Connecting the dots: could microbial translocation explain commonly reported symptoms in HIV disease?

PubMed

Wilson, Natalie L; Vance, David E; Moneyham, Linda D; Raper, James L; Mugavero, Michael J; Heath, Sonya L; Kempf, Mirjam-Colette

2014-01-01

Microbial translocation within the context of HIV disease has been described as one of the contributing causes of inflammation and disease progression in HIV infection. HIV-associated symptoms have been related to inflammatory markers and sCD14, a surrogate marker for microbial translocation, suggesting a plausible link between microbial translocation and symptom burden in HIV disease. Similar pathophysiological responses and symptoms have been reported in inflammatory bowel disease. We provide a comprehensive review of microbial translocation, HIV-associated symptoms, and symptoms connected with inflammation. We identify studies showing a relationship among inflammatory markers, sCD14, and symptoms reported in HIV disease. A conceptual framework and rationale to investigate the link between microbial translocation and symptoms is presented. The impact of inflammation on symptoms supports recommendations to reduce inflammation as part of HIV symptom management. Research in reducing microbial translocation-induced inflammation is limited, but needed, to further promote positive health outcomes among HIV-infected patients. Published by Elsevier Inc.

Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity.

PubMed

Schirmer, Melanie; Smeekens, Sanne P; Vlamakis, Hera; Jaeger, Martin; Oosting, Marije; Franzosa, Eric A; Ter Horst, Rob; Jansen, Trees; Jacobs, Liesbeth; Bonder, Marc Jan; Kurilshikov, Alexander; Fu, Jingyuan; Joosten, Leo A B; Zhernakova, Alexandra; Huttenhower, Curtis; Wijmenga, Cisca; Netea, Mihai G; Xavier, Ramnik J

2016-11-03

Gut microbial dysbioses are linked to aberrant immune responses, which are often accompanied by abnormal production of inflammatory cytokines. As part of the Human Functional Genomics Project (HFGP), we investigate how differences in composition and function of gut microbial communities may contribute to inter-individual variation in cytokine responses to microbial stimulations in healthy humans. We observe microbiome-cytokine interaction patterns that are stimulus specific, cytokine specific, and cytokine and stimulus specific. Validation of two predicted host-microbial interactions reveal that TNFα and IFNγ production are associated with specific microbial metabolic pathways: palmitoleic acid metabolism and tryptophan degradation to tryptophol. Besides providing a resource of predicted microbially derived mediators that influence immune phenotypes in response to common microorganisms, these data can help to define principles for understanding disease susceptibility. The three HFGP studies presented in this issue lay the groundwork for further studies aimed at understanding the interplay between microbial, genetic, and environmental factors in the regulation of the immune response in humans. PAPERCLIP. Copyright © 2016 Elsevier Inc. All rights reserved.

Linking microbial and ecosystem ecology using ecological stoichiometry: a synthesis of conceptual and empirical approaches

USGS Publications Warehouse

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

2011-01-01

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

Microbial Communities as Experimental Units

PubMed Central

DAY, MITCH D.; BECK, DANIEL; FOSTER, JAMES A.

2011-01-01

Artificial ecosystem selection is an experimental technique that treats microbial communities as though they were discrete units by applying selection on community-level properties. Highly diverse microbial communities associated with humans and other organisms can have significant impacts on the health of the host. It is difficult to find correlations between microbial community composition and community-associated diseases, in part because it may be impossible to define a universal and robust species concept for microbes. Microbial communities are composed of potentially thousands of unique populations that evolved in intimate contact, so it is appropriate in many situations to view the community as the unit of analysis. This perspective is supported by recent discoveries using metagenomics and pangenomics. Artificial ecosystem selection experiments can be costly, but they bring the logical rigor of biological model systems to the emerging field of microbial community analysis. PMID:21731083

Both the intratumoral immune and microbial microenvironment are linked to recurrence in human colon cancer: results from a prospective, multicenter nodal ultrastaging trial

PubMed Central

Noguti, Juliana; Chan, Alfred A.; Bandera, Bradley; Brislawn, Colin J.; Protic, Mladjan; Sim, Myung S.; Jansson, Janet K.; Bilchik, Anton J.; Lee, Delphine J.

2018-01-01

Colon cancer (CC) is the third most common cancer diagnosed in the United States and the incidence has been rising among young adults. We and others have shown a relationship between the immune infiltrate and prognosis, with improved disease-free survival (DFS) being associated with a higher expression of CD8+ T cells. We hypothesized that a microbial signature might be associated with intratumoral immune cells as well as DFS. We found that the relative abundance of one Operational Taxonomic Unit (OTU), OTU_104, was significantly associated with recurrence even after applying false discovery correction (HR 1.21, CI 1.08 to 1.36). The final multivariable model showed that DFS was influenced by three parameters: N-stage, CD8+ labeling, as well as this OTU_104 belonging to the order Clostridiales. Not only were CD8+ labeling and OTU_104 significant contributors in the final DFS model, but they were also inversely correlated to each other (p=0.022). Interestingly, CD8+ was also significantly associated with the microbiota composition in the tumor: CD8+ T cells was inversely correlated with alpha diversity (p=0.027) and significantly associated with the beta diversity. This study is the first to demonstrate an association among the intratumoral microbiome, CD8+ T cells, and recurrence in CC. An increased relative abundance of a specific OTU_104 was inversely associated with CD8+ T cells and directly associated with CC recurrence. The link between this microbe, CD8+ T cells, and DFS has not been previously shown.

Microbial community variation and its relationship with nitrogen mineralization in historically altered forests

Treesearch

Jennifer M. Fraterrigo; Teri C. Balser; Monica g. Turner

2006-01-01

Past land use can impart soil legacies that have important implications for ecosystem function. Although these legacies have been linked with microbially mediated processes, little is known about the long-term influence of land use on soil microbial communities themselves. We examined whether historical land use affected soil microbial community composition (lipid...

Linking genes to ecosystem trace gas fluxes in a large-scale model system

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Soil microbial communities drive the resistance of ecosystem multifunctionality to global change in drylands across the globe.

PubMed

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

2017-10-01

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

The United States Culture Collection Network (USCCN): Enhancing Microbial Genomics Research through Living Microbe Culture Collections

DOE PAGES

Boundy-Mills, Kyria; Hess, Matthias; Bennett, A. Rick; ...

2015-06-19

The mission of the United States Culture Collection Network (USCCN;http://usccn.org) is “to facilitate the safe and responsible utilization of microbial resources for research, education, industry, medicine, and agriculture for the betterment of human kind.” Microbial culture collections are a key component of life science research, biotechnology, and emerging global biobased economies. Here, representatives and users of several microbial culture collections from the United States and Europe gathered at the University of California, Davis, to discuss how collections of microorganisms can better serve users and stakeholders and to showcase existing resources available in public culture collections.

The United States Culture Collection Network (USCCN): Enhancing Microbial Genomics Research through Living Microbe Culture Collections

PubMed Central

Boundy-Mills, Kyria; Hess, Matthias; Bennett, A. Rick; Ryan, Matthew; Kang, Seogchan; Nobles, David; Eisen, Jonathan A.; Inderbitzin, Patrik; Sitepu, Irnayuli R.; Torok, Tamas; Brown, Daniel R.; Cho, Juliana; Wertz, John E.; Mukherjee, Supratim; Cady, Sherry L.

2015-01-01

The mission of the United States Culture Collection Network (USCCN; http://usccn.org) is “to facilitate the safe and responsible utilization of microbial resources for research, education, industry, medicine, and agriculture for the betterment of human kind.” Microbial culture collections are a key component of life science research, biotechnology, and emerging global biobased economies. Representatives and users of several microbial culture collections from the United States and Europe gathered at the University of California, Davis, to discuss how collections of microorganisms can better serve users and stakeholders and to showcase existing resources available in public culture collections. PMID:26092453

The United States Culture Collection Network (USCCN): Enhancing Microbial Genomics Research through Living Microbe Culture Collections

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boundy-Mills, Kyria; Hess, Matthias; Bennett, A. Rick

The mission of the United States Culture Collection Network (USCCN;http://usccn.org) is “to facilitate the safe and responsible utilization of microbial resources for research, education, industry, medicine, and agriculture for the betterment of human kind.” Microbial culture collections are a key component of life science research, biotechnology, and emerging global biobased economies. Here, representatives and users of several microbial culture collections from the United States and Europe gathered at the University of California, Davis, to discuss how collections of microorganisms can better serve users and stakeholders and to showcase existing resources available in public culture collections.

The United States Culture Collection Network (USCCN): Enhancing Microbial Genomics Research through Living Microbe Culture Collections

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boundy-Mills, K.; Hess, Matthias; Bennett, A. R.

The mission of the United States Culture Collection Network (USCCN; http://usccn.org) is "to facilitate the safe and responsible utilization of microbial resources for research, education, industry, medicine, and agriculture for the betterment of human kind." Microbial culture collections are a key component of life science research, biotechnology, and emerging global biobased economies. Representatives and users of several microbial culture collections from the United States and Europe gathered at the University of California, Davis, to discuss how collections of microorganisms can better serve users and stakeholders and to showcase existing resources available in public culture collections.

LABORATORY AND FIELD RESULTS LINKING HIGH BULK CONDUCTIVITIES TO THE MICROBIAL DEGRADATION OF PETROLEUM HYDROCARBONS

EPA Science Inventory

Diesel contaminated layer (i.e. 32-45 cm) was the most geoelectrically conductive and showed the peak microbial activity. Below the saturated zone microbial enhanced mineral weathering increases the ionic concentration of pore fluids, leading to increased bulk electrical conducit...

PCB126 modulates fecal microbial fermentation of the dietary fiber inulin

USDA-ARS?s Scientific Manuscript database

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...

Microbial communities associated with wet flue gas desulfurization systems

PubMed Central

Brown, Bryan P.; Brown, Shannon R.; Senko, John M.

2012-01-01

Flue gas desulfurization (FGD) systems are employed to remove SOx gasses that are produced by the combustion of coal for electric power generation, and consequently limit acid rain associated with these activities. Wet FGDs represent a physicochemically extreme environment due to the high operating temperatures and total dissolved solids (TDS) of fluids in the interior of the FGD units. Despite the potential importance of microbial activities in the performance and operation of FGD systems, the microbial communities associated with them have not been evaluated. Microbial communities associated with distinct process points of FGD systems at several coal-fired electricity generation facilities were evaluated using culture-dependent and -independent approaches. Due to the high solute concentrations and temperatures in the FGD absorber units, culturable halothermophilic/tolerant bacteria were more abundant in samples collected from within the absorber units than in samples collected from the makeup waters that are used to replenish fluids inside the absorber units. Evaluation of bacterial 16S rRNA genes recovered from scale deposits on the walls of absorber units revealed that the microbial communities associated with these deposits are primarily composed of thermophilic bacterial lineages. These findings suggest that unique microbial communities develop in FGD systems in response to physicochemical characteristics of the different process points within the systems. The activities of the thermophilic microbial communities that develop within scale deposits could play a role in the corrosion of steel structures in FGD systems. PMID:23226147

Reintroduction of locally extinct vertebrates impacts arid soil fungal communities.

PubMed

Clarke, Laurence J; Weyrich, Laura S; Cooper, Alan

2015-06-01

Introduced species have contributed to extinction of native vertebrates in many parts of the world. Changes to vertebrate assemblages are also likely to alter microbial communities through coextinction of some taxa and the introduction of others. Many attempts to restore degraded habitats involve removal of exotic vertebrates (livestock and feral animals) and reintroduction of locally extinct species, but the impact of such reintroductions on microbial communities is largely unknown. We used high-throughput DNA sequencing of the fungal internal transcribed spacer I (ITS1) region to examine whether replacing exotic vertebrates with reintroduced native vertebrates led to changes in soil fungal communities at a reserve in arid central Australia. Soil fungal diversity was significantly different between dune and swale (interdune) habitats. Fungal communities also differed significantly between sites with exotic or reintroduced native vertebrates after controlling for the effect of habitat. Several fungal operational taxonomic units (OTUs) found exclusively inside the reserve were present in scats from reintroduced native vertebrates, providing a direct link between the vertebrate assemblage and soil microbial communities. Our results show that changes to vertebrate assemblages through local extinctions and the invasion of exotic species can alter soil fungal communities. If local extinction of one or several species results in the coextinction of microbial taxa, the full complement of ecological interactions may never be restored. © 2015 John Wiley & Sons Ltd.

The United States Culture Collection Network (USCCN): Enhancing Microbial Genomics Research through Living Microbe Culture Collections.

PubMed

Boundy-Mills, Kyria; Hess, Matthias; Bennett, A Rick; Ryan, Matthew; Kang, Seogchan; Nobles, David; Eisen, Jonathan A; Inderbitzin, Patrik; Sitepu, Irnayuli R; Torok, Tamas; Brown, Daniel R; Cho, Juliana; Wertz, John E; Mukherjee, Supratim; Cady, Sherry L; McCluskey, Kevin

2015-09-01

The mission of the United States Culture Collection Network (USCCN; http://usccn.org) is "to facilitate the safe and responsible utilization of microbial resources for research, education, industry, medicine, and agriculture for the betterment of human kind." Microbial culture collections are a key component of life science research, biotechnology, and emerging global biobased economies. Representatives and users of several microbial culture collections from the United States and Europe gathered at the University of California, Davis, to discuss how collections of microorganisms can better serve users and stakeholders and to showcase existing resources available in public culture collections. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Microbial Source Tracking: Current and Future Molecular Tools in Microbial Water Quality Forensics

EPA Science Inventory

Current regulations in the United States stipulate that the microbial quality of waters used for consumption and recreational activities should be determined regularly by measuring microbial indicators of fecal pollution. Hence, the microbial risk associated with these waters is...

Effects of Resource Chemistry on the Composition and Function of Stream Hyporheic Biofilms

PubMed Central

Hall, E. K.; Besemer, K.; Kohl, L.; Preiler, C.; Riedel, K.; Schneider, T.; Wanek, W.; Battin, T. J.

