. Ballast water samples from a Great Lakes ship were collected from the intake and discharge of both control and NaOH (pH 12) treated tanks and were analyzed in duplicates. One set of duplicates was treated with the membrane-impermeable DNA cross-linking reagent propidium mono-azide (PMA) prior to PCR amplification to differentiate between live and dead microorganisms. Ion Torrent sequencing generated nearly 580,000 reads for 31 bar-coded samples and revealed alterations of the microbial community structure in ballast water that had been treated with NaOH. Rarefaction analysis of the Ion Torrent sequencing data showed that BWT using NaOH significantly decreased microbial community diversity relative to control discharge (pbased principal coordinate analysis (PCoA) plots and UPGMA tree analysis revealed that NaOH-treated ballast water microbial communities differed from both intake communities and control discharge communities. After NaOH treatment, bacteria from the genus Alishewanella became dominant in the NaOH-treated samples, accounting for alkali ballast water treatment in reducing ballast water microbial diversity and demonstrated the application of new Ion Torrent sequencing techniques to microbial community studies. PMID:25222021

Spatial and seasonal variation in diversity and structure of microbial biofilms on marine plastics in Northern European waters.

Science.gov (United States)

Oberbeckmann, Sonja; Loeder, Martin G J; Gerdts, Gunnar; Osborn, A Mark

2014-11-01

Plastic pollution is now recognised as a major threat to marine environments and marine biota. Recent research highlights that diverse microbial species are found to colonise plastic surfaces (the plastisphere) within marine waters. Here, we investigate how the structure and diversity of marine plastisphere microbial community vary with respect to season, location and plastic substrate type. We performed a 6-week exposure experiment with polyethylene terephthalate (PET) bottles in the North Sea (UK) as well as sea surface sampling of plastic polymers in Northern European waters. Scanning electron microscopy revealed diverse plastisphere communities comprising prokaryotic and eukaryotic microorganisms. Denaturing gradient gel electrophoresis (DGGE) and sequencing analysis revealed that plastisphere microbial communities on PET fragments varied both with season and location and comprised of bacteria belonging to Bacteroidetes, Proteobacteria, Cyanobacteria and members of the eukaryotes Bacillariophyceae and Phaeophyceae. Polymers sampled from the sea surface mainly comprised polyethylene, polystyrene and polypropylene particles. Variation within plastisphere communities on different polymer types was observed, but communities were primarily dominated by Cyanobacteria. This research reveals that the composition of plastisphere microbial communities in marine waters varies with season, geographical location and plastic substrate type. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Response of African marigold (Tagetes erecta L. to different concentrations of chlorpyrifos and microbial diversity in root rhizosphere

Directory of Open Access Journals (Sweden)

Mani Santhoshkumar

2017-04-01

Full Text Available Objective: To assess the response of African marigold (Tagetes erecta L. to exposed different concentration of chlorpyrifos by evaluating morphology (root and shoot length, biomass (fresh weight and dry weight, photosynthetic pigments (chlorophyll a and b, protein and microbial diversity in root rhizosphere. Methods: The study was carried out in pot culture and treated with various concentrations (0.5%, 1.0%, 2.0%, and 2.5% as well as control treatments. The morphological, biomass, photosynthetic pigments, protein, and microbial diversity were analyzed on 30, 60, and 90 days. Results: The obtained results revealed that the tested pesticide reduced the growth, biomass and photosynthetic pigment of African marigold when applied at higher concentration than the optimum dosage. But the lower dose the pesticide had some stimulatory effect of analyzed parameters. A similar effect of pesticide was observed on the microbial population of root rhizosphere that is decreased in microbial population was caused at higher doses. But it was increased at lower doses. Conclusions: It can be concluded that pesticide above the certain dosage level adversely affect all the analyzed parameters at higher doses. The application of recommended doses should be discouraged. Further study is needed for the effect of pesticide use on microbial diversity, since these studies are carried out in a controlled pot experiment, including the current study. Thus, future study directed towards by studying the phyoremediation of theses contaminted site with intraction of microbes.

Relating Anaerobic Digestion Microbial Community and Process Function.

Science.gov (United States)

Venkiteshwaran, Kaushik; Bocher, Benjamin; Maki, James; Zitomer, Daniel

2015-01-01

Anaerobic digestion (AD) involves a consortium of microorganisms that convert substrates into biogas containing methane for renewable energy. The technology has suffered from the perception of being periodically unstable due to limited understanding of the relationship between microbial community structure and function. The emphasis of this review is to describe microbial communities in digesters and quantitative and qualitative relationships between community structure and digester function. Progress has been made in the past few decades to identify key microorganisms influencing AD. Yet, more work is required to realize robust, quantitative relationships between microbial community structure and functions such as methane production rate and resilience after perturbations. Other promising areas of research for improved AD may include methods to increase/control (1) hydrolysis rate, (2) direct interspecies electron transfer to methanogens, (3) community structure-function relationships of methanogens, (4) methanogenesis via acetate oxidation, and (5) bioaugmentation to study community-activity relationships or improve engineered bioprocesses.

Pyrosequencing reveals diverse microbial community associated with the zoanthid Palythoa australiae from the South China Sea.

Science.gov (United States)

Sun, Wei; Zhang, Fengli; He, Liming; Li, Zhiyong

2014-05-01

Diverse sessile organisms inhabit the coral reef ecosystems, including corals, sponges, and sea anemones. In the past decades, scleractinian corals (Cnidaria, Anthozoa, Scleractinia) and their associated microorganisms have attracted much attention. Zoanthids (Cnidaria, Anthozoa, Zoanthidea) are commonly found in coral reefs. However, little is known about the community structure of zoanthid-associated microbiota. In this study, the microbial community associated with the zoanthid Palythoa australiae in the South China Sea was investigated by 454 pyrosequencing. As a result, 2,353 bacterial, 583 archaeal, and 36 eukaryotic microbial ribotypes were detected, respectively. A total of 22 bacterial phyla (16 formally described phyla and six candidate phyla) were recovered. Proteobacteria was the most abundant group, followed by Chloroflexi and Actinobacteria. High-abundance Rhizobiales and diverse Chloroflexi were observed in the bacterial community. The archaeal population was composed of Crenarchaeota and Euryarchaeota, with Marine Group I as the dominant lineage. In particular, Candidatus Nitrosopumilus dominated the archaeal community. Besides bacteria and archaea, the zoanthid harbored eukaryotic microorganisms including fungi and algae though their diversity was very low. This study provided the first insights into the microbial community associated with P. australiae by 454 pyrosequencing, consequently laid a basis for the understanding of the association of P. australiae-microbes symbioses.

Desert farming benefits from microbial potential in arid soils and promotes diversity and plant health.

Directory of Open Access Journals (Sweden)

Martina Köberl

Full Text Available BACKGROUND: To convert deserts into arable, green landscapes is a global vision, and desert farming is a strong growing area of agriculture world-wide. However, its effect on diversity of soil microbial communities, which are responsible for important ecosystem services like plant health, is still not known. METHODOLOGY/PRINCIPAL FINDINGS: We studied the impact of long-term agriculture on desert soil in one of the most prominent examples for organic desert farming in Sekem (Egypt. Using a polyphasic methodological approach to analyse microbial communities in soil as well as associated with cultivated plants, drastic effects caused by 30 years of agriculture were detected. Analysing bacterial fingerprints, we found statistically significant differences between agricultural and native desert soil of about 60%. A pyrosequencing-based analysis of the 16S rRNA gene regions showed higher diversity in agricultural than in desert soil (Shannon diversity indices: 11.21/7.90, and displayed structural differences. The proportion of Firmicutes in field soil was significantly higher (37% than in the desert (11%. Bacillus and Paenibacillus play the key role: they represented 96% of the antagonists towards phytopathogens, and identical 16S rRNA sequences in the amplicon library and for isolates were detected. The proportion of antagonistic strains was doubled in field in comparison to desert soil (21.6%/12.4%; disease-suppressive bacteria were especially enriched in plant roots. On the opposite, several extremophilic bacterial groups, e.g., Acidimicrobium, Rubellimicrobium and Deinococcus-Thermus, disappeared from soil after agricultural use. The N-fixing Herbaspirillum group only occurred in desert soil. Soil bacterial communities were strongly driven by the a-biotic factors water supply and pH. CONCLUSIONS/SIGNIFICANCE: After long-term farming, a drastic shift in the bacterial communities in desert soil was observed. Bacterial communities in agricultural

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)

Microbial diversity in the floral nectar of seven Epipactis (Orchidaceae) species

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Jacquemyn, Hans; Lenaerts, Marijke; Tyteca, Daniel; Lievens, Bart

2013-01-01

Abstract Floral nectar of animal-pollinated plants is commonly infested with microorganisms, yet little is known about the microorganisms inhabiting the floral nectar of orchids. In this study, we investigated microbial communities occurring in the floral nectar of seven Epipactis (Orchidaceae) species. Culturable bacteria and yeasts were isolated and identified by partially sequencing the small subunit (SSU) ribosomal RNA (rRNA) gene and the D1/D2 domains of the large subunit (LSU) rRNA gene, respectively. Using three different culture media, we found that bacteria were common inhabitants of the floral nectar of Epipactis. The most widely distributed bacterial operational taxonomic units (OTUs) in nectar of Epipactis were representatives of the family of Enterobacteriaceae, with an unspecified Enterobacteriaceae bacterium as the most common. In contrast to previous studies investigating microbial communities in floral nectar, very few yeast species (mainly of the genus Cryptococcus) were observed, and most of them occurred in very low densities. Total OTU richness (i.e., the number of bacterial and yeast OTUs per orchid species) varied between 4 and 20. Cluster analysis revealed that microbial communities of allogamous species differed from those of autogamous and facultatively autogamous species. This study extends previous efforts to identify microbial communities in floral nectar and indicates that the floral nectar of the orchids investigated mainly contained bacterial communities with moderate phylogenetic diversity. PMID:23836678

Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity

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Parfrey, Laura Wegener; Walters, William A.; Lauber, Christian L.; Clemente, Jose C.; Berg-Lyons, Donna; Teiling, Clotilde; Kodira, Chinnappa; Mohiuddin, Mohammed; Brunelle, Julie; Driscoll, Mark; Fierer, Noah; Gilbert, Jack A.; Knight, Rob

2014-06-19

Eukaryotic microbes (protists) residing in the vertebrate gut influence host health and disease, but their diversity and distribution in healthy hosts is poorly understood. Protists found in the gut are typically considered parasites, but many are commensal and some are beneficial. Further, the hygiene hypothesis predicts that association with our co-evolved microbial symbionts may be important to overall health. It is therefore imperative that we understand the normal diversity of our eukaryotic gut microbiota to test for such effects and avoid eliminating commensal organisms. We assembled a dataset of healthy individuals from two populations, one with traditional, agrarian lifestyles and a second with modern, westernized lifestyles, and characterized the human eukaryotic microbiota via high-throughput sequencing. To place the human gut microbiota within a broader context our dataset also includes gut samples from diverse mammals and samples from other aquatic and terrestrial environments. We curated the SILVA ribosomal database to reflect current knowledge of eukaryotic taxonomy and employ it as a phylogenetic framework to compare eukaryotic diversity across environment. We show that adults from the non-western population harbor a diverse community of protists, and diversity in the human gut is comparable to that in other mammals. However, the eukaryotic microbiota of the western population appears depauperate. The distribution of symbionts found in mammals reflects both host phylogeny and diet. Eukaryotic microbiota in the gut are less diverse and more patchily distributed than bacteria. More broadly, we show that eukaryotic communities in the gut are less diverse than in aquatic and terrestrial habitats, and few taxa are shared across habitat types, and diversity patterns of eukaryotes are correlated with those observed for bacteria. These results outline the distribution and diversity of microbial eukaryotic communities in the mammalian gut and across

Microbial Diversity and Bioremediation of a Hydrocarbon-Contaminated Aquifer (Vega Baja, Puerto Rico

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Arturo A. Massol-Deyá

2006-09-01

Full Text Available Hydrocarbon contamination of groundwater resources has become a major environmental and human health concern in many parts of the world. Our objectives were to employ both culture and culture-independent techniques to characterize the dynamics of microbial community structure within a fluidized bed reactor used to bioremediate a diesel-contaminated groundwater in a tropical environment. Under normal operating conditions, 97 to 99% of total hydrocarbons were removed with only 14 min hydraulic retention time. Over 25 different cultures were isolated from the treatment unit (96% which utilized diesel constituents as sole carbon source. Approximately 20% of the isolates were also capable of complete denitrification to nitrogen gas. Sequence analysis of 16S rDNA demonstrated ample diversity with most belonging to the ∝, β and γ subdivision of the Proteobacteria, Bacilli, and Actinobacteria groups. Moreover, the genetic constitution of the microbial community was examined at multiple time points with a Functional Gene Array (FGA containing over 12,000 probes for genes involved in organic degradation and major biogeochemical cycles. Total community DNA was extracted and amplified using an isothermal φ29 polymerase-based technique, labeled with Cy5 dye, and hybridized to the arrays in 50% formimide overnight at 50°C. Cluster analysis revealed comparable profiles over the course of treatment suggesting the early selection of a very stable microbial community. A total of 270 genes for organic contaminant degradation (including naphthalene, toluene [aerobic and anaerobic], octane, biphenyl, pyrene, xylene, phenanthrene, and benzene; and 333 genes involved in metabolic activities (nitrite and nitrous oxide reductases [nirS, nirK, and nosZ], dissimilatory sulfite reductases [dsrAB], potential metal reducing C-type cytochromes, and methane monooxygenase [pmoA] were repeatedly detected. Genes for degradation of MTBE

An integrated study to analyze soil microbial community structure and metabolic potential in two forest types.

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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.

Differential Microbial Diversity in Drosophila melanogaster: Are Fruit Flies Potential Vectors of Opportunistic Pathogens?

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Luis A. Ramírez-Camejo

2017-01-01

Full Text Available Drosophila melanogaster has become a model system to study interactions between innate immunity and microbial pathogens, yet many aspects regarding its microbial community and interactions with pathogens remain unclear. In this study wild D. melanogaster were collected from tropical fruits in Puerto Rico to test how the microbiota is distributed and to compare the culturable diversity of fungi and bacteria. Additionally, we investigated whether flies are potential vectors of human and plant pathogens. Eighteen species of fungi and twelve species of bacteria were isolated from wild flies. The most abundant microorganisms identified were the yeast Candida inconspicua and the bacterium Klebsiella sp. The yeast Issatchenkia hanoiensis was significantly more common internally than externally in flies. Species richness was higher in fungi than in bacteria, but diversity was lower in fungi than in bacteria. The microbial composition of flies was similar internally and externally. We identified a variety of opportunistic human and plant pathogens in flies such as Alcaligenes faecalis, Aspergillus flavus, A. fumigatus, A. niger, Fusarium equiseti/oxysporum, Geotrichum candidum, Klebsiella oxytoca, Microbacterium oxydans, and Stenotrophomonas maltophilia. Despite its utility as a model system, D. melanogaster can be a vector of microorganisms that represent a potential risk to plant and public health.

Stochastic Community Assembly: Does It Matter in Microbial Ecology?

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Zhou, Jizhong; Ning, Daliang

2017-12-01

Understanding the mechanisms controlling community diversity, functions, succession, and biogeography is a central, but poorly understood, topic in ecology, particularly in microbial ecology. Although stochastic processes are believed to play nonnegligible roles in shaping community structure, their importance relative to deterministic processes is hotly debated. The importance of ecological stochasticity in shaping microbial community structure is far less appreciated. Some of the main reasons for such heavy debates are the difficulty in defining stochasticity and the diverse methods used for delineating stochasticity. Here, we provide a critical review and synthesis of data from the most recent studies on stochastic community assembly in microbial ecology. We then describe both stochastic and deterministic components embedded in various ecological processes, including selection, dispersal, diversification, and drift. We also describe different approaches for inferring stochasticity from observational diversity patterns and highlight experimental approaches for delineating ecological stochasticity in microbial communities. In addition, we highlight research challenges, gaps, and future directions for microbial community assembly research. Copyright © 2017 American Society for Microbiology.

Community Structure of Lithotrophically-Driven Hydrothermal Microbial Mats from the Mariana Arc and Back-Arc

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Kevin W. Hager

2017-08-01

Full Text Available The Mariana region exhibits a rich array of hydrothermal venting conditions in a complex geological setting, which provides a natural laboratory to study the influence of local environmental conditions on microbial community structure as well as large-scale patterns in microbial biogeography. We used high-throughput amplicon sequencing of the bacterial small subunit (SSU rRNA gene from 22 microbial mats collected from four hydrothermally active locations along the Mariana Arc and back-arc to explore the structure of lithotrophically-based microbial mat communities. The vent effluent was classified as iron- or sulfur-rich corresponding with two distinct community types, dominated by either Zetaproteobacteria or Epsilonproteobacteria, respectively. The Zetaproteobacterial-based communities had the highest richness and diversity, which supports the hypothesis that Zetaproteobacteria function as ecosystem engineers creating a physical habitat within a chemical environment promoting enhanced microbial diversity. Gammaproteobacteria were also high in abundance within the iron-dominated mats and some likely contribute to primary production. In addition, we also compare sampling scale, showing that bulk sampling of microbial mats yields higher diversity than micro-scale sampling. We present a comprehensive analysis and offer new insights into the community structure and diversity of lithotrophically-driven microbial mats from a hydrothermal region associated with high microbial biodiversity. Our study indicates an important functional role of for the Zetaproteobacteria altering the mat habitat and enhancing community interactions and complexity.

Distinct microbial communities in the active and permafrost layers on the Tibetan Plateau.

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Chen, Yong-Liang; Deng, Ye; Ding, Jin-Zhi; Hu, Hang-Wei; Xu, Tian-Le; Li, Fei; Yang, Gui-Biao; Yang, Yuan-He

2017-12-01

Permafrost represents an important understudied genetic resource. Soil microorganisms play important roles in regulating biogeochemical cycles and maintaining ecosystem function. However, our knowledge of patterns and drivers of permafrost microbial communities is limited over broad geographic scales. Using high-throughput Illumina sequencing, this study compared soil bacterial, archaeal and fungal communities between the active and permafrost layers on the Tibetan Plateau. Our results indicated that microbial alpha diversity was significantly higher in the active layer than in the permafrost layer with the exception of fungal Shannon-Wiener index and Simpson's diversity index, and microbial community structures were significantly different between the two layers. Our results also revealed that environmental factors such as soil fertility (soil organic carbon, dissolved organic carbon and total nitrogen contents) were the primary drivers of the beta diversity of bacterial, archaeal and fungal communities in the active layer. In contrast, environmental variables such as the mean annual precipitation and total phosphorus played dominant roles in driving the microbial beta diversity in the permafrost layer. Spatial distance was important for predicting the bacterial and archaeal beta diversity in both the active and permafrost layers, but not for fungal communities. Collectively, these results demonstrated different driving factors of microbial beta diversity between the active layer and permafrost layer, implying that the drivers of the microbial beta diversity observed in the active layer cannot be used to predict the biogeographic patterns of the microbial beta diversity in the permafrost layer. © 2017 John Wiley & Sons Ltd.

The maturing of microbial ecology.

