Metaproteomics: extracting and mining proteome information to characterize metabolic activities in microbial communities.

Science.gov (United States)

Abraham, Paul E; Giannone, Richard J; Xiong, Weili; Hettich, Robert L

2014-06-17

Contemporary microbial ecology studies usually employ one or more "omics" approaches to investigate the structure and function of microbial communities. Among these, metaproteomics aims to characterize the metabolic activities of the microbial membership, providing a direct link between the genetic potential and functional metabolism. The successful deployment of metaproteomics research depends on the integration of high-quality experimental and bioinformatic techniques for uncovering the metabolic activities of a microbial community in a way that is complementary to other "meta-omic" approaches. The essential, quality-defining informatics steps in metaproteomics investigations are: (1) construction of the metagenome, (2) functional annotation of predicted protein-coding genes, (3) protein database searching, (4) protein inference, and (5) extraction of metabolic information. In this article, we provide an overview of current bioinformatic approaches and software implementations in metaproteome studies in order to highlight the key considerations needed for successful implementation of this powerful community-biology tool. Copyright © 2014 John Wiley & Sons, Inc.

Microbial Metabolism and Inhibition Studies of Phenobarbital

African Journals Online (AJOL)

Erah

techniques, high performance liquid chromatography (HPLC), mass spectrometry (MS) ... Keywords: Microbial metabolism, Phenobarbital, Inhibition studies, Rhizopus stolonifer, CYP 2C9, .... 24 h of incubation 0.5 ml of drug solution was ... mode, positive: spray voltage, 3.5 KV: ... Rhizopus stolonifer showed an extra peak at.

Microbial diversity and metabolic networks in acid mine drainage habitats

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Celia eMendez-Garcia

2015-05-01

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

An Inquiry-Based Laboratory Design for Microbial Ecology

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Tessier, Jack T.; Penniman, Clayton A.

2006-01-01

There is a collective need to increase the use of inquiry-based instruction at the college level. This paper provides of an example of how inquiry was successfully used in the laboratory component of an undergraduate course in microbial ecology. Students were offered a collection of field and laboratory methods to choose from, and they developed a…

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

Science.gov (United States)

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

2017-01-01

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

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

Directory of Open Access Journals (Sweden)

María Camila Alvarez-Silva

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

Metabolomic applications to decipher gut microbial metabolic influence in health and disease

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Francois-Pierre eMartin

2012-04-01

Full Text Available Dietary preferences and nutrients composition have been shown to influence human and gut microbial metabolism, which ultimately has specific effects on health and diseases’ risk. Increasingly, results from molecular biology and microbiology demonstrate the key role of the gut microbiota metabolic interface to the overall mammalian host’s health status. There is therefore raising interest in nutrition research to characterize the molecular foundations of the gut microbial mammalian cross-talk at both physiological and biochemical pathway levels. Tackling these challenges can be achieved through systems biology approaches, such as metabolomics, to underpin the highly complex metabolic exchanges between diverse biological compartments, including organs, systemic biofluids and microbial symbionts. By the development of specific biomarkers for prediction of health and disease, metabolomics is increasingly used in clinical applications as regard to disease aetiology, diagnostic stratification and potentially mechanism of action of therapeutical and nutraceutical solutions. Surprisingly, an increasing number of metabolomics investigations in pre-clinical and clinical studies based on proton nuclear magnetic resonance (1H NMR spectroscopy and mass spectrometry (MS provided compelling evidence that system wide and organ-specific biochemical processes are under the influence of gut microbial metabolism. This review aims at describing recent applications of metabolomics in clinical fields where main objective is to discern the biochemical mechanisms under the influence of the gut microbiota, with insight into gastrointestinal health and diseases diagnostics and improvement of homeostasis metabolic regulation.

Nitrification-driven forms of nitrogen metabolism in microbial mat communities thriving along an ammonium-enriched subsurface geothermal stream

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Nishizawa, Manabu; Koba, Keisuke; Makabe, Akiko; Yoshida, Naohiro; Kaneko, Masanori; Hirao, Shingo; Ishibashi, Jun-ichiro; Yamanaka, Toshiro; Shibuya, Takazo; Kikuchi, Tohru; Hirai, Miho; Miyazaki, Junichi; Nunoura, Takuro; Takai, Ken

2013-07-01

We report here the concurrence and interaction among forms of nitrogen metabolism in thermophilic microbial mat communities that developed in an ammonium-abundant subsurface geothermal stream. First, the physical and chemical conditions of the stream water at several representative microbial mat habitats (including upper, middle and downstream sites) were characterized. A thermodynamic calculation using these physical and chemical conditions predicted that nitrification consisting of ammonia and nitrite oxidations would provide one of the largest energy yields of chemolithotrophic metabolisms. Second, near-complete prokaryotic 16S rRNA gene clone analysis was conducted for representative microbial mat communities at the upper, middle and downstream sites. The results indicated a dynamic shift in the 16S rRNA gene phylotype composition through physical and chemical variations of the stream water. The predominant prokaryotic components varied from phylotypes related to hydrogeno (H2)- and thio (S)-trophic Aquificales, thermophilic methanotrophs and putative ammonia-oxidizing Archaea (AOA) located upstream (72 °C) to the phylotypes affiliated with putative AOA and nitrite-oxidizing bacteria (NOB) located at the middle and downstream sites (65 and 57 °C, respectively). In addition, the potential in situ metabolic activities of different forms of nitrogen metabolism were estimated through laboratory experiments using bulk microbial mat communities. Finally, the compositional and isotopic variation in nitrogen compounds was investigated in the stream water flowing over the microbial mats and in the interstitial water inside the mats. Although the stream water was characterized by a gradual decrease in the total ammonia concentration (ΣNH3: the sum of ammonia and ammonium concentrations) and a gradual increase in the total concentration of nitrite and nitrate (NO2- + NO3-), the total inorganic nitrogen concentration (TIN: the sum of ΣNH3, NO2- and NO3- concentrations

Genome-scale modelling of microbial metabolism with temporal and spatial resolution.

Science.gov (United States)

Henson, Michael A

2015-12-01

Most natural microbial systems have evolved to function in environments with temporal and spatial variations. A major limitation to understanding such complex systems is the lack of mathematical modelling frameworks that connect the genomes of individual species and temporal and spatial variations in the environment to system behaviour. The goal of this review is to introduce the emerging field of spatiotemporal metabolic modelling based on genome-scale reconstructions of microbial metabolism. The extension of flux balance analysis (FBA) to account for both temporal and spatial variations in the environment is termed spatiotemporal FBA (SFBA). Following a brief overview of FBA and its established dynamic extension, the SFBA problem is introduced and recent progress is described. Three case studies are reviewed to illustrate the current state-of-the-art and possible future research directions are outlined. The author posits that SFBA is the next frontier for microbial metabolic modelling and a rapid increase in methods development and system applications is anticipated. © 2015 Authors; published by Portland Press Limited.

Gut Microbial Glycerol Metabolism as an Endogenous Acrolein Source

OpenAIRE

Zhang, Jianbo; Sturla, Shana; Lacroix, Christophe; Schwab, Clarissa

2018-01-01

ABSTRACT Acrolein is a highly reactive electrophile causing toxic effects, such as DNA and protein adduction, oxidative stress, endoplasmic reticulum stress, immune dysfunction, and membrane damage. This Opinion/Hypothesis provides an overview of endogenous and exogenous acrolein sources, acrolein’s mode of action, and its metabolic fate. Recent reports underpin the finding that gut microbial glycerol metabolism leading to the formation of reuterin is an additional source of endogenous acrole...

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

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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

Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0.

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Brian R Granger

2016-04-01

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

Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0.

Science.gov (United States)

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

2016-04-01

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

Soil Microbial Community Contribution to Small Headwater Stream Metabolism.

Science.gov (United States)

Clapcott, J. E.; Gooderham, J. P.; Barmuta, L. A.; Davies, P. E.

2005-05-01

The temporal dynamics of sediment respiration were examined in seven small headwater streams in forested catchments in 2004. A strong seasonal response was observed with higher respiration rates in depositional zones than in gravel runs. The data were also examined in the context of proportional habitat distributions that highlighted the importance of high flow events in shaping whole stream metabolic budgets. This study specifically examines the question of terrestrial soil respiration contribution to whole stream metabolism by the controlled inundation of terrestrial soils. The experiment included six experimentally inundated terrestrial zones, six terrestrial controls, and six in-stream depositional zones. Sediment bacterial respiration was measured using 14C leucine incorporation and cotton strip bioassays were also employed to provide an indicative measure of sediment microbial activity. Despite high variability and exhibiting significantly lower bacterial activity than in-stream sediments, modelling using flow data and habitat mapping illustrated the important contribution of terrestrial soil respiration to the whole stream metabolic budgets of small headwater streams. In addition, microbial community composition examined using phospholipid fatty acid analysis clearly differentiated between terrestrial and aquatic communities. Freshly inundated terrestrial communities remained similar to un-inundated controls after 28 days.

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.

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

Science.gov (United States)

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.

Does canine inflammatory bowel disease influence gut microbial profile and host metabolism?

OpenAIRE

Xu, Jia; Verbrugghe, Adronie; Louren?o, Marta; Janssens, Geert P. J.; Liu, Daisy J. X.; Van de Wiele, Tom; Eeckhaut, Venessa; Van Immerseel, Filip; Van de Maele, Isabel; Niu, Yufeng; Bosch, Guido; Junius, Greet; Wuyts, Brigitte; Hesta, Myriam

2016-01-01

Background Inflammatory bowel disease (IBD) refers to a diverse group of chronic gastrointestinal diseases, and gut microbial dysbiosis has been proposed as a modulating factor in its pathogenesis. Several studies have investigated the gut microbial ecology of dogs with IBD but it is yet unclear if this microbial profile can alter the nutrient metabolism of the host. The aim of the present study was to characterize the faecal bacterial profile and functionality as well as to determine host me...

Balancing cellular redox metabolism in microbial electrosynthesis and electro fermentation - A chance for metabolic engineering.

Science.gov (United States)

Kracke, Frauke; Lai, Bin; Yu, Shiqin; Krömer, Jens O

2018-01-01

More and more microbes are discovered that are capable of extracellular electron transfer, a process in which they use external electrodes as electron donors or acceptors for metabolic reactions. This feature can be used to overcome cellular redox limitations and thus optimizing microbial production. The technologies, termed microbial electrosynthesis and electro-fermentation, have the potential to open novel bio-electro production platforms from sustainable energy and carbon sources. However, the performance of reported systems is currently limited by low electron transport rates between microbes and electrodes and our limited ability for targeted engineering of these systems due to remaining knowledge gaps about the underlying fundamental processes. Metabolic engineering offers many opportunities to optimize these processes, for instance by genetic engineering of pathways for electron transfer on the one hand and target product synthesis on the other hand. With this review, we summarize the status quo of knowledge and engineering attempts around chemical production in bio-electrochemical systems from a microbe perspective. Challenges associated with the introduction or enhancement of extracellular electron transfer capabilities into production hosts versus the engineering of target compound synthesis pathways in natural exoelectrogens are discussed. Recent advances of the research community in both directions are examined critically. Further, systems biology approaches, for instance using metabolic modelling, are examined for their potential to provide insight into fundamental processes and to identify targets for metabolic engineering. Copyright © 2017 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Fire vs. Metal: A Laboratory Study Demonstrating Microbial Responses to Soil Disturbances

Science.gov (United States)

Stromberger, Mary E.

2005-01-01

Incubation studies are traditionally used in soil microbiology laboratory classes to demonstrate microbial respiration and N mineralization-immobilization processes. Sometimes these exercises are done to calculate a N balance in N fertilizer-amended soils. However, examining microbial responses to environmental perturbations would appeal to soil…

Genome-driven evolutionary game theory helps understand the rise of metabolic interdependencies in microbial communities.

Science.gov (United States)

Zomorrodi, Ali R; Segrè, Daniel

2017-11-16

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

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

Science.gov (United States)

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

2014-01-01

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

Functional Gene Diversity and Metabolic Potential of the Microbial Community in an Estuary-Shelf Environment

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Yu Wang

2017-06-01

Full Text Available Microbes play crucial roles in various biogeochemical processes in the ocean, including carbon (C, nitrogen (N, and phosphorus (P cycling. Functional gene diversity and the structure of the microbial community determines its metabolic potential and therefore its ecological function in the marine ecosystem. However, little is known about the functional gene composition and metabolic potential of bacterioplankton in estuary areas. The East China Sea (ECS is a dynamic marginal ecosystem in the western Pacific Ocean that is mainly affected by input from the Changjiang River and the Kuroshio Current. Here, using a high-throughput functional gene microarray (GeoChip, we analyzed the functional gene diversity, composition, structure, and metabolic potential of microbial assemblages in different ECS water masses. Four water masses determined by temperature and salinity relationship showed different patterns of functional gene diversity and composition. Generally, functional gene diversity [Shannon–Weaner’s H and reciprocal of Simpson’s 1/(1-D] in the surface water masses was higher than that in the bottom water masses. The different presence and proportion of functional genes involved in C, N, and P cycling among the bacteria of the different water masses showed different metabolic preferences of the microbial populations in the ECS. Genes involved in starch metabolism (amyA and nplT showed higher proportion in microbial communities of the surface water masses than of the bottom water masses. In contrast, a higher proportion of genes involved in chitin degradation was observed in microorganisms of the bottom water masses. Moreover, we found a higher proportion of nitrogen fixation (nifH, transformation of hydroxylamine to nitrite (hao and ammonification (gdh genes in the microbial communities of the bottom water masses compared with those of the surface water masses. The spatial variation of microbial functional genes was significantly correlated

Metabolic modelling of polyhydroxyalkanoate copolymers production by mixed microbial cultures

Directory of Open Access Journals (Sweden)

Reis Maria AM

2008-07-01

Full Text Available Abstract Background This paper presents a metabolic model describing the production of polyhydroxyalkanoate (PHA copolymers in mixed microbial cultures, using mixtures of acetic and propionic acid as carbon source material. Material and energetic balances were established on the basis of previously elucidated metabolic pathways. Equations were derived for the theoretical yields for cell growth and PHA production on mixtures of acetic and propionic acid as functions of the oxidative phosphorylation efficiency, P/O ratio. The oxidative phosphorylation efficiency was estimated from rate measurements, which in turn allowed the estimation of the theoretical yield coefficients. Results The model was validated with experimental data collected in a sequencing batch reactor (SBR operated under varying feeding conditions: feeding of acetic and propionic acid separately (control experiments, and the feeding of acetic and propionic acid simultaneously. Two different feast and famine culture enrichment strategies were studied: (i either with acetate or (ii with propionate as carbon source material. Metabolic flux analysis (MFA was performed for the different feeding conditions and culture enrichment strategies. Flux balance analysis (FBA was used to calculate optimal feeding scenarios for high quality PHA polymers production, where it was found that a suitable polymer would be obtained when acetate is fed in excess and the feeding rate of propionate is limited to ~0.17 C-mol/(C-mol.h. The results were compared with published pure culture metabolic studies. Conclusion Acetate was more conducive toward the enrichment of a microbial culture with higher PHA storage fluxes and yields as compared to propionate. The P/O ratio was not only influenced by the selected microbial culture, but also by the carbon substrate fed to each culture, where higher P/O ratio values were consistently observed for acetate than propionate. MFA studies suggest that when mixtures of

Genome-resolved metagenomics reveals that sulfur metabolism dominates the microbial ecology of rising hydrothermal plumes

Science.gov (United States)

Anantharaman, K.; Breier, J. A., Jr.; Jain, S.; Reed, D. C.; Dick, G.

2015-12-01

Deep-sea hydrothermal plumes occur when hot fluids from hydrothermal vents replete with chemically reduced elements and compounds like sulfide, methane, hydrogen, ammonia, iron and manganese mix with cold, oxic seawater. Chemosynthetic microbes use these reduced chemicals to power primary production and are pervasive throughout the deep sea, even at sites far removed from hydrothermal vents. Although neutrally-buoyant hydrothermal plumes have been well-studied, rising hydrothermal plumes have received little attention even though they represent an important interface in the deep-sea where microbial metabolism and particle formation processes control the transformation of important elements and impact global biogeochemical cycles. In this study, we used genome-resolved metagenomic analyses and thermodynamic-bioenergetic modeling to study the microbial ecology of rising hydrothermal plumes at five different hydrothermal vents spanning a range of geochemical gradients at the Eastern Lau Spreading Center (ELSC) in the Western Pacific Ocean. Our analyses show that differences in the geochemistry of hydrothermal vents do not manifest in microbial diversity and community composition, both of which display only minor variance across ELSC hydrothermal plumes. Microbial metabolism is dominated by oxidation of reduced sulfur species and supports a diversity of bacteria, archaea and viruses that provide intriguing insights into metabolic plasticity and virus-mediated horizontal gene transfer in the microbial community. The manifestation of sulfur oxidation genes in hydrogen and methane oxidizing organisms hints at metabolic opportunism in deep-sea microbes that would enable them to respond to varying redox conditions in hydrothermal plumes. Finally, we infer that the abundance, diversity and metabolic versatility of microbes associated with sulfur oxidation impart functional redundancy that could allow it to persist in the dynamic settings of hydrothermal plumes.

Microbial community assembly and metabolic function during mammalian corpse decomposition

Energy Technology Data Exchange (ETDEWEB)

Metcalf, J. L.; Xu, Z. Z.; Weiss, S.; Lax, S.; Van Treuren, W.; Hyde, E. R.; Song, S. J.; Amir, A.; Larsen, P.; Sangwan, N.; Haarmann, D.; Humphrey, G. C.; Ackermann, G.; Thompson, L. R.; Lauber, C.; Bibat, A.; Nicholas, C.; Gebert, M. J.; Petrosino, J. F.; Reed, S. C.; Gilbert, J. A.; Lynne, A. M.; Bucheli, S. R.; Carter, D. O.; Knight, R.

2015-12-10

Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups that contribute to nitrogen cycling and a reproducible network of decomposers that emerge on predictable time scales. Our results show that this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in low abundance. Soil type was not a dominant factor driving community development, and the process of decomposition is sufficiently reproducible to offer new opportunities for forensic investigations.

Microbial community assembly and metabolic function during mammalian corpse decomposition

Science.gov (United States)

Metcalf, Jessica L; Xu, Zhenjiang Zech; Weiss, Sophie; Lax, Simon; Van Treuren, Will; Hyde, Embriette R.; Song, Se Jin; Amir, Amnon; Larsen, Peter; Sangwan, Naseer; Haarmann, Daniel; Humphrey, Greg C; Ackermann, Gail; Thompson, Luke R; Lauber, Christian; Bibat, Alexander; Nicholas, Catherine; Gebert, Matthew J; Petrosino, Joseph F; Reed, Sasha C.; Gilbert, Jack A; Lynne, Aaron M; Bucheli, Sibyl R; Carter, David O; Knight, Rob

2016-01-01

Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups that contribute to nitrogen cycling and a reproducible network of decomposers that emerge on predictable time scales. Our results show that this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in low abundance. Soil type was not a dominant factor driving community development, and the process of decomposition is sufficiently reproducible to offer new opportunities for forensic investigations.

Changes in Microbial Energy Metabolism Measured by Nanocalorimetry during Growth Phase Transitions

Science.gov (United States)

Robador, Alberto; LaRowe, Douglas E.; Finkel, Steven E.; Amend, Jan P.; Nealson, Kenneth H.

2018-01-01

Calorimetric measurements of the change in heat due to microbial metabolic activity convey information about the kinetics, as well as the thermodynamics, of all chemical reactions taking place in a cell. Calorimetric measurements of heat production made on bacterial cultures have recorded the energy yields of all co-occurring microbial metabolic reactions, but this is a complex, composite signal that is difficult to interpret. Here we show that nanocalorimetry can be used in combination with enumeration of viable cell counts, oxygen consumption rates, cellular protein content, and thermodynamic calculations to assess catabolic rates of an isolate of Shewanella oneidensis MR-1 and infer what fraction of the chemical energy is assimilated by the culture into biomass and what fraction is dissipated in the form of heat under different limiting conditions. In particular, our results demonstrate that catabolic rates are not necessarily coupled to rates of cell division, but rather, to physiological rearrangements of S. oneidensis MR-1 upon growth phase transitions. In addition, we conclude that the heat released by growing microorganisms can be measured in order to understand the physiochemical nature of the energy transformation and dissipation associated with microbial metabolic activity in conditions approaching those found in natural systems. PMID:29449836

Biodegradation of crude oil by introduced psychotropic microbial association and indigenous bacteria under laboratory and field conditions in soils of Moscow region, Russia

Energy Technology Data Exchange (ETDEWEB)

Filonov, A.; Boronin, A. [Pushchino State Univ., Moscow (Russian Federation). Inst. of Biochemistry and Physiology of Microorganisms; Nechaeva, I.; Akhmetov, L.; Gafarov, A.; Puntus, I. [Pushchino State Univ., Moscow (Russian Federation)

2007-07-01

This paper presented an in-situ bioremediation method that accelerates the degradation of crude oil. Laboratory and field studies were conducted to determine the effect of adding mineral fertilizers such as nitrogen and phosphorus to stimulate the growth of microorganisms and accelerate microbial metabolism. The strongest effect was observed when nitrogen, phosphorous and potassium sources were added with microbial association jointly, particularly in field soil experiments. A 22 per cent oil spill removal was achieved due to metabolic activity of indigenous bacteria after only 2 months of experimenting. This study examined the kinetics of total number and crude oil degrading bacteria in the soil resulting from nutrient inoculation. It was shown that the rate of hydrocarbon degradation by microorganisms in the environment is determined by a range of factors such as temperature, soil pH, oxygen, water and nutritive availability. The use of psychotrophic degrader strains resulted in a higher degree of oil degradation in the field than in the laboratory. The study also revealed that the biodegradation process in polluted Arctic soils polluted with diesel was accelerated with the addition of degrader microorganisms. It was recommended that in cold climates, nitrogen, phosphorous and potassium should be introduced simultaneously. 21 refs., 1 tab., 4 figs.

Gut Microbial Glycerol Metabolism as an Endogenous Acrolein Source

Directory of Open Access Journals (Sweden)

Jianbo Zhang

2018-01-01

Full Text Available Acrolein is a highly reactive electrophile causing toxic effects, such as DNA and protein adduction, oxidative stress, endoplasmic reticulum stress, immune dysfunction, and membrane damage. This Opinion/Hypothesis provides an overview of endogenous and exogenous acrolein sources, acrolein’s mode of action, and its metabolic fate. Recent reports underpin the finding that gut microbial glycerol metabolism leading to the formation of reuterin is an additional source of endogenous acrolein. Reuterin is an antimicrobial multicomponent system consisting of 3-hydroxypropionaldehyde, its dimer and hydrate, and also acrolein. The major conclusion is that gut microbes can metabolize glycerol to reuterin and that this transformation occurs in vivo. Given the known toxicity of acrolein, the observation that acrolein is formed in the gut necessitates further investigations on functional relevance for gut microbiota and the host.

In situ metabolism in halite endolithic microbial communities of the hyperarid Atacama Desert

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Alfonso F Davila

2015-10-01

Full Text Available The Atacama Desert of northern Chile is one of the driest regions on Earth, with areas that exclude plants and where soils have extremely low microbial biomass. However, in the driest parts of the desert there are microorganisms that colonize the interior of halite nodules in fossil continental evaporites, where they are sustained by condensation of atmospheric water triggered by the salt substrate. Using a combination of in situ observations of variable chlorophyll fluorescence and controlled laboratory experiments, we show that this endolithic community is capable of carbon fixation both through oxygenic photosynthesis and potentially ammonia oxidation. We also present evidence that photosynthetic activity is finely tuned to moisture availability and solar insolation and can be sustained for days, and perhaps longer, after a wetting event. This is the first demonstration of in situ active metabolism in the hyperarid core of the Atacama Desert, and it provides the basis for proposing a self-contained, endolithic community that relies exclusively on non-rainfall sources of water. Our results contribute to an increasing body of evidence that even in hyperarid environments active metabolism, adaptation and growth can occur in highly specialized microhabitats.

Laboratory Course on "Streptomyces" Genetics and Secondary Metabolism

Science.gov (United States)

Siitonen, Vilja; Räty, Kaj; Metsä-Ketelä, Mikko

2016-01-01

The "'Streptomyces' genetics and secondary metabolism" laboratory course gives an introduction to the versatile soil dwelling Gram-positive bacteria "Streptomyces" and their secondary metabolism. The course combines genetic modification of "Streptomyces"; growing of the strain and protoplast preparation, plasmid…

The Importance of Transition Metals in the Expanding Network of Microbial Metabolism in the Archean Eon

Science.gov (United States)

Moore, E. K.; Jelen, B. I.; Giovannelli, D.; Prabhu, A.; Raanan, H.; Falkowski, P. G.

2017-12-01

Deep time changes in Earth surface redox conditions, particularly due to global oxygenation, has impacted the availability of different metals and substrates that are central in biology. Oxidoreductase proteins are molecular nanomachines responsible for all biological electron transfer processes across the tree of life. These enzymes largely contain transition metals in their active sites. Microbial metabolic pathways form a global network of electron transfer, which expanded throughout the Archean eon. Older metabolisms (sulfur reduction, methanogenesis, anoxygenic photosynthesis) accessed negative redox potentials, while later evolving metabolisms (oxygenic photosynthesis, nitrification/denitrification, aerobic respiration) accessed positive redox potentials. The incorporation of different transition metals facilitated biological innovation and the expansion of the network of microbial metabolism. Network analysis was used to examine the connections between microbial taxa, metabolic pathways, crucial metallocofactors, and substrates in deep time by incorporating biosignatures preserved in the geologic record. Nitrogen fixation and aerobic respiration have the highest level of betweenness among metabolisms in the network, indicating that the oldest metabolisms are not the most central. Fe has by far the highest betweenness among metals. Clustering analysis largely separates High Metal Bacteria (HMB), Low Metal Bacteria (LMB), and Archaea showing that simple un-weighted links between taxa, metabolism, and metals have phylogenetic relevance. On average HMB have the highest betweenness among taxa, followed by Archaea and LMB. There is a correlation between the number of metallocofactors and metabolic pathways in representative bacterial taxa, but Archaea do not follow this trend. In many cases older and more recently evolved metabolisms were clustered together supporting previous findings that proliferation of metabolic pathways is not necessarily chronological.

Effects of Pheretima Guillelmi Cultivation Time on Microbial Community Diversity and Characteristics of Carbon Metabolism in Vegetable Soil

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ZHENG Xian-qing

2015-12-01

Full Text Available In order to study the effect of different biological tillage time (Pheretima guillelmi on soil microbial community metabolic functions in different soil depths, we set a location test in vegetable field at Chongming Island in Shanghai to analyze the changes of soil microbial community and carbon utilization abilities (Average well- color development, AWCD by using biolog eco-plate method. The three-year results showed that: Bio-tillage significantly improved microbial community activity, and with the increase of tillage years, biological tillage could make the average AWCD 3 to 7 times higher. The Simpson index and Shannon index of the biological tillage treatments were significantly higher than that of the control. The cumulative increase of 0~5 cm soil layer was 49 and 6.28 respectively, and the cumulative increase of 5~20 cm soil layer was 31 and 2.55 respectively. Earthworm bio-tillage significantly increased the soil microbial metabolic ability of 6 kinds of carbon sources, and increased the carbohydrate metabolism activity. In this study, earthworm bio-tillage is an effective way to increase the microbial activity of microbial soil.

Kinetic modeling of microbially-driven redox chemistry of radionuclides in subsurface environments: Coupling transport, microbial metabolism and geochemistry

International Nuclear Information System (INIS)

Wang, Yifeng; Papenguth, Hans W.

2000-01-01

Microbial degradation of organic matter is a driving force in many subsurface geochemical systems, and therefore may have significant impacts on the fate of radionuclides released into subsurface environments. In this paper, the authors present a general reaction-transport model for microbial metabolism, redox chemistry, and radionuclide migration in subsurface systems. The model explicitly accounts for biomass accumulation and the coupling of radionuclide redox reactions with major biogeochemical processes. Based on the consideration that the biomass accumulation in subsurface environments is likely to achieve a quasi-steady state, they have accordingly modified the traditional microbial growth kinetic equation. They justified the use of the biogeochemical models without the explicit representation of biomass accumulation, if the interest of modeling is in the net impact of microbial reactions on geochemical processes. They then applied their model to a scenario in which an oxic water flow containing both uranium and completing organic ligands is recharged into an oxic aquifer in a carbonate formation. The model simulation shows that uranium can be reduced and therefore immobilized in the anoxic zone created by microbial degradation

Kinetic modeling of microbially-driven redox chemistry of radionuclides in subsurface environments: Coupling transport, microbial metabolism and geochemistry

Energy Technology Data Exchange (ETDEWEB)

WANG,YIFENG; PAPENGUTH,HANS W.

2000-05-04

Microbial degradation of organic matter is a driving force in many subsurface geochemical systems, and therefore may have significant impacts on the fate of radionuclides released into subsurface environments. In this paper, the authors present a general reaction-transport model for microbial metabolism, redox chemistry, and radionuclide migration in subsurface systems. The model explicitly accounts for biomass accumulation and the coupling of radionuclide redox reactions with major biogeochemical processes. Based on the consideration that the biomass accumulation in subsurface environments is likely to achieve a quasi-steady state, they have accordingly modified the traditional microbial growth kinetic equation. They justified the use of the biogeochemical models without the explicit representation of biomass accumulation, if the interest of modeling is in the net impact of microbial reactions on geochemical processes. They then applied their model to a scenario in which an oxic water flow containing both uranium and completing organic ligands is recharged into an oxic aquifer in a carbonate formation. The model simulation shows that uranium can be reduced and therefore immobilized in the anoxic zone created by microbial degradation.

A Status Report on the Global Research in Microbial Metabolic Engineering

Energy Technology Data Exchange (ETDEWEB)

Joe, Min Ho; Lim, Sang Yong; Kim, Dong Ho

2008-09-15

Biotechnology industry is now a global 'Mega-Trend' and metabolic engineering technology has important role is this area. Therefore, many countries has made efforts in this field to produce top value added bio-products efficiently using microorganisms. It has been applied to increase the production of chemicals that are already produced by the host organism, to produce desired chemical substances from less expensive feedstock, and to generate products that are new to the host organism. Recent experimental advances, the so-called '-omics' technologies, mainly functional genomics, proteomics and metabolomics, have enabled wholesale generation of new genomic, transcriptomic, proteomic, and metabolomic data. This report provides the insights of the integrated view of metabolism generated by metabolic engineering for biotechnological applications of microbial metabolic engineering.

A Status Report on the Global Research in Microbial Metabolic Engineering

International Nuclear Information System (INIS)

Joe, Min Ho; Lim, Sang Yong; Kim, Dong Ho

2008-09-01

Biotechnology industry is now a global 'Mega-Trend' and metabolic engineering technology has important role is this area. Therefore, many countries has made efforts in this field to produce top value added bio-products efficiently using microorganisms. It has been applied to increase the production of chemicals that are already produced by the host organism, to produce desired chemical substances from less expensive feedstock, and to generate products that are new to the host organism. Recent experimental advances, the so-called '-omics' technologies, mainly functional genomics, proteomics and metabolomics, have enabled wholesale generation of new genomic, transcriptomic, proteomic, and metabolomic data. This report provides the insights of the integrated view of metabolism generated by metabolic engineering for biotechnological applications of microbial metabolic engineering

A Status Report on the Global Research in Microbial Metabolic Engineering

Energy Technology Data Exchange (ETDEWEB)

Joe, Min Ho; Lim, Sang Yong; Kim, Dong Ho

2008-09-15

Biotechnology industry is now a global 'Mega-Trend' and metabolic engineering technology has important role is this area. Therefore, many countries has made efforts in this field to produce top value added bio-products efficiently using microorganisms. It has been applied to increase the production of chemicals that are already produced by the host organism, to produce desired chemical substances from less expensive feedstock, and to generate products that are new to the host organism. Recent experimental advances, the so-called '-omics' technologies, mainly functional genomics, proteomics and metabolomics, have enabled wholesale generation of new genomic, transcriptomic, proteomic, and metabolomic data. This report provides the insights of the integrated view of metabolism generated by metabolic engineering for biotechnological applications of microbial metabolic engineering.

Biodegradation of crude oil by introduced psychotropic microbial association and indigenous bacteria under laboratory and field conditions in soils of Moscow region, Russia. Volume 1

International Nuclear Information System (INIS)

Filonov, A.; Boronin, A.

2007-01-01

This paper presented an in-situ bioremediation method that accelerates the degradation of crude oil. Laboratory and field studies were conducted to determine the effect of adding mineral fertilizers such as nitrogen and phosphorus to stimulate the growth of microorganisms and accelerate microbial metabolism. The strongest effect was observed when nitrogen, phosphorous and potassium sources were added with microbial association jointly, particularly in field soil experiments. A 22 per cent oil spill removal was achieved due to metabolic activity of indigenous bacteria after only 2 months of experimenting. This study examined the kinetics of total number and crude oil degrading bacteria in the soil resulting from nutrient inoculation. It was shown that the rate of hydrocarbon degradation by microorganisms in the environment is determined by a range of factors such as temperature, soil pH, oxygen, water and nutritive availability. The use of psychotrophic degrader strains resulted in a higher degree of oil degradation in the field than in the laboratory. The study also revealed that the biodegradation process in polluted Arctic soils polluted with diesel was accelerated with the addition of degrader microorganisms. It was recommended that in cold climates, nitrogen, phosphorous and potassium should be introduced simultaneously. 21 refs., 1 tab., 4 figs

Biodegradation of crude oil by introduced psychotropic microbial association and indigenous bacteria under laboratory and field conditions in soils of Moscow region, Russia. Volume 1

Energy Technology Data Exchange (ETDEWEB)

Filonov, A.; Boronin, A. [Pushchino State Univ., Moscow (Russian Federation). Inst. of Biochemistry and Physiology of Microorganisms; Nechaeva, I.; Akhmetov, L.; Gafarov, A.; Puntus, I. [Pushchino State Univ., Moscow (Russian Federation)

2007-07-01

This paper presented an in-situ bioremediation method that accelerates the degradation of crude oil. Laboratory and field studies were conducted to determine the effect of adding mineral fertilizers such as nitrogen and phosphorus to stimulate the growth of microorganisms and accelerate microbial metabolism. The strongest effect was observed when nitrogen, phosphorous and potassium sources were added with microbial association jointly, particularly in field soil experiments. A 22 per cent oil spill removal was achieved due to metabolic activity of indigenous bacteria after only 2 months of experimenting. This study examined the kinetics of total number and crude oil degrading bacteria in the soil resulting from nutrient inoculation. It was shown that the rate of hydrocarbon degradation by microorganisms in the environment is determined by a range of factors such as temperature, soil pH, oxygen, water and nutritive availability. The use of psychotrophic degrader strains resulted in a higher degree of oil degradation in the field than in the laboratory. The study also revealed that the biodegradation process in polluted Arctic soils polluted with diesel was accelerated with the addition of degrader microorganisms. It was recommended that in cold climates, nitrogen, phosphorous and potassium should be introduced simultaneously. 21 refs., 1 tab., 4 figs.

Microbial production of antioxidant food ingredients via metabolic engineering.

Science.gov (United States)

Lin, Yuheng; Jain, Rachit; Yan, Yajun

2014-04-01

Antioxidants are biological molecules with the ability to protect vital metabolites from harmful oxidation. Due to this fascinating role, their beneficial effects on human health are of paramount importance. Traditional approaches using solvent-based extraction from food/non-food sources and chemical synthesis are often expensive, exhaustive, and detrimental to the environment. With the advent of metabolic engineering tools, the successful reconstitution of heterologous pathways in Escherichia coli and other microorganisms provides a more exciting and amenable alternative to meet the increasing demand of natural antioxidants. In this review, we elucidate the recent progress in metabolic engineering efforts for the microbial production of antioxidant food ingredients - polyphenols, carotenoids, and antioxidant vitamins. Copyright © 2013 Elsevier Ltd. All rights reserved.

Mineralogical controls on surface colonization by sulfur-metabolizing microbial communities

Science.gov (United States)

Jones, A. A.; Bennett, P.

2012-12-01

When characterizing microbial diversity and the microbial ecosystem of the shallow subsurface the mineral matrix is generally assumed to be homogenous and unreactive. We report here experimental evidence that microorganisms colonize rock surfaces according to the rock's chemistry and the organism's metabolic requirements and tolerances. We investigated this phenomenon using laboratory biofilm reactors with both a pure culture of sulfur-oxidizing Thiothrix unzii and a mixed environmental sulfur-metabolizing community from Lower Kane, Cave, WY, USA. Reactors contained rock and mineral chips (calcite, albite, microcline, quartz, chert, Madison Limestone (ML), Madison Dolostone (MD), and basalt) amended with one of the two inoculants. Biomass of attached microorganisms on each mineral surface was quantified. The 16S rRNA of attached microbial communities were compared using Roche FLX and Titanium 454 next generation pyrosequencing. A primary controlling factor on taxonomy of attached microorganisms in both pure and mixed culture experiments was mineral buffering capacity. In mixed culture experiments acid-buffering carbonates were preferentially colonized by neutrophilic sulfur-oxidizing microorganisms (~18% to ~27% of microorganisms), while acidophilic sulfur-oxidizing microorganisms colonized non-buffering quartz exclusively (~46% of microorganisms). The nutrient content of the rock was a controlling factor on biomass accumulation, with neutrophilic organisms selecting between carbonate surfaces of equivalent buffer capacities according to the availability of phosphate. Dry biomass on ML was 17.8 ± 2.3 mg/cm2 and MD was 20.6 ± 6.8 mg/cm2; while nutrient poor calcite accumulated 2.4 ± 0.3 mg/cm2. Biomass accumulation was minimal on non-buffering nutrient-limited surfaces. These factors are countered by the competitive exclusion of some populations. A pure culture of T. unzii preferentially colonizes carbonates while a very closely related Thiothrix spp is excluded

From Field to Laboratory: A New Database Approach for Linking Microbial Field Ecology with Laboratory Studies

Science.gov (United States)

Bebout, Leslie; Keller, R.; Miller, S.; Jahnke, L.; DeVincenzi, D. (Technical Monitor)

2002-01-01

The Ames Exobiology Culture Collection Database (AECC-DB) has been developed as a collaboration between microbial ecologists and information technology specialists. It allows for extensive web-based archiving of information regarding field samples to document microbial co-habitation of specific ecosystem micro-environments. Documentation and archiving continues as pure cultures are isolated, metabolic properties determined, and DNA extracted and sequenced. In this way metabolic properties and molecular sequences are clearly linked back to specific isolates and the location of those microbes in the ecosystem of origin. Use of this database system presents a significant advancement over traditional bookkeeping wherein there is generally little or no information regarding the environments from which microorganisms were isolated. Generally there is only a general ecosystem designation (i.e., hot-spring). However within each of these there are a myriad of microenvironments with very different properties and determining exactly where (which microenvironment) a given microbe comes from is critical in designing appropriate isolation media and interpreting physiological properties. We are currently using the database to aid in the isolation of a large number of cyanobacterial species and will present results by PI's and students demonstrating the utility of this new approach.

An Open-Ended Investigative Microbial Ecology Laboratory for Introductory Biology

Science.gov (United States)

Jones-Held, Susan; Paoletti, Robert; Glick, David; Held, Michael E.

2010-01-01

In this article we describe a multi-week investigative laboratory in microbial ecology/diversity and nitrogen cycling that we have used in our introductory biology course. This module encourages active student involvement in experimental design, using the scientific literature and quantitative analysis of large data sets. Students analyze soil…

Using isotopic tracers to assess the impact of tillage and straw management on the microbial metabolic network in soil

Science.gov (United States)

Van Groenigen, K.; Forristal, D.; Jones, M. B.; Schwartz, E.; Hungate, B. A.; Dijkstra, P.

2013-12-01

By decomposing soil organic matter, microbes gain energy and building blocks for biosynthesis and release CO2 to the atmosphere. Therefore, insight into the effect of management practices on microbial metabolic pathways and C use efficiency (CUE; microbial C produced per substrate C utilized) may help to predict long term changes in soil C stocks. We studied the effects of reduced (RT) and conventional tillage (CT) on the microbial central C metabolic network, using soil samples from a 12-year-old field experiment in an Irish winter wheat cropping system. Each year after harvest, straw was removed from half of the RT and CT plots or incorporated into the soil in the other half, resulting in four treatment combinations. We added 1-13C and 2,3-13C pyruvate and 1-13C and U-13C glucose as metabolic tracer isotopomers to composite soil samples taken at two depths (0-15 cm and 15-30 cm) from each treatment and used the rate of position-specific respired 13CO2 to parameterize a metabolic model. Model outcomes were then used to calculate CUE of the microbial community. We found that the composite samples differed in CUE, but the changes were small, with values ranging between 0.757-0.783 across treatments and soil depth. Increases in CUE were associated with a decrease in tricarboxylic acid cycle and reductive pentose phosphate pathway activity and increased consumption of metabolic intermediates for biosynthesis. Our results indicate that RT and straw incorporation promote soil C storage without substantially changing CUE or any of the microbial metabolic pathways. This suggests that at our site, RT and straw incorporation promote soil C storage mostly through direct effects such as increased soil C input and physical protection from decomposition, rather than by feedback responses of the microbial community.

Genome-enabled Modeling of Microbial Biogeochemistry using a Trait-based Approach. Does Increasing Metabolic Complexity Increase Predictive Capabilities?

Science.gov (United States)

King, E.; Karaoz, U.; Molins, S.; Bouskill, N.; Anantharaman, K.; Beller, H. R.; Banfield, J. F.; Steefel, C. I.; Brodie, E.

2015-12-01

The biogeochemical functioning of ecosystems is shaped in part by genomic information stored in the subsurface microbiome. Cultivation-independent approaches allow us to extract this information through reconstruction of thousands of genomes from a microbial community. Analysis of these genomes, in turn, gives an indication of the organisms present and their functional roles. However, metagenomic analyses can currently deliver thousands of different genomes that range in abundance/importance, requiring the identification and assimilation of key physiologies and metabolisms to be represented as traits for successful simulation of subsurface processes. Here we focus on incorporating -omics information into BioCrunch, a genome-informed trait-based model that represents the diversity of microbial functional processes within a reactive transport framework. This approach models the rate of nutrient uptake and the thermodynamics of coupled electron donors and acceptors for a range of microbial metabolisms including heterotrophs and chemolithotrophs. Metabolism of exogenous substrates fuels catabolic and anabolic processes, with the proportion of energy used for cellular maintenance, respiration, biomass development, and enzyme production based upon dynamic intracellular and environmental conditions. This internal resource partitioning represents a trade-off against biomass formation and results in microbial community emergence across a fitness landscape. Biocrunch was used here in simulations that included organisms and metabolic pathways derived from a dataset of ~1200 non-redundant genomes reflecting a microbial community in a floodplain aquifer. Metagenomic data was directly used to parameterize trait values related to growth and to identify trait linkages associated with respiration, fermentation, and key enzymatic functions such as plant polymer degradation. Simulations spanned a range of metabolic complexities and highlight benefits originating from simulations

Does canine inflammatory bowel disease influence gut microbial profile and host metabolism?

Science.gov (United States)

Xu, Jia; Verbrugghe, Adronie; Lourenço, Marta; Janssens, Geert P J; Liu, Daisy J X; Van de Wiele, Tom; Eeckhaut, Venessa; Van Immerseel, Filip; Van de Maele, Isabel; Niu, Yufeng; Bosch, Guido; Junius, Greet; Wuyts, Brigitte; Hesta, Myriam

2016-06-16

Inflammatory bowel disease (IBD) refers to a diverse group of chronic gastrointestinal diseases, and gut microbial dysbiosis has been proposed as a modulating factor in its pathogenesis. Several studies have investigated the gut microbial ecology of dogs with IBD but it is yet unclear if this microbial profile can alter the nutrient metabolism of the host. The aim of the present study was to characterize the faecal bacterial profile and functionality as well as to determine host metabolic changes in IBD dogs. Twenty-three dogs diagnosed with IBD and ten healthy control dogs were included. Dogs with IBD were given a clinical score using the canine chronic enteropathy clinical activity index (CCECAI). Faecal short-chain fatty acids (SCFA) and ammonia concentrations were measured and quantitative PCR was performed. The concentration of plasma amino acids, acylcarnitines, serum folate, cobalamin, and indoxyl sulfate was determined. No significant differences in the abundance of a selection of bacterial groups and fermentation metabolites were observed between the IBD and control groups. However, significant negative correlations were found between CCECAI and the faecal proportion of Lactobacillus as well as between CCECAI and total SCFA concentration. Serum folate and plasma citrulline were decreased and plasma valine was increased in IBD compared to control dogs. Increased plasma free carnitine and total acylcarnitines were observed in IBD compared with control dogs, whereas short-chain acylcarnitines (butyrylcarnitine + isobutyrylcarnitine and, methylmalonylcarnitine) to free carnitine ratios decreased. Dogs with IBD had a higher 3-hydroxyisovalerylcarnitine + isovalerylcarnitine to leucine ratio compared to control dogs. Canine IBD induced a wide range of changes in metabolic profile, especially for the plasma concentrations of short-chain acylcarnitines and amino acids, which could have evolved from tissue damage and alteration in host metabolism. In

MbT-Tool: An open-access tool based on Thermodynamic Electron Equivalents Model to obtain microbial-metabolic reactions to be used in biotechnological process.

Science.gov (United States)

Araujo, Pablo Granda; Gras, Anna; Ginovart, Marta

2016-01-01

Modelling cellular metabolism is a strategic factor in investigating microbial behaviour and interactions, especially for bio-technological processes. A key factor for modelling microbial activity is the calculation of nutrient amounts and products generated as a result of the microbial metabolism. Representing metabolic pathways through balanced reactions is a complex and time-consuming task for biologists, ecologists, modellers and engineers. A new computational tool to represent microbial pathways through microbial metabolic reactions (MMRs) using the approach of the Thermodynamic Electron Equivalents Model has been designed and implemented in the open-access framework NetLogo. This computational tool, called MbT-Tool (Metabolism based on Thermodynamics) can write MMRs for different microbial functional groups, such as aerobic heterotrophs, nitrifiers, denitrifiers, methanogens, sulphate reducers, sulphide oxidizers and fermenters. The MbT-Tool's code contains eighteen organic and twenty inorganic reduction-half-reactions, four N-sources (NH4 (+), NO3 (-), NO2 (-), N2) to biomass synthesis and twenty-four microbial empirical formulas, one of which can be determined by the user (CnHaObNc). MbT-Tool is an open-source program capable of writing MMRs based on thermodynamic concepts, which are applicable in a wide range of academic research interested in designing, optimizing and modelling microbial activity without any extensive chemical, microbiological and programing experience.

Microbial population heterogeneity versus bioreactor heterogeneity: evaluation of Redox Sensor Green as an exogenous metabolic biosensor

DEFF Research Database (Denmark)

Baert, Jonathan; Delepierre, Anissa; Telek, Samuel

2016-01-01

Microbial heterogeneity in metabolic performances has attracted a lot of attention, considering its potential impact on industrial bioprocesses. However, little is known about the impact of extracellular perturbations (i.e. bioreactor heterogeneity) on cell-to-cell variability in metabolic...

Metabolic engineering for the microbial production of isoprenoids: Carotenoids and isoprenoid-based biofuels

Directory of Open Access Journals (Sweden)

Fu-Xing Niu

2017-09-01

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

Metal availability and the expanding network of microbial metabolisms in the Archaean eon

Science.gov (United States)

Moore, Eli K.; Jelen, Benjamin I.; Giovannelli, Donato; Raanan, Hagai; Falkowski, Paul G.

2017-09-01

Life is based on energy gained by electron-transfer processes; these processes rely on oxidoreductase enzymes, which often contain transition metals in their structures. The availability of different metals and substrates has changed over the course of Earth's history as a result of secular changes in redox conditions, particularly global oxygenation. New metabolic pathways using different transition metals co-evolved alongside changing redox conditions. Sulfur reduction, sulfate reduction, methanogenesis and anoxygenic photosynthesis appeared between about 3.8 and 3.4 billion years ago. The oxidoreductases responsible for these metabolisms incorporated metals that were readily available in Archaean oceans, chiefly iron and iron-sulfur clusters. Oxygenic photosynthesis appeared between 3.2 and 2.5 billion years ago, as did methane oxidation, nitrogen fixation, nitrification and denitrification. These metabolisms rely on an expanded range of transition metals presumably made available by the build-up of molecular oxygen in soil crusts and marine microbial mats. The appropriation of copper in enzymes before the Great Oxidation Event is particularly important, as copper is key to nitrogen and methane cycling and was later incorporated into numerous aerobic metabolisms. We find that the diversity of metals used in oxidoreductases has increased through time, suggesting that surface redox potential and metal incorporation influenced the evolution of metabolism, biological electron transfer and microbial ecology.

IMGMD: A platform for the integration and standardisation of In silico Microbial Genome-scale Metabolic Models.

Science.gov (United States)

Ye, Chao; Xu, Nan; Dong, Chuan; Ye, Yuannong; Zou, Xuan; Chen, Xiulai; Guo, Fengbiao; Liu, Liming

2017-04-07

Genome-scale metabolic models (GSMMs) constitute a platform that combines genome sequences and detailed biochemical information to quantify microbial physiology at the system level. To improve the unity, integrity, correctness, and format of data in published GSMMs, a consensus IMGMD database was built in the LAMP (Linux + Apache + MySQL + PHP) system by integrating and standardizing 328 GSMMs constructed for 139 microorganisms. The IMGMD database can help microbial researchers download manually curated GSMMs, rapidly reconstruct standard GSMMs, design pathways, and identify metabolic targets for strategies on strain improvement. Moreover, the IMGMD database facilitates the integration of wet-lab and in silico data to gain an additional insight into microbial physiology. The IMGMD database is freely available, without any registration requirements, at http://imgmd.jiangnan.edu.cn/database.

Microbial Communities and Their Predicted Metabolic Functions in Growth Laminae of a Unique Large Conical Mat from Lake Untersee, East Antarctica

Directory of Open Access Journals (Sweden)

Hyunmin Koo

2017-08-01

Full Text Available In this study, we report the distribution of microbial taxa and their predicted metabolic functions observed in the top (U1, middle (U2, and inner (U3 decadal growth laminae of a unique large conical microbial mat from perennially ice-covered Lake Untersee of East Antarctica, using NextGen sequencing of the 16S rRNA gene and bioinformatics tools. The results showed that the U1 lamina was dominated by cyanobacteria, specifically Phormidium sp., Leptolyngbya sp., and Pseudanabaena sp. The U2 and U3 laminae had high abundances of Actinobacteria, Verrucomicrobia, Proteobacteria, and Bacteroidetes. Closely related taxa within each abundant bacterial taxon found in each lamina were further differentiated at the highest taxonomic resolution using the oligotyping method. PICRUSt analysis, which determines predicted KEGG functional categories from the gene contents and abundances among microbial communities, revealed a high number of sequences belonging to carbon fixation, energy metabolism, cyanophycin, chlorophyll, and photosynthesis proteins in the U1 lamina. The functional predictions of the microbial communities in U2 and U3 represented signal transduction, membrane transport, zinc transport and amino acid-, carbohydrate-, and arsenic- metabolisms. The Nearest Sequenced Taxon Index (NSTI values processed through PICRUSt were 0.10, 0.13, and 0.11 for U1, U2, and U3 laminae, respectively. These values indicated a close correspondence with the reference microbial genome database, implying high confidence in the predicted metabolic functions of the microbial communities in each lamina. The distribution of microbial taxa observed in each lamina and their predicted metabolic functions provides additional insight into the complex microbial ecosystem at Lake Untersee, and lays the foundation for studies that will enhance our understanding of the mechanisms responsible for the formation of these unique mat structures and their evolutionary significance.

Microbial pathways in colonic sulfur metabolism and links with health and disease

Directory of Open Access Journals (Sweden)

Franck eCarbonero

2012-11-01

Full Text Available Sulfur is both crucial to life and a potential threat to health. While colonic sulfur metabolism mediated by eukaryotic cells is relatively well studied, much less is known about sulfur metabolism within gastrointestinal microbes. Sulfated compounds in the colon are either of inorganic (e.g., sulfates, sulfites or organic (e.g., dietary amino acids and host mucins origin. The most extensively studied of the microbes involved in colonic sulfur metabolism are the sulfate-reducing bacteria, which are common colonic inhabitants. Many other microbial pathways are likely to shape colonic sulfur metabolism as well as the composition and availability of sulfated compounds, and these interactions need to be examined in more detail. Hydrogen sulfide is the sulfur derivative that has attracted the most attention in the context of colonic health, and the extent to which it is detrimental or beneficial remains in debate. Several lines of evidence point to sulfate-reducing bacteria or exogenous hydrogen sulfide as potential players in the etiology of intestinal disorders, inflammatory bowel diseases and colorectal cancer in particular. Generation of hydrogen sulfide via pathways other than dissimilatory sulfate reduction may be as, or more, important than those involving the sulfate-reducing bacteria. We suggest here that a novel axis of research is to assess the effects of hydrogen sulfide in shaping colonic microbiome structure. Clearly, in-depth characterization of the microbial pathways involved in colonic sulfur metabolism is necessary for a better understanding of its contribution to colonic disorders and development of therapeutic strategies.

MbT-Tool: An open-access tool based on Thermodynamic Electron Equivalents Model to obtain microbial-metabolic reactions to be used in biotechnological process

Directory of Open Access Journals (Sweden)

Pablo Araujo Granda

2016-01-01

Full Text Available Modelling cellular metabolism is a strategic factor in investigating microbial behaviour and interactions, especially for bio-technological processes. A key factor for modelling microbial activity is the calculation of nutrient amounts and products generated as a result of the microbial metabolism. Representing metabolic pathways through balanced reactions is a complex and time-consuming task for biologists, ecologists, modellers and engineers. A new computational tool to represent microbial pathways through microbial metabolic reactions (MMRs using the approach of the Thermodynamic Electron Equivalents Model has been designed and implemented in the open-access framework NetLogo. This computational tool, called MbT-Tool (Metabolism based on Thermodynamics can write MMRs for different microbial functional groups, such as aerobic heterotrophs, nitrifiers, denitrifiers, methanogens, sulphate reducers, sulphide oxidizers and fermenters. The MbT-Tool's code contains eighteen organic and twenty inorganic reduction-half-reactions, four N-sources (NH4+, NO3−, NO2−, N2 to biomass synthesis and twenty-four microbial empirical formulas, one of which can be determined by the user (CnHaObNc. MbT-Tool is an open-source program capable of writing MMRs based on thermodynamic concepts, which are applicable in a wide range of academic research interested in designing, optimizing and modelling microbial activity without any extensive chemical, microbiological and programing experience.