2012-01-01

Fluvial ecosystems process large quantities of dissolved organic matter as it moves from the headwater streams to the sea. In particular, hyporheic sediments are centers of high biogeochemical reactivity due to their elevated residence time and high microbial biomass and activity. However, the interaction between organic matter and microbial dynamics in the hyporheic zone remains poorly understood. We evaluated how variance in resource chemistry affected the microbial community and its associated activity in experimentally grown hyporheic biofilms. To do this we fed beech leaf leachates that differed in chemical composition to a series of bioreactors filled with sediment from a sub-alpine stream. Differences in resource chemistry resulted in differences in diversity and phylogenetic origin of microbial proteins, enzyme activity, and microbial biomass stoichiometry. Specifically, increased lignin, phenolics, and manganese in a single leachate resulted in increased phenoloxidase and peroxidase activity, elevated microbial biomass carbon:nitrogen ratio, and a greater proportion of proteins of Betaproteobacteria origin. We used this model system to attempt to link microbial form (community composition and metaproteome) with function (enzyme activity) in order to better understand the mechanisms that link resource heterogeneity to ecosystem function in stream ecosystems. PMID:22347877

Effects of resource chemistry on the composition and function of stream hyporheic biofilms.

USGS Publications Warehouse

Hall, E.K.; Besemer, K.; Kohl, L.; Preiler, C.; Reidel, K.; Schneider, T.; Wanek, W.; Battin, T.J.

2012-01-01

Fluvial ecosystems process large quantities of dissolved organic matter as it moves from the headwater streams to the sea. In particular, hyporheic sediments are centers of high biogeochemical reactivity due to their elevated residence time and high microbial biomass and activity. However, the interaction between organic matter and microbial dynamics in the hyporheic zone remains poorly understood. We evaluated how variance in resource chemistry affected the microbial community and its associated activity in experimentally grown hyporheic biofilms. To do this we fed beech leaf leachates that differed in chemical composition to a series of bioreactors filled with sediment from a sub-alpine stream. Differences in resource chemistry resulted in differences in diversity and phylogenetic origin of microbial proteins, enzyme activity, and microbial biomass stoichiometry. Specifically, increased lignin, phenolics, and manganese in a single leachate resulted in increased phenoloxidase and peroxidase activity, elevated microbial biomass carbon:nitrogen ratio, and a greater proportion of proteins of Betaproteobacteria origin. We used this model system to attempt to link microbial form (community composition and metaproteome) with function (enzyme activity) in order to better understand the mechanisms that link resource heterogeneity to ecosystem function in stream ecosystems.

Role of microbial processes in linking sandstone diagenesis with organic-rich clays

USGS Publications Warehouse

McMahon, P.B.; Chapelle, F.H.; Falls, W.F.; Bradley, P.M.

1992-01-01

Shows that the processes of microbial organic-acid production (via fermentation) in clays and microbial organic-acid consumption (via sulfate reduction) in sands effectively link organic-rich clays to sandstone diagenesis in the Black Creek Formation of South Carolina. Diagenetic processes have resulted in the formation of 10 volume percent calcite cement, 0.1 volume percent authigenic pyrite, and 1.5 volume percent secondary porosity in Black Creek sands. However, the distribution of these diagenetic processes is not uniform, resulting in net destruction of porosity in some parts of the sand and net porosity enchancement in other parts. -from Authors

Microbial community responses in forest mineral soil to compaction, organic matter removal, and vegetation control

Treesearch

Matt D. Busse; Samual E. Beattie; Robert F. Powers; Felipe G. Sanchez; Allan E. Tiarks

2006-01-01

We tested three disturbance hypotheses in young conifer plantations: H1: soil compaction and removal of surface organic matter produces sustained changes in microbial community size, activity, and structure in mineral soil; H2: microbial community characteristics in mineral soil are linked to the recovery of plant diversity...

Interactions between Snow Chemistry, Mercury Inputs and Microbial Population Dynamics in an Arctic Snowpack

PubMed Central

Larose, Catherine; Prestat, Emmanuel; Cecillon, Sébastien; Berger, Sibel; Malandain, Cédric; Lyon, Delina; Ferrari, Christophe; Schneider, Dominique; Dommergue, Aurélien; Vogel, Timothy M.

2013-01-01

We investigated the interactions between snowpack chemistry, mercury (Hg) contamination and microbial community structure and function in Arctic snow. Snowpack chemistry (inorganic and organic ions) including mercury (Hg) speciation was studied in samples collected during a two-month field study in a high Arctic site, Svalbard, Norway (79°N). Shifts in microbial community structure were determined by using a 16S rRNA gene phylogenetic microarray. We linked snowpack and meltwater chemistry to changes in microbial community structure by using co-inertia analyses (CIA) and explored changes in community function due to Hg contamination by q-PCR quantification of Hg-resistance genes in metagenomic samples. Based on the CIA, chemical and microbial data were linked (p = 0.006) with bioavailable Hg (BioHg) and methylmercury (MeHg) contributing significantly to the ordination of samples. Mercury was shown to influence community function with increases in merA gene copy numbers at low BioHg levels. Our results show that snowpacks can be considered as dynamic habitats with microbial and chemical components responding rapidly to environmental changes. PMID:24282515

Longitudinal analysis of microbiota in microalga Nannochloropsis salina cultures

DOE PAGES

Geng, Haifeng; Sale, Kenneth L.; Tran-Gyamfi, Mary Bao; ...

2016-03-08

Here, large-scale open microalgae cultivation has tremendous potential to make a significant contribution to replacing petroleum-based fuels with biofuels. Open algal cultures are unavoidably inhabited with a diversity of microbes that live on, influence, and shape the fate of these ecosystems. However, there is little understanding of the resilience and stability of the microbial communities in engineered semicontinuous algal systems. To evaluate the dynamics and resilience of the microbial communities in microalgae biofuel cultures, we conducted a longitudinal study on open systems to compare the temporal profiles of the microbiota from two multigenerational algal cohorts, which include one seeded withmore » the microbiota from an in-house culture and the other exogenously seeded with a natural-occurring consortia of bacterial species harvested from the Pacific Ocean. From these month-long, semicontinuous open microalga Nannochloropsis salina cultures, we sequenced a time-series of 46 samples, yielding 8804 operational taxonomic units derived from 9,160,076 high-quality partial 16S rRNA sequences. We provide quantitative evidence that clearly illustrates the development of microbial community is associated with microbiota ancestry. In addition, N. salina growth phases were linked with distinct changes in microbial phylotypes. Alteromonadeles dominated the community in the N. salina exponential phase whereas Alphaproteobacteria and Flavobacteriia were more prevalent in the stationary phase. We also demonstrate that the N. salina-associated microbial community in open cultures is diverse, resilient, and dynamic in response to environmental perturbations. This knowledge has general implications for developing and testing design principles of cultivated algal systems.« less

Microbial Diversity in Engineered Haloalkaline Environments Shaped by Shared Geochemical Drivers Observed in Natural Analogues

PubMed Central

Warren, Lesley A.; Kendra, Kathryn E.

2015-01-01

Microbial communities in engineered terrestrial haloalkaline environments have been poorly characterized relative to their natural counterparts and are geologically recent in formation, offering opportunities to explore microbial diversity and assembly in dynamic, geochemically comparable contexts. In this study, the microbial community structure and geochemical characteristics of three geographically dispersed bauxite residue environments along a remediation gradient were assessed and subsequently compared with other engineered and natural haloalkaline systems. In bauxite residues, bacterial communities were similar at the phylum level (dominated by Proteobacteria and Firmicutes) to those found in soda lakes, oil sands tailings, and nuclear wastes; however, they differed at lower taxonomic levels, with only 23% of operational taxonomic units (OTUs) shared with other haloalkaline environments. Although being less diverse than natural analogues, bauxite residue harbored substantial novel bacterial taxa, with 90% of OTUs nonmatchable to cultured representative sequences. Fungal communities were dominated by Ascomycota and Basidiomycota, consistent with previous studies of hypersaline environments, and also harbored substantial novel (73% of OTUs) taxa. In bauxite residues, community structure was clearly linked to geochemical and physical environmental parameters, with 84% of variation in bacterial and 73% of variation in fungal community structures explained by environmental parameters. The major driver of bacterial community structure (salinity) was consistent across natural and engineered environments; however, drivers differed for fungal community structure between natural (pH) and engineered (total alkalinity) environments. This study demonstrates that both engineered and natural terrestrial haloalkaline environments host substantial repositories of microbial diversity, which are strongly shaped by geochemical drivers. PMID:25979895

Microbial electrohydrogenesis linked to dark fermentation as integrated application for enhanced biohydrogen production: A review on process characteristics, experiences and lessons.

PubMed

Bakonyi, Péter; Kumar, Gopalakrishnan; Koók, László; Tóth, Gábor; Rózsenberszki, Tamás; Bélafi-Bakó, Katalin; Nemestóthy, Nándor

2018-03-01

Microbial electrohydrogenesis cells (MECs) are devices that have attracted significant attention from the scientific community to generate hydrogen gas electrochemically with the aid of exoelectrogen microorganisms. It has been demonstrated that MECs are capable to deal with the residual organic materials present in effluents generated along with dark fermentative hydrogen bioproduction (DF). Consequently, MECs stand as attractive post-treatment units to enhance the global H 2 yield as a part of a two-stage, integrated application (DF-MEC). In this review article, it is aimed (i) to assess results communicated in the relevant literature on cascade DF-MEC systems, (ii) describe the characteristics of each steps involved and (iii) discuss the experiences as well as the lessons in order to facilitate knowledge transfer and help the interested readers with the construction of more efficient coupled set-ups, leading eventually to the improvement of overall biohydrogen evolution performances. Copyright © 2017 Elsevier Ltd. All rights reserved.

Generating Germ-Free Drosophila to Study Gut-Microbe Interactions: Protocol to Rear Drosophila Under Axenic Conditions.

PubMed

Kietz, Christa; Pollari, Vilma; Meinander, Annika

2018-06-22

As several diseases have been linked to dysbiosis of the human intestinal microflora, manipulation of the microbiota has emerged as an exciting new strategy for potentially treating and preventing diseases. However, the human microbiota consists of a plethora of different species, and distinguishing the impact of a specific bacterial species on human health is challenging. In tackling this challenge, the fruit fly Drosophila melanogaster, with its far simpler microbial composition, has emerged as a powerful model for unraveling host-microbe interactions. To study the interplay between the resident commensal microbiome and the host, flies can be made germ-free, or axenic. To elucidate the impact of specific bacteria, axenic flies can then be re-introduced to specific microbial species. In this unit, we provide a step-by-step protocol on how to rear Drosophila melanogaster under axenic conditions and confirm the axenity of flies. © 2018 by John Wiley & Sons, Inc. © 2018 John Wiley & Sons, Inc.

How agricultural management shapes soil microbial communities: patterns emerging from genetic and genomic studies

NASA Astrophysics Data System (ADS)

Daly, Amanda; Grandy, A. Stuart

2016-04-01

Agriculture is a predominant land use and thus a large influence on global carbon (C) and nitrogen (N) balances, climate, and human health. If we are to produce food, fiber, and fuel sustainably we must maximize agricultural yield while minimizing negative environmental consequences, goals towards which we have made great strides through agronomic advances. However, most agronomic strategies have been designed with a view of soil as a black box, largely ignoring the way management is mediated by soil biota. Because soil microbes play a central role in many of the processes that deliver nutrients to crops and support their health and productivity, agricultural management strategies targeted to exploit or support microbial activity should deliver additional benefits. To do this we must determine how microbial community structure and function are shaped by agricultural practices, but until recently our characterizations of soil microbial communities in agricultural soils have been largely limited to broad taxonomic classes due to methodological constraints. With advances in high-throughput genetic and genomic sequencing techniques, better taxonomic resolution now enables us to determine how agricultural management affects specific microbes and, in turn, nutrient cycling outcomes. Here we unite findings from published research that includes genetic or genomic data about microbial community structure (e.g. 454, Illumina, clone libraries, qPCR) in soils under agricultural management regimes that differ in type and extent of tillage, cropping selections and rotations, inclusion of cover crops, organic amendments, and/or synthetic fertilizer application. We delineate patterns linking agricultural management to microbial diversity, biomass, C- and N-content, and abundance of microbial taxa; furthermore, where available, we compare patterns in microbial communities to patterns in soil extracellular enzyme activities, catabolic profiles, inorganic nitrogen pools, and nitrogen transforming processes. Where genetic data are scarce, we further inform our observations with data from phosopholipid fatty acid, ribosomal intergenic spacer, (terminal) restriction fragment length polymorphism, and denaturing gradient gel electrophoresis analyses. By summarizing the most current information about microbial community structure under different agricultural management strategies, we hope to jumpstart a dialogue that could ultimately inspire novel - and sustainable - agronomic approaches that work with and through soil microbes.

Effect of plant harvesting on the performance of constructed wetlands during winter: radial oxygen loss and microbial characteristics.

PubMed

Wang, Qian; Xie, Huijun; Zhang, Jian; Liang, Shuang; Ngo, Huu Hao; Guo, Wenshan; Liu, Chen; Zhao, Congcong; Li, Hao

2015-05-01

The aboveground tissue of plants is important for providing roots with constant photosynthetic resources. However, the aboveground biomass is usually harvested before winter to maintain the permanent removal of nutrients. In this work, the effects of harvest on plants' involvement in oxygen input as well as in microbial abundance and activity were investigated in detail. Three series of constructed wetlands with integrated plants ("unharvested"), harvested plants ("harvested"), and fully cleared plants ("cleared") were set up. Better performance was found in the unharvested units, with the radial oxygen loss (ROL) rates ranging from 0.05 to 0.59 μmol O₂/h/plant, followed by the harvested units that had relatively lower ROL rates (0.01 to 0.52 μmol O₂/h/plant). The cleared units had the lowest removal efficiency, which had no rhizome resources from the plants. The microbial population and activity were highest in the unharvested units, followed by the harvested and cleared units. Results showed that bacterial abundances and enhanced microbial activity were ten times higher on root surfaces compared with sands. These results indicate that late autumn harvesting of the aboveground biomass exhibited negative effects on plant ROL as well as on the microbial population and activity during the following winter.

Linking Specific Heterotrophic Bacterial Populations to Bioreduction of Uranium and Nitrate in Contaminated Subsurface Sediments by Using Stable Isotope Probing▿†

PubMed Central

Akob, Denise M.; Kerkhof, Lee; Küsel, Kirsten; Watson, David B.; Palumbo, Anthony V.; Kostka, Joel E.

2011-01-01

Shifts in terminal electron-accepting processes during biostimulation of uranium-contaminated sediments were linked to the composition of stimulated microbial populations using DNA-based stable isotope probing. Nitrate reduction preceded U(VI) and Fe(III) reduction in [13C]ethanol-amended microcosms. The predominant, active denitrifying microbial groups were identified as members of the Betaproteobacteria, whereas Actinobacteria dominated under metal-reducing conditions. PMID:21948831

Microbial communities in carbonate rocks-from soil via groundwater to rocks.