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Schmidt, Thomas M

2006-09-01

A.J. Kluyver and C.B. van Niel introduced many scientists to the exceptional metabolic capacity of microbes and their remarkable ability to adapt to changing environments in The Microbe's Contribution to Biology. Beyond providing an overview of the physiology and adaptability of microbes, the book outlined many of the basic principles for the emerging discipline of microbial ecology. While the study of pure cultures was highlighted, provided a unifying framework for understanding the vast metabolic potential of microbes and their roles in the global cycling of elements, extrapolation from pure cultures to natural environments has often been overshadowed by microbiologists inability to culture many of the microbes seen in natural environments. A combination of genomic approaches is now providing a culture-independent view of the microbial world, revealing a more diverse and dynamic community of microbes than originally anticipated. As methods for determining the diversity of microbial communities become increasingly accessible, a major challenge to microbial ecologists is to link the structure of natural microbial communities with their functions. This article presents several examples from studies of aquatic and terrestrial microbial communities in which culture and culture-independent methods are providing an enhanced appreciation for the microbe's contribution to the evolution and maintenance of life on Earth, and offers some thoughts about the graduate-level educational programs needed to enhance the maturing field of microbial ecology.

Determining the Diversity and Species Abundance Patterns in Arctic Soils using Rational Methods for Exploring Microbial Diversity

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Ovreas, L.; Quince, C.; Sloan, W.; Lanzen, A.; Davenport, R.; Green, J.; Coulson, S.; Curtis, T.

2012-12-01

Arctic microbial soil communities are intrinsically interesting and poorly characterised. We have inferred the diversity and species abundance distribution of 6 Arctic soils: new and mature soil at the foot of a receding glacier, Arctic Semi Desert, the foot of bird cliffs and soil underlying Arctic Tundra Heath: all near Ny-Ålesund, Spitsbergen. Diversity, distribution and sample sizes were estimated using the rational method of Quince et al., (Isme Journal 2 2008:997-1006) to determine the most plausible underlying species abundance distribution. A log-normal species abundance curve was found to give a slightly better fit than an inverse Gaussian curve if, and only if, sequencing error was removed. The median estimates of diversity of operational taxonomic units (at the 3% level) were 3600-5600 (lognormal assumed) and 2825-4100 (inverse Gaussian assumed). The nature and origins of species abundance distributions are poorly understood but may yet be grasped by observing and analysing such distributions in the microbial world. The sample size required to observe the distribution (by sequencing 90% of the taxa) varied between ~ 106 and ~105 for the lognormal and inverse Gaussian respectively. We infer that between 5 and 50 GB of sequencing would be required to capture 90% or the metagenome. Though a principle components analysis clearly divided the sites into three groups there was a high (20-45%) degree of overlap in between locations irrespective of geographical proximity. Interestingly, the nearest relatives of the most abundant taxa at a number of most sites were of alpine or polar origin. Samples plotted on first two principal components together with arbitrary discriminatory OTUs

From vineyard to winery: a source map of microbial diversity driving wine fermentation.

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Morrison-Whittle, Peter; Goddard, Matthew R

2018-01-01

Humans have been making wine for thousands of years and microorganisms play an integral part in this process as they not only drive fermentation, but also significantly influence the flavour, aroma and quality of finished wines. Since fruits are ephemeral, they cannot comprise a permanent microbial habitat; thus, an age-old unanswered question concerns the origin of fruit and ferment associated microbes. Here we use next-generation sequencing approaches to examine and quantify the roles of native forest, vineyard soil, bark and fruit habitats as sources of fungal diversity in ferments. We show that microbial communities in harvested juice and ferments vary significantly across regions, and that while vineyard fungi account for ∼40% of the source of this diversity, uncultivated ecosystems outside of vineyards also prove a significant source. We also show that while communities in harvested juice resemble those found on grapes, these increasingly resemble fungi present on vine bark as the ferment proceeds. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Invasion by Cordgrass Increases Microbial Diversity and Alters Community Composition in a Mangrove Nature Reserve

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Min Liu

2017-12-01

Full Text Available Invasion by exotic plant species can alter ecosystem function and reduce native plant diversity, but relatively little is known about their effects on belowground microbial communities. Here we investigated the effects of exotic cordgrass (Spartina alterniflora invasion on the distribution of soil bacterial communities in a mangrove nature reserve of the Jiulong River Estuary, southeast China using high-throughput sequencing of 16S rRNA gene and multivariate statistical analysis. Our results showed that S. alterniflora invasion altered soil properties, and significantly increased soil bacterial taxa richness, primarily by stimulating an increase in conditionally rare or rare taxa, and changes in community composition and function. Abundant, conditionally rare and rare subcommunities exhibited similar response patterns to environment changes, with both conditionally rare and rare taxa showing a stronger response than abundant ones. Habitat generalists were detected among abundant, conditionally rare and rare taxa, whereas habitat specialists were only identified among conditionally rare taxa and rare taxa. In addition, we found that vegetation was the key factor driving these patterns. However, our comparative analysis indicated that both environmental selection, and neutral process, significantly contributed to soil bacterial community assembly. These results could improve the understanding of the microbial processes and mechanisms of cordgrass invasion, and offer empirical data of use in the restoration and management of the mangrove wetlands.

Taxonomic and functional characteristics of microbial communities and their correlation with physicochemical properties of four geothermal springs in Odisha, India.

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Badhai, Jhasketan; Ghosh, Tarini S; Das, Subrata K

2015-01-01

This study describes microbial diversity in four tropical hot springs representing moderately thermophilic environments (temperature range: 40-58°C; pH: 7.2-7.4) with discrete geochemistry. Metagenome sequence data showed a dominance of Bacteria over Archaea; the most abundant phyla were Chloroflexi and Proteobacteria, although other phyla were also present, such as Acetothermia, Nitrospirae, Acidobacteria, Firmicutes, Deinococcus-Thermus, Bacteroidetes, Thermotogae, Euryarchaeota, Verrucomicrobia, Ignavibacteriae, Cyanobacteria, Actinobacteria, Planctomycetes, Spirochaetes, Armatimonadetes, Crenarchaeota, and Aquificae. The distribution of major genera and their statistical correlation analyses with the physicochemical parameters predicted that the temperature, aqueous concentrations of ions (such as sodium, chloride, sulfate, and bicarbonate), total hardness, dissolved solids and conductivity were the main environmental variables influencing microbial community composition and diversity. Despite the observed high taxonomic diversity, there were only little variations in the overall functional profiles of the microbial communities in the four springs. Genes involved in the metabolism of carbohydrates and carbon fixation were the most abundant functional class of genes present in these hot springs. The distribution of genes involved in carbon fixation predicted the presence of all the six known autotrophic pathways in the metagenomes. A high prevalence of genes involved in membrane transport, signal transduction, stress response, bacterial chemotaxis, and flagellar assembly were observed along with genes involved in the pathways of xenobiotic degradation and metabolism. The analysis of the metagenomic sequences affiliated to the candidate phylum Acetothermia from spring TB-3 provided new insight into the metabolism and physiology of yet-unknown members of this lineage of bacteria.

Taxonomic and functional characteristics of microbial communities and their correlation with physicochemical properties of four geothermal springs in Odisha, India

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Subrata K Das

2015-10-01

Full Text Available This study describes microbial diversity in four tropical hot springs representing moderately thermophilic environments (temperature range: 40-58 °C; pH: 7.2-7.4 with discrete geochemistry. Metagenome sequence data showed a dominance of Bacteria over Archaea; the most abundant phyla were Chloroflexi and Proteobacteria, although other phyla were also present, such as Acetothermia, Nitrospirae, Acidobacteria, Firmicutes, Deinococcus-Thermus, Bacteroidetes, Thermotogae, Euryarchaeota, Verrucomicrobia, Ignavibacteriae, Cyanobacteria, Actinobacteria, Planctomycetes, Spirochaetes, Armatimonadetes, Crenarchaeota, and Aquificae. The distribution of major genera and their statistical correlation analyses with the physicochemical parameters predicted that the temperature, aqueous concentrations of ions (such as sodium, chloride, sulfate, and bicarbonate, total hardness, dissolved solids and conductivity were the main environmental variables influencing microbial community composition and diversity. Despite the observed high taxonomic diversity, there were only little variations in the overall functional profiles of the microbial communities in the four springs. Genes involved in the metabolism of carbohydrates and carbon fixation were the most abundant functional class of genes present in these hot springs. The distribution of genes involved in carbon fixation predicted the presence of all the six known autotrophic pathways in the metagenomes. A high prevalence of genes involved in membrane transport, signal transduction, stress response, bacterial chemotaxis and flagellar assembly were observed along with genes involved in the pathways of xenobiotic degradation and metabolism. The analysis of the metagenomic sequences affiliated to the candidate phylum Acetothermia from spring TB-3 provided new insight into the metabolism and physiology of yet-unknown members of this lineage of bacteria.

Optimized cryopreservation of mixed microbial communities for conserved functionality and diversity.

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Frederiek-Maarten Kerckhof

Full Text Available The use of mixed microbial communities (microbiomes for biotechnological applications has steadily increased over the past decades. However, these microbiomes are not readily available from public culture collections, hampering their potential for widespread use. The main reason for this lack of availability is the lack of an effective cryopreservation protocol. Due to this critical need, we evaluated the functionality as well as the community structure of three different types of microbiomes before and after cryopreservation with two cryoprotective agents (CPA. Microbiomes were selected based upon relevance towards applications: (1 a methanotrophic co-culture (MOB, with potential for mitigation of greenhouse gas emissions, environmental pollutants removal and bioplastics production; (2 an oxygen limited autotrophic nitrification/denitrification (OLAND biofilm, with enhanced economic and ecological benefits for wastewater treatment, and (3 fecal material from a human donor, with potential applications for fecal transplants and pre/probiotics research. After three months of cryopreservation at -80 °C, we found that metabolic activity, in terms of the specific activity recovery of MOB, aerobic ammonium oxidizing bacteria (AerAOB and anaerobic AOB (AnAOB, anammox in the OLAND mixed culture, resumes sooner when one of our selected CPA [dimethyl sulfoxide (DMSO and DMSO plus trehalose and tryptic soy broth (DMSO+TT] was added. However, the activity of the fecal community was not influenced by the CPA addition, although the preservation of the community structure (as determined by 16S rRNA gene sequencing was enhanced by addition of CPA. In summary, we have evaluated a cryopreservation protocol that succeeded in preserving both community structure and functionality of value-added microbiomes. This will allow individual laboratories and culture collections to boost the use of microbiomes in biotechnological applications.