Water type and irrigation time effects on microbial metabolism of a soil cultivated with Bermuda-grass Tifton 85

Directory of Open Access Journals (Sweden)

Sandra Furlan Nogueira

2011-06-01

Full Text Available This study investigated the microbial metabolism in Bermuda-grass Tifton 85 areas after potable-water and effluent irrigation treatments. The experiment was carried out in Lins/SP with samples taken in the rainy and dry seasons (2006 after one year and three years of irrigation management, and set up on an entirely randomized block design with four treatments: C (control, without irrigation or fertilization, PW (potable water + 520 kg of N ha-1 year-1; TE3 and TE0 (treated effluent + 520 kg of N ha-1 year-1 for three years and one year, respectively. The parameters determined were: microbial biomass carbon, microbial activity, and metabolic quotient. Irrigation with wastewater after three years indicated no alteration in soil quality for C and ET3; for PW, a negative impact on soil quality (microbial biomass decrease suggested that water-potable irrigation in Lins is not an adequate option. Microbial activity alterations observed in TE0 characterize a priming effect.

A bioenergetics-kinetics coupled modeling study on subsurface microbial metabolism in a field biostimulation experiment

Science.gov (United States)

Jin, Q.; Zheng, Z.; Zhu, C.

2006-12-01

Microorganisms in nature conserve energy by catalyzing various geochemical reactions. To build a quantitative relationship between geochemical conditions and metabolic rates, we propose a bioenergetics-kinetics coupled modeling approach. This approach describes microbial community as a metabolic network, i.e., fermenting microbes degrade organic substrates while aerobic respirer, nitrate reducer, metal reducer, sulfate reducer, and methanogen consume the fermentation products. It quantifies the control of substrate availability and biological energy conservation on the metabolic rates using thermodynamically consistent rate laws. We applied this simulation approach to study the progress of microbial metabolism during a field biostimulation experiment conducted in Oak Ridge, Tennessee. In the experiment, ethanol was injected into a monitoring well and groundwater was sampled to monitor changes in the chemistry. With time, concentrations of ethanol and SO42- decreased while those of NH4+, Fe2+, and Mn2+ increased. The simulation results fitted well to the observation, indicating simultaneous ethanol degradation and terminal electron accepting processes. The rates of aerobic respiration and denitrification were mainly controlled by substrate concentrations while those of ethanol degradation, sulfate reduction, and methanogenesis were controlled dominantly by the energy availability. The simulation results suggested two different microbial growth statuses in the subsurface. For the functional groups with significant growth, variations with time in substrate concentrations demonstrated a typical S curve. For the groups without significant growth, initial decreases in substrate concentrations were linear with time. Injecting substrates followed by monitoring environmental chemistry therefore provides a convenient approach to characterize microbial growth in the subsurface where methods for direct observation are currently unavailable. This research was funded by the

Frozen in Time? Microbial strategies for survival and carbon metabolism over geologic time in a Pleistocene permafrost chronosequence

Science.gov (United States)

Mackelprang, R.; Douglas, T. A.; Waldrop, M. P.

2014-12-01

Permafrost soils have received tremendous interest due to their importance as a global carbon store with the potential to be thawed over the coming centuries. Instead of being 'frozen in time,' permafrost contains active microbes. Most metagenomic studies have focused on Holocene aged permafrost. Here, we target Pleistocene aged ice and carbon rich permafrost (Yedoma), which can differ in carbon content and stage of decay. Our aim was to understand how microbes in the permafrost transform organic matter over geologic time and to identify physiological and biochemical adaptations that enable long-term survival. We used next-generation sequencing to characterize microbial communities along a permafrost age gradient. Samples were collected from the Cold Regions Research and Engineering Laboratory (CRREL) Permafrost Tunnel near Fox, AK, which penetrates a hillside providing access to permafrost ranging in age from 12 to 40 kyr. DNA was extracted directly from unthawed samples. 16S rRNA amplicon (16S) and shotgun metagenome sequencing revealed significant age-driven differences. First, microbial diversity declines with permafrost age, likely due to long-term exposure to environmental stresses and a reduction in metabolic resources. Second, we observed taxonomic differences among ages, with an increasing abundance of Firmicutes (endospore-formers) in older samples, suggesting that dormancy is a common survival strategy in older permafrost. Ordination of 16S and metagenome data revealed age-based clustering. Genes differing significantly between age categories included those involved in lipopolysaccharide assembly, cold-response, and carbon processing. These data point to the physiological adaptations to long-term frozen conditions and to the metabolic processes utilized in ancient permafrost. In fact, a gene common in older samples is involved in cadaverine production, which could potentially explain the putrefied smell of Pleistocene aged permafrost. Coupled with soil

Microbial catabolic activities are naturally selected by metabolic energy harvest rate.

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González-Cabaleiro, Rebeca; Ofiţeru, Irina D; Lema, Juan M; Rodríguez, Jorge

2015-12-01

The fundamental trade-off between yield and rate of energy harvest per unit of substrate has been largely discussed as a main characteristic for microbial established cooperation or competition. In this study, this point is addressed by developing a generalized model that simulates competition between existing and not experimentally reported microbial catabolic activities defined only based on well-known biochemical pathways. No specific microbial physiological adaptations are considered, growth yield is calculated coupled to catabolism energetics and a common maximum biomass-specific catabolism rate (expressed as electron transfer rate) is assumed for all microbial groups. Under this approach, successful microbial metabolisms are predicted in line with experimental observations under the hypothesis of maximum energy harvest rate. Two microbial ecosystems, typically found in wastewater treatment plants, are simulated, namely: (i) the anaerobic fermentation of glucose and (ii) the oxidation and reduction of nitrogen under aerobic autotrophic (nitrification) and anoxic heterotrophic and autotrophic (denitrification) conditions. The experimentally observed cross feeding in glucose fermentation, through multiple intermediate fermentation pathways, towards ultimately methane and carbon dioxide is predicted. Analogously, two-stage nitrification (by ammonium and nitrite oxidizers) is predicted as prevailing over nitrification in one stage. Conversely, denitrification is predicted in one stage (by denitrifiers) as well as anammox (anaerobic ammonium oxidation). The model results suggest that these observations are a direct consequence of the different energy yields per electron transferred at the different steps of the pathways. Overall, our results theoretically support the hypothesis that successful microbial catabolic activities are selected by an overall maximum energy harvest rate.

Microbial analysis of the buffer/container experiment at AECL's underground research laboratory

International Nuclear Information System (INIS)

Stroes-Gascoyne, S.

1996-07-01

The Buffer/Container Experiment (BCE) was carried out at AECL's Underground Research Laboratory (URL) for 2.5 years to examine the in situ performance of compacted buffer material in a single emplacement borehole under vault-relevant conditions. During decommissioning of this experiment, numerous samples were taken for microbial analysis to determine if the naturally present microbial population in buffer material survived the conditions (i.e., compaction, heat and desiccation) in the BCE and to determine which group(s) of microorganisms would be dominant in such a simulated vault environment. Such knowledge will be very useful in assessing the potential effects of microbial activity on the concept for deep disposal of Canada's nuclear fuel waste, proposed by AECL. 46 refs., 31 tabs., 35 figs

Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism.

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Broman, Elias; Sjöstedt, Johanna; Pinhassi, Jarone; Dopson, Mark

2017-08-09

A key characteristic of eutrophication in coastal seas is the expansion of hypoxic bottom waters, often referred to as 'dead zones'. One proposed remediation strategy for coastal dead zones in the Baltic Sea is to mix the water column using pump stations, circulating oxygenated water to the sea bottom. Although microbial metabolism in the sediment surface is recognized as key in regulating bulk chemical fluxes, it remains unknown how the microbial community and its metabolic processes are influenced by shifts in oxygen availability. Here, coastal Baltic Sea sediments sampled from oxic and anoxic sites, plus an intermediate area subjected to episodic oxygenation, were experimentally exposed to oxygen shifts. Chemical, 16S rRNA gene, metagenomic, and metatranscriptomic analyses were conducted to investigate changes in chemistry fluxes, microbial community structure, and metabolic functions in the sediment surface. Compared to anoxic controls, oxygenation of anoxic sediment resulted in a proliferation of bacterial populations in the facultative anaerobic genus Sulfurovum that are capable of oxidizing toxic sulfide. Furthermore, the oxygenated sediment had higher amounts of RNA transcripts annotated as sqr, fccB, and dsrA involved in sulfide oxidation. In addition, the importance of cryptic sulfur cycling was highlighted by the oxidative genes listed above as well as dsvA, ttrB, dmsA, and ddhAB that encode reductive processes being identified in anoxic and intermediate sediments turned oxic. In particular, the intermediate site sediments responded differently upon oxygenation compared to the anoxic and oxic site sediments. This included a microbial community composition with more habitat generalists, lower amounts of RNA transcripts attributed to methane oxidation, and a reduced rate of organic matter degradation. These novel data emphasize that genetic expression analyses has the power to identify key molecular mechanisms that regulate microbial community responses

Towards a universal microbial inoculum for dissolved organic carbon degradation experiments

Science.gov (United States)

Pastor, Ada; Catalán, Núria; Gutiérrez, Carmen; Nagar, Nupur; Casas-Ruiz, Joan P.; Obrador, Biel; von Schiller, Daniel; Sabater, Sergi; Petrovic, Mira; Borrego, Carles M.; Marcé, Rafael

2017-04-01

Dissolved organic carbon (DOC) is the largest biologically available pool of organic carbon in aquatic ecosystems and its degradation along the land-to-ocean continuum has implications for carbon cycling from local to global scales. DOC biodegradability is usually assessed by incubating filtered water inoculated with native microbial assemblages in the laboratory. However, the use of a native inoculum from several freshwaters, without having a microbial-tailored design, hampers our ability to tease apart the relative contribution of the factors driving DOC degradation from the effects of local microbial communities. The use of a standard microbial inoculum would allow researchers to disentangle the drivers of DOC degradation from the metabolic capabilities of microbial communities operating in situ. With this purpose, we designed a bacterial inoculum to be used in experiments of DOC degradation in freshwater habitats. The inoculum is composed of six bacterial strains that easily grow under laboratory conditions, possess a versatile metabolism and are able to grow under both aerobic and anaerobic conditions. The mixed inoculum showed higher DOC degradation rates than those from their isolated bacterial components and the consumption of organic substrates was consistently replicated. Moreover, DOC degradation rates obtained using the designed inoculum were responsive across a wide range of natural water types differing in DOC concentration and composition. Overall, our results show the potential of the designed inoculum as a tool to discriminate between the effects of environmental drivers and intrinsic properties of DOC on degradation dynamics.

Adaptive laboratory evolution – principles and applications for biotechnology

Science.gov (United States)

2013-01-01

Adaptive laboratory evolution is a frequent method in biological studies to gain insights into the basic mechanisms of molecular evolution and adaptive changes that accumulate in microbial populations during long term selection under specified growth conditions. Although regularly performed for more than 25 years, the advent of transcript and cheap next-generation sequencing technologies has resulted in many recent studies, which successfully applied this technique in order to engineer microbial cells for biotechnological applications. Adaptive laboratory evolution has some major benefits as compared with classical genetic engineering but also some inherent limitations. However, recent studies show how some of the limitations may be overcome in order to successfully incorporate adaptive laboratory evolution in microbial cell factory design. Over the last two decades important insights into nutrient and stress metabolism of relevant model species were acquired, whereas some other aspects such as niche-specific differences of non-conventional cell factories are not completely understood. Altogether the current status and its future perspectives highlight the importance and potential of adaptive laboratory evolution as approach in biotechnological engineering. PMID:23815749

Coupling Spatiotemporal Community Assembly Processes to Changes in Microbial Metabolism

Energy Technology Data Exchange (ETDEWEB)

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

2016-12-16

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

Microbial Dark Matter Phase II: Stepping deeper into unknown territory

Energy Technology Data Exchange (ETDEWEB)

Jarett, Jessica; Dunfield, Peter; Peura, Sari; Wielen, Paul van der; Hedlund, Brian; Elshahed, Mostafa; Kormas, Konstantinos; Stott, Andreas Teske8, Matt; Birkeland, Nils-Kare; Zhang, Chuanlun; Rengefors, Karin; Lindemann, Stephen; Ravin, Nikolai V.; Spear, John; Hallam, Steven; Crowe, Sean; Steele, Jillian; Goudeau, Danielle; Malmstrom, Rex; Kyrpides, Nikos; Stepanauskas, Ramunas; Woyke, Tanja

2014-10-27

Currently available microbial genomes are of limited phylogenetic breadth due to our historical inability to cultivate most microorganisms in the laboratory. The first phase of the Microbial Dark Matter project used single-cell genomics to sequence 201 single cells from uncultivated lineages, and was able to resolve new superphyla and reveal novel metabolic features in bacteria and archaea. However, many fundamental questions about the evolution and function of microbes remain unanswered, and many candidate phyla remain uncharacterized. Phase II of the Microbial Dark Matter project will target candidate phyla with no sequenced representatives at a variety of new sites using a combination of single-cell sequencing and shotgun metagenomics approaches.

Nanoscale zero-valent iron/persulfate enhanced upflow anaerobic sludge blanket reactor for dye removal: Insight into microbial metabolism and microbial community

Science.gov (United States)

Pan, Fei; Zhong, Xiaohan; Xia, Dongsheng; Yin, Xianze; Li, Fan; Zhao, Dongye; Ji, Haodong; Liu, Wen

2017-03-01

This study investigated the efficiency of nanoscale zero-valent iron combined with persulfate (NZVI/PS) for enhanced degradation of brilliant red X-3B in an upflow anaerobic sludge blanket (UASB) reactor, and examined the effects of NZVI/PS on anaerobic microbial communities during the treatment process. The addition of NZVI (0.5 g/L) greatly enhanced the decolourization rate of X-3B from 63.8% to 98.4%. The Biolog EcoPlateTM technique was utilized to examine microbial metabolism in the reactor, and the Illumina MiSeq high-throughput sequencing revealed 22 phyla and 88 genera of the bacteria. The largest genera (Lactococcus) decreased from 33.03% to 7.94%, while the Akkermansia genera increased from 1.69% to 20.23% according to the abundance in the presence of 0.2 g/L NZVI during the biological treatment process. Meanwhile, three strains were isolated from the sludge in the UASB reactors and identified by 16 S rRNA analysis. The distribution of three strains was consistent with the results from the Illumina MiSeq high throughput sequencing. The X-ray photoelectron spectroscopy results indicated that Fe(0) was transformed into Fe(II)/Fe(III) during the treatment process, which are beneficial for the microorganism growth, and thus promoting their metabolic processes and microbial community.

Nanoscale zero-valent iron/persulfate enhanced upflow anaerobic sludge blanket reactor for dye removal: Insight into microbial metabolism and microbial community

Science.gov (United States)

Pan, Fei; Zhong, Xiaohan; Xia, Dongsheng; Yin, Xianze; Li, Fan; Zhao, Dongye; Ji, Haodong; Liu, Wen

2017-01-01

This study investigated the efficiency of nanoscale zero-valent iron combined with persulfate (NZVI/PS) for enhanced degradation of brilliant red X-3B in an upflow anaerobic sludge blanket (UASB) reactor, and examined the effects of NZVI/PS on anaerobic microbial communities during the treatment process. The addition of NZVI (0.5 g/L) greatly enhanced the decolourization rate of X-3B from 63.8% to 98.4%. The Biolog EcoPlateTM technique was utilized to examine microbial metabolism in the reactor, and the Illumina MiSeq high-throughput sequencing revealed 22 phyla and 88 genera of the bacteria. The largest genera (Lactococcus) decreased from 33.03% to 7.94%, while the Akkermansia genera increased from 1.69% to 20.23% according to the abundance in the presence of 0.2 g/L NZVI during the biological treatment process. Meanwhile, three strains were isolated from the sludge in the UASB reactors and identified by 16 S rRNA analysis. The distribution of three strains was consistent with the results from the Illumina MiSeq high throughput sequencing. The X-ray photoelectron spectroscopy results indicated that Fe(0) was transformed into Fe(II)/Fe(III) during the treatment process, which are beneficial for the microorganism growth, and thus promoting their metabolic processes and microbial community. PMID:28300176

Soil Metabolome and Metabolic Fate: Microbial Insights into Freshwater Tidal Wetland Redox Biogeochemistry

Science.gov (United States)

Roy Chowdhury, T.; Bramer, L.; Hoyt, D. W.; Kim, Y. M.; Metz, T. O.; McCue, L. A.; Jansson, J.; Bailey, V. L.

2017-12-01

Earth System Models predict climate extremes that will impact regional and global hydrology. Aquatic-terrestrial transition zones like wetlands will experience the immediate consequence of climate change as shifts in the magnitude and dynamics of hydrologic flow. Such fluctuating hydrology can alter the structure and function of the soil microbial populations that in turn will alter the nature and rate of biogeochemical transformations and significantly impact the carbon balance of the ecosystem. We tested the impacts of shifting hydrology on the soil microbiome and the role of antecedent moisture condition on redox active microbial processes in soils sampled from a tidal freshwater wetland system in the lower Columbia River, WA, USA. Our objectives were to characterize changes in the soil microbial community composition in response to soil moisture legacy effects, and to elucidate relationships between community response, geochemical signatures and metabolite profiles in this soil. The 16S rRNA gene sequencing showed significant decreases in bacterial abundance capable of anaerobic metabolism in response to drying, but quickly recovered to the antecedent moisture condition, as observed by redox processes. Metabolomics and biogeochemical process rates generated evidence for moisture-driven redox conditions as principal controls on the community and metabolic function. Fluctuating redox conditions altered terminal electron acceptor and donor availability and recovery strengths of these pools in soil such that a disproportionate release of carbon dioxide stemmed from alternative anaerobic degradation processes like sulfate and iron reduction in compared to methanogenesis. Our results show that anoxic conditions impact microbial communities in both permanently and temporarily saturated conditions and that rapid change in hydrology can increase substrate availability for both aerobic and anaerobic decomposition processes, including methanogenesis.

Influence of Wastewater Discharge on the Metabolic Potential of the Microbial Community in River Sediments.

Science.gov (United States)

Li, Dong; Sharp, Jonathan O; Drewes, Jörg E

2016-01-01

To reveal the variation of microbial community functions during water filtration process in river sediments, which has been utilized widely in natural water treatment systems, this study investigates the influence of municipal wastewater discharge to streams on the phylotype and metabolic potential of the microbiome in upstream and particularly various depths of downstream river sediments. Cluster analyses based on both microbial phylogenetic and functional data collectively revealed that shallow upstream sediments grouped with those from deeper subsurface downstream regions. These sediment samples were distinct from those found in shallow downstream sediments. Functional genes associated with carbohydrate, xenobiotic, and certain amino acid metabolisms were overrepresented in upstream and deep downstream samples. In contrast, the more immediate contact with wastewater discharge in shallow downstream samples resulted in an increase in the relative abundance of genes associated with nitrogen, sulfur, purine and pyrimidine metabolisms, as well as restriction-modification systems. More diverse bacterial phyla were associated with upstream and deep downstream sediments, mainly including Actinobacteria, Planctomycetes, and Firmicutes. In contrast, in shallow downstream sediments, genera affiliated with Betaproteobacteria and Gammaproteobacteria were enriched with putative functions that included ammonia and sulfur oxidation, polyphosphate accumulation, and methylotrophic bacteria. Collectively, these results highlight the enhanced capabilities of microbial communities residing in deeper stream sediments for the transformation of water contaminants and thus provide a foundation for better design of natural water treatment systems to further improve the removal of contaminants.

Influence of Wastewater Discharge on the Metabolic Potential of the Microbial Community in River Sediments

KAUST Repository

Li, Dong

2015-09-24

To reveal the variation of microbial community functions during water filtration process in river sediments, which has been utilized widely in natural water treatment systems, this study investigates the influence of municipal wastewater discharge to streams on the phylotype and metabolic potential of the microbiome in upstream and particularly various depths of downstream river sediments. Cluster analyses based on both microbial phylogenetic and functional data collectively revealed that shallow upstream sediments grouped with those from deeper subsurface downstream regions. These sediment samples were distinct from those found in shallow downstream sediments. Functional genes associated with carbohydrate, xenobiotic, and certain amino acid metabolisms were overrepresented in upstream and deep downstream samples. In contrast, the more immediate contact with wastewater discharge in shallow downstream samples resulted in an increase in the relative abundance of genes associated with nitrogen, sulfur, purine and pyrimidine metabolisms, as well as restriction–modification systems. More diverse bacterial phyla were associated with upstream and deep downstream sediments, mainly including Actinobacteria, Planctomycetes, and Firmicutes. In contrast, in shallow downstream sediments, genera affiliated with Betaproteobacteria and Gammaproteobacteria were enriched with putative functions that included ammonia and sulfur oxidation, polyphosphate accumulation, and methylotrophic bacteria. Collectively, these results highlight the enhanced capabilities of microbial communities residing in deeper stream sediments for the transformation of water contaminants and thus provide a foundation for better design of natural water treatment systems to further improve the removal of contaminants. © 2015, Springer Science+Business Media New York.

Photochemical alteration of organic carbon draining permafrost soils shifts microbial metabolic pathways and stimulates respiration.

Science.gov (United States)

Ward, Collin P; Nalven, Sarah G; Crump, Byron C; Kling, George W; Cory, Rose M

2017-10-03

In sunlit waters, photochemical alteration of dissolved organic carbon (DOC) impacts the microbial respiration of DOC to CO 2 . This coupled photochemical and biological degradation of DOC is especially critical for carbon budgets in the Arctic, where thawing permafrost soils increase opportunities for DOC oxidation to CO 2 in surface waters, thereby reinforcing global warming. Here we show how and why sunlight exposure impacts microbial respiration of DOC draining permafrost soils. Sunlight significantly increases or decreases microbial respiration of DOC depending on whether photo-alteration produces or removes molecules that native microbial communities used prior to light exposure. Using high-resolution chemical and microbial approaches, we show that rates of DOC processing by microbes are likely governed by a combination of the abundance and lability of DOC exported from land to water and produced by photochemical processes, and the capacity and timescale that microbial communities have to adapt to metabolize photo-altered DOC.The role of dissolved organic carbon (DOC) photo-alteration in the microbial respiration of DOC to CO 2 is unclear. Here, the authors show that the impact of this mechanism depends on whether photo-alteration of DOC produces or removes molecules used by native microbial communities prior to light exposure.

Anaerobic 4-hydroxyproline utilization: Discovery of a new glycyl radical enzyme in the human gut microbiome uncovers a widespread microbial metabolic activity.

Science.gov (United States)

Huang, Yolanda Y; Martínez-Del Campo, Ana; Balskus, Emily P

2018-02-06

The discovery of enzymes responsible for previously unappreciated microbial metabolic pathways furthers our understanding of host-microbe and microbe-microbe interactions. We recently identified and characterized a new gut microbial glycyl radical enzyme (GRE) responsible for anaerobic metabolism of trans-4-hydroxy-l-proline (Hyp). Hyp dehydratase (HypD) catalyzes the removal of water from Hyp to generate Δ 1 -pyrroline-5-carboxylate (P5C). This enzyme is encoded in the genomes of a diverse set of gut anaerobes and is prevalent and abundant in healthy human stool metagenomes. Here, we discuss the roles HypD may play in different microbial metabolic pathways as well as the potential implications of this activity for colonization resistance and pathogenesis within the human gut. Finally, we present evidence of anaerobic Hyp metabolism in sediments through enrichment culturing of Hyp-degrading bacteria, highlighting the wide distribution of this pathway in anoxic environments beyond the human gut.

Diagnosis of In Situ Metabolic State and Rates of Microbial Metabolism During In Situ Uranium Bioremediation with Molecular Techniques

Energy Technology Data Exchange (ETDEWEB)

Lovley, Derek R. [University of Massachusetts, Amherst

2012-11-28

The goal of these projects was to develop molecule tools to tract the metabolic activity and physiological status of microorganisms during in situ uranium bioremediation. Such information is important in able to design improved bioremediation strategies. As summarized below, the research was highly successful with new strategies developed for estimating in situ rates of metabolism and diagnosing the physiological status of the predominant subsurface microorganisms. This is a first not only for groundwater bioremediation studies, but also for subsurface microbiology in general. The tools and approaches developed in these studies should be applicable to the study of microbial communities in a diversity of soils and sediments.

Spatial variation in microbial processes controlling carbon mineralization within soils and sediments

Energy Technology Data Exchange (ETDEWEB)

Fendorf, Scott [Stanford Univ., CA (United States); Kleber, Markus [Oregon State Univ., Corvallis, OR (United States); Nico, Peter [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

2017-10-19

Soils have a defining role in global carbon cycling, having one of the largest dynamic stocks of C on earth—3300 Pg of C are stored in soils, which is three-times the amount stored in the atmosphere and more than the terrestrial land plants. An important control on soil organic matter (SOM) quantities is the mineralization rate. It is well recognized that the rate and extent of SOM mineralization is affected by climatic factors and mineral-organic matter associations. What remained elusive is to what extent constraints on microbial metabolism induced by the respiratory pathway, and specifically the electron acceptor in respiration, control overall rates of carbon mineralization in soils. Therefore, physical factors limiting oxygen diffusion such as soil texture and aggregate size (soil structure) may therefore be central controls on C mineralization rates. The goal of our research was therefore to determine if variations in microbial metabolic rates induced by anaerobic microsites in soils are a major control on SOM mineralization rates and thus storage. We performed a combination of laboratory experiments and field investigations will be performed to fulfill our research objectives. We used laboratory studies to examine fundamental factors of respiratory constraints (i.e., electron acceptor) on organic matter mineralization rates. We ground our laboratory studies with both manipulation of field samples and in-field measurements. Selection of the field sites is guided by variation in soil texture and structure while having (other environmental/soil factors constant. Our laboratory studies defined redox gradients and variations in microbial metabolism operating at the aggregate-scale (cm-scale) within soils using a novel constructed diffusion reactor. We further examined micro-scale variation in terminal electron accepting processes and resulting C mineralization rates within re-packed soils. A major outcome of our research is the ability to quantitatively place

Reply to 'Comment on kinetic modeling of microbially-driven redox chemistry of subsurface environments: coupling transport, microbial metabolism and geochemistry' by J. Griffioen

Science.gov (United States)

Hunter, K. S.; Van Cappellen, P.

2000-01-01

Our paper, 'Kinetic modeling of microbially-driven redox chemistry of subsurface environments: coupling transport, microbial metabolism and geochemistry' (Hunter et al., 1998), presents a theoretical exploration of biogeochemical reaction networks and their importance to the biogeochemistry of groundwater systems. As with any other model, the kinetic reaction-transport model developed in our paper includes only a subset of all physically, biologically and chemically relevant processes in subsurface environments. It considers aquifer systems where the primary energy source driving microbial activity is the degradation of organic matter. In addition to the primary biodegradation pathways of organic matter (i.e. respiration and fermentation), the redox chemistry of groundwaters is also affected by reactions not directly involving organic matter oxidation. We refer to the latter as secondary reactions. By including secondary redox reactions which consume reduced reaction products (e.g., Mn2+, FeS, H2S), and in the process compete with microbial heterotrophic populations for available oxidants (i.e. O2, NO3-, Mn(IV), Fe(III), SO42-), we predict spatio-temporal distributions of microbial activity which differ significantly from those of models which consider only the biodegradation reactions. That is, the secondary reactions have a significant impact on the distributions of the rates of heterotrophic and chemolithotrophic metabolic pathways. We further show that secondary redox reactions, as well as non-redox reactions, significantly influence the acid-base chemistry of groundwaters. The distributions of dissolved inorganic redox species along flowpaths, however, are similar in simulations with and without secondary reactions (see Figs. 3(b) and 7(b) in Hunter et al., 1998), indicating that very different biogeochemical reaction dynamics may lead to essentially the same chemical redox zonation of a groundwater system.

Metabolic engineering of microbial competitive advantage for industrial fermentation processes.

Science.gov (United States)

Shaw, A Joe; Lam, Felix H; Hamilton, Maureen; Consiglio, Andrew; MacEwen, Kyle; Brevnova, Elena E; Greenhagen, Emily; LaTouf, W Greg; South, Colin R; van Dijken, Hans; Stephanopoulos, Gregory

2016-08-05

Microbial contamination is an obstacle to widespread production of advanced biofuels and chemicals. Current practices such as process sterilization or antibiotic dosage carry excess costs or encourage the development of antibiotic resistance. We engineered Escherichia coli to assimilate melamine, a xenobiotic compound containing nitrogen. After adaptive laboratory evolution to improve pathway efficiency, the engineered strain rapidly outcompeted a control strain when melamine was supplied as the nitrogen source. We additionally engineered the yeasts Saccharomyces cerevisiae and Yarrowia lipolytica to assimilate nitrogen from cyanamide and phosphorus from potassium phosphite, and they outcompeted contaminating strains in several low-cost feedstocks. Supplying essential growth nutrients through xenobiotic or ecologically rare chemicals provides microbial competitive advantage with minimal external risks, given that engineered biocatalysts only have improved fitness within the customized fermentation environment. Copyright © 2016, American Association for the Advancement of Science.

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

Replicating the microbial community and water quality performance of full-scale slow sand filters in laboratory-scale filters.

Science.gov (United States)

Haig, Sarah-Jane; Quince, Christopher; Davies, Robert L; Dorea, Caetano C; Collins, Gavin

2014-09-15

Previous laboratory-scale studies to characterise the functional microbial ecology of slow sand filters have suffered from methodological limitations that could compromise their relevance to full-scale systems. Therefore, to ascertain if laboratory-scale slow sand filters (L-SSFs) can replicate the microbial community and water quality production of industrially operated full-scale slow sand filters (I-SSFs), eight cylindrical L-SSFs were constructed and were used to treat water from the same source as the I-SSFs. Half of the L-SSFs sand beds were composed of sterilized sand (sterile) from the industrial filters and the other half with sand taken directly from the same industrial filter (non-sterile). All filters were operated for 10 weeks, with the microbial community and water quality parameters sampled and analysed weekly. To characterize the microbial community phyla-specific qPCR assays and 454 pyrosequencing of the 16S rRNA gene were used in conjunction with an array of statistical techniques. The results demonstrate that it is possible to mimic both the water quality production and the structure of the microbial community of full-scale filters in the laboratory - at all levels of taxonomic classification except OTU - thus allowing comparison of LSSF experiments with full-scale units. Further, it was found that the sand type composing the filter bed (non-sterile or sterile), the water quality produced, the age of the filters and the depth of sand samples were all significant factors in explaining observed differences in the structure of the microbial consortia. This study is the first to the authors' knowledge that demonstrates that scaled-down slow sand filters can accurately reproduce the water quality and microbial consortia of full-scale slow sand filters. Copyright © 2014 Elsevier Ltd. All rights reserved.

Effect of silver nanoparticles on growth performance, metabolism and microbial profile of broiler chickens

DEFF Research Database (Denmark)

Pineda, Lane Manalili; Chwalibog, André; Sawosz, Ewa

2012-01-01

and intestinal content were collected to evaluate the effects of AgNano on plasma concentration of immunoglobulins and the intestinal microflora, respectively. The provision of water solutions containing different concentrations of AgNano had no effect on postnatal growth performance and the energy metabolism...... (IgG) in the blood plasma of broilers supplemented with AgNano decreased at day 36 (p = 0.012). The results demonstrated that AgNano affects N utilisation and plasma IgG concentration; however, it does not influence the microbial populations in the digestive tract, the energy metabolism and growth...

Gut Microbial Metabolism of Polyphenols from Black Tea and Red Wine/Grape Juice Is Source-Specific and Colon-Region Dependent

NARCIS (Netherlands)

Dorsten, van F.A.; Peters, S.; Gross, G.; Gomez-Roldan, V.; Klinkenberg, M.; Vos, de Ric; Vaughan, E.E.; Duynhoven, van J.P.M.; Possemiers, S.; Wiele, van der T.; Jacobs, D.M.

2012-01-01

The colonic microbial degradation of a polyphenol-rich black tea extract (BTE) and red wine/grape juice extract (RWGE) was compared in a five-stage in vitro gastrointestinal model (TWINSHIME). Microbial metabolism of BTE and RWGE polyphenols in the TWINSHIME was studied subsequently in single- and

2012 Molecular Basis of Microbial One-Carbon Metabolism Gordon Research Conferences and Gordon Research Seminar, August 4-10,2012

Energy Technology Data Exchange (ETDEWEB)

Hanson, Thomas

2012-08-10

The 2012 Gordon Conference will present and discuss cutting-edge research in the field of microbial metabolism of C1 compounds. The conference will feature the roles and application of C1 metabolism in natural and synthetic systems at scales from molecules to ecosystems. The conference will stress molecular aspects of the unique metabolism exhibited by autotrophic bacteria, methanogens, methylotrophs, aerobic and anaerobic methanotrophs, and acetogens.

[Advances in metabolic engineering for the microbial production of naturally occurring terpenes-limonene and bisabolene: a mini review].

Science.gov (United States)

Pang, Yaru; Hu, Zhihui; Xiao, Dongguang; Yu, Aiqun

2018-01-25

Limonene (C₁₀H₁₆) and bisabolene (C₁₅H₂₄) are both naturally occurring terpenes in plants. Depending on the number of C₅ units, limonene and bisabolene are recognized as representative monoterpenes and sesquiterpenes, respectively. Limonene and bisabolene are important pharmaceutical and nutraceutical products used in the prevention and treatment of cancer and many other diseases. In addition, they can be used as starting materials to produce a range of commercially valuable products, such as pharmaceuticals, nutraceuticals, cosmetics, and biofuels. The low abundance or yield of limonene and bisabolene in plants renders their isolation from plant sources non-economically viable. Isolation of limonene and bisabolene from plants also suffers from low efficiency and often requires harsh reaction conditions, prolonged reaction times, and expensive equipment cost. Recently, the rapid developments in metabolic engineering of microbes provide a promising alternative route for producing these plant natural products. Therefore, producing limonene and bisabolene by engineering microbial cells into microbial factories is becoming an attractive alternative approach that can overcome the bottlenecks, making it more sustainable, environmentally friendly and economically competitive. Here, we reviewed the status of metabolic engineering of microbes that produce limonene and bisabolene including microbial hosts, key enzymes, metabolic pathways and engineering of limonene/bisabolene biosynthesis. Furthermore, key challenges and future perspectives were discussed.

A Synthetic Ecology Perspective: How Well Does Behavior of Model Organisms in the Laboratory Predict Microbial Activities in Natural Habitats?

Science.gov (United States)

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

2016-01-01

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

Metagenomic analysis of an ecological wastewater treatment plant's microbial communities and their potential to metabolize pharmaceuticals.

Science.gov (United States)

Balcom, Ian N; Driscoll, Heather; Vincent, James; Leduc, Meagan

2016-01-01

Pharmaceuticals and other micropollutants have been detected in drinking water, groundwater, surface water, and soil around the world. Even in locations where wastewater treatment is required, they can be found in drinking water wells, municipal water supplies, and agricultural soils. It is clear conventional wastewater treatment technologies are not meeting the challenge of the mounting pressures on global freshwater supplies. Cost-effective ecological wastewater treatment technologies have been developed in response. To determine whether the removal of micropollutants in ecological wastewater treatment plants (WWTPs) is promoted by the plant-microbe interactions, as has been reported for other recalcitrant xenobiotics, biofilm microbial communities growing on the surfaces of plant roots were profiled by whole metagenome sequencing and compared to the microbial communities residing in the wastewater. In this study, the concentrations of pharmaceuticals and personal care products (PPCPs) were quantified in each treatment tank of the ecological WWTP treating human wastewater at a highway rest stop and visitor center in Vermont. The concentrations of detected PPCPs were substantially greater than values reported for conventional WWTPs likely due to onsite recirculation of wastewater. The greatest reductions in PPCPs concentrations were observed in the anoxic treatment tank where Bacilli dominated the biofilm community. Benzoate degradation was the most abundant xenobiotic metabolic category identified throughout the system. Collectively, the microbial communities residing in the wastewater were taxonomically and metabolically more diverse than the immersed plant root biofilm. However, greater heterogeneity and higher relative abundances of xenobiotic metabolism genes was observed for the root biofilm.

2004 Molecular Basis of Microbial One-Carbon Metabolism Gordon Conference - August 1-6, 2004

Energy Technology Data Exchange (ETDEWEB)

Joseph A. Krzycki

2005-09-15

The Gordon Research Conference (GRC) on 2004 Molecular Basis of Microbial One-Carbon Metabolism Gordon Conference - August 1-6, 2004 was held at Mount Holyoke College, South Hadley, MA from August 1-6, 2004. The Conference was well-attended with 117 participants (attendees list attached). The attendees represented the spectrum of endeavor in this field coming from academia, industry, and government laboratories, both U.S. and foreign scientists, senior researchers, young investigators, and students. In designing the formal speakers program, emphasis was placed on current unpublished research and discussion of the future target areas in this field. There was a conscious effort to stimulate lively discussion about the key issues in the field today. Time for formal presentations was limited in the interest of group discussions. In order that more scientists could communicate their most recent results, poster presentation time was scheduled. Attached is a copy of the formal schedule and speaker program and the poster program. In addition to these formal interactions, 'free time' was scheduled to allow informal discussions. Such discussions are fostering new collaborations and joint efforts in the field.

Metabolic commensalism and competition in a two-species microbial consortium

DEFF Research Database (Denmark)

Christensen, Bjarke Bak; Haagensen, Janus Anders Juul; Heydorn, Arne

2002-01-01

We analyzed metabolic interactions and the importance of specific structural relationships in a benzyl alcohol-degrading microbial consortium comprising two species, Pseudomonas putida strain R1 and Acinetobacter strain C6, both of which are able to utilize benzyl alcohol as their sole carbon...... alcohol, which apparently gives Acinetobacter strain C6 a growth advantage, probably because it converts benzyl alcohol to benzoate with a higher yield per time unit than P. putida R1. In biofilms, however, the organisms establish structured, surface-attached consortia, in which heterogeneous ecological...... niches develop, and under these conditions competition for the primary carbon source is not the only determinant of biomass and population structure....

Energy Harvesting From River Sediment Using a Microbial Fuel Cell: Preliminary Results

Directory of Open Access Journals (Sweden)

Philippe Namour

2014-05-01

Full Text Available We have built a sedimentary fuel cell or Sediment Microbial Fuel Cell (SMFC. The device works on the principle of microbial fuel cells by exploiting directly the energy contained in sedimentary organic matter. It converts in electricity the sediment potential, thanks to microorganisms able to waste electrons from their metabolism directly to a solid anode instead of their natural electron acceptors, such as oxygen or nitrate. The sediment microbial fuel cell was made of a non-corrodible anode (graphite buried in anoxic sediments layer and connected via an electrical circuit to a cathode installed in surface water. We present the first results of laboratory sedimentary fuel cell and a prototype installed in the river.

Laboratory Diagnosis of Carbohydrate Metabolism Disorders. Diagnosis Algorithm in Hyperglycemic States

Directory of Open Access Journals (Sweden)

V.I. Pankiv

2014-04-01

Full Text Available The article is devoted to the laboratory diagnosis of disorders of carbohydrate metabolism. Presents criteria for diagnosis of diabetes, an algorithm for oral glucose tolerance test, determine type of diabetes based on clinical and laboratory data. The article also raised the issues of diagnosis of gestational diabetes and a diagnostic algorithm of hyperglycemia conditions during pregnancy.

Calibration and analysis of genome-based models for microbial ecology.

Science.gov (United States)

Louca, Stilianos; Doebeli, Michael

2015-10-16

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

Good laboratory practices for biochemical genetic testing and newborn screening for inherited metabolic disorders.

Science.gov (United States)

2012-04-06

Biochemical genetic testing and newborn screening are essential laboratory services for the screening, detection, diagnosis, and monitoring of inborn errors of metabolism or inherited metabolic disorders. Under the Clinical Laboratory Improvement Amendments of 1988 (CLIA) regulations, laboratory testing is categorized on the basis of the level of testing complexity as either waived (i.e., from routine regulatory oversight) or nonwaived testing (which includes tests of moderate and high complexity). Laboratories that perform biochemical genetic testing are required by CLIA regulations to meet the general quality systems requirements for nonwaived testing and the personnel requirements for high-complexity testing. Laboratories that perform public health newborn screening are subject to the same CLIA regulations and applicable state requirements. As the number of inherited metabolic diseases that are included in state-based newborn screening programs continues to increase, ensuring the quality of performance and delivery of testing services remains a continuous challenge not only for public health laboratories and other newborn screening facilities but also for biochemical genetic testing laboratories. To help ensure the quality of laboratory testing, CDC collaborated with the Centers for Medicare & Medicaid Services, the Food and Drug Administration, the Health Resources and Services Administration, and the National Institutes of Health to develop guidelines for laboratories to meet CLIA requirements and apply additional quality assurance measures for these areas of genetic testing. This report provides recommendations for good laboratory practices that were developed based on recommendations from the Clinical Laboratory Improvement Advisory Committee, with additional input from the Secretary's Advisory Committee on Genetics, Health, and Society; the Secretary's Advisory Committee on Heritable Disorders in Newborns and Children; and representatives of newborn

Microbial metaproteomics for characterizing the range of metabolic functions and activities of human gut microbiota.

Science.gov (United States)

Xiong, Weili; Abraham, Paul E; Li, Zhou; Pan, Chongle; Hettich, Robert L

2015-10-01

The human gastrointestinal tract is a complex, dynamic ecosystem that consists of a carefully tuned balance of human host and microbiota membership. The microbiome is not merely a collection of opportunistic parasites, but rather provides important functions to the host that are absolutely critical to many aspects of health, including nutrient transformation and absorption, drug metabolism, pathogen defense, and immune system development. Microbial metaproteomics provides the ability to characterize the human gut microbiota functions and metabolic activities at a remarkably deep level, revealing information about microbiome development and stability as well as their interactions with their human host. Generally, microbial and human proteins can be extracted and then measured by high performance MS-based proteomics technology. Here, we review the field of human gut microbiome metaproteomics, with a focus on the experimental and informatics considerations involved in characterizing systems ranging from low-complexity model gut microbiota in gnotobiotic mice, to the emerging gut microbiome in the GI tract of newborn human infants, and finally to an established gut microbiota in human adults. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Microbial Reduction of Fe(III) and SO42- and Associated Microbial Communities in the Alluvial Aquifer Groundwater and Sediments.

Science.gov (United States)

Lee, Ji-Hoon; Lee, Bong-Joo

2017-11-25

Agricultural demands continuously increased use of groundwater, causing drawdown of water table and need of artificial recharge using adjacent stream waters. River water intrusion into groundwater can alter the geochemical and microbiological characteristics in the aquifer and subsurface. In an effort to investigate the subsurface biogeochemical activities before operation of artificial recharge at the test site, established at the bank of Nakdong River, Changwon, South Korea, organic carbon transported from river water to groundwater was mimicked and the effect on the indigenous microbial communities was investigated with the microcosm incubations of the groundwater and subsurface sediments. Laboratory incubations indicated microbial reduction of Fe(III) and sulfate. Next-generation Illumina MiSeq sequences of V4 region of 16S rRNA gene provided that the shifts of microbial taxa to Fe(III)-reducing and/or sulfate-reducing microorganisms such as Geobacter, Albidiferax, Desulfocapsa, Desulfuromonas, and Desulfovibrio were in good correlation with the sequential flourishment of microbial reduction of Fe(III) and sulfate as the incubations progressed. This suggests the potential role of dissolved organic carbons migrated with the river water into groundwater in the managed aquifer recharge system on the indigenous microbial community composition and following alterations of subsurface biogeochemistry and microbial metabolic activities.

Variation in antibiotic-induced microbial recolonization impacts on the host metabolic phenotypes of rats.

Science.gov (United States)

Swann, Jonathan R; Tuohy, Kieran M; Lindfors, Peter; Brown, Duncan T; Gibson, Glenn R; Wilson, Ian D; Sidaway, James; Nicholson, Jeremy K; Holmes, Elaine

2011-08-05

The interaction between the gut microbiota and their mammalian host is known to have far-reaching consequences with respect to metabolism and health. We investigated the effects of eight days of oral antibiotic exposure (penicillin and streptomycin sulfate) on gut microbial composition and host metabolic phenotype in male Han-Wistar rats (n = 6) compared to matched controls. Early recolonization was assessed in a third group exposed to antibiotics for four days followed by four days recovery (n = 6). Fluorescence in situ hybridization analysis of the intestinal contents collected at eight days showed a significant reduction in all bacterial groups measured (control, 10(10.7) cells/g feces; antibiotic-treated, 10(8.4)). Bacterial suppression reduced the excretion of mammalian-microbial urinary cometabolites including hippurate, phenylpropionic acid, phenylacetylglycine and indoxyl-sulfate whereas taurine, glycine, citrate, 2-oxoglutarate, and fumarate excretion was elevated. While total bacterial counts remained notably lower in the recolonized animals (10(9.1) cells/g faeces) compared to the controls, two cage-dependent subgroups emerged with Lactobacillus/Enterococcus probe counts dominant in one subgroup. This dichotomous profile manifested in the metabolic phenotypes with subgroup differences in tricarboxylic acid cycle metabolites and indoxyl-sulfate excretion. Fecal short chain fatty acids were diminished in all treated animals. Antibiotic treatment induced a profound effect on the microbiome structure, which was reflected in the metabotype. Moreover, the recolonization process was sensitive to the microenvironment, which may impact on understanding downstream consequences of antibiotic consumption in human populations.

Effects of Conservation Tillage on Topsoil Microbial Metabolic Characteristics and Organic Carbon within Aggregates under a Rice (Oryza sativa L.) –Wheat (Triticum aestivum L.) Cropping System in Central China

Science.gov (United States)

Liu, Tian-Qi; Cao, Cou-Gui; Li, Cheng-Fang

2016-01-01

Investigating microbial metabolic characteristics and soil organic carbon (SOC) within aggregates and their relationships under conservation tillage may be useful in revealing the mechanism of SOC sequestration in conservation tillage systems. However, limited studies have been conducted to investigate the relationship between SOC and microbial metabolic characteristics within aggregate fractions under conservation tillage. We hypothesized that close relationships can exist between SOC and microbial metabolic characteristics within aggregates under conservation tillage. In this study, a field experiment was conducted from June 2011 to June 2013 following a split-plot design of a randomized complete block with tillage practices [conventional intensive tillage (CT) and no tillage (NT)] as main plots and straw returning methods [preceding crop residue returning (S, 2100−2500 kg C ha−1) and removal (NS, 0 kg C ha-1)] as subplots with three replications. The objective of this study was to reveal the effects of tillage practices and residue-returning methods on topsoil microbial metabolic characteristics and organic carbon (SOC) fractions within aggregates and their relationships under a rice–wheat cropping system in central China. Microbial metabolic characteristics investigated using the Biolog system was examined within two aggregate fractions (>0.25 and 0.25 aggregate, and 0.25 mm aggregate (11.3%), and 0.25 mm aggregate, and 0.25 mm aggregate, and tillage (NT and S) increased microbial metabolic activities and Shannon index in >0.25 and directly improved SOC by promoting DOC in >0.25 mm aggregate in the upper (0−5 cm) soil layer under conservation tillage systems, as well as directly and indirectly by promoting DOC and MBC in tillage increased SOC in aggregates in the topsoil by improving microbial metabolic activities. PMID:26731654

[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

Metabolic and demographic feedbacks shape the emergent spatial structure and function of microbial communities.

Directory of Open Access Journals (Sweden)

Sylvie Estrela

Full Text Available Microbes are predominantly found in surface-attached and spatially structured polymicrobial communities. Within these communities, microbial cells excrete a wide range of metabolites, setting the stage for interspecific metabolic interactions. The links, however, between metabolic and ecological interactions (functional relationships, and species spatial organization (structural relationships are still poorly understood. Here, we use an individual-based modelling framework to simulate the growth of a two-species surface-attached community where food (resource is traded for detoxification (service and investigate how metabolic constraints of individual species shape the emergent structural and functional relationships of the community. We show that strong metabolic interdependence drives the emergence of mutualism, robust interspecific mixing, and increased community productivity. Specifically, we observed a striking and highly stable emergent lineage branching pattern, generating a persistent lineage mixing that was absent when the metabolic exchange was removed. These emergent community properties are driven by demographic feedbacks, such that aid from neighbouring cells directly enhances focal cell growth, which in turn feeds back to neighbour fecundity. In contrast, weak metabolic interdependence drives conflict (exploitation or competition, and in turn greater interspecific segregation. Together, these results support the idea that species structural and functional relationships represent the net balance of metabolic interdependencies.

Computational design of auxotrophy-dependent microbial biosensors for combinatorial metabolic engineering experiments.

Science.gov (United States)

Tepper, Naama; Shlomi, Tomer

2011-01-21

Combinatorial approaches in metabolic engineering work by generating genetic diversity in a microbial population followed by screening for strains with improved phenotypes. One of the most common goals in this field is the generation of a high rate chemical producing strain. A major hurdle with this approach is that many chemicals do not have easy to recognize attributes, making their screening expensive and time consuming. To address this problem, it was previously suggested to use microbial biosensors to facilitate the detection and quantification of chemicals of interest. Here, we present novel computational methods to: (i) rationally design microbial biosensors for chemicals of interest based on substrate auxotrophy that would enable their high-throughput screening; (ii) predict engineering strategies for coupling the synthesis of a chemical of interest with the production of a proxy metabolite for which high-throughput screening is possible via a designed bio-sensor. The biosensor design method is validated based on known genetic modifications in an array of E. coli strains auxotrophic to various amino-acids. Predicted chemical production rates achievable via the biosensor-based approach are shown to potentially improve upon those predicted by current rational strain design approaches. (A Matlab implementation of the biosensor design method is available via http://www.cs.technion.ac.il/~tomersh/tools).

Sulfur metabolizing microbes dominate microbial communities in Andesite-hosted shallow-sea hydrothermal systems.

Directory of Open Access Journals (Sweden)

Yao Zhang

Full Text Available To determine microbial community composition, community spatial structure and possible key microbial processes in the shallow-sea hydrothermal vent systems off NE Taiwan's coast, we examined the bacterial and archaeal communities of four samples collected from the water column extending over a redoxocline gradient of a yellow and four from a white hydrothermal vent. Ribosomal tag pyrosequencing based on DNA and RNA showed statistically significant differences between the bacterial and archaeal communities of the different hydrothermal plumes. The bacterial and archaeal communities from the white hydrothermal plume were dominated by sulfur-reducing Nautilia and Thermococcus, whereas the yellow hydrothermal plume and the surface water were dominated by sulfide-oxidizing Thiomicrospira and Euryarchaeota Marine Group II, respectively. Canonical correspondence analyses indicate that methane (CH(4 concentration was the only statistically significant variable that explains all community cluster patterns. However, the results of pyrosequencing showed an essential absence of methanogens and methanotrophs at the two vent fields, suggesting that CH(4 was less tied to microbial processes in this shallow-sea hydrothermal system. We speculated that mixing between hydrothermal fluids and the sea or meteoric water leads to distinctly different CH(4 concentrations and redox niches between the yellow and white vents, consequently influencing the distribution patterns of the free-living Bacteria and Archaea. We concluded that sulfur-reducing and sulfide-oxidizing chemolithoautotrophs accounted for most of the primary biomass synthesis and that microbial sulfur metabolism fueled microbial energy flow and element cycling in the shallow hydrothermal systems off the coast of NE Taiwan.

Sulfur metabolizing microbes dominate microbial communities in Andesite-hosted shallow-sea hydrothermal systems.

Science.gov (United States)

Zhang, Yao; Zhao, Zihao; Chen, Chen-Tung Arthur; Tang, Kai; Su, Jianqiang; Jiao, Nianzhi

2012-01-01

To determine microbial community composition, community spatial structure and possible key microbial processes in the shallow-sea hydrothermal vent systems off NE Taiwan's coast, we examined the bacterial and archaeal communities of four samples collected from the water column extending over a redoxocline gradient of a yellow and four from a white hydrothermal vent. Ribosomal tag pyrosequencing based on DNA and RNA showed statistically significant differences between the bacterial and archaeal communities of the different hydrothermal plumes. The bacterial and archaeal communities from the white hydrothermal plume were dominated by sulfur-reducing Nautilia and Thermococcus, whereas the yellow hydrothermal plume and the surface water were dominated by sulfide-oxidizing Thiomicrospira and Euryarchaeota Marine Group II, respectively. Canonical correspondence analyses indicate that methane (CH(4)) concentration was the only statistically significant variable that explains all community cluster patterns. However, the results of pyrosequencing showed an essential absence of methanogens and methanotrophs at the two vent fields, suggesting that CH(4) was less tied to microbial processes in this shallow-sea hydrothermal system. We speculated that mixing between hydrothermal fluids and the sea or meteoric water leads to distinctly different CH(4) concentrations and redox niches between the yellow and white vents, consequently influencing the distribution patterns of the free-living Bacteria and Archaea. We concluded that sulfur-reducing and sulfide-oxidizing chemolithoautotrophs accounted for most of the primary biomass synthesis and that microbial sulfur metabolism fueled microbial energy flow and element cycling in the shallow hydrothermal systems off the coast of NE Taiwan.

Electronic Nose Technology to Measure Soil Microbial Activity and Classify Soil Metabolic Status

OpenAIRE

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

2011-01-01

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

Detrital microbial community development and phosphorus dynamics in a stream ecosystem

International Nuclear Information System (INIS)

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

1986-06-01

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

Microbial Metabolic Roles in Bedrock Degradation and the Genesis of Biomineral and Biopattern Biosignatures in Caves and Mines

Science.gov (United States)

Boston, P. J.

2016-12-01

In subsurface environments like natural or anthropogenic caves (aka mines), microorganisms facilitate considerable bedrock degradation under a variety of circumstances. Mobilization of materials from these processes frequently produces distinctive biominerals, identifiable biotextures, and unique biopatterns. Microbial activities can even determine the form of speleothems (secondary mineral cave decorations), thus providing highly conspicuous macroscopic biosignatures. It is critical to understand microbial-mineral interactions, recognizing that while the lithology controls important aspects of the environment, in turn, the geochemistry is greatly affected by the biology. Microbial communities can contribute to the actual formation of cavities (speleogenesis), and subsequent enlargement of caves and vugs and the mineral deposits that enrich many subterranean spaces. A major challenge is to quantify such influences. Genetic analysis is revealing a vast but highly partitioned biodiversity in the overall rock fracture habitat of Earth's crust especially in caves and mines where the three phases of matter (solid rock, fluids, and gases) typically interact producing high niche richness. Lessons learned from the microbial/geochemical systems that we have studied include: 1) significant similarities in metabolic functions between different geochemical systems, 2) ubiquity of metal oxidation for energy, 3) ubiquity of biofilms, some highly mineralized, 4) highly interdependent, multi-species communities that can only transform materials in consortia, 5) complex ecological succession including characteristic pioneer species, 6) often very slow growth rates in culture, 7) prevalence of very small cell sizes, ( 100 - 500 nm diam.), 8) mineral reprecipitation of mobilized materials, often dependent on the presence of live microbial communities to produce initial amorphous compounds followed by gradual crystallization, and 9) resultant in situ self-fossilization. Microbial

Deep subsurface microbial processes

Science.gov (United States)

Lovley, D.R.; Chapelle, F.H.