PubMed

Meier, Aileen; Singh, Manu K; Kastner, Anne; Merten, Dirk; Büchel, Georg; Kothe, Erika

2017-09-01

Microbial communities in soil, groundwater, and rock of two sites in limestone were investigated to determine community parameters differentiating habitats in two lithostratigraphic untis. Lower Muschelkalk and Middle Muschelkalk associated soils, groundwater, and rock samples showed different, but overlapping microbial communities linked to carbon fluxes. The microbial diversities in soil were highest, groundwater revealed overlapping taxa but lower diversity, and rock samples were predominantly characterized by endospore forming bacteria and few archaea. Physiological profiles could establish a differentiation between habitats (soil, groundwater, rock). From community analyses and physiological profiles, different element cycles in limestone could be identified for the three habitats. While in soil, nitrogen cycling was identified as specific determinant, in rock methanogenesis linked carbonate rock to atmospheric methane cycles. These patterns specifically allowed for delineation of lithostratigraphic connections to physiological parameters. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Evaluation of microbial profile in dental unit waterlines and assessment of antimicrobial efficacy of two treating agents.

PubMed

Mungara, J; Dilna, N C; Joseph, E; Reddy, N

2013-01-01

The quality of water in a dental unit used for cooling and flushing the high and low speed handpiece, air/water syringes and the scalers is of considerable importance. The present study was carried out to enumerate and identify the microorganisms present in water samples collected from dental unit waterlines of different dental specialty clinics and to find out the efficacy of two treating agents in disinfecting dental unit waterlines. Sample included 70 dental unit waterlines from different speciality dental clinics which were checked for microbial contamination. From these dental units 40 units were randomly selected and divided into two groups of 20 each. Group A, treatment was done in 20 dental units with 0.2% Chlorhexidine gluconate solution and Group B, treatment was done in 20 dental units with 10% Povidone iodine solution and the reduction in the microbial levels were assessed. Five dental units were randomly selected and checked the microbial contamination using mineral water sterile distilled water fresh tap water as a water source in the dental unit reservoir bottles. Also from the test group, five from each group were checked for the duration of efficacy of treating agent for one week by analyzing the water samples collected on 3,5 and 7 day intervals. Most of the identified microorganisms are Gram negative and pseudomonas predominating up to 98.59% of the total isolates. Usage of disinfectants 0.2% Chlorhexidine and 10% Povidone Iodine were found to be very effective in reducing the microbial contamination and 10% Povidone iodine was found to be more efficient (97.13%) and active for a period of 3 days and gradually loosing its efficacy by 7th day. No significant difference were found in microbial contamination of water samples collected from different water outlets such as handpiece outlets, air water syringe outlets, scaler lines. To continue maintaining the sterility of the Dental unit waterlines and to complete the infection control measures adopted in the dental clinics, suitable disinfectants like 0.2% Chlorhexidine on daily basis or 10% Povidone iodine on every 3rd day basis intermittently maintain the sterility of dental unit waterlines it is essential to have a good water source and an effective disinfectant.

Environmental context affects microbial ecophysiological mechanisms underpinning soil carbon storage under different land use

NASA Astrophysics Data System (ADS)

Malik, A. A.; Puissant, J.; Buckeridge, K. M.; Goodall, T.; Jehmlich, N.; Chowdhury, S.; Gleixner, G.; Griffiths, R.

2017-12-01

Soil microorganisms act as gatekeepers for soil-atmosphere carbon exchange by balancing the accumulation and release of organic matter in soil. Increasing evidence now exists to suggest that microbial biomass contributes significantly to soil organic carbon formation. However, we do not fully understand the microbial mechanisms of organic matter processing and this hinders the development of effective land management strategies to enhance soil carbon storage. Here we empirically link key microbial ecophysiological traits to soil carbon storage in temperate grassland habitats ranging in land use from pristine species-rich grasslands to intensive croplands in 56 different soils across Britain. Physiological mechanisms of soil microorganisms were assessed using stable carbon isotope tracing and soil proteomics. Through spatial patterns and path analysis of structural equation modeling we discern two distinct pH-related mechanisms of soil carbon storage and highlight that the response of these mechanistic indicators is shaped by the environmental context. Land use intensification in low pH soils that increases soil pH above a threshold value ( 6.2) leads to loss of carbon due to increased microbial degradation as a result of lower acid retardation of organic matter decomposition. On the contrary, the loss of carbon through intensification in high pH (> 6.2) soils was linked to decreased microbial biomass and reduced carbon use efficiency that was linked to tradeoffs with stress alleviation and resource acquisition. We conclude that land use intensification-induced changes in soil pH can be used as a proxy to determine the effect of land management strategies on microbial soil carbon cycling processes and emphasize that more extensive land management practices at higher soil pH have greater potential for soil carbon storage through increased microbial metabolic efficiency, whereas in acidic soils abiotic factors exert a greater influence on the fate of soil carbon.

Bench-to-bedside review: Functional relationships between coagulation and the innate immune response and their respective roles in the pathogenesis of sepsis

PubMed Central

Opal, Steven M; Esmon, Charles T

2003-01-01

The innate immune response system is designed to alert the host rapidly to the presence of an invasive microbial pathogen that has breached the integument of multicellular eukaryotic organisms. Microbial invasion poses an immediate threat to survival, and a vigorous defense response ensues in an effort to clear the pathogen from the internal milieu of the host. The innate immune system is able to eradicate many microbial pathogens directly, or innate immunity may indirectly facilitate the removal of pathogens by activation of specific elements of the adaptive immune response (cell-mediated and humoral immunity by T cells and B cells). The coagulation system has traditionally been viewed as an entirely separate system that has arisen to prevent or limit loss of blood volume and blood components following mechanical injury to the circulatory system. It is becoming increasingly clear that coagulation and innate immunity have coevolved from a common ancestral substrate early in eukaryotic development, and that these systems continue to function as a highly integrated unit for survival defense following tissue injury. The mechanisms by which these highly complex and coregulated defense strategies are linked together are the focus of the present review. PMID:12617738

Methanogenesis-induced pH–Eh shifts drives aqueous metal(loid) mobility in sulfide mineral systems under CO2 enriched conditions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harvey, Omar R.; Qafoku, Nikolla; Cantrell, Kirk J.

2016-01-15

Accounting for microbially-mediated CO2 transformation is pivotal to assessing geochemical implications for elevated CO2 in subsurface environments. A series of batch-reactor experiments were conducted to decipher links between autotrophic methanogenesis, CO2 dynamics and aqueous Fe, As and Pb concentrations in the presence of sulfide minerals. Microbially-mediated solubility-trapping followed by pseudo-first order reduction of HCO3- to CH4 (k’ = 0.28-0.59 d-1) accounted for 95% of the CO2 loss from methanogenic experiments. Bicarbonate-to-methane reduction was pivotal in the mitigation of CO2-induced acidity (~1 pH unit) and enhancement of reducing conditions (Eh change from -0.215 to -0.332V ). Methanogenesis-associated shifts in pH-Eh valuesmore » showed no significant effect on aqueous Pb but favored, 1) increased aqueous As as a result of microbially-mediated dissolution of arsenopyrite and 2) decreased aqueous Fe due to mineral-trapping of CO2-mobilized Fe as Fe-carbonate. Its order of occurrence (and magnitude), relative to solubility- and mineral-trapping, highlighted the potential for autotrophic methanogenesis to modulate both carbon sequestration and contaminant mobility in CO2-impacted subsurface environments.« less

SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments.

PubMed

Youngblut, Nicholas D; Barnett, Samuel E; Buckley, Daniel H

2018-01-01

DNA Stable isotope probing (DNA-SIP) is a powerful method that links identity to function within microbial communities. The combination of DNA-SIP with multiplexed high throughput DNA sequencing enables simultaneous mapping of in situ assimilation dynamics for thousands of microbial taxonomic units. Hence, high throughput sequencing enabled SIP has enormous potential to reveal patterns of carbon and nitrogen exchange within microbial food webs. There are several different methods for analyzing DNA-SIP data and despite the power of SIP experiments, it remains difficult to comprehensively evaluate method accuracy across a wide range of experimental parameters. We have developed a toolset (SIPSim) that simulates DNA-SIP data, and we use this toolset to systematically evaluate different methods for analyzing DNA-SIP data. Specifically, we employ SIPSim to evaluate the effects that key experimental parameters (e.g., level of isotopic enrichment, number of labeled taxa, relative abundance of labeled taxa, community richness, community evenness, and beta-diversity) have on the specificity, sensitivity, and balanced accuracy (defined as the product of specificity and sensitivity) of DNA-SIP analyses. Furthermore, SIPSim can predict analytical accuracy and power as a function of experimental design and community characteristics, and thus should be of great use in the design and interpretation of DNA-SIP experiments.

SIPSim: A Modeling Toolkit to Predict Accuracy and Aid Design of DNA-SIP Experiments

PubMed Central

Youngblut, Nicholas D.; Barnett, Samuel E.; Buckley, Daniel H.

2018-01-01

DNA Stable isotope probing (DNA-SIP) is a powerful method that links identity to function within microbial communities. The combination of DNA-SIP with multiplexed high throughput DNA sequencing enables simultaneous mapping of in situ assimilation dynamics for thousands of microbial taxonomic units. Hence, high throughput sequencing enabled SIP has enormous potential to reveal patterns of carbon and nitrogen exchange within microbial food webs. There are several different methods for analyzing DNA-SIP data and despite the power of SIP experiments, it remains difficult to comprehensively evaluate method accuracy across a wide range of experimental parameters. We have developed a toolset (SIPSim) that simulates DNA-SIP data, and we use this toolset to systematically evaluate different methods for analyzing DNA-SIP data. Specifically, we employ SIPSim to evaluate the effects that key experimental parameters (e.g., level of isotopic enrichment, number of labeled taxa, relative abundance of labeled taxa, community richness, community evenness, and beta-diversity) have on the specificity, sensitivity, and balanced accuracy (defined as the product of specificity and sensitivity) of DNA-SIP analyses. Furthermore, SIPSim can predict analytical accuracy and power as a function of experimental design and community characteristics, and thus should be of great use in the design and interpretation of DNA-SIP experiments. PMID:29643843

Identifying protist consumers of photosynthetic picoeukaryotes in the surface ocean using stable isotope probing.

PubMed

Orsi, William D; Wilken, Susanne; Del Campo, Javier; Heger, Thierry; James, Erick; Richards, Thomas A; Keeling, Patrick J; Worden, Alexandra Z; Santoro, Alyson E

2018-02-01

Photosynthetic picoeukaryotes contribute a significant fraction of primary production in the upper ocean. Micromonas pusilla is an ecologically relevant photosynthetic picoeukaryote, abundantly and widely distributed in marine waters. Grazing by protists may control the abundance of picoeukaryotes such as M. pusilla, but the diversity of the responsible grazers is poorly understood. To identify protists consuming photosynthetic picoeukaryotes in a productive North Pacific Ocean region, we amended seawater with living 15 N, 13 C-labelled M. pusilla cells in a 24-h replicated bottle experiment. DNA stable isotope probing, combined with high-throughput sequencing of V4 hypervariable regions from 18S rRNA gene amplicons (Tag-SIP), identified 19 operational taxonomic units (OTUs) of microbial eukaryotes that consumed M. pusilla. These OTUs were distantly related to cultured taxa within the dinoflagellates, ciliates, stramenopiles (MAST-1C and MAST-3 clades) and Telonema flagellates, thus, far known only from their environmental 18S rRNA gene sequences. Our discovery of eukaryotic prey consumption by MAST cells confirms that their trophic role in marine microbial food webs includes grazing upon picoeukaryotes. Our study provides new experimental evidence directly linking the genetic identity of diverse uncultivated microbial eukaryotes to the consumption of picoeukaryotic phytoplankton in the upper ocean. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Observing and modeling links between soil moisture, microbes and CH4 fluxes from forest soils

NASA Astrophysics Data System (ADS)

Christiansen, Jesper; Levy-Booth, David; Barker, Jason; Prescott, Cindy; Grayston, Sue

2017-04-01

Soil moisture is a key driver of methane (CH4) fluxes in forest soils, both of the net uptake of atmospheric CH4 and emission from the soil. Climate and land use change will alter spatial patterns of soil moisture as well as temporal variability impacting the net CH4 exchange. The impact on the resultant net CH4 exchange however is linked to the underlying spatial and temporal distribution of the soil microbial communities involved in CH4 cycling as well as the response of the soil microbial community to environmental changes. Significant progress has been made to target specific CH4 consuming and producing soil organisms, which is invaluable in order to understand the microbial regulation of the CH4 cycle in forest soils. However, it is not clear as to which extent soil moisture shapes the structure, function and abundance of CH4 specific microorganisms and how this is linked to observed net CH4 exchange under contrasting soil moisture regimes. Here we report on the results from a research project aiming to understand how the CH4 net exchange is shaped by the interactive effects soil moisture and the spatial distribution CH4 consuming (methanotrophs) and producing (methanogens). We studied the growing season variations of in situ CH4 fluxes, microbial gene abundances of methanotrophs and methanogens, soil hydrology, and nutrient availability in three typical forest types across a soil moisture gradient in a temperate rainforest on the Canadian Pacific coast. Furthermore, we conducted laboratory experiments to determine whether the net CH4 exchange from hydrologically contrasting forest soils responded differently to changes in soil moisture. Lastly, we modelled the microbial mediation of net CH4 exchange along the soil moisture gradient using structural equation modeling. Our study shows that it is possible to link spatial patterns of in situ net exchange of CH4 to microbial abundance of CH4 consuming and producing organisms. We also show that the microbial community responds different to environmental change dependent on the soil moisture regime. These results are important to include in future modeling efforts to predict changes in soil-atmosphere exchange of CH4 under global change.

Metals other than uranium affected microbial community composition in a historical uranium-mining site.