Microbial diversity in acidic thermal pools in the Uzon Caldera, Kamchatka.

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Mardanov, Andrey V; Gumerov, Vadim M; Beletsky, Alexey V; Ravin, Nikolai V

2018-01-01

Microbial communities of four acidic thermal pools in the Uzon Caldera, Kamchatka, Russia, were studied using amplification and pyrosequencing of 16S rRNA gene fragments. The sites differed in temperature and pH: 1805 (60 °C, pH 3.7), 1810 (90 °C, pH 4.1), 1818 (80 °C, pH 3.5), and 1807 (86 °C, pH 5.6). Archaea of the order Sulfolobales were present among the dominant groups in all four pools. Acidilobales dominated in pool 1818 but were a minor fraction at the higher temperature in pool 1810. Uncultivated Archaea of the Hot Thaumarchaeota-related clade were present in significant quantities in pools 1805 and 1807, but they were not abundant in pools 1810 and 1818, where high temperatures were combined with low pH. Nanoarchaeota were present in all pools, but were more abundant in pools 1810 and 1818. A similar abundance pattern was observed for Halobacteriales. Thermophilic Bacteria were less diverse and were mostly represented by aerobic hydrogen- and sulfur-oxidizers of the phylum Aquificae and sulfur-oxidising Proteobacteria of the genus Acidithiobacillus. Thus we showed that extremely acidic hot pools contain diverse microbial communities comprising different metabolic groups of prokaryotes, including putative lithoautotrophs using energy sources of volcanic origin, and various facultative and obligate heterotrophs.

Microbial ecology and biogeochemistry of continental Antarctic soils.

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Cowan, Don A; Makhalanyane, Thulani P; Dennis, Paul G; Hopkins, David W

2014-01-01

The Antarctica Dry Valleys are regarded as the coldest hyperarid desert system on Earth. While a wide variety of environmental stressors including very low minimum temperatures, frequent freeze-thaw cycles and low water availability impose severe limitations to life, suitable niches for abundant microbial colonization exist. Antarctic desert soils contain much higher levels of microbial diversity than previously thought. Edaphic niches, including cryptic and refuge habitats, microbial mats and permafrost soils all harbor microbial communities which drive key biogeochemical cycling processes. For example, lithobionts (hypoliths and endoliths) possess a genetic capacity for nitrogen and carbon cycling, polymer degradation, and other system processes. Nitrogen fixation rates of hypoliths, as assessed through acetylene reduction assays, suggest that these communities are a significant input source for nitrogen into these oligotrophic soils. Here we review aspects of microbial diversity in Antarctic soils with an emphasis on functionality and capacity. We assess current knowledge regarding adaptations to Antarctic soil environments and highlight the current threats to Antarctic desert soil communities.

Microbial biogeography of San Francisco Bay sediments

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Lee, J. A.; Francis, C. A.

2014-12-01

The largest estuary on the west coast of North America, San Francisco Bay is an ecosystem of enormous biodiversity, and also enormous human impact. The benthos has experienced dredging, occupation by invasive species, and over a century of sediment input as a result of hydraulic mining. Although the Bay's great cultural and ecological importance has inspired numerous surveys of the benthic macrofauna, to date there has been almost no investigation of the microbial communities on the Bay floor. An understanding of those microbial communities would contribute significantly to our understanding of both the biogeochemical processes (which are driven by the microbiota) and the physical processes (which contribute to microbial distributions) in the Bay. Here, we present the first broad survey of bacterial and archaeal taxa in the sediments of the San Francisco Bay. We conducted 16S rRNA community sequencing of bacteria and archaea in sediment samples taken bimonthly for one year, from five sites spanning the salinity gradient between Suisun and Central Bay, in order to capture the effect of both spatial and temporal environmental variation on microbial diversity. From the same samples we also conducted deep sequencing of a nitrogen-cycling functional gene, nirS, allowing an assessment of evolutionary diversity at a much finer taxonomic scale within an important and widespread functional group of bacteria. We paired these sequencing projects with extensive geochemical metadata as well as information about macrofaunal distribution. Our data reveal a diversity of distinct biogeographical patterns among different taxa: clades ubiquitous across sites; clades that respond to measurable environmental drivers; and clades that show geographical site-specificity. These community datasets allow us to test the hypothesis that salinity is a major driver of both overall microbial community structure and community structure of the denitrifying bacteria specifically; and to assess

Microbial diversity in opalinus clay and interaction of dominant microbial strains with actinides

International Nuclear Information System (INIS)

Moll, Henry; Luetke, Laura; Bachvarova, Velina; Steudtner, Robin; Geissler, Andrea; Krawczyk-Baersch, Evelyn; Selenska-Pobell, Sonja; Bernhardt, Gert

2013-01-01

For the first time microbial tDNA could be isolated from 50 g unperturbed Mont Terri Opalinus Clay. Based on the analysis of the tDNA the bacterial diversity of the unperturbed clay is dominated by representatives of Firmicutes, Betaproteobacteria, and Bacteriodetes. Firmicutes also dominate after treatment of the clay with R2A medium. Bacteria isolated from Mont Terri Opalinus Clay on R2A medium were related to Sporomusa spp., Paenibacillus spp., and Clostridium spp. All further investigations are concentrated on the unique isolates Sporomusa sp. MT-2 and Paenibacillus sp. MT-2. Cells of the type Sporomusa sp. MT-2 and Paenibacillus sp. MT-2 were comprehensively analyzed in terms of growing, morphology, functional groups of the cell envelope, and cell membrane structure. Strong actinide(An)/lanthanide(Ln)-interactions with the Opalinus Clay isolates and the Aespoe-strain Pseudomonas fluorescens (CCUG 32456) could be determined within a broad pH range (2-8). The metals bind as a function of pH on protonated phosphoryl, carboxyl and deprotonated phosphoryl sites of the respective cell membrane. The thermodynamic surface complexation constants of bacterial An/Ln-species were determined and can be used in modeling programs. Depending on the used An different interaction mechanisms were found (U(VI): biosorption, partly biomineralisation; Cm(III): biosorption, indications for embedded Cm(III); Pu: biosorption, bioreduction and indications for embedded Pu). Different strategies of coping with U(VI) were observed comparing P. fluorescens planktonic cells and biofilms under the chosen experimental conditions. An enhanced capability of the biofilm to form meta-autunite in comparison to the planktonic cells was proven. Conclusively, the P. fluorescens biofilm is more efficient in U(VI) detoxification. In conclusion, Mont Terri Opalinus Clay contains bacterial communities, that may influence the speciation and hence the migration behavior of selected An/Ln under

Microbial diversity in opalinus clay and interaction of dominant microbial strains with actinides

Energy Technology Data Exchange (ETDEWEB)

Moll, Henry; Luetke, Laura; Bachvarova, Velina; Steudtner, Robin; Geissler, Andrea; Krawczyk-Baersch, Evelyn; Selenska-Pobell, Sonja; Bernhardt, Gert

2013-07-01

For the first time microbial tDNA could be isolated from 50 g unperturbed Mont Terri Opalinus Clay. Based on the analysis of the tDNA the bacterial diversity of the unperturbed clay is dominated by representatives of Firmicutes, Betaproteobacteria, and Bacteriodetes. Firmicutes also dominate after treatment of the clay with R2A medium. Bacteria isolated from Mont Terri Opalinus Clay on R2A medium were related to Sporomusa spp., Paenibacillus spp., and Clostridium spp. All further investigations are concentrated on the unique isolates Sporomusa sp. MT-2 and Paenibacillus sp. MT-2. Cells of the type Sporomusa sp. MT-2 and Paenibacillus sp. MT-2 were comprehensively analyzed in terms of growing, morphology, functional groups of the cell envelope, and cell membrane structure. Strong actinide(An)/lanthanide(Ln)-interactions with the Opalinus Clay isolates and the Aespoe-strain Pseudomonas fluorescens (CCUG 32456) could be determined within a broad pH range (2-8). The metals bind as a function of pH on protonated phosphoryl, carboxyl and deprotonated phosphoryl sites of the respective cell membrane. The thermodynamic surface complexation constants of bacterial An/Ln-species were determined and can be used in modeling programs. Depending on the used An different interaction mechanisms were found (U(VI): biosorption, partly biomineralisation; Cm(III): biosorption, indications for embedded Cm(III); Pu: biosorption, bioreduction and indications for embedded Pu). Different strategies of coping with U(VI) were observed comparing P. fluorescens planktonic cells and biofilms under the chosen experimental conditions. An enhanced capability of the biofilm to form meta-autunite in comparison to the planktonic cells was proven. Conclusively, the P. fluorescens biofilm is more efficient in U(VI) detoxification. In conclusion, Mont Terri Opalinus Clay contains bacterial communities, that may influence the speciation and hence the migration behavior of selected An/Ln under

Phylogenetic and functional diversity of metagenomic libraries of phenol degrading sludge from petroleum refinery wastewater treatment system.