1995-01-01

Information on the microbiology of the deep subsurface is necessary in order to understand the factors controlling the rate and extent of the microbially catalyzed redox reactions that influence the geophysical properties of these environments. Furthermore, there is an increasing threat that deep aquifers, an important drinking water resource, may be contaminated by man's activities, and there is a need to predict the extent to which microbial activity may remediate such contamination. Metabolically active microorganisms can be recovered from a diversity of deep subsurface environments. The available evidence suggests that these microorganisms are responsible for catalyzing the oxidation of organic matter coupled to a variety of electron acceptors just as microorganisms do in surface sediments, but at much slower rates. The technical difficulties in aseptically sampling deep subsurface sediments and the fact that microbial processes in laboratory incubations of deep subsurface material often do not mimic in situ processes frequently necessitate that microbial activity in the deep subsurface be inferred through nonmicrobiological analyses of ground water. These approaches include measurements of dissolved H2, which can predict the predominant microbially catalyzed redox reactions in aquifers, as well as geochemical and groundwater flow modeling, which can be used to estimate the rates of microbial processes. Microorganisms recovered from the deep subsurface have the potential to affect the fate of toxic organics and inorganic contaminants in groundwater. Microbial activity also greatly influences 1 the chemistry of many pristine groundwaters and contributes to such phenomena as porosity development in carbonate aquifers, accumulation of undesirably high concentrations of dissolved iron, and production of methane and hydrogen sulfide. Although the last decade has seen a dramatic increase in interest in deep subsurface microbiology, in comparison with the study of

Effect of co-existing plant specie on soil microbial activity under heavy metal stress

International Nuclear Information System (INIS)

Nwuche, C. O.; Ugoji, E. O.

2010-01-01

The influence of plant primary compounds on the activity of soil microbial communities under heavy metal stress was studied in a pot-culture field experiment conducted in a green house. Amaranthus spinosus was cultivated in an agricultural soil previously amended in the laboratory with solutions of different trace elements in two separate treatment modes: singly and in combination. Culture-independent metabolism based indices such as the rate of carbon and nitrogen mineralization, microbial biomass carbon and soil basal respiration were monitored fortnightly over a period of six weeks. Result shows that plant detritus have significant modifying effect on soil microbe-metal interactions. Data on microbial and biochemical processes in the respective mesocosms did not vary from control; not even in mesocosms containing very high concentrations of copper, zinc and nickel. The soil microbial biomass carbon and the rate of carbon and nitrogen cycling were not impeded by the respective metal treatment while the respiration responses increased as a result of increase in metabolic activity of the soil microbes. The plant based substrates enabled the soil microflora to resist high metal contamination because of its tendency to absorb large amounts of inorganic cations.

Elevated CO2 shifts the functional structure and metabolic potentials of soil microbial communities in a C4 agroecosystem.

Science.gov (United States)

Xiong, Jinbo; He, Zhili; Shi, Shengjing; Kent, Angela; Deng, Ye; Wu, Liyou; Van Nostrand, Joy D; Zhou, Jizhong

2015-03-20

Atmospheric CO2 concentration is continuously increasing, and previous studies have shown that elevated CO2 (eCO2) significantly impacts C3 plants and their soil microbial communities. However, little is known about effects of eCO2 on the compositional and functional structure, and metabolic potential of soil microbial communities under C4 plants. Here we showed that a C4 maize agroecosystem exposed to eCO2 for eight years shifted the functional and phylogenetic structure of soil microbial communities at both soil depths (0-5 cm and 5-15 cm) using EcoPlate and functional gene array (GeoChip 3.0) analyses. The abundances of key genes involved in carbon (C), nitrogen (N) and phosphorus (P) cycling were significantly stimulated under eCO2 at both soil depths, although some differences in carbon utilization patterns were observed between the two soil depths. Consistently, CO2 was found to be the dominant factor explaining 11.9% of the structural variation of functional genes, while depth and the interaction of depth and CO2 explained 5.2% and 3.8%, respectively. This study implies that eCO2 has profound effects on the functional structure and metabolic potential/activity of soil microbial communities associated with C4 plants, possibly leading to changes in ecosystem functioning and feedbacks to global change in C4 agroecosystems.

Nitrogen metabolism and microbial production of dairy cows fed sugarcane and nitrogen compounds

OpenAIRE

Gonçalves,Geógenes da Silva; Pedreira,Marcio dos Santos; Pereira,Mara Lúcia Albuquerque; Santos,Dimas Oliveira; Souza,Dicastro Dias de; Porto Junior,Antonio Ferraz

2014-01-01

The aim of this study was to evaluate the effect of dairy cow diets containing two different sources of urea on nitrogen metabolism and microbial synthesis. Eight crossbred cows were confined and distributed in two 4x4 Latin: FS - soybean meal (control), conventional urea (UC) 100%; ULL 44 UC = 56% / 44% ULL, ULL 88 UC = 12% / 88% ULL. Diets were offered to animals during 21 days with 14 days of adaptation. The N intake, retained nitrogen balance, nitrogen excretion in milk, urine, feces and ...

Genome-reconstruction for eukaryotes from complex natural microbial communities.

Science.gov (United States)

West, Patrick T; Probst, Alexander J; Grigoriev, Igor V; Thomas, Brian C; Banfield, Jillian F

2018-04-01

Microbial eukaryotes are integral components of natural microbial communities, and their inclusion is critical for many ecosystem studies, yet the majority of published metagenome analyses ignore eukaryotes. In order to include eukaryotes in environmental studies, we propose a method to recover eukaryotic genomes from complex metagenomic samples. A key step for genome recovery is separation of eukaryotic and prokaryotic fragments. We developed a k -mer-based strategy, EukRep, for eukaryotic sequence identification and applied it to environmental samples to show that it enables genome recovery, genome completeness evaluation, and prediction of metabolic potential. We used this approach to test the effect of addition of organic carbon on a geyser-associated microbial community and detected a substantial change of the community metabolism, with selection against almost all candidate phyla bacteria and archaea and for eukaryotes. Near complete genomes were reconstructed for three fungi placed within the Eurotiomycetes and an arthropod. While carbon fixation and sulfur oxidation were important functions in the geyser community prior to carbon addition, the organic carbon-impacted community showed enrichment for secreted proteases, secreted lipases, cellulose targeting CAZymes, and methanol oxidation. We demonstrate the broader utility of EukRep by reconstructing and evaluating relatively high-quality fungal, protist, and rotifer genomes from complex environmental samples. This approach opens the way for cultivation-independent analyses of whole microbial communities. © 2018 West et al.; Published by Cold Spring Harbor Laboratory Press.

Microbial Metabolism in Soil at Subzero Temperatures: Adaptation Mechanisms Revealed by Position-Specific 13C Labeling

Directory of Open Access Journals (Sweden)

Ezekiel K. Bore

2017-05-01

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

Rumen microbial communities influence metabolic phenotypes in lambs

Directory of Open Access Journals (Sweden)

Diego P. Morgavi

2015-10-01

Full Text Available The rumen microbiota is an essential part of ruminants forging their nutrition and health. Despite its importance, it is not fully understood how various groups of rumen microbes affect host-microbe relationships and functions. The aim of the study was to simultaneously explore the rumen microbiota and the metabolic phenotype of lambs for identifying host-microbe associations and potential biomarkers of digestive functions. Twin lambs, separated in two groups after birth were exposed to practices (isolation and gavage with rumen fluid with protozoa or protozoa-depleted that differentially restricted the acquisition of microbes. Rumen microbiota, fermentation parameters, digestibility and growth were monitored for up to 31 weeks of age. Microbiota assembled in isolation from other ruminants lacked protozoa and had low bacterial and archaeal diversity whereas digestibility was not affected. Exposure to adult sheep microbiota increased bacterial and archaeal diversity independently of protozoa presence. For archaea, Methanomassiliicoccales displaced Methanosphaera. Notwithstanding, protozoa induced differences in functional traits such as digestibility and significantly shaped bacterial community structure, notably Ruminococcaceae and Lachnospiraceae lower up to 6 folds, Prevotellaceae lower by ~40%, and Clostridiaceae and Veillonellaceae higher up to 10 folds compared to microbiota without protozoa. An orthogonal partial least squares-discriminant analysis of urinary metabolome matched differences in microbiota structure. Discriminant metabolites were mainly involved in amino acids and protein metabolic pathways while a negative interaction was observed between methylotrophic methanogens Methanomassiliicoccales and trimethylamine N-oxide. These results stress the influence of gut microbes on animal phenotype and show the potential of metabolomics for monitoring rumen microbial functions.

Detrital microbial community development and phosphorus dynamics in a stream ecosystem

Energy Technology Data Exchange (ETDEWEB)

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

1986-06-01

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

Genome-Enabled Modeling of Biogeochemical Processes Predicts Metabolic Dependencies that Connect the Relative Fitness of Microbial Functional Guilds

Science.gov (United States)

Brodie, E.; King, E.; Molins, S.; Karaoz, U.; Steefel, C. I.; Banfield, J. F.; Beller, H. R.; Anantharaman, K.; Ligocki, T. J.; Trebotich, D.

2015-12-01

Pore-scale processes mediated by microorganisms underlie a range of critical ecosystem services, regulating carbon stability, nutrient flux, and the purification of water. Advances in cultivation-independent approaches now provide us with the ability to reconstruct thousands of genomes from microbial populations from which functional roles may be assigned. With this capability to reveal microbial metabolic potential, the next step is to put these microbes back where they belong to interact with their natural environment, i.e. the pore scale. At this scale, microorganisms communicate, cooperate and compete across their fitness landscapes with communities emerging that feedback on the physical and chemical properties of their environment, ultimately altering the fitness landscape and selecting for new microbial communities with new properties and so on. We have developed a trait-based model of microbial activity that simulates coupled functional guilds that are parameterized with unique combinations of traits that govern fitness under dynamic conditions. Using a reactive transport framework, we simulate the thermodynamics of coupled electron donor-acceptor reactions to predict energy available for cellular maintenance, respiration, biomass development, and enzyme production. From metagenomics, we directly estimate some trait values related to growth and identify the linkage of key traits associated with respiration and fermentation, macromolecule depolymerizing enzymes, and other key functions such as nitrogen fixation. Our simulations were carried out to explore abiotic controls on community emergence such as seasonally fluctuating water table regimes across floodplain organic matter hotspots. Simulations and metagenomic/metatranscriptomic observations highlighted the many dependencies connecting the relative fitness of functional guilds and the importance of chemolithoautotrophic lifestyles. Using an X-Ray microCT-derived soil microaggregate physical model combined

Impact of metabolism and growth phase on the hydrogen isotopic composition of microbial fatty acids

Science.gov (United States)

Heinzelmann, Sandra M.; Villanueva, Laura; Sinke-Schoen, Danielle; Sinninghe Damsté, Jaap S.; Schouten, Stefan; van der Meer, Marcel T. J.

2015-01-01

Microorganisms are involved in all elemental cycles and therefore it is important to study their metabolism in the natural environment. A recent technique to investigate this is the hydrogen isotopic composition of microbial fatty acids, i.e., heterotrophic microorganisms produce fatty acids enriched in deuterium (D) while photoautotrophic and chemoautotrophic microorganisms produce fatty acids depleted in D compared to the water in the culture medium (growth water). However, the impact of factors other than metabolism have not been investigated. Here, we evaluate the impact of growth phase compared to metabolism on the hydrogen isotopic composition of fatty acids of different environmentally relevant microorganisms with heterotrophic, photoautotrophic and chemoautotrophic metabolisms. Fatty acids produced by heterotrophs are enriched in D compared to growth water with εlipid/water between 82 and 359‰ when grown on glucose or acetate, respectively. Photoautotrophs (εlipid/water between −149 and −264‰) and chemoautotrophs (εlipid/water between −217 and −275‰) produce fatty acids depleted in D. Fatty acids become, in general, enriched by between 4 and 46‰ with growth phase which is minor compared to the influence of metabolisms. Therefore, the D/H ratio of fatty acids is a promising tool to investigate community metabolisms in nature. PMID:26005437

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.

Bacterial communities associated with Shinkaia crosnieri from the Iheya North, Okinawa Trough: Microbial diversity and metabolic potentials

Science.gov (United States)

Zhang, Jian; Zeng, Zhi-gang; Chen, Shuai; Sun, Li

2018-04-01

Shinkaia crosnieri is a galatheid crab endemic to the deep-sea hydrothermal systems in the Okinawa Trough. In this study, we systematically analyzed and compared the diversity and metabolic potentials of the microbial communities in different tissues (setae, gill, and intestine) of S. crosnieri by high-throughput sequencing technology and quantitative real-time polymerase chain reaction. Sequence analysis based on the V3-V4 regions of the 16S rRNA gene obtained 408,079 taxon tags, which covered 15 phyla, 22 classes, 32 orders, 42 families, and 25 genera. Overall, the microbial communities in all tissues were dominated by Epsilonproteobacteria and Gammaproteobacteria, of which Epsilonproteobacteria was the largest class and accounted for 85.24% of the taxon tags. In addition, 20 classes of bacteria were discovered for the first time to be associated with S. crosnieri and no archaea were detected. Comparative analysis showed that (i) bacteria from different tissues fell into different groups by β-diversity analysis, (ii) bacterial communities in intestine were similar to that in gill and much more diverse than that in setae, and the sulfur-oxidizing genus Sulfurovum was markedly enriched in intestine and gill. Furthermore, bacteria potentially involved in methane, nitrogen, and metal metabolisms were detected in all samples. The key genes of aprA/dsrA and pmoA involved in sulfate reducing and methane oxidization, respectively, were detected in the gill and gut communities for the first time, and pmoA was significantly more abundant in gill and setae than in intestine. These results provide the first comparative and relatively complete picture of the diversity and metabolic potentials of the bacteria in different tissues of S. crosnieri. These results also indicate that the composition of the microbial communities in hydrothermal fauna changes with time, suggesting the importance of environmental influence.

Microbial syntrophy: interaction for the common good.

Science.gov (United States)

Morris, Brandon E L; Henneberger, Ruth; Huber, Harald; Moissl-Eichinger, Christine

2013-05-01

Classical definitions of syntrophy focus on a process, performed through metabolic interaction between dependent microbial partners, such as the degradation of complex organic compounds under anoxic conditions. However, examples from past and current scientific discoveries suggest that a new, simple but wider definition is necessary to cover all aspects of microbial syntrophy. We suggest the term 'obligately mutualistic metabolism', which still focuses on microbial metabolic cooperation but also includes an ecological aspect: the benefit for both partners. By the combined metabolic activity of microorganisms, endergonic reactions can become exergonic through the efficient removal of products and therefore enable a microbial community to survive with minimal energy resources. Here, we explain the principles of classical and non-classical syntrophy and illustrate the concepts with various examples. We present biochemical fundamentals that allow microorganism to survive under a range of environmental conditions and to drive important biogeochemical processes. Novel technologies have contributed to the understanding of syntrophic relationships in cultured and uncultured systems. Recent research highlights that obligately mutualistic metabolism is not limited to certain metabolic pathways nor to certain environments or microorganisms. This beneficial microbial interaction is not restricted to the transfer of reducing agents such as hydrogen or formate, but can also involve the exchange of organic, sulfurous- and nitrogenous compounds or the removal of toxic compounds. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Uranium Biomineralization by Natural Microbial Phosphatase Activities in the Subsurface

Energy Technology Data Exchange (ETDEWEB)

Sobecky, Patricia A. [Univ. of Alabama, Tuscaloosa, AL (United States)

2015-04-06

In this project, inter-disciplinary research activities were conducted in collaboration among investigators at The University of Alabama (UA), Georgia Institute of Technology (GT), Lawrence Berkeley National Laboratory (LBNL), Brookhaven National Laboratory (BNL), the DOE Joint Genome Institute (JGI), and the Stanford Synchrotron Radiation Light source (SSRL) to: (i) confirm that phosphatase activities of subsurface bacteria in Area 2 and 3 from the Oak Ridge Field Research Center result in solid U-phosphate precipitation in aerobic and anaerobic conditions; (ii) investigate the eventual competition between uranium biomineralization via U-phosphate precipitation and uranium bioreduction; (iii) determine subsurface microbial community structure changes of Area 2 soils following organophosphate amendments; (iv) obtain the complete genome sequences of the Rahnella sp. Y9-602 and the type-strain Rahnella aquatilis ATCC 33071 isolated from these soils; (v) determine if polyphosphate accumulation and phytate hydrolysis can be used to promote U(VI) biomineralization in subsurface sediments; (vi) characterize the effect of uranium on phytate hydrolysis by a new microorganism isolated from uranium-contaminated sediments; (vii) utilize positron-emission tomography to label and track metabolically-active bacteria in soil columns, and (viii) study the stability of the uranium phosphate mineral product. Microarray analyses and mineral precipitation characterizations were conducted in collaboration with DOE SBR-funded investigators at LBNL. Thus, microbial phosphorus metabolism has been shown to have a contributing role to uranium immobilization in the subsurface.

Uranium Biomineralization by Natural Microbial Phosphatase Activities in the Subsurface

International Nuclear Information System (INIS)

Sobecky, Patricia A.

2015-01-01

In this project, inter-disciplinary research activities were conducted in collaboration among investigators at The University of Alabama (UA), Georgia Institute of Technology (GT), Lawrence Berkeley National Laboratory (LBNL), Brookhaven National Laboratory (BNL), the DOE Joint Genome Institute (JGI), and the Stanford Synchrotron Radiation Light source (SSRL) to: (i) confirm that phosphatase activities of subsurface bacteria in Area 2 and 3 from the Oak Ridge Field Research Center result in solid U-phosphate precipitation in aerobic and anaerobic conditions; (ii) investigate the eventual competition between uranium biomineralization via U-phosphate precipitation and uranium bioreduction; (iii) determine subsurface microbial community structure changes of Area 2 soils following organophosphate amendments; (iv) obtain the complete genome sequences of the Rahnella sp. Y9-602 and the type-strain Rahnella aquatilis ATCC 33071 isolated from these soils; (v) determine if polyphosphate accumulation and phytate hydrolysis can be used to promote U(VI) biomineralization in subsurface sediments; (vi) characterize the effect of uranium on phytate hydrolysis by a new microorganism isolated from uranium-contaminated sediments; (vii) utilize positron-emission tomography to label and track metabolically-active bacteria in soil columns, and (viii) study the stability of the uranium phosphate mineral product. Microarray analyses and mineral precipitation characterizations were conducted in collaboration with DOE SBR-funded investigators at LBNL. Thus, microbial phosphorus metabolism has been shown to have a contributing role to uranium immobilization in the subsurface.

Characterization of the microbial community composition and the distribution of Fe-metabolizing bacteria in a creek contaminated by acid mine drainage.

Science.gov (United States)

Sun, Weimin; Xiao, Enzong; Krumins, Valdis; Dong, Yiran; Xiao, Tangfu; Ning, Zengping; Chen, Haiyan; Xiao, Qingxiang

2016-10-01

A small watershed heavily contaminated by long-term acid mine drainage (AMD) from an upstream abandoned coal mine was selected to study the microbial community developed in such extreme system. The watershed consists of AMD-contaminated creek, adjacent contaminated soils, and a small cascade aeration unit constructed downstream, which provide an excellent contaminated site to study the microbial response in diverse extreme AMD-polluted environments. The results showed that the innate microbial communities were dominated by acidophilic bacteria, especially acidophilic Fe-metabolizing bacteria, suggesting that Fe and pH are the primary environmental factors in governing the indigenous microbial communities. The distribution of Fe-metabolizing bacteria showed distinct site-specific patterns. A pronounced shift from diverse communities in the upstream to Proteobacteria-dominated communities in the downstream was observed in the ecosystem. This location-specific trend was more apparent at genus level. In the upstream samples (sampling sites just below the coal mining adit), a number of Fe(II)-oxidizing bacteria such as Alicyclobacillus spp., Metallibacterium spp., and Acidithrix spp. were dominant, while Halomonas spp. were the major Fe(II)-oxidizing bacteria observed in downstream samples. Additionally, Acidiphilium, an Fe(III)-reducing bacterium, was enriched in the upstream samples, while Shewanella spp. were the dominant Fe(III)-reducing bacteria in downstream samples. Further investigation using linear discriminant analysis (LDA) effect size (LEfSe), principal coordinate analysis (PCoA), and unweighted pair group method with arithmetic mean (UPGMA) clustering confirmed the difference of microbial communities between upstream and downstream samples. Canonical correspondence analysis (CCA) and Spearman's rank correlation indicate that total organic carbon (TOC) content is the primary environmental parameter in structuring the indigenous microbial communities

Does iron inhibit cryptoendolithic microbial communities?

Science.gov (United States)

Johnston, C. G.; Vestal, J. R.; Friedmann, E. I. (Principal Investigator)

1988-01-01

Photosynthetic activity of three cryptoendolithic microbial communities was studied under controlled conditions in the laboratory. In two of these communities, the dominant organisms were lichens, collected from Linnaeus Terrace and from Battleship Promontory. The third community, dominated by cyanobacteria, was collected from Battleship Promontory. Both sites are in the ice-free valleys of southern Victoria Land. Previous efforts have shown how physical conditions can influence metabolic activity in endolithic communities (Kappen and Friedmann 1983; Kappen, Friedmann, and Garty 1981; Vestal, Federle, and Friedmann 1984). Biological activity can also be strongly influenced by the chemical environment. Inorganic nutrients such as nitrate, ammonia, and phosphate are often limiting factors, so their effects on photosynthetic carbon-14 bicarbonate incorporation were investigated. Iron and manganese are two metals present in Linnaeus Terrace and Battleship Promontory sandstones, and their effects on photosynthesis were also studied. The results may add to our understanding of biogeochemical interactions within this unique microbial community.

Structural and metabolic responses of microbial community to sewage-borne chlorpyrifos in constructed wetlands.

Science.gov (United States)

Zhang, Dan; Wang, Chuan; Zhang, Liping; Xu, Dong; Liu, Biyun; Zhou, Qiaohong; Wu, Zhenbin

2016-06-01

Long-term use of chlorpyrifos poses a potential threat to the environment that cannot be ignored, yet little is known about the succession of substrate microbial communities in constructed wetlands (CWs) under chlorpyrifos stress. Six pilot-scale CW systems receiving artificial wastewater containing 1mg/L chlorpyrifos were established to investigate the effects of chlorpyrifos and wetland vegetation on the microbial metabolism pattern of carbon sources and community structure, using BIOLOG and denaturing gradient gel electrophoresis (DGGE) approaches. Based on our samples, BIOLOG showed that Shannon diversity (H') and richness (S) values distinctly increased after 30days when chlorpyrifos was added. At the same time, differences between the vegetated and the non-vegetated systems disappeared. DGGE profiles indicated that H' and S had no significant differences among four different treatments. The effect of chlorpyrifos on the microbial community was mainly reflected at the physiological level. Principal component analysis (PCA) of both BIOLOG and DGGE showed that added chlorpyrifos made a difference on test results. Meanwhile, there was no difference between the vegetation and no-vegetation treatments after addition of chlorpyrifos at the physiological level. Moreover, the vegetation had no significant effect on the microbial community at the genetic level. Comparisons were made between bacteria in this experiment and other known chlorpyrifos-degrading bacteria. The potential chlorpyrifos-degrading ability of bacteria in situ may be considerable. Copyright © 2016. Published by Elsevier B.V.

Engineering Robustness of Microbial Cell Factories.

Science.gov (United States)

Gong, Zhiwei; Nielsen, Jens; Zhou, Yongjin J

2017-10-01

Metabolic engineering and synthetic biology offer great prospects in developing microbial cell factories capable of converting renewable feedstocks into fuels, chemicals, food ingredients, and pharmaceuticals. However, prohibitively low production rate and mass concentration remain the major hurdles in industrial processes even though the biosynthetic pathways are comprehensively optimized. These limitations are caused by a variety of factors unamenable for host cell survival, such as harsh industrial conditions, fermentation inhibitors from biomass hydrolysates, and toxic compounds including metabolic intermediates and valuable target products. Therefore, engineered microbes with robust phenotypes is essential for achieving higher yield and productivity. In this review, the recent advances in engineering robustness and tolerance of cell factories is described to cope with these issues and briefly introduce novel strategies with great potential to enhance the robustness of cell factories, including metabolic pathway balancing, transporter engineering, and adaptive laboratory evolution. This review also highlights the integration of advanced systems and synthetic biology principles toward engineering the harmony of overall cell function, more than the specific pathways or enzymes. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effect of Bioprocessing on the In Vitro Colonic Microbial Metabolism of Phenolic Acids from Rye Bran Fortified Breads

DEFF Research Database (Denmark)

Koistinen, Ville M; Nordlund, Emilia; Katina, Kati

2017-01-01

in an in vitro colon model, the metabolites were analyzed using two different methods applying mass spectrometry. While phenolic acids were released more extensively from the bioprocessed bran bread and ferulic acid had consistently higher concentrations in the bread type during fermentation, there were only......Cereal bran is an important source of dietary fiber and bioactive compounds, such as phenolic acids. We aimed to study the phenolic acid metabolism of native and bioprocessed rye bran fortified refined wheat bread and to elucidate the microbial metabolic route of phenolic acids. After incubation...

Characterizing bacterial gene expression in nitrogen cycle metabolism with RT-qPCR.

Science.gov (United States)

Graham, James E; Wantland, Nicholas B; Campbell, Mark; Klotz, Martin G

2011-01-01

Recent advances in DNA sequencing have greatly accelerated our ability to obtain the raw information needed to recognize both known and potential novel modular microbial genomic capacity for nitrogen metabolism. With PCR-based approaches to quantifying microbial mRNA expression now mainstream in most laboratories, researchers can now more efficiently propose and test hypotheses on the contributions of individual microbes to the biological accessibility of nitrogen upon which all other life depends. We review known microbial roles in these key nitrogen transformations, and describe the necessary steps in carrying out relevant gene expression studies. An example experimental design is then provided characterizing Nitrosococcus oceani mRNA expression in cultures responding to ammonia. The approach described, that of assessing microbial genome inventory and testing putative modular gene expression by mRNA quantification, is likely to remain an important tool in understanding individual microbial contributions within microbial community activities that maintain the Earth's nitrogen balance. Copyright © 2011 Elsevier Inc. All rights reserved.

Tracing biofouling to the structure of the microbial community and its metabolic products: a study of the three-stage MBR process.

Science.gov (United States)

Gao, Dawen; Fu, Yuan; Ren, Nanqi

2013-11-01

The biofouling characteristics of a sequential anoxic/aerobic-membrane bioreactor (A/O MBR) were analyzed during the three-stage process (fast-slow-fast transmembrane pressure (TMP) increasing). The results indicated: during the stage 1 (before day 1), the microbial communities in the activated sludge (AS), cake sludge (CS) and biofilm (BF) were similar to each other, and the adsorption of microbes and the metabolic products was the main factor that led to TMP increase; during the stage 2 (between day 1 and day 7), the cake layer begun to form and the TMP continued to rise gradually at a reduced rate compared to stage 1, at this point a characteristic microbial community colonized the CS with microorganisms such as Saprospiraceae and Comamonadaceae thriving on the membrane surface (BF) probably due to greater nutrient availability, and the predominance of these species in the microbial population led to the accumulation of biofouling metabolic products in the CS, which resulted in membrane fouling and the associated rise in TMP; during the final stage (after day 7), the biofilm had matured, and the activity of anaerobes stimulated cake compaction. The statistical analysis showed a correlation between the TMP changing rate and the carbonhydrates of soluble microbial products (SMPc) content in the CS. When the SMPc concentration rose slowly there was a low level of biofouling. However, when the SMPc accumulating rate was greater, it resulted in the more severe biofouling associated with the TMP jump. Furthermore, the correlation coefficient for the TMP increase and protein concentrations of extracellular polymeric substances (EPSp) in the CS was highly significant. The cluster analysis suggested that the AS microbial community remained stable during the three TMP change stages, while the CS and BF community were changed accompanied with the TMP change. The interaction between the microbial communities and the metabolic products lead to the significant correlation

Characterization of microbial metabolism of Syrah grape products in an in vitro colon model using targeted and non-targeted analytical approaches

OpenAIRE

Aura, Anna-Marja; Mattila, Ismo; Hyötyläinen, Tuulia; Gopalacharyulu, Peddinti; Cheynier, Veronique; Souquet, Jean-Marc; Bes, Magali; Le Bourvellec, Carine; Guyot, Sylvain; Orešič, Matej

2012-01-01

Purpose Syrah red grapes are used in the production of tannin-rich red wines. Tannins are high molecular weight molecules, proanthocyanidins (PAs), and poorly absorbed in the upper intestine. In this study, gut microbial metabolism of Syrah grape phenolic compounds was investigated. Methods Syrah grape pericarp was subjected to an enzymatic in vitro digestion model, and red wine and grape skin PA fraction were prepared. Microbial conversion was screened using an in vitro colon model with faec...

Studies about behavior of microbial degradation of organic compounds

International Nuclear Information System (INIS)

Ohtsuka, Makiko

2003-02-01

Some of TRU waste include organic compounds, thus these organic compounds might be nutrients for microbial growth at disposal site. This disposal system might be exposed to high alkali condition by cement compounds as engineering barrier material. In the former experimental studies, it has been supposed that microbial exist under pH = 12 and the microbial activity acclimated to high alkali condition are able to degrade asphalt under anaerobic condition. Microbes are called extremophile that exist in cruel habitat as high alkali or reductive condition. We know less information about the activity of extremophile, though any recent studies reveal them. In this study, the first investigation is metabolic pathway as microbial activity, the second is microbial degradation of aromatic compounds in anaerobic condition, and the third is microbial activity under high alkali. Microbial metabolic pathway consist of two systems that fulfill their function each other. One system is to generate energy for microbial activities and the other is to convert substances for syntheses of organisms' structure materials. As these systems are based on redox reaction between substances, it is made chart of the microbial activity region using pH, Eh, and depth as parameter, There is much report that microbe is able to degrade aromatic compounds under aerobic or molecular O 2 utilizing condition. For degradation of aromatic compounds in anaerobic condition, supplying electron acceptor is required. Co-metabolism and microbial consortia has important role, too. Alcalophile has individual transporting system depending Na + and acidic compounds contained in cell wall. Generating energy is key for survival and growth under high alkali condition. Co-metabolism and microbial consortia are effective for microbial degradation of aromatic compounds under high alkali and reductive condition, and utilizable electron acceptor and degradable organic compounds are required for keeping microbial activity and

The effect of gluten on the host-microbial metabolism assessed by urinary metabolomics

DEFF Research Database (Denmark)

Roager, Henrik Munch; Frandsen, Henrik Lauritz; Gøbel, Rikke Juul

A gluten-free diet clearly improves the life of patients with celiac disease, but the scientific evidence supporting possible health benefits of a gluten-free diet for non-celiac adults is limited. Therefore, as urine reflects the host and gut microbial metabolism, the study aimed to assess...... a gluten-rich (21.6±5.7g/day) or a gluten-poor (~1g/day) diet for 8 weeks, crossing over to the other diet after 6 weeks washout. Urine samples were standardised collected at the beginning and end of each diet intervention period and were analysed by gas chromatography mass spectrometry (GC-MS) and liquid...... the long-term metabolic effect of gluten on the urine metabolome of non-celiac individuals by a cross-over intervention study (gluten-poor and gluten rich, respectively) using a non-targeted metabolomics approach. Fifty-one non-celiac adult participants (30 female, 21 male) were randomized to either...

Microbial stratification and microbially catalyzed processes along a hypersaline chemocline

Science.gov (United States)

Hyde, A.; Joye, S. B.; Teske, A.

2017-12-01

Orca Basin is the largest deep hypersaline anoxic basin in the world, covering over 400 km2. Located at the bottom of the Gulf of Mexico, this body of water reaches depths of 200 meters and is 8 times denser (and more saline) than the overlying seawater. The sharp pycnocline prevents any significant vertical mixing and serves as a particle trap for sinking organic matter. These rapid changes in salinity, oxygen, organic matter, and other geochemical parameters present unique conditions for the microbial communities present. We collected samples in 10m intervals throughout the chemocline. After filtering the water, we used high-throughput bacterial and archaeal 16S rRNA gene sequencing to characterize the changing microbial community along the Orca Basin chemocline. The results reveal a dominance of microbial taxa whose biogeochemical function is entirely unknown. We then used metagenomic sequencing and reconstructed genomes for select samples, revealing the potential dominant metabolic processes in the Orca Basin chemocline. Understanding how these unique geochemical conditions shape microbial communities and metabolic capabilities will have implications for the ocean's biogeochemical cycles and the consequences of expanding oxygen minimum zones.

Laboratory treatability studies preparatory to field testing a resting-cell in situ microbial filter bioremediation strategy

International Nuclear Information System (INIS)

Taylor, R.T.; Hanna, M.L.

1995-04-01

Prior to a down-hole-column treatability test of a Methylosinus trichosporium OB3b attached-resting-cell in situ biofilter strategy, a set of three sequential laboratory experiments were carried out to define several key operational parameters and to evaluate the likely degree of success at a NASA Kennedy Space Center site. They involved the cell attachment to site-specific sediments, the intrinsic resting-cell biotransformation capacities for the contaminants of interest plus their time-dependent extents of biodegradative removal at the concentrations of concern, and a scaled in situ mini-flow-through-column system that closely mimics the subsurface conditions during a field-treatability or pilot test of an emplaced resting-cell filter. These experiments established the conditions required for the complete metabolic removal of a vinyl chloride (VC), cis-dichlororthylene (cis-DCE) and trichloroethylene (TCE) mixture. However, the gas chromatographic (GC) procedures that we utilized and the mini-flow-through column data demonstrated that, at most, only about 50--70% of the site-water VC, cis-DCE, and TCE would be biodegraded. This occurred because of a limiting level of dissolved oxygen, which was exacerbated by the simultaneous presence of several additional previously unrecognized groundwater components, especially methane, that are also competing substrates for the whole-cell soluble methane monooxygenase (sMMO) enzyme complex. Irrespective, collectively the simplicity of the methods that we have developed and the results obtainable with them appear to provide relevant laboratory-based test-criteria before taking our microbial filter strategy to an in situ field treatability or pilot demonstration stage at other sites in the future

Effects of microbial processes on gas generation under expected WIPP repository conditions: Annual report through 1992

International Nuclear Information System (INIS)

Francis, A.J.; Gillow, J.B.

1993-09-01

Microbial processes involved in gas generation from degradation of the organic constituents of transuranic waste under conditions expected at the Waste Isolation Pilot Plant (WIPP) repository are being investigated at Brookhaven National Laboratory. These laboratory studies are part of the Sandia National Laboratories -- WIPP Gas Generation Program. Gas generation due to microbial degradation of representative cellulosic waste was investigated in short-term ( 6 months) experiments by incubating representative paper (filter paper, paper towels, and tissue) in WIPP brine under initially aerobic (air) and anaerobic (nitrogen) conditions. Samples from the WIPP surficial environment and underground workings harbor gas-producing halophilic microorganisms, the activities of which were studied in short-term experiments. The microorganisms metabolized a variety of organic compounds including cellulose under aerobic, anaerobic, and denitrifying conditions. In long-term experiments, the effects of added nutrients (trace amounts of ammonium nitrate, phosphate, and yeast extract), no nutrients, and nutrients plus excess nitrate on gas production from cellulose degradation

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

Utilization of Alternate Chirality Enantiomers in Microbial Communities

Science.gov (United States)

Pikuta, Elena V.; Hoover, Richard B.

2010-01-01

Our previous study of chirality led to interesting findings for some anaerobic extremophiles: the ability to metabolize substrates with alternate chirality enantiomers of amino acids and sugars. We have subsequently found that not just separate microbial species or strains but entire microbial communities have this ability. The functional division within a microbial community on proteo- and sugarlytic links was also reflected in a microbial diet with L-sugars and D-amino acids. Several questions are addressed in this paper. Why and when was this feature developed in a microbial world? Was it a secondary de novo adaptation in a bacterial world? Or is this a piece of genetic information that has been left in modern genomes as an atavism? Is it limited exclusively to prokaryotes, or does this ability also occur in eukaryotes? In this article, we have used a broader approach to study this phenomenon using anaerobic extremophilic strains from our laboratory collection. A series of experiments were performed on physiologically different groups of extremophilic anaerobes (pure and enrichment cultures). The following characteristics were studied: 1) the ability to grow on alternate chirality enantiomers -- L-sugars and D- amino acids; 2) Growth-inhibitory effect of alternate chirality enantiomers; 3) Stickland reaction with alternate chirality amino acids. The results of this research are presented in this paper.

Robust metabolic responses to varied carbon sources in natural and laboratory strains of Saccharomyces cerevisiae.

Directory of Open Access Journals (Sweden)

Wayne A Van Voorhies

Full Text Available Understanding factors that regulate the metabolism and growth of an organism is of fundamental biologic interest. This study compared the influence of two different carbon substrates, dextrose and galactose, on the metabolic and growth rates of the yeast Saccharomyces cerevisiae. Yeast metabolic and growth rates varied widely depending on the metabolic substrate supplied. The metabolic and growth rates of a yeast strain maintained under long-term laboratory conditions was compared to strain isolated from natural condition when grown on different substrates. Previous studies had determined that there are numerous genetic differences between these two strains. However, the overall metabolic and growth rates of a wild isolate of yeast was very similar to that of a strain that had been maintained under laboratory conditions for many decades. This indicates that, at in least this case, metabolism and growth appear to be well buffered against genetic differences. Metabolic rate and cell number did not co-vary in a simple linear manner. When grown in either dextrose or galactose, both strains showed a growth pattern in which the number of cells continued to increase well after the metabolic rate began a sharp decline. Previous studied have reported that O₂ consumption in S. cerevisiae grown in reduced dextrose levels were elevated compared to higher levels. Low dextrose levels have been proposed to induce caloric restriction and increase life span in yeast. However, there was no evidence that reduced levels of dextrose increased metabolic rates, measured by either O₂ consumption or CO₂ production, in the strains used in this study.

Microbial risk in wastewater irrigated lettuce: comparing Escherichia coli contamination from an experimental site with a laboratory approach.

Science.gov (United States)

Makkaew, P; Miller, M; Fallowfield, H J; Cromar, N J

This study assessed the contamination of Escherichia coli, in lettuce grown with treated domestic wastewater in four different irrigation configurations: open spray, spray under plastic sheet cover, open drip and drip under plastic sheet cover. Samples of lettuce from each irrigation configuration and irrigating wastewater were collected during the growing season. No E. coli was detected in lettuce from drip irrigated beds. All lettuce samples from spray beds were positive for E. coli, however, no statistical difference (p > 0.05) was detected between lettuces grown in open spray or covered spray beds. The results from the field experiment were also compared to a laboratory experiment which used submersion of lettuce in wastewater of known E. coli concentration as a surrogate method to assess contamination following irrigation. The microbial quality of spray bed lettuces was not significantly different from submersed lettuce when irrigated with wastewater containing 1,299.7 E. coli MPN/100 mL (p > 0.05). This study is significant since it is the first to validate that the microbial contamination of lettuce irrigated with wastewater in the field is comparable with a laboratory technique frequently applied in the quantitative microbial risk assessment of the consumption of wastewater irrigated salad crops.

Investigation of the microbial metabolism of carbon dioxide and hydrogen in the kangaroo foregut by stable isotope probing.

Science.gov (United States)

Godwin, Scott; Kang, Alicia; Gulino, Lisa-Maree; Manefield, Mike; Gutierrez-Zamora, Maria-Luisa; Kienzle, Marco; Ouwerkerk, Diane; Dawson, Kerri; Klieve, Athol V

2014-09-01

Kangaroos ferment forage material in an enlarged forestomach analogous to the rumen, but in contrast to ruminants, they produce little or no methane. The objective of this study was to identify the dominant organisms and pathways involved in hydrogenotrophy in the kangaroo forestomach, with the broader aim of understanding how these processes are able to predominate over methanogenesis. Stable isotope analysis of fermentation end products and RNA stable isotope probing (RNA-SIP) were used to investigate the organisms and biochemical pathways involved in the metabolism of hydrogen and carbon dioxide in the kangaroo forestomach. Our results clearly demonstrate that the activity of bacterial reductive acetogens is a key factor in the reduced methane output of kangaroos. In in vitro fermentations, the microbial community of the kangaroo foregut produced very little methane, but produced a significantly greater proportion of acetate derived from carbon dioxide than the microbial community of the bovine rumen. A bacterial operational taxonomic unit closely related to the known reductive acetogen Blautia coccoides was found to be associated with carbon dioxide and hydrogen metabolism in the kangaroo foregut. Other bacterial taxa including members of the genera Prevotella, Oscillibacter and Streptococcus that have not previously been reported as containing hydrogenotrophic organisms were also significantly associated with metabolism of hydrogen and carbon dioxide in the kangaroo forestomach.

Towards the understanding of microbial metabolism in relation to microbial enhanced oil recovery

DEFF Research Database (Denmark)

Halim, Amalia Yunita; Nielsen, Sidsel Marie; Nielsen, Kristian Fog

2017-01-01

In this study, Bacillus licheniformis 421 was used as a model organism to understand the effects of microbial cell growth and metabolite production under anaerobic conditions in relation to microbial enhanced oil recovery. The bacterium was able to grow anaerobically on different carbon compounds...

Colonization Habitat Controls Biomass, Composition, and Metabolic Activity of Attached Microbial Communities in the Columbia River Hyporheic Corridor

Energy Technology Data Exchange (ETDEWEB)

Stern, Noah; Ginder-Vogel, Matthew; Stegen, James C.; Arntzen, Evan; Kennedy, David W.; Larget, Bret R.; Roden, Eric E.; Kostka, Joel E.

2017-06-09

Hydrologic exchange plays a critical role in biogeochemical cycling within the hyporheic zone (the interface between river water and groundwater) of riverine ecosystems. Such exchange may set limits on the rates of microbial metabolism and impose deterministic selection on microbial communities that adapt to dynamically changing dissolved organic carbon (DOC) sources. This study examined the response of attached microbial communities (in situcolonized sand packs) from groundwater, hyporheic, and riverbed habitats within the Columbia River hyporheic corridor to “cross-feeding” with either groundwater, river water, or DOC-free artificial fluids. Our working hypothesis was that deterministic selection duringin situcolonization would dictate the response to cross-feeding, with communities displaying maximal biomass and respiration when supplied with their native fluid source. In contrast to expectations, the major observation was that the riverbed colonized sand had much higher biomass and respiratory activity, as well as a distinct community structure, compared with those of the hyporheic and groundwater colonized sands. 16S rRNA gene amplicon sequencing revealed a much higher proportion of certain heterotrophic taxa as well as significant numbers of eukaryotic algal chloroplasts in the riverbed colonized sand. Significant quantities of DOC were released from riverbed sediment and colonized sand, and separate experiments showed that the released DOC stimulated respiration in the groundwater and piezometer colonized sand. These results suggest that the accumulation and degradation of labile particulate organic carbon (POC) within the riverbed are likely to release DOC, which may enter the hyporheic corridor during hydrologic exchange, thereby stimulating microbial activity and imposing deterministic selective pressure on the microbial community composition.

IMPORTANCEThe influence of river water

Molecular Basis of Microbial One-Carbon Metabolism 2008 Gordon Research Conference (July 20-25, 2008)

Energy Technology Data Exchange (ETDEWEB)

Stephen W. Ragsdale

2009-08-12

One-carbon (C-1) compounds play a central role in microbial metabolism. C-1 compounds include methane, carbon monoxide, CO2, and methanol as well as coenzyme-bound one-carbon compounds (methyl-B12, CH3-H4folate, etc). Such compounds are of broad global importance because several C-1 compounds (e.g., CH4) are important energy sources, some (e.g., CO2 and CH4) are potent greenhouse gases, and others (e.g., CH2Cl2) are xenobiotics. They are central in pathways of energy metabolism and carbon fixation by microbes and many are of industrial interest. Research on the pathways of one-carbon metabolism has added greatly to our understanding of evolution, structural biology, enzyme mechanisms, gene regulation, ecology, and applied biology. The 2008 meeting will include recent important findings in the following areas: (a) genomics, metagenomics, and proteomic studies that have expanded our understanding of autotrophy and C-1 metabolism and the evolution of these pathways; (b) redox regulation of carbon cycles and the interrelationship between the carbon cycle and other biogeochemical cycles (sulfur, nitrogen, oxygen); (c) novel pathways for carbon assimilation; (d) biotechnology related to C-1 metabolism; (e) novel enzyme mechanisms including channeling of C-1 intermediates during metabolism; and (f) the relationship between metal homeostasis and the global carbon cycle. The conference has a diverse and gender-balanced slate of speakers and session leaders. The wide variety of disciplines brought to the study of C-1 metabolism make the field an excellent one in which to train young researchers.

Methane Metabolizing Microbial Communities in the Cold Seep Areas in the Northern Continental Shelf of South China Sea

Science.gov (United States)

Wang, F.; Liang, Q.

2016-12-01

Marine sediment contains large amount of methane, estimated approximately 500-2500 gigatonnes of dissolved and hydrated methane carbon stored therein, mainly in continental margins. In localized specific areas named cold seeps, hydrocarbon (mainly methane) containing fluids rise to the seafloor, and support oases of ecosystem composed of various microorganisms and faunal assemblages. South China Sea (SCS) is surrounded by passive continental margins in the west and north and convergent margins in the south and east. Thick organic-rich sediments have accumulated in the SCS since the late Mesozoic, which are continuing sources to form gas hydrates in the sediments of SCS. Here, Microbial ecosystems, particularly those involved in methane transformations were investigated in the cold seep areas (Qiongdongnan, Shenhu, and Dongsha) in the northern continental shelf of SCS. Multiple interdisciplinary analytic tools such as stable isotope probing, geochemical analysis, and molecular ecology, were applied for a comprehensive understanding of the microbe mediated methane transformation in this project. A variety of sediments cores have been collected, the geochemical profiles and the associated microbial distribution along the sediment cores were recorded. The major microbial groups involved in the methane transformation in these sediment cores were revealed, known methane producing and oxidizing archaea including Methanosarcinales, anaerobic methane oxidizing groups ANME-1, ANME-2 and their niche preference in the SCS sediments were found. In-depth comparative analysis revealed the presence of SCS-specific archaeal subtypes which probably reflected the evolution and adaptation of these methane metabolizing microbes to the SCS environmental conditions. Our work represents the first comprehensive analysis of the methane metabolizing microbial communities in the cold seep areas along the northern continental shelf of South China Sea, would provide new insight into the

Microbial communities from different subsystems in biological heap leaching system play different roles in iron and sulfur metabolisms.

Science.gov (United States)

Xiao, Yunhua; Liu, Xueduan; Ma, Liyuan; Liang, Yili; Niu, Jiaojiao; Gu, Yabing; Zhang, Xian; Hao, Xiaodong; Dong, Weiling; She, Siyuan; Yin, Huaqun

2016-08-01

The microbial communities are important for minerals decomposition in biological heap leaching system. However, the differentiation and relationship of composition and function of microbial communities between leaching heap (LH) and leaching solution (LS) are still unclear. In this study, 16S rRNA gene sequencing was used to assess the microbial communities from the two subsystems in ZiJinShan copper mine (Fujian province, China). Results of PCoA and dissimilarity test showed that microbial communities in LH samples were significantly different from those in LS samples. The dominant genera of LH was Acidithiobacillus (57.2 ∼ 87.9 %), while Leptospirillum (48.6 ∼ 73.7 %) was predominant in LS. Environmental parameters (especially pH) were the major factors to influence the composition and structure of microbial community by analysis of Mantel tests. Results of functional test showed that microbial communities in LH utilized sodium thiosulfate more quickly and utilized ferrous sulfate more slowly than those in LS, which further indicated that the most sulfur-oxidizing processes of bioleaching took place in LH and the most iron-oxidizing processes were in LS. Further study found that microbial communities in LH had stronger pyrite leaching ability, and iron extraction efficiency was significantly positively correlated with Acidithiobacillus (dominated in LH), which suggested that higher abundance ratio of sulfur-oxidizing microbes might in favor of minerals decomposition. Finally, a conceptual model was designed through the above results to better exhibit the sulfur and iron metabolism in bioleaching systems.

Impact of anti-acidification microbial consortium on carbohydrate metabolism of key microbes during food waste composting.

Science.gov (United States)

Song, Caihong; Li, Mingxiao; Qi, Hui; Zhang, Yali; Liu, Dongming; Xia, Xunfeng; Pan, Hongwei; Xi, Beidou

2018-07-01

This study investigated the effect of anti-acidification microbial consortium (AAMC), which act synergistically for rapid bioconversion of organic acids on carbohydrate metabolism of key microbes in the course of food waste (FW) composting by metaproteomics. AAMC was inoculated to the composting mass and compared with treatment with alkaline compounds and the control without any amendment. Inoculating AAMC could effectively accelerate carbohydrate degradation process and improve composting efficiency. Carbohydrate metabolic network profiles showed the inoculation with AAMC could increase significantly the types of enzymes catalysing the degradation of lignin, cellulose and hemicellulose. Furthermore, AAMC inoculum could increase not only diversities of microbes producing key enzymes in metabolism pathways of acetic and propionic acids, but also the amounts of these key enzymes. The increase of diversities of microbes could disperse the pressure from acidic adversity on microorganisms which were capable to degrade acetic and propionic acids. Copyright © 2018 Elsevier Ltd. All rights reserved.

Reprint of Design of synthetic microbial communities for biotechnological production processes.

Science.gov (United States)

Jagmann, Nina; Philipp, Bodo

2014-12-20

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

Assessing coral reefs on a Pacific-wide scale using the microbialization score.

Directory of Open Access Journals (Sweden)

Tracey McDole

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

Assessing coral reefs on a Pacific-wide scale using the microbialization score.

Science.gov (United States)

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

2012-01-01

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

The Influence of Tallow on Rumen Metabolism, Microbial Biomass Synthesis and Fatty Acid Composition of Bacteria and Protozoa

DEFF Research Database (Denmark)

Weisbjerg, Martin Riis; Børsting, Christian Friis; Hvelplund, Torben

1992-01-01

Rumen metabolism, microbial biomass synthesis and microbial long chain fatty acid composition were studied in lactating cows fed at two levels of dry matter intake (L, 8.6 kg DM and H, 12.6 kg DM) with 0, 4 and 6% added tallow at the low feed level (L0, L4 and L6) and 0, 2, 4 and 6% at the high...... feed level (H0, H2, H4 and H6). Fibre digestibility was not significantly affected by tallow addition. Increasing tallow level in the diet decreased the total VFA concentration, the ratio of acetic acid to propionic acid and the ammonia concentration in the rumen. Crude fat and fatty acid content...... in bacterial and protozoal dry matter increased with increased tallow level, especially due to an increase in fatty acids originating from the feeds. Microbial synthesis in the rumen and flow of amino acids to the duodenum was highest for medium fat intake at the high feed level....

Strong linkage between active microbial communities and microbial carbon usage in a deglaciated terrain of the High Arctic

Science.gov (United States)

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

2017-12-01

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

Influence of diet and microbial activity in the digestive tract on digestibility, and nitrogen and energy metabolism in rats and pigs

DEFF Research Database (Denmark)

Eggum, B O; Thorbek, G; Beames, R M

1982-01-01

-55 kg. Measurements were made on the influence of microbial activity in the digestive tract on digestibility and nitrogen and energy metabolism. Dietary inclusion of the antibiotic Nebacitin was the method used to reduce the microbial population. 2. The microbial activity in the hind-gut (mumol ATP....../g air-dry contents) of antibiotic-treated rats was reduced to approximately one-tenth of that of untreated rats. 3. Live-weight gain was not significantly affected in either species by a reduction in the microbial activity, in spite of a reduction in dry matter digestibility in animals with reduced...... microflora. 4. For rats on low-crude-fibre diets, a reduction in microflora reduced digestibility of all nutrients and energy and metabolizability of digestible energy by approximately 5.4%. All differences were highly significant. On high-crude-fibre diets the decrease was approximately 5.9%. In pigs...

In situ hydrogen consumption kinetics as an indicator of subsurface microbial activity

Science.gov (United States)

Harris, S.H.; Smith, R.L.; Suflita, J.M.

2007-01-01

There are few methods available for broadly assessing microbial community metabolism directly within a groundwater environment. In this study, hydrogen consumption rates were estimated from in situ injection/withdrawal tests conducted in two geochemically varying, contaminated aquifers as an approach towards developing such a method. The hydrogen consumption first-order rates varied from 0.002 nM h-1 for an uncontaminated, aerobic site to 2.5 nM h-1 for a contaminated site where sulfate reduction was a predominant process. The method could accommodate the over three orders of magnitude range in rates that existed between subsurface sites. In a denitrifying zone, the hydrogen consumption rate (0.02 nM h-1) was immediately abolished in the presence of air or an antibiotic mixture, suggesting that such measurements may also be sensitive to the effects of environmental perturbations on field microbial activities. Comparable laboratory determinations with sediment slurries exhibited hydrogen consumption kinetics that differed substantially from the field estimates. Because anaerobic degradation of organic matter relies on the rapid consumption of hydrogen and subsequent maintenance at low levels, such in situ measures of hydrogen turnover can serve as a key indicator of the functioning of microbial food webs and may be more reliable than laboratory determinations. ?? 2007 Federation of European Microbiological Societies.

Unusual metabolic diversity of hyperalkaliphilic microbial communities associated with subterranean serpentinization at The Cedars.

Science.gov (United States)

Suzuki, Shino; Ishii, Shun'ichi; Hoshino, Tatsuhiko; Rietze, Amanda; Tenney, Aaron; Morrill, Penny L; Inagaki, Fumio; Kuenen, J Gijs; Nealson, Kenneth H

2017-11-01

Water from The Cedars springs that discharge from serpentinized ultramafic rocks feature highly basic (pH=~12), highly reducing (E h serpentinizing system, was dominated by several bacterial taxa from the phyla OD1 ('Parcubacteria') and Chloroflexi. Members of the GPS1 community had, for the most part, the smallest genomes reported for their respective taxa, and encoded only archaeal (A-type) ATP synthases or no ATP synthases at all. Furthermore, none of the members encoded respiration-related genes and some of the members also did not encode key biosynthesis-related genes. In contrast, BS5, fed by shallow water, appears to have a community driven by hydrogen metabolism and was dominated by a diverse group of Proteobacteria similar to those seen in many terrestrial serpentinization sites. Our findings indicated that the harsh ultrabasic geological setting supported unexpectedly diverse microbial metabolic strategies and that the deep-water-fed springs supported a community that was remarkable in its unusual metagenomic and genomic constitution.

The maturing of microbial ecology.

Science.gov (United States)

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.

Biotechnology in petroleum recovery. The microbial EOR

Energy Technology Data Exchange (ETDEWEB)

Sen, Ramkrishna [Department of Biotechnology, Indian Institute of Technology (IIT), Kharagpur, West Bengal 721302 (India)

2008-12-15

Biotechnology has played a significant role in enhancing crude oil recovery from the depleted oil reservoirs to solve stagnant petroleum production, after a three-stage recovery process employing mechanical, physical and chemical methods. Biotechnologically enhanced oil recovery processes, known as microbial enhanced oil recovery (MEOR), involve stimulating indigenous reservoir microbes or injecting specially selected consortia of natural bacteria into the reservoir to produce specific metabolic events that lead to improved oil recovery. This also involves flooding with oil recovery agents produced ex situ by industrial or pilot scale fermentation. This paper essentially reviews the operating mechanisms and the progress made in enhanced oil recovery through the use of microbes and their metabolic products. Improvement in oil recovery by injecting solvents and gases or by energizing the reservoir microflora to produce them in situ for carbonate rock dissolution and reservoir re-pressurization has been enunciated. The role of biosurfactants in oil mobilization through emulsification and that of biopolymers for selective plugging of oil-depleted zones and for biofilm formation have been delineated. The spoil sport played by sulfate-reducing bacteria (SRB) in MEOR has also been briefly reviewed. The importance of mathematical models used in predicting the applicability of an MEOR strategy and the microbial growth and transport has been qualitatively discussed. The results of some laboratory studies and worldwide field trials applying ex situ and in situ MEOR technologies were compiled and interpreted. However, the potential of the MEOR technologies has not been fully realized due to poor yield of the useful microbial metabolic products, growth inhibition by accumulated toxic metabolites and longer time of incubation. A complete evaluation and assessment of MEOR from an engineering standpoint based on economics, applicability and performance is required to further

Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life.