PubMed

Sitte, Jana; Löffler, Sylvia; Burkhardt, Eva-Maria; Goldfarb, Katherine C; Büchel, Georg; Hazen, Terry C; Küsel, Kirsten

2015-12-01

To understand the links between the long-term impact of uranium and other metals on microbial community composition, ground- and surface water-influenced soils varying greatly in uranium and metal concentrations were investigated at the former uranium-mining district in Ronneburg, Germany. A soil-based 16S PhyloChip approach revealed 2358 bacterial and 35 archaeal operational taxonomic units (OTU) within diverse phylogenetic groups with higher OTU numbers than at other uranium-contaminated sites, e.g., at Oak Ridge. Iron- and sulfate-reducing bacteria (FeRB and SRB), which have the potential to attenuate uranium and other metals by the enzymatic and/or abiotic reduction of metal ions, were found at all sites. Although soil concentrations of solid-phase uranium were high, ranging from 5 to 1569 μg·g (dry weight) soil(-1), redundancy analysis (RDA) and forward selection indicated that neither total nor bio-available uranium concentrations contributed significantly to the observed OTU distribution. Instead, microbial community composition appeared to be influenced more by redox potential. Bacterial communities were also influenced by bio-available manganese and total cobalt and cadmium concentrations. Bio-available cadmium impacted FeRB distribution while bio-available manganese and copper as well as solid-phase zinc concentrations in the soil affected SRB composition. Archaeal communities were influenced by the bio-available lead as well as total zinc and cobalt concentrations. These results suggest that (i) microbial richness was not impacted by heavy metals and radionuclides and that (ii) redox potential and secondary metal contaminants had the strongest effect on microbial community composition, as opposed to uranium, the primary source of contamination.

Role of hydraulic retention time and granular medium in microbial removal in tertiary treatment reed beds.

PubMed

García, Joan; Vivar, Joan; Aromir, Maria; Mujeriego, Rafael

2003-06-01

The main objective of this paper is to evaluate the role of hydraulic retention time (HRT) and granular medium in faecal coliform (FC) and somatic coliphage (SC) removal in tertiary reed beds. Experiments were carried out in a pilot plant with four parallel reed beds (horizontal subsurface flow constructed wetlands), each one containing a different type of granular medium. This pilot plant is located in a wastewater treatment plant in Montcada i Reixac, near Barcelona, in northeastern Spain. The microbial inactivation ratios obtained in the different beds are compared as a function of three selected HRTs. Secondary effluent from the wastewater treatment plant was used as the influent of the pilot system. The microbial inactivation ratio ranged between 0.1 and 2.7 log-units for FC and from 0.5 to 1.7 log-units for SC in beds with coarser granular material (5-25mm), while it ranged between 0.7 and 3.4 log-units for FC and from 0.9 to 2.6 log-units for SC in the bed with finer material (2-13mm). HRT and granular medium are both key factors in microbial removal in the tertiary reed beds. The microbial inactivation ratio rises as the HRT increases until it reaches a saturation value (in general at an HRT of 3 days). The value of the microbial inactivation ratio at the saturation level depends on the granular medium contained in the bed. The specific surface area necessary to reach 2-3 log-units of FC and SC is approximately 3m(2)/person-equivalent.

Soil microbial diversity and activity as terroir elements of Sangiovese vineyards in the Chianti Classico region (Italy)

NASA Astrophysics Data System (ADS)

Fabiani, Arturo; Mocali, Stefano; Priori, Simone; Valboa, Giuseppe; Vignozzi, Nadia; Pellegrini, Sergio; Storchi, Paolo; Perria, Rita; Costantini, Edoardo

2016-04-01

Linking the uniqueness and quality of grapes and wine to the environment they are produced, based on the terroir concept, have recently become popular in many parts of world. The natural components of terroir are actually a set of processes, which together create a delicate equilibrium and regulation of its effect on products in both space and time. Climate, geology, geomorphology and soil are therefore the main environmental factors which make up the terroir effect on different scales. However, information on the impact of soil microbial communities on soil functions, grapevine plants and wine quality is still lacking. Thus, four of the most suitable areas (so called "cru") for the production of Sangiovese wine were chosen within the Barone Ricasoli farm of Brolio, the largest winery in the Chianti Classico area in central Italy: Fattoio, Miniera, Ceni and Colli-Agresto. Based on previous pedological and sensing technologies surveys, each area was further divided into two distinct homogeneous areas of about 1.5 ha called Basic Terroir Unit (UTB), which were monitored over 3 years (2012-2014) for the soil the chemical-physical variability (moisture, organic matter, nitrogen, potassium), the vineyard physiological status (water stress, grape production, characteristics of the grapes and wine) and the structure and activity of soil microbial communities (determined through DGGE, soil respiration and microbial biomass, respectively). The aim of the work was to assess the relationships among soil parameters and vine quality at intra- and inter- UTB level and, in particular, the potential impact of microbial composition and/or function on the terroir concept. The overall results highlighted a microbial community structure specific for each cru area and, in particular, associated to each UTB. Furthermore, microbial activity in Miniera and Ceni appeared to be positively related to Sangiovese quality, as determined through the Sangiovese Performance Index. However, except for Fattoio area which showed a higher stability over time, all the other cru displayed a remarkably higher variability in terms of both microbial community structure and functions, suggesting a predominant role of annual climatic variations.

LABORATORY AND FIELD RESULTS LINKING HIGH CONDUCTIVITIES TO THE MICROBIAL DEGRADATION OF PETROLEUM HYDROCARBONS

EPA Science Inventory

The results of a field and laboratory investigation of unconsolidated sediments contaminated by petroleum hydrocarbons and undergoing natural biodegradation are presented. Fundamental to geophysical investigations of hydrocarbon impacted sediments is the assessment of how microbi...

Construction and Analysis of Functional Networks in the Gut Microbiome of Type 2 Diabetes Patients.

PubMed

Li, Lianshuo; Wang, Zicheng; He, Peng; Ma, Shining; Du, Jie; Jiang, Rui

2016-10-01

Although networks of microbial species have been widely used in the analysis of 16S rRNA sequencing data of a microbiome, the construction and analysis of a complete microbial gene network are in general problematic because of the large number of microbial genes in metagenomics studies. To overcome this limitation, we propose to map microbial genes to functional units, including KEGG orthologous groups and the evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG) orthologous groups, to enable the construction and analysis of a microbial functional network. We devised two statistical methods to infer pairwise relationships between microbial functional units based on a deep sequencing dataset of gut microbiome from type 2 diabetes (T2D) patients as well as healthy controls. Networks containing such functional units and their significant interactions were constructed subsequently. We conducted a variety of analyses of global properties, local properties, and functional modules in the resulting functional networks. Our data indicate that besides the observations consistent with the current knowledge, this study provides novel biological insights into the gut microbiome associated with T2D. Copyright © 2016. Production and hosting by Elsevier Ltd.

Microbial quality of water in dental unit waterlines.

PubMed

Nikaeen, Mahnaz; Hatamzadeh, Maryam; Sabzevari, Zohre; Zareh, Omolbanin

2009-09-01

Dental unit waterlines (DUWLs) are ideal environment for development of microbial biofilms. Microbial contamination of water in DUWLs is thought to be the result of biofilm formation as it could serves as a haven for pathogens. The aim of this study was to assess microbial quality of water in dental unit waterlines of dental units located at the dental school of Isfahan University of Medical Sciences. Water samples were collected from air/water syringe and high-speed handpiece. Generally, 100-200 ml water samples were collected aseptically in sterile containers with sodium thiosulfate at the beginning of the day after a 2 minute purge. Samples were transferred to the laboratory in insulated box with cooling packs and examined for total viable heterotrophic bacteria and fungi. The heterotrophic plate count levels were significantly exceeded the American Dental Association recommendations for DUWL water quality (< 200 CFU/ml), in both air/water syringe (84%, CFU/ml: 500-20000) and high-speed handpiece (96%, CFU/ml: 710-36800) samples. However, there was no significant difference between the level of contamination in the air/water syringe and high-speed handpiece. Fungi were found in 28% and 36% of air/water syringe and high-speed handpiece samples, respectively; and filamentous fungi were the most frequently isolated fungi. DUWLs should be subjected to routine microbial monitoring and to a decontamination protocol in order to minimize the risk of exposure to potential pathogens from dental units.

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

PubMed

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.

Biomass-C specific temperature responses of microbial C transformations reveal consistency regardless of microbial community structure across diverse timescales of inquiry

NASA Astrophysics Data System (ADS)

Min, K.; Buckeridge, K. M.; Ziegler, S. E.; Edwards, K. A.; Bagchi, S.; Billings, S. A.

2016-12-01

The responses of heterotrophic microbial process rates to temperature in soils are often investigated in the short-term (hours to months), making it difficult to predict longer-term temperature responses. Here, we integrate the temperature sensitivity obtained from the Arrhenius model with the concepts of microbial resistance, resilience, and susceptibility to assess temporal dynamics of microbial temperature responses. We collected soils along a boreal forest climate gradient (long-term effect), and quantified exo-enzyme activities and CO2 respiration at 5, 15, and 25°C for 84 days (relatively short-term effect). Microbial process rates were examined at two levels (per g microbial biomass-C; and per g dry soil) along with community structure, to characterize driving mechanisms for temporal patterns (e.g., size of biomass, physiological plasticity, community composition). Although temperature sensitivity of exo-enzyme activities on a per g dry soil basis showed both resistance and resilience depending on the types of exo-enzyme, biomass -C-specific responses always exhibited resistance regardless of distinct community composition. Temperature sensitivity of CO2 respiration was constant across time and different communities at both units. This study advances our knowledge in two ways. First, resistant temperature sensitivity of exo-enzymes and respiration at biomass-C specific level across distinct communities and diverse timescales indicates a common relationship between microbial physiology and temperature at a fundamental level, a useful feature allowing microbial process models to be reasonably simplified. Second, different temporal responses of exo-enzymes depending on the unit selected provide a cautionary tale for those projecting future microbial behaviors, because interpretation of ecosystem process rates may vary with the unit of observation.

Microbial ecology in a future climate: effects of temperature and moisture on microbial communities of two boreal fens.

PubMed

Peltoniemi, Krista; Laiho, Raija; Juottonen, Heli; Kiikkilä, Oili; Mäkiranta, Päivi; Minkkinen, Kari; Pennanen, Taina; Penttilä, Timo; Sarjala, Tytti; Tuittila, Eeva-Stiina; Tuomivirta, Tero; Fritze, Hannu

2015-07-01

Impacts of warming with open-top chambers on microbial communities in wet conditions and in conditions resulting from moderate water-level drawdown (WLD) were studied across 0-50 cm depth in northern and southern boreal sedge fens. Warming alone decreased microbial biomass especially in the northern fen. Impact of warming on microbial PLFA and fungal ITS composition was more obvious in the northern fen and linked to moisture regime and sample depth. Fungal-specific PLFA increased in the surface peat in the drier regime and decreased in layers below 10 cm in the wet regime after warming. OTUs representing Tomentella and Lactarius were observed in drier regime and Mortierella in wet regime after warming in the northern fen. The ectomycorrhizal fungi responded only to WLD. Interestingly, warming together with WLD decreased archaeal 16S rRNA copy numbers in general, and fungal ITS copy numbers in the northern fen. Expectedly, many results indicated that microbial response on warming may be linked to the moisture regime. Results indicated that microbial community in the northern fen representing Arctic soils would be more sensitive to environmental changes. The response to future climate change clearly may vary even within a habitat type, exemplified here by boreal sedge fen. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Environmental implications of herbicide resistance: soil biology and ecology

USDA-ARS?s Scientific Manuscript database

Soil microbial community structure and activity are clearly linked to plant communities established in natural and agricultural ecosystems. A limited number of studies confirm that weeds alter their soil environment and select for specific microbial communities in the rhizosphere. Such rhizosphere m...

Linking Soil Microbial Ecology to Ecosystem Functioning in Integrated Crop-Livestock Systems

USDA-ARS?s Scientific Manuscript database

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

Long-term treatment with green tea polyphenols modifies the gut microbiome of female sprague-dawley rats.

PubMed

Wang, Jincheng; Tang, Lili; Zhou, Hongyuan; Zhou, Jun; Glenn, Travis C; Shen, Chwan-Li; Wang, Jia-Sheng

2018-06-01

Green tea polyphenols (GTP) have been shown to exert a spectrum of health benefits to animals and humans. It is plausible that the beneficial effects of GTP are a result of its interaction with the gut microbiota. This study evaluated the effect of long-term treatment with GTP on the gut microbiota of experimental rats and the potential linkage between changes of the gut microbiota with the beneficial effects of GTP. Six-month-old Sprague-Dawley rats were randomly allocated into three dosing regimens (0, 0.5%, and 1.5% of GTP) and followed for 6 months. At the end of month 3 or month 6, half of the animals from each group were sacrificed and their colon contents were collected for microbiome analysis using 16S ribosomal RNA and shotgun metagenomic community sequencing. GTP treatment significantly decreased the biodiversity and modified the microbial community in a dose-dependent manner; similar patterns were observed at both sampling times. Multiple operational taxonomic units and phylotypes were modified: the phylotypes Bacteroidetes and Oscillospira, previously linked to the lean phenotype in human and animal studies, were enriched; and Peptostreptococcaceae previously linked to colorectal cancer phenotype was depleted in GTP treated groups in a dose-dependent manner. Several microbial gene orthologs were modified, among which genes related to energy production and conversion were consistently enriched in samples from month 6 in a dose-dependent manner. This study showed that long-term treatment with GTP induced a dose-dependent modification of the gut microbiome in experimental rats, which might be linked to beneficial effects of GTP. Copyright © 2018 Elsevier Inc. All rights reserved.

Linking microbial heterotrophic activity and sediment lithology in oxic, oligotrophic sub-seafloor sediments of the north atlantic ocean.

PubMed

Picard, Aude; Ferdelman, Timothy G

2011-01-01

Microbial heterotrophic activity was investigated in oxic sub-seafloor sediments at North Pond, a sediment pond situated at 23°N on the western flank of the Mid-Atlantic Ridge. The North Pond sediments underlie the oligotrophic North Atlantic Gyre at 4580-m water depth and cover a 7-8 million-year-old basaltic crust aquifer through which seawater flows. Discrete samples for experimentation were obtained from up to ~9 m-long gravity cores taken at 14 stations in the North Pond area. Potential respiration rates were determined in sediment slurries incubated under aerobic conditions with (14)C-acetate. Microbial heterotrophic activity, as defined by oxidation of acetate to CO(2) (with O(2) as electron acceptor), was detected in all 14 stations and all depths sampled. Potential respiration rates were generally low (<0.2 nmol of respired acetate cm(-3) d(-1)) in the sediment, but indicate that microbial heterotrophic activity occurs in deep-sea, oxic, sub-seafloor sediments. Furthermore, discernable differences in activity existed between sites and within given depth profiles. At seven stations, activity was increased by several orders of magnitude at depth (up to ~12 nmol of acetate respired cm(-3) d(-1)). We attempted to correlate the measures of activity with high-resolution color and element stratigraphy. Increased activities at certain depths may be correlated to variations in the sediment geology, i.e., to the presence of dark clay-rich layers, of sandy layers, or within clay-rich horizons presumably overlying basalts. This would suggest that the distribution of microbial heterotrophic activity in deeply buried sediments may be linked to specific lithologies. Nevertheless, high-resolution microbial examination at the level currently enjoyed by sedimentologists will be required to fully explore this link.