Science.gov (United States)

Silva, Cynthia C; Hayden, Helen; Sawbridge, Tim; Mele, Pauline; Kruger, Ricardo H; Rodrigues, Marili Vn; Costa, Gustavo Gl; Vidal, Ramon O; Sousa, Maíra P; Torres, Ana Paula R; Santiago, Vânia Mj; Oliveira, Valéria M

2012-03-27

In petrochemical refinery wastewater treatment plants (WWTP), different concentrations of pollutant compounds are received daily in the influent stream, including significant amounts of phenolic compounds, creating propitious conditions for the development of particular microorganisms that can rapidly adapt to such environment. In the present work, the microbial sludge from a refinery WWTP was enriched for phenol, cloned into fosmid vectors and pyrosequenced. The fosmid libraries yielded 13,200 clones and a comprehensive bioinformatic analysis of the sequence data set revealed a complex and diverse bacterial community in the phenol degrading sludge. The phylogenetic analyses using MEGAN in combination with RDP classifier showed a massive predominance of Proteobacteria, represented mostly by the genera Diaphorobacter, Pseudomonas, Thauera and Comamonas. The functional classification of phenol degrading sludge sequence data set generated by MG-RAST showed the wide metabolic diversity of the microbial sludge, with a high percentage of genes involved in the aerobic and anaerobic degradation of phenol and derivatives. In addition, genes related to the metabolism of many other organic and xenobiotic compounds, such as toluene, biphenyl, naphthalene and benzoate, were found. Results gathered herein demonstrated that the phenol degrading sludge has complex phylogenetic and functional diversities, showing the potential of such community to degrade several pollutant compounds. This microbiota is likely to represent a rich resource of versatile and unknown enzymes which may be exploited for biotechnological processes such as bioremediation.

A user's guide to functional diversity indices

OpenAIRE

Schleuter, D.; Daufresne, M.; Massol, F.; Argillier, C.

2010-01-01

Functional diversity is the diversity of species traits in ecosystems. This concept is increasingly used in ecological research, yet its formal definition and measurements are currently under discussion. As the overall behaviour and consistency of functional diversity indices have not been described so far, the novice user risks choosing an inaccurate index or a set of redundant indices to represent functional diversity. In our study we closely examine functional diversity indices to clari...

Investigating Microbial Habitats in Hydrothermal Chimneys using Ti-Thermocouple Arrays: Microbial Diversity

Science.gov (United States)

Pagé, A.; Tivey, M. K.; Stakes, D. S.; Bradley, A. M.; Seewald, J. S.; Wheat, C. G.; Reysenbach, A.

2004-12-01

In order to examine the changes that occur in the microbial community composition as a deep-sea hydrothermal vent chimney develops, we deployed Ti-thermocouple arrays over high temperature vents at two active sites of the Guaymas Basin Southern Trough. Chimney material that precipitated around the arrays was recovered after 4 and 72 days. Chimney material that precipitated prior to deployment of the arrays was also recovered at one of the sites (Busted Shroom). Culture-independent analysis based on the small subunit rRNA sequence (cloning and DGGE) was used to determine the microbial diversity associated with subsamples of each chimney. The original Busted Shroom chimney (BSO) was dominated by members of the Crenarchaeota Marine Group I, a group of cosmopolitan marine Archaea, ɛ -Proteobacteria, and γ -Proteobacteria, two divisions of Bacteria that are common to deep-sea vents. The 4 days old Busted Shroom chimney (BSD1) was dominated by members of the Methanocaldococcaceae, hyperthermophilic methanogens, and the 72 days old chimney (BSD2) by members of the Methanosarcinaceae, mesophilic and thermophilic methanogens. At the second site, Toadstool, the 72 days old chimney material that had precipitated around the array (TS) revealed the dominance of sequences from uncultured marine Archaea, the DHVE group I and II, and from the ɛ -Proteobacteria. Additionally, sequences belonging to the Methanocaldococcaceae and Desulfurococcaceae were recovered next to thermocouples that were at temperatures of 109° C (at Busted Shroom) and 116° C (at Toadstool), respectively. These temperatures are higher than the upper limit for growth of cultured representatives from each family.

Comparison of the Microbial Diversity and Abundance Between the Freshwater Land-Locked Lakes of Schirmacher Oasis and the Perennially Ice-Covered Lake Untersee in East Antarctica

Science.gov (United States)

Huang, Jonathan; Hoover, Richard B.; Swain, Ashit; Murdock, Chris; Bej, Asim K.

2010-01-01

Extreme conditions such as low temperature, dryness, and constant UV-radiation in terrestrial Antarctica are limiting factors of the survival of microbial populations. The objective of this study was to investigate the microbial diversity and enumeration between the open water lakes of Schirmacher Oasis and the permanently ice-covered Lake Untersee. The lakes in Schirmacher Oasis possessed abundant and diverse group of microorganisms compared to the Lake Untersee. Furthermore, the microbial diversity between two lakes in Schirmacher Oasis (Lake L27C and L47) was compared by culture-based molecular approach. It was determined that L27Chad a richer microbial diversity representing 5 different phyla and 7 different genera. In contrast L47 consisted of 4 different phyla and 6 different genera. The difference in microbial community could be due to the wide range of pH between L27C (pH 9.1) and L47 (pH 5.7). Most of the microbes isolated from these lakes consisted of adaptive biological pigmentation. Characterization of the microbial community found in the freshwater lakes of East Antarctica is important because it gives a further glimpse into the adaptation and survival strategies found in extreme conditions.

Functional Enzyme-Based Approach for Linking Microbial Community Functions with Biogeochemical Process Kinetics

Energy Technology Data Exchange (ETDEWEB)

Li, Minjing [School; Qian, Wei-jun [Pacific Northwest National Laboratory, Richland, Washington 99354, United States; Gao, Yuqian [Pacific Northwest National Laboratory, Richland, Washington 99354, United States; Shi, Liang [School; Liu, Chongxuan [Pacific Northwest National Laboratory, Richland, Washington 99354, United States; School

2017-09-28

The kinetics of biogeochemical processes in natural and engineered environmental systems are typically described using Monod-type or modified Monod-type models. These models rely on biomass as surrogates for functional enzymes in microbial community that catalyze biogeochemical reactions. A major challenge to apply such models is the difficulty to quantitatively measure functional biomass for constraining and validating the models. On the other hand, omics-based approaches have been increasingly used to characterize microbial community structure, functions, and metabolites. Here we proposed an enzyme-based model that can incorporate omics-data to link microbial community functions with biogeochemical process kinetics. The model treats enzymes as time-variable catalysts for biogeochemical reactions and applies biogeochemical reaction network to incorporate intermediate metabolites. The sequences of genes and proteins from metagenomes, as well as those from the UniProt database, were used for targeted enzyme quantification and to provide insights into the dynamic linkage among functional genes, enzymes, and metabolites that are necessary to be incorporated in the model. The application of the model was demonstrated using denitrification as an example by comparing model-simulated with measured functional enzymes, genes, denitrification substrates and intermediates

Microbial Diversity and Characteristics in Anaerobic Environments in KURT Groundwater

International Nuclear Information System (INIS)

Roh, Yul; Oh, Jong Min; Rhee, Sung Keun; Yong, Jong Joong

2008-03-01

The Underground Research Tunnel (URT) located in Korea Atomic Energy Research Institute (KAERI), Daejeon, South Korea was recently constructed as an experimental site to study radionuclide transport, biogeochemistry, radionuclide-mineral interactions for the geological disposal of high level nuclear waste. Groundwater sampled from URT was used to examine microbial diversity and to enrich metal reducing bacteria for studying microbe-metal interactions. Genomic analysis indicated that the groundwater contained diverse microorganisms such as metal reducers, metal oxidizers, anaerobic denitrifying bacteria, and bacteria for reductive dechlorination. Metal-reducing bacteria enriched from the groundwater was used to study metal reduction and biomineralization. The metal-reducing bacteria enriched with acetate or lactate as the electron donors showed the bacteria reduced Fe(III)-citrate, Fe(III) oxyhydroxide, Mn(IV) oxide, and Cr(VI) as the electron acceptors. Preliminary study indicated that the enriched bacteria were able to use glucose, lactate, acetate, and hydrogen as electron donors while reducing Fe(III)-citrate or Fe(III) oxyhydroxide as the electron acceptor. The bacteria exhibited diverse mineral precipitation capabilities including the formation of magnetite, siderite, and rhodochrosite. The results indicated that Fe(III)- and metal-reducing communities are present in URT at the KAERI

Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers

Directory of Open Access Journals (Sweden)

Ren Bai

2017-05-01

Full Text Available Paddy rice fields occupy broad agricultural area in China and cover diverse soil types. Microbial community in paddy soils is of great interest since many microorganisms are involved in soil functional processes. In the present study, Illumina Mi-Seq sequencing and functional gene array (GeoChip 4.2 techniques were combined to investigate soil microbial communities and functional gene patterns across the three soil types including an Inceptisol (Binhai, an Oxisol (Leizhou, and an Ultisol (Taoyuan along four profile depths (up to 70 cm in depth in mesocosm incubation columns. Detrended correspondence analysis revealed that distinctly differentiation in microbial community existed among soil types and profile depths, while the manifest variance in functional structure was only observed among soil types and two rice growth stages, but not across profile depths. Along the profile depth within each soil type, Acidobacteria, Chloroflexi, and Firmicutes increased whereas Cyanobacteria, β-proteobacteria, and Verrucomicrobia declined, suggesting their specific ecophysiological properties. Compared to bacterial community, the archaeal community showed a more contrasting pattern with the predominant groups within phyla Euryarchaeota, Thaumarchaeota, and Crenarchaeota largely varying among soil types and depths. Phylogenetic molecular ecological network (pMEN analysis further indicated that the pattern of bacterial and archaeal communities interactions changed with soil depth and the highest modularity of microbial community occurred in top soils, implying a relatively higher system resistance to environmental change compared to communities in deeper soil layers. Meanwhile, microbial communities had higher connectivity in deeper soils in comparison with upper soils, suggesting less microbial interaction in surface soils. Structure equation models were developed and the models indicated that pH was the most representative characteristics of soil type and

Microbial Community and Functional Structure Significantly Varied among Distinct Types of Paddy Soils But Responded Differently along Gradients of Soil Depth Layers.