Science.gov (United States)

Brown, Christopher T; Sharon, Itai; Thomas, Brian C; Castelle, Cindy J; Morowitz, Michael J; Banfield, Jillian F

2013-12-17

The premature infant gut has low individual but high inter-individual microbial diversity compared with adults. Based on prior 16S rRNA gene surveys, many species from this environment are expected to be similar to those previously detected in the human microbiota. However, the level of genomic novelty and metabolic variation of strains found in the infant gut remains relatively unexplored. To study the stability and function of early microbial colonizers of the premature infant gut, nine stool samples were taken during the third week of life of a premature male infant delivered via Caesarean section. Metagenomic sequences were assembled and binned into near-complete and partial genomes, enabling strain-level genomic analysis of the microbial community.We reconstructed eleven near-complete and six partial bacterial genomes representative of the key members of the microbial community. Twelve of these genomes share >90% putative ortholog amino acid identity with reference genomes. Manual curation of the assembly of one particularly novel genome resulted in the first essentially complete genome sequence (in three pieces, the order of which could not be determined due to a repeat) for Varibaculum cambriense (strain Dora), a medically relevant species that has been implicated in abscess formation.During the period studied, the microbial community undergoes a compositional shift, in which obligate anaerobes (fermenters) overtake Escherichia coli as the most abundant species. Other species remain stable, probably due to their ability to either respire anaerobically or grow by fermentation, and their capacity to tolerate fluctuating levels of oxygen. Metabolic predictions for V. cambriense suggest that, like other members of the microbial community, this organism is able to process various sugar substrates and make use of multiple different electron acceptors during anaerobic respiration. Genome comparisons within the family Actinomycetaceae reveal important differences

QT correction formulas and laboratory analysis on patients with metabolic syndrome and diabetes

Science.gov (United States)

Wong, Sara; Rivera, Pedro; Rodríguez, María. G.; Severeyn, Érika; Altuve, Miguel

2013-11-01

This article presents a study of ventricular repolarization in diabetic and metabolic syndrome subjects. The corrected QT interval (QTc) was estimated using four correction formulas commonly employed in the literature: Bazett, Fridericia, Framingham and Hodges. After extracting the Q, R and T waves from the electrocardiogram of 52 subjects (19 diabetic, 15 with metabolic syndrome and 18 control), using a wavelet-based approach, the RR interval and QT interval were determined. Then, QTc interval was computed using the formulas previously mentioned. Additionally, laboratory test (fasting glucose, cholesterol, triglycerides) were also evaluated. Results show that metabolic syndrome subjects have normal QTc. However, a longer QTc in this population may be a sign of future complication. The corrected QT interval by Fridericia's formula seems to be the most appropriated for metabolic syndrome subjects (low correlation coefficient between RR and QTc). Significant differences were obtained in the blood glucose and triglyceride levels, principally due to the abnormal sugar metabolization of metabolic syndrome and diabetic subjects. Further studies are focused on the acquisition of a larger database of metabolic syndrome and diabetics subjects and the repetition of this study using other populations, like high performance athletes.

Microbial degradation of low-level radioactive waste

International Nuclear Information System (INIS)

Rogers, R.D.; Hamilton, M.A.; Veeh, R.H.; McConnell, J.W. Jr.

1994-04-01

The Nuclear Regulatory Commission stipulates that disposed low-level radioactive waste (LLW) be stabilized. Because of apparent ease of use and normal structural integrity, cement has been widely used as a binder to solidify LLW. However, the resulting waste forms are sometimes susceptible to failure due to the actions of waste constituents, stress, and environment. This report reviews laboratory efforts that are being developed to address the effects of microbiologically influenced chemical attack on cement-solidified LLW. Groups of microorganisms are being employed that are capable of metabolically converting organic and inorganic substrates into organic and mineral acids. Such acids aggressively react with cement and can ultimately lead to structural failure. Results on the application of mechanisms inherent in microbially influenced degradation of cement-based material are the focus of this report. Sufficient data-validated evidence of the potential for microbially influenced deterioration of cement-solidified LLW has been developed during the course of this study. These data support the continued development of appropriate tests necessary to determine the resistance of cement-solidified LLW to microbially induced degradation that could impact the stability of the waste form. They also justify the continued effort of enumeration of the conditions necessary to support the microbiological growth and population expansion

Hydrodynamic chronoamperometry for probing kinetics of anaerobic microbial metabolism - case study of Faecalibacterium prausnitzii

Science.gov (United States)

Prévoteau, Antonin; Geirnaert, Annelies; Arends, Jan B. A.; Lannebère, Sylvain; van de Wiele, Tom; Rabaey, Korneel

2015-07-01

Monitoring in vitro the metabolic activity of microorganisms aids bioprocesses and enables better understanding of microbial metabolism. Redox mediators can be used for this purpose via different electrochemical techniques that are either complex or only provide non-continuous data. Hydrodynamic chronoamperometry using a rotating disc electrode (RDE) can alleviate these issues but was seldom used and is poorly characterized. The kinetics of Faecalibacterium prausnitzii A2-165, a beneficial gut microbe, were determined using a RDE with riboflavin as redox probe. This butyrate producer anaerobically ferments glucose and reduces riboflavin whose continuous monitoring on a RDE provided highly accurate kinetic measurements of its metabolism, even at low cell densities. The metabolic reaction rate increased linearly over a broad range of cell concentrations (9 × 104 to 5 × 107 cells.mL-1). Apparent Michaelis-Menten kinetics was observed with respect to riboflavin (KM = 6 μM kcat = 5.3×105 s-1, at 37 °C) and glucose (KM = 6 μM kcat = 2.4 × 105 s-1). The short temporal resolution allows continuous monitoring of fast cellular events such as kinetics inhibition with butyrate. Furthermore, we detected for the first time riboflavin reduction by another potential probiotic, Butyricicoccus pullicaecorum. The ability of the RDE for fast, accurate, simple and continuous measurements makes it an ad hoc tool for assessing bioprocesses at high resolution.

Hydrodynamic chronoamperometry for probing kinetics of anaerobic microbial metabolism--case study of Faecalibacterium prausnitzii.

Science.gov (United States)

Prévoteau, Antonin; Geirnaert, Annelies; Arends, Jan B A; Lannebère, Sylvain; Van de Wiele, Tom; Rabaey, Korneel

2015-07-01

Monitoring in vitro the metabolic activity of microorganisms aids bioprocesses and enables better understanding of microbial metabolism. Redox mediators can be used for this purpose via different electrochemical techniques that are either complex or only provide non-continuous data. Hydrodynamic chronoamperometry using a rotating disc electrode (RDE) can alleviate these issues but was seldom used and is poorly characterized. The kinetics of Faecalibacterium prausnitzii A2-165, a beneficial gut microbe, were determined using a RDE with riboflavin as redox probe. This butyrate producer anaerobically ferments glucose and reduces riboflavin whose continuous monitoring on a RDE provided highly accurate kinetic measurements of its metabolism, even at low cell densities. The metabolic reaction rate increased linearly over a broad range of cell concentrations (9 × 10(4) to 5 × 10(7) cells.mL(-1)). Apparent Michaelis-Menten kinetics was observed with respect to riboflavin (KM = 6 μM; kcat = 5.3 × 10(5) s(-1), at 37 °C) and glucose (KM = 6 μM; kcat = 2.4 × 10(5) s(-1)). The short temporal resolution allows continuous monitoring of fast cellular events such as kinetics inhibition with butyrate. Furthermore, we detected for the first time riboflavin reduction by another potential probiotic, Butyricicoccus pullicaecorum. The ability of the RDE for fast, accurate, simple and continuous measurements makes it an ad hoc tool for assessing bioprocesses at high resolution.

Rhizosphere effect of colonizer plant species on the development of soil microbial community during primary succession on postmining sites

Energy Technology Data Exchange (ETDEWEB)

Elhottova, D.; Kristufek, V.; Maly, S.; Frouz, J. [Academy of Sciences of the Czech Republic, Ceske Budejovice (Czech Republic). Inst. for Soil Biology

2009-07-01

The impact of pioneer plant species Tussilago farfara on structural, functional, and growth characterization of microbial community colonizing the spoil colliery substrate was studied in a laboratory microcosm experiment. Microcosms consisting of spoil substrate (0.7 dm{sup 3} of tertiary alkaline clay sediment from Sokolov brown-coal mine area) from a pioneer site (without vegetation, 5 years after heaping) were cultivated in a greenhouse with one plant of this species. Plant roots substantially increased microbial diversity and biomass after one season (7 months) of cultivation. Roots influenced the microbial community and had nearly twice the size, higher growth, and metabolic potential in comparison to the control. The development of microbial specialists improves the plant nutrient status. Bacterial nitrogen (N{sub 2}) fixators (Bradyrhizobium japonicum, Rhizobium radiobacter) and arbuscular mycorrhizal fungi were confirmed in the rhizosphere of Tussilago farfara.

Laboratory-Cultured Strains of the Sea Anemone Exaiptasia Reveal Distinct Bacterial Communities

KAUST Repository

Herrera Sarrias, Marcela; Ziegler, Maren; Voolstra, Christian R.; Aranda, Manuel

2017-01-01

Exaiptasia is a laboratory sea anemone model system for stony corals. Two clonal strains are commonly used, referred to as H2 and CC7, that originate from two genetically distinct lineages and that differ in their Symbiodinium specificity. However, little is known about their other microbial associations. Here, we examined and compared the taxonomic composition of the bacterial assemblages of these two symbiotic Exaiptasia strains, both of which have been cultured in the laboratory long-term under identical conditions. We found distinct bacterial microbiota for each strain, indicating the presence of host-specific microbial consortia. Putative differences in the bacterial functional profiles (i.e., enrichment and depletion of various metabolic processes) based on taxonomic inference were also detected, further suggesting functional differences of the microbiomes associated with these lineages. Our study contributes to the current knowledge of the Exaiptasia holobiont by comparing the bacterial diversity of two commonly used strains as models for coral research.

Laboratory-Cultured Strains of the Sea Anemone Exaiptasia Reveal Distinct Bacterial Communities

KAUST Repository

Herrera Sarrias, Marcela

2017-05-02

Exaiptasia is a laboratory sea anemone model system for stony corals. Two clonal strains are commonly used, referred to as H2 and CC7, that originate from two genetically distinct lineages and that differ in their Symbiodinium specificity. However, little is known about their other microbial associations. Here, we examined and compared the taxonomic composition of the bacterial assemblages of these two symbiotic Exaiptasia strains, both of which have been cultured in the laboratory long-term under identical conditions. We found distinct bacterial microbiota for each strain, indicating the presence of host-specific microbial consortia. Putative differences in the bacterial functional profiles (i.e., enrichment and depletion of various metabolic processes) based on taxonomic inference were also detected, further suggesting functional differences of the microbiomes associated with these lineages. Our study contributes to the current knowledge of the Exaiptasia holobiont by comparing the bacterial diversity of two commonly used strains as models for coral research.

Recent advances in engineering propionyl-CoA metabolism for microbial production of value-added chemicals and biofuels.

Science.gov (United States)

Srirangan, Kajan; Bruder, Mark; Akawi, Lamees; Miscevic, Dragan; Kilpatrick, Shane; Moo-Young, Murray; Chou, C Perry

2017-09-01

Diminishing fossil fuel reserves and mounting environmental concerns associated with petrochemical manufacturing practices have generated significant interests in developing whole-cell biocatalytic systems for the production of value-added chemicals and biofuels. Although acetyl-CoA is a common natural biogenic precursor for the biosynthesis of numerous metabolites, propionyl-CoA is unpopular and non-native to most organisms. Nevertheless, with its C3-acyl moiety as a discrete building block, propionyl-CoA can serve as another key biogenic precursor to several biological products of industrial importance. As a result, engineering propionyl-CoA metabolism, particularly in genetically tractable hosts with the use of inexpensive feedstocks, has paved an avenue for novel biomanufacturing. Herein, we present a systematic review on manipulation of propionyl-CoA metabolism as well as relevant genetic and metabolic engineering strategies for microbial production of value-added chemicals and biofuels, including odd-chain alcohols and organic acids, bio(co)polymers and polyketides. [Formula: see text].

Effects of simulated acid rain on microbial characteristics in a lateritic red soil.

Science.gov (United States)

Xu, Hua-qin; Zhang, Jia-en; Ouyang, Ying; Lin, Ling; Quan, Guo-ming; Zhao, Ben-liang; Yu, Jia-yu

2015-11-01

A laboratory experiment was performed to examine the impact of simulated acid rain (SAR) on nutrient leaching, microbial biomass, and microbial activities in a lateritic red soil in South China. The soil column leaching experiment was conducted over a 60-day period with the following six SAR pH treatments (levels): 2.5, 3.0, 3.5, 4.0, 4.5, and 5.0 and one control treatment (pH = 7). Compared with the control treatment, the concentrations of soil organic matter, total nitrogen, total phosphorus, total potassium, soil microbial biomass carbon (MBC), soil microbial biomass nitrogen (MBN), and average well color density (AWCD) in the Ecoplates were all significantly decreased by leaching with SAR at different pH levels. The decrease in MBC and MBN indicated that acid rain reduced the soil microbial population, while the decrease in AWCD revealed that acid rain had a negative effect on soil bacterial metabolic function. Soil basal respiration increased gradually from pH 4.0 to 7.0 but decreased dramatically from pH 2.5 to 3.0. The decrease in soil nutrient was the major reason for the change of soil microbial functions. A principal component analysis showed that the major carbon sources used by the bacteria were carbohydrates and carboxylic acids.

Measuring maximum and standard metabolic rates using intermittent-flow respirometry: a student laboratory investigation of aerobic metabolic scope and environmental hypoxia in aquatic breathers.

Science.gov (United States)

Rosewarne, P J; Wilson, J M; Svendsen, J C

2016-01-01

Metabolic rate is one of the most widely measured physiological traits in animals and may be influenced by both endogenous (e.g. body mass) and exogenous factors (e.g. oxygen availability and temperature). Standard metabolic rate (SMR) and maximum metabolic rate (MMR) are two fundamental physiological variables providing the floor and ceiling in aerobic energy metabolism. The total amount of energy available between these two variables constitutes the aerobic metabolic scope (AMS). A laboratory exercise aimed at an undergraduate level physiology class, which details the appropriate data acquisition methods and calculations to measure oxygen consumption rates in rainbow trout Oncorhynchus mykiss, is presented here. Specifically, the teaching exercise employs intermittent flow respirometry to measure SMR and MMR, derives AMS from the measurements and demonstrates how AMS is affected by environmental oxygen. Students' results typically reveal a decline in AMS in response to environmental hypoxia. The same techniques can be applied to investigate the influence of other key factors on metabolic rate (e.g. temperature and body mass). Discussion of the results develops students' understanding of the mechanisms underlying these fundamental physiological traits and the influence of exogenous factors. More generally, the teaching exercise outlines essential laboratory concepts in addition to metabolic rate calculations, data acquisition and unit conversions that enhance competency in quantitative analysis and reasoning. Finally, the described procedures are generally applicable to other fish species or aquatic breathers such as crustaceans (e.g. crayfish) and provide an alternative to using higher (or more derived) animals to investigate questions related to metabolic physiology. © 2016 The Fisheries Society of the British Isles.

A review of metabolic and enzymatic engineering strategies for designing and optimizing performance of microbial cell factories

Directory of Open Access Journals (Sweden)

Amanda K. Fisher

2014-08-01

Full Text Available Microbial cell factories (MCFs are of considerable interest to convert low value renewable substrates to biofuels and high value chemicals. This review highlights the progress of computational models for the rational design of an MCF to produce a target bio-commodity. In particular, the rational design of an MCF involves: (i product selection, (ii de novo biosynthetic pathway identification (i.e., rational, heterologous, or artificial, (iii MCF chassis selection, (iv enzyme engineering of promiscuity to enable the formation of new products, and (v metabolic engineering to ensure optimal use of the pathway by the MCF host. Computational tools such as (i de novo biosynthetic pathway builders, (ii docking, (iii molecular dynamics (MD and steered MD (SMD, and (iv genome-scale metabolic flux modeling all play critical roles in the rational design of an MCF. Genome-scale metabolic flux models are of considerable use to the design process since they can reveal metabolic capabilities of MCF hosts. These can be used for host selection as well as optimizing precursors and cofactors of artificial de novo biosynthetic pathways. In addition, recent advances in genome-scale modeling have enabled the derivation of metabolic engineering strategies, which can be implemented using the genomic tools reviewed here as well.

Biotechnological Aspects of Microbial Extracellular Electron Transfer

Science.gov (United States)

Kato, Souichiro

2015-01-01

Extracellular electron transfer (EET) is a type of microbial respiration that enables electron transfer between microbial cells and extracellular solid materials, including naturally-occurring metal compounds and artificial electrodes. Microorganisms harboring EET abilities have received considerable attention for their various biotechnological applications, in addition to their contribution to global energy and material cycles. In this review, current knowledge on microbial EET and its application to diverse biotechnologies, including the bioremediation of toxic metals, recovery of useful metals, biocorrosion, and microbial electrochemical systems (microbial fuel cells and microbial electrosynthesis), were introduced. Two potential biotechnologies based on microbial EET, namely the electrochemical control of microbial metabolism and electrochemical stimulation of microbial symbiotic reactions (electric syntrophy), were also discussed. PMID:26004795

MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data

Science.gov (United States)

Vallenet, David; Belda, Eugeni; Calteau, Alexandra; Cruveiller, Stéphane; Engelen, Stefan; Lajus, Aurélie; Le Fèvre, François; Longin, Cyrille; Mornico, Damien; Roche, David; Rouy, Zoé; Salvignol, Gregory; Scarpelli, Claude; Thil Smith, Adam Alexander; Weiman, Marion; Médigue, Claudine

2013-01-01

MicroScope is an integrated platform dedicated to both the methodical updating of microbial genome annotation and to comparative analysis. The resource provides data from completed and ongoing genome projects (automatic and expert annotations), together with data sources from post-genomic experiments (i.e. transcriptomics, mutant collections) allowing users to perfect and improve the understanding of gene functions. MicroScope (http://www.genoscope.cns.fr/agc/microscope) combines tools and graphical interfaces to analyse genomes and to perform the manual curation of gene annotations in a comparative context. Since its first publication in January 2006, the system (previously named MaGe for Magnifying Genomes) has been continuously extended both in terms of data content and analysis tools. The last update of MicroScope was published in 2009 in the Database journal. Today, the resource contains data for >1600 microbial genomes, of which ∼300 are manually curated and maintained by biologists (1200 personal accounts today). Expert annotations are continuously gathered in the MicroScope database (∼50 000 a year), contributing to the improvement of the quality of microbial genomes annotations. Improved data browsing and searching tools have been added, original tools useful in the context of expert annotation have been developed and integrated and the website has been significantly redesigned to be more user-friendly. Furthermore, in the context of the European project Microme (Framework Program 7 Collaborative Project), MicroScope is becoming a resource providing for the curation and analysis of both genomic and metabolic data. An increasing number of projects are related to the study of environmental bacterial (meta)genomes that are able to metabolize a large variety of chemical compounds that may be of high industrial interest. PMID:23193269

Establishment and metabolic analysis of a model microbial community for understanding trophic and electron accepting interactions of subsurface anaerobic environments

Directory of Open Access Journals (Sweden)

Yang Zamin K

2010-05-01

Full Text Available Abstract Background Communities of microorganisms control the rates of key biogeochemical cycles, and are important for biotechnology, bioremediation, and industrial microbiological processes. For this reason, we constructed a model microbial community comprised of three species dependent on trophic interactions. The three species microbial community was comprised of Clostridium cellulolyticum, Desulfovibrio vulgaris Hildenborough, and Geobacter sulfurreducens and was grown under continuous culture conditions. Cellobiose served as the carbon and energy source for C. cellulolyticum, whereas D. vulgaris and G. sulfurreducens derived carbon and energy from the metabolic products of cellobiose fermentation and were provided with sulfate and fumarate respectively as electron acceptors. Results qPCR monitoring of the culture revealed C. cellulolyticum to be dominant as expected and confirmed the presence of D. vulgaris and G. sulfurreducens. Proposed metabolic modeling of carbon and electron flow of the three-species community indicated that the growth of C. cellulolyticum and D. vulgaris were electron donor limited whereas G. sulfurreducens was electron acceptor limited. Conclusions The results demonstrate that C. cellulolyticum, D. vulgaris, and G. sulfurreducens can be grown in coculture in a continuous culture system in which D. vulgaris and G. sulfurreducens are dependent upon the metabolic byproducts of C. cellulolyticum for nutrients. This represents a step towards developing a tractable model ecosystem comprised of members representing the functional groups of a trophic network.

Microbial Cell Dynamics Lab (MCDL)

Data.gov (United States)

Federal Laboratory Consortium — The Microbial Cell Dynamics Laboratory at PNNL enables scientists to study the molecular details of microbes under relevant environmental conditions. The MCDL seeks...

[Effects of heavy metals pollution on soil microbial communities metabolism and soil enzyme activities in coal mining area of Tongchuan, Shaanxi Province of Northwest China].

Science.gov (United States)

Guo, Xing-Liang; Gu, Jie; Chen, Zhi-Xue; Gao, Hua; Qin, Qing-Jun; Sun, Wei; Zhang, Wei-Juan

2012-03-01

This paper studied the metabolism of soil microbes, functions of soil microbial communities, and activities of soil enzymes in a coal mining area of Tongchuan. In the coal mining area, the concentrations of soil Cu, Zn, Cd, and Pb were significantly higher than those in the non-mining area, of which, Cd contributed most to the heavy metals pollution. By adopting Biolog method combining with principal component analysis (PCA) and cluster analysis, it was found that the metabolic characteristics of different soil microbial communities varied significantly with increasing soil heavy metals pollution, and the variation was mainly manifested in the metabolic patterns of carbon sources such as saccharides and amino acids. In slightly and moderately polluted soils, the utilization of carbon sources by soil microbial communities was activated; while in heavily polluted soils, the carbon sources utilization was inhibited. The activities of soil urease, protease, alkaline phosphatase, and catalase all tended to decline with intensifying soil heavy metals pollution. The soil urease, protease, alkaline phosphatase, and catalase activities in the coal mining area were 50.5%-65.1%, 19.1%-57.1%, 87.2%-97.5%, and 77.3%-86.0% higher than those in the non-mining area, respectively. The activities of soil sucrase and cellulase were activated in slightly and moderately polluted soils, but inhibited in heavily polluted soils.

Systems Biology of Microbial Exopolysaccharides Production.

Science.gov (United States)

Ates, Ozlem

2015-01-01

Exopolysaccharides (EPSs) produced by diverse group of microbial systems are rapidly emerging as new and industrially important biomaterials. Due to their unique and complex chemical structures and many interesting physicochemical and rheological properties with novel functionality, the microbial EPSs find wide range of commercial applications in various fields of the economy such as food, feed, packaging, chemical, textile, cosmetics and pharmaceutical industry, agriculture, and medicine. EPSs are mainly associated with high-value applications, and they have received considerable research attention over recent decades with their biocompatibility, biodegradability, and both environmental and human compatibility. However, only a few microbial EPSs have achieved to be used commercially due to their high production costs. The emerging need to overcome economic hurdles and the increasing significance of microbial EPSs in industrial and medical biotechnology call for the elucidation of the interrelations between metabolic pathways and EPS biosynthesis mechanism in order to control and hence enhance its microbial productivity. Moreover, a better understanding of biosynthesis mechanism is a significant issue for improvement of product quality and properties and also for the design of novel strains. Therefore, a systems-based approach constitutes an important step toward understanding the interplay between metabolism and EPS biosynthesis and further enhances its metabolic performance for industrial application. In this review, primarily the microbial EPSs, their biosynthesis mechanism, and important factors for their production will be discussed. After this brief introduction, recent literature on the application of omics technologies and systems biology tools for the improvement of production yields will be critically evaluated. Special focus will be given to EPSs with high market value such as xanthan, levan, pullulan, and dextran.

Systems biology of microbial exopolysaccharides production

Directory of Open Access Journals (Sweden)

Ozlem eAtes

2015-12-01

Full Text Available Exopolysaccharides (EPS produced by diverse group of microbial systems are rapidly emerging as new and industrially important biomaterials. Due to their unique and complex chemical structures and many interesting physicochemical and rheological properties with novel functionality, the microbial EPSs find wide range of commercial applications in various fields of the economy such as food, feed, packaging, chemical, textile, cosmetics and pharmaceutical industry, agriculture and medicine. EPSs are mainly associated with high-value applications and they have received considerable research attention over recent decades with their biocompatibility, biodegradability, and both environmental and human compatibility. However only a few microbial EPSs have achieved to be used commercially due to their high production costs. The emerging need to overcome economic hurdles and the increasing significance of microbial EPSs in industrial and medical biotechnology call for the elucidation of the interrelations between metabolic pathways and EPS biosynthesis mechanism in order to control and hence enhance its microbial productivity. Moreover a better understanding of biosynthesis mechanism is a significant issue for improvement of product quality and properties and also for the design of novel strains. Therefore a systems-based approach constitutes an important step towards understanding the interplay between metabolism and EPS biosynthesis and further enhances its metabolic performance for industrial application. In this review, primarily the microbial EPSs, their biosynthesis mechanism and important factors for their production will be discussed. After this brief introduction, recent literature on the application of omics technologies and systems biology tools for the improvement of production yields will be critically evaluated. Special focus will be given to EPSs with high market value such as xanthan, levan, pullulan and dextran.

The information science of microbial ecology.

Science.gov (United States)

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

2016-06-01

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

Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations.

Science.gov (United States)

Wu, Xiaofen; Holmfeldt, Karin; Hubalek, Valerie; Lundin, Daniel; Åström, Mats; Bertilsson, Stefan; Dopson, Mark

2016-05-01

Microorganisms in the terrestrial deep biosphere host up to 20% of the earth's biomass and are suggested to be sustained by the gases hydrogen and carbon dioxide. A metagenome analysis of three deep subsurface water types of contrasting age (from 86% coverage. The populations were dominated by Proteobacteria, Candidate divisions, unclassified archaea and unclassified bacteria. The estimated genome sizes of the biosphere. The data were finally used to create a combined metabolic model of the deep terrestrial biosphere microbial community.

Bacillus licheniformis affects the microbial community and metabolic profile in the spontaneous fermentation of Daqu starter for Chinese liquor making.

Science.gov (United States)

Wang, Peng; Wu, Qun; Jiang, Xuejian; Wang, Zhiqiang; Tang, Jingli; Xu, Yan

2017-06-05

Chinese liquor is produced from spontaneous fermentation starter (Daqu) that provides the microbes, enzymes and flavors for liquor fermentation. To improve the flavor character of Daqu, we inoculated Bacillus licheniformis and studied the effect of this strain on the community structure and metabolic profile in Daqu fermentation. The microbial relative abundance changed after the inoculation, including the increase in Bacillus, Clavispora and Aspergillus, and the decrease in Pichia, Saccharomycopsis and some other genera. This variation was also confirmed by pure culture and coculture experiments. Seventy-three metabolites were identified during Daqu fermentation process. After inoculation, the average content of aromatic compounds were significantly enriched from 0.37mg/kg to 0.90mg/kg, and the average content of pyrazines significantly increased from 0.35mg/kg to 5.71mg/kg. The increase in pyrazines was positively associated with the metabolism of the inoculated Bacillus and the native genus Clavispora, because they produced much more pyrazines in their cocultures. Whereas the increase in aromatic compounds might be related to the change of in situ metabolic activity of several native genera, in particular, Aspergillus produced more aromatic compounds in cocultures with B. licheniformis. It indicated that the inoculation of B. licheniformis altered the flavor character of Daqu by both its own metabolic activity and the variation of in situ metabolic activity. Moreover, B. licheniformis inoculation influenced the enzyme activity of Daqu, including the significant increase in amylase activity (from 1.3gstarch/g/h to 1.7gstarch/g/h), and the significant decrease in glucoamylase activity (from 627.6mgglucose/g/h to 445.6mgglucose/g/h) and esterase activity (from 28.1mgethylcaproate/g/100h to 17.2mgethylcaproate/g/100h). These effects of inoculation were important factors for regulating the metabolism of microbial communities, hence for improving the flavor profile

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

Long-term performance of anaerobic digestion for crop residues containing heavy metals and response of microbial communities.

Science.gov (United States)

Lee, Jongkeun; Kim, Joonrae Roger; Jeong, Seulki; Cho, Jinwoo; Kim, Jae Young

2017-01-01

In order to investigate the long-term stability on the performance of the anaerobic digestion process, a laboratory-scale continuous stirred-tank reactor (CSTR) was operated for 1100 days with sunflower harvested in a heavy metal contaminated site. Changes of microbial communities during digestion were identified using pyrosequencing. According to the results, soluble heavy metal concentrations were lower than the reported inhibitory level and the reactor performance remained stable up to OLR of 2.0g-VS/L/day at HRT of 20days. Microbial communities commonly found in anaerobic digestion for cellulosic biomass were observed and stably established with respect to the substrate. Thus, the balance of microbial metabolism was maintained appropriately and anaerobic digestion seems to be feasible for disposal of heavy metal-containing crop residues from phytoremediation sites. Copyright © 2016 Elsevier Ltd. All rights reserved.

Advances in metabolic engineering in the microbial production of fuels and chemicals from C1 gas.

Science.gov (United States)

Humphreys, Christopher M; Minton, Nigel P

2018-04-01

The future sustainable production of chemicals and fuels from non-petrochemical sources, while at the same time reducing greenhouse gas (GHG) emissions, represent two of society's greatest challenges. Microbial chassis able to grow on waste carbon monoxide (CO) and carbon dioxide (CO 2 ) can provide solutions to both. Ranging from the anaerobic acetogens, through the aerobic chemoautotrophs to the photoautotrophic cyanobacteria, they are able to convert C1 gases into a range of chemicals and fuels which may be enhanced and extended through appropriate metabolic engineering. The necessary improvements will be facilitated by the increasingly sophisticated gene tools that are beginning to emerge as part of the Synthetic Biology revolution. These tools, in combination with more accurate metabolic and genome scale models, will enable C1 chassis to deliver their full potential. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

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

Science.gov (United States)

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.

The Microbial DNA Index System (MiDIS): A tool for microbial pathogen source identification

Energy Technology Data Exchange (ETDEWEB)

Velsko, S. P. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

2010-08-09

The microbial DNA Index System (MiDIS) is a concept for a microbial forensic database and investigative decision support system that can be used to help investigators identify the sources of microbial agents that have been used in a criminal or terrorist incident. The heart of the proposed system is a rigorous method for calculating source probabilities by using certain fundamental sampling distributions associated with the propagation and mutation of microbes on disease transmission networks. This formalism has a close relationship to mitochondrial and Y-chromosomal human DNA forensics, and the proposed decision support system is somewhat analogous to the CODIS and SWGDAM mtDNA databases. The MiDIS concept does not involve the use of opportunistic collections of microbial isolates and phylogenetic tree building as a basis for inference. A staged approach can be used to build MiDIS as an enduring capability, beginning with a pilot demonstration program that must meet user expectations for performance and validation before evolving into a continuing effort. Because MiDIS requires input from a a broad array of expertise including outbreak surveillance, field microbial isolate collection, microbial genome sequencing, disease transmission networks, and laboratory mutation rate studies, it will be necessary to assemble a national multi-laboratory team to develop such a system. The MiDIS effort would lend direction and focus to the national microbial genetics research program for microbial forensics, and would provide an appropriate forensic framework for interfacing to future national and international disease surveillance efforts.

Microbial metatranscriptomics in a permanent marine oxygen minimum zone

OpenAIRE

Stewart, Frank J.; Ulloa, Osvaldo; DeLong, Edward

2010-01-01

Simultaneous characterization of taxonomic composition, metabolic gene content and gene expression in marine oxygen minimum zones (OMZs) has potential to broaden perspectives on the microbial and biogeochemical dynamics in these environments. Here, we present a metatranscriptomic survey of microbial community metabolism in the Eastern Tropical South Pacific OMZ off northern Chile. Community RNA was sampled in late austral autumn from four depths (50, 85, 110, 200 m) extending across the oxycl...

Modular co-culture engineering, a new approach for metabolic engineering.

Science.gov (United States)

Zhang, Haoran; Wang, Xiaonan

2016-09-01

With the development of metabolic engineering, employment of a selected microbial host for accommodation of a designed biosynthetic pathway to produce a target compound has achieved tremendous success in the past several decades. Yet, increasing requirements for sophisticated microbial biosynthesis call for establishment and application of more advanced metabolic engineering methodologies. Recently, important progress has been made towards employing more than one engineered microbial strains to constitute synthetic co-cultures and modularizing the biosynthetic labor between the co-culture members in order to improve bioproduction performance. This emerging approach, referred to as modular co-culture engineering in this review, presents a valuable opportunity for expanding the scope of the broad field of metabolic engineering. We highlight representative research accomplishments using this approach, especially those utilizing metabolic engineering tools for microbial co-culture manipulation. Key benefits and major challenges associated with modular co-culture engineering are also presented and discussed. Copyright © 2016 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Arabinoxylo-Oligosaccharides and Inulin Impact Inter-Individual Variation on Microbial Metabolism and Composition, Which Immunomodulates Human Cells.

Science.gov (United States)

Van den Abbeele, Pieter; Taminiau, Bernard; Pinheiro, Iris; Duysburgh, Cindy; Jacobs, Heidi; Pijls, Loek; Marzorati, Massimo

2018-02-07

Fecal batch fermentations coupled to cocultures of epithelial cells and macrophages were used to compare how arabinoxylo-oligosaccharides (AXOS) and inulin modulate gut microbial activity and composition of three different human donors and subsequently the epithelial permeability and immune response. Both inulin and AXOS decreased the pH during incubation (-1.5 pH units), leading to increased productions of acetate, propionate, and butyrate. Differences in terms of metabolites production could be linked to specific microbial alterations at genus level upon inulin/AXOS supplementation (i.e., Bifidobacterium, Bacteroides, Prevotella and unclassified Erysipelotrichaceae), as shown by 16S-targeted Illumina sequencing. Both products stimulated gut barrier and immune function with increases in TEER, NF-KB, IL-10, and IL-6. Ingredients with different structures selectively modulate the microbiota of a specific donor leading to differential changes at metabolic level. The extent of this effect is donor specific and is linked to a final specific modulation of the host's immune system.

Field Evidence for Co-Metabolism of Trichloroethene Stimulated by Addition of Electron Donor to Groundwater

Energy Technology Data Exchange (ETDEWEB)

Conrad, Mark E.; Brodie, Eoin L.; Radtke, Corey W.; Bill, Markus; Delwiche, Mark E.; Lee, M. Hope; Swift, Dana L.; Colwell, Frederick S.

2010-05-17

For more than 10 years, electron donor has been injected into the Snake River aquifer beneath the Test Area North site of the Idaho National Laboratory for the purpose of stimulating microbial reductive dechlorination of trichloroethene (TCE) in groundwater. This has resulted in significant TCE removal from the source area of the contaminant plume and elevated dissolved CH4 in the groundwater extending 250 m from the injection well. The delta13C of the CH4 increases from 56o/oo in the source area to -13 o/oo with distance from the injection well, whereas the delta13C of dissolved inorganic carbon decreases from 8 o/oo to -13 o/oo, indicating a shift from methanogenesis to methane oxidation. This change in microbial activity along the plume axis is confirmed by PhyloChip microarray analyses of 16S rRNA genes obtained from groundwater microbial communities, which indicate decreasing abundances of reductive dechlorinating microorganisms (e.g., Dehalococcoides ethenogenes) and increasing CH4-oxidizing microorganisms capable of aerobic co-metabolism of TCE (e.g., Methylosinus trichosporium). Incubation experiments with 13C-labeled TCE introduced into microcosms containing basalt and groundwater from the aquifer confirm that TCE co-metabolism is possible. The results of these studies indicate that electron donor amendment designed to stimulate reductive dechlorination of TCE may also stimulate co-metabolism of TCE.

Environmental spread of microbes impacts the development of metabolic phenotypes in mice transplanted with microbial communities from humans

DEFF Research Database (Denmark)

Zhang, Li; Bahl, Martin Iain; Roager, Henrik Munch

2017-01-01

Microbiota transplantation to germ-free animals is a powerful method to study involvement of gut microbes in the aetiology of metabolic syndrome. Owing to large interpersonal variability in gut microbiota, studies with broad coverage of donors are needed to elucidate the establishment of human......, thereby allowing us to explore the extent of microbial spread between cages in a well-controlled environment. Despite high group-wise similarity between obese and control human microbiotas, transplanted mice in the four isolators developed distinct gut bacterial composition and activity, body mass gain......, and insulin resistance. Spread of microbes between cages within isolators interacted with establishment of the transplanted microbiotas in mice, and contributed to the transmission of metabolic phenotypes. Our findings highlight the impact of donor variability and reveal that inter-individual spread...

A Metabolic Murder Mystery: A Case-Based Experiment for the Undergraduate Biochemistry Laboratory

Science.gov (United States)

Childs-Disney, Jessica L.; Kauffmann, Andrew D.; Poplawski, Shane G.; Lysiak, Daniel R.; Stewart, Robert J.; Arcadi, Jane K.; Dinan, Frank J.

2010-01-01

In 1990, a woman was wrongly convicted of poisoning her infant son and was sentenced to life in prison. Her conviction was based on laboratory work that wrongly identified ethylene glycol as present in her son's blood and in the formula he drank prior to his death. The actual cause of the infant's death, a metabolic disease, was eventually…

Microbial Diversity of a Heavily Polluted Microbial Mat and Its Community Changes following Degradation of Petroleum Compounds

Science.gov (United States)

Abed, Raeid M. M.; Safi, Nimer M. D.; Köster, Jürgen; de Beer, Dirk; El-Nahhal, Yasser; Rullkötter, Jürgen; Garcia-Pichel, Ferran

2002-01-01

We studied the microbial diversity of benthic cyanobacterial mats inhabiting a heavily polluted site in a coastal stream (Wadi Gaza) and monitored the microbial community response induced by exposure to and degradation of four model petroleum compounds in the laboratory. Phormidium- and Oscillatoria-like cyanobacterial morphotypes were dominant in the field. Bacteria belonging to different groups, mainly the Cytophaga-Flavobacterium-Bacteriodes group, the γ and β subclasses of the class Proteobacteria, and the green nonsulfur bacteria, were also detected. In slurry experiments, these communities efficiently degraded phenanthrene and dibenzothiophene completely in 7 days both in the light and in the dark. n-Octadecane and pristane were degraded to 25 and 34% of their original levels, respectively, within 7 days, but there was no further degradation until 40 days. Both cyanobacterial and bacterial communities exhibited noticeable changes concomitant with degradation of the compounds. The populations enriched by exposure to petroleum compounds included a cyanobacterium affiliated phylogenetically with Halomicronema. Bacteria enriched both in the light and in the dark, but not bacteria enriched in any of the controls, belonged to the newly described Holophaga-Geothrix-Acidobacterium phylum. In addition, another bacterial population, found to be a member of green nonsulfur bacteria, was detected only in the bacteria treated in the light. All or some of the populations may play a significant role in metabolizing the petroleum compounds. We concluded that the microbial mats from Wadi Gaza are rich in microorganisms with high biodegradative potential. PMID:11916684

Effect of UV on De-NOx performance and microbial community of a hybrid catalytic membrane biofilm reactor

Science.gov (United States)

Chen, Zhouyang; Huang, Zhensha; He, Yiming; Xiao, Xiaoliang; Wei, Zaishan

2018-02-01

The hybrid membrane catalytic biofilm reactor provides a new way of flue gas denitration. However, the effects of UV on denitrification performance, microbial community and microbial nitrogen metabolism are still unknown. In this study, the effects of UV on deNO x performance, nitrification and denitrification, microbial community and microbial nitrogen metabolism of a bench scale N-TiO2/PSF hybrid catalytic membrane biofilm reactor (HCMBR) were evaluated. The change from nature light to UV in the HCMBR leads to the fall of NO removal efficiency of HCMBR from 92.8% to 81.8%. UV affected the microbial community structure, but did not change microbial nitrogen metabolism, as shown by metagenomics sequencing method. Some dominant phyla, such as Gammaproteobacteria, Bacteroidetes, Firmicutes, Actinobacteria, and Alphaproteobacteria, increased in abundance, whereas others, such as Proteobacteria and Betaproteobacteria, decreased. There were nitrification, denitrification, nitrogen fixation, and organic nitrogen metabolism in the HCMBR.

Something new from something old? Fracking stimulated microbial processes

Science.gov (United States)

Wrighton, K. C.; Daly, R. A.; Hoyt, D.; Trexler, R.; McRae, J.; Wilkins, M.; Mouser, P. J.

2015-12-01

Hydraulic fracturing, colloquially known as "fracking", is employed for effective gas and oil recovery in deep shales. This process injects organisms and liquids from the surface into the deep subsurface (~2500 m), exposing microorganisms to high pressures, elevated temperatures, chemical additives, and brine-level salinities. Here we use assembly-based metagenomics to create a metabolic blueprint from an energy-producing Marcellus shale well over a 328-day period. Using this approach we ask the question: What abiotic and biotic factors drive microbial metabolism and thus biogeochemical cycling during natural gas extraction? We found that after 49 days, increased salinity in produced waters corresponded to a shift in the microbial community, with only organisms that encode salinity adaptations detected. We posit that organic compatible solutes, produced by organisms adapting to increased salinity, fuels a methylamine-driven ecosystem in fractured shale. This metabolic network ultimately results in biogenic methane production from members of Methanohalophilus and Methanolobus. Proton NMR validated these genomic hypotheses, with mono-methylamine being highest in the input material, but detected throughout the sampling. Beyond abiotic constraints, our genomic investigations revealed that viruses can be linked to key members of the microbial community, potentially releasing methylamine osmoprotectants and impacting bacterial strain variation. Collectively our results indicate that adaptation to high salinity, metabolism in the absence of oxidized electron acceptors, and viral predation are controlling factors mediating microbial community metabolism during hydraulic fracturing of the deep subsurface.

Impact of an indigenous microbial enhanced oil recovery field trial on microbial community structure in a high pour-point oil reservoir

Energy Technology Data Exchange (ETDEWEB)

Zhang, Fan; Zhang, Xiao-Tao; Hou, Du-Jie [China Univ. of Geosciences, Beijing (China). The Key Lab. of Marine Reservoir Evolution and Hydrocarbon Accumulation Mechanism; She, Yue-Hui [Yangtze Univ., Jingzhou, Hubei (China). College of Chemistry and Environmental Engineering; Huazhong Univ. of Science and Technology, Wuhan (China). College of Life Science and Technology; Li, Hua-Min [Beijing Bioscience Research Center (China); Shu, Fu-Chang; Wang, Zheng-Liang [Yangtze Univ., Jingzhou, Hubei (China). College of Chemistry and Environmental Engineering; Yu, Long-Jiang [Huazhong Univ. of Science and Technology, Wuhan (China). College of Life Science and Technology

2012-08-15

Based on preliminary investigation of microbial populations in a high pour-point oil reservoir, an indigenous microbial enhanced oil recovery (MEOR) field trial was carried out. The purpose of the study is to reveal the impact of the indigenous MEOR process on microbial community structure in the oil reservoir using 16Sr DNA clone library technique. The detailed monitoring results showed significant response of microbial communities during the field trial and large discrepancies of stimulated microorganisms in the laboratory and in the natural oil reservoir. More specifically, after nutrients injection, the original dominant populations of Petrobacter and Alishewanella in the production wells almost disappeared. The expected desirable population of Pseudomonas aeruginosa, determined by enrichment experiments in laboratory, was stimulated successfully in two wells of the five monitored wells. Unexpectedly, another potential population of Pseudomonas pseudoalcaligenes which were not detected in the enrichment culture in laboratory was stimulated in the other three monitored production wells. In this study, monitoring of microbial community displayed a comprehensive alteration of microbial populations during the field trial to remedy the deficiency of culture-dependent monitoring methods. The results would help to develop and apply more MEOR processes. (orig.)

Impact of an indigenous microbial enhanced oil recovery field trial on microbial community structure in a high pour-point oil reservoir.

Science.gov (United States)

Zhang, Fan; She, Yue-Hui; Li, Hua-Min; Zhang, Xiao-Tao; Shu, Fu-Chang; Wang, Zheng-Liang; Yu, Long-Jiang; Hou, Du-Jie

2012-08-01

Based on preliminary investigation of microbial populations in a high pour-point oil reservoir, an indigenous microbial enhanced oil recovery (MEOR) field trial was carried out. The purpose of the study is to reveal the impact of the indigenous MEOR process on microbial community structure in the oil reservoir using 16Sr DNA clone library technique. The detailed monitoring results showed significant response of microbial communities during the field trial and large discrepancies of stimulated microorganisms in the laboratory and in the natural oil reservoir. More specifically, after nutrients injection, the original dominant populations of Petrobacter and Alishewanella in the production wells almost disappeared. The expected desirable population of Pseudomonas aeruginosa, determined by enrichment experiments in laboratory, was stimulated successfully in two wells of the five monitored wells. Unexpectedly, another potential population of Pseudomonas pseudoalcaligenes which were not detected in the enrichment culture in laboratory was stimulated in the other three monitored production wells. In this study, monitoring of microbial community displayed a comprehensive alteration of microbial populations during the field trial to remedy the deficiency of culture-dependent monitoring methods. The results would help to develop and apply more MEOR processes.

Recent advances in systems metabolic engineering tools and strategies.

Science.gov (United States)

Chae, Tong Un; Choi, So Young; Kim, Je Woong; Ko, Yoo-Sung; Lee, Sang Yup

2017-10-01

Metabolic engineering has been playing increasingly important roles in developing microbial cell factories for the production of various chemicals and materials to achieve sustainable chemical industry. Nowadays, many tools and strategies are available for performing systems metabolic engineering that allows systems-level metabolic engineering in more sophisticated and diverse ways by adopting rapidly advancing methodologies and tools of systems biology, synthetic biology and evolutionary engineering. As an outcome, development of more efficient microbial cell factories has become possible. Here, we review recent advances in systems metabolic engineering tools and strategies together with accompanying application examples. In addition, we describe how these tools and strategies work together in simultaneous and synergistic ways to develop novel microbial cell factories. Copyright © 2017 Elsevier Ltd. All rights reserved.

Metabolite secretion in microorganisms: the theory of metabolic overflow put to the test

DEFF Research Database (Denmark)

Pinu, Farhana R.; Granucci, Ninna; Daniell, James

2018-01-01

Introduction Microbial cells secrete many metabolites during growth, including important intermediates of the central carbon metabolism. This has not been taken into account by researchers when modeling microbial metabolism for metabolic engineering and systems biology studies. Materials and Meth...

Metabolic-flux dependent regulation of microbial physiology.

Science.gov (United States)

Litsios, Athanasios; Ortega, Álvaro D; Wit, Ernst C; Heinemann, Matthias

2018-04-01

According to the most prevalent notion, changes in cellular physiology primarily occur in response to altered environmental conditions. Yet, recent studies have shown that changes in metabolic fluxes can also trigger phenotypic changes even when environmental conditions are unchanged. This suggests that cells have mechanisms in place to assess the magnitude of metabolic fluxes, that is, the rate of metabolic reactions, and use this information to regulate their physiology. In this review, we describe recent evidence for metabolic flux-sensing and flux-dependent regulation. Furthermore, we discuss how such sensing and regulation can be mechanistically achieved and present a set of new candidates for flux-signaling metabolites. Similar to metabolic-flux sensing, we argue that cells can also sense protein translation flux. Finally, we elaborate on the advantages that flux-based regulation can confer to cells. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Mass spectral molecular networking of living microbial colonies

NARCIS (Netherlands)

Watrous, J.; Roach, P.; Alexandrov, T.; Heath, B.S.; Yang, J.Y.; Kersten, R.D.; Voort, van der M.; Pogliano, K.; Gross, H.; Raaijmakers, J.; Moore, B.S.; Laskin, J.; Bandeira, N.; Dorrestein, P.C.

2012-01-01

Integrating the governing chemistry with the genomics and phenotypes of microbial colonies has been a “holy grail” in microbiology. This work describes a highly sensitive, broadly applicable, and cost-effective approach that allows metabolic profiling of live microbial colonies directly from a Petri

Genetic and metabolic engineering for microbial production of poly-γ-glutamic acid.

Science.gov (United States)

Cao, Mingfeng; Feng, Jun; Sirisansaneeyakul, Sarote; Song, Cunjiang; Chisti, Yusuf

2018-05-28

Poly-γ-glutamic acid (γ-PGA) is a natural biopolymer of glutamic acid. The repeating units of γ-PGA may be derived exclusively from d-glutamic acid, or l-glutamic acid, or both. The monomer units are linked by amide bonds between the α-amino group and the γ-carboxylic acid group. γ-PGA is biodegradable, edible and water-soluble. It has numerous existing and emerging applications in processing of foods, medicines and cosmetics. This review focuses on microbial production of γ-PGA via genetically and metabolically engineered recombinant bacteria. Strategies for improving production of γ-PGA include modification of its biosynthesis pathway, enhancing the production of its precursor (glutamic acid), and preventing loss of the precursor to competing byproducts. These and other strategies are discussed. Heterologous synthesis of γ-PGA in industrial bacterial hosts that do not naturally produce γ-PGA is discussed. Emerging trends and the challenges affecting the production of γ-PGA are reviewed. Copyright © 2018. Published by Elsevier Inc.

Mineral solubility and free energy controls on microbial reaction kinetics: Application to contaminant transport in the subsurface

Energy Technology Data Exchange (ETDEWEB)

Taillefert, Martial [Georgia Inst. of Technology, Atlanta, GA (United States); Van Cappellen, Philippe [Univ. of Waterloo, ON (Canada)

2016-11-14

Recent developments in the theoretical treatment of geomicrobial reaction processes have resulted in the formulation of kinetic models that directly link the rates of microbial respiration and growth to the corresponding thermodynamic driving forces. The overall objective of this project was to verify and calibrate these kinetic models for the microbial reduction of uranium(VI) in geochemical conditions that mimic as much as possible field conditions. The approach combined modeling of bacterial processes using new bioenergetic rate laws, laboratory experiments to determine the bioavailability of uranium during uranium bioreduction, evaluation of microbial growth yield under energy-limited conditions using bioreactor experiments, competition experiments between metabolic processes in environmentally relevant conditions, and model applications at the field scale. The new kinetic descriptions of microbial U(VI) and Fe(III) reduction should replace those currently used in reactive transport models that couple catabolic energy generation and growth of microbial populations to the rates of biogeochemical redox processes. The above work was carried out in collaboration between the groups of Taillefert (batch reactor experiments and reaction modeling) at Georgia Tech and Van Cappellen (retentostat experiments and reactive transport modeling) at University of Waterloo (Canada).

Succession of the functional microbial communities and the metabolic functions in maize straw composting process.

Science.gov (United States)

Wei, Huawei; Wang, Liuhong; Hassan, Muhammad; Xie, Bing

2018-05-01

Illumina MiSeq sequencing and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) were applied to study the dynamic changes and effects of microbial community structures as well as the metabolic function of bacterial community in maize straw composting process. Results showed that humic acid contents in loosely combined humus (HA1) and stably combined humus (HA2) increased after composting and Staphylococcus, Cellulosimicrobium and Ochrobactrum possibly participated in the transformation of the process. The bacterial communities differed in different stages of the composting. Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria were reported the dominant phyla throughout the process and the relative abundance of the dominant phyla varied significantly (p composting. Copyright © 2018 Elsevier Ltd. All rights reserved.

Microbial heterotrophic metabolic rates constrain the microbial carbon pump

Digital Repository Service at National Institute of Oceanography (India)

Robinson, C.; Ramaiah, N.

(2008). 10. P.A. del Giorgio, J. J. Cole, in MicrobialEcologyoftheOceans D. L. Kirchman Ed. (JohnWiley & Sons, Inc. NewYork ed. 1. 2000),pp. 289–325. 11. A. B. Burd etal., DeepSeaRes.II 57, 1557 (2010). 12. S. Martinez-García, E. Fernández, M.... R.A. Straza, D. L. Kirchman, Aquat.Microb.Ecol. 62, 267(2011). 16. O. Hoegh-Guldberg, J. F. Bruno, Science 328,1523 (2010). 17. J. Piontek, M. Lunau, N. Handel, C. Borchard, M.Wurst,A. Engel, Biogeosciences 7, 1615 (2010). 18. J. K.Apple, P.A. del...

Microbial metabolism and community structure in response to bioelectrochemically enhanced remediation of petroleum hydrocarbon-contaminated soil.

Science.gov (United States)

Lu, Lu; Huggins, Tyler; Jin, Song; Zuo, Yi; Ren, Zhiyong Jason

2014-04-01

This study demonstrates that electrodes in a bioelectrochemical system (BES) can potentially serve as a nonexhaustible electron acceptor for in situ bioremediation of hydrocarbon contaminated soil. The deployment of BES not only eliminates aeration or supplement of electron acceptors as in contemporary bioremediation but also significantly shortens the remediation period and produces sustainable electricity. More interestingly, the study reveals that microbial metabolism and community structure distinctively respond to the bioelectrochemically enhanced remediation. Tubular BESs with carbon cloth anode (CCA) or biochar anode (BCA) were inserted into raw water saturated soils containing petroleum hydrocarbons for enhancing in situ remediation. Results show that total petroleum hydrocarbon (TPH) removal rate almost doubled in soils close to the anode (63.5-78.7%) than that in the open circuit positive controls (37.6-43.4%) during a period of 64 days. The maximum current density from the BESs ranged from 73 to 86 mA/m(2). Comprehensive microbial and chemical characterizations and statistical analyses show that the residual TPH has a strongly positive correlation with hydrocarbon-degrading microorganisms (HDM) numbers, dehydrogenase activity, and lipase activity and a negative correlation with soil pH, conductivity, and catalase activity. Distinctive microbial communities were identified at the anode, in soil with electrodes, and soil without electrodes. Uncommon electrochemically active bacteria capable of hydrocarbon degradation such as Comamonas testosteroni, Pseudomonas putida, and Ochrobactrum anthropi were selectively enriched on the anode, while hydrocarbon oxidizing bacteria were dominant in soil samples. Results from genus or phylum level characterizations well agree with the data from cluster analysis. Data from this study suggests that a unique constitution of microbial communities may play a key role in BES enhancement of petroleum hydrocarbons

Host genes related to paneth cells and xenobiotic metabolism are associated with shifts in human ileum-associated microbial composition.