Linking Microbial Heterotrophic Activity and Sediment Lithology in Oxic, Oligotrophic Sub-Seafloor Sediments of the North Atlantic Ocean

PubMed Central

Picard, Aude; Ferdelman, Timothy G.

2011-01-01

Microbial heterotrophic activity was investigated in oxic sub-seafloor sediments at North Pond, a sediment pond situated at 23°N on the western flank of the Mid-Atlantic Ridge. The North Pond sediments underlie the oligotrophic North Atlantic Gyre at 4580-m water depth and cover a 7–8 million-year-old basaltic crust aquifer through which seawater flows. Discrete samples for experimentation were obtained from up to ~9 m-long gravity cores taken at 14 stations in the North Pond area. Potential respiration rates were determined in sediment slurries incubated under aerobic conditions with 14C-acetate. Microbial heterotrophic activity, as defined by oxidation of acetate to CO2 (with O2 as electron acceptor), was detected in all 14 stations and all depths sampled. Potential respiration rates were generally low (<0.2 nmol of respired acetate cm−3 d−1) in the sediment, but indicate that microbial heterotrophic activity occurs in deep-sea, oxic, sub-seafloor sediments. Furthermore, discernable differences in activity existed between sites and within given depth profiles. At seven stations, activity was increased by several orders of magnitude at depth (up to ~12 nmol of acetate respired cm−3 d−1). We attempted to correlate the measures of activity with high-resolution color and element stratigraphy. Increased activities at certain depths may be correlated to variations in the sediment geology, i.e., to the presence of dark clay-rich layers, of sandy layers, or within clay-rich horizons presumably overlying basalts. This would suggest that the distribution of microbial heterotrophic activity in deeply buried sediments may be linked to specific lithologies. Nevertheless, high-resolution microbial examination at the level currently enjoyed by sedimentologists will be required to fully explore this link. PMID:22207869

Gastrointestinal microbial ecology and the safety of our food supply as related to Salmonella.

PubMed

Callaway, T R; Edrington, T S; Anderson, R C; Byrd, J A; Nisbet, D J

2008-04-01

Salmonella causes an estimated 1.3 million human foodborne illnesses and more than 500 deaths each year in the United States, representing an annual estimated cost to the economy of approximately $2.4 billion. Salmonella enterica comprises more than 2,500 serotypes. With this genetic and environmental diversity, serotypes are adapted to live in a variety of hosts, which may or may not manifest with clinical illness. Thus, Salmonella presents a multifaceted threat to food production and safety. Salmonella have been isolated from all food animals and can cause morbidity and mortality in swine, cattle, sheep, and poultry. The link between human salmonellosis and host animals is most clear in poultry. During the early part of the 20th century, a successful campaign was waged to eliminate fowl typhoid caused by Salmonella Gallinarum/Pullorum. Microbial ecology is much like macroecology; environmental niches are filled by adapted and specialized species. Elimination of S. Gallinarum cleared a niche in the on-farm and intestinal microbial ecology that was quickly exploited by Salmonella Enteritidis and other serotypes that live in other hosts, such as rodents. In the years since, human salmonellosis cases linked to poultry have increased to the point that uncooked chicken and eggs are regarded as toxic in the zeitgeist. Salmonellosis caused by poultry products have increased significantly in the past 5 yr, leading to a USDA Food Safety and Inspection Service "Salmonella Attack Plan" that aims to reduce the incidence of Salmonella in chickens below the current 19%. The prevalence of Salmonella in swine and cattle is lower, but still poses a threat to food safety and production efficiency. Thus, approaches to reducing Salmonella in animals must take into consideration that the microbial ecology of the animal is a critical factor that should be accounted for when designing intervention strategies. Use of competitive exclusion, sodium chlorate, vaccination, and bacteriophage are all strategies that can reduce Salmonella in the live animal, but it is vital to understand how they function so that we do not invoke the law of unintended consequences.

Electricity generation coupled with wastewater treatment using a microbial fuel cell composed of a modified cathode with a ceramic membrane and cellulose acetate film.

PubMed

Seo, Ha Na; Lee, Woo Jin; Hwang, Tae Sik; Park, Doo Hyun

2009-09-01

A noncompartmented microbial fuel cell (NCMFC) composed of a Mn(IV)-carbon plate and a Fe(III)-carbon plate was used for electricity generation from organic wastewater without consumption of external energy. The Fe(III)-carbon plate, coated with a porous ceramic membrane and a semipermeable cellulose acetate film, was used as a cathode, which substituted for the catholyte and cathode. The Mn(IV)-carbon plate was used as an anode without a membrane or film coating. A solar cell connected to the NCMFC activated electricity generation and bacterial consumption of organic matter contained in the wastewater. More than 99 degrees of the organic matter was biochemically oxidized during wastewater flow through the four NCMFC units. A predominant bacterium isolated from the anode surface in both the conventional and the solar cell-linked NCMFC was found to be more than 99 degrees similar to a Mn(II)-oxidizing bacterium and Burkeholderia sp., based on 16S rDNA sequence analysis. The isolate reacted electrochemically with the Mn(IV)-modified anode and produced electricity in the NCMFC. After 90 days of incubation, a bacterial species that was enriched on the Mn(IV)-modified anode surface in all of the NCMFC units was found to be very similar to the initially isolated predominant species by comparing 16S rDNA sequences.

Contrasting digestive strategies in four New Zealand herbivorous fishes as reflected by carbohydrase activity profiles.

PubMed

Skea, G L; Mountfort, D O; Clements, K D

2007-01-01

Enzymatic degradation of algal carbohydrates was examined in the New Zealand herbivorous fishes Parma alboscapularis (Pomacentridae), Aplodactylus etheridgii (Aplodactylidae), Girella tricuspidata and G. cyanea (Girellidae). Enzyme extract taken from the anterior gut wall, gut fluid and microbial pellet from sections sampled along the gut were tested for activity against starch, carrageenan, agarose and carboxymethylcellulose. Hydrolysis of starch was greater than for all other substrates tested. Endogenous (host-produced) activity in the anterior gut fluid varied between species in the order G. tricuspidata (7700 units mL(-1))>G. cyanea (2300 units mL(-1))>P. alboscapularis (2000)>A. etheridgii (1400 units mL(-1)) where one unit is equivalent to 1 mug of reducing sugar released per minute. Activity decreased markedly along the gut in all cases, so that at the posterior end of the gut only 0.3-8% of the anterior activity remained in the gut fluid. Enzyme activity against structural carbohydrates was lower than that against starch, and was of exogenous (produced by resident microbiota) origin in all species although the location of activity along the gut differed. The microbial extract of A. etheridgii displayed the highest activity against carrageenan and agarose in all gut sections, reaching maxima of 47 units mL(-1) against carrageenan and 35 units mL(-1) against agarose in the mid-gut microbial extract. Carrageenase and agarase activity in the other three species was <10 units mL(-1) for all gut sections. Results suggest that carrageenan and agarose are potentially important substrates for microbial fermentation, particularly in A. etheridgii, and that there is microbial activity in the mid-gut of this species, rather than primarily in the hind-gut as in other herbivorous species.

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

PubMed

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

2011-03-01

Microbial communities and their associated enzyme activities affect the amount and chemical quality of carbon (C) in soils. Increasing nitrogen (N) deposition, particularly in N-rich tropical forests, is likely to change the composition and behavior of microbial communities and feed back on ecosystem structure and function. This study presents a novel assessment of mechanistic links between microbial responses to N deposition and shifts in soil organic matter (SOM) quality and quantity. We used phospholipid fatty acid (PLFA) analysis and microbial enzyme assays in soils to assess microbial community responses to long-term N additions in two distinct tropical rain forests. We used soil density fractionation and 13C nuclear magnetic resonance (NMR) spectroscopy to measure related changes in SOM pool sizes and chemical quality. Microbial biomass increased in response to N fertilization in both tropical forests and corresponded to declines in pools of low-density SOM. The chemical quality of this soil C pool reflected ecosystem-specific changes in microbial community composition. In the lower-elevation forest, there was an increase in gram-negative bacteria PLFA biomass, and there were significant losses of labile C chemical groups (O-alkyls). In contrast, the upper-elevation tropical forest had an increase in fungal PLFAs with N additions and declines in C groups associated with increased soil C storage (alkyls). The dynamics of microbial enzymatic activities with N addition provided a functional link between changes in microbial community structure and SOM chemistry. Ecosystem-specific changes in microbial community composition are likely to have far-reaching effects on soil carbon storage and cycling. This study indicates that microbial communities in N-rich tropical forests can be sensitive to added N, but we can expect significant variability in how ecosystem structure and function respond to N deposition among tropical forest types.

The effects of mixotrophy on the stability and dynamics of a simple planktonic food web

USGS Publications Warehouse

Jost, Christian; Lawrence, Cathryn A.; Campolongo, Francesca; Wouter, van de Bund; Hill, Sheryl; DeAngelis, Donald L.

2004-01-01

Recognition of the microbial loop as an important part of aquatic ecosystems disrupted the notion of simple linear food chains. However, current research suggests that even the microbial loop paradigm is a gross simplification of microbial interactions due to the presence of mixotrophs—organisms that both photosynthesize and graze. We present a simple food web model with four trophic species, three of them arranged in a food chain (nutrients–autotrophs–herbivores) and the fourth as a mixotroph with links to both the nutrients and the autotrophs. This model is used to study the general implications of inclusion of the mixotrophic link in microbial food webs and the specific predictions for a parameterization that describes open ocean mixed layer plankton dynamics. The analysis indicates that the system parameters reside in a region of the parameter space where the dynamics converge to a stable equilibrium rather than displaying periodic or chaotic solutions. However, convergence requires weeks to months, suggesting that the system would never reach equilibrium in the ocean due to alteration of the physical forcing regime. Most importantly, the mixotrophic grazing link seems to stabilize the system in this region of the parameter space, particularly when nutrient recycling feedback loops are included.

Toward Linking Aboveground Vegetation Properties and Soil Microbial Communities Using Remote Sensing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hamada, Yuki; Gilbert, Jack A.; Larsen, Peter E.

2014-04-01

Despite their vital role in terrestrial ecosystem function, the distributions and dynamics of soil microbial communities (SMCs) are poorly understood. Vegetation and soil properties are the primary factors that influence SMCs. This paper discusses the potential effectiveness of remote sensing science and technologies for mapping SMC biogeography by characterizing surface biophysical properties (e.g., plant traits and community composition) strongly correlated with SMCs. Using remotely sensed biophysical properties to predict SMC distributions is extremely challenging because of the intricate interactions between biotic and abiotic factors and between above- and belowground ecosystems. However, the integration of biophysical and soil remote sensing withmore » geospatial information about the e nvironment holds great promise for mapping SMC biogeography. Additional research needs invol ve microbial taxonomic definition, soil environmental complexity, and scaling strategies. The collaborative effort of experts from diverse disciplines is essential to linking terrestrial surface biosphere observations with subsurface microbial community distributions using remote sensing.« less

Toward Linking Aboveground Vegetation Properties and Soil Microbial Communities Using Remote Sensing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hamada, Yuki; Gilbert, Jack A.; Larsen, Peter E.

2014-04-01

Despite their vital role in terrestrial ecosystem function, the distributions and dynamics of soil microbial communities (SMCs) are poorly understood. Vegetation and soil properties are the primary factors that influence SMCs. This paper discusses the potential effectiveness of remote sensing science and technologies for mapping SMC biogeography by characterizing surface biophysical properties (e.g., plant traits and community composition) strongly correlated with SMCs. Using remotely sensed biophysical properties to predict SMC distributions is extremely challenging because of the intricate interactions between biotic and abiotic factors and between above- and below-ground ecosystems. However, the integration of biophysical and soil remote sensing withmore » geospatial information about the environment holds great promise for mapping SMC biogeography. Additional research needs involve microbial taxonomic definition, soil environmental complexity, and scaling strategies. The collaborative effort of experts from diverse disciplines is essential to linking terrestrial surface biosphere observations with subsurface microbial community distributions using remote sensing.« less

Effects of microbial loading and sporulation temperature on atmospheric plasma inactivation of Bacillus subtilis spores

NASA Astrophysics Data System (ADS)

Deng, X. T.; Shi, J. J.; Shama, G.; Kong, M. G.

2005-10-01

Current inactivation studies of Bacillus subtilis spores using atmospheric-pressure glow discharges (APGD) do not consider two important factors, namely microbial loading at the surface of a substrate and sporulation temperature. Yet these are known to affect significantly microbial resistance to heat and hydrogen peroxide. This letter investigates effects of microbial loading and sporulation temperature on spore resistance to APGD. It is shown that microbial loading can lead to a stacking structure as a protective shield against APGD treatment and that high sporulation temperature increases spore resistance by altering core water content and cross-linked muramic acid content of B. subtilis spores.

Bovine Host Genetic Variation Influences Rumen Microbial Methane Production with Best Selection Criterion for Low Methane Emitting and Efficiently Feed Converting Hosts Based on Metagenomic Gene Abundance

PubMed Central

Roehe, Rainer; Dewhurst, Richard J.; Duthie, Carol-Anne; Rooke, John A.; McKain, Nest; Ross, Dave W.; Hyslop, Jimmy J.; Waterhouse, Anthony; Freeman, Tom C.

2016-01-01

Methane produced by methanogenic archaea in ruminants contributes significantly to anthropogenic greenhouse gas emissions. The host genetic link controlling microbial methane production is unknown and appropriate genetic selection strategies are not developed. We used sire progeny group differences to estimate the host genetic influence on rumen microbial methane production in a factorial experiment consisting of crossbred breed types and diets. Rumen metagenomic profiling was undertaken to investigate links between microbial genes and methane emissions or feed conversion efficiency. Sire progeny groups differed significantly in their methane emissions measured in respiration chambers. Ranking of the sire progeny groups based on methane emissions or relative archaeal abundance was consistent overall and within diet, suggesting that archaeal abundance in ruminal digesta is under host genetic control and can be used to genetically select animals without measuring methane directly. In the metagenomic analysis of rumen contents, we identified 3970 microbial genes of which 20 and 49 genes were significantly associated with methane emissions and feed conversion efficiency respectively. These explained 81% and 86% of the respective variation and were clustered in distinct functional gene networks. Methanogenesis genes (e.g. mcrA and fmdB) were associated with methane emissions, whilst host-microbiome cross talk genes (e.g. TSTA3 and FucI) were associated with feed conversion efficiency. These results strengthen the idea that the host animal controls its own microbiota to a significant extent and open up the implementation of effective breeding strategies using rumen microbial gene abundance as a predictor for difficult-to-measure traits on a large number of hosts. Generally, the results provide a proof of principle to use the relative abundance of microbial genes in the gastrointestinal tract of different species to predict their influence on traits e.g. human metabolism, health and behaviour, as well as to understand the genetic link between host and microbiome. PMID:26891056

Bovine Host Genetic Variation Influences Rumen Microbial Methane Production with Best Selection Criterion for Low Methane Emitting and Efficiently Feed Converting Hosts Based on Metagenomic Gene Abundance.