Science.gov (United States)

Bai, Ren; Wang, Jun-Tao; Deng, Ye; He, Ji-Zheng; Feng, Kai; Zhang, Li-Mei

2017-01-01

Paddy rice fields occupy broad agricultural area in China and cover diverse soil types. Microbial community in paddy soils is of great interest since many microorganisms are involved in soil functional processes. In the present study, Illumina Mi-Seq sequencing and functional gene array (GeoChip 4.2) techniques were combined to investigate soil microbial communities and functional gene patterns across the three soil types including an Inceptisol (Binhai), an Oxisol (Leizhou), and an Ultisol (Taoyuan) along four profile depths (up to 70 cm in depth) in mesocosm incubation columns. Detrended correspondence analysis revealed that distinctly differentiation in microbial community existed among soil types and profile depths, while the manifest variance in functional structure was only observed among soil types and two rice growth stages, but not across profile depths. Along the profile depth within each soil type, Acidobacteria , Chloroflexi , and Firmicutes increased whereas Cyanobacteria , β -proteobacteria , and Verrucomicrobia declined, suggesting their specific ecophysiological properties. Compared to bacterial community, the archaeal community showed a more contrasting pattern with the predominant groups within phyla Euryarchaeota , Thaumarchaeota , and Crenarchaeota largely varying among soil types and depths. Phylogenetic molecular ecological network (pMEN) analysis further indicated that the pattern of bacterial and archaeal communities interactions changed with soil depth and the highest modularity of microbial community occurred in top soils, implying a relatively higher system resistance to environmental change compared to communities in deeper soil layers. Meanwhile, microbial communities had higher connectivity in deeper soils in comparison with upper soils, suggesting less microbial interaction in surface soils. Structure equation models were developed and the models indicated that pH was the most representative characteristics of soil type and

Diversity of nitrogen-fixing bacteria in cyanobacterial mats

NARCIS (Netherlands)

Severin, I.; Acinas, S.G.; Stal, L.J.

2010-01-01

The structure of the microbial community and the diversity of the functional gene for dinitrogenase reductase and its transcripts were investigated by analyzing >1400 16S rRNA gene and nifH sequences from two microbial mats situated in the intertidal zone of the Dutch barrier island Schiermonnikoog.

Archaeal and bacterial diversity in two hot spring microbial mats from a geothermal region in Romania.

Science.gov (United States)

Coman, Cristian; Drugă, Bogdan; Hegedus, Adriana; Sicora, Cosmin; Dragoş, Nicolae

2013-05-01

The diversity of archaea and bacteria was investigated in two slightly alkaline, mesophilic hot springs from the Western Plain of Romania. Phylogenetic analysis showed a low diversity of Archaea, only three Euryarchaeota taxa being detected: Methanomethylovorans thermophila, Methanomassiliicoccus luminyensis and Methanococcus aeolicus. Twelve major bacterial groups were identified, both springs being dominated by Cyanobacteria, Chloroflexi and Proteobacteria. While at the phylum/class-level the microbial mats share a similar biodiversity; at the species level the geothermal springs investigated seem to be colonized by specific consortia. The dominant taxa were filamentous heterocyst-containing Fischerella, at 45 °C and non-heterocyst Leptolyngbya and Geitlerinema, at 55 °C. Other bacterial taxa (Thauera sp., Methyloversatilis universalis, Pannonibacter phragmitetus, Polymorphum gilvum, Metallibacterium sp. and Spartobacteria) were observed for the first time in association with a geothermal habitat. Based on their bacterial diversity the two mats were clustered together with other similar habitats from Europe and part of Asia, most likely the water temperature playing a major role in the formation of specific microbial communities that colonize the investigated thermal springs.

Recovery of microbial diversity and activity during bioremediation following chemical oxidation of diesel contaminated soils

NARCIS (Netherlands)

Sutton, N.B.; Langenhoff, A.A.M.; Hidalgo Lasso, D.; Zaan, van der B.M.; Gaans, van P.; Maphosa, F.; Smidt, H.; Grotenhuis, J.T.C.; Rijnaarts, H.H.M.

2014-01-01

To improve the coupling of in situ chemical oxidation and in situ bioremediation, a systematic analysis was performed of the effect of chemical oxidation with Fenton's reagent, modified Fenton's reagent, permanganate, or persulfate, on microbial diversity and activity during 8 weeks of incubation in

Application of ion torrent sequencing to the assessment of the effect of alkali ballast water treatment on microbial community diversity.

Science.gov (United States)

Fujimoto, Masanori; Moyerbrailean, Gregory A; Noman, Sifat; Gizicki, Jason P; Ram, Michal L; Green, Phyllis A; Ram, Jeffrey L

2014-01-01

The impact of NaOH as a ballast water treatment (BWT) on microbial community diversity was assessed using the 16S rRNA gene based Ion Torrent sequencing with its new 400 base chemistry. Ballast water samples from a Great Lakes ship were collected from the intake and discharge of both control and NaOH (pH 12) treated tanks and were analyzed in duplicates. One set of duplicates was treated with the membrane-impermeable DNA cross-linking reagent propidium mono-azide (PMA) prior to PCR amplification to differentiate between live and dead microorganisms. Ion Torrent sequencing generated nearly 580,000 reads for 31 bar-coded samples and revealed alterations of the microbial community structure in ballast water that had been treated with NaOH. Rarefaction analysis of the Ion Torrent sequencing data showed that BWT using NaOH significantly decreased microbial community diversity relative to control discharge (pPCoA) plots and UPGMA tree analysis revealed that NaOH-treated ballast water microbial communities differed from both intake communities and control discharge communities. After NaOH treatment, bacteria from the genus Alishewanella became dominant in the NaOH-treated samples, accounting for microbial community structure between PMA-processed and non-PMA samples occurred in intake water samples, which exhibited a significantly higher amount of PMA-sensitive cyanobacteria/chloroplast 16S rRNA than their corresponding non-PMA total DNA samples. The community assembly obtained using Ion Torrent sequencing was comparable to that obtained from a subset of samples that were also subjected to 454 pyrosequencing. This study showed the efficacy of alkali ballast water treatment in reducing ballast water microbial diversity and demonstrated the application of new Ion Torrent sequencing techniques to microbial community studies.

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.

Culture-dependent and -independent investigations of microbial diversity on urinary catheters

DEFF Research Database (Denmark)

Xu, Yijuan; Moser, Claus Ernst; Abu Al-Soud, Waleed

2012-01-01

Catheter-associated urinary tract infection is caused by bacteria, which ascend the catheter along its external or internal surface to the bladder and subsequently develop into biofilms on the catheter and uroepithelium. Antibiotic-treated bacteria and bacteria residing in biofilm can be difficult...... to culture. In this study we used culture-based and 16S rRNA gene-based culture-independent methods (fingerprinting, cloning, and pyrosequencing) to determine the microbial diversity of biofilms on 24 urinary catheters. Most of the patients were catheterized for...

Soil microbial functionality in response to the inclusion of cover crop mixtures in agricultural systems

Directory of Open Access Journals (Sweden)

Diego N. Chavarría

2016-06-01

Full Text Available Agricultural systems where monoculture prevails are characterized by fertility losses and reduced contribution to ecosystem services. Including cover crops (CC as part of an agricultural system is a promising choice in sustainable intensification of those demanding systems. We evaluated soil microbial functionality in cash crops in response to the inclusion of CC by analyzing soil microbial functions at two different periods of the agricultural year (cash crop harvest and CC desiccation during 2013 and 2014. Three plant species were used as CC: oat (Avena sativa L., vetch (Vicia sativa L. and radish (Raphanus sativus L. which were sown in two different mixtures of species: oat and radish mix (CC1 and oat, radish and vetch mix (CC2, with soybean monoculture and soybean/corn being the cash crops. The study of community level physiological profiles showed statistical differences in respiration of specific C sources indicating an improvement of catabolic diversity in CC treatments. Soil enzyme activities were also increased with the inclusion of CC mixtures, with values of dehydrogenase activity and fluorescein diacetate hydrolysis up to 38.1% and 35.3% higher than those of the control treatment, respectively. This research evidenced that CC inclusion promotes soil biological quality through a contribution of soil organic carbon, improving the sustainability of agrosystems. The use of a CC mixture of three plant species including the legume vetch increased soil biological processes and catabolic diversity, with no adverse effects on cash crop grain yield.

Soil microbial functionality in response to the inclusion of cover crop mixtures in agricultural systems

Energy Technology Data Exchange (ETDEWEB)

Chavarría, D.N.; Verdenelli, R.A.; Muñoz, M.J.; Conforto, C.; Restovich, S.B.; Andriulo, A.E.; Meriles, J.M.; Vargas-Gil, S.

2016-11-01

Agricultural systems where monoculture prevails are characterized by fertility losses and reduced contribution to ecosystem services. Including cover crops (CC) as part of an agricultural system is a promising choice in sustainable intensification of those demanding systems. We evaluated soil microbial functionality in cash crops in response to the inclusion of CC by analyzing soil microbial functions at two different periods of the agricultural year (cash crop harvest and CC desiccation) during 2013 and 2014. Three plant species were used as CC: oat (Avena sativa L.), vetch (Vicia sativa L.) and radish (Raphanus sativus L.) which weresown in two different mixtures of species: oat and radish mix (CC1) and oat, radish and vetch mix (CC2), with soybean monoculture and soybean/corn being the cash crops. The study of community level physiological profiles showed statistical differences in respiration of specific C sources indicating an improvement of catabolic diversity in CC treatments. Soil enzyme activities were also increased with the inclusion of CC mixtures, with values of dehydrogenase activity and fluorescein diacetate hydrolysis up to 38.1% and 35.3% higher than those of the control treatment, respectively. This research evidenced that CC inclusion promotes soil biological quality through a contribution of soil organic carbon, improving the sustainability of agrosystems. The use of a CC mixture of three plant species including the legume vetch increased soil biological processes and catabolic diversity, with no adverse effects on cash crop grain yield. (Author)

Geochemical Influence on Microbial Diversity in the Warm, Salty, Stinking Spring, Utah, USA

Science.gov (United States)

Spear, J. R.