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Tianyi Zhang

Full Text Available The aim of this study was to integrate human clinical, genotype, mRNA microarray and 16 S rRNA sequence data collected on 84 subjects with ileal Crohn's disease, ulcerative colitis or control patients without inflammatory bowel diseases in order to interrogate how host-microbial interactions are perturbed in inflammatory bowel diseases (IBD. Ex-vivo ileal mucosal biopsies were collected from the disease unaffected proximal margin of the ileum resected from patients who were undergoing initial intestinal surgery. Both RNA and DNA were extracted from the mucosal biopsy samples. Patients were genotyped for the three major NOD2 variants (Leufs1007, R702W, and G908R and the ATG16L1T300A variant. Whole human genome mRNA expression profiles were generated using Agilent microarrays. Microbial composition profiles were determined by 454 pyrosequencing of the V3-V5 hypervariable region of the bacterial 16 S rRNA gene. The results of permutation based multivariate analysis of variance and covariance (MANCOVA support the hypothesis that host mucosal Paneth cell and xenobiotic metabolism genes play an important role in host microbial interactions.

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

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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.

The effect of feed rations containing high moisture crimped corn ensiled with microbial inoculant or chemical additive on milk production and metabolism of dairy cows

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László Könyves

2015-01-01

Full Text Available The study evaluated the effects of crimped corn preserved either with organic acids or with a microbial inoculant on a range of metabolic and production indicators of dairy cows. Two hundred and sixty in-calf, second and third parity cows were selected into pairs on basis of age, parity, milk production in previous lactation, days in milk and body condition score with the greatest possible conformity within pairs. Cow pairs were assigned into a 2-period crossover experiment (2 × 45 days and kept in separate groups within the same shed. Dietary treatments were TMR with crimped corn preserved with either organic acids (treatment K or microbial inoculant (treatment B. Ten superbly matched cow-pairs were selected to form nucleus pairs for metabolic studies. The preservatives had no effect on the nutrient content of crimped corn. Crimped corn preserved with the microbial inoculant were found mouldy, predominantly with Mucor sp. at a number high enough to inhibit the growth of lactic acid bacteria, and had significantly higher pH and ammonium concentration compared to the chemical treatment. The milk yield of treatment K cows was significantly higher than that of treatment B cows with identical feed intake. Blood beta-hydroxy-butyrate concentration was lower and blood aspartate amino transferase activity higher with treatment K compared to treatment B. Results of this study suggest the superiority of total mixed rations containing chemically preserved crimped corn in terms of ammonia and microbiological indicators of crimped corn, significantly higher milk yield, and balanced energy metabolism.

Integrating the protein and metabolic engineering toolkits for next-generation chemical biosynthesis.

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Pirie, Christopher M; De Mey, Marjan; Jones Prather, Kristala L; Ajikumar, Parayil Kumaran

2013-04-19

Through microbial engineering, biosynthesis has the potential to produce thousands of chemicals used in everyday life. Metabolic engineering and synthetic biology are fields driven by the manipulation of genes, genetic regulatory systems, and enzymatic pathways for developing highly productive microbial strains. Fundamentally, it is the biochemical characteristics of the enzymes themselves that dictate flux through a biosynthetic pathway toward the product of interest. As metabolic engineers target sophisticated secondary metabolites, there has been little recognition of the reduced catalytic activity and increased substrate/product promiscuity of the corresponding enzymes compared to those of central metabolism. Thus, fine-tuning these enzymatic characteristics through protein engineering is paramount for developing high-productivity microbial strains for secondary metabolites. Here, we describe the importance of protein engineering for advancing metabolic engineering of secondary metabolism pathways. This pathway integrated enzyme optimization can enhance the collective toolkit of microbial engineering to shape the future of chemical manufacturing.

Microbial production strategies and applications of lycopene and other terpenoids.

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Ma, Tian; Deng, Zixin; Liu, Tiangang

2016-01-01

Terpenoids are a large class of compounds that have far-reaching applications and economic value, particularly those most commonly found in plants; however, the extraction and synthesis of these compounds is often expensive and technically challenging. Recent advances in microbial metabolic engineering comprise a breakthrough that may enable the efficient, cost-effective production of these limited natural resources. Via the engineering of safe, industrial microorganisms that encode product-specific enzymes, and even entire metabolic pathways of interest, microbial-derived semisynthetic terpenoids may soon replace plant-derived terpenoids as the primary source of these valuable compounds. Indeed, the recent metabolic engineering of an Escherichia coli strain that produces the precursor to lycopene, a commercially and medically important compound, with higher yields than those in tomato plants serves as a successful example. Here, we review the recent developments in the metabolic engineering of microbes for the production of certain terpenoid compounds, particularly lycopene, which has been increasingly used in pharmaceuticals, nutritional supplements, and cosmetics. Furthermore, we summarize the metabolic engineering strategies used to achieve successful microbial production of some similar compounds. Based on this overview, there is a reason to believe that metabolic engineering comprises an optimal approach for increasing the production of lycopene and other terpenoids.

Gut microbiota and metabolic syndrome.

Science.gov (United States)

Festi, Davide; Schiumerini, Ramona; Eusebi, Leonardo Henry; Marasco, Giovanni; Taddia, Martina; Colecchia, Antonio

2014-11-21

Gut microbiota exerts a significant role in the pathogenesis of the metabolic syndrome, as confirmed by studies conducted both on humans and animal models. Gut microbial composition and functions are strongly influenced by diet. This complex intestinal "superorganism" seems to affect host metabolic balance modulating energy absorption, gut motility, appetite, glucose and lipid metabolism, as well as hepatic fatty storage. An impairment of the fine balance between gut microbes and host's immune system could culminate in the intestinal translocation of bacterial fragments and the development of "metabolic endotoxemia", leading to systemic inflammation and insulin resistance. Diet induced weight-loss and bariatric surgery promote significant changes of gut microbial composition, that seem to affect the success, or the inefficacy, of treatment strategies. Manipulation of gut microbiota through the administration of prebiotics or probiotics could reduce intestinal low grade inflammation and improve gut barrier integrity, thus, ameliorating metabolic balance and promoting weight loss. However, further evidence is needed to better understand their clinical impact and therapeutic use.

Starter Culture Selection for Making Chinese Sesame-Flavored Liquor Based on Microbial Metabolic Activity in Mixed-Culture Fermentation

Science.gov (United States)

Wu, Qun; Ling, Jie

2014-01-01

Selection of a starter culture with excellent viability and metabolic activity is important for inoculated fermentation of traditional food. To obtain a suitable starter culture for making Chinese sesame-flavored liquor, the yeast and bacterium community structures were investigated during spontaneous and solid-state fermentations of this type of liquor. Five dominant species in spontaneous fermentation were identified: Saccharomyces cerevisiae, Pichia membranaefaciens, Issatchenkia orientalis, Bacillus licheniformis, and Bacillus amyloliquefaciens. The metabolic activity of each species in mixed and inoculated fermentations of liquor was investigated in 14 different cocultures that used different combinations of these species. The relationships between the microbial species and volatile metabolites were analyzed by partial least-squares (PLS) regression analysis. We found that S. cerevisiae was positively correlated to nonanal, and B. licheniformis was positively associated with 2,3-butanediol, isobutyric acid, guaiacol, and 4-vinyl guaiacol, while I. orientalis was positively correlated to butyric acid, isovaleric acid, hexanoic acid, and 2,3-butanediol. These three species are excellent flavor producers for Chinese liquor. Although P. membranaefaciens and B. amyloliquefaciens were not efficient flavor producers, the addition of them alleviated competition among the other three species and altered their growth rates and flavor production. As a result, the coculture of all five dominant species produced the largest amount of flavor compounds. The result indicates that flavor producers and microbial interaction regulators are important for inoculated fermentation of Chinese sesame-flavored liquor. PMID:24814798

Metabolic effects of dark chocolate consumption on energy, gut microbiota, and stress-related metabolism in free-living subjects.

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Martin, Francois-Pierre J; Rezzi, Serge; Peré-Trepat, Emma; Kamlage, Beate; Collino, Sebastiano; Leibold, Edgar; Kastler, Jürgen; Rein, Dietrich; Fay, Laurent B; Kochhar, Sunil

2009-12-01

Dietary preferences influence basal human metabolism and gut microbiome activity that in turn may have long-term health consequences. The present study reports the metabolic responses of free living subjects to a daily consumption of 40 g of dark chocolate for up to 14 days. A clinical trial was performed on a population of 30 human subjects, who were classified in low and high anxiety traits using validated psychological questionnaires. Biological fluids (urine and blood plasma) were collected during 3 test days at the beginning, midtime and at the end of a 2 week study. NMR and MS-based metabonomics were employed to study global changes in metabolism due to the chocolate consumption. Human subjects with higher anxiety trait showed a distinct metabolic profile indicative of a different energy homeostasis (lactate, citrate, succinate, trans-aconitate, urea, proline), hormonal metabolism (adrenaline, DOPA, 3-methoxy-tyrosine) and gut microbial activity (methylamines, p-cresol sulfate, hippurate). Dark chocolate reduced the urinary excretion of the stress hormone cortisol and catecholamines and partially normalized stress-related differences in energy metabolism (glycine, citrate, trans-aconitate, proline, beta-alanine) and gut microbial activities (hippurate and p-cresol sulfate). The study provides strong evidence that a daily consumption of 40 g of dark chocolate during a period of 2 weeks is sufficient to modify the metabolism of free living and healthy human subjects, as per variation of both host and gut microbial metabolism.

Strategies for microbial synthesis of high-value phytochemicals

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Li, Sijin; Li, Yanran; Smolke, Christina D.

2018-03-01

Phytochemicals are of great pharmaceutical and agricultural importance, but often exhibit low abundance in nature. Recent demonstrations of industrial-scale production of phytochemicals in yeast have shown that microbial production of these high-value chemicals is a promising alternative to sourcing these molecules from native plant hosts. However, a number of challenges remain in the broader application of this approach, including the limited knowledge of plant secondary metabolism and the inefficient reconstitution of plant metabolic pathways in microbial hosts. In this Review, we discuss recent strategies to achieve microbial biosynthesis of complex phytochemicals, including strategies to: (1) reconstruct plant biosynthetic pathways that have not been fully elucidated by mining enzymes from native and non-native hosts or by enzyme engineering; (2) enhance plant enzyme activity, specifically cytochrome P450 activity, by improving efficiency, selectivity, expression or electron transfer; and (3) enhance overall reaction efficiency of multi-enzyme pathways by dynamic control, compartmentalization or optimization with the host's metabolism. We also highlight remaining challenges to — and future opportunities of — this approach.

Kinetic modeling of cell metabolism for microbial production.

Science.gov (United States)

Costa, Rafael S; Hartmann, Andras; Vinga, Susana

2016-02-10

Kinetic models of cellular metabolism are important tools for the rational design of metabolic engineering strategies and to explain properties of complex biological systems. The recent developments in high-throughput experimental data are leading to new computational approaches for building kinetic models of metabolism. Herein, we briefly survey the available databases, standards and software tools that can be applied for kinetic models of metabolism. In addition, we give an overview about recently developed ordinary differential equations (ODE)-based kinetic models of metabolism and some of the main applications of such models are illustrated in guiding metabolic engineering design. Finally, we review the kinetic modeling approaches of large-scale networks that are emerging, discussing their main advantages, challenges and limitations. Copyright © 2015 Elsevier B.V. All rights reserved.

Microbial diversity in restored wetlands of San Francisco Bay

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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 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

Microbial transformation of xenobiotics for environmental ...

African Journals Online (AJOL)

Microbial transformation of xenobiotics for environmental bioremediation. ... anaerobic and reductive biotransformation by co-metabolic processes and an overview of ... of xenobiotic compounds in context to the modern day biotechnology.

MICROBIAL MATS - A JOINT VENTURE

NARCIS (Netherlands)

VANGEMERDEN, H

Microbial mats characteristically are dominated by a few functional groups of microbes: cyanobacteria, colorless sulfur bacteria, purple sulfur bacteria, and sulfate-reducing bacteria. Their combined metabolic activities result in steep environmental microgradients, particularly of oxygen and

Bioreactor microbial ecosystems for thiocyanate and cyanide degradation unravelled with genome-resolved metagenomics.

Science.gov (United States)

Kantor, Rose S; van Zyl, A Wynand; van Hille, Robert P; Thomas, Brian C; Harrison, Susan T L; Banfield, Jillian F

2015-12-01

Gold ore processing uses cyanide (CN(-) ), which often results in large volumes of thiocyanate- (SCN(-) ) contaminated wastewater requiring treatment. Microbial communities can degrade SCN(-) and CN(-) , but little is known about their membership and metabolic potential. Microbial-based remediation strategies will benefit from an ecological understanding of organisms involved in the breakdown of SCN(-) and CN(-) into sulfur, carbon and nitrogen compounds. We performed metagenomic analysis of samples from two laboratory-scale bioreactors used to study SCN(-) and CN(-) degradation. Community analysis revealed the dominance of Thiobacillus spp., whose genomes harbour a previously unreported operon for SCN(-) degradation. Genome-based metabolic predictions suggest that a large portion of each bioreactor community is autotrophic, relying not on molasses in reactor feed but using energy gained from oxidation of sulfur compounds produced during SCN(-) degradation. Heterotrophs, including a bacterium from a previously uncharacterized phylum, compose a smaller portion of the reactor community. Predation by phage and eukaryotes is predicted to affect community dynamics. Genes for ammonium oxidation and denitrification were detected, indicating the potential for nitrogen removal, as required for complete remediation of wastewater. These findings suggest optimization strategies for reactor design, such as improved aerobic/anaerobic partitioning and elimination of organic carbon from reactor feed. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

COMBINED MICROBIAL SURFACTANT-POLYMER SYSTEM FOR IMPROVED OIL MOBILITY AND CONFORMANCE CONTROL

Energy Technology Data Exchange (ETDEWEB)

Jorge Gabitto; Maria Barrufet

2004-08-01

Many domestic oil fields are facing abandonment even though they still contain two-thirds of their original oil. A significant number of these fields can yield additional oil using advanced oil recovery (AOR) technologies. To maintain domestic oil production at current levels, AOR technologies are needed that are affordable and can be implemented by independent oil producers of the future. Microbial enhanced oil recovery (MEOR) technologies have become established as cost-effective solutions for declining oil production. MEOR technologies are affordable for independent producers operating stripper wells and can be used to extend the life of marginal fields. The demonstrated versatility of microorganisms can be used to design advanced microbial systems to treat multiple production problems in complex, heterogeneous reservoirs. The proposed research presents the concept of a combined microbial surfactant-polymer system for advanced oil recovery. The surfactant-polymer system utilizes bacteria that are capable of both biosurfactant production and metabolically-controlled biopolymer production. This novel technology combines complementary mechanisms to extend the life of marginal fields and is applicable to a large number of domestic reservoirs. The research project described in this report is performed jointly by, Bio-Engineering Inc., a woman owned small business, Texas A&M University and Prairie View A&M University, a Historically Black College and University. This report describes the results of our laboratory work to grow microbial cultures and the work done on recovery experiments on core rocks. We have selected two bacterial strains capable of producing both surfactant and polymers. We have conducted laboratory experiments to determine under what conditions surfactants and polymers can be produced from one single strain. We have conduct recovery experiments to determine the performance of these strains under different conditions. Our results do not show a

EFFECTS OF STIMULATOR SUBSTANCES ON AEROBIC METHYL TERT-BUTYL ETHER BIODEGRADATION BY MICROBIAL CONSORTIUM

Directory of Open Access Journals (Sweden)

M. Farrokhi ، S. Ahmadizad

2009-04-01

Full Text Available In this study dissolved humic substances and yeast extract were tested in different concentrations for enhancing methyl tert-butyl ether mineralization by isolated microorganisms from a variety of sources. All experiments were conducted at a constant temperature of 25ºC. Vials of 50 mL and 125 mL volume sealed with Teflon-lined Mini-Nert caps was used for microcosm experiments. In all experiments 1% sodium azide were used as control. Samples of bacterial cultures that metabolize methyl tert-butyl ether have been analysed by direct GC analysis using flame ionization detector. Cultures able to metabolize have been found in activated sludge and soils. These microorganisms weregram-positive bacterium. An aerobic microbial consortium was enriched in laboratory for four months. Methyl tert-butyl ether has been shown to biodegrade under aerobic and co-metabolic conditions. A microbial consortium isolated from activated sludges was identified as Cocobacillus. The concentration of the initial attached biomass was about 0.11 g/L of dry weight. The maximum mineralization rate and beneficial effects of stimulator substances on aerobic biodegradation of methyl tert-butyl ether occurred with the culture by combined concentrations of 500 mg/L of yeast extract and 20 mg/L of peat humic growth support of microbial consortium within 216 h and in presence of high oxygen levels and well mixing conditions. It was shown that adding, peat humic and yeast extract together, had better stimulatory effect on methyl tert-butyl ether biodegradation. Results clearly showed a stimulatory effect on methyl tert-butyl ether consumption higher than 20%. Consortium was capable of degrading concentrations of ≤1000 mg/L, whereas concentrations of >1000 mg/L, were not degraded.

Are Chicken Embryos Endotherms or Ectotherms? A Laboratory Exercise Integrating Concepts in Thermoregulation and Metabolism

Science.gov (United States)

Hiebert, Sara M; Noveral, Jocelyne

2007-01-01

This investigative laboratory exercise uses the different relations between ambient temperature and metabolic rate in endotherms and ectotherms as a core concept to answer the following question: What thermoregulatory mode is employed by chicken embryos? Emphasis is placed on the physiological concepts that can be taught with this exercise,…

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.

Assessment of microbial processes on radionuclide mobility in shallow land burial

International Nuclear Information System (INIS)

Colombo, P.; Tate, R.L. III; Weiss, A.J.

1982-07-01

The impact of microbial metabolism of the organic substituents of low level radioactive wastes on radionuclide mobility in disposal sites, the nature of the microbial transformations involved in this metabolism and the effect of the prevailing environmental parameters on the quantities and types of metabolic intermediates accumulated were examined. Since both aerobic and anaerobic periods can occur during trench ecosystem development, oxidation capacities of the microbial community in the presence and absence of oxygen were analyzed. Results of gas studies performed at three commercial low level radioactive waste disposal sites were reviewed. Several deficiencies in available data were determined. Further research needs are suggested. This assessment has demonstrated that the biochemical capabilities expressed within the low level radioactive waste disposal site are common to a wide variety of soil bacteria. Hence, assuming trenches would not be placed in sites with such extreme abiotic conditions that all microbial activity is precluded, the microbial populations needed for colonization and decomposition of the organic waste substances are readily provided from the waste itself and from the soil of existing and any proposed disposal sites. Indeed, considering the ubiquity of occurrence of the microorganisms responsible for waste decomposition and the chemical nature of the organic waste material, long-term prevention of biodecomposition is difficult, if not impossible

CHARACTERISTICS OF METABOLISM AND WORKING OUT THE METHODS OF DETERMINATION OF SYNTHETIC CANNABINOID THJ-2201 IN THE URINE OF LABORATORY ANIMALS

Directory of Open Access Journals (Sweden)

D. Yu. Apushkin

2017-01-01

Full Text Available The proposed article touches upon the study of metabolism of new synthetic cannabinoids. In the work the data on synthetic cannabinoid 3-(Naftalin-1-yloxomethyl-1-(5-fluoropentyl-1H-indazole (THJ-2201, as well as the products of its metabolism in the laboratory rats of the Wistar line are given, i. e. Mass spectra and chromatograms of the native substance (THJ-2201 obtained by high-performance liquid chromatography with mass-selective detection (HPLC-MS and gas chromatography with mass-selective detection (GC-MS are given. The paper presents a complex technique for qualitative determination of cannabimimetics THJ-2201 and methods for obtaining a metabolic profile model for the test substance that can be useful for the tasks of qualitative detection and detection of new psychoactive substances in biological objects for the purposes of forensic analysis.The aim of this work was to develop methods for determination of the test substance (THJ-2201 and its metabolites in the urine of laboratory animals, as well as the study of the metabolic characteristics of synthetic cannabinoids on the whole.Materials and methods. The following equipment was used for the experiment: a liquid chromatograph from the firm “Shimadzu LCMC-8050” in combination with a mass-selective detector. The detector type is a triple quadrupole with a double ionization source (chemical ionization at atmospheric pressure and electrospray. The separation of the substances occurred in a chromatographic column (the material is stainless steel, the characteristics are: 150 * 3.0 mm, Luna 3uC18 (2, 100A. The Sorbent is reversed-phase. The investigations were carried out on Agilent 7890A gas chromatograph with Agilent 5975C mass spectrometer and a 103 polar HP-5ms column of 28 m × 0.25 mm. The animals were mature male white laboratory rats of the Wistar line, aged 4–6 months, weighing 190-230 grams.Results and discussion. As a result of the studies, a comprehensive methodology for

Metabolic Flux Analysis of Shewanella spp. Reveals Evolutionary Robustness in Central Carbon Metabolism

Energy Technology Data Exchange (ETDEWEB)

Tang, Yinjie J.; Martin, Hector Garcia; Dehal, Paramvir S.; Deutschbauer, Adam; Llora, Xavier; Meadows, Adam; Arkin, Adam; Keasling, Jay D.

2009-08-19

Shewanella spp. are a group of facultative anaerobic bacteria widely distributed in marine and fresh-water environments. In this study, we profiled the central metabolic fluxes of eight recently sequenced Shewanella species grown under the same condition in minimal med-ium with [3-13C] lactate. Although the tested Shewanella species had slightly different growth rates (0.23-0.29 h31) and produced different amounts of acetate and pyruvate during early exponential growth (pseudo-steady state), the relative intracellular metabolic flux distributions were remarkably similar. This result indicates that Shewanella species share similar regulation in regard to central carbon metabolic fluxes under steady growth conditions: the maintenance of metabolic robustness is not only evident in a single species under genetic perturbations (Fischer and Sauer, 2005; Nat Genet 37(6):636-640), but also observed through evolutionary related microbial species. This remarkable conservation of relative flux profiles through phylogenetic differences prompts us to introduce the concept of metabotype as an alternative scheme to classify microbial fluxomics. On the other hand, Shewanella spp. display flexibility in the relative flux profiles when switching their metabolism from consuming lactate to consuming pyruvate and acetate.

Quantitative analysis of microbial biomass yield in aerobic bioreactor.

Science.gov (United States)

Watanabe, Osamu; Isoda, Satoru

2013-12-01

We have studied the integrated model of reaction rate equations with thermal energy balance in aerobic bioreactor for food waste decomposition and showed that the integrated model has the capability both of monitoring microbial activity in real time and of analyzing biodegradation kinetics and thermal-hydrodynamic properties. On the other hand, concerning microbial metabolism, it was known that balancing catabolic reactions with anabolic reactions in terms of energy and electron flow provides stoichiometric metabolic reactions and enables the estimation of microbial biomass yield (stoichiometric reaction model). We have studied a method for estimating real-time microbial biomass yield in the bioreactor during food waste decomposition by combining the integrated model with the stoichiometric reaction model. As a result, it was found that the time course of microbial biomass yield in the bioreactor during decomposition can be evaluated using the operational data of the bioreactor (weight of input food waste and bed temperature) by the combined model. The combined model can be applied to manage a food waste decomposition not only for controlling system operation to keep microbial activity stable, but also for producing value-added products such as compost on optimum condition. Copyright © 2013 The Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences. Published by Elsevier B.V. All rights reserved.

Impact of the gut microbiota on inflammation, obesity, and metabolic disease.

Science.gov (United States)

Boulangé, Claire L; Neves, Ana Luisa; Chilloux, Julien; Nicholson, Jeremy K; Dumas, Marc-Emmanuel

2016-04-20

The human gut harbors more than 100 trillion microbial cells, which have an essential role in human metabolic regulation via their symbiotic interactions with the host. Altered gut microbial ecosystems have been associated with increased metabolic and immune disorders in animals and humans. Molecular interactions linking the gut microbiota with host energy metabolism, lipid accumulation, and immunity have also been identified. However, the exact mechanisms that link specific variations in the composition of the gut microbiota with the development of obesity and metabolic diseases in humans remain obscure owing to the complex etiology of these pathologies. In this review, we discuss current knowledge about the mechanistic interactions between the gut microbiota, host energy metabolism, and the host immune system in the context of obesity and metabolic disease, with a focus on the importance of the axis that links gut microbes and host metabolic inflammation. Finally, we discuss therapeutic approaches aimed at reshaping the gut microbial ecosystem to regulate obesity and related pathologies, as well as the challenges that remain in this area.

Colonic transit time is related to bacterial metabolism and mucosal turnover in the gut

DEFF Research Database (Denmark)

Roager, Henrik Munch; Hansen, Lea Benedicte Skov; Bahl, Martin Iain

2016-01-01

Little is known about how colonic transit time relates to human colonic metabolism and its importance for host health, although a firm stool consistency, a proxy for a long colonic transit time, has recently been positively associated with gut microbial richness. Here, we show that colonic transi...... does not per se imply a healthy gut microbial ecosystem and points at colonic transit time as a highly important factor to consider in microbiome and metabolomics studies.......Little is known about how colonic transit time relates to human colonic metabolism and its importance for host health, although a firm stool consistency, a proxy for a long colonic transit time, has recently been positively associated with gut microbial richness. Here, we show that colonic transit...... time in humans, assessed using radio-opaque markers, is associated with overall gut microbial composition, diversity and metabolism. We find that a long colonic transit time associates with high microbial richness and is accompanied by a shift in colonic metabolism from carbohydrate fermentation...

Carbon use efficiency (CUE) and biomass turnover of soil microbial communities as affected by bedrock, land management and soil temperature and moisture

Science.gov (United States)

Zheng, Qing; Hu, Yuntao; Richter, Andreas; Wanek, Wolfgang

2017-04-01

Soil microbial carbon use efficiency (CUE), defined as the proportion of organic C taken up that is allocated to microbial growth, represents an important synthetic representation of microbial community C metabolism that describes the flux partitioning between microbial respiration and growth. Therefore, studying microbial CUE is critical for the understanding of soil C cycling. Microbial CUE is thought to vary with environmental conditions (e.g. temperature and soil moisture). Microbial CUE is thought to decrease with increasing temperature and declining soil moisture, as the latter may trigger stress responses (e.g. the synthesis of stress metabolites), which may consequently lower microbial community CUE. However, these effects on microbial CUE have not been adequately measured so far due to methodological restrictions. The most widely used methods for microbial CUE estimation are based on tracing 13C-labeled substrates into microbial biomass and respiratory CO2, approaches that are known to overestimate microbial CUE of native organic matter in soil. Recently, a novel substrate-independent approach based on the measurement of (i) respiration rates and (ii) the incorporation rates of 18O from labelled water into newly formed microbial DNA has been developed in our laboratory for measuring microbial CUE. This approach overcomes the shortcomings of previously used methods and has already been shown to yield realistic estimations of soil microbial CUE. This approach can also be applied to concurrently measure microbial biomass turnover rates, which also influence the sequestration of soil organic C. Microbial turnover rates are also thought to be impacted by environmental factors, but rarely have been directly measured so far. Here, we aimed at determining the short-term effects of environmental factors (soil temperature and soil moisture) on microbial CUE and microbial biomass turnover rates based on the novel 18O approach. Soils from three land-use types (arable

Fifteen years of microbiological investigation in Opalinus Clay at the Mont Terri rock laboratory (Switzerland)

Energy Technology Data Exchange (ETDEWEB)

Leupin, O.X. [National Cooperative for the Disposal of Radioactive Waste (NAGRA), Wettingen (Switzerland); Bernier-Latmani, R.; Bagnoud, A. [Swiss Federal Office of Technology EPFL, Lausanne (Switzerland); Moors, H.; Leys, N.; Wouters, K. [Belgian Nuclear Research Centre SCK-CEN, Mol (Belgium); Stroes-Gascoyne, S. [University of Saskatchewan, Saskatoon (Canada)

2017-04-15

Microbiological studies related to the geological disposal of radioactive waste have been conducted at the Mont Terri rock laboratory in Opalinus Clay, a potential host rock for a deep geologic repository, since 2002. The metabolic potential of microorganisms and their response to excavation-induced effects have been investigated in undisturbed and disturbed claystone cores and in pore- (borehole) water. Results from nearly 15 years of research at the Mont Terri rock laboratory have shown that microorganisms can potentially affect the environment of a repository by influencing redox conditions, metal corrosion and gas production and consumption under favourable conditions. However, the activity of microorganisms in undisturbed Opalinus Clay is limited by the very low porosity, the low water activity, and the largely recalcitrant nature of organic matter in the claystone formation. The presence of microorganisms in numerous experiments at the Mont Terri rock laboratory has suggested that excavation activities and perturbation of the host rock combined with additional contamination during the installation of experiments in boreholes create favourable conditions for microbial activity by providing increased space, water and substrates. Thus effects resulting from microbial activity might be expected in the proximity of a geological repository i.e., in the excavation damaged zone, the engineered barriers, and first containments (the containers). (authors)

Fifteen years of microbiological investigation in Opalinus Clay at the Mont Terri rock laboratory (Switzerland)

International Nuclear Information System (INIS)

Leupin, O.X.; Bernier-Latmani, R.; Bagnoud, A.; Moors, H.; Leys, N.; Wouters, K.; Stroes-Gascoyne, S.

2017-01-01

Microbiological studies related to the geological disposal of radioactive waste have been conducted at the Mont Terri rock laboratory in Opalinus Clay, a potential host rock for a deep geologic repository, since 2002. The metabolic potential of microorganisms and their response to excavation-induced effects have been investigated in undisturbed and disturbed claystone cores and in pore- (borehole) water. Results from nearly 15 years of research at the Mont Terri rock laboratory have shown that microorganisms can potentially affect the environment of a repository by influencing redox conditions, metal corrosion and gas production and consumption under favourable conditions. However, the activity of microorganisms in undisturbed Opalinus Clay is limited by the very low porosity, the low water activity, and the largely recalcitrant nature of organic matter in the claystone formation. The presence of microorganisms in numerous experiments at the Mont Terri rock laboratory has suggested that excavation activities and perturbation of the host rock combined with additional contamination during the installation of experiments in boreholes create favourable conditions for microbial activity by providing increased space, water and substrates. Thus effects resulting from microbial activity might be expected in the proximity of a geological repository i.e., in the excavation damaged zone, the engineered barriers, and first containments (the containers). (authors)

Microbial changes during pregnancy, birth and infancy

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Meital Nuriel-Ohayon

2016-07-01

Full Text Available Several healthy developmental processes such as pregnancy, fetal development and infant development include a multitude of physiological changes: weight gain, hormonal and metabolic changes, as well as immune changes. In this review we present an additional important factor which both influences and is affected by these physiological processes- the microbiome. We summarize the known changes in microbiota composition at a variety of body sites including gut, vagina, oral cavity and placenta, throughout pregnancy, fetal development and early childhood. There is still a lot to be discovered; yet several pieces of research point to the healthy desired microbial changes. Future research is likely to unravel precise roles and mechanisms of the microbiota in gestation; perhaps linking the metabolic, hormonal and immune changes together. Although some research has started to link microbial dysbiosis and specific microbial populations with unhealthy pregnancy complications, it is important to first understand the context of the natural healthy microbial changes occurring. Until recently the placenta and developing fetus were considered to be germ free, containing no apparent microbiome. We present multiple study results showing distinct microbiota compositions in the placenta and meconium, alluding to early microbial colonization. These results may change dogmas and our overall understanding of the importance and roles of microbiota from the beginning of life. We further review the main factors shaping the infant microbiome- modes of delivery, feeding, weaning, and exposure to antibiotics. Taken together, we are starting to build a broader understanding of healthy vs. abnormal microbial alterations throughout major developmental time-points.

ReacKnock: identifying reaction deletion strategies for microbial strain optimization based on genome-scale metabolic network.

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Zixiang Xu

Full Text Available Gene knockout has been used as a common strategy to improve microbial strains for producing chemicals. Several algorithms are available to predict the target reactions to be deleted. Most of them apply mixed integer bi-level linear programming (MIBLP based on metabolic networks, and use duality theory to transform bi-level optimization problem of large-scale MIBLP to single-level programming. However, the validity of the transformation was not proved. Solution of MIBLP depends on the structure of inner problem. If the inner problem is continuous, Karush-Kuhn-Tucker (KKT method can be used to reformulate the MIBLP to a single-level one. We adopt KKT technique in our algorithm ReacKnock to attack the intractable problem of the solution of MIBLP, demonstrated with the genome-scale metabolic network model of E. coli for producing various chemicals such as succinate, ethanol, threonine and etc. Compared to the previous methods, our algorithm is fast, stable and reliable to find the optimal solutions for all the chemical products tested, and able to provide all the alternative deletion strategies which lead to the same industrial objective.

Global microbialization of coral reefs.

Science.gov (United States)

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

2016-04-25

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

Molecular analysis of microbial community structures in pristine and contaminated aquifers--Field and laboratory microcosm experiments

Science.gov (United States)

Shi, Y.; Zwolinski, M.D.; Schreiber, M.E.; Bahr, J.M.; Sewell, G.W.; Hickey, W.J.

1999-01-01

Molecular Analysis of Microbial Community Structures in Pristine and Contaminated Aquifers: Field and Laboratory Microcosm Experimentsvar callbackToken='531E8ACDB6C8511'; var subCode='asmjournal_sub'; var OAS_sitepage = 'aem.asm.org'; This study used phylogenetic probes in hybridization analysis to (i) determine in situ microbial community structures in regions of a shallow sand aquifer that were oxygen depleted and fuel contaminated (FC) or aerobic and noncontaminated (NC) and (ii) examine alterations in microbial community structures resulting from exposure to toluene and/or electron acceptor supplementation (nitrate). The latter objective was addressed by using the NC and FC aquifer materials for anaerobic microcosm studies in which phylogenetic probe analysis was complemented by microbial activity assays. Domain probe analysis of the aquifer samples showed that the communities were predominantlyBacteria; Eucarya and Archaea were not detectable. At the phylum and subclass levels, the FC and NC aquifer material had similar relative abundance distributions of 43 to 65% β- and γ-Proteobacteria (B+G), 31 to 35% α-Proteobacteria (ALF), 15 to 18% sulfate-reducing bacteria, and 5 to 10% high G+C gram positive bacteria. Compared to that of the NC region, the community structure of the FC material differed mainly in an increased abundance of B+G relative to that of ALF. The microcosm communities were like those of the field samples in that they were predominantly Bacteria (83 to 101%) and lacked detectable Archaea but differed in that a small fraction (2 to 8%) of Eucarya was detected regardless of the treatment applied. The latter result was hypothesized to reflect enrichment of anaerobic protozoa. Addition of nitrate and/or toluene stimulated microbial activity in the microcosms, but only supplementation of toluene alone significantly altered community structures. For the NC material, the dominant subclass shifted from B+G to ALF, while in the FC microcosms 55 to 65

D/H Ratios in Lipids as a Tool to Elucidate Microbial Metabolism

Science.gov (United States)

Wijker, Reto S.; Sessions, Alex L.

2016-04-01

Large D/H fractionations have been observed in the lipids and growth water of most organisms studied today. These fractionations have generally been assumed to be constant across most biota because they originate solely from isotope effects imposed by the highly conserved lipid biosynthetic pathway. Recent data is illustrating this conclusion as incomplete. Lipids from field and laboratory samples exhibit huge variations in D/H fractionation. In environmental samples, lipids vary in δD by up to 300 ‰ and in laboratory cultures the documented variation is up to 500 ‰ within the same organism. Remarkably, the isotope fractionation appears to be correlated with the type of metabolism employed by the host organism. However, the underlying biochemical mechanisms leading to these isotopic variations are not yet fully understood. Because the largest proportion of H-bound C in fatty acids is derived directly from NADPH during biosynthesis, the original hypothesis was that large differences in the isotopic composition of NADPH, generated by different central metabolic pathways, were the primary source of D/H variation in lipids. However, recent observations indicate that this cannot be the whole story and lead us to the conclusion that additional processes must affect the isotope composition of NADPH. These processes may include the isotopic exchange of NADPH with water as well as fractionation of NADPH by transhydrogenases, interconverting NADH to NADPH by exhibiting large isotope effects. In this project, our objective is to ascertain whether D/H fractionation and these biochemical processes are correlated. We investigate correlations between cellular NADPH/NADP+ as well as NADH/NAD+ pool sizes and the D/H fractionation in a set of different microorganisms and will present the trends here. Our results will contribute to a more comprehensive understanding of the basic biological regulations over D/H fractionation and potentially enables their use as tracers and

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

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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.

Direct fed microbial supplementation repartitions host energy to the immune system.

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Qiu, R; Croom, J; Ali, R A; Ballou, A L; Smith, C D; Ashwell, C M; Hassan, H M; Chiang, C-C; Koci, M D

2012-08-01

Direct fed microbials and probiotics are used to promote health in livestock and poultry; however, their mechanism of action is still poorly understood. We previously reported that direct fed microbial supplementation in young broilers reduced ileal respiration without changing whole-body energy expenditure. The current studies were conducted to further investigate the effects of a direct fed microbial on energy metabolism in different tissues of broilers. One hundred ninety-two 1-d-old broiler chicks (16 chicks/pen) were randomly assigned to 2 dietary groups: standard control starter diet (CSD) and CSD plus direct fed microbial (DFMD; 0.3%) with 6 pens/treatment. Body weight, feed consumption, whole-body energy expenditure, organ mass, tissue respiration rates, and peripheral blood mononuclear cell (PBMC) ATP concentrations were measured to estimate changes in energy metabolism. No differences in whole body energy expenditure or BW gain were observed; however, decreased ileal O(2) respiration (P energy consumption by PBMC corresponded with an altered immune response, broilers were immunized with sheep red blood cells (SRBC) and assayed for differences in their humoral response. The DFMD-fed broilers had a faster rate of antigen specific IgG production (P direct fed microbial used in this study resulted in energy re-partitioning to the immune system and an increase in antibody production independent of changes in whole body metabolism or growth performance.

IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes.

Science.gov (United States)

Hadjithomas, Michalis; Chen, I-Min A; Chu, Ken; Huang, Jinghua; Ratner, Anna; Palaniappan, Krishna; Andersen, Evan; Markowitz, Victor; Kyrpides, Nikos C; Ivanova, Natalia N

2017-01-04

Secondary metabolites produced by microbes have diverse biological functions, which makes them a great potential source of biotechnologically relevant compounds with antimicrobial, anti-cancer and other activities. The proteins needed to synthesize these natural products are often encoded by clusters of co-located genes called biosynthetic gene clusters (BCs). In order to advance the exploration of microbial secondary metabolism, we developed the largest publically available database of experimentally verified and predicted BCs, the Integrated Microbial Genomes Atlas of Biosynthetic gene Clusters (IMG-ABC) (https://img.jgi.doe.gov/abc/). Here, we describe an update of IMG-ABC, which includes ClusterScout, a tool for targeted identification of custom biosynthetic gene clusters across 40 000 isolate microbial genomes, and a new search capability to query more than 700 000 BCs from isolate genomes for clusters with similar Pfam composition. Additional features enable fast exploration and analysis of BCs through two new interactive visualization features, a BC function heatmap and a BC similarity network graph. These new tools and features add to the value of IMG-ABC's vast body of BC data, facilitating their in-depth analysis and accelerating secondary metabolite discovery. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Transport of microbial tracers in clean and organically contaminated silica sand in laboratory columns compared with their transport in the field

International Nuclear Information System (INIS)

Weaver, Louise; Sinton, Lester W.; Pang, Liping; Dann, Rod; Close, Murray

2013-01-01

Waste disposal on land and the consequent transport of bacterial and viral pathogens in soils and aquifers are of major concern worldwide. Pathogen transport can be enhanced in the presence of organic matter due to occupation of attachment sites in the aquifer materials thus preventing pathogen attachment leading to their faster transport for longer distances. Laboratory column studies were carried out to investigate the effect of organic matter, in the form of dissolved organic carbon (DOC), on the transport of Escherichia coli and MS2 phage in saturated clean silica sand. Transport rates of these microbial tracers were also studied in a contaminated field site. Laboratory column studies showed that low concentrations (0.17 mg L −1 ) of DOC had little effect on E. coli J6-2 removal and slightly reduced the attachment of MS2 phage. After progressive conditioning of the column with DOC (1.7 mg L −1 and 17 mg L −1 ), neither E. coli J6-2 nor MS2 phage showed any attachment and recovery rates increased dramatically (up to 100%). The results suggest that DOC can affect the transport rates of microbial contaminants. For E. coli J6-2 the predominant effect appeared to be an increase in the secondary energy minimum leading to an increase in E. coli attachment initially. However, after 17 mg L −1 DOC conditioning of the silica sand no attachment of E. coli was observed as the DOC took up attachment sites in the porous media. MS2 phage appeared to be affected predominantly by out-competition of binding sites in the clean silica sand and a steady reduction in attachment was observed as the DOC conditioning increased. Field study showed a high removal of both E. coli and MS2 phage, although E. coli was removed at a lower rate than MS2 phage. In the field it is likely that a combination of effects are seen as the aquifer material will be heterogeneous in its surface nanoscale properties, demonstrated by the differing removal of E. coli and MS2 phage compared to the

Transport of microbial tracers in clean and organically contaminated silica sand in laboratory columns compared with their transport in the field

Energy Technology Data Exchange (ETDEWEB)

Weaver, Louise, E-mail: louise.weaver@esr.cri.nz; Sinton, Lester W.; Pang, Liping; Dann, Rod; Close, Murray

2013-01-15

Waste disposal on land and the consequent transport of bacterial and viral pathogens in soils and aquifers are of major concern worldwide. Pathogen transport can be enhanced in the presence of organic matter due to occupation of attachment sites in the aquifer materials thus preventing pathogen attachment leading to their faster transport for longer distances. Laboratory column studies were carried out to investigate the effect of organic matter, in the form of dissolved organic carbon (DOC), on the transport of Escherichia coli and MS2 phage in saturated clean silica sand. Transport rates of these microbial tracers were also studied in a contaminated field site. Laboratory column studies showed that low concentrations (0.17 mg L{sup −1}) of DOC had little effect on E. coli J6-2 removal and slightly reduced the attachment of MS2 phage. After progressive conditioning of the column with DOC (1.7 mg L{sup −1} and 17 mg L{sup −1}), neither E. coli J6-2 nor MS2 phage showed any attachment and recovery rates increased dramatically (up to 100%). The results suggest that DOC can affect the transport rates of microbial contaminants. For E. coli J6-2 the predominant effect appeared to be an increase in the secondary energy minimum leading to an increase in E. coli attachment initially. However, after 17 mg L{sup −1} DOC conditioning of the silica sand no attachment of E. coli was observed as the DOC took up attachment sites in the porous media. MS2 phage appeared to be affected predominantly by out-competition of binding sites in the clean silica sand and a steady reduction in attachment was observed as the DOC conditioning increased. Field study showed a high removal of both E. coli and MS2 phage, although E. coli was removed at a lower rate than MS2 phage. In the field it is likely that a combination of effects are seen as the aquifer material will be heterogeneous in its surface nanoscale properties, demonstrated by the differing removal of E. coli and MS2 phage

The microbial community of a passive biochemical reactor treating arsenic, zinc and sulfate-rich seepage

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Susan Anne Baldwin

2015-03-01

Full Text Available Sulfidogenic biochemical reactors for metal removal that use complex organic carbon have been shown to be effective in laboratory studies, but their performance in the field is highly variable. Successful operation depends on the types of microorganisms supported by the organic matrix, and factors affecting the community composition are unknown. A molecular survey of a field-based biochemical reactor that had been removing zinc and arsenic for over six years revealed that the microbial community was dominated by methanogens related to Methanocorpusculum sp. and Methanosarcina sp., which co-occurred with Bacteroidetes environmental groups, such as Vadin HA17, in places where the organic matter was more degraded. The metabolic potential for organic matter decomposition by Ruminococcaceae was prevalent in samples with more pyrolysable carbon. Rhodobium- and Hyphomicrobium-related genera within the Rhizobiales Order that have the metabolic potential for dark hydrogen fermentation and methylotrophy, and unclassified Comamonadaceae were the dominant Proteobacteria. The unclassified environmental group Sh765B-TzT-29 was an important Delta-Proteobacteria group in this BCR, that co-occurred with the dominant Rhizobiales OTUs. Organic matter degradation is one driver for shifting the microbial community composition and therefore possibly the performance of these bioreactors over time.

PCB126 modulates fecal microbial fermentation of the dietary fiber inulin

Science.gov (United States)

Exposure to environmental pollutants can alter gut microbial populations. Short-chain fatty acids (SCFAs), produced from gut microbial fermentation of dietary fibers such as inulin, exert numerous effects on host energy metabolism. SCFAs are also linked to health promoting effects, including a red...

Review of Micro/Nanotechnologies for Microbial Biosensors

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Ji Won eLim

2015-05-01

Full Text Available A microbial biosensor is an analytical device with a biologically integrated transducer that generates a measurable signal indicating the analyte concentration. This method is ideally suited for the analysis of extracellular chemicals and the environment, and for metabolic sensory-regulation. Although microbial biosensors show promise for application in various detection fields, some limitations still remain such as poor selectivity, low sensitivity, and impractical portability. To overcome such limitations, microbial biosensors have been integrated with many recently developed micro/nanotechnologies and applied to a wide range of detection purposes. This review article discusses micro/nanotechnologies that have been integrated with microbial biosensors and summarizes recent advances and the applications achieved through such novel integration. Future perspectives on the combination of micro/nanotechnologies and microbial biosensors will be discussed, and the necessary developments and improvements will be strategically deliberated.

Proteomic signatures differentiating Bacillus anthracis Sterne sporulation on soil relative to laboratory media.

Science.gov (United States)

Wunschel, D S; Hutchison, J R; Deatherage Kaiser, B L; Merkley, E D; Hess, B M; Lin, A; Warner, M G

2017-12-18

The process of sporulation is vital for the stability and infectious cycle of Bacillus anthracis. The spore is the infectious form of the organism and therefore relevant to biodefense. While the morphological and molecular events occurring during sporulation have been well studied, the influence of growth medium and temperature on the proteins expressed in sporulated cultures is not well understood. Understanding the features of B. anthracis sporulation specific to natural vs. laboratory production will address an important question in microbial forensics. In an effort to bridge this knowledge gap, a system for sporulation on two types of agar-immobilized soils was used for comparison to cultures sporulated on two common types of solid laboratory media, and one liquid sporulation medium. The total number of proteins identified as well as their identity differed between samples generated in each medium and growth temperature, demonstrating that sporulation environment significantly impacts the protein content of the spore. In addition, a subset of proteins common in all of the soil-cultivated samples was distinct from the expression profiles in laboratory medium (and vice versa). These differences included proteins involved in thiamine and phosphate metabolism in the sporulated cultures produced on soils with a notable increase in expression of ATP binding cassette (ABC) transporters annotated to be for phosphate and antimicrobial peptides. A distinct set of ABC transporters for amino acids, sugars and oligopeptides were found in cultures produced on laboratory media as well as increases in carbon and amino acid metabolism-related proteins. These protein expression changes indicate that the sporulation environment impacts the protein profiles in specific ways that are reflected in the metabolic and membrane transporter proteins present in sporulated cultures.

Genome-scale biological models for industrial microbial systems.

Science.gov (United States)

Xu, Nan; Ye, Chao; Liu, Liming

2018-04-01

The primary aims and challenges associated with microbial fermentation include achieving faster cell growth, higher productivity, and more robust production processes. Genome-scale biological models, predicting the formation of an interaction among genetic materials, enzymes, and metabolites, constitute a systematic and comprehensive platform to analyze and optimize the microbial growth and production of biological products. Genome-scale biological models can help optimize microbial growth-associated traits by simulating biomass formation, predicting growth rates, and identifying the requirements for cell growth. With regard to microbial product biosynthesis, genome-scale biological models can be used to design product biosynthetic pathways, accelerate production efficiency, and reduce metabolic side effects, leading to improved production performance. The present review discusses the development of microbial genome-scale biological models since their emergence and emphasizes their pertinent application in improving industrial microbial fermentation of biological products.

Final Scientific/Technical Report, DE-FG02-06ER64171, Integrated Nucleic Acid System for In-Field Monitoring of Microbial Community Dynamics and Metabolic Activity – Subproject to Co-PI Eric E. Roden

Energy Technology Data Exchange (ETDEWEB)

Eric E. Roden

2009-07-08

This report summarizes research conducted in conjunction with a project entitled “Integrated Nucleic Acid System for In-Field Monitoring of Microbial Community Dynamics and Metabolic Activity”, which was funded through the Integrative Studies Element of the former NABIR Program (now the Environmental Remediation Sciences Program) within the Office of Biological and Environmental Research. Dr. Darrell Chandler (originally at Argonne National Laboratory, now with Akonni Biosystems) was the overall PI/PD for the project. The overall project goals were to (1) apply a model iron-reducer and sulfate-reducer microarray and instrumentation systems to sediment and groundwater samples from the Scheibe et al. FRC Area 2 field site, UMTRA sediments, and other DOE contaminated sites; (2) continue development and expansion of a 16S rRNA/rDNA¬-targeted probe suite for microbial community dynamics as new sequences are obtained from DOE-relevant sites; and (3) address the fundamental molecular biology and analytical chemistry associated with the extraction, purification and analysis of functional genes and mRNA in environmental samples. Work on the UW subproject focused on conducting detailed batch and semicontinuous culture reactor experiments with uranium-contaminated FRC Area 2 sediment. The reactor experiments were designed to provide coherent geochemical and microbiological data in support of microarray analyses of microbial communities in Area 2 sediments undergoing biostimulation with ethanol. A total of four major experiments were conducted (one batch and three semicontinuous culture), three of which (the batch and two semicontinuous culture) provided samples for DNA microarray analysis. A variety of other molecular analyses (clone libraries, 16S PhyloChip, RT-PCR, and T-RFLP) were conducted on parallel samples from the various experiments in order to provide independent information on microbial community response to biostimulation.

New microbial resource: microbial diversity, function and dynamics in Chinese liquor starter.

Science.gov (United States)

Huang, Yuhong; Yi, Zhuolin; Jin, Yanling; Zhao, Yonggui; He, Kaize; Liu, Dayu; Zhao, Dong; He, Hui; Luo, Huibo; Zhang, Wenxue; Fang, Yang; Zhao, Hai

2017-11-06

Traditional Chinese liquor (Baijiu) solid state fermentation technology has lasted for several thousand years. The microbial communities that enrich in liquor starter are important for fermentation. However, the microbial communities are still under-characterized. In this study, 454 pyrosequencing technology was applied to comprehensively analyze the microbial diversity, function and dynamics of two most-consumed liquor starters (Jiang- and Nong-flavor) during production. In total, 315 and 83 bacterial genera and 72 and 47 fungal genera were identified in Jiang- and Nong-flavor liquor starter, respectively. The relatively high diversity was observed when the temperature increased to 70 and 62 °C for Jiang- and Nong-flavor liquor starter, respectively. Some thermophilic fungi have already been isolated. Microbial communities that might contribute to ethanol fermentation, saccharification and flavor development were identified and shown to be core communities in correlation-based network analysis. The predictively functional profile of bacterial communities showed significant difference in energy, carbohydrate and amino acid metabolism and the degradation of aromatic compounds between the two kinds of liquor starters. Here we report these liquor starters as a new functionally microbial resource, which can be used for discovering thermophilic and aerobic enzymes and for food and feed preservation.

Long-term oil contamination causes similar changes in microbial communities of two distinct soils.

Science.gov (United States)

Liao, Jingqiu; Wang, Jie; Jiang, Dalin; Wang, Michael Cai; Huang, Yi

2015-12-01

Since total petroleum hydrocarbons (TPH) are toxic and persistent in environments, studying the impact of oil contamination on microbial communities in different soils is vital to oil production engineering, effective soil management and pollution control. This study analyzed the impact of oil contamination on the structure, activity and function in carbon metabolism of microbial communities of Chernozem soil from Daqing oil field and Cinnamon soil from Huabei oil field through both culture-dependent techniques and a culture-independent technique-pyrosequencing. Results revealed that pristine microbial communities in these two soils presented disparate patterns, where Cinnamon soil showed higher abundance of alkane, (polycyclic aromatic hydrocarbons) PAHs and TPH degraders, number of cultivable microbes, bacterial richness, bacterial biodiversity, and stronger microbial activity and function in carbon metabolism than Chernozem soil. It suggested that complicated properties of microbes and soils resulted in the difference in soil microbial patterns. However, the changes of microbial communities caused by oil contamination were similar in respect of two dominant phenomena. Firstly, the microbial community structures were greatly changed, with higher abundance, higher bacterial biodiversity, occurrence of Candidate_division_BRC1 and TAO6, disappearance of BD1-5 and Candidate_division_OD1, dominance of Streptomyces, higher percentage of hydrocarbon-degrading groups, and lower percentage of nitrogen-transforming groups. Secondly, microbial activity and function in carbon metabolism were significantly enhanced. Based on the characteristics of microbial communities in the two soils, appropriate strategy for in situ bioremediation was provided for each oil field. This research underscored the usefulness of combination of culture-dependent techniques and next-generation sequencing techniques both to unravel the microbial patterns and understand the ecological impact of

Integrated co-regulation of bacterial arsenic and phosphorus metabolisms.

Science.gov (United States)

Kang, Yoon-Suk; Heinemann, Joshua; Bothner, Brian; Rensing, Christopher; McDermott, Timothy R

2012-12-01

Arsenic ranks first on the US Environmental Protection Agency Superfund List of Hazardous Substances. Its mobility and toxicity depend upon chemical speciation, which is significantly driven by microbial redox transformations. Genome sequence-enabled surveys reveal that in many microorganisms genes essential to arsenite (AsIII) oxidation are located immediately adjacent to genes coding for functions associated with phosphorus (Pi) acquisition, implying some type of functional importance to the metabolism of As, Pi or both. We extensively document how expression of genes key to AsIII oxidation and the Pi stress response are intricately co-regulated in the soil bacterium Agrobacterium tumefaciens. These observations significantly expand our understanding of how environmental factors influence microbial AsIII metabolism and contribute to the current discussion of As and P metabolism in the microbial cell. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Microbial Propionic Acid Production

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R. Axayacatl Gonzalez-Garcia

2017-05-01

Full Text Available Propionic acid (propionate is a commercially valuable carboxylic acid produced through microbial fermentation. Propionic acid is mainly used in the food industry but has recently found applications in the cosmetic, plastics and pharmaceutical industries. Propionate can be produced via various metabolic pathways, which can be classified into three major groups: fermentative pathways, biosynthetic pathways, and amino acid catabolic pathways. The current review provides an in-depth description of the major metabolic routes for propionate production from an energy optimization perspective. Biological propionate production is limited by high downstream purification costs which can be addressed if the target yield, productivity and titre can be achieved. Genome shuffling combined with high throughput omics and metabolic engineering is providing new opportunities, and biological propionate production is likely to enter the market in the not so distant future. In order to realise the full potential of metabolic engineering and heterologous expression, however, a greater understanding of metabolic capabilities of the native producers, the fittest producers, is required.

Engineering microbial consortia for controllable outputs

Energy Technology Data Exchange (ETDEWEB)

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

2016-03-11

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

Characterization of microbial metabolism of Syrah grape products in an in vitro colon model using targeted and non-targeted analytical approaches.