PubMed

Roehe, Rainer; Dewhurst, Richard J; Duthie, Carol-Anne; Rooke, John A; McKain, Nest; Ross, Dave W; Hyslop, Jimmy J; Waterhouse, Anthony; Freeman, Tom C; Watson, Mick; Wallace, R John

2016-02-01

Methane produced by methanogenic archaea in ruminants contributes significantly to anthropogenic greenhouse gas emissions. The host genetic link controlling microbial methane production is unknown and appropriate genetic selection strategies are not developed. We used sire progeny group differences to estimate the host genetic influence on rumen microbial methane production in a factorial experiment consisting of crossbred breed types and diets. Rumen metagenomic profiling was undertaken to investigate links between microbial genes and methane emissions or feed conversion efficiency. Sire progeny groups differed significantly in their methane emissions measured in respiration chambers. Ranking of the sire progeny groups based on methane emissions or relative archaeal abundance was consistent overall and within diet, suggesting that archaeal abundance in ruminal digesta is under host genetic control and can be used to genetically select animals without measuring methane directly. In the metagenomic analysis of rumen contents, we identified 3970 microbial genes of which 20 and 49 genes were significantly associated with methane emissions and feed conversion efficiency respectively. These explained 81% and 86% of the respective variation and were clustered in distinct functional gene networks. Methanogenesis genes (e.g. mcrA and fmdB) were associated with methane emissions, whilst host-microbiome cross talk genes (e.g. TSTA3 and FucI) were associated with feed conversion efficiency. These results strengthen the idea that the host animal controls its own microbiota to a significant extent and open up the implementation of effective breeding strategies using rumen microbial gene abundance as a predictor for difficult-to-measure traits on a large number of hosts. Generally, the results provide a proof of principle to use the relative abundance of microbial genes in the gastrointestinal tract of different species to predict their influence on traits e.g. human metabolism, health and behaviour, as well as to understand the genetic link between host and microbiome.

DOE Office of Scientific and Technical Information (OSTI.GOV)

O'Brien, Sarah L.; Gibbons, Sean M.; Owens, Sarah M.

Soil microbial communities are essential for ecosystem function, but linking community composition to biogeochemical processes is challenging because of high microbial diversity and large spatial variability of most soil characteristics. We investigated soil bacterial community structure in a switchgrass stand planted on soil with a history of grassland vegetation at high spatial resolution to determine whether biogeographic trends occurred at the centimeter scale. Moreover, we tested whether such heterogeneity, if present, influenced community structure within or among ecosystems. Pronounced heterogeneity was observed at centimeter scales, with abrupt changes in relative abundance of phyla from sample to sample. At the ecosystemmore » scale (> 10 m), however, bacterial community composition and structure were subtly, but significantly, altered by fertilization, with higher alpha diversity in fertilized plots. Moreover, by comparing these data with data from 1772 soils from the Earth Microbiome Project, it was found that 20% diverse globally sourced soil samples, while grassland soils shared approximately 40% of their operational taxonomic units with the current study. By spanning several orders of magnitude, the analysis suggested that extreme patchiness characterized community structure at smaller scales but that coherent patterns emerged at larger length scales.« less

Effect of 0.2% chlorhexidine on microbial and fungal contamination of dental unit waterlines

PubMed Central

Agahi, Raha Habib; Hashemipour, Maryam Alsadat; Kalantari, Mahsa; Ayatollah-Mosavi, Amin; Aghassi, Hossein; Nassab, Amir Hossein Gandjalikhan

2014-01-01

Background: It is known that dental unit waterline can be a source of infection. The aim of this study was to evaluate the efficacy of a mouthwash, chlorhexidine, in controlling microbial and fungal contamination of dental unit waterlines. Materials and Methods: In the present experimental study, the water in high-speed handpieces and air/water syringes of 35 dental units in a dental school was investigated microbiologically. Five of the units and one tap water served as controls; 100-200-mL water samples were collected aseptically in sterile containers in the morning after a 2-min purge. Water reservoir bottles were emptied and 50 mL of 0.2% chlorhexidine mouthwash was introduced into the tank. Then the water syringe was used to flush the waterline until the pink-colored chlorhexidine was observed to flow from the water syringe. Before the next day's session and before the students used the unit, two water samples from the water syringe and water turbine was collected. The samples were transferred to the laboratory. After 48 h at 37°C, the microbial colonies were counted. The number of these colonies was evaluated using colony forming unit CFU. Data were analyzed with Mann — Whitney U test and SPSS 13.5 statistical program. The statistical significance was defined at P ≤ 0.05. Results: All 35 units were contaminated before chlorhexidine use; no contamination was detected after adding chlorhexidine to the waterlines of the units. After week 1, 28 of the 30 treated dental unit waterlines (DUWLs) had values of CFU/mL less than 200. Conclusion: The present study showed that the use of chlorhexidine could reduce microbial counts in dental unit waterlines. PMID:25097645

Effect of 0.2% chlorhexidine on microbial and fungal contamination of dental unit waterlines.

PubMed

Agahi, Raha Habib; Hashemipour, Maryam Alsadat; Kalantari, Mahsa; Ayatollah-Mosavi, Amin; Aghassi, Hossein; Nassab, Amir Hossein Gandjalikhan

2014-05-01

It is known that dental unit waterline can be a source of infection. The aim of this study was to evaluate the efficacy of a mouthwash, chlorhexidine, in controlling microbial and fungal contamination of dental unit waterlines. In the present experimental study, the water in high-speed handpieces and air/water syringes of 35 dental units in a dental school was investigated microbiologically. Five of the units and one tap water served as controls; 100-200-mL water samples were collected aseptically in sterile containers in the morning after a 2-min purge. Water reservoir bottles were emptied and 50 mL of 0.2% chlorhexidine mouthwash was introduced into the tank. Then the water syringe was used to flush the waterline until the pink-colored chlorhexidine was observed to flow from the water syringe. Before the next day's session and before the students used the unit, two water samples from the water syringe and water turbine was collected. The samples were transferred to the laboratory. After 48 h at 37°C, the microbial colonies were counted. The number of these colonies was evaluated using colony forming unit CFU. Data were analyzed with Mann - Whitney U test and SPSS 13.5 statistical program. The statistical significance was defined at P ≤ 0.05. All 35 units were contaminated before chlorhexidine use; no contamination was detected after adding chlorhexidine to the waterlines of the units. After week 1, 28 of the 30 treated dental unit waterlines (DUWLs) had values of CFU/mL less than 200. The present study showed that the use of chlorhexidine could reduce microbial counts in dental unit waterlines.

Climate variability and change in the United States: potential impacts on water- and foodborne diseases caused by microbiologic agents.

PubMed Central

Rose, J B; Epstein, P R; Lipp, E K; Sherman, B H; Bernard, S M; Patz, J A

2001-01-01

Exposure to waterborne and foodborne pathogens can occur via drinking water (associated with fecal contamination), seafood (due to natural microbial hazards, toxins, or wastewater disposal) or fresh produce (irrigated or processed with contaminated water). Weather influences the transport and dissemination of these microbial agents via rainfall and runoff and the survival and/or growth through such factors as temperature. Federal and state laws and regulatory programs protect much of the U.S. population from waterborne disease; however, if climate variability increases, current and future deficiencies in areas such as watershed protection, infrastructure, and storm drainage systems will probably increase the risk of contamination events. Knowledge about transport processes and the fate of microbial pollutants associated with rainfall and snowmelt is key to predicting risks from a change in weather variability. Although recent studies identified links between climate variability and occurrence of microbial agents in water, the relationships need further quantification in the context of other stresses. In the marine environment as well, there are few studies that adequately address the potential health effects of climate variability in combination with other stresses such as overfishing, introduced species, and rise in sea level. Advances in monitoring are necessary to enhance early-warning and prevention capabilities. Application of existing technologies, such as molecular fingerprinting to track contaminant sources or satellite remote sensing to detect coastal algal blooms, could be expanded. This assessment recommends incorporating a range of future scenarios of improvement plans for current deficiencies in the public health infrastructure to achieve more realistic risk assessments. PMID:11359688

Climate variability and change in the United States: potential impacts on water- and foodborne diseases caused by microbiologic agents.

PubMed

Rose, J B; Epstein, P R; Lipp, E K; Sherman, B H; Bernard, S M; Patz, J A

2001-05-01

Exposure to waterborne and foodborne pathogens can occur via drinking water (associated with fecal contamination), seafood (due to natural microbial hazards, toxins, or wastewater disposal) or fresh produce (irrigated or processed with contaminated water). Weather influences the transport and dissemination of these microbial agents via rainfall and runoff and the survival and/or growth through such factors as temperature. Federal and state laws and regulatory programs protect much of the U.S. population from waterborne disease; however, if climate variability increases, current and future deficiencies in areas such as watershed protection, infrastructure, and storm drainage systems will probably increase the risk of contamination events. Knowledge about transport processes and the fate of microbial pollutants associated with rainfall and snowmelt is key to predicting risks from a change in weather variability. Although recent studies identified links between climate variability and occurrence of microbial agents in water, the relationships need further quantification in the context of other stresses. In the marine environment as well, there are few studies that adequately address the potential health effects of climate variability in combination with other stresses such as overfishing, introduced species, and rise in sea level. Advances in monitoring are necessary to enhance early-warning and prevention capabilities. Application of existing technologies, such as molecular fingerprinting to track contaminant sources or satellite remote sensing to detect coastal algal blooms, could be expanded. This assessment recommends incorporating a range of future scenarios of improvement plans for current deficiencies in the public health infrastructure to achieve more realistic risk assessments.

The emerging relevance of the gut microbiome in cardiometabolic health

USDA-ARS?s Scientific Manuscript database

Host metabolic pathways and physiological responses are regulated by signals linking the host to the gut microbial community or microbiome. Here, we draw a spotlight on lipid and bile acid metabolism and inflammatory response as they pertain to cardiometabolic dysfunction. Gut microbial dysbiosis al...

Effects of redox fluctuations on microbial community ecology post-wildfire in a high elevation mixed-conifer catchment in northern New Mexico.

NASA Astrophysics Data System (ADS)

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

2015-12-01

Wildfires are increasing in size and severity across the western United States with impacts on regional biogeochemical cycling. The resiliency of resident soil microbial communities determines rates of nutrient transformations as well as forest structure and recovery. Redox conditions in soil determine metabolic activities of microorganisms, which first consume oxygen and a succession of alternative terminal electron acceptors to support growth and metabolism using a variety of carbon sources. Controls on redox zonation are largely unknown in dominantly oxic soils, and microbial community adaptation and response to fluctuations in redox potential in a sub-alpine forested post-disturbance catchment has not been studied. Previous work has shown that fluctuating or rising water tables result in redox-dynamic sites, which can be 'hot spots' of biogeochemical activity depending on landscape position. Fire-induced tree mortality results in altered hydrologic flow paths and decreased evapotranspiration, leading to potential for intensified hot spot activity. We are testing such coupling of microbial activity with fluctuations in redox status using field measurements and laboratory incubation experiments. The 2013 Thompson Ridge Fire in the Jemez River Basin (NM) Critical Zone Observatory provides a highly-contextualized opportunity to examine how disturbance regime affects changes in soil microbial community dynamics and fluctuations in reduction-oxidation potential (as quantified by continuous CZO measurements of O2, CO2 and Eh as a function of soil depth and landscape location). We hypothesize that areas of depositional convergence in the catchment, which have been shown to exhibit more reducing conditions, will host microbial communities that are better adapted to fluctuating redox conditions and exhibit a greater diversity in functional capabilities. In these mixed conifer forests we find shifts in redox potential status in relation to depth and topography where more reducing conditions typically occur in convergent zones and at depth. These results highlight the significance of fluctuating oxygen-depleted zones in aerobic soils on microbial community activity and structure, linking community response to larger scale ecosystem processes.

Temporal changes in soil water repellency linked to the soil respiration and CH4 and CO2 fluxes

NASA Astrophysics Data System (ADS)

Qassem, Khalid; Urbanek, Emilia; van Keulen, Geertje

2014-05-01

Soil water repellency (SWR) is known to be a spatially and temporally variable phenomenon. The seasonal changes in soil moisture lead to development of soil water repellency, which in consequence may affect the microbial activity and in consequence alter the CO2 and CH4 fluxes from soils. Soil microbial activity is strongly linked to the temperature and moisture status of the soil. In terms of CO2 flux intermediate moisture contents are most favourable for the optimal microbial activity and highest CO2 fluxes. Methanogenesis occurs primarily in anaerobic water-logged habitats while methanotrophy is a strictly aerobic process. In the study we hypothesise that the changes in CO2 and CH4 fluxes are closely linked to critical moisture thresholds for soil water repellency. This research project aims to adopt a multi-disciplinary approach to comprehensively determine the effect of SWR on CO2 and CH4 fluxes. Research is conducted in situ at four sites exhibiting SWR in the southern UK. Flux measurements are carried out concomitant with meteorological and SWR observations Field observations are supported by laboratory measurements carried out on intact soil samples collected at the above identified field sites. The laboratory analyses are conducted under constant temperatures with controlled changes of soil moisture content. Methanogenic and Methanotrophic microbial populations are being analysed at different SWR and moisture contents using the latest metagenomic and metatranscriptomic approaches. Currently available data show that greenhouse gas flux are closely linked with soil moisture thresholds for SWR development.

Mechanistic links between gut microbial community dynamics, microbial functions and metabolic health.