2012-12-01

Little is known of the geochemistry and microbiology in the Stinking Springs, a sulfidic, saline, warm spring northeast of the Great Salt Lake, Utah. The International Geobiology Course of 2012 investigated the geochemistry, lipid abundances, dissolved inorganic carbon (DIC) uptake rates and microbial diversity on different kinds of samples from a number of locations in the spring. The measured pH, temperature, salinity, and sulfide concentration along the 100 m flow path ranged from 6.64-7.77, 40-28° C, 2.9-2.2%, and 250 μM - negligible, respectively. Five sites were selected along the flow path and within each site microbial mats were sub-sampled according to their morphological characteristics; a range from floating to streamer-style in zones of higher flow rates to highly-layered mats in low- or sheet-flow zones. Geochemical characterization of the above plus metals, anions and cations were conducted at each site. Genomic DNA was extracted from each microbial sample / layer, and 16S rRNA genes were amplified and subjected to pyrosequencing. Fatty acids and pigments were extracted from the mat samples / layers and analyzed by liquid chromatography and mass spectrometry for lipid / pigment composition. Bicarbonate uptake rates for mat samples / layers were determined with 24 hour light and dark incubations of 13HCO3-spiked spring water. Microbial diversity varied by site and was generally high in all three domains of life with phototrophs, sulfur oxidizers, sulfate reducers, methanogens, and other bacteria / archaea identified by 16S rRNA gene sequence. Diatoms, identified by both microscopy and lipid analyses were found to increase in abundance with distance from the source. Methanogens were generally more abundant in deeper mat laminae and underlying sediments. Photoheterotrophs were found in all mat layers. Microbial diversity increased significantly with depth at most sites. In addition, two distinct microbial streamers were also identified and

On the Use of Diversity Measures in Longitudinal Sequencing Studies of Microbial Communities.

Science.gov (United States)

Wagner, Brandie D; Grunwald, Gary K; Zerbe, Gary O; Mikulich-Gilbertson, Susan K; Robertson, Charles E; Zemanick, Edith T; Harris, J Kirk

2018-01-01

Identification of the majority of organisms present in human-associated microbial communities is feasible with the advent of high throughput sequencing technology. As substantial variability in microbiota communities is seen across subjects, the use of longitudinal study designs is important to better understand variation of the microbiome within individual subjects. Complex study designs with longitudinal sample collection require analytic approaches to account for this additional source of variability. A common approach to assessing community changes is to evaluate the change in alpha diversity (the variety and abundance of organisms in a community) over time. However, there are several commonly used alpha diversity measures and the use of different measures can result in different estimates of magnitude of change and different inferences. It has recently been proposed that diversity profile curves are useful for clarifying these differences, and may provide a more complete picture of the community structure. However, it is unclear how to utilize these curves when interest is in evaluating changes in community structure over time. We propose the use of a bi-exponential function in a longitudinal model that accounts for repeated measures on each subject to compare diversity profiles over time. Furthermore, it is possible that no change in alpha diversity (single community/sample) may be observed despite the presence of a highly divergent community composition. Thus, it is also important to use a beta diversity measure (similarity between multiple communities/samples) that captures changes in community composition. Ecological methods developed to evaluate temporal turnover have currently only been applied to investigate changes of a single community over time. We illustrate the extension of this approach to multiple communities of interest (i.e., subjects) by modeling the beta diversity measure over time. With this approach, a rate of change in community

Diversity patterns of microbial eukaryotes mirror those of bacteria in Antarctic cryoconite holes.

Science.gov (United States)

Sommers, Pacifica; Darcy, John L; Gendron, Eli M S; Stanish, Lee F; Bagshaw, Elizabeth A; Porazinska, Dorota L; Schmidt, Steven K

2018-01-01

Ice-lidded cryoconite holes on glaciers in the Taylor Valley, Antarctica, provide a unique system of natural mesocosms for studying community structure and assembly. We used high-throughput DNA sequencing to characterize both microbial eukaryotic communities and bacterial communities within cryoconite holes across three glaciers to study similarities in their spatial patterns. We expected that the alpha (phylogenetic diversity) and beta (pairwise community dissimilarity) diversity patterns of eukaryotes in cryoconite holes would be related to those of bacteria, and that they would be related to the biogeochemical gradient within the Taylor Valley. We found that eukaryotic alpha and beta diversity were strongly related to those of bacteria across scales ranging from 140 m to 41 km apart. Alpha diversity of both was significantly related to position in the valley and surface area of the cryoconite hole, with pH also significantly correlated with the eukaryotic diversity. Beta diversity for both bacteria and eukaryotes was significantly related to position in the valley, with bacterial beta diversity also related to nitrate. These results are consistent with transport of sediments onto glaciers occurring primarily at local scales relative to the size of the valley, thus creating feedbacks in local chemistry and diversity. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Metabolic diversity of the heterotrophic microorganisms and potential link to pollution of the Rouge River

International Nuclear Information System (INIS)

Tiquia, S.M.

2010-01-01

The heterotrophic microbial communities of the Rouge River were tracked using Biolog Ecoplates to understand the metabolic diversity at different temporal and spatial scales, and potential link to river pollution. Site less impacted by anthrophogenic sources (site 1), showed markedly lower metabolic diversity. The only substrates that were utilized in the water samples were carbohydrates. Sites more impacted by anthrophogenic sources (sites 8 and 9) showed higher metabolic diversity. Higher functional diversity was linked to the physico-chemical and biological properties of the water samples (i.e. higher concentrations of DO, DOC, chlorophyll, and bacterial density). Biolog analysis was found to be useful in differentiating metabolic diversity between microbial communities; in determining factors that most influence the separation of communities; and in identifying which substrates were most utilized by the communities. It can also be used as an effective ecological indicator of changes in river function attributable to urbanization and pollution. - BIOLOG differentiated metabolic diversity between microbial communities and can be used as ecological indicator of river function attributable to urbanization and pollution.

Metabolic diversity of the heterotrophic microorganisms and potential link to pollution of the Rouge River

Energy Technology Data Exchange (ETDEWEB)

Tiquia, S.M., E-mail: smtiquia@umd.umich.ed [Department of Natural Sciences, University of Michigan, 115F Science Building, Dearborn, MI 48128 (United States)

2010-05-15

The heterotrophic microbial communities of the Rouge River were tracked using Biolog Ecoplates to understand the metabolic diversity at different temporal and spatial scales, and potential link to river pollution. Site less impacted by anthrophogenic sources (site 1), showed markedly lower metabolic diversity. The only substrates that were utilized in the water samples were carbohydrates. Sites more impacted by anthrophogenic sources (sites 8 and 9) showed higher metabolic diversity. Higher functional diversity was linked to the physico-chemical and biological properties of the water samples (i.e. higher concentrations of DO, DOC, chlorophyll, and bacterial density). Biolog analysis was found to be useful in differentiating metabolic diversity between microbial communities; in determining factors that most influence the separation of communities; and in identifying which substrates were most utilized by the communities. It can also be used as an effective ecological indicator of changes in river function attributable to urbanization and pollution. - BIOLOG differentiated metabolic diversity between microbial communities and can be used as ecological indicator of river function attributable to urbanization and pollution.

Ecosystem Functions across Trophic Levels Are Linked to Functional and Phylogenetic Diversity

Science.gov (United States)

Thompson, Patrick L.; Davies, T. Jonathan; Gonzalez, Andrew

2015-01-01

In experimental systems, it has been shown that biodiversity indices based on traits or phylogeny can outperform species richness as predictors of plant ecosystem function. However, it is unclear whether this pattern extends to the function of food webs in natural ecosystems. Here we tested whether zooplankton functional and phylogenetic diversity explains the functioning of 23 natural pond communities. We used two measures of ecosystem function: (1) zooplankton community biomass and (2) phytoplankton abundance (Chl a). We tested for diversity-ecosystem function relationships within and across trophic levels. We found a strong correlation between zooplankton diversity and ecosystem function, whereas local environmental conditions were less important. Further, the positive diversity-ecosystem function relationships were more pronounced for measures of functional and phylogenetic diversity than for species richness. Zooplankton and phytoplankton biomass were best predicted by different indices, suggesting that the two functions are dependent upon different aspects of diversity. Zooplankton community biomass was best predicted by zooplankton trait-based functional richness, while phytoplankton abundance was best predicted by zooplankton phylogenetic diversity. Our results suggest that the positive relationship between diversity and ecosystem function can extend across trophic levels in natural environments, and that greater insight into variation in ecosystem function can be gained by combining functional and phylogenetic diversity measures. PMID:25693188

Molecular analysis of microbial diversity in advanced caries.

Science.gov (United States)

Chhour, Kim-Ly; Nadkarni, Mangala A; Byun, Roy; Martin, F Elizabeth; Jacques, Nicholas A; Hunter, Neil

2005-02-01

Real-time PCR analysis of the total bacterial load in advanced carious lesions has shown that the total load exceeds the number of cultivable bacteria. This suggests that an unresolved complexity exists in bacteria associated with advanced caries. In this report, the profile of the microflora of carious dentine was explored by using DNA extracted from 10 lesions selected on the basis of comparable total microbial load and on the relative abundance of Prevotella spp. Using universal primers for the 16S rRNA gene, PCR amplicons were cloned, and approximately 100 transformants were processed for each lesion. Phylogenetic analysis of 942 edited sequences demonstrated the presence of 75 species or phylotypes in the 10 carious lesions. Up to 31 taxa were represented in each sample. A diverse array of lactobacilli were found to comprise 50% of the species, with prevotellae also abundant, comprising 15% of the species. Other taxa present in a number of lesions or occurring with high abundance included Selenomonas spp., Dialister spp., Fusobacterium nucleatum, Eubacterium spp., members of the Lachnospiraceae family, Olsenella spp., Bifidobacterium spp., Propionibacterium sp., and Pseudoramibacter alactolyticus. The mechanisms by which such diverse patterns of bacteria extend carious lesions, including the aspect of infection of the vital dental pulp, remain unclear.