Science.gov (United States)

Aura, Anna-Marja; Mattila, Ismo; Hyötyläinen, Tuulia; Gopalacharyulu, Peddinti; Cheynier, Veronique; Souquet, Jean-Marc; Bes, Magali; Le Bourvellec, Carine; Guyot, Sylvain; Orešič, Matej

2013-03-01

Syrah red grapes are used in the production of tannin-rich red wines. Tannins are high molecular weight molecules, proanthocyanidins (PAs), and poorly absorbed in the upper intestine. In this study, gut microbial metabolism of Syrah grape phenolic compounds was investigated. Syrah grape pericarp was subjected to an enzymatic in vitro digestion model, and red wine and grape skin PA fraction were prepared. Microbial conversion was screened using an in vitro colon model with faecal microbiota, by measurement of short-chain fatty acids by gas chromatography (GC) and microbial phenolic metabolites using GC with mass detection (GC-MS). Red wine metabolites were further profiled using two-dimensional GC mass spectrometry (GCxGC-TOFMS). In addition, the effect of PA structure and dose on conversion efficiency was investigated by GC-MS. Red wine exhibited a higher degree of C1-C3 phenolic acid formation than PA fraction or grape pericarp powders. Hydroxyphenyl valeric acid (flavanols and PAs as precursors) and 3,5-dimethoxy-4-hydroxybenzoic acid (anthocyanin as a precursor) were identified from the red wine metabolite profile. In the absence of native grape pericarp or red wine matrix, the isolated PAs were found to be effective in the dose-dependent inhibition of microbial conversions and short-chain fatty acid formation. Metabolite profiling was complementary to targeted analysis. The identified metabolites had biological relevance, because the structures of the metabolites resembled fragments of their grape phenolic precursors or were in agreement with literature data.

Distance-dependent varieties of microbial community structure and metabolic functions in the rhizosphere of Sedum alfredii Hance during phytoextraction of a cadmium-contaminated soil.

Science.gov (United States)

Yang, Wenhao; Zhang, Taoxiang; Lin, Sen; Ni, Wuzhong

2017-06-01

The recovery of microbial community and activities is crucial to the remediation of contaminated soils. Distance-dependent variations of microbial community composition and metabolic characteristics in the rhizospheric soil of hyperaccumulator during phytoextraction are poorly understood. A 12-month phytoextraction experiment with Sedum alfredii in a Cd-contaminated soil was conducted. A pre-stratified rhizobox was used for separating sub-layer rhizospheric (0-2, 2-4, 4-6, 6-8, 8-10 mm from the root mat)/bulk soils. Soil microbial structure and function were analyzed by phospholipid fatty acid (PLFA) and MicroResp™ methods. The concentrations of total and specified PLFA biomarkers and the utilization rates for the 14 substrates (organic carbon) in the 0-2-mm sub-layer rhizospheric soil were significantly increased, as well as decreased with the increase in the distance from the root mat. Microbial structure measured by the ratios of different groups of PLFAs such as fungal/bacterial, monounsaturated/saturated, ratios of Gram-positive to Gram-negative (GP/GN) bacterial, and cyclopropyl/monoenoic precursors and 19:0 cyclo/18:1ω7c were significantly changed in the 0-2-mm soil. The PLFA contents and substrate utilization rates were negatively correlated with pH and total, acid-soluble, and reducible fractions of Cd, while positively correlated with labile carbon. The dynamics of microbial community were likely due to root exudates and Cd uptake by S. alfredii. This study revealed the stimulations and gradient changes of rhizosphere microbial community through phytoextraction, as reduced Cd concentration, pH, and increased labile carbons are due to the microbial community responses.

Metabolic engineering in methanotrophic bacteria

Energy Technology Data Exchange (ETDEWEB)

Kalyuzhnaya, MG; Puri, AW; Lidstrom, ME

2015-05-01

Methane, as natural gas or biogas, is the least expensive source of carbon for (bio)chemical synthesis. Scalable biological upgrading of this simple alkane to chemicals and fuels can bring new sustainable solutions to a number of industries with large environmental footprints, such as natural gas/petroleum production, landfills, wastewater treatment, and livestock. Microbial biocatalysis with methane as a feedstock has been pursued off and on for almost a half century, with little enduring success. Today, biological engineering and systems biology provide new opportunities for metabolic system modulation and give new optimism to the concept of a methane-based bio-industry. Here we present an overview of the most recent advances pertaining to metabolic engineering of microbial methane utilization. Some ideas concerning metabolic improvements for production of acetyl-CoA and pyruvate, two main precursors for bioconversion, are presented. We also discuss main gaps in the current knowledge of aerobic methane utilization, which must be solved in order to release the full potential of methane-based biosystems. (C) 2015 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Patterns of nutrient utilization. Implications for nitrogen metabolism

International Nuclear Information System (INIS)

Oldham, J.D.

1983-01-01

Nutrients react within both the rumen and the ruminant body, and the patterns of availability of different nutrients greatly influence their net utilization. In the rumen, microbial capture of N substrates, especially ammonia, depends on the degree of synchronization between rates of production of N substrates and of ATP to drive microbial protein synthesis. The form of dietary carbohydrate and of dietary N and the frequency of feeding can all affect the efficiency of microbial growth and digestion. The pattern of supply of nutrients to the body will also influence nutrient utilization. Disparities between diurnal patterns of supply of volatile fatty acids from the rumen and amino acids from the intestines will result in changes in balance of metabolic pathways. The balance between supply of glucogenic and lipogenic nutrients will influence efficiency of fattening. A major factor determining the pattern of utilization/metabolism of amino acids is the metabolic demand for protein synthesis, which varies with physiological state. (author)

Aerobic microbial dolomite at the nanometer scale : Implications for the geologic record

NARCIS (Netherlands)

Sánchez-Román, Mónica; Vasconcelos, Crisógono; Schmid, Thomas; Dittrich, Maria; McKenzie, Judith A.; Zenobi, Renato; Rivadeneyra, Maria A.

2008-01-01

Microbial experiments are the only proven approach to produce experimental dolomite under Earth's surface conditions. Although microbial metabolisms are known to induce dolomite precipitation by favoring dolomite growth kinetics, the involvement of microbes in the dolomite nucleation process is

Dissecting the genetic and metabolic mechanisms of adaptation to the knockout of a major metabolic enzyme in Escherichia coli

DEFF Research Database (Denmark)

Long, Christopher P.; Gonzalez, Jacqueline E.; Feist, Adam M.

2018-01-01

Unraveling the mechanisms of microbial adaptive evolution following genetic or environmental challenges is of fundamental interest in biological science and engineering. When the challenge is the loss of a metabolic enzyme, adaptive responses can also shed significant insight into metabolic...

Microbial metabolism alters pore water chemistry and increases consolidation of oil sands tailings.

Science.gov (United States)

Arkell, Nicholas; Kuznetsov, Petr; Kuznetsova, Alsu; Foght, Julia M; Siddique, Tariq

2015-01-01

Tailings produced during bitumen extraction from surface-mined oil sands ores (tar sands) comprise an aqueous suspension of clay particles that remain dispersed for decades in tailings ponds. Slow consolidation of the clays hinders water recovery for reuse and retards volume reduction, thereby increasing the environmental footprint of tailings ponds. We investigated mechanisms of tailings consolidation and revealed that indigenous anaerobic microorganisms altered porewater chemistry by producing CO and CH during metabolism of acetate added as a labile carbon amendment. Entrapped biogenic CO decreased tailings pH, thereby increasing calcium (Ca) and magnesium (Mg) cations and bicarbonate (HCO) concentrations in the porewater through dissolution of carbonate minerals. Soluble ions increased the porewater ionic strength, which, with higher exchangeable Ca and Mg, decreased the diffuse double layer of clays and increased consolidation of tailings compared with unamended tailings in which little microbial activity was observed. These results are relevant to effective tailings pond management strategies. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

Using ATP-driven bioluminescence assay to monitor microbial safety in a contemporary human cadaver laboratory.

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Benninger, Brion; Maier, Thomas

2015-03-01

The objective of this study was to utilize a cost-effective method for assessing the levels of bacterial, yeast, and mold activity during a human dissection laboratory course. Nowadays, compliance with safety regulations is policed by institutions at higher standards than ever before. Fear of acquiring an unknown infection is one of the top concerns of professional healthcare students, and it provokes anti-laboratory anxiety. Human cadavers are not routinely tested for bacteria and viruses prior to embalming. Human anatomy dissecting rooms that house embalmed cadavers are normally cleaned after the dissected cadavers have been removed. There is no evidence that investigators have ever assessed bacterial and fungal activities using adenosine triphosphate (ATP)-driven bioluminescence assays. A literature search was conducted on texts, journals, and websites regarding bacterial, yeast, and mold activities in an active cadaver laboratory. Midway into a clinical anatomy course, ATP bioluminescence assays were used to swab various sites within the dissection room, including entrance and exiting door handles, water taps, cadaver tables, counter tops, imaging material, X-ray box switches, and the cadaver surfaces. The results demonstrated very low activities on cadaver tables, washing up areas, and exiting door handles. There was low activity on counter tops and X-ray boxes. There was medium activity on the entrance door handles. These findings suggest an inexpensive and accurate method for monitoring safety compliance and microbial activity. Students can feel confident and safe in the environment in which they work. © 2014 Wiley Periodicals, Inc.

Investigation of microbial-mineral interactions by Moessbauer spectroscopy

International Nuclear Information System (INIS)

Sawicki, J.A.; Brown, D.A.

1998-01-01

Moessbauer spectroscopy was used to investigate the reactions of microbes with iron minerals in aqueous solutions and as components of rocks in banded iron formations and granite. A microbial biofilm that formed on a wall of an excavated granite vault in a deep underground laboratory initiated this research. At the aerobic face of the biofilm, iron was found in a form of ferrihydrite; in the anaerobic face against the rock, iron was found as very small siderite particles. Laboratory incubations of the biofilm microbial consortium showed different mineral species could be formed. When the microbial consortium from the biofilm was incubated with magnetite grains, up to about 10% of the iron was altered in three weeks to hematite. The ability of the consortium to precipitate iron both as Fe 2+ and Fe 3+ in close proximity may have a bearing on the deposition of banded iron formations. These reactions could also be important in microbially induced corrosion

Microbial bioinformatics 2020.

Science.gov (United States)

Pallen, Mark J

2016-09-01

Microbial bioinformatics in 2020 will remain a vibrant, creative discipline, adding value to the ever-growing flood of new sequence data, while embracing novel technologies and fresh approaches. Databases and search strategies will struggle to cope and manual curation will not be sustainable during the scale-up to the million-microbial-genome era. Microbial taxonomy will have to adapt to a situation in which most microorganisms are discovered and characterised through the analysis of sequences. Genome sequencing will become a routine approach in clinical and research laboratories, with fresh demands for interpretable user-friendly outputs. The "internet of things" will penetrate healthcare systems, so that even a piece of hospital plumbing might have its own IP address that can be integrated with pathogen genome sequences. Microbiome mania will continue, but the tide will turn from molecular barcoding towards metagenomics. Crowd-sourced analyses will collide with cloud computing, but eternal vigilance will be the price of preventing the misinterpretation and overselling of microbial sequence data. Output from hand-held sequencers will be analysed on mobile devices. Open-source training materials will address the need for the development of a skilled labour force. As we boldly go into the third decade of the twenty-first century, microbial sequence space will remain the final frontier! © 2016 The Author. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

The Canadian approach to microbial studies in nuclear waste management and disposal

International Nuclear Information System (INIS)

Stroes-Gascoyne, S.; Sargent, F.P.

1998-01-01

Many countries considering radioactive waste disposal have, or are considering programs to study and quantify microbial effects in terms of their particular disposal concept. Although there is an abundance of qualitative information, there is a need for quantitative data. Quantitative research should cover topics such as the kinetics of microbial activity in geological media, microbial effects on radionuclide migration in host rock (including effects of biofilms), tolerance to extreme conditions of radiation, heat and desiccation, microbially-influenced corrosion of waste containers and microbial gas production. The research should be performed in relevant disposal environments with the ultimate objective to quantify those effects that need to be included in models for predictive and safety assessment purposes. The Canadian approach to dealing with microbial effects involves a combination of pertinent, quantitative measurements from carefully designed laboratory studies and from large scale engineering experiments in AECL's Underground Research Laboratory (URL). The validity of these quantitative data is measured against observations from natural environments and analogues. An example is the viability of microbes in clay-based scaling materials. Laboratory studies have shown that the clay content of these barriers strongly affects microbial activity and movement. This is supported by natural environment and analogue observations that show clay deposits to contain very old tree segments and dense clay lenses in sediments to contain much smaller, less diverse and less active microbial populations than more porous sediments. This approach has allowed for focused, quantitative research on microbial effects in Canada. (author)

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.

Bioremediation of hydrocarbon degradation in a petroleum-contaminated soil and microbial population and activity determination.

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Wu, Manli; Li, Wei; Dick, Warren A; Ye, Xiqiong; Chen, Kaili; Kost, David; Chen, Liming

2017-02-01

Bioremediation of hydrocarbon degradation in petroleum-polluted soil is carried out by various microorganisms. However, little information is available for the relationships between hydrocarbon degradation rates in petroleum-contaminated soil and microbial population and activity in laboratory assay. In a microcosm study, degradation rate and efficiency of total petroleum hydrocarbons (TPH), alkanes, and polycyclic aromatic hydrocarbons (PAH) in a petroleum-contaminated soil were determined using an infrared photometer oil content analyzer and a gas chromatography mass spectrometry (GC-MS). Also, the populations of TPH, alkane, and PAH degraders were enumerated by a modified most probable number (MPN) procedure, and the hydrocarbon degrading activities of these degraders were determined by the Biolog (MT2) MicroPlates assay. Results showed linear correlations between the TPH and alkane degradation rates and the population and activity increases of TPH and alkane degraders, but no correlation was observed between the PAH degradation rates and the PAH population and activity increases. Petroleum hydrocarbon degrading microbial population measured by MPN was significantly correlated with metabolic activity in the Biolog assay. The results suggest that the MPN procedure and the Biolog assay are efficient methods for assessing the rates of TPH and alkane, but not PAH, bioremediation in oil-contaminated soil in laboratory. Copyright © 2016 Elsevier Ltd. All rights reserved.

Predictive tools for the evaluation of microbial effects on drugs during gastrointestinal passage.

Science.gov (United States)

Pieper, Ines A; Bertau, Martin

2010-06-01

Predicting drug metabolism after oral administration is highly complex, yet indispensable. Hitherto, drug metabolism mainly focuses on hepatic processes. In the intestine, drug molecules encounter the metabolic activity of microorganisms prior to absorption through the gut wall. Drug biotransformation through the gastrointestinal microflora has the potential to evoke serious problems because the metabolites formed may cause unexpected and undesired side effects in patients. Hence, in the course of drug development, the question has to be addressed if microbially formed metabolites are physiologically active, pharmaceutically active or even toxic. In order to provide answers to these questions and to keep the number of laboratory tests needed low, predictive tools - in vivo as well as in silico - are invaluable. This review gives an outline of the current state of the art in the field of predicting the drug biotransformation through the gastrointestinal microflora on several levels of modelling. A comprehensive review of the literature with a thorough discussion on assets and drawbacks of the different modelling approaches. The impact of the gastrointestinal drug biotransformation on patients' health will grow with increasing complexity of drug entities. Predicting metabolic fates of drugs by combining in vitro and in silico models provides invaluable information which will be suitable to particularly reduce in vivo studies.

Insights from quantitative metaproteomics and protein-stable isotope probing into microbial ecology.

Science.gov (United States)

von Bergen, Martin; Jehmlich, Nico; Taubert, Martin; Vogt, Carsten; Bastida, Felipe; Herbst, Florian-Alexander; Schmidt, Frank; Richnow, Hans-Hermann; Seifert, Jana

2013-10-01

The recent development of metaproteomics has enabled the direct identification and quantification of expressed proteins from microbial communities in situ, without the need for microbial enrichment. This became possible by (1) significant increases in quality and quantity of metagenome data and by improvements of (2) accuracy and (3) sensitivity of modern mass spectrometers (MS). The identification of physiologically relevant enzymes can help to understand the role of specific species within a community or an ecological niche. Beside identification, relative and absolute quantitation is also crucial. We will review label-free and label-based methods of quantitation in MS-based proteome analysis and the contribution of quantitative proteome data to microbial ecology. Additionally, approaches of protein-based stable isotope probing (protein-SIP) for deciphering community structures are reviewed. Information on the species-specific metabolic activity can be obtained when substrates or nutrients are labeled with stable isotopes in a protein-SIP approach. The stable isotopes ((13)C, (15)N, (36)S) are incorporated into proteins and the rate of incorporation can be used for assessing the metabolic activity of the corresponding species. We will focus on the relevance of the metabolic and phylogenetic information retrieved with protein-SIP studies and for detecting and quantifying the carbon flux within microbial consortia. Furthermore, the combination of protein-SIP with established tools in microbial ecology such as other stable isotope probing techniques are discussed.

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

Science.gov (United States)

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

Microbial biosensors for environmental monitoring

Directory of Open Access Journals (Sweden)

David VOGRINC

2015-12-01

Full Text Available Microbial biosensors are analytical devices capable of sensing substances in the environment due to the specific biological reaction of the microorganism or its parts. Construction of a microbial biosensor requires knowledge of microbial response to the specific analyte. Linking this response with the quantitative data, using a transducer, is the crucial step in the construction of a biosensor. Regarding the transducer type, biosensors are divided into electrochemical, optical biosensors and microbial fuel cells. The use of the proper configuration depends on the selection of the biosensing element. With the use of transgenic E. coli strains, bioluminescence or fluorescence based biosensors were developed. Microbial fuel cells enable the use of the heterogeneous microbial populations, isolated from wastewater. Different microorganisms are used for different pollutants – pesticides, heavy metals, phenolic compounds, organic waste, etc. Biosensing enables measurement of their concentration and their toxic or genotoxic effects on the microbes. Increasing environmental awareness has contributed to the increase of interest for biomonitoring. Although technologies, such as bioinformatics and genetic engineering, allow us to design complex and efficient microbial biosensors for environmental pollutants, the transfer of the laboratory work to the field still remains a problem to solve.

Soil microbial metabolic quotient (qCO2) of twelve ecosystems of Mt. Kilimanjaro

Science.gov (United States)

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

2014-05-01

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

Available nitrogen is the key factor influencing soil microbial functional gene diversity in tropical rainforest.

Science.gov (United States)

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

2015-08-20

Tropical rainforests cover over 50% of all known plant and animal species and provide a variety of key resources and ecosystem services to humans, largely mediated by metabolic activities of soil microbial communities. A deep analysis of soil microbial communities and their roles in ecological processes would improve our understanding on biogeochemical elemental cycles. However, soil microbial functional gene diversity in tropical rainforests and causative factors remain unclear. GeoChip, contained almost all of the key functional genes related to biogeochemical cycles, could be used as a specific and sensitive tool for studying microbial gene diversity and metabolic potential. In this study, soil microbial functional gene diversity in tropical rainforest was analyzed by using GeoChip technology. Gene categories detected in the tropical rainforest soils were related to different biogeochemical processes, such as carbon (C), nitrogen (N) and phosphorus (P) cycling. The relative abundance of genes related to C and P cycling detected mostly derived from the cultured bacteria. C degradation gene categories for substrates ranging from labile C to recalcitrant C were all detected, and gene abundances involved in many recalcitrant C degradation gene categories were significantly (P rainforest. Soil available N could be the key factor in shaping the soil microbial functional gene structure and metabolic potential.

Imaging microbial metal metabolism in situ under conditions of the deep-sea hydrothermal vents

Science.gov (United States)

Oger, P. M.; Daniel, I.; Simionovici, A.; Picard, A.

2006-12-01

High-pressure biotopes are the most widely spread biotopes on Earth. They represent one possible location for the origin of life. They also share striking similarities with extraterrestrial biotopes such as those postulated for Europe or Mars. In absence of light, dissimilatory reduction of metals (DMR) is fueling the ecosystem. Monitoring the metabolism of the deep-sea hydrothermal vent microbial fauna under P, T and chemical conditions relevant to their isolation environment can be difficult because of the confinement and because most spectroscopic probes do not sense metallic ions in solution. We demonstrated the possibility to use Xray spectroscopy to monitor the speciation of metallic species in solution. Experiments were performed at The ESRF using Selenium (Se) detoxification by Agrobacterium tumefaciens as an analog of DMR. The reduction of Se from selenite to the metal was monitored by a combiantion of two Xray spectroscopic techniques (XANES and μXRF). Cells were incubated in the low pressure DAC in growth medium supplemented with 5mM Selenite and incubated under pressures up to 60 Mpa at 30°C for 24h. The evolution of the speciation can be easily monitored and the concentration of each Se species determined from the Xray spectra by linear combinations of standard spectra. Selenite is transformed by the bacterium into a mixture of metal Se and methylated Se after 24 hours. Se detoxification is observed in situ up to at least 25 MPa. The technique, developped for Se can be adapted to monitor other elements more relevant to DMR such as As, Fe or S, which should allow to monitor in situ under controlled pressure and temperature the metabolism of vent organisms. It is also amenable to the monitoring of toxic metals. Xray spectroscopy and the lpDAC are compatible with other spectroscopic techniques, such as Raman, UV or IR spectroscopies, allowing to probe other metabolic activities. Hence, enlarging the range of metabolic information that can be obtained in

Characterization of microbial communities in former neutral uranium mines in Saxony and studies on the microbial immobilization of uranium and arsenic

International Nuclear Information System (INIS)

Gagell, Corinna

2015-01-01

applied in addition to the DNA based approach indicated that detected and dominant microorganisms (Bacteria as well as Archaea) in planktonic communities from Schlema and in biofilms were metabolically active. In the planktonic community from Zobes greater abundances were determined for Verrucomicrobia, Acidobacteria, and Alphaproteobacteria compared to data from the DNA based analysis. However, the meaning of these results remains open. Investigations on the microbial metabolic potential of planktonic communities by CFU and MPN analyses revealed that microorganisms of all uranium mines covered a broad range of anaerobic reactions (reduction of nitrate, iron, manganese, arsenate and sulfate as well as acetogenesis) under laboratory conditions. In good agreement with sequencing results methanogenic Archaea were only detected in flood water from Poehla and Zobes. The metaproteomic analysis revealed that 61,6% of analyzed peptides in the planktonic community of Schlema originated from dominant Epsilonproteobacteria. Whereas for Zobes the majority of detected peptides were assigned to methylotrophic and iron oxidizing Betaproteobacteria of the families Methylophilaceae and Gallionellaceae, respectively, as well as methylotrophic Gammaproteobacteria of Methylococcaceae. Although the majority of proteins was related to translation, a total of 49 protein groups was determined with relevance for energy metabolism. Especially Gammaproteobacteria from Zobes have been associated with carbon and sulfur cycle. The potential influence of microbial communities from Schlema on the mobility of arsenic and uranium in flood water was analyzed by means of laboratory microcosms and acetate as electron donor under anaerobic conditions over a period of 98 days. In comparison to controls the stimulated planktonic community as well as biofilms were capable to remove almost all of the natural arsenic from the aqueous phase. However, the subsequent increase of dissolved arsenic indicated that the

Soil ecology of a rock outcrop ecosystem: Abiotic stresses, soil respiration, and microbial community profiles in limestone cedar glades

Science.gov (United States)

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

2015-01-01

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

Microbial production of value-added nutraceuticals.

Science.gov (United States)

Wang, Jian; Guleria, Sanjay; Koffas, Mattheos Ag; Yan, Yajun

2016-02-01

Nutraceuticals are important natural bioactive compounds that confer health-promoting and medical benefits to humans. Globally growing demands for value-added nutraceuticals for prevention and treatment of human diseases have rendered nutraceuticals a multi-billion dollar market. However, supply limitations and extraction difficulties from natural sources such as plants, animals or fungi, restrict the large-scale use of nutraceuticals. Metabolic engineering via microbial production platforms has been advanced as an eco-friendly alternative approach for production of value-added nutraceuticals from simple carbon sources. Microbial platforms like the most widely used Escherichia coli and Saccharomyces cerevisiae have been engineered as versatile cell factories for production of diverse and complex value-added chemicals such as phytochemicals, prebiotics, polysaccaharides and poly amino acids. This review highlights the recent progresses in biological production of value-added nutraceuticals via metabolic engineering approaches. Copyright © 2015 Elsevier Ltd. All rights reserved.

Salmonella source attribution based on microbial subtyping

DEFF Research Database (Denmark)

Barco, Lisa; Barrucci, Federica; Olsen, John Elmerdahl

2013-01-01

Source attribution of cases of food-borne disease represents a valuable tool for identifying and prioritizing effective food-safety interventions. Microbial subtyping is one of the most common methods to infer potential sources of human food-borne infections. So far, Salmonella microbial subtyping...... source attribution through microbial subtyping approach. It summarizes the available microbial subtyping attribution models and discusses the use of conventional phenotypic typing methods, as well as of the most commonly applied molecular typing methods in the European Union (EU) laboratories...

Microbial functional diversity plays an important role in the degradation of polyhydroxybutyrate (PHB) in soil.

Science.gov (United States)

Dey, Samrat; Tribedi, Prosun

2018-03-01

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

Marked Response in Microbial Community and Metabolism in the Ileum and Cecum of Suckling Piglets After Early Antibiotics Exposure

Directory of Open Access Journals (Sweden)

Miao Yu

2018-05-01

Full Text Available In modern swine husbandry systems, antibiotics have been used as growth promoters for piglets during suckling or weaning period. However, while early colonization of intestinal microbiota has been regarded crucial for the host’s later life performance and well-being, little is known about the impact of antibiotics on intestinal microbiota in suckling piglets. The present study aimed to investigate the effects of early antibiotics exposure on gut microbiota and microbial metabolism of suckling piglets. Sixteen litters of suckling piglets were fed a creep feed diet with (Antibiotic or without (Control antibiotics from postnatal days 7–23 (n = 8. The ileal and cecal digesta were obtained for microbial composition and microbial metabolites analysis. The results showed that the antibiotics significantly altered the bacterial community composition by decreasing (P < 0.05 the diversity and richness in the ileum. The antibiotics significantly reduced the abundance of Lactobacillus in both the ileum and cecum, increased the abundance of Streptococcus, unclassified Enterococcaceae, unclassified Fusobacteriales, and Corynebacterium in the ileum, and the abundance of unclassified Ruminococcaceae and unclassified Erysipelotrichaceae in the cecum. The antibiotics decreased (P < 0.05 ileal lactate concentration and cecal concentration of total short-chain fatty acids (SCFAs. But the antibiotics enhanced protein fermentation (P < 0.05 in the ileum and cecum, as ileal concentrations of putrescine and cadaverine, and cecal concentrations of isobutyrate, isovalerate, putrescine, cadaverine, spermine, and spermidine were significantly increased (P < 0.05. These results indicated that early antibiotics exposure significantly altered the microbial composition of suckling piglets toward a vulnerable and unhealthy gut environment. The findings provide a new insight on the antibiotics impact on neonates and may provide new framework for designing alternatives to the

Biotechnological Processes in Microbial Amylase Production.

Science.gov (United States)

Gopinath, Subash C B; Anbu, Periasamy; Arshad, M K Md; Lakshmipriya, Thangavel; Voon, Chun Hong; Hashim, Uda; Chinni, Suresh V

2017-01-01

Amylase is an important and indispensable enzyme that plays a pivotal role in the field of biotechnology. It is produced mainly from microbial sources and is used in many industries. Industrial sectors with top-down and bottom-up approaches are currently focusing on improving microbial amylase production levels by implementing bioengineering technologies. The further support of energy consumption studies, such as those on thermodynamics, pinch technology, and environment-friendly technologies, has hastened the large-scale production of the enzyme. Herein, the importance of microbial (bacteria and fungi) amylase is discussed along with its production methods from the laboratory to industrial scales.

Microbial contamination and preservative capacity of some brands ...

African Journals Online (AJOL)

Purpose: Cosmetic and topical products need not be sterile but may contain low levels of microbial load during use. This study was conducted to determine and compare the level and type of microbial contaminants in commercial cosmetic products sold in the market and a laboratory prepared aqueous cream and their ...

Biodegradation of different petroleum hydrocarbons by free and immobilized microbial consortia.

Science.gov (United States)

Shen, Tiantian; Pi, Yongrui; Bao, Mutai; Xu, Nana; Li, Yiming; Lu, Jinren

2015-12-01

The efficiencies of free and immobilized microbial consortia in the degradation of different types of petroleum hydrocarbons were investigated. In this study, the biodegradation rates of naphthalene, phenanthrene, pyrene and crude oil reached about 80%, 30%, 56% and 48% under the optimum environmental conditions of free microbial consortia after 7 d. We evaluated five unique co-metabolic substances with petroleum hydrocarbons, α-lactose was the best co-metabolic substance among glucose, α-lactose, soluble starch, yeast powder and urea. The orthogonal biodegradation analysis results showed that semi-coke was the best immobilized carrier followed by walnut shell and activated carbon. Meanwhile, the significance of various factors that contribute to the biodegradation of semi-coke immobilized microbial consortia followed the order of: α-lactose > semi-coke > sodium alginate > CaCl2. Moreover, the degradation rate of the immobilized microbial consortium (47%) was higher than that of a free microbial consortium (26%) under environmental conditions such as the crude oil concentration of 3 g L(-1), NaCl concentration of 20 g L(-1), pH at 7.2-7.4 and temperature of 25 °C after 5 d. SEM and FTIR analyses revealed that the structure of semi-coke became more porous and easily adhered to the microbial consortium; the functional groups (e.g., hydroxy and phosphate) were identified in the microbial consortium and were changed by immobilization. This study demonstrated that the ability of microbial adaptation to the environment can be improved by immobilization which expands the application fields of microbial remediation.

Arsenic and selenium in microbial metabolism

Science.gov (United States)

Stolz, John F.; Basu, Partha; Santini, Joanne M.; Oremland, Ronald S.

2006-01-01

Arsenic and selenium are readily metabolized by prokaryotes, participating in a full range of metabolic functions including assimilation, methylation, detoxification, and anaerobic respiration. Arsenic speciation and mobility is affected by microbes through oxidation/reduction reactions as part of resistance and respiratory processes. A robust arsenic cycle has been demonstrated in diverse environments. Respiratory arsenate reductases, arsenic methyltransferases, and new components in arsenic resistance have been recently described. The requirement for selenium stems primarily from its incorporation into selenocysteine and its function in selenoenzymes. Selenium oxyanions can serve as an electron acceptor in anaerobic respiration, forming distinct nanoparticles of elemental selenium that may be enriched in (76)Se. The biogenesis of selenoproteins has been elucidated, and selenium methyltransferases and a respiratory selenate reductase have also been described. This review highlights recent advances in ecology, biochemistry, and molecular biology and provides a prelude to the impact of genomics studies.

Transitory microbial habitat in the hyperarid Atacama Desert

Science.gov (United States)

Schulze-Makuch, Dirk; Wagner, Dirk; Kounaves, Samuel P.; Mangelsdorf, Kai; Devine, Kevin G.; de Vera, Jean-Pierre; Schmitt-Kopplin, Philippe; Grossart, Hans-Peter; Parro, Victor; Kaupenjohann, Martin; Galy, Albert; Schneider, Beate; Airo, Alessandro; Frösler, Jan; Davila, Alfonso F.; Arens, Felix L.; Cáceres, Luis; Solís Cornejo, Francisco; Carrizo, Daniel; Dartnell, Lewis; DiRuggiero, Jocelyne; Flury, Markus; Ganzert, Lars; Gessner, Mark O.; Grathwohl, Peter; Guan, Lisa; Heinz, Jacob; Hess, Matthias; Keppler, Frank; Maus, Deborah; McKay, Christopher P.; Meckenstock, Rainer U.; Montgomery, Wren; Oberlin, Elizabeth A.; Probst, Alexander J.; Sáenz, Johan S.; Sattler, Tobias; Schirmack, Janosch; Sephton, Mark A.; Schloter, Michael; Uhl, Jenny; Valenzuela, Bernardita; Vestergaard, Gisle; Wörmer, Lars; Zamorano, Pedro

2018-03-01

Traces of life are nearly ubiquitous on Earth. However, a central unresolved question is whether these traces always indicate an active microbial community or whether, in extreme environments, such as hyperarid deserts, they instead reflect just dormant or dead cells. Although microbial biomass and diversity decrease with increasing aridity in the Atacama Desert, we provide multiple lines of evidence for the presence of an at times metabolically active, microbial community in one of the driest places on Earth. We base this observation on four major lines of evidence: (i) a physico-chemical characterization of the soil habitability after an exceptional rain event, (ii) identified biomolecules indicative of potentially active cells [e.g., presence of ATP, phospholipid fatty acids (PLFAs), metabolites, and enzymatic activity], (iii) measurements of in situ replication rates of genomes of uncultivated bacteria reconstructed from selected samples, and (iv) microbial community patterns specific to soil parameters and depths. We infer that the microbial populations have undergone selection and adaptation in response to their specific soil microenvironment and in particular to the degree of aridity. Collectively, our results highlight that even the hyperarid Atacama Desert can provide a habitable environment for microorganisms that allows them to become metabolically active following an episodic increase in moisture and that once it decreases, so does the activity of the microbiota. These results have implications for the prospect of life on other planets such as Mars, which has transitioned from an earlier wetter environment to today’s extreme hyperaridity.

Does canine inflammatory bowel disease influence gut microbial profile and host metabolism?

NARCIS (Netherlands)

Xu, Jia; Verbrugghe, Adronie; Lourenço, Marta; Janssens, Geert P.J.; Liu, Daisy J.X.; Wiele, Van de Tom; Eeckhaut, Venessa; Immerseel, Van Filip; Maele, Van de Isabel; Niu, Yufeng; Bosch, Guido; Junius, Greet; Wuyts, Brigitte; Hesta, Myriam

2016-01-01

Background: Inflammatory bowel disease (IBD) refers to a diverse group of chronic gastrointestinal diseases, and gut microbial dysbiosis has been proposed as a modulating factor in its pathogenesis. Several studies have investigated the gut microbial ecology of dogs with IBD but it is yet unclear

Investigation of metabolic encephalopathy

African Journals Online (AJOL)

cycle defects is the X-linked recessive disorder, ornithine ... life, or if the child is fed the compounds that they are unable .... as learning difficulties, drowsiness and avoidance of ... Table 2. Laboratory investigation of suspected metabolic encephalopathy. Laboratory .... Clinical approach to treatable inborn metabolic diseases:.

Center for Advancing Microbial Risk Assessment

Data.gov (United States)

Federal Laboratory Consortium — The Center for Advancing Microbial Risk Assessment (CAMRA), based at Michigan State University and jointly funded by the U.S. Department of Homeland Security and the...

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 respiration per unit microbial biomass increases with carbon-to-nutrient ratios in soils

Science.gov (United States)

Spohn, Marie; Chodak, Marcin

2015-04-01

The ratio of carbon-to-nutrient in forest floors is usually much higher than the ratio of carbon-to-nutrient that soil microorganisms require for their nutrition. In order to understand how this mismatch affects carbon cycling, the respiration rate per unit soil microbial biomass carbon - the metabolic quotient (qCO2) - was studied. This was done in a field study (Spohn and Chodak, 2015) and in a meta-analysis of published data (Spohn, 2014). Cores of beech, spruce, and mixed spruce-beech forest soils were cut into slices of 1 cm from the top of the litter layer down to 5 cm in the mineral soil, and the relationship between the qCO2 and the soil carbon-to-nitrogen (C:N) and the soil carbon-to-phosphorus (C:P) ratio was analyzed. We found that the qCO2 was positively correlated with soil C:N ratio in spruce soils (R = 0.72), and with the soil C:P ratio in beech (R = 0.93), spruce (R = 0.80) and mixed forest soils (R = 0.96). We also observed a close correlation between the qCO2 and the soil C concentration in all three forest types. Yet, the qCO2 decreased less with depth than the C concentration in all three forest types, suggesting that the change in qCO2 is not only controlled by the soil C concentration. We conclude that microorganisms increase their respiration rate per unit biomass with increasing soil C:P ratio and C concentration, which adjusts the substrate to their nutritional demands in terms of stoichiometry. In an analysis of literature data, I tested the effect of the C:N ratio of soil litter layers on microbial respiration in absolute terms and per unit microbial biomass C. For this purpose, a global dataset on the microbial respiration rate per unit microbial biomass C - termed the metabolic quotient (qCO2) - was compiled form literature data. It was found that the qCO2 in the soil litter layers was positively correlated with the litter C:N ratio and negatively related with the litter nitrogen (N) concentration. The positive relation between the qCO2

Reconstructing each cell's genome within complex microbial communities-dream or reality?

Science.gov (United States)

Clingenpeel, Scott; Clum, Alicia; Schwientek, Patrick; Rinke, Christian; Woyke, Tanja

2014-01-01

As the vast majority of microorganisms have yet to be cultivated in a laboratory setting, access to their genetic makeup has largely been limited to cultivation-independent methods. These methods, namely metagenomics and more recently single-cell genomics, have become cornerstones for microbial ecology and environmental microbiology. One ultimate goal is the recovery of genome sequences from each cell within an environment to move toward a better understanding of community metabolic potential and to provide substrate for experimental work. As single-cell sequencing has the ability to decipher all sequence information contained in an individual cell, this method holds great promise in tackling such challenge. Methodological limitations and inherent biases however do exist, which will be discussed here based on environmental and benchmark data, to assess how far we are from reaching this goal.

The functional potential of microbial communities in hydraulic fracturing source water and produced water from natural gas extraction characterized by metagenomic sequencing.

Directory of Open Access Journals (Sweden)

Arvind Murali Mohan

Full Text Available Microbial activity in produced water from hydraulic fracturing operations can lead to undesired environmental impacts and increase gas production costs. However, the metabolic profile of these microbial communities is not well understood. Here, for the first time, we present results from a shotgun metagenome of microbial communities in both hydraulic fracturing source water and wastewater produced by hydraulic fracturing. Taxonomic analyses showed an increase in anaerobic/facultative anaerobic classes related to Clostridia, Gammaproteobacteria, Bacteroidia and Epsilonproteobacteria in produced water as compared to predominantly aerobic Alphaproteobacteria in the fracturing source water. The metabolic profile revealed a relative increase in genes responsible for carbohydrate metabolism, respiration, sporulation and dormancy, iron acquisition and metabolism, stress response and sulfur metabolism in the produced water samples. These results suggest that microbial communities in produced water have an increased genetic ability to handle stress, which has significant implications for produced water management, such as disinfection.

Phyllosphere Microbiota Composition and Microbial Community Transplantation on Lettuce Plants Grown Indoors

Science.gov (United States)

Williams, Thomas R.

2014-01-01

ABSTRACT The aerial surfaces of plants, or phyllosphere, are microbial habitats important to plant and human health. In order to accurately investigate microbial interactions in the phyllosphere under laboratory conditions, the composition of the phyllosphere microbiota should be representative of the diversity of microorganisms residing on plants in nature. We found that Romaine lettuce grown in the laboratory contained 10- to 100-fold lower numbers of bacteria than age-matched, field-grown lettuce. The bacterial diversity on laboratory-grown plants was also significantly lower and contained relatively higher proportions of Betaproteobacteria as opposed to the Gammaproteobacteria-enriched communities on field lettuce. Incubation of field-grown Romaine lettuce plants in environmental growth chambers for 2 weeks resulted in bacterial cell densities and taxa similar to those on plants in the field but with less diverse bacterial populations overall. In comparison, the inoculation of laboratory-grown Romaine lettuce plants with either freshly collected or cryopreserved microorganisms recovered from field lettuce resulted in the development of a field-like microbiota on the lettuce within 2 days of application. The survival of an inoculated strain of Escherichia coli O157:H7 was unchanged by microbial community transfer; however, the inoculation of E. coli O157:H7 onto those plants resulted in significant shifts in the abundance of certain taxa. This finding was strictly dependent on the presence of a field-associated as opposed to a laboratory-associated microbiota on the plants. Phyllosphere microbiota transplantation in the laboratory will be useful for elucidating microbial interactions on plants that are important to agriculture and microbial food safety. PMID:25118240

Microbial synthesis of alka(enes

Directory of Open Access Journals (Sweden)

Weihua eWang

2013-10-01

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

Microbial metabolomics in open microscale platforms

Science.gov (United States)

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

2016-01-01

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

Association between degradation of pharmaceuticals and endocrine-disrupting compounds and microbial communities along a treated wastewater effluent gradient in Lake Mead

Science.gov (United States)

Blunt, Susanna M.; Sackett, Joshua D.; Rosen, Michael R.; Benotti, Mark J.; Trenholm, Rebecca A.; Vanderford, Brett J.; Hedlund, Brian P.; Moser, Duane P.

2018-01-01

The role of microbial communities in the degradation of trace organic contaminants in the environment is little understood. In this study, the biotransformation potential of 27 pharmaceuticals and endocrine-disrupting compounds was examined in parallel with a characterization of the native microbial community in water samples from four sites variously impacted by urban run-off and wastewater discharge in Lake Mead, Nevada and Arizona, USA. Samples included relatively pristine Colorado River water at the upper end of the lake, nearly pure tertiary-treated municipal wastewater entering via the Las Vegas Wash, and waters of mixed influence (Las Vegas Bay and Boulder Basin), which represented a gradient of treated wastewater effluent impact. Microbial diversity analysis based on 16S rRNA gene censuses revealed the community at this site to be distinct from the less urban-impacted locations, although all sites were similar in overall diversity and richness. Similarly, Biolog EcoPlate assays demonstrated that the microbial community at Las Vegas Wash was the most metabolically versatile and active. Organic contaminants added as a mixture to laboratory microcosms were more rapidly and completely degraded in the most wastewater-impacted sites (Las Vegas Wash and Las Vegas Bay), with the majority exhibiting shorter half-lives than at the other sites or in a bacteriostatic control. Although the reasons for enhanced degradation capacity in the wastewater-impacted sites remain to be established, these data are consistent with the acclimatization of native microorganisms (either through changes in community structure or metabolic regulation) to effluent-derived trace contaminants. This study suggests that in urban, wastewater-impacted watersheds, prior exposure to organic contaminants fundamentally alters the structure and function of microbial communities, which in turn translates into greater potential for the natural attenuation of these compounds compared to more pristine

Engineering microbial cell factories for the production of plant natural products: from design principles to industrial-scale production.

Science.gov (United States)

Liu, Xiaonan; Ding, Wentao; Jiang, Huifeng

2017-07-19

Plant natural products (PNPs) are widely used as pharmaceuticals, nutraceuticals, seasonings, pigments, etc., with a huge commercial value on the global market. However, most of these PNPs are still being extracted from plants. A resource-conserving and environment-friendly synthesis route for PNPs that utilizes microbial cell factories has attracted increasing attention since the 1940s. However, at the present only a handful of PNPs are being produced by microbial cell factories at an industrial scale, and there are still many challenges in their large-scale application. One of the challenges is that most biosynthetic pathways of PNPs are still unknown, which largely limits the number of candidate PNPs for heterologous microbial production. Another challenge is that the metabolic fluxes toward the target products in microbial hosts are often hindered by poor precursor supply, low catalytic activity of enzymes and obstructed product transport. Consequently, despite intensive studies on the metabolic engineering of microbial hosts, the fermentation costs of most heterologously produced PNPs are still too high for industrial-scale production. In this paper, we review several aspects of PNP production in microbial cell factories, including important design principles and recent progress in pathway mining and metabolic engineering. In addition, implemented cases of industrial-scale production of PNPs in microbial cell factories are also highlighted.

Data-driven integration of genome-scale regulatory and metabolic network models

Science.gov (United States)

Imam, Saheed; Schäuble, Sascha; Brooks, Aaron N.; Baliga, Nitin S.; Price, Nathan D.

2015-01-01

Microbes are diverse and extremely versatile organisms that play vital roles in all ecological niches. Understanding and harnessing microbial systems will be key to the sustainability of our planet. One approach to improving our knowledge of microbial processes is through data-driven and mechanism-informed computational modeling. Individual models of biological networks (such as metabolism, transcription, and signaling) have played pivotal roles in driving microbial research through the years. These networks, however, are highly interconnected and function in concert—a fact that has led to the development of a variety of approaches aimed at simulating the integrated functions of two or more network types. Though the task of integrating these different models is fraught with new challenges, the large amounts of high-throughput data sets being generated, and algorithms being developed, means that the time is at hand for concerted efforts to build integrated regulatory-metabolic networks in a data-driven fashion. In this perspective, we review current approaches for constructing integrated regulatory-metabolic models and outline new strategies for future development of these network models for any microbial system. PMID:25999934

Biotechnological Processes in Microbial Amylase Production

Directory of Open Access Journals (Sweden)

Subash C. B. Gopinath

2017-01-01

Full Text Available Amylase is an important and indispensable enzyme that plays a pivotal role in the field of biotechnology. It is produced mainly from microbial sources and is used in many industries. Industrial sectors with top-down and bottom-up approaches are currently focusing on improving microbial amylase production levels by implementing bioengineering technologies. The further support of energy consumption studies, such as those on thermodynamics, pinch technology, and environment-friendly technologies, has hastened the large-scale production of the enzyme. Herein, the importance of microbial (bacteria and fungi amylase is discussed along with its production methods from the laboratory to industrial scales.

Microbial network for waste activated sludge cascade utilization in an integrated system of microbial electrolysis and anaerobic fermentation

DEFF Research Database (Denmark)

Liu, Wenzong; He, Zhangwei; Yang, Chunxue

2016-01-01

in an integrated system of microbial electrolysis cell (MEC) and anaerobic digestion (AD) for waste activated sludge (WAS). Microbial communities in integrated system would build a thorough energetic and metabolic interaction network regarding fermentation communities and electrode respiring communities...... to Firmicutes (Acetoanaerobium, Acetobacterium, and Fusibacter) showed synergistic relationship with exoelectrogensin the degradation of complex organic matter or recycling of MEC products (H2). High protein and polysaccharide but low fatty acid content led to the dominance of Proteiniclasticum...... biofilm. The overall performance of WAS cascade utilization was substantially related to the microbial community structures, which in turn depended on the initial pretreatment to enhance WAS fermentation. It is worth noting that species in AD and MEC communities are able to build complex networks...

Metabolic and phylogenetic analysis of microbial communities during phytoremediation of soil contaminated with weathered hydrocarbons and heavy metals.

Science.gov (United States)

Palmroth, Marja R T; Koskinen, Perttu E P; Kaksonen, Anna H; Münster, Uwe; Pichtel, John; Puhakka, Jaakko A

2007-12-01

In the current study, the microbial ecology of weathered hydrocarbon and heavy metal contaminated soil undergoing phytoremediation was studied. The relationship of functional diversity, measured as carbon source utilisation in Biolog plates and extracellular enzymatic activities, and genetic diversity of bacteria was evaluated. Denaturing gradient gel electrophoresis was used for community analyses at the species level. Bulk soil and rhizosphere soil from pine and poplar plantations were analysed separately to determine if the plant rhizosphere impacted hydrocarbon degradation. Prevailing microbial communities in the field site were both genetically and metabolically diverse. Furthermore, both tree rhizosphere and fertilisation affected the compositions of these communities and increased activities of extracellular aminopeptidases. In addition, the abundance of alkane hydroxylase and naphthalene dioxygenase genes in the communities was low, but the prevalence of these genes was increased by the addition of bioavailable hydrocarbons. Tree rhizosphere communities had greater hydrocarbon degradation potential than those of bulk soil. Hydrocarbon utilising communities were dominated generally by the species Ralstonia eutropha and bacteria belonging to the genus Burkholderia. Despite the presence of viable hydrocarbon-degrading microbiota, decomposition of hydrocarbons from weathered hydrocarbon contaminated soil over four years, regardless of the presence of vegetation, was low in unfertilised soil. Compost addition enhanced the removal of hydrocarbons.

Duodenal histopathology and laboratory deficiencies related to bone metabolism in coeliac disease.

Science.gov (United States)

Posthumus, Lotte; Al-Toma, Abdul

2017-08-01

Coeliac disease (CD) is a chronic immune-mediated small intestine enteropathy precipitated by gluten in genetically predisposed individuals. Adult presentation is often atypical and malabsorption of vitamins and minerals is common, with a consequent disturbance of bone metabolism. We aim to evaluate laboratory deficiencies related to bone metabolism and the relationship between severity of histological damage and degree of bone mass loss at diagnosis of CD. A retrospective cross-sectional study of 176 adult coeliac patients was carried out. All patients fulfilled the histopathological criteria for CD. Biochemical data were analysed (calcium/phosphate/alkaline-phosphatase/vitamin D/parathormone). Duodenal histology was classified according to the Marsh classification. Bone mass density (BMD) at the lumbar and femoral regions measured by dual X-ray absorptiometry. A P-value of less than 0.05 was considered significant. No correlation was found between the presence of gastrointestinal symptoms and the Marsh histopathological stage (P>0.05). Vitamin D deficiency was most common (44.5%), whereas only 5.7% had hypocalcaemia. Calcium was lower (Pcoeliac patients older than 30 years, evaluation of bone biomarkers and dual X-ray absorptiometry examination should be considered.

MICROBIAL SURFACTANTS IN ENVIRONMENTAL TECHNOLOGIES

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T. P. Pirog

2015-08-01

Full Text Available It was shown literature and own experimental data concerning the use of microbial surface active glycolipids (rhamno-, sophoro- and trehalose lipids and lipopeptides for water and soil purification from oil and other hydrocarbons, removing toxic heavy metals (Cu2+, Cd2+, Ni2+, Pb2+, degradation of complex pollution (oil and other hydrocarbons with heavy metals, and the role of microbial surfactants in phytoremediation processes. The factors that limit the use of microbial surfactants in environmental technologies are discussed. Thus, at certain concentrations biosurfactant can exhibit antimicrobial properties and inhibit microorganisms destructing xenobiotics. Microbial biodegradability of surfactants may also reduce the effectiveness of bioremediation. Development of effective technologies using microbial surfactants should include the following steps: monitoring of contaminated sites to determine the nature of pollution and analysis of the autochthonous microbiota; determining the mode of surfactant introduction (exogenous addition of stimulation of surfactant synthesis by autochthonous microbiota; establishing an optimal concentration of surfactant to prevent exhibition of antimicrobial properties and rapid biodegradation; research both in laboratory and field conditions.

Microbiology Meets Archaeology: Soil Microbial Communities Reveal Different Human Activities at Archaic Monte Iato (Sixth Century BC).

Science.gov (United States)

Margesin, Rosa; Siles, José A; Cajthaml, Tomas; Öhlinger, Birgit; Kistler, Erich

2017-05-01

Microbial ecology has been recognized as useful in archaeological studies. At Archaic Monte Iato in Western Sicily, a native (indigenous) building was discovered. The objective of this study was the first examination of soil microbial communities related to this building. Soil samples were collected from archaeological layers at a ritual deposit (food waste disposal) in the main room and above the fireplace in the annex. Microbial soil characterization included abundance (cellular phospholipid fatty acids (PLFA), viable bacterial counts), activity (physiological profiles, enzyme activities of viable bacteria), diversity, and community structure (bacterial and fungal Illumina amplicon sequencing, identification of viable bacteria). PLFA-derived microbial abundance was lower in soils from the fireplace than in soils from the deposit; the opposite was observed with culturable bacteria. Microbial communities in soils from the fireplace had a higher ability to metabolize carboxylic and acetic acids, while those in soils from the deposit metabolized preferentially carbohydrates. The lower deposit layer was characterized by higher total microbial and bacterial abundance and bacterial richness and by a different carbohydrate metabolization profile compared to the upper deposit layer. Microbial community structures in the fireplace were similar and could be distinguished from those in the two deposit layers, which had different microbial communities. Our data confirmed our hypothesis that human consumption habits left traces on microbiota in the archaeological evidence; therefore, microbiological residues as part of the so-called ecofacts are, like artifacts, key indicators of consumer behavior in the past.

Microbial network of the carbonate precipitation process induced by microbial consortia and the potential application to crack healing in concrete.

Science.gov (United States)

Zhang, Jiaguang; Zhou, Aijuan; Liu, Yuanzhen; Zhao, Bowei; Luan, Yunbo; Wang, Sufang; Yue, Xiuping; Li, Zhu

2017-11-06

Current studies have employed various pure-cultures for improving concrete durability based on microbially induced carbonate precipitation (MICP). However, there have been very few reports concerned with microbial consortia, which could perform more complex tasks and be more robust in their resistance to environmental fluctuations. In this study, we constructed three microbial consortia that are capable of MICP under aerobic (AE), anaerobic (AN) and facultative anaerobic (FA) conditions. The results showed that AE consortia showed more positive effects on inorganic carbon conversion than AN and FA consortia. Pyrosequencing analysis showed that clear distinctions appeared in the community structure between different microbial consortia systems. Further investigation on microbial community networks revealed that the species in the three microbial consortia built thorough energetic and metabolic interaction networks regarding MICP, nitrate-reduction, bacterial endospores and fermentation communities. Crack-healing experiments showed that the selected cracks of the three consortia-based concrete specimens were almost completely healed in 28 days, which was consistent with the studies using pure cultures. Although the economic advantage might not be clear yet, this study highlights the potential implementation of microbial consortia on crack healing in concrete.

Microbial biofilm formation and its consequences for the CELSS program

Science.gov (United States)

Mitchell, R.

1994-01-01

A major goal of the Controlled Ecology Life Support System (CELSS) program is to provide reliable and efficient life support systems for long-duration space flights. A principal focus of the program is on the growth of higher plants in growth chambers. These crops should be grown without the risk of damage from microbial contamination. While it is unlikely that plant pathogens will pose a risk, there are serious hazards associated with microorganisms carried in the nutrient delivery systems and in the atmosphere of the growth chamber. Our experience in surface microbiology showed that colonization of surfaces with microorganisms is extremely rapid even when the inoculum is small. After initial colonization extensive biofilms accumulate on moist surfaces. These microbial films metabolize actively and slough off continuously to the air and water. During plant growth in the CELSS program, microbial biofilms have the potential to foul sensors and to plug nutrient delivery systems. In addition both metabolic products of microbial growth and degradation products of materials being considered for use as nutrient reservoirs and for delivery are likely sources of chemicals known to adversly affect plant growth.