PubMed

Ha, Connie W Y; Lam, Yan Y; Holmes, Andrew J

2014-11-28

Gut microbes comprise a high density, biologically active community that lies at the interface of an animal with its nutritional environment. Consequently their activity profoundly influences many aspects of the physiology and metabolism of the host animal. A range of microbial structural components and metabolites directly interact with host intestinal cells and tissues to influence nutrient uptake and epithelial health. Endocrine, neuronal and lymphoid cells in the gut also integrate signals from these microbial factors to influence systemic responses. Dysregulation of these host-microbe interactions is now recognised as a major risk factor in the development of metabolic dysfunction. This is a two-way process and understanding the factors that tip host-microbiome homeostasis over to dysbiosis requires greater appreciation of the host feedbacks that contribute to regulation of microbial community composition. To date, numerous studies have employed taxonomic profiling approaches to explore the links between microbial composition and host outcomes (especially obesity and its comorbidities), but inconsistent host-microbe associations have been reported. Available data indicates multiple factors have contributed to discrepancies between studies. These include the high level of functional redundancy in host-microbiome interactions combined with individual variation in microbiome composition; differences in study design, diet composition and host system between studies; and inherent limitations to the resolution of rRNA-based community profiling. Accounting for these factors allows for recognition of the common microbial and host factors driving community composition and development of dysbiosis on high fat diets. New therapeutic intervention options are now emerging.

Mechanistic links between gut microbial community dynamics, microbial functions and metabolic health

PubMed Central

Ha, Connie WY; Lam, Yan Y; Holmes, Andrew J

2014-01-01

Gut microbes comprise a high density, biologically active community that lies at the interface of an animal with its nutritional environment. Consequently their activity profoundly influences many aspects of the physiology and metabolism of the host animal. A range of microbial structural components and metabolites directly interact with host intestinal cells and tissues to influence nutrient uptake and epithelial health. Endocrine, neuronal and lymphoid cells in the gut also integrate signals from these microbial factors to influence systemic responses. Dysregulation of these host-microbe interactions is now recognised as a major risk factor in the development of metabolic dysfunction. This is a two-way process and understanding the factors that tip host-microbiome homeostasis over to dysbiosis requires greater appreciation of the host feedbacks that contribute to regulation of microbial community composition. To date, numerous studies have employed taxonomic profiling approaches to explore the links between microbial composition and host outcomes (especially obesity and its comorbidities), but inconsistent host-microbe associations have been reported. Available data indicates multiple factors have contributed to discrepancies between studies. These include the high level of functional redundancy in host-microbiome interactions combined with individual variation in microbiome composition; differences in study design, diet composition and host system between studies; and inherent limitations to the resolution of rRNA-based community profiling. Accounting for these factors allows for recognition of the common microbial and host factors driving community composition and development of dysbiosis on high fat diets. New therapeutic intervention options are now emerging. PMID:25469018

Microbial Changes during Pregnancy, Birth, and Infancy

PubMed Central

Nuriel-Ohayon, Meital; Neuman, Hadar; Koren, Omry

2016-01-01

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. PMID:27471494

The effect of compost on carbon cycling in soil

NASA Astrophysics Data System (ADS)

Singer, E.; Woyke, T.

2013-12-01

Rangelands cover an estimated 40-70% of global landmass, approximately one-third of the landmass of the United States and half of California. The soils of this vast land area has high carbon (C) storage capacity, which makes it an important target ecosystem for the mitigation of greenhouse gas emission and effects on climate change, in particular under land management techniques that favor increased C sequestration rates. While microbial communities are key players in the processes responsible for C storage and loss in soils, we have barely shed light on these highly complex processes in part due to the tremendous and seemingly intractable diversity of microbes, largely uncultured, that inhabit soil ecosystems. In our study, we compare Mediterranean grassland soil plots that were amended with greenwaste of various C:N ratios and biochar in a single event. Monthly subsampling of control and amended plots over the course of three months was performed in depth increments of 0-12 cm and 12-24 cm. We present data on greenhouse gas emissions and budgets of carbon, nitrogen, phosphorus, and micronutrients in dependence of amendment types and seasonality. Changes in the active members of the soil microbial community were assessed using a novel approach combining flow cytometry and metagenomic sequencing disclosing 'who does what'. This is the first study revealing the nature of actively metabolizing microbial community members linked to the geochemical characteristics of compost-amended soil.

BinSanity: unsupervised clustering of environmental microbial assemblies using coverage and affinity propagation

PubMed Central

Heidelberg, John F.; Tully, Benjamin J.

2017-01-01

Metagenomics has become an integral part of defining microbial diversity in various environments. Many ecosystems have characteristically low biomass and few cultured representatives. Linking potential metabolisms to phylogeny in environmental microorganisms is important for interpreting microbial community functions and the impacts these communities have on geochemical cycles. However, with metagenomic studies there is the computational hurdle of ‘binning’ contigs into phylogenetically related units or putative genomes. Binning methods have been implemented with varying approaches such as k-means clustering, Gaussian mixture models, hierarchical clustering, neural networks, and two-way clustering; however, many of these suffer from biases against low coverage/abundance organisms and closely related taxa/strains. We are introducing a new binning method, BinSanity, that utilizes the clustering algorithm affinity propagation (AP), to cluster assemblies using coverage with compositional based refinement (tetranucleotide frequency and percent GC content) to optimize bins containing multiple source organisms. This separation of composition and coverage based clustering reduces bias for closely related taxa. BinSanity was developed and tested on artificial metagenomes varying in size and complexity. Results indicate that BinSanity has a higher precision, recall, and Adjusted Rand Index compared to five commonly implemented methods. When tested on a previously published environmental metagenome, BinSanity generated high completion and low redundancy bins corresponding with the published metagenome-assembled genomes. PMID:28289564

The effect of compost on carbon cycling and the active soil microbiota

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singer, Esther; Woyke, Tanja; Ryals, Rebecca

2014-09-02

Rangelands cover an estimated 40-70percent of global landmass, approximately one-third of the landmass of the United States and half of California. The soils of this vast land area has high carbon (C) storage capacity, which makes it an important target ecosystem for the mitigation of greenhouse gas emission and effects on climate change, in particular under land management techniques that favor increased C sequestration rates. While microbial communities are key players in the processes responsible for C storage and loss in soils, we have barely shed light on these highly complex processes in part due to the tremendous and seeminglymore » intractable diversity of microbes, largely uncultured, that inhabit soil ecosystems. In our study, we compare Mediterranean grassland soil plots that were amended with greenwaste compost in a single event 6 years ago. Subsampling of control and amended plots was performed in depth increments of 0-10 cm. We present data on greenhouse gas emissions and budgets of carbon, nitrogen, phosphorus, and micronutrients in dependence of compost amendment. Changes in the active members of the soil microbial community were assessed using a novel approach combining flow cytometry and 16S tag sequencing disclosing who is active. This is the first study revealing the nature of actively metabolizing microbial community members linked to the geochemical characteristics of compost-amended soil.« less

The Microbial Fuel Cell as an Education Tool

ERIC Educational Resources Information Center

Dewan, Alim; Van Wie, Bernard; Beyenal, Haluk; Lewandowski, Zbigniew

2010-01-01

Many chemical engineering programs offer courses from a variety of disciplines to teach their students multidisciplinary concepts, but often these courses lack appropriate tools for linking newly learned concepts to principles learned in the core courses. This paper describes our experience of incorporating a microbial fuel cell education module…

Disbiome database: linking the microbiome to disease.

PubMed

Janssens, Yorick; Nielandt, Joachim; Bronselaer, Antoon; Debunne, Nathan; Verbeke, Frederick; Wynendaele, Evelien; Van Immerseel, Filip; Vandewynckel, Yves-Paul; De Tré, Guy; De Spiegeleer, Bart

2018-06-04

Recent research has provided fascinating indications and evidence that the host health is linked to its microbial inhabitants. Due to the development of high-throughput sequencing technologies, more and more data covering microbial composition changes in different disease types are emerging. However, this information is dispersed over a wide variety of medical and biomedical disciplines. Disbiome is a database which collects and presents published microbiota-disease information in a standardized way. The diseases are classified using the MedDRA classification system and the micro-organisms are linked to their NCBI and SILVA taxonomy. Finally, each study included in the Disbiome database is assessed for its reporting quality using a standardized questionnaire. Disbiome is the first database giving a clear, concise and up-to-date overview of microbial composition differences in diseases, together with the relevant information of the studies published. The strength of this database lies within the combination of the presence of references to other databases, which enables both specific and diverse search strategies within the Disbiome database, and the human annotation which ensures a simple and structured presentation of the available data.

MICROBIAL TRANSFORMATION OF SELECTED ORGANIC CHEMICALS IN NATURAL AQUATIC SYSTEMS

EPA Science Inventory

A method for describing the microbial degradation of xenobiotics through the use of a second-order reaction equation was tested in several water bodies in the United States and Russia. he experiment was aimed at studying the microbial transformation of a herbicide widely used in ...

Microbial Source Module (MSM): Documenting the Science and Software for Discovery, Evaluation, and Integration

EPA Science Inventory

The Microbial Source Module (MSM) estimates microbial loading rates to land surfaces from non-point sources, and to streams from point sources for each subwatershed within a watershed. A subwatershed, the smallest modeling unit, represents the common basis for information consume...

Comparing the Effect of Echinacea and Chlorhexidine Mouthwash on the Microbial Flora of Intubated Patients Admitted to the Intensive Care Unit.

PubMed

Safarabadi, Mehdi; Ghaznavi-Rad, Ehsanollah; Pakniyat, Abdolghader; Rezaie, Korosh; Jadidi, Ali

2017-01-01

Providing intubated patients admitted to the intensive care units with oral healthcare is one of the main tasks of nurses in order to prevent Ventilator-Associated Pneumonia (VAP). This study aimed at comparing the effects of two mouthwash solutions (echinacea and chlorhexidine) on the oral microbial flora of patients hospitalized in the intensive care units. In this clinical trial, 70 patients aged between18 and 65 years undergoing tracheal intubation through the mouth in three hospitals in Arak, were selected using simple random sampling and were randomly divided into two groups: the intervention group and the control group. The oral health checklist was used to collect the data (before and after the intervention). The samples were obtained from the orally intubated patients and were then cultured in selective media. Afterwards, the aerobic microbial growth was investigated in all culture media. The data were analyzed using SPSS software. The microbial flora in the echinacea group significantly decreased after the intervention ( p < 0.0001) and it was also the case withmicrobial flora of the patients in the chlorhexidine group ( p < 0.001). After 4 days, the oral microbial flora of the patients in the intervention group was lower than that of the patients in the control group ( p < 0.001). The results showed that the echinacea solution was more effective in decreasing the oral microbial flora of patients in the intensive care unit. Given the benefits of the components of the herb Echinacea, it can be suggested as a viable alternative to chlorhexidine.

Biogeochemical Processes in Microbial Ecosystems

NASA Technical Reports Server (NTRS)

DesMarais, David J.

2001-01-01

The hierarchical organization of microbial ecosystems determines process rates that shape Earth's environment, create the biomarker sedimentary and atmospheric signatures of life, and define the stage upon which major evolutionary events occurred. In order to understand how microorganisms have shaped the global environment of Earth and, potentially, other worlds, we must develop an experimental paradigm that links biogeochemical processes with ever-changing temporal and spatial distributions of microbial populations and their metabolic properties. Additional information is contained in the original extended abstract.

Land scale biogeography of arsenic biotransformation genes in estuarine wetland.

PubMed

Zhang, Si-Yu; Su, Jian-Qiang; Sun, Guo-Xin; Yang, Yunfeng; Zhao, Yi; Ding, Junjun; Chen, Yong-Shan; Shen, Yu; Zhu, Guibing; Rensing, Christopher; Zhu, Yong-Guan

2017-06-01

As an analogue of phosphorus, arsenic (As) has a biogeochemical cycle coupled closely with other key elements on the Earth, such as iron, sulfate and phosphate. It has been documented that microbial genes associated with As biotransformation are widely present in As-rich environments. Nonetheless, their presence in natural environment with low As levels remains unclear. To address this issue, we investigated the abundance levels and diversities of aioA, arrA, arsC and arsM genes in estuarine sediments at low As levels across Southeastern China to uncover biogeographic patterns at a large spatial scale. Unexpectedly, genes involved in As biotransformation were characterized by high abundance and diversity. The functional microbial communities showed a significant decrease in similarity along the geographic distance, with higher turnover rates than taxonomic microbial communities based on the similarities of 16S rRNA genes. Further investigation with niche-based models showed that deterministic processes played primary roles in shaping both functional and taxonomic microbial communities. Temperature, pH, total nitrogen concentration, carbon/nitrogen ratio and ferric iron concentration rather than As content in these sediments were significantly linked to functional microbial communities, while sediment temperature and pH were linked to taxonomic microbial communities. We proposed several possible mechanisms to explain these results. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale

PubMed Central

Schmidt, Thomas S. B.; Matias Rodrigues, João F.; von Mering, Christian

2014-01-01

Operational Taxonomic Units (OTUs), usually defined as clusters of similar 16S/18S rRNA sequences, are the most widely used basic diversity units in large-scale characterizations of microbial communities. However, it remains unclear how well the various proposed OTU clustering algorithms approximate ‘true’ microbial taxa. Here, we explore the ecological consistency of OTUs – based on the assumption that, like true microbial taxa, they should show measurable habitat preferences (niche conservatism). In a global and comprehensive survey of available microbial sequence data, we systematically parse sequence annotations to obtain broad ecological descriptions of sampling sites. Based on these, we observe that sequence-based microbial OTUs generally show high levels of ecological consistency. However, different OTU clustering methods result in marked differences in the strength of this signal. Assuming that ecological consistency can serve as an objective external benchmark for cluster quality, we conclude that hierarchical complete linkage clustering, which provided the most ecologically consistent partitions, should be the default choice for OTU clustering. To our knowledge, this is the first approach to assess cluster quality using an external, biologically meaningful parameter as a benchmark, on a global scale. PMID:24763141

Metabolites associated with adaptation of microorganisms to an acidophilic, metal-rich environment identified by stable-isotope-enabled metabolomics.