A resurgence in field research is essential to better understand the diversity, ecology, and evolution of microbial eukaryotes.

Science.gov (United States)

Heger, Thierry J; Edgcomb, Virginia P; Kim, Eunsoo; Lukeš, Julius; Leander, Brian S; Yubuki, Naoji

2014-01-01

The discovery and characterization of protist communities from diverse environments are crucial for understanding the overall evolutionary history of life on earth. However, major questions about the diversity, ecology, and evolutionary history of protists remain unanswered, notably because data obtained from natural protist communities, especially of heterotrophic species, remain limited. In this review, we discuss the challenges associated with "field protistology", defined here as the exploration, characterization, and interpretation of microbial eukaryotic diversity within the context of natural environments or field experiments, and provide suggestions to help fill this important gap in knowledge. We also argue that increased efforts in field studies that combine molecular and microscopical methods offer the most promising path toward (1) the discovery of new lineages that expand the tree of eukaryotes; (2) the recognition of novel evolutionary patterns and processes; (3) the untangling of ecological interactions and functions, and their roles in larger ecosystem processes; and (4) the evaluation of protist adaptations to a changing climate. © 2013 The Author(s) Journal of Eukaryotic Microbiology © 2013 International Society of Protistologists.

New directions in coral reef microbial ecology.

Science.gov (United States)

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.

Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.

KAUST Repository

Ferreira, Ari J S

2014-06-12

Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world\\'s oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light.

Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.

KAUST Repository

Ferreira, Ari J S; Siam, Rania; Setubal, Joã o C; Moustafa, Ahmed; Sayed, Ahmed; Chambergo, Felipe S; Dawe, Adam S; Ghazy, Mohamed A; Sharaf, Hazem; Ouf, Amged; Alam, Intikhab; Abdel-Haleem, Alyaa M; Lehvä slaiho, Heikki; Ramadan, Eman; Antunes, André ; Stingl, Ulrich; Archer, John A.C.; Jankovic, Boris R; Sogin, Mitchell; Bajic, Vladimir B.; El-Dorry, Hamza

2014-01-01

Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs) of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light.

Core microbial functional activities in ocean environments revealed by global metagenomic profiling analyses.

Directory of Open Access Journals (Sweden)

Ari J S Ferreira

Full Text Available Metagenomics-based functional profiling analysis is an effective means of gaining deeper insight into the composition of marine microbial populations and developing a better understanding of the interplay between the functional genome content of microbial communities and abiotic factors. Here we present a comprehensive analysis of 24 datasets covering surface and depth-related environments at 11 sites around the world's oceans. The complete datasets comprises approximately 12 million sequences, totaling 5,358 Mb. Based on profiling patterns of Clusters of Orthologous Groups (COGs of proteins, a core set of reference photic and aphotic depth-related COGs, and a collection of COGs that are associated with extreme oxygen limitation were defined. Their inferred functions were utilized as indicators to characterize the distribution of light- and oxygen-related biological activities in marine environments. The results reveal that, while light level in the water column is a major determinant of phenotypic adaptation in marine microorganisms, oxygen concentration in the aphotic zone has a significant impact only in extremely hypoxic waters. Phylogenetic profiling of the reference photic/aphotic gene sets revealed a greater variety of source organisms in the aphotic zone, although the majority of individual photic and aphotic depth-related COGs are assigned to the same taxa across the different sites. This increase in phylogenetic and functional diversity of the core aphotic related COGs most probably reflects selection for the utilization of a broad range of alternate energy sources in the absence of light.

Development of functional composts using spent coffee grounds, poultry manure and biochar through microbial bioaugmentation.

Science.gov (United States)

Emmanuel, S Aalfin; Yoo, Jangyeon; Kim, Eok-Jo; Chang, Jae-Soo; Park, Young-In; Koh, Sung-Cheol

2017-11-02

Spent coffee grounds (SCG), poultry manure, and agricultural waste-derived biochar were used to manufacture functional composts through microbial bioaugmentation. The highest yield of tomato stalk-based biochar (40.7%) was obtained at 450°C with a surface area of 2.35 m 2 g -1 . Four pilot-scale composting reactors were established to perform composting for 45 days. The ratios of NH 4 + -N/NO 3 - -N, which served as an indicator of compost maturity, indicate rapid, and successful composting via microbial bioaugmentation and biochar amendment. Moreover, germination indices for radish also increased by 14-34% through augmentation and biochar amendment. Microbial diversity was also enhanced in the augmented and biochar-amended composts by 7.1-8.9%, where two species of Sphingobacteriaceae were dominant (29-43%). The scavenging activities of 2,2-diphenyl-1-picrylhydrazyl (DPPH) were enhanced by 14.1% and 8.6% in the fruits of pepper plants grown in the presence of the TR-2 (augmentation applied only) and TR-3 (both augmentation and biochar amendment applied) composts, respectively. Total phenolic content was also enhanced by 68% in the fruits of the crops grown in TR-3. Moreover, the other compost, TR-L (augmentation applied only), boosted DPPH scavenging activity by 111% in leeks compared with commercial organic fertilizer, while TR-3 increased the phenolic content by 44.8%. Composting facilitated by microbial augmentation and biochar amendment shortened the composting time and enhanced the quality of the functional compost. These results indicate that functional compost has great potential to compete with commercially available organic fertilizers and that the novel composting technology could significantly contribute to the eco-friendly recycling of organic wastes such as spent coffee grounds, poultry manure, and agricultural wastes.

Interpreting ecological diversity indices applied to terminal restriction fragment length polymorphism data: insights from simulated microbial communities.

Science.gov (United States)

Blackwood, Christopher B; Hudleston, Deborah; Zak, Donald R; Buyer, Jeffrey S

2007-08-01

Ecological diversity indices are frequently applied to molecular profiling methods, such as terminal restriction fragment length polymorphism (T-RFLP), in order to compare diversity among microbial communities. We performed simulations to determine whether diversity indices calculated from T-RFLP profiles could reflect the true diversity of the underlying communities despite potential analytical artifacts. These include multiple taxa generating the same terminal restriction fragment (TRF) and rare TRFs being excluded by a relative abundance (fluorescence) threshold. True community diversity was simulated using the lognormal species abundance distribution. Simulated T-RFLP profiles were generated by assigning each species a TRF size based on an empirical or modeled TRF size distribution. With a typical threshold (1%), the only consistently useful relationship was between Smith and Wilson evenness applied to T-RFLP data (TRF-E(var)) and true Shannon diversity (H'), with correlations between 0.71 and 0.81. TRF-H' and true H' were well correlated in the simulations using the lowest number of species, but this correlation declined substantially in simulations using greater numbers of species, to the point where TRF-H' cannot be considered a useful statistic. The relationships between TRF diversity indices and true indices were sensitive to the relative abundance threshold, with greatly improved correlations observed using a 0.1% threshold, which was investigated for comparative purposes but is not possible to consistently achieve with current technology. In general, the use of diversity indices on T-RFLP data provides inaccurate estimates of true diversity in microbial communities (with the possible exception of TRF-E(var)). We suggest that, where significant differences in T-RFLP diversity indices were found in previous work, these should be reinterpreted as a reflection of differences in community composition rather than a true difference in community diversity.

Microbial ecology and biogeochemistry of continental Antarctic soils

Directory of Open Access Journals (Sweden)

Don A Cowan

2014-04-01

Full Text Available The Antarctica Dry Valleys are regarded as the coldest hyperarid desert system on Earth. While a wide variety of environmental stressors including very low minimum temperatures, frequent freeze-thaw cycles and low water availability impose severe limitations to life, suitable niches for abundant microbial colonization exist. Antarctic desert soils contain much higher levels of microbial diversity than previously thought. Edaphic niches, including cryptic and refuge habitats, microbial mats and permafrost soils all harbour microbial communities which drive key biogeochemical cycling processes. For example, lithobionts (hypoliths and endoliths possess a genetic capacity for nitrogen and carbon cycling, polymer degradation and other system processes. Nitrogen fixation rates of hypoliths, as assessed through acetylene reduction assays, suggest that these communities are a significant input source for nitrogen into these oligotrophic soils. Here we review aspects of microbial diversity in Antarctic soils with an emphasis on functionality and capacity. We assess current knowledge regarding adaptations to Antarctic soil environments and highlight the current threats to Antarctic desert soil communities.

A survey of microbial community diversity in marine sediments impacted by petroleum hydrocarbons from the Gulf of Mexico and Atlantic shorelines, Texas to Florida

Science.gov (United States)

Lisle, John T.; Stellick, Sarah H.

2011-01-01

Microbial community genomic DNA was extracted from sediment samples collected along the Gulf of Mexico and Atlantic coasts from Texas to Florida. Sample sites were identified as being ecologically sensitive and (or) as having high potential of being impacted by Macondo-1 (M-1) well oil from the Deepwater Horizon blowout. The diversity within the microbial communities associated with the collected sediments provides a baseline dataset to which microbial community-diversity data from impacted sites could be compared. To determine the microbial community diversity in the samples, genetic fingerprints were generated and compared. Specific sequences within the community genomic DNA were first amplified using the polymerase chain reaction (PCR) with a primer set that provides possible resolution to the species level. A second nested PCR was performed on the primary PCR products using a primer set on which a GC-clamp was attached to one of the primers. The nested PCR products were separated using denaturing-gradient gel electrophoresis (DGGE) that resolves the nested PCR products based on sequence dissimilarities (or similarities), forming a genomic fingerprint of the microbial diversity within the respective samples. Samples with similar fingerprints were grouped and compared to oil-fingerprint data from the same sites (Rosenbauer and others, 2011). The microbial community fingerprints were generally grouped into sites that had been shown to contain background concentrations of non-Deepwater Horizon oil. However, these groupings also included sites where no oil signature was detected. This report represents some of the first information on naturally occurring microbial communities in sediment from shorelines along the Gulf of Mexico and Atlantic coasts from Texas to Florida.