Microbial Development and Metabolic Engineering | Bioenergy | NREL

Science.gov (United States)

Diversity Our genetically engineered microbes utilize a variety of feedstock including cellulose, xylan , syngas, simple sugars, organic acids, and carbon dioxide (CO2). We have modified the metabolic pathways

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

Science.gov (United States)

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 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

Microbial Life in an Underground Gas Storage Reservoir

Science.gov (United States)

Bombach, Petra; van Almsick, Tobias; Richnow, Hans H.; Zenner, Matthias; Krüger, Martin

2015-04-01

While underground gas storage is technically well established for decades, the presence and activity of microorganisms in underground gas reservoirs have still hardly been explored today. Microbial life in underground gas reservoirs is controlled by moderate to high temperatures, elevated pressures, the availability of essential inorganic nutrients, and the availability of appropriate chemical energy sources. Microbial activity may affect the geochemical conditions and the gas composition in an underground reservoir by selective removal of anorganic and organic components from the stored gas and the formation water as well as by generation of metabolic products. From an economic point of view, microbial activities can lead to a loss of stored gas accompanied by a pressure decline in the reservoir, damage of technical equipment by biocorrosion, clogging processes through precipitates and biomass accumulation, and reservoir souring due to a deterioration of the gas quality. We present here results from molecular and cultivation-based methods to characterize microbial communities inhabiting a porous rock gas storage reservoir located in Southern Germany. Four reservoir water samples were obtained from three different geological horizons characterized by an ambient reservoir temperature of about 45 °C and an ambient reservoir pressure of about 92 bar at the time of sampling. A complementary water sample was taken at a water production well completed in a respective horizon but located outside the gas storage reservoir. Microbial community analysis by Illumina Sequencing of bacterial and archaeal 16S rRNA genes indicated the presence of phylogenetically diverse microbial communities of high compositional heterogeneity. In three out of four samples originating from the reservoir, the majority of bacterial sequences affiliated with members of the genera Eubacterium, Acetobacterium and Sporobacterium within Clostridiales, known for their fermenting capabilities. In

Deciphering the microbial ecology in bio- gas reactors for optimizing the anaerobic digestion process

DEFF Research Database (Denmark)

Zhu, Xinyu

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

pH and Organic Carbon Dose Rates Control Microbially Driven Bioremediation Efficacy in Alkaline Bauxite Residue.

Science.gov (United States)

Santini, Talitha C; Malcolm, Laura I; Tyson, Gene W; Warren, Lesley A

2016-10-18

Bioremediation of alkaline tailings, based on fermentative microbial metabolisms, is a novel strategy for achieving rapid pH neutralization and thus improving environmental outcomes associated with mining and refining activities. Laboratory-scale bioreactors containing bauxite residue (an alkaline, saline tailings material generated as a byproduct of alumina refining), to which a diverse microbial inoculum was added, were used in this study to identify key factors (pH, salinity, organic carbon supply) controlling the rates and extent of microbially driven pH neutralization (bioremediation) in alkaline tailings. Initial tailings pH and organic carbon dose rates both significantly affected bioremediation extent and efficiency with lower minimum pHs and higher extents of pH neutralization occurring under low initial pH or high organic carbon conditions. Rates of pH neutralization (up to 0.13 mM H + produced per day with pH decreasing from 9.5 to ≤6.5 in three days) were significantly higher in low initial pH treatments. Representatives of the Bacillaceae and Enterobacteriaceae, which contain many known facultative anaerobes and fermenters, were identified as key contributors to 2,3-butanediol and/or mixed acid fermentation as the major mechanism(s) of pH neutralization. Initial pH and salinity significantly influenced microbial community successional trajectories, and microbial community structure was significantly related to markers of fermentation activity. This study provides the first experimental demonstration of bioremediation in bauxite residue, identifying pH and organic carbon dose rates as key controls on bioremediation efficacy, and will enable future development of bioreactor technologies at full field scale.

Microbial electron transport and energy conservation – the foundation for optimizing bioelectrochemical systems

Science.gov (United States)

Kracke, Frauke; Vassilev, Igor; Krömer, Jens O.

2015-01-01

Microbial electrochemical techniques describe a variety of emerging technologies that use electrode–bacteria interactions for biotechnology applications including the production of electricity, waste and wastewater treatment, bioremediation and the production of valuable products. Central in each application is the ability of the microbial catalyst to interact with external electron acceptors and/or donors and its metabolic properties that enable the combination of electron transport and carbon metabolism. And here also lies the key challenge. A wide range of microbes has been discovered to be able to exchange electrons with solid surfaces or mediators but only a few have been studied in depth. Especially electron transfer mechanisms from cathodes towards the microbial organism are poorly understood but are essential for many applications such as microbial electrosynthesis. We analyze the different electron transport chains that nature offers for organisms such as metal respiring bacteria and acetogens, but also standard biotechnological organisms currently used in bio-production. Special focus lies on the essential connection of redox and energy metabolism, which is often ignored when studying bioelectrochemical systems. The possibility of extracellular electron exchange at different points in each organism is discussed regarding required redox potentials and effect on cellular redox and energy levels. Key compounds such as electron carriers (e.g., cytochromes, ferredoxin, quinones, flavins) are identified and analyzed regarding their possible role in electrode–microbe interactions. This work summarizes our current knowledge on electron transport processes and uses a theoretical approach to predict the impact of different modes of transfer on the energy metabolism. As such it adds an important piece of fundamental understanding of microbial electron transport possibilities to the research community and will help to optimize and advance bioelectrochemical

Metabolic engineering of Bacillus subtilis fueled by systems biology: Recent advances and future directions.

Science.gov (United States)

Liu, Yanfeng; Li, Jianghua; Du, Guocheng; Chen, Jian; Liu, Long

By combining advanced omics technology and computational modeling, systems biologists have identified and inferred thousands of regulatory events and system-wide interactions of the bacterium Bacillus subtilis, which is commonly used both in the laboratory and in industry. This dissection of the multiple layers of regulatory networks and their interactions has provided invaluable information for unraveling regulatory mechanisms and guiding metabolic engineering. In this review, we discuss recent advances in the systems biology and metabolic engineering of B. subtilis and highlight current gaps in our understanding of global metabolism and global pathway engineering in this organism. We also propose future perspectives in the systems biology of B. subtilis and suggest ways that this approach can be used to guide metabolic engineering. Specifically, although hundreds of regulatory events have been identified or inferred via systems biology approaches, systematic investigation of the functionality of these events in vivo has lagged, thereby preventing the elucidation of regulatory mechanisms and further rational pathway engineering. In metabolic engineering, ignoring the engineering of multilayer regulation hinders metabolic flux redistribution. Post-translational engineering, allosteric engineering, and dynamic pathway analyses and control will also contribute to the modulation and control of the metabolism of engineered B. subtilis, ultimately producing the desired cellular traits. We hope this review will aid metabolic engineers in making full use of available systems biology datasets and approaches for the design and perfection of microbial cell factories through global metabolism optimization. Copyright © 2016 Elsevier Inc. All rights reserved.

Investigating the impact of microbial interactions with geologic media on geophysical properties

Science.gov (United States)

Davis, Caroline Ann

The goals of this study were to investigate the effect of: (1) microbial metabolic byproducts, microbial growth, and biofilm formation on the low frequency electrical properties of porous media, (2) biofilm formation on acoustic wave properties, and (3) the natural electrical (self-potential) signatures associated with an in-situ biological permeable reactive barrier (PRB). The results suggest: (1) increases in electrolytic conductivity are consistent with increased concentrations of organic acids and biosurfactants; (2) mineral weathering promoted by organic acids causes increases in electrolytic conductivity, concomitant with increases in major cation concentrations; (3) interfacial conductivity generally parallels microbial cell concentrations and biofilm formation; (4) variations in microbial growth and biofilms causes spatiotemporal heterogeneity in the elastic properties of porous media; (5) SP signatures associated with the injection of groundwater into an in-situ biological PRB are dominated by diffusion potentials induced by the injections. The results suggest that electrolytic conductivity may be useful as an indicator of metabolism, while interfacial conductivity may be used as proxy indicator for microbial growth and biofilm formation in porous media. In addition, acoustic measurements may provide diagnostic spatiotemporal data for the validation of bioclogging models/simulations. Collectively, this study provides further evidence that geophysical measurements are sensitive to microbial-induced changes to geologic media, and may be useful for the detection and monitoring of subsurface microbial growth, activity, and distribution such as in microbial enhanced oil recovery, assessing biofilm barriers used for contaminant remediation, or as sealants for reservoirs in CO2 sequestration studies.

A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems.

Science.gov (United States)

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

2017-01-01

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

Microbial enhanced oil recovery: Entering the log phase

Energy Technology Data Exchange (ETDEWEB)

Bryant, R.S.

1995-12-31

Microbial enhanced oil recovery (MEOR) technology has advanced internationally since 1980 from a laboratory-based evaluation of microbial processes to field applications. In order to adequately support the decline in oil production in certain areas, research on cost-effective technologies such as microbial enhanced oil recovery processes must focus on both near-term and long-term applications. Many marginal wells are desperately in need of an inexpensive improved oil recovery technology today that can assist producers in order to prevent their abandonment. Microbial enhanced waterflooding technology has also been shown to be an economically feasible technology in the United States. Complementary environmental research and development will also be required to address any potential environmental impacts of microbial processes. In 1995 at this conference, the goal is to further document and promote microbial processes for improved oil recovery and related technology for solving environmental problems.

Data-driven integration of genome-scale regulatory and metabolic network models

Directory of Open Access Journals (Sweden)

Saheed eImam

2015-05-01

Full Text Available Microbes are diverse and extremely versatile organisms that play vital roles in all ecological niches. Understanding and harnessing microbial systems will be key to the sustainability of our planet. One approach to improving our knowledge of microbial processes is through data-driven and mechanism-informed computational modeling. Individual models of biological networks (such as metabolism, transcription and signaling have played pivotal roles in driving microbial research through the years. These networks, however, are highly interconnected and function in concert – a fact that has led to the development of a variety of approaches aimed at simulating the integrated functions of two or more network types. Though the task of integrating these different models is fraught with new challenges, the large amounts of high-throughput data sets being generated, and algorithms being developed, means that the time is at hand for concerted efforts to build integrated regulatory-metabolic networks in a data-driven fashion. In this perspective, we review current approaches for constructing integrated regulatory-metabolic models and outline new strategies for future development of these network models for any microbial system.

Quantitative microbiome profiling links gut community variation to microbial load.

Science.gov (United States)

Vandeputte, Doris; Kathagen, Gunter; D'hoe, Kevin; Vieira-Silva, Sara; Valles-Colomer, Mireia; Sabino, João; Wang, Jun; Tito, Raul Y; De Commer, Lindsey; Darzi, Youssef; Vermeire, Séverine; Falony, Gwen; Raes, Jeroen

2017-11-23

Current sequencing-based analyses of faecal microbiota quantify microbial taxa and metabolic pathways as fractions of the sample sequence library generated by each analysis. Although these relative approaches permit detection of disease-associated microbiome variation, they are limited in their ability to reveal the interplay between microbiota and host health. Comparative analyses of relative microbiome data cannot provide information about the extent or directionality of changes in taxa abundance or metabolic potential. If microbial load varies substantially between samples, relative profiling will hamper attempts to link microbiome features to quantitative data such as physiological parameters or metabolite concentrations. Saliently, relative approaches ignore the possibility that altered overall microbiota abundance itself could be a key identifier of a disease-associated ecosystem configuration. To enable genuine characterization of host-microbiota interactions, microbiome research must exchange ratios for counts. Here we build a workflow for the quantitative microbiome profiling of faecal material, through parallelization of amplicon sequencing and flow cytometric enumeration of microbial cells. We observe up to tenfold differences in the microbial loads of healthy individuals and relate this variation to enterotype differentiation. We show how microbial abundances underpin both microbiota variation between individuals and covariation with host phenotype. Quantitative profiling bypasses compositionality effects in the reconstruction of gut microbiota interaction networks and reveals that the taxonomic trade-off between Bacteroides and Prevotella is an artefact of relative microbiome analyses. Finally, we identify microbial load as a key driver of observed microbiota alterations in a cohort of patients with Crohn's disease, here associated with a low-cell-count Bacteroides enterotype (as defined through relative profiling).

The electric picnic: synergistic requirements for exoelectrogenic microbial communities

KAUST Repository

Kiely, Patrick D

2011-06-01

Characterization of the various microbial populations present in exoelectrogenic biofilms provides insight into the processes required to convert complex organic matter in wastewater streams into electrical current in bioelectrochemical systems (BESs). Analysis of the community profiles of exoelectrogenic microbial consortia in BESs fed different substrates gives a clearer picture of the different microbial populations present in these exoelectrogenic biofilms. Rapid utilization of fermentation end products by exoelectrogens (typically Geobacter species) relieves feedback inhibition for the fermentative consortia, allowing for rapid metabolism of organics. Identification of specific syntrophic processes and the communities characteristic of these anodic biofilms will be a valuable aid in improving the performance of BESs. © 2011 Elsevier Ltd.

Feasible metabolisms in high pH springs of the Philippines.

Science.gov (United States)

Cardace, Dawn; Meyer-Dombard, D'Arcy R; Woycheese, Kristin M; Arcilla, Carlo A

2015-01-01

A field campaign targeting high pH, H2-, and CH4-emitting serpentinite-associated springs in the Zambales and Palawan Ophiolites of the Philippines was conducted in 2012-2013, and enabled description of several springs sourced in altered pillow basalts, gabbros, and peridotites. We combine field observations of pH, temperature, conductivity, dissolved oxygen, and oxidation-reduction potential with analyses of major ions, dissolved inorganic carbon, dissolved organic carbon, and dissolved gas phases in order to model the activities of selected phases important to microbial metabolism, and to rank feasible metabolic reactions based on energy yield. We document changing geochemical inventories in these springs between sampling years, and examine how the environment supports or prevents the function of certain microbial metabolisms. In all, this geochemistry-based assessment of feasible metabolisms indicates methane cycling, hydrogen oxidation, some iron and sulfur metabolisms, and ammonia oxidation are feasible reactions in this continental site of serpentinization.

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

The ability to link microbial community structure to function has long been a primary focus of environmental microbiology. With the advent of community genomic and proteomic techniques, along with advances in microscopic imaging techniques, it is now possible to gain insights into the organismal and functional makeup of microbial communities. Biofilms growing within highly acidic solutions inside the Richmond Mine (Iron Mountain, Redding, California) exhibit distinct macro- and microscopic morphologies. They are composed of microorganisms belonging to the three domains of life, including archaea, bacteria and eukarya. The proportion of each organismal type depends on sampling location and developmental stage. For example, mature biofilms floating on top of acid mine drainage (AMD) pools exhibit layers consisting of a densely packed bottom layer of the chemoautolithotroph Leptospirillum group II, a less dense top layer composed mainly of archaea, and fungal filaments spanning across the entire biofilm. The expression of cytochrome 579 (the most highly abundant protein in the biofilm, believed to be central to iron oxidation and encoded by Leptospirillum group II) is localized at the interface of the biofilm with the AMD solution, highlighting that biofilm architecture is reflected at the functional gene expression level. Distinct functional partitioning is also apparent in a biological wastewater treatment system that selects for distinct polyphosphate accumulating organisms. Community genomic data from " Candidatus Accumulibacter phosphatis" dominated activated sludge has enabled high mass-accuracy shotgun proteomics for identification of key metabolic pathways. Comprehensive genome-wide alignment of orthologous proteins suggests distinct partitioning of protein variants involved in both core-metabolism and specific metabolic pathways among the dominant population and closely related species. In addition, strain- resolved proteogenomic analysis of the AMD biofilms

Microbes at Surface-Air Interfaces: The Metabolic Harnessing of Relative Humidity, Surface Hygroscopicity, and Oligotrophy for Resilience

Science.gov (United States)

Stone, Wendy; Kroukamp, Otini; Korber, Darren R.; McKelvie, Jennifer; Wolfaardt, Gideon M.

2016-01-01

The human environment is predominantly not aqueous, and microbes are ubiquitous at the surface-air interfaces with which we interact. Yet microbial studies at surface-air interfaces are largely survival-oriented, whilst microbial metabolism has overwhelmingly been investigated from the perspective of liquid saturation. This study explored microbial survival and metabolism under desiccation, particularly the influence of relative humidity (RH), surface hygroscopicity, and nutrient availability on the interchange between these two phenomena. The combination of a hygroscopic matrix (i.e., clay or 4,000 MW polyethylene glycol) and high RH resulted in persistent measurable microbial metabolism during desiccation. In contrast, no microbial metabolism was detected at (a) hygroscopic interfaces at low RH, and (b) less hygroscopic interfaces (i.e., sand and plastic/glass) at high or low RH. Cell survival was conversely inhibited at high RH and promoted at low RH, irrespective of surface hygroscopicity. Based on this demonstration of metabolic persistence and survival inhibition at high RH, it was proposed that biofilm metabolic rates might inversely influence whole-biofilm resilience, with ‘resilience’ defined in this study as a biofilm’s capacity to recover from desiccation. The concept of whole-biofilm resilience being promoted by oligotrophy was supported in desiccation-tolerant Arthrobacter spp. biofilms, but not in desiccation-sensitive Pseudomonas aeruginosa biofilms. The ability of microbes to interact with surfaces to harness water vapor during desiccation was demonstrated, and potentially to harness oligotrophy (the most ubiquitous natural condition facing microbes) for adaptation to desiccation. PMID:27746774

Shift in the microbial community composition of surface water and sediment along an urban river.

Science.gov (United States)

Wang, Lan; Zhang, Jing; Li, Huilin; Yang, Hong; Peng, Chao; Peng, Zhengsong; Lu, Lu

2018-06-15

Urban rivers represent a unique ecosystem in which pollution occurs regularly, leading to significantly altered of chemical and biological characteristics of the surface water and sediments. However, the impact of urbanization on the diversity and structure of the river microbial community has not been well documented. As a major tributary of the Yangtze River, the Jialing River flows through many cities. Here, a comprehensive analysis of the spatial microbial distribution in the surface water and sediments in the Nanchong section of Jialing River and its two urban branches was conducted using 16S rRNA gene-based Illumina MiSeq sequencing. The results revealed distinct differences in surface water bacterial composition along the river with a differential distribution of Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes and Acidobacteria (P urban water. PICRUSt metabolic inference analysis revealed a growing number of genes associated with xenobiotic metabolism and nitrogen metabolism in the urban water, indicating that urban discharges might act as the dominant selective force to alter the microbial communities. Redundancy analysis suggested that the microbial community structure was influenced by several environmental factors. TP (P urban river. These results highlight that river microbial communities exhibit spatial variation in urban areas due to the joint influence of chemical variables associated with sewage discharging and construction of hydropower stations. Copyright © 2018 Elsevier B.V. All rights reserved.

Potential of wheat bran to promote indigenous microbial enhanced oil recovery.

Science.gov (United States)

Zhan, Yali; Wang, Qinghong; Chen, Chunmao; Kim, Jung Bong; Zhang, Hongdan; Yoza, Brandon A; Li, Qing X

2017-06-01

Microbial enhanced oil recovery (MEOR) is an emerging oil extraction technology that utilizes microorganisms to facilitate recovery of crude oil in depleted petroleum reservoirs. In the present study, effects of wheat bran utilization were investigated on stimulation of indigenous MEOR. Biostimulation conditions were optimized with the response surface methodology. The co-application of wheat bran with KNO 3 and NH 4 H 2 PO 4 significantly promoted indigenous MEOR (IMEOR) and exhibited sequential aerobic (O-), facultative (A n -) and anaerobic (A 0 -) metabolic stages. The surface tension of fermented broth decreased by approximately 35%, and the crude oil was highly emulsified. Microbial community structure varied largely among and in different IMEOR metabolic stages. Pseudomonas sp., Citrobacter sp., and uncultured Burkholderia sp. dominated the O-, A n - and early A 0 -stages. Bacillus sp., Achromobacter sp., Rhizobiales sp., Alcaligenes sp. and Clostridium sp. dominated the later A 0 -stage. This study illustrated occurrences of microbial community succession driven by wheat bran stimulation and its industrial potential.

Insights into the phylogeny and coding potential of microbial dark matter

Energy Technology Data Exchange (ETDEWEB)

Rinke, Christian; Schwientek, Patrick; Sczyrba, Alexander; Ivanova, Natalia N.; Anderson, Iain J.; Cheng, Jan-Fang; Darling, Aaron; Malfatti, Stephanie; Swan, Brandon K.; Gies, Esther A.; Dodsworth, Jeremy A.; Hedlund, Brian P.; Tsiamis, George; Sievert, Stefan M.; Liu, Wen-Tso; Eisen, Jonathan A.; Hallam, Steven J.; Kyrpides, Nikos C.; Stepanauskas, Ramunas; Rubin, Edward M.; Hugenholtz, Philip; Woyke, Tanja

2013-07-01

Genome sequencing enhances our understanding of the biological world by providing blueprints for the evolutionary and functional diversity that shapes the biosphere. However, microbial genomes that are currently available are of limited phylogenetic breadth, owing to our historical inability to cultivate most microorganisms in the laboratory. We apply single-cell genomics to target and sequence 201 uncultivated archaeal and bacterial cells fromnine diverse habitats belonging to 29 major mostly uncharted branches of the tree of life, so-called microbial dark matter. With this additional genomic information, we are able to resolve many intra- and inter-phylum-level relationships and to propose two new superphyla. We uncover unexpected metabolic features that extend our understanding of biology and challenge established boundaries between the three domains of life. These include a novel amino acid use for the opal stop codon, an archaeal-type purine synthesis in Bacteria and complete sigma factors in Archaea similar to those in Bacteria. The single-cell genomes also served to phylogenetically anchor up to 20percent of metagenomic reads in some habitats, facilitating organism-level interpretation of ecosystem function. This study greatly expands the genomic representation of the tree of life and provides a systematic step towards a better understanding of biological evolution on our planet.

COMBINED MICROBIAL SURFACTANT-POLYMER SYSTEM FOR IMPROVED OIL MOBILITY AND CONFORMANCE CONTROL

Energy Technology Data Exchange (ETDEWEB)

Jorge Gabitto; Maria Barrufet

2005-08-01

Many domestic oil fields are facing abandonment even though they still contain two-thirds of their original oil. A significant number of these fields can yield additional oil using advanced oil recovery (AOR) technologies. To maintain domestic oil production at current levels, AOR technologies are needed that are affordable and can be implemented by the independent oil producers of the future. Microbial enhanced oil recovery (MEOR) technologies have become established as cost-effective solutions for declining oil production. MEOR technologies are affordable for independent producers operating stripper wells and can be used to extend the life of marginal fields. The demonstrated versatility of microorganisms can be used to design advanced microbial systems to treat multiple production problems in complex, heterogeneous reservoirs. The proposed research presents the concept of a combined microbial surfactant-polymer system for advanced oil recovery. The surfactant-polymer system utilizes bacteria that are capable of both biosurfactant production and metabolically-controlled biopolymer production. This novel technology combines complementary mechanisms to extend the life of marginal fields and is applicable to a large number of domestic reservoirs. The research project described in this report was performed by Bio-Engineering Inc., a woman owned small business, Texas A&M University and Prairie View A&M University, a Historically Black College and University. This report describes the results of our laboratory work to grow microbial cultures, the work done on recovery experiments on core rocks, and computer simulations. We have selected two bacterial strains capable of producing both surfactant and polymers. We have conducted laboratory experiments to determine under what conditions surfactants and polymers can be produced from one single strain. We have conduct recovery experiments to determine the performance of these strains under different conditions. Our results

Metabolic Potential and Activity in Fluids of the Coast Range Ophiolite Microbial Observatory, California, USA

Science.gov (United States)

Hoehler, T.; Som, S.; Schrenk, M.; McCollom, T.; Cardace, D.

2016-01-01

Metabolic potential and activity associated with hydrogen and carbon monoxide were characterized in fluids sampled from the the Coast Range Ophiolite Microbial Observatory (CROMO). CROMO consists of two clusters of science-dedicated wells drilled to varying depths up to 35m in the actively serpentinizing, Jurassic-age Coast Range Ophiolite of Northern California, along with a suite of pre-existing monitoring wells at the same site. Consistent with the fluid chemistry observed in other serpentinizing systems, CROMO fluids are highly alkaline, with pH up to 12.5, high in methane, with concentrations up 1600 micromolar, and low in dissolved inorganic carbon (DIC), with concentrations of 10's to 100's of micromolar. CROMO is conspicuous for fluid H2 concentrations that are consistently sub-micromolar, orders of magnitude lower than is typical of other systems. However, higher H2 concentrations (10's -100's of micromolar) at an earlier stage of fluid chemical evolution are predicted by, or consistent with: thermodynamic models for fluid chemistry based on parent rock composition equivalent to local peridotite and with water:rock ratio constrained by observed pH; the presence of magnetite at several wt% in CROMO drill cores; and concentrations of formate and carbon monoxide that would require elevated H2 if formed in equilibrium with H2 and DIC. Calculated Gibbs energy changes for reaction of H2 and CO in each of several metabolisms, across the range of fluid composition encompassed by the CROMO wells, range from bioenergetically feasible (capable of driving ATP synthesis) to thermodynamically unfavorable. Active consumption relative to killed controls was observed for both CO and H2 during incubation of fluids from the pre-existing monitoring wells; in incubations of freshly cored solids, consumption was only observed in one sample set (corresponding to the lowest pH) out of three. The specific metabolisms by which H2 and CO are consumed remain to be determined.

The effects of laboratory housing and spatial enrichment on brain size and metabolic rate in the eastern mosquitofish, Gambusia holbrooki

Directory of Open Access Journals (Sweden)

Mischa P. Turschwell

2016-03-01

Full Text Available It has long been hypothesised that there is a functional correlation between brain size and metabolic rate in vertebrates. The present study tested this hypothesis in wild-caught adult mosquitofish Gambusia holbrooki by testing for an intra-specific association between resting metabolic rate (RMR and brain size while controlling for variation in body size, and through the examination of the effects of spatial enrichment and laboratory housing on body mass-independent measures of brain size and RMR. Controlling for body mass, there was no relationship between brain size and RMR in wild-caught fish. Contrary to predictions, spatial enrichment caused a decrease in mass-independent brain size, highlighting phenotypic plasticity in the adult brain. As expected, after controlling for differences in body size, wild-caught fish had relatively larger brains than fish that had been maintained in the laboratory for a minimum of six weeks, but wild-caught fish also had significantly lower mass-independent RMR. This study demonstrates that an organisms' housing environment can cause significant plastic changes to fitness related traits including brain size and RMR. We therefore conclude that current standard laboratory housing conditions may cause captive animals to be non-representative of their wild counterparts, potentially undermining the transferability of previous laboratory-based studies of aquatic ectothermic vertebrates to wild populations.

Significance, mechanisms and environmental implications of microbial bio-mineralization

International Nuclear Information System (INIS)

Benzerara, K.; Miot, J.; Morin, G.; Ona-Nguema, G.; Skouri-Panet, F.; Ferard, C.

2011-01-01

Microorganisms can mediate the formation of minerals by a process called bio-mineralization. This process offers an efficient way to sequester inorganic pollutants within relatively stable solid phases. Here we review some of the main mechanisms involved in the mediation of mineral precipitation by microorganisms. This includes supersaturation caused by metabolic activity, the triggering of nucleation by production of more or less specific organic molecules, and the impact of mineral growth. While these processes have been widely studied in the laboratory, assessment of their importance in the environment is more difficult. We illustrate this difficulty using a case study on an As-contaminated acid mine drainage located in the South of France (Carnoules, Gard). In particular, we explore the potential relationships that might exist between microbial diversity and mineral precipitation. The present review, far from being exhaustive, highlights some recent advances in the field of bio-mineralogy and provides non-specialists an introduction to some of the main approaches and some questions that remain unanswered. (authors)

Microbial analysis of the buffer/container experiment at AECL's Underground Research Laboratory

International Nuclear Information System (INIS)

Stroes-Gascoyne, S.; Hamon, C.J.; Haveman, S.A.; Delaney, T.L.

1996-05-01

The Buffer/Container experiment was carried out for 2.5 years to examine the in-situ performance of compacted buffer material in a single emplacement borehole under vault-relevant conditions. During decommissioning of this experiment, numerous samples were taken for microbial analysis to determine if the naturally present microbial population in buffer material survived to conditions and to determine which groups of microorganisms would be dominant in such a simulated vault environment. Microbial analyses were initiated within 24 hour of sampling for all types of samples taken. The culture results showed an almost universal disappearance of viable microorganisms in the samples taken from near the heater surface. The microbial activity measurements confirmed the lack of viable organisms with very weak or no activity measured in most of these samples. Generally, aerobic heterotrophic culture conditions gave the highest mean colony-forming units (CFU) values at both 25 and 50 C. Under anaerobic conditions, and especially at 50 C, lower mean CFU values were obtained. In all samples analyzed, numbers of sulfate reducing bacteria were less than 1000 CFU/g dry material. Methanogens were either not present or were found in very low numbers. Anaerobic sulfur oxidizing bacteria were found in higher numbers in most sample types with sufficient moisture. The statistical evaluation of the culture data demonstrated clearly that the water content was the variable limiting the viability of the bacteria present, and not the temperature. 68 refs, 35 figs, 37 tabs

Functional tradeoffs underpin salinity-driven divergence in microbial community composition.

Directory of Open Access Journals (Sweden)

Chris L Dupont

Full Text Available Bacterial community composition and functional potential change subtly across gradients in the surface ocean. In contrast, while there are significant phylogenetic divergences between communities from freshwater and marine habitats, the underlying mechanisms to this phylogenetic structuring yet remain unknown. We hypothesized that the functional potential of natural bacterial communities is linked to this striking divide between microbiomes. To test this hypothesis, metagenomic sequencing of microbial communities along a 1,800 km transect in the Baltic Sea area, encompassing a continuous natural salinity gradient from limnic to fully marine conditions, was explored. Multivariate statistical analyses showed that salinity is the main determinant of dramatic changes in microbial community composition, but also of large scale changes in core metabolic functions of bacteria. Strikingly, genetically and metabolically different pathways for key metabolic processes, such as respiration, biosynthesis of quinones and isoprenoids, glycolysis and osmolyte transport, were differentially abundant at high and low salinities. These shifts in functional capacities were observed at multiple taxonomic levels and within dominant bacterial phyla, while bacteria, such as SAR11, were able to adapt to the entire salinity gradient. We propose that the large differences in central metabolism required at high and low salinities dictate the striking divide between freshwater and marine microbiomes, and that the ability to inhabit different salinity regimes evolved early during bacterial phylogenetic differentiation. These findings significantly advance our understanding of microbial distributions and stress the need to incorporate salinity in future climate change models that predict increased levels of precipitation and a reduction in salinity.

Early warning system for detection of microbial contamination of source waters

DEFF Research Database (Denmark)

Mogensen, Claus Tilsted; Bentien, Anders; Lau, Mogens

2011-01-01

Ensuring chemical and microbial water quality is an ever increasing important issue world-wide. Currently, determination of microbial water quality is a time (and money) consuming manual laboratory process. We have developed and field-tested an online and real-time sensor for measuring the microb...

The biofilm ecology of microbial biofouling, biocide resistance and corrosion

Energy Technology Data Exchange (ETDEWEB)

White, D.C. [Univ. of Tennessee, Knoxville, TN (United States). Center for Environmental Biotechnology]|[Oak Ridge National Lab., TN (United States). Environmental Science Div.; Kirkegaard, R.D.; Palmer, R.J. Jr.; Flemming, C.A.; Chen, G.; Leung, K.T.; Phiefer, C.B. [Univ. of Tennessee, Knoxville, TN (United States). Center for Environmental Biotechnology; Arrage, A.A. [Univ. of Tennessee, Knoxville, TN (United States). Center for Environmental Biotechnology]|[Microbial Insights, Inc., Rockford, TN (United States)

1997-06-01

In biotechnological or bioremediation processes it is often the aim to promote biofilm formation, and maintain active, high density biomass. In other situations, biofouling can seriously restrict effective heat transport, membrane processes, and potentate macrofouling with loss of transportation efficiency. In biotechnological or bioremediation processes it is often the aim to promote biofilm formation, and maintain active, high density biomass. In other situations, biofouling can seriously restrict effective heat transport, membrane processes, and potentate macrofouling with loss of transportation efficiency. Heterogeneous distribution of microbes and/or their metabolic activity can promote microbially influenced corrosion (MIC) which is a multibillion dollar problem. Consequently, it is important that biofilm microbial ecology be understood so it can be manipulated rationally. It is usually simple to select organisms that form biofilms by flowing a considerably dilute media over a substratum, and propagating the organisms that attach. To examine the biofilm most expeditiously, the biomass accumulation, desquamation, and metabolic activities need to be monitored on-line and non-destructively. This on-line monitoring becomes even more valuable if the activities can be locally mapped in time and space within the biofilm. Herein the authors describe quantitative measures of microbial biofouling, the ecology of pathogens in drinking water distributions systems, and localization of microbial biofilms and activities with localized MIC.

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.

Emergent biosynthetic capacity in simple microbial communities.

Directory of Open Access Journals (Sweden)

Hsuan-Chao Chiu

2014-07-01

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

Evaluation of some feedstuffs with special emphasis on the effect of nitrate and other non-protein nitrogen fractions on ruminal microbial metabolism

International Nuclear Information System (INIS)

Nikolic, J.A.

1988-01-01

Green herbage grown under widely different conditions was examined for nitrate content. The mean value was 0.14% (range 0.01-0.32%) NO 3 -N in the dry matter (DM). It was concluded that the cut green fodder would induce high levels of blood methaemoglobin when fed to ruminants in mixed diets. Nevertheless, experiments in vitro indicated that relatively small amounts of dietary nitrate induced considerable microbial nitrate reducing activity in rumen contents. Moreover, nitrate reduction to ammonia was accompanied by alterations in microbial sulphur and energy metabolism. A technique for determining organic matter digestibility (OMD) in vitro was standardized and used to evaluate the potential nutritive value of some fruit wastes. Studies on apple pomace silage indicated that added urea did not significantly increase the silage protein content but remained as a potential source of non-protein nitrogen for rumen microorganisms. Apple pomace ensiled alone or preferably with other ingredients was acceptable to sheep and cattle, particularly as a supplement to their winter rations. (author). 27 refs, 2 figs, 5 tabs

Intestinal Crosstalk between Bile Acids and Microbiota and Its Impact on Host Metabolism

DEFF Research Database (Denmark)

Wahlström, Annika; Sayin, Sama I; Marschall, Hanns-Ulrich

2016-01-01

The gut microbiota is considered a metabolic "organ" that not only facilitates harvesting of nutrients and energy from the ingested food but also produces numerous metabolites that signal through their cognate receptors to regulate host metabolism. One such class of metabolites, bile acids......, is produced in the liver from cholesterol and metabolized in the intestine by the gut microbiota. These bioconversions modulate the signaling properties of bile acids via the nuclear farnesoid X receptor and the G protein-coupled membrane receptor 5, which regulate numerous metabolic pathways in the host....... Conversely, bile acids can modulate gut microbial composition both directly and indirectly through activation of innate immune genes in the small intestine. Thus, host metabolism can be affected through microbial modifications of bile acids, which lead to altered signaling via bile acid receptors, but also...

Biotechnological Applications of Microbial (Per)chlorate Reduction.

Science.gov (United States)

Wang, Ouwei; Coates, John D

2017-11-24

While the microbial degradation of a chloroxyanion-based herbicide was first observed nearly ninety years ago, only recently have researchers elucidated the underlying mechanisms of perchlorate and chlorate [collectively, (per)chlorate] respiration. Although the obvious application of these metabolisms lies in the bioremediation and attenuation of (per)chlorate in contaminated environments, a diversity of alternative and innovative biotechnological applications has been proposed based on the unique metabolic abilities of dissimilatory (per)chlorate-reducing bacteria (DPRB). This is fueled in part by the unique ability of these organisms to generate molecular oxygen as a transient intermediate of the central pathway of (per)chlorate respiration. This ability, along with other novel aspects of the metabolism, have resulted in a wide and disparate range of potential biotechnological applications being proposed, including enzymatic perchlorate detection; gas gangrene therapy; enhanced xenobiotic bioremediation; oil reservoir bio-souring control; chemostat hygiene control; aeration enhancement in industrial bioreactors; and, biogenic oxygen production for planetary exploration. While previous reviews focus on the fundamental science of microbial (per)chlorate reduction (for example see Youngblut et al., 2016), here, we provide an overview of the emerging biotechnological applications of (per)chlorate respiration and the underlying organisms and enzymes to environmental and biotechnological industries.

Application of meta-omics techniques to understand greenhouse gas emissions originating from ruminal metabolism.

Science.gov (United States)

Wallace, Robert J; Snelling, Timothy J; McCartney, Christine A; Tapio, Ilma; Strozzi, Francesco

2017-01-16

Methane emissions from ruminal fermentation contribute significantly to total anthropological greenhouse gas (GHG) emissions. New meta-omics technologies are beginning to revolutionise our understanding of the rumen microbial community structure, metabolic potential and metabolic activity. Here we explore these developments in relation to GHG emissions. Microbial rumen community analyses based on small subunit ribosomal RNA sequence analysis are not yet predictive of methane emissions from individual animals or treatments. Few metagenomics studies have been directly related to GHG emissions. In these studies, the main genes that differed in abundance between high and low methane emitters included archaeal genes involved in methanogenesis, with others that were not apparently related to methane metabolism. Unlike the taxonomic analysis up to now, the gene sets from metagenomes may have predictive value. Furthermore, metagenomic analysis predicts metabolic function better than only a taxonomic description, because different taxa share genes with the same function. Metatranscriptomics, the study of mRNA transcript abundance, should help to understand the dynamic of microbial activity rather than the gene abundance; to date, only one study has related the expression levels of methanogenic genes to methane emissions, where gene abundance failed to do so. Metaproteomics describes the proteins present in the ecosystem, and is therefore arguably a better indication of microbial metabolism. Both two-dimensional polyacrylamide gel electrophoresis and shotgun peptide sequencing methods have been used for ruminal analysis. In our unpublished studies, both methods showed an abundance of archaeal methanogenic enzymes, but neither was able to discriminate high and low emitters. Metabolomics can take several forms that appear to have predictive value for methane emissions; ruminal metabolites, milk fatty acid profiles, faecal long-chain alcohols and urinary metabolites have all

The contribution of microbial mats to the arsenic geochemistry of an ancient gold mine

International Nuclear Information System (INIS)

Drewniak, Lukasz; Maryan, Natalia; Lewandowski, Wiktor; Kaczanowski, Szymon; Sklodowska, Aleksandra

2012-01-01

The ancient Zloty Stok (SW Poland) gold mine is such an environment, where different microbial communities, able to utilize inorganic arsenic species As(III) and As(V), are found. The purpose of the present study was to (i) estimate prokaryotic diversity in the microbial mats in bottom sediments of this gold mine, (ii) identify microorganisms that can metabolize arsenic, and (iii) estimate their potential role in the arsenic geochemistry of the mine and in the environment. The oxidation/reduction experiments showed that the microbial mat community may significantly contribute to arsenic contamination in groundwater. The presence of both arsenite oxidizing and dissimilatory arsenate reducing bacteria in the mat was confirmed by the detection of arsenite oxidase and dissimilatory arsenate reductase genes, respectively. This work also demonstrated that microorganisms utilizing other compounds that naturally co-occur with arsenic are present within the microbial mat community and may contribute to the arsenic geochemistry in the environment. - Highlights: ► The microbial mats from this ancient gold mine are highly diverse community. ► As(III) oxidizing and As(V) reducing bacteria are present in the mats. ► As redox transformations are linked to the metabolism of microbial mats bacteria. ► Microbial mats play a crucial role in the As biogeochemical cycle within the mine. - The microbial mats from this ancient gold mine can mediate oxidation/reduction reaction of arsenic and in this way may significantly contribute to arsenic contamination in groundwater.

Microbial corrosion of metallic materials in a deep nuclear-waste repository

Directory of Open Access Journals (Sweden)

Stoulil J.

2016-06-01

Full Text Available The study summarises current knowledge on microbial corrosion in a deep nuclear-waste repository. The first part evaluates the general impact of microbial activity on corrosion mechanisms. Especially, the impact of microbial metabolism on the environment and the impact of biofilms on the surface of structure materials were evaluated. The next part focuses on microbial corrosion in a deep nuclear-waste repository. The study aims to suggest the development of the repository environment and in that respect the viability of bacteria, depending on the probable conditions of the environment, such as humidity of bentonite, pressure in compact bentonite, the impact of ionizing radiation, etc. The last part is aimed at possible techniques for microbial corrosion mechanism monitoring in the conditions of a deep repository. Namely, electrochemical and microscopic techniques were discussed.

The use of tracer techniques in pesticide balance and metabolism studies

International Nuclear Information System (INIS)

Fuehr, F.

1977-01-01

The radioisotope tracing technique has been a useful tool in obtaining extensive information on the fate of pesticides in the soil-plant systems, including their uptake, transport and metabolism by plants; their photochemical, chemical and microbial degradation; their adsorption, desorption and translocation in soil; and their bioavailability to untreated crops. A pesticide balance study under practical field conditions using radio labelling can examine a number of factors affecting the fate of a compound at the same time and assess the magnitude of the major processes involved. On the basis of these results, more detailed studies are then formulated to be conducted under an exactly defined environment of a growth chamber or a laboratory. The use of tracer techniques in such studies is reported. (author)

Colonic transit time is related to bacterial metabolism and mucosal turnover in the human gut

DEFF Research Database (Denmark)

Roager, Henrik Munch; Hansen, Lea Benedicte Skov; Bahl, Martin Iain

Little is known about how colonic transit time relates to human colonic metabolism, and its importance for host health, although stool consistency, a proxy for colonic transit time, has recently been negatively associated with gut microbial richness. To address the relationships between colonic t...... imply a healthy gut microbial ecosystem and points at colonic transit time as a highly important factor to consider in microbiome and metabolomics studies.......Little is known about how colonic transit time relates to human colonic metabolism, and its importance for host health, although stool consistency, a proxy for colonic transit time, has recently been negatively associated with gut microbial richness. To address the relationships between colonic...... transit time and the gut microbial composition and metabolism, we assessed the colonic transit time of 98 subjects using radiopaque markers, and profiled their gut microbiota by16S rRNA gene sequencing and their urine metabolome by ultra performance liquid chromatography mass spectrometry. Based...

Microbial degradation of furanic compounds : Biochemistry, genetics, and impact

NARCIS (Netherlands)

Wierckx, N.; Koopman, F.; Ruijssenaars, H.J.; De Winde, J.H.

2011-01-01

Microbial metabolism of furanic compounds, especially furfural and 5-hydroxymethylfurfural (HMF), is rapidly gaining interest in the scientific community. This interest can largely be attributed to the occurrence of toxic furanic aldehydes in lignocellulosic hydrolysates. However, these compounds

Enhanced microbial coalbed methane generation: A review of research, commercial activity, and remaining challenges

Science.gov (United States)

Ritter, Daniel J.; Vinson, David S.; Barnhart, Elliott P.; Akob, Denise M.; Fields, Matthew W.; Cunningham, Al B.; Orem, William H.; McIntosh, Jennifer C.

2015-01-01

Coalbed methane (CBM) makes up a significant portion of the world’s natural gas resources. The discovery that approximately 20% of natural gas is microbial in origin has led to interest in microbially enhanced CBM (MECoM), which involves stimulating microorganisms to produce additional CBM from existing production wells. This paper reviews current laboratory and field research on understanding processes and reservoir conditions which are essential for microbial CBM generation, the progress of efforts to stimulate microbial methane generation in coal beds, and key remaining knowledge gaps. Research has been primarily focused on identifying microbial communities present in areas of CBM generation and attempting to determine their function, in-situ reservoir conditions that are most favorable for microbial CBM generation, and geochemical indicators of metabolic pathways of methanogenesis (i.e., acetoclastic or hydrogenotrophic methanogenesis). Meanwhile, researchers at universities, government agencies, and companies have focused on four primary MECoM strategies: 1) microbial stimulation (i.e., addition of nutrients to stimulate native microbes); 2) microbial augmentation (i.e., addition of microbes not native to or abundant in the reservoir of interest); 3) physically increasing microbial access to coal and distribution of amendments; and 4) chemically increasing the bioavailability of coal organics. Most companies interested in MECoM have pursued microbial stimulation: Luca Technologies, Inc., successfully completed a pilot scale field test of their stimulation strategy, while two others, Ciris Energy and Next Fuel, Inc., have undertaken smaller scale field tests. Several key knowledge gaps remain that need to be addressed before MECoM strategies can be implemented commercially. Little is known about the bacterial community responsible for coal biodegradation and how these microorganisms may be stimulated to enhance microbial methanogenesis. In addition, research

Predicting bioremediation of hydrocarbons: Laboratory to field scale

International Nuclear Information System (INIS)

Diplock, E.E.; Mardlin, D.P.; Killham, K.S.; Paton, G.I.

2009-01-01

There are strong drivers to increasingly adopt bioremediation as an effective technique for risk reduction of hydrocarbon impacted soils. Researchers often rely solely on chemical data to assess bioremediation efficiently, without making use of the numerous biological techniques for assessing microbial performance. Where used, laboratory experiments must be effectively extrapolated to the field scale. The aim of this research was to test laboratory derived data and move to the field scale. In this research, the remediation of over thirty hydrocarbon sites was studied in the laboratory using a range of analytical techniques. At elevated concentrations, the rate of degradation was best described by respiration and the total hydrocarbon concentration in soil. The number of bacterial degraders and heterotrophs as well as quantification of the bioavailable fraction allowed an estimation of how bioremediation would progress. The response of microbial biosensors proved a useful predictor of bioremediation in the absence of other microbial data. Field-scale trials on average took three times as long to reach the same endpoint as the laboratory trial. It is essential that practitioners justify the nature and frequency of sampling when managing remediation projects and estimations can be made using laboratory derived data. The value of bioremediation will be realised when those that practice the technology can offer transparent lines of evidence to explain their decisions. - Detailed biological, chemical and physical characterisation reduces uncertainty in predicting bioremediation.

Microbial-Host Co-metabolites Are Prodromal Markers Predicting Phenotypic Heterogeneity in Behavior, Obesity, and Impaired Glucose Tolerance

Directory of Open Access Journals (Sweden)

Marc-Emmanuel Dumas

2017-07-01

Full Text Available The influence of the gut microbiome on metabolic and behavioral traits is widely accepted, though the microbiome-derived metabolites involved remain unclear. We carried out untargeted urine 1H-NMR spectroscopy-based metabolic phenotyping in an isogenic C57BL/6J mouse population (n = 50 and show that microbial-host co-metabolites are prodromal (i.e., early markers predicting future divergence in metabolic (obesity and glucose homeostasis and behavioral (anxiety and activity outcomes with 94%–100% accuracy. Some of these metabolites also modulate disease phenotypes, best illustrated by trimethylamine-N-oxide (TMAO, a product of microbial-host co-metabolism predicting future obesity, impaired glucose tolerance (IGT, and behavior while reducing endoplasmic reticulum stress and lipogenesis in 3T3-L1 adipocytes. Chronic in vivo TMAO treatment limits IGT in HFD-fed mice and isolated pancreatic islets by increasing insulin secretion. We highlight the prodromal potential of microbial metabolites to predict disease outcomes and their potential in shaping mammalian phenotypic heterogeneity.

Laboratory-Scale Simulation and Real-Time Tracking of a Microbial Contamination Event and Subsequent Shock-Chlorination in Drinking Water

Directory of Open Access Journals (Sweden)

Michael D. Besmer

2017-10-01

Full Text Available Rapid contamination of drinking water in distribution and storage systems can occur due to pressure drop, backflow, cross-connections, accidents, and bio-terrorism. Small volumes of a concentrated contaminant (e.g., wastewater can contaminate large volumes of water in a very short time with potentially severe negative health impacts. The technical limitations of conventional, cultivation-based microbial detection methods neither allow for timely detection of such contaminations, nor for the real-time monitoring of subsequent emergency remediation measures (e.g., shock-chlorination. Here we applied a newly developed continuous, ultra high-frequency flow cytometry approach to track a rapid pollution event and subsequent disinfection of drinking water in an 80-min laboratory scale simulation. We quantified total (TCC and intact (ICC cell concentrations as well as flow cytometric fingerprints in parallel in real-time with two different staining methods. The ingress of wastewater was detectable almost immediately (i.e., after 0.6% volume change, significantly changing TCC, ICC, and the flow cytometric fingerprint. Shock chlorination was rapid and detected in real time, causing membrane damage in the vast majority of bacteria (i.e., drop of ICC from more than 380 cells μl-1 to less than 30 cells μl-1 within 4 min. Both of these effects as well as the final wash-in of fresh tap water followed calculated predictions well. Detailed and highly quantitative tracking of microbial dynamics at very short time scales and for different characteristics (e.g., concentration, membrane integrity is feasible. This opens up multiple possibilities for targeted investigation of a myriad of bacterial short-term dynamics (e.g., disinfection, growth, detachment, operational changes both in laboratory-scale research and full-scale system investigations in practice.

Bioinformatic approaches reveal metagenomic characterization of soil microbial community.

Directory of Open Access Journals (Sweden)

Zhuofei Xu

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

From position-specific isotope labeling towards soil fluxomics: a novel toolbox to assess the microbial impact on biogeochemical cycles

Science.gov (United States)

Apostel, C.; Dippold, M. A.; Kuzyakov, Y.

2015-12-01

Understanding the microbial impact on C and nutrient cycles is one of the most important challenges in terrestrial biogeochemistry. Transformation of low molecular weight organic substances (LMWOS) is a key step in all biogeochemical cycles because 1) all high molecular substances pass the LMWOS pool during their degradation and 2) only LMWOS can be taken up by microorganisms intact. Thus, the transformations of LMWOS are dominated by biochemical pathways of the soil microorganisms. Thus, understanding fluxes and transformations in soils requires a detailed knowledge on the microbial metabolic network and its control mechanism. Tracing C fate in soil by isotopes became on of the most applied and promising biogeochemistry tools but studies were nearly exclusively based on uniformly labeled substances. However, such tracers do not allow the differentiation of the intact use of the initial substances from its transformation to metabolites. The novel tool of position-specific labeling enables to trace molecule atoms separately and thus to determine the cleavage of molecules - a prerequisite for metabolic tracing. Position-specific labeling of basic metabolites and quantification of isotope incorporation in CO2 and bulk soil enabled following the basic metabolic pathways of microorganisms. However, the combination of position-specific 13C labeling with compound-specific isotope analysis of microbial biomarkers and metabolites like phospholipid fatty acids (PLFA) or amino sugars revealed new insights into the soil fluxome: First, it enables tracing specific anabolic pathways in diverse microbial communities in soils e.g. carbon starvation pathways versus pathways reflecting microbial growth. Second, it allows identification of specific pathways of individual functional microbial groups in soils in situ. Tracing metabolic pathways and understanding their regulating factors are crucial for soil C fluxomics i.e. the unravaling of the complex network of C transformations

An open source platform for multi-scale spatially distributed simulations of microbial ecosystems

Energy Technology Data Exchange (ETDEWEB)

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

2014-08-14

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

Glyphosate toxicity and the effects of long-term vegetation control on soil microbial communities

Science.gov (United States)

Matt D. Busse; Alice W. Ratcliff; Carol J. Stestak; Robert F. Powers

2001-01-01

We assessed the direct and indirect effect of the herbicide glyphosate on soil microbial communities from soil bioassays at glyphosate concentrations up to 100-fold greater than expected following a single field application. Indirect effects on microbial biomass, respiration, and metabolic diversity (Biolog and catabolic response profile) were compared seasonally after...

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.

Impact of some selected insecticides application on soil microbial respiration.

Science.gov (United States)

Latif, M A; Razzaque, M A; Rahman, M M

2008-08-15

The aim of present study was to investigate the impact of selected insecticides used for controlling brinjal shoot and fruit borer on soil microorganisms and to find out the insecticides or nontoxic to soil microorganism the impact of nine selected insecticides on soil microbial respiration was studied in the laboratory. After injection of different insecticides solutions, the soil was incubated in the laboratory at room temperature for 32 days. The amount of CO2 evolved due to soil microbial respiration was determined at 2, 4, 8, 16, 24 and 32 days of incubation. Flubendiamide, nimbicidine, lambda-cyhalothrin, abamectin and thiodicarb had stimulatory effect on microbial respiration during the initial period of incubation. Chlorpyriphos, cartap and carbosulfan had inhibitory effect on microbial respiration and cypermethrin had no remarkable effect during the early stage of incubation. The negative effect of chlorpyriphos, cartap and carbosulfan was temporary, which was disappeared after 4 days of insecticides application. No effect of the selected insecticides on soil microorganisms was observed after 24 or 32 days of incubation.

Elucidating Microbial Species-Specific Effects on Organic Matter Transformation in Marine Sediments

Science.gov (United States)

Mahmoudi, N.; Enke, T. N.; Beaupre, S. R.; Teske, A.; Cordero, O. X.; Pearson, A.

2017-12-01

Microbial transformation and decomposition of organic matter in sediments constitutes one of the largest fluxes of carbon in marine environments. Mineralization of sedimentary organic matter by microorganisms results in selective degradation such that bioavailable or accessible compounds are rapidly metabolized while more recalcitrant, complex compounds are preserved and buried in sediment. Recent studies have found that the ability to use different carbon sources appears to vary among microorganisms, suggesting that the availability of certain pools of carbon can be specific to the taxa that utilize the pool. This implies that organic matter mineralization in marine environments may depend on the metabolic potential of the microbial populations that are present and active. The goal of our study was to investigate the extent to which organic matter availability and transformation may be species-specific using sediment from Guaymas Basin (Gulf of California). We carried out time-series incubations using bacterial isolates and sterilized sediment in the IsoCaRB system which allowed us to measure the production rates and natural isotopic signatures (δ13C and Δ14C) of microbially-respired CO2. Separate incubations using two different marine bacterial isolates (Vibrio sp. and Pseudoalteromonas sp.) and sterilized Guaymas Basin sediment under oxic conditions showed that the rate and total quantity of organic matter metabolized by these two species differs. Approximately twice as much CO2 was collected during the Vibrio sp. incubation compared to the Pseudoalteromonas sp. incubation. Moreover, the rate at which organic matter was metabolized by the Vibrio sp. was much higher than the Pseudoalteromonas sp. indicating the intrinsic availability of organic matter in sediments may depend on the species that is present and active. Isotopic analyses of microbially respired CO2 will be used to constrain the type and age of organic matter that is accessible to each species

The Genome-Based Metabolic Systems Engineering to Boost Levan Production in a Halophilic Bacterial Model.

Science.gov (United States)

Aydin, Busra; Ozer, Tugba; Oner, Ebru Toksoy; Arga, Kazim Yalcin

2018-03-01

Metabolic systems engineering is being used to redirect microbial metabolism for the overproduction of chemicals of interest with the aim of transforming microbial hosts into cellular factories. In this study, a genome-based metabolic systems engineering approach was designed and performed to improve biopolymer biosynthesis capability of a moderately halophilic bacterium Halomonas smyrnensis AAD6 T producing levan, which is a fructose homopolymer with many potential uses in various industries and medicine. For this purpose, the genome-scale metabolic model for AAD6 T was used to characterize the metabolic resource allocation, specifically to design metabolic engineering strategies for engineered bacteria with enhanced levan production capability. Simulations were performed in silico to determine optimal gene knockout strategies to develop new strains with enhanced levan production capability. The majority of the gene knockout strategies emphasized the vital role of the fructose uptake mechanism, and pointed out the fructose-specific phosphotransferase system (PTS fru ) as the most promising target for further metabolic engineering studies. Therefore, the PTS fru of AAD6 T was restructured with insertional mutagenesis and triparental mating techniques to construct a novel, engineered H. smyrnensis strain, BMA14. Fermentation experiments were carried out to demonstrate the high efficiency of the mutant strain BMA14 in terms of final levan concentration, sucrose consumption rate, and sucrose conversion efficiency, when compared to the AAD6 T . The genome-based metabolic systems engineering approach presented in this study might be considered an efficient framework to redirect microbial metabolism for the overproduction of chemicals of interest, and the novel strain BMA14 might be considered a potential microbial cell factory for further studies aimed to design levan production processes with lower production costs.