PubMed

Mosier, Annika C; Justice, Nicholas B; Bowen, Benjamin P; Baran, Richard; Thomas, Brian C; Northen, Trent R; Banfield, Jillian F

2013-03-12

Microorganisms grow under a remarkable range of extreme conditions. Environmental transcriptomic and proteomic studies have highlighted metabolic pathways active in extremophilic communities. However, metabolites directly linked to their physiology are less well defined because metabolomics methods lag behind other omics technologies due to a wide range of experimental complexities often associated with the environmental matrix. We identified key metabolites associated with acidophilic and metal-tolerant microorganisms using stable isotope labeling coupled with untargeted, high-resolution mass spectrometry. We observed >3,500 metabolic features in biofilms growing in pH ~0.9 acid mine drainage solutions containing millimolar concentrations of iron, sulfate, zinc, copper, and arsenic. Stable isotope labeling improved chemical formula prediction by >50% for larger metabolites (>250 atomic mass units), many of which were unrepresented in metabolic databases and may represent novel compounds. Taurine and hydroxyectoine were identified and likely provide protection from osmotic stress in the biofilms. Community genomic, transcriptomic, and proteomic data implicate fungi in taurine metabolism. Leptospirillum group II bacteria decrease production of ectoine and hydroxyectoine as biofilms mature, suggesting that biofilm structure provides some resistance to high metal and proton concentrations. The combination of taurine, ectoine, and hydroxyectoine may also constitute a sulfur, nitrogen, and carbon currency in the communities. Microbial communities are central to many critical global processes and yet remain enigmatic largely due to their complex and distributed metabolic interactions. Metabolomics has the possibility of providing mechanistic insights into the function and ecology of microbial communities. However, our limited knowledge of microbial metabolites, the difficulty of identifying metabolites from complex samples, and the inability to link metabolites directly to community members have proven to be major limitations in developing advances in systems interactions. Here, we show that combining stable-isotope-enabled metabolomics with genomics, transcriptomics, and proteomics can illuminate the ecology of microorganisms at the community scale.

Two-stage conversion of crude glycerol to energy using dark fermentation linked with microbial fuel cell or microbial electrolysis cell.

PubMed

Chookaew, Teera; Prasertsan, Poonsuk; Ren, Zhiyong Jason

2014-03-25

Crude glycerol is a main byproduct of the biodiesel industry, and the beneficial use of waste glycerol has been a major challenge. This study characterises the conversion of crude glycerol into bioenergy such as H2 and electricity using a two-stage process linking dark fermentation with a microbial fuel cell (MFC) or microbial electrolysis cell (MEC). The results showed that fermentation achieved a maximum H2 rate of 332 mL/L and a yield of 0.55 mol H2/mol glycerol, accompanied by 20% of organic removal. Fed with the raw fermentation products with an initial COD of 7610 mg/L, a two-chamber MFC produced 92 mW/m(2) in power density and removed 50% of COD. The Columbic efficiency was 14%. When fed with 50% diluted fermentation product, a similar power output (90m W/m(2)) and COD removal (49%) were obtained, but the CE doubled to 27%. Similar substrates were used to produce H2 in two-chamber MECs, and the diluted influent had a higher performance, with the highest yield at 106 mL H2/g COD and a CE of 24%. These results demonstrate that dark fermentation linked with MFC/MEC can be a feasible option for conversion of waste glycerol into bioenergy. Copyright © 2013 Elsevier B.V. All rights reserved.

Topic Outlines in Microbiology: An Instructor's Guide for Junior and Community Colleges.

ERIC Educational Resources Information Center

American Society for Microbiology, Washington, DC.

This resource guide presents subject matter organized in outline form for four topical areas: introductory microbiology; medical microbiology; microbial genetics; and microbial physiology. The first two units comprise the two most frequently taught microbiology courses in community and junior colleges. The outlines for microbial genetics and…

Dolomite Formation within Microbial Mats in the Sabkha of Abu Dhabi (UAE) and Associated Microsedimentary Structures

NASA Astrophysics Data System (ADS)

Bontognali, T. R.; Vasconcelos, C.; McKenzie, J. A.

2008-12-01

The link between microbial activity and dolomite formation has been evaluated in the coastal sabkha of Abu Dhabi (UAE). This modern dolomite-forming environment is frequently cited as the type analogue for the interpretation of many ancient evaporitic sequences. The investigation of sabkha sediments along a transect from intertidal to supratidal zones revealed a close association between microbial mats and dolomite. Authigenic dolomite occurs within surface and buried microbial mats, which are comprised of exopolymeric substances (EPS). Dolomite forms as a direct consequence of mineral nucleation and growth within microbially produced EPS. The cation-binding effect of the EPS molecules influences the composition of the precipitate. The early stage of this process is characterized by the complexation of an amorphous Mg-Si precipitate, which promotes dolomite development. Mineral formation within EPS appears to be enhanced by evaporation with consequent supersaturation of the pore waters with respect to dolomite. Partial EPS degradation during diagenesis may also provide an additional source of cations. However, the specific mineral-template property of EPS, rather than an increase in cation concentrations, is the key factor for dolomite formation in the studied area of the sabkha. Indeed, within the modern microbial mat located at the surface, dolomite precipitates from pore waters whose composition is very close to seawater. In the supratidal zone, pore water analysis and stable isotope values did not reveal any linkage between dolomite formation and microbial excretion and/or consumption of metabolites along the sediment profiles. This is in contrast with current models, in which dolomite formation is mainly linked to microbial increase of pH and alkalinity or consumption of dissolved SO4 in pore-waters. The EPS of the microbial mats is characterized by an alveolar microfabric, which can be mineralized during early diagenesis, preserving fossil imprints of the original biofilm. Recognition of this biostructure, combined with the atypical Mg-Si phase, may be used to interpret ancient microbial dolomite throughout the geological record.

Soil microbial diversity and activity linked to crop yield and quality in a dryland organic wheat production system

USDA-ARS?s Scientific Manuscript database

One of the primary goals of organic agriculture is increasing soil quality through the enhancement of soil biological diversity and activity. Greater soil microbial activity and diversity increase soil organic matter turnover and contribute to soil fertility, one of the main challenges associated wi...

Phylogenetic and functional potential links pH and N2O emissions in pasture soils.

PubMed

Samad, Md Sainur; Biswas, Ambarish; Bakken, Lars R; Clough, Timothy J; de Klein, Cecile A M; Richards, Karl G; Lanigan, Gary J; Morales, Sergio E

2016-10-26

Denitrification is mediated by microbial, and physicochemical, processes leading to nitrogen loss via N 2 O and N 2 emissions. Soil pH regulates the reduction of N 2 O to N 2 , however, it can also affect microbial community composition and functional potential. Here we simultaneously test the link between pH, community composition, and the N 2 O emission ratio (N 2 O/(NO + N 2 O + N 2 )) in 13 temperate pasture soils. Physicochemical analysis, gas kinetics, 16S rRNA amplicon sequencing, metagenomic and quantitative PCR (of denitrifier genes: nirS, nirK, nosZI and nosZII) analysis were carried out to characterize each soil. We found strong evidence linking pH to both N 2 O emission ratio and community changes. Soil pH was negatively associated with N 2 O emission ratio, while being positively associated with both community diversity and total denitrification gene (nir &nos) abundance. Abundance of nosZII was positively linked to pH, and negatively linked to N 2 O emissions. Our results confirm that pH imposes a general selective pressure on the entire community and that this results in changes in emission potential. Our data also support the general model that with increased microbial diversity efficiency increases, demonstrated in this study with lowered N 2 O emission ratio through more efficient conversion of N 2 O to N 2 .

Phylogenetic and functional potential links pH and N2O emissions in pasture soils

NASA Astrophysics Data System (ADS)

Samad, M. D. Sainur; Biswas, Ambarish; Bakken, Lars R.; Clough, Timothy J.; de Klein, Cecile A. M.; Richards, Karl G.; Lanigan, Gary J.; Morales, Sergio E.

2016-10-01

Denitrification is mediated by microbial, and physicochemical, processes leading to nitrogen loss via N2O and N2 emissions. Soil pH regulates the reduction of N2O to N2, however, it can also affect microbial community composition and functional potential. Here we simultaneously test the link between pH, community composition, and the N2O emission ratio (N2O/(NO + N2O + N2)) in 13 temperate pasture soils. Physicochemical analysis, gas kinetics, 16S rRNA amplicon sequencing, metagenomic and quantitative PCR (of denitrifier genes: nirS, nirK, nosZI and nosZII) analysis were carried out to characterize each soil. We found strong evidence linking pH to both N2O emission ratio and community changes. Soil pH was negatively associated with N2O emission ratio, while being positively associated with both community diversity and total denitrification gene (nir & nos) abundance. Abundance of nosZII was positively linked to pH, and negatively linked to N2O emissions. Our results confirm that pH imposes a general selective pressure on the entire community and that this results in changes in emission potential. Our data also support the general model that with increased microbial diversity efficiency increases, demonstrated in this study with lowered N2O emission ratio through more efficient conversion of N2O to N2.

Phylogenetic and functional potential links pH and N2O emissions in pasture soils

PubMed Central

Samad, M. d. Sainur; Biswas, Ambarish; Bakken, Lars R.; Clough, Timothy J.; de Klein, Cecile A. M.; Richards, Karl G.; Lanigan, Gary J.; Morales, Sergio E.

2016-01-01

Denitrification is mediated by microbial, and physicochemical, processes leading to nitrogen loss via N2O and N2 emissions. Soil pH regulates the reduction of N2O to N2, however, it can also affect microbial community composition and functional potential. Here we simultaneously test the link between pH, community composition, and the N2O emission ratio (N2O/(NO + N2O + N2)) in 13 temperate pasture soils. Physicochemical analysis, gas kinetics, 16S rRNA amplicon sequencing, metagenomic and quantitative PCR (of denitrifier genes: nirS, nirK, nosZI and nosZII) analysis were carried out to characterize each soil. We found strong evidence linking pH to both N2O emission ratio and community changes. Soil pH was negatively associated with N2O emission ratio, while being positively associated with both community diversity and total denitrification gene (nir & nos) abundance. Abundance of nosZII was positively linked to pH, and negatively linked to N2O emissions. Our results confirm that pH imposes a general selective pressure on the entire community and that this results in changes in emission potential. Our data also support the general model that with increased microbial diversity efficiency increases, demonstrated in this study with lowered N2O emission ratio through more efficient conversion of N2O to N2. PMID:27782174

Geochemical heterogeneity of a gasoline-contaminated aquifer

USGS Publications Warehouse

Cozzarelli, Isabelle M.; Herman, Janet S.; Baedecker, Mary Jo; Fischer, Jeffrey M.

1999-01-01

The scale of biogeochemical reactions was studied in a physically and chemically heterogeneous surficial Coastal Plain aquifer contaminated by a gasoline spill. The physical heterogeneity of the aquifer is manifested in two hydrologic units, a shallow local aquifer of perched water and a regional sandy aquifer. Over the studied vertical interval of 21.3 ft (6.5 m), concentrations of reactive species varied by orders of magnitude, and the impact of biodegradation was expressed to widely varying degrees. A thin (3 ft thick) section of the perched-water zone was the most contaminated; total aromatic hydrocarbons were as high as 19.4 mg/l. Hydrocarbons were degraded by microbially mediated reactions that varied over short vertical distances and time. Anaerobic processes dominated within the low-permeability clay unit, whereas in the more permeable sandy layers nitrate reduction and aerobic degradation occurred. Hydrocarbons were more persistent over time in the low-permeability layer due to the limited availability of electron acceptors for degradation. The microbial degradation of hydrocarbons was linked to sulfate and iron reduction in the clay unit and led to alterations in the aquifer solids; electron microscopy revealed the presence of FeS minerals encrusting primary aquifer grains. High concentrations of Fe2+ in groundwater, up to 34.5 mg/l, persist in kinetic disequilibrium in the presence of elevated H2S levels of 1.0 mg/l. Assessment of aquifer heterogeneities and groundwater contamination was possible due to sample discrimination at a scale of approximately 2 ft (∼0.6 m), a much finer resolution than is attempted in many remedial investigations of polluted aquifers. The information obtained in this type of study is essential to the development of models capable of estimating the fate of hydrocarbons at a site scale.

Ecogenomics: Ensemble Analysis of Gene Expression in Microbial Communities

NASA Technical Reports Server (NTRS)

Sogin, Mitchell; DesMarais, David J.; Stahl, D. A.; Pace, Norman R.

2001-01-01

The hierarchical organization of microbial ecosystems determines process rates that shape Earth's environment, create the biomarker sedimentary and atmospheric signatures of life, and define the stage upon which major evolutionary events occurred. In order to understand how microorganisms have shaped the global environment of Earth and, potentially, other worlds, we must develop an experimental paradigm that links biogeochemical processes with ever-changing temporal and spatial distributions of microbial populations and their metabolic properties. Additional information is contained in the original extended abstract.

Influence of geogenic factors on microbial communities in metallogenic Australian soils

PubMed Central

Reith, Frank; Brugger, Joel; Zammit, Carla M; Gregg, Adrienne L; Goldfarb, Katherine C; Andersen, Gary L; DeSantis, Todd Z; Piceno, Yvette M; Brodie, Eoin L; Lu, Zhenmei; He, Zhili; Zhou, Jizhong; Wakelin, Steven A

2012-01-01

Links between microbial community assemblages and geogenic factors were assessed in 187 soil samples collected from four metal-rich provinces across Australia. Field-fresh soils and soils incubated with soluble Au(III) complexes were analysed using three-domain multiplex-terminal restriction fragment length polymorphism, and phylogenetic (PhyloChip) and functional (GeoChip) microarrays. Geogenic factors of soils were determined using lithological-, geomorphological- and soil-mapping combined with analyses of 51 geochemical parameters. Microbial communities differed significantly between landforms, soil horizons, lithologies and also with the occurrence of underlying Au deposits. The strongest responses to these factors, and to amendment with soluble Au(III) complexes, was observed in bacterial communities. PhyloChip analyses revealed a greater abundance and diversity of Alphaproteobacteria (especially Sphingomonas spp.), and Firmicutes (Bacillus spp.) in Au-containing and Au(III)-amended soils. Analyses of potential function (GeoChip) revealed higher abundances of metal-resistance genes in metal-rich soils. For example, genes that hybridised with metal-resistance genes copA, chrA and czcA of a prevalent aurophillic bacterium, Cupriavidus metallidurans CH34, occurred only in auriferous soils. These data help establish key links between geogenic factors and the phylogeny and function within soil microbial communities. In particular, the landform, which is a crucial factor in determining soil geochemistry, strongly affected microbial community structures. PMID:22673626

Influence of geogenic factors on microbial communities in metallogenic Australian soils.

PubMed

Reith, Frank; Brugger, Joel; Zammit, Carla M; Gregg, Adrienne L; Goldfarb, Katherine C; Andersen, Gary L; DeSantis, Todd Z; Piceno, Yvette M; Brodie, Eoin L; Lu, Zhenmei; He, Zhili; Zhou, Jizhong; Wakelin, Steven A

2012-11-01

Links between microbial community