Microbial stress tolerance for biofuels. Systems biology

Energy Technology Data Exchange (ETDEWEB)

Liu, Zonglin Lewis (ed.) [National Center for Agricultural Utilization Research, USDA-ARS, Peoria, IL (United States)

2012-07-01

The development of sustainable and renewable biofuels is attracting growing interest. It is vital to develop robust microbial strains for biocatalysts that are able to function under multiple stress conditions. This Microbiology Monograph provides an overview of methods for studying microbial stress tolerance for biofuels applications using a systems biology approach. Topics covered range from mechanisms to methodology for yeast and bacteria, including the genomics of yeast tolerance and detoxification; genetics and regulation of glycogen and trehalose metabolism; programmed cell death; high gravity fermentations; ethanol tolerance; improving biomass sugar utilization by engineered Saccharomyces; the genomics on tolerance of Zymomonas mobilis; microbial solvent tolerance; control of stress tolerance in bacterial host organisms; metabolomics for ethanologenic yeast; automated proteomics work cell systems for strain improvement; and unification of gene expression data for comparable analyses under stress conditions. (orig.)

Microbial Metabolism and Inhibition Studies of Phenobarbital ...

African Journals Online (AJOL)

Purpose: Screening scale studies were performed with eight cultures for their ability to metabolize phenobarbital, an antiepileptic, sedative, hypnotic and substrate for CYP 2C9 and 2C19. Methods: The transformation of phenobarbital was confirmed and characterized by fermentation techniques, high performance liquid ...

Methane-metabolizing microbial communities in sediments of the Haima cold seep area, northwest slope of the South China Sea.

Science.gov (United States)

Niu, Mingyang; Fan, Xibei; Zhuang, Guangchao; Liang, Qianyong; Wang, Fengping

2017-09-01

Cold seeps are widespread chemosynthetic ecosystems in the deep-sea environment, and cold seep microbial communities of the South China Sea are poorly constrained. Here we report on the archaeal communities, particularly those involved in methane metabolization, in sediments of a newly discovered cold seep (named 'Haima') on the northwest slope of the South China Sea. Archaeal diversity, abundance and distribution were investigated in two piston cores collected from a seep area (QDN-14B) and a non-seep control site (QDN-31B). Geochemical investigation of the QDN-14B core identified an estimated sulfate-methane transition zone (Estimated SMTZ) at 300-400 cm below sea floor (cmbsf), where a high abundance of anaerobic methane-oxidizing archaea (ANME) occurred, as revealed by analysis of the 16S rRNA gene and the gene (mcrA) encoding the α-subunit of the key enzyme methyl-coenzyme M reductase. ANME-2a/b was predominant in the upper and middle layers of the estimated SMTZ, whereas ANME-1b outcompeted ANME-2 in the sulfate-depleted bottom layers of the estimated SMTZ and the methanogenic zone. Fine-scale phylogenetic analysis further divided the ANME-1b group into three subgroups with different distribution patterns: ANME-1bI, ANME-1bII and ANME-1bIII. Multivariate analyses indicated that dissolved inorganic carbon and sulfate may be important factors controlling the composition of the methane-metabolizing community. Our study on ANME niche separation and interactions with other archaeal groups improves our understanding of the metabolic diversity and flexibility of ANME, and the findings further suggest that ANME subgroups may have evolved diversified/specified metabolic capabilities other than syntrophic anaerobic oxidation of methane coupled with sulfate reduction in marine sediments. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Weedy lignocellulosic feedstock and microbial metabolic engineering. Advancing the generation of 'Biofuel'

Energy Technology Data Exchange (ETDEWEB)

Chandel, Anuj K. [Jawaharlal Nehru Technological Univ., Hyderabad (India). Centre of Biotechnology; Singh, Om V. [Pittsburgh Univ., Bradford, PA (United States). Div. of Biological and Health Sciences

2011-03-15

Lignocellulosic materials are the most abundant renewable organic resources ({proportional_to}200 billion tons annually) on earth that are readily available for conversion to ethanol and other value-added products, but they have not yet been tapped for the commercial production of fuel ethanol. The lignocellulosic substrates include woody substrates such as hardwood (birch and aspen, etc.) and softwood (spruce and pine, etc.), agro residues (wheat straw, sugarcane bagasse, corn stover, etc.), dedicated energy crops (switch grass, and Miscanthus etc.), weedy materials (Eicchornia crassipes, Lantana camara etc.), and municipal solid waste (food and kitchen waste, etc.). Despite the success achieved in the laboratory, there are limitations to success with lignocellulosic substrates on a commercial scale. The future of lignocellulosics is expected to lie in improvements of plant biomass, metabolic engineering of ethanol, and cellulolytic enzyme-producing microorganisms, fullest exploitation of weed materials, and process integration of the individual steps involved in bioethanol production. Issues related to the chemical composition of various weedy raw substrates for bioethanol formation, including chemical composition-based structural hydrolysis of the substrate, need special attention. This area could be opened up further by exploring genetically modified metabolic engineering routes in weedy materials and in biocatalysts that would make the production of bioethanol more efficient. (orig.)

Microbial products II

Energy Technology Data Exchange (ETDEWEB)

Pape, H; Rehm, H J [eds.

1986-01-01

The present volume deals mainly with compounds which have been detected as natural microbial products. Part 1 of this volume introduces the general aspects of the overproduction of metabolites and the concepts and genetics of secondary metabolism. Compounds such as nucleosides, nucleotides, coenzymes, vitamins and lipids are dealt with in part 2. Part 3 then is devoted to products and antibiotics with uses im medicine, veterinary medicine, plant protection and metabolites with antitumor activity. Several secondary metabolites have found uses in human and animal health care. With 244 figs., 109 tabs.

Visualizing Microbial Biogeochemistry: NanoSIMS and Stable Isotope Probing (Invited)

Science.gov (United States)

Pett-Ridge, J.; Weber, P. K.

2009-12-01

oligonucleotide, functional enzyme and metabolic image data and should help unravel the metabolic processes of complex microbial communities in soils, biofilms and aquatic systems.

A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems.

Directory of Open Access Journals (Sweden)

Marko Budinich

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

Insights into the Microbial and Viral Dynamics of a Coastal Downwelling-Upwelling Transition.

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Gustavo Bueno Gregoracci

Full Text Available Although previous studies have described opposing states in upwelling regions, i.e., the rise of cold nutrient-rich waters and prevalence of surface warm nutrient-poor waters, few have addressed the transition from one state to the other. This study aimed to describe the microbial and viral structure during this transition and was able to obtain the taxonomic and metabolic compositions as well as physical-chemical data. This integrated approach allowed for a better understanding of the dynamics of the downwelling upwelling transition, suggesting that a wealth of metabolic processes and ecological interactions are occurring in the minute fractions of the plankton (femto, pico, nano. These processes and interactions included evidence of microbial predominance during downwelling (with nitrogen recycling and aerobic anoxygenic photosynthesis, different viral predation pressures over primary production in different states (cyanobacteria vs eukaryotes, and a predominance of diatoms and selected bacterial and archaeal groups during upwelling (with the occurrence of a wealth of nitrogen metabolism involving ammonia. Thus, the results provided insights into which microbes, viruses and microbial-mediated processes are probably important in the functioning of upwelling systems.

Microbial genome analysis: the COG approach.

Science.gov (United States)

Galperin, Michael Y; Kristensen, David M; Makarova, Kira S; Wolf, Yuri I; Koonin, Eugene V

2017-09-14

For the past 20 years, the Clusters of Orthologous Genes (COG) database had been a popular tool for microbial genome annotation and comparative genomics. Initially created for the purpose of evolutionary classification of protein families, the COG have been used, apart from straightforward functional annotation of sequenced genomes, for such tasks as (i) unification of genome annotation in groups of related organisms; (ii) identification of missing and/or undetected genes in complete microbial genomes; (iii) analysis of genomic neighborhoods, in many cases allowing prediction of novel functional systems; (iv) analysis of metabolic pathways and prediction of alternative forms of enzymes; (v) comparison of organisms by COG functional categories; and (vi) prioritization of targets for structural and functional characterization. Here we review the principles of the COG approach and discuss its key advantages and drawbacks in microbial genome analysis. Published by Oxford University Press 2017. This work is written by US Government employees and is in the public domain in the US.

Gut Microbiota, Obesity and Metabolic Dysfunction

Directory of Open Access Journals (Sweden)

Anna Meiliana

2011-12-01

Full Text Available BACKGROUND: The prevalence of obesity and related disorders such as metabolic syndrome and diabetes has vastly increased throughout the world. Recent insights have generated an entirely new perspective suggesting that our microbiota might be involved in the development of these disorders. This represents an area of scientific need, opportunity and challenge. The insights gleaned should help to address several pressing global health problems. CONTENT: Our bowels have two major roles: the digestion and absorption of nutrients and the maintenance of a barrier against the external environment. They fulfill these functions in the context of, and with the help from, tens of trillions of resident microbes, known as the gut microbiota. Studies have demonstrated that obesity and metabolic syndrome may be associated with profound microbiotal changes, and the induction of a metabolic syndrome phenotype through fecal transplants corroborates the important role of the microbiota in this disease. Dietary composition and caloric intake appear to swiftly regulate intestinal microbial composition and function. SUMMARY: The interaction of the intestinal microbial world with its host, and its mutual regulation, will become one of the important topics of biomedical research and will provide us with further insights at the interface of microbiota, metabolism, metabolic syndrome, and obesity. A better understanding of the interaction between certain diets and the human gut microbiome should help to develop new guidelines for feeding humans at various time points in their life, help to improve global human health, and establish ways to prevent or treat various food-related diseases. KEYWORDS: gut microbiota, obesity, metabolic syndrome, type 2 diabetes.

Environmental controls on microbial communities in continental serpentinite fluids

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Melitza eCrespo-Medina

2014-11-01

Full Text Available Geochemical reactions associated with serpentinization alter the composition of dissolved organic compounds in circulating fluids and potentially liberate mantle-derived carbon and reducing power to support subsurface microbial communities. Previous studies have identified Betaproteobacteria from the order Burkholderiales and bacteria from the order Clostridiales as key components of the serpentinite–hosted microbiome, however there is limited knowledge of their metabolic capabilities or growth characteristics. In an effort to better characterize microbial communities, their metabolism, and factors limiting their activities, microcosm experiments were designed with fluids collected from several monitoring wells at the Coast Range Ophiolite Microbial Observatory (CROMO in northern California during expeditions in March and August 2013. The incubations were initiated with a hydrogen atmosphere and a variety of carbon sources (carbon dioxide, methane, acetate and formate, with and without the addition of nutrients and electron acceptors. Growth was monitored by direct microscopic counts; DNA yield and community composition was assessed at the end of the three month incubation. For the most part, results indicate that bacterial growth was favored by the addition of acetate and methane, and that the addition of nutrients and electron acceptors had no significant effect on microbial growth, suggesting no nutrient- or oxidant-limitation. However the addition of sulfur amendments led to different community compositions. The dominant organisms at the end of the incubations were closely related to Dethiobacter sp. and to the family Comamonadaceae, which are also prominent in culture-independent gene sequencing surveys. These experiments provide one of first insights into the biogeochemical dynamics of the serpentinite subsurface environment and will facilitate experiments to trace microbial activities in serpentinizing ecosystems.

Feasible Metabolic Schema Associated with High pH Springs in the Philippines

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DAWN eCARDACE

2015-02-01

Full Text Available A field campaign targeting high pH springs in the Zambales and Palawan Ophiolites of the Philippines was conducted in 2012-2013, and enabled description of several springs sourced in altered pillow basalts, gabbros, and peridotites. We combine field observations of pH, temperature, conductivity, dissolved oxygen, and oxidation-reduction potential with analyses of major ions, dissolved inorganic carbon, dissolved organic carbon, and dissolved gas phases in order to model the activities of selected phases important to microbial metabolism, and to evaluate feasible metabolic reactions based on energy yield. We document changing geochemical inventories in these springs, and examine how the environment supports or prevents the function of certain microbial metabolisms.

From Position-Specific Labeling to Environmental Fluxomics: Elucidating Biogeochemical Cycles from the Metabolic Perspective (BG Division Outstanding ECS Award Lecture)

Science.gov (United States)

Dippold, Michaela; Apostel, Carolin; Dijkstra, Paul; Kuzyakov, Yakov

2017-04-01

Understanding soil and sedimentary organic matter (SOM) dynamics is one of the most important challenges in biogeoscience. To disentangle the fluxes and transformations of C in soils a detailed knowledge on the biochemical pathways and its controlling factors is required. Biogeochemists' view on the C transformation of microorganisms in soil has rarely exceed a strongly simplified concept assuming that C gets either oxidized to CO2 via the microbial catabolism or incorporated into biomass via the microbial anabolism. Biochemists, however, thoroughly identified in the past decades the individual reactions of glycolysis, pentose-phosphate pathway and citric acid cycle underlying the microbial catabolism. At various points within that metabolic network the anabolic fluxes feeding biomass formation branch off. Recent studies on metabolic flux tracing by position-specific isotope labeling allowed tracing these C transformations in soils in situ, an approach which is qunatitatively complemented by metabolic flux modeling. This approach has reached new impact by the cutting-edge combination of position-specific 13C labeling with compound-specific isotope analysis of microbial biomarkers and metabolites which allows 1) tracing specific anabolic pathways in diverse microbial communities in soils and 2) identification of specific pathways of individual functional microbial groups. Thus, the combination of position-specific labeling, compound-specific isotope incorporation in biomarkers and quantitative metabolic flux modelling provide the toolbox for quantitative soil fluxomics. Our studies combining position-specific labeled glucose with amino sugar 13C analysis showed that up to 55% of glucose, incorporated into the glucose derivative glucosamine, first passed glycolysis before allocated back via gluconeogenesis. Similarly, glutamate-derived C is allocated via anaplerotic pathways towards fatty acid synthesis and in parallel to its oxidation in citric acid cycle. Thus

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.

First Microbial Community Assessment of Borehole Fluids from the Deep Underground Science and Engineering Laboratory (DUSEL)

Science.gov (United States)

Moser, D. P.; Anderson, C.; Bang, S.; Jones, T. L.; Boutt, D.; Kieft, T.; Sherwood Lollar, B.; Murdoch, L. C.; Pfiffner, S. M.; Bruckner, J.; Fisher, J. C.; Newburn, J.; Wheatley, A.; Onstott, T. C.

2010-12-01

Fluid and gas samples were collected from two flowing boreholes at the 4100 (1,250 m) and 4850 ft (1478 m) levels of the former Homestake Gold Mine in Lead, South Dakota. Service- and flood water samples were also collected as comparative benchmarks. With a maximum depth of 8,000 ft, (2,438 m), this mine currently hosts the Sanford Laboratory and is the proposed location for the US Deep Underground Science and Engineering Laboratory (DUSEL). The uncased 4100L hole is a legacy of mining; whereas, the cased 4850 hole was drilled in 2009 in support of large cavity construction. Both were packered or valved to exclude mine air and sampled anaerobically using aseptic technique. Physical measurements, aquatic and dissolved gas chemistry, cell counts, and microbial community assessments (SSU rRNA libraries) were performed on all samples. This study represents the first at Sanford Lab/DUSEL specifically focused on the deep biosphere rather than mine microbiology. Fluids from the two holes differed markedly, with that from 4100L being characterized by NaHCO3 and 4850 by Na2SO4. pH values of 8.2 vs. 7.5, conductivities (μS) of 1790 vs. 7667 and alkalinities (mg/L) of 767 vs. 187 were obtained from 4100L and 4850, respectively. As expected, the deeper 4850L hole had the higher temperature (38 vs. 30 oC). Neither had measureable nitrate, but both had similar dissolved organic C (DOC) concentrations (0.8 vs. 0.9 mg/L). Sulfate was present at 337 vs. 4,470 mg/L in 4100L and 4850L. Major dissolved gases were N2 (91 and 81 vol%), O2 (12 and 16 vol%) and CH4 (0.07 and 3.35 vol%) in 4100L and 4850L. The δ13C of CH4 was -51 and -56.7 permil in 4100L and 4850, respectively. The uncorrected 14C age of DIC was calculated at 25,310 (+/- 220) and 47,700 (+/-3,100) years for the two fluids. Cell counts were 5.9e3 and 2.01e5 in 4100L and 4850. Microbial community structure was diverse in both holes and distinct from that of service water. A large proportion of rRNA library clones were

Long-term high-solids anaerobic digestion of food waste: Effects of ammonia on process performance and microbial community.

Science.gov (United States)

Peng, Xuya; Zhang, ShangYi; Li, Lei; Zhao, Xiaofei; Ma, Yao; Shi, Dezhi

2018-04-22

A long-term high solids anaerobic digestion of food waste was conducted to identify microbial mechanisms of ammonia inhibition during digestion and to clarify correlations between ammonia accumulation, microbial community dynamics (diversity, composition, and interactions), and process stability. Results show that the effects of ammonia on process performance and microbial community were indirectly caused by volatile fatty acid accumulation. Excess free ammonia blocked acetate metabolism, leading to process instability. Accumulated acetate caused feedback inhibition at the acetogenesis stage, which resulted in considerable accumulation of propionate, valerate, and other long-chain fatty acids. This high concentration of volatile fatty acids reduced the abundance of syntrophic acetogenic bacteria and allowed hydrolytic fermentative bacteria to dominate. The normally interactive and orderly metabolic network was broken, which further exacerbated the process instability. These results improve the understanding of microbial mechanisms which contribute to process instability and provide guidance for the microbial management of anaerobic digesters. Copyright © 2018 Elsevier Ltd. All rights reserved.

The woodrat gut microbiota as an experimental system for understanding microbial metabolism of dietary toxins

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Kevin D. Kohl

2016-07-01

Full Text Available The microbial communities inhabiting the alimentary tracts of mammals, particularly those of herbivores, are estimated to be one of the densest microbial reservoirs on Earth. The significance of these gut microbes in influencing the physiology, ecology and evolution of their hosts is only beginning to be realized. To understand the microbiome of herbivores with a focus on nutritional ecology, while evaluating the roles of host evolution and environment in sculpting microbial diversity, we have developed an experimental system consisting of the microbial communities of several species of herbivorous woodrats (genus Neotoma that naturally feed on a variety of dietary toxins. We designed this system to investigate the long-standing, but experimentally neglected hypothesis that ingestion of toxic diets by herbivores is facilitated by the gut microbiota. Like several other rodent species, the woodrat stomach has a sacculated, nongastric foregut portion. We have documented a dense and diverse community of microbes in the woodrat foregut, with several genera potentially capable of degrading dietary toxins and/or playing a role in stimulating hepatic detoxification enzymes of the host. The biodiversity of these gut microbes appears to be a function of host evolution, ecological experience and diet, such that dietary toxins increase microbial diversity in hosts with experience with these toxins while novel toxins depress microbial diversity. These microbial communities are critical to the ingestion of a toxic diet as reducing the microbial community with antibiotics impairs the host’s ability to feed on dietary toxins. Furthermore, the detoxification capacity of gut microbes can be transferred from Neotoma both intra and interspecifically to naïve animals that lack ecological and evolutionary history with these toxins. In addition to advancing our knowledge of complex host-microbes interactions, this system holds promise for identifying microbes that

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

Science.gov (United States)

Maharjan, M.

2016-12-01

Land-use change from native forest to intensive agricultural systems can negatively impact numerous soil parameters. Understanding the effects of forest ecosystem transformations on markers of long-term soil health is particularly important in rapidly developing regions such as Nepal, where unprecedented levels of agriculturally-driven deforestation have occurred in recent decades. However, the effects of widespread land use changes on soil quality in this region have yet to be properly characterized. Microbial indicators (soil microbial biomass, metabolic quotient and enzymes activities) are particularly suited to assessing the consequences of such ecosystem disturbances, as microbial communities are especially sensitive to environmental change. Thus, the aim of this study was to assess the effect of land use system; i.e. forest, organic and conventional farming, on soil quality in Chitwan, Nepal using markers of microbial community size and activity. Total organic C and N contents were higher in organic farming compared with conventional farming and forest, suggesting higher nutrient retention and soil preservation with organic farming practices compared to conventional. These differences in soil composition were reflected in the health of the soil microbial communities: Organic farm soil exhibited higher microbial biomass C, elevated β-glucosidase and chitinase activities, and a lower metabolic quotient relative to other soils, indicating a larger, more active, and less stressed microbial community, respectively. These results collectively demonstrate that application of organic fertilizers and organic residues positively influence nutrient availability, with subsequent improvements in soil quality and productivity. Furthermore, the sensitivity of microbial indicators to different management practices demonstrated in this study supports their use as effective markers of ecosystem disturbance in subtropical soils.

Microbial Communities: Tracing Growth Processes from Antarctic Lakes to Early Earth to Other Planets

Science.gov (United States)

Sumner, D. Y.

2014-12-01

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

Stimulating soil microorganisms for mineralizing the herbicide isoproturon by means of microbial electroremediating cells.

Science.gov (United States)

Rodrigo Quejigo, Jose; Dörfler, Ulrike; Schroll, Reiner; Esteve-Núñez, Abraham

2016-05-01

The absence of suitable terminal electron acceptors (TEA) in soil might limit the oxidative metabolism of environmental microbial populations. Microbial electroremediating cells (MERCs) consist in a variety of bioelectrochemical devices that aim to overcome electron acceptor limitation and maximize metabolic oxidation with the purpose of enhancing the biodegradation of a pollutant in the environment. The objective of this work was to use MERCs principles for stimulating soil bacteria to achieve the complete biodegradation of the herbicide (14) C-isoproturon (IPU) to (14) CO(2) in soils. Our study concludes that using electrodes at a positive potential [+600 mV (versus Ag/AgCl)] enhanced the mineralization by 20-fold respect the electrode-free control. We also report an overall profile of the (14) C-IPU metabolites and a (14) C mass balance in response to the different treatments. The remarkable impact of electrodes on the microbial activity of natural communities suggests a promising future for this emerging environmental technology that we propose to name bioelectroventing. © 2016 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Metagenomic insights into evolution of heavy metal-contaminated groundwater microbial community

Energy Technology Data Exchange (ETDEWEB)

Hemme, C.L.; Deng, Y.; Gentry, T.J.; Fields, M.W.; Wu, L.; Barua, S.; Barry, K.; Green-Tringe, S.; Watson, D.B.; He, Z.; Hazen, T.C.; Tiedje, J.M.; Rubin, E.M.; Zhou, J.

2010-07-01

Understanding adaptation of biological communities to environmental change is a central issue in ecology and evolution. Metagenomic analysis of a stressed groundwater microbial community reveals that prolonged exposure to high concentrations of heavy metals, nitric acid and organic solvents ({approx}50 years) has resulted in a massive decrease in species and allelic diversity as well as a significant loss of metabolic diversity. Although the surviving microbial community possesses all metabolic pathways necessary for survival and growth in such an extreme environment, its structure is very simple, primarily composed of clonal denitrifying {gamma}- and {beta}-proteobacterial populations. The resulting community is overabundant in key genes conferring resistance to specific stresses including nitrate, heavy metals and acetone. Evolutionary analysis indicates that lateral gene transfer could have a key function in rapid response and adaptation to environmental contamination. The results presented in this study have important implications in understanding, assessing and predicting the impacts of human-induced activities on microbial communities ranging from human health to agriculture to environmental management, and their responses to environmental changes.

Effect of Temperature on Precipitation Rate of Calcium Carbonate Produced through Microbial Metabolic Process of Bio Materials

Directory of Open Access Journals (Sweden)

Prima Yane Putri

2016-09-01

Full Text Available Concrete is the most widely used construction material in civil engineering. But plain concrete is a brittle material and has little resistance to cracking. The cracking in concrete promotes deterioration such as the corrosion of reinforcing rebar, therefore, repair in filling the crack is often carried out. Recently, repair methods using bio-based materials associated with microbial metabolic processes leading to precipitation of calcium carbonate have been intensively studied. In this study, influencing factors on the precipitation rate depending on the constituents of bio-based material comprising yeast, glucose and calcium acetate mixed in tris buffer solution was examined for improving the rate of initial reactions. In addition, effect of temperature change on the amount of calcium carbonate precipitation was also investigated. The precipitates were identified by X-ray diffraction. It was shown that the increase of temperature lead to a change on calcium carbonate precipitation and caused the pH decrease under 7.0.

Laboratory studies of oil spill bioremediation; toward understanding field behavior

International Nuclear Information System (INIS)

Prince, R.C.; Hinton, S.M.; Elmendorf, D.L.; Lute, J.R.; Grossman, M.J.; Robbins, W.K.; Hsu, Chang S.; Richard, B.E.; Haith, C.E.; Senius, J.D.; Minak-Bernero, V.; Chianelli, R.R.; Bragg, J.R.; Douglas, G.S.

1993-01-01

Oil spill remediation aims to enhance the natural process of microbial hydrocarbon biodegradation. The microbial foundations have been studied throughout this century, but the focus of most of this work has been on the degradation of well defined compounds by well defined microbial species. This paper addresses laboratory studies on crude oil biodegradation by microbial consortia obtained from oiled beaches in Prince William Sound, Alaska following the spill from the Exxon Valdez. It demonstrates that oil degradation is indeed likely to be nitrogen-limited in Prince William Sound, the different molecular classes in crude oil that are subjected to biodegradation, the identification of conserved species in the oil that can be used for assessing biodegradation and bioremediation in the field, the effectiveness of fertilizers in stimulating sub-surface biodegradation, the role of the olephilic fertilizer Inipol EAP22, and the identification of the oil-degrading microorganisms in Prince William Sound. Together, these laboratory studies provided guidance and important insights into the microbial phenomena underlying the successful bioremediation of the oiled shorelines

Improving Microbial Genome Annotations in an Integrated Database Context

Science.gov (United States)

Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken; Anderson, Iain; Mavromatis, Konstantinos; Kyrpides, Nikos C.; Ivanova, Natalia N.

2013-01-01

Effective comparative analysis of microbial genomes requires a consistent and complete view of biological data. Consistency regards the biological coherence of annotations, while completeness regards the extent and coverage of functional characterization for genomes. We have developed tools that allow scientists to assess and improve the consistency and completeness of microbial genome annotations in the context of the Integrated Microbial Genomes (IMG) family of systems. All publicly available microbial genomes are characterized in IMG using different functional annotation and pathway resources, thus providing a comprehensive framework for identifying and resolving annotation discrepancies. A rule based system for predicting phenotypes in IMG provides a powerful mechanism for validating functional annotations, whereby the phenotypic traits of an organism are inferred based on the presence of certain metabolic reactions and pathways and compared to experimentally observed phenotypes. The IMG family of systems are available at http://img.jgi.doe.gov/. PMID:23424620

Improving microbial genome annotations in an integrated database context.

Directory of Open Access Journals (Sweden)

I-Min A Chen

Full Text Available Effective comparative analysis of microbial genomes requires a consistent and complete view of biological data. Consistency regards the biological coherence of annotations, while completeness regards the extent and coverage of functional characterization for genomes. We have developed tools that allow scientists to assess and improve the consistency and completeness of microbial genome annotations in the context of the Integrated Microbial Genomes (IMG family of systems. All publicly available microbial genomes are characterized in IMG using different functional annotation and pathway resources, thus providing a comprehensive framework for identifying and resolving annotation discrepancies. A rule based system for predicting phenotypes in IMG provides a powerful mechanism for validating functional annotations, whereby the phenotypic traits of an organism are inferred based on the presence of certain metabolic reactions and pathways and compared to experimentally observed phenotypes. The IMG family of systems are available at http://img.jgi.doe.gov/.

Untargeted metabolomics studies employing NMR and LC-MS reveal metabolic coupling between Nanoarcheum equitans and its archaeal host Ignicoccus hospitalis.

Science.gov (United States)

Hamerly, Timothy; Tripet, Brian P; Tigges, Michelle; Giannone, Richard J; Wurch, Louie; Hettich, Robert L; Podar, Mircea; Copié, Valerie; Bothner, Brian

2015-08-01

Interspecies interactions are the basis of microbial community formation and infectious diseases. Systems biology enables the construction of complex models describing such interactions, leading to a better understanding of disease states and communities. However, before interactions between complex organisms can be understood, metabolic and energetic implications of simpler real-world host-microbe systems must be worked out. To this effect, untargeted metabolomics experiments were conducted and integrated with proteomics data to characterize key molecular-level interactions between two hyperthermophilic microbial species, both of which have reduced genomes. Metabolic changes and transfer of metabolites between the archaea Ignicoccus hospitalis and Nanoarcheum equitans were investigated using integrated LC-MS and NMR metabolomics. The study of such a system is challenging, as no genetic tools are available, growth in the laboratory is challenging, and mechanisms by which they interact are unknown. Together with information about relative enzyme levels obtained from shotgun proteomics, the metabolomics data provided useful insights into metabolic pathways and cellular networks of I. hospitalis that are impacted by the presence of N. equitans , including arginine, isoleucine, and CTP biosynthesis. On the organismal level, the data indicate that N. equitans exploits metabolites generated by I. hospitalis to satisfy its own metabolic needs. This finding is based on N. equitans 's consumption of a significant fraction of the metabolite pool in I. hospitalis that cannot solely be attributed to increased biomass production for N. equitans . Combining LC-MS and NMR metabolomics datasets improved coverage of the metabolome and enhanced the identification and quantitation of cellular metabolites.

Microbial metabolic potential for carbon degradation and nutrient (nitrogen and phosphorus) acquisition in an ombrotrophic peatland.

Science.gov (United States)

Lin, Xueju; Tfaily, Malak M; Green, Stefan J; Steinweg, J Megan; Chanton, Patrick; Imvittaya, Aopeau; Chanton, Jeffrey P; Cooper, William; Schadt, Christopher; Kostka, Joel E

2014-06-01

This study integrated metagenomic and nuclear magnetic resonance (NMR) spectroscopic approaches to investigate microbial metabolic potential for organic matter decomposition and nitrogen (N) and phosphorus (P) acquisition in soils of an ombrotrophic peatland in the Marcell Experimental Forest (MEF), Minnesota, USA. This analysis revealed vertical stratification in key enzymatic pathways and taxa containing these pathways. Metagenomic analyses revealed that genes encoding laccases and dioxygenases, involved in aromatic compound degradation, declined in relative abundance with depth, while the relative abundance of genes encoding metabolism of amino sugars and all four saccharide groups increased with depth in parallel with a 50% reduction in carbohydrate content. Most Cu-oxidases were closely related to genes from Proteobacteria and Acidobacteria, and type 4 laccase-like Cu-oxidase genes were >8 times more abundant than type 3 genes, suggesting an important and overlooked role for type 4 Cu-oxidase in phenolic compound degradation. Genes associated with sulfate reduction and methanogenesis were the most abundant anaerobic respiration genes in these systems, with low levels of detection observed for genes of denitrification and Fe(III) reduction. Fermentation genes increased in relative abundance with depth and were largely affiliated with Syntrophobacter. Methylocystaceae-like small-subunit (SSU) rRNA genes, pmoA, and mmoX genes were more abundant among methanotrophs. Genes encoding N2 fixation, P uptake, and P regulons were significantly enriched in the surface peat and in comparison to other ecosystems, indicating N and P limitation. Persistence of inorganic orthophosphate throughout the peat profile in this P-limiting environment indicates that P may be bound to recalcitrant organic compounds, thus limiting P bioavailability in the subsurface. Comparative metagenomic analysis revealed a high metabolic potential for P transport and starvation, N2 fixation, and

Study on Dynamic Characteristics of Microbial Enhanced Oil Recovery

Science.gov (United States)

Zhao, Yang; Shi, Fang; Qin, Wuying; Yan, Jing

2018-01-01

With the rapid development of economy, the demand for oil is increasing day by day. MEOR has the advantages of low cost and no pollution to the environment, attracted widespread attention. In this paper, the dynamic characteristics of microbial enhanced oil recovery were studied by laboratory experiments. The result showed that all the microbial flooding recovery rate could reach more than 5%, and the total recovery could reach more than 35% and if the injection period of microbial composite system was advanced, the whole oil displacement process could be shortened and the workload would be reduced.

The mind-body-microbial continuum

OpenAIRE

Gonzalez, Antonio; Stombaugh, Jesse; Lozupone, Catherine; Turnbaugh, Peter J.; Gordon, Jeffrey I.; Knight, Rob

2011-01-01

Our understanding of the vast collection of microbes that live on and inside us (microbiota) and their collective genes (microbiome) has been revolutionized by culture-independent ?metagenomic? techniques and DNA sequencing technologies. Most of our microbes live in our gut, where they function as a metabolic organ and provide attributes not encoded in our human genome. Metagenomic studies are revealing shared and distinctive features of microbial communities inhabiting different humans. A ce...

Microbial and molecular techniques to evaluate and to implement in-situ biodegradation potential and activity at sites contaminated with aromatic and chlorinated hydrocarbons

International Nuclear Information System (INIS)

Karg, F.; Henkler, Ch.

2005-01-01

Intrinsic bio-remediation harnesses the ability of indigenous microorganisms to degrade contaminants that are present in soil and groundwater. Over the past decade many environmental regulatory agencies especially in Europe have come to recognize the importance of these natural processes in contaminant attenuation. In order to use in-situ bio-remediation to clean up a site successfully it is necessary to investigate the indigenous microbial population and its potential activity to degrade the contaminants of concern (COCs). The evaluation of naturally-occurring degradative activity in initial screening of soil and groundwater samples using recently developed molecular and microbial methods may allow for the implementation of a contaminant reduction and management program without the need for fully engineered remediation intervention. Limited engineering approaches (nutrient delivery etc.) can be implemented to support naturally-occurring bio-restoration processes to achieve a controlled, dynamic attenuation of COCs. Techniques for monitoring pollutant-degrading microorganisms were previously limited to standard culturing techniques. More recently, techniques based upon detection of genetic elements and metabolic activities have been developed in collaboration with university partners Europe, especially in France. The modern techniques are more sensitive for monitoring microbial populations, metabolic activity and the genetic potential to degrade the COCs, and avoid the need for cultivation of microbes under artificial conditions in the laboratory. Especially the application of PCR-Tests (Polymerase Chain Reaction) are able to quantify the Genetic Potential of Pollutant Microbiological Degradation on a contaminated site. This enables to use very economic in-situ site rehabilitation strategies as for example (Dynamic Natural Attenuation). For this modern application of these new strategies PLANREAL created with HPC Envirotec and together with a French University

Assessment of microbial processes on radionuclide mobility in shallow land burial. [West Valley, NY; Beatty, Nevada; Maxey Flats, Kentucky

Energy Technology Data Exchange (ETDEWEB)

Colombo, P.; Tate, R.L. III; Weiss, A.J.

1982-07-01

The impact of microbial metabolism of the organic substituents of low level radioactive wastes on radionuclide mobility in disposal sites, the nature of the microbial transformations involved in this metabolism and the effect of the prevailing environmental parameters on the quantities and types of metabolic intermediates accumulated were examined. Since both aerobic and anaerobic periods can occur during trench ecosystem development, oxidation capacities of the microbial community in the presence and absence of oxygen were analyzed. Results of gas studies performed at three commercial low level radioactive waste disposal sites were reviewed. Several deficiencies in available data were determined. Further research needs are suggested. This assessment has demonstrated that the biochemical capabilities expressed within the low level radioactive waste disposal site are common to a wide variety of soil bacteria. Hence, assuming trenches would not be placed in sites with such extreme abiotic conditions that all microbial activity is precluded, the microbial populations needed for colonization and decomposition of the organic waste substances are readily provided from the waste itself and from the soil of existing and any proposed disposal sites. Indeed, considering the ubiquity of occurrence of the microorganisms responsible for waste decomposition and the chemical nature of the organic waste material, long-term prevention of biodecomposition is difficult, if not impossible.

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

Science.gov (United States)

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

Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine.

Science.gov (United States)

Louis, Petra; Flint, Harry J

2009-05-01

Butyrate-producing bacteria play a key role in colonic health in humans. This review provides an overview of the current knowledge of the diversity, metabolism and microbial ecology of this functionally important group of bacteria. Human colonic butyrate producers are Gram-positive firmicutes, but are phylogenetically diverse, with the two most abundant groups related to Eubacterium rectale/Roseburia spp. and to Faecalibacterium prausnitzii. Five different arrangements have been identified for the genes of the central pathway involved in butyrate synthesis, while in most cases butyryl-CoA : acetate CoA-transferase, rather than butyrate kinase, appears to perform the final step in butyrate synthesis. Mechanisms have been proposed recently in non-gut Clostridium spp. whereby butyrate synthesis can result in energy generation via both substrate-level phosphorylation and proton gradients. Here we suggest that these mechanisms also apply to the majority of butyrate producers from the human colon. The roles of these bacteria in the gut community and their influence on health are now being uncovered, taking advantage of the availability of cultured isolates and molecular methodologies. Populations of F. prausnitzii are reported to be decreased in Crohn's disease, for example, while populations of Roseburia relatives appear to be particularly sensitive to the diet composition in human volunteer studies.

The microbial community of a biofilm contact reactor for the treatment of winery wastewater.

Science.gov (United States)

de Beer, D M; Botes, M; Cloete, T E

2018-02-01

To utilize a three-tiered approach to provide insight into the microbial community structure, the spatial distribution and the metabolic capabilities of organisms of a biofilm in the two towers of a high-rate biological contact reactor treating winery wastewater. Next-generation sequencing indicated that bacteria primarily responsible for the removal of carbohydrates, sugars and alcohol were more abundant in tower 1 than tower 2 while nitrifying and denitrifying bacteria were more abundant in tower 2. Yeast populations differed in each tower. Fluorescent in situ hybridization coupled with confocal microscopy showed distribution of organisms confirming an oxygen gradient across the biofilm depth. The Biolog system (ECO plates) specified the different carbon-metabolizing profiles of the two biofilms. The three-tiered approach confirmed that the addition of a second subunit to the bioreactor, expanded the treatment capacity by augmenting the microbial and metabolic diversity of the system, improving the treatment scope of the system. A three-tiered biofilm analysis provided data required to optimize the design of a bioreactor to provide favourable conditions for the development of a microbial consortium, which has optimal waste removal properties for the treatment requirements at hand. © 2017 The Society for Applied Microbiology.

Recent applications of synthetic biology tools for yeast metabolic engineering

DEFF Research Database (Denmark)

Jensen, Michael Krogh; Keasling, Jay

2015-01-01

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

Use of genome-scale microbial models for metabolic engineering

DEFF Research Database (Denmark)

Patil, Kiran Raosaheb; Åkesson, M.; Nielsen, Jens

2004-01-01

Metabolic engineering serves as an integrated approach to design new cell factories by providing rational design procedures and valuable mathematical and experimental tools. Mathematical models have an important role for phenotypic analysis, but can also be used for the design of optimal metaboli...... network structures. The major challenge for metabolic engineering in the post-genomic era is to broaden its design methodologies to incorporate genome-scale biological data. Genome-scale stoichiometric models of microorganisms represent a first step in this direction....

Survey of safety practices among hospital laboratories in Oromia Regional State, Ethiopia.

Science.gov (United States)

Sewunet, Tsegaye; Kebede, Wakjira; Wondafrash, Beyene; Workalemau, Bereket; Abebe, Gemeda

2014-10-01

Unsafe working practices, working environments, disposable waste products, and chemicals in clinical laboratories contribute to infectious and non-infectious hazards. Staffs, the community, and patients are less safe. Furthermore, such practices compromise the quality of laboratory services. We conducted a study to describe safety practices in public hospital laboratories of Oromia Regional State, Ethiopia. Randomly selected ten public hospital laboratories in Oromia Regional State were studied from Oct 2011- Feb 2012. Self-administered structured questionnaire and observation checklists were used for data collection. The respondents were heads of the laboratories, senior technicians, and safety officers. The questionnaire addressed biosafety label, microbial hazards, chemical hazards, physical/mechanical hazards, personal protective equipment, first aid kits and waste disposal system. The data was analyzed using descriptive analysis with SPSS version16 statistical software. All of the respondents reported none of the hospital laboratories were labeled with the appropriate safety label and safety symbols. These respondents also reported they may contain organisms grouped under risk group IV in the absence of microbiological safety cabinets. Overall, the respondents reported that there were poor safety regulations or standards in their laboratories. There were higher risks of microbial, chemical and physical/mechanical hazards. Laboratory safety in public hospitals of Oromia Regional State is below the standard. The laboratory workers are at high risk of combined physical, chemical and microbial hazards. Prompt recognition of the problem and immediate action is mandatory to ensure safe working environment in health laboratories.

Unveiling Microbial Carbon Cycling Processes in Key U.S. Soils using ''Omics''

Energy Technology Data Exchange (ETDEWEB)

Myrold, David D. [Oregon State Univ., Corvallis, OR (United States); Bottomely, Peter J. [Oregon State Univ., Corvallis, OR (United States); Jumpponen, Ari [Kansas State Univ., Manhattan, KS (United States); Rice, Charles W. [Kansas State Univ., Manhattan, KS (United States); Zeglin, Lydia H. [Kansas State Univ., Manhattan, KS (United States); David, Maude M. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Jansson, Janet K. [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Prestat, Emmanuel [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Hettich, Robert L. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

2014-09-17

biology approach, considering the complex soil microbial community as a functioning system and using state-of-the-art metatranscriptomic, metaproteomic, and metabolomic approaches. These omics tools were refined, applied to field experiments, and confirmed with controlled laboratory studies. Our experiments were designed to specifically identify microbial community members and processes that are instrumental players in processing of C in the prairie soils and how these processes are impacted by wetting and drying events. This project addresses a key ecosystem in the United States that current climate models predict will be subjected to dramatic changes in rainfall patterns as a result of global warming. Currently Mollisols, such as those of the tallgrass prairie, are thought to sequester more C than is released into the atmosphere, but it is not known what changes in rainfall patterns will have on future C fluxes. Through an analysis of the molecular response of the soil microbial community to shifts in precipitation cycles that are accompanied by phenologically driven changes in quality of plant C rhizodeposits, we gained deeper insight into how the metabolism of microbes has adapted to different precipitation regimes and the impact of this adaption on the fate of C deposited into soil. In doing so, we addressed key questions about the microbial cycling of C in soils that have been identified by the DOE.

Microbial analysis of the buffer/container experiment at AECL`s Underground Research Laboratory

Energy Technology Data Exchange (ETDEWEB)

Stroes-Gascoyne, S; Hamon, C J; Haveman, S A; Delaney, T L [Atomic Energy of Canada Ltd., Pinawa, MB (Canada). Whiteshell Labs; Pedersen, K; Ekendahl, S; Jahromi, N; Arlinger, J; Hallbeck, L [Univ. of Goeteborg, (Sweden). Dept. of General and Marine Microbiology; Daumas, S; Dekeyser, K [Guiges Recherche Appliquee en Microbiologie, Aix-en-Provence, (France)

1996-05-01

The Buffer/Container experiment was carried out for 2.5 years to examine the in-situ performance of compacted buffer material in a single emplacement borehole under vault-relevant conditions. During decommissioning of this experiment, numerous samples were taken for microbial analysis to determine if the naturally present microbial population in buffer material survived to conditions and to determine which groups of microorganisms would be dominant in such a simulated vault environment. Microbial analyses were initiated within 24 hour of sampling for all types of samples taken. The culture results showed an almost universal disappearance of viable microorganisms in the samples taken from near the heater surface. The microbial activity measurements confirmed the lack of viable organisms with very weak or no activity measured in most of these samples. Generally, aerobic heterotrophic culture conditions gave the highest mean colony-forming units (CFU) values at both 25 and 50 C. Under anaerobic conditions, and especially at 50 C, lower mean CFU values were obtained. In all samples analyzed, numbers of sulfate reducing bacteria were less than 1000 CFU/g dry material. Methanogens were either not present or were found in very low numbers. Anaerobic sulfur oxidizing bacteria were found in higher numbers in most sample types with sufficient moisture. The statistical evaluation of the culture data demonstrated clearly that the water content was the variable limiting the viability of the bacteria present, and not the temperature. 68 refs, 35 figs, 37 tabs.

Simultaneous efficient removal of oxyfluorfen with electricity generation in a microbial fuel cell and its microbial community analysis.

Science.gov (United States)

Zhang, Qinghua; Zhang, Lei; Wang, Han; Jiang, Qinrui; Zhu, Xiaoyu

2018-02-01

The performance of a microbial fuel cell (MFC) to degrade oxyfluorfen was investigated. Approximately 77% of 50 mg/L oxyfluorfen was degraded within 24 h by anodic biofilm. The temperature, pH, and initial oxyfluorfen concentration had a significant effect on oxyfluorfen degrading, and a maximum degradation rate of 94.95% could theoretically be achieved at 31.96 °C, a pH of 7.65, and an initial oxyfluorfen concentration of 120.05 mg/L. Oxyfluorfen was further catabolized through various microbial metabolism pathways. Moreover, the anodic biofilm exhibited multiple catabolic capacities to 4-nitrophenol, chloramphenicol, pyraclostrobin, and sulfamethoxazole. Microbial community analysis indicated that functional bacteria Arcobacter, Acinetobacter, Azospirillum, Azonexus, and Comamonas were the predominant genera in the anodic biofilm. In terms of the efficient removal of various organic compounds and energy recovery, the MFC seemed to be a promising approach for the treatment of environmental contaminants. Copyright © 2017 Elsevier Ltd. All rights reserved.

Molecular Paths Linking Metabolic Diseases, Gut Microbiota Dysbiosis and Enterobacteria Infections.

Science.gov (United States)

Serino, Matteo

2018-03-02

Alterations of both ecology and functions of gut microbiota are conspicuous traits of several inflammatory pathologies, notably metabolic diseases such as obesity and type 2 diabetes. Moreover, the proliferation of enterobacteria, subdominant members of the intestinal microbial ecosystem, has been shown to be favored by Western diet, the strongest inducer of both metabolic diseases and gut microbiota dysbiosis. The inner interdependence between the host and the gut microbiota is based on a plethora of molecular mechanisms by which host and intestinal microbes modify each other. Among these mechanisms are as follows: (i) the well-known metabolic impact of short chain fatty acids, produced by microbial fermentation of complex carbohydrates from plants; (ii) a mutual modulation of miRNAs expression, both on the eukaryotic (host) and prokaryotic (gut microbes) side; (iii) the production by enterobacteria of virulence factors such as the genotoxin colibactin, shown to alter the integrity of host genome and induce a senescence-like phenotype in vitro; (iv) the microbial excretion of outer-membrane vesicles, which, in addition to other functions, may act as a carrier for multiple molecules such as toxins to be delivered to target cells. In this review, I describe the major molecular mechanisms by which gut microbes exert their metabolic impact at a multi-organ level (the gut barrier being in the front line) and support the emerging triad of metabolic diseases, gut microbiota dysbiosis and enterobacteria infections. Copyright © 2018 Elsevier Ltd. All rights reserved.

Biochar affects soil organic matter cycling and microbial functions but does not alter microbial community structure in a paddy soil.

Science.gov (United States)

Tian, Jing; Wang, Jingyuan; Dippold, Michaela; Gao, Yang; Blagodatskaya, Evgenia; Kuzyakov, Yakov

2016-06-15

The application of biochar (BC) in conjunction with mineral fertilizers is one of the most promising management practices recommended to improve soil quality. However, the interactive mechanisms of BC and mineral fertilizer addition affecting microbial communities and functions associated with soil organic matter (SOM) cycling are poorly understood. We investigated the SOM in physical and chemical fractions, microbial community structure (using phospholipid fatty acid analysis, PLFA) and functions (by analyzing enzymes involved in C and N cycling and Biolog) in a 6-year field experiment with BC and NPK amendment. BC application increased total soil C and particulate organic C for 47.4-50.4% and 63.7-74.6%, respectively. The effects of BC on the microbial community and C-cycling enzymes were dependent on fertilization. Addition of BC alone did not change the microbial community compared with the control, but altered the microbial community structure in conjunction with NPK fertilization. SOM fractions accounted for 55% of the variance in the PLFA-related microbial community structure. The particulate organic N explained the largest variation in the microbial community structure. Microbial metabolic activity strongly increased after BC addition, particularly the utilization of amino acids and amines due to an increase in the activity of proteolytic (l-leucine aminopeptidase) enzymes. These results indicate that microorganisms start to mine N from the SOM to compensate for high C:N ratios after BC application, which consequently accelerate cycling of stable N. Concluding, BC in combination with NPK fertilizer application strongly affected microbial community composition and functions, which consequently influenced SOM cycling. Copyright © 2016 Elsevier B.V. All rights reserved.

Inferred effects of cloud deposition on forest floor nutrient cycling and microbial properties along a short elevation gradient

International Nuclear Information System (INIS)

Lavoie, M.; Bradley, R.L.

2003-01-01

Higher cloud cover significantly decreases forest floor pH, decrease exchangeable cations, modifies mineral-N speciation and increases physiological stress within microbial communities. - Cloud water deposition often increases with elevation, and it is widely accepted that this cloud water increases acid loading to upland forest ecosystems. A study was undertaken in south-eastern Quebec to determine if a 250 m elevation gradient (i.e. 420-665 m), along a uniform sugar-maple stand on the slope of Mount Orford, corresponded to a pH gradient in the forest floor and to predictable changes in soil nutrient availability and microbial properties. Precipitation data from a nearby study, and a photographic survey, provided presumptive evidence that this elevation gradient corresponded to a strong gradient in cloud water deposition. Forest floor temperature did not differ significantly across elevations. Forest floor moisture content was significantly higher, whereas pH and exchangeable Ca and Mg were significantly lower, at the higher elevations. Average seasonal net nitrification rates, determined by long-term laboratory incubations, did not differ significantly across elevations, whereas average seasonal net ammonification rates were significantly higher at higher elevations. Basal respiration rates and microbial biomass did not differ significantly across elevations, but metabolic quotient was significantly higher at higher elevations indicating possible environmental stress on forest floor microbial communities due to cloud water deposition. Anaerobic N mineralisation rates were significantly higher at higher elevations suggesting that N-limited microbial communities frequently exposed to cloud cover can be important short-term sinks for atmospheric N, thereby contributing to increase the active-N fraction of forest floors. We conclude that, where no significant changes in vegetation or temperature occur, elevation gradients can still be used to understand the spatial

The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. II. Metabolic Functions of Abundant Community Members Predicted from Metagenomic Analyses.

Science.gov (United States)

Thiel, Vera; Hügler, Michael; Ward, David M; Bryant, Donald A

2017-01-01

Microbial mat communities in the effluent channels of Octopus and Mushroom Springs within the Lower Geyser Basin of Yellowstone National Park have been extensively characterized. Previous studies have focused on the chlorophototrophic organisms of the phyla Cyanobacteria and Chloroflexi . However, the diversity and metabolic functions of the other portion of the community in the microoxic/anoxic region of the mat are poorly understood. We recently described the diverse but extremely uneven microbial assemblage in the undermat of Mushroom Spring based on 16S rRNA amplicon sequences, which was dominated by Roseiflexus members, filamentous anoxygenic chlorophototrophs. In this study, we analyzed the orange-colored undermat portion of the community of Mushroom Spring mats in a genome-centric approach and discuss the metabolic potentials of the major members. Metagenome binning recovered partial genomes of all abundant community members, ranging in completeness from ~28 to 96%, and allowed affiliation of function with taxonomic identity even for representatives of novel and Candidate phyla. Less complete metagenomic bins correlated with high microdiversity. The undermat portion of the community was found to be a mixture of phototrophic and chemotrophic organisms, which use bicarbonate as well as organic carbon sources derived from different cell components and fermentation products. The presence of rhodopsin genes in many taxa strengthens the hypothesis that light energy is of major importance. Evidence for the usage of all four bacterial carbon fixation pathways was found in the metagenome. Nitrogen fixation appears to be limited to Synechococcus spp. in the upper mat layer and Thermodesulfovibrio sp. in the undermat, and nitrate/nitrite metabolism was limited. A closed sulfur cycle is indicated by biological sulfate reduction combined with the presence of genes for sulfide oxidation mainly in phototrophs. Finally, a variety of undermat microorganisms have genes for

The Dark Side of the Mushroom Spring Microbial Mat: Life in the Shadow of Chlorophototrophs. II. Metabolic Functions of Abundant Community Members Predicted from Metagenomic Analyses

Directory of Open Access Journals (Sweden)

Vera Thiel

2017-06-01

Full Text Available Microbial mat communities in the effluent channels of Octopus and Mushroom Springs within the Lower Geyser Basin of Yellowstone National Park have been extensively characterized. Previous studies have focused on the chlorophototrophic organisms of the phyla Cyanobacteria and Chloroflexi. However, the diversity and metabolic functions of the other portion of the community in the microoxic/anoxic region of the mat are poorly understood. We recently described the diverse but extremely uneven microbial assemblage in the undermat of Mushroom Spring based on 16S rRNA amplicon sequences, which was dominated by Roseiflexus members, filamentous anoxygenic chlorophototrophs. In this study, we analyzed the orange-colored undermat portion of the community of Mushroom Spring mats in a genome-centric approach and discuss the metabolic potentials of the major members. Metagenome binning recovered partial genomes of all abundant community members, ranging in completeness from ~28 to 96%, and allowed affiliation of function with taxonomic identity even for representatives of novel and Candidate phyla. Less complete metagenomic bins correlated with high microdiversity. The undermat portion of the community was found to be a mixture of phototrophic and chemotrophic organisms, which use bicarbonate as well as organic carbon sources derived from different cell components and fermentation products. The presence of rhodopsin genes in many taxa strengthens the hypothesis that light energy is of major importance. Evidence for the usage of all four bacterial carbon fixation pathways was found in the metagenome. Nitrogen fixation appears to be limited to Synechococcus spp. in the upper mat layer and Thermodesulfovibrio sp. in the undermat, and nitrate/nitrite metabolism was limited. A closed sulfur cycle is indicated by biological sulfate reduction combined with the presence of genes for sulfide oxidation mainly in phototrophs. Finally, a variety of undermat

Microbial succession and the functional potential during the fermentation of Chinese soy sauce brine.

Science.gov (United States)

Sulaiman, Joanita; Gan, Han Ming; Yin, Wai-Fong; Chan, Kok-Gan

2014-01-01

The quality of traditional Chinese soy sauce is determined by microbial communities and their inter-related metabolic roles in the fermentation tank. In this study, traditional Chinese soy sauce brine samples were obtained periodically to monitor the transitions of the microbial population and functional properties during the 6 months of fermentation process. Whole genome shotgun method revealed that the fermentation brine was dominated by the bacterial genus Weissella and later dominated by the fungal genus Candida. Metabolic reconstruction of the metagenome sequences demonstrated a characteristic profile of heterotrophic fermentation of proteins and carbohydrates. This was supported by the detection of ethanol with stable decrease of pH values. To the best of our knowledge, this is the first study that explores the temporal changes in microbial successions over a period of 6 months, through metagenome shotgun sequencing in traditional Chinese soy sauce fermentation and the biological processes therein.

The YNP Metagenome Project: Environmental Parameters Responsible for Microbial Distribution in the Yellowstone Geothermal Ecosystem

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William P. Inskeep

2013-05-01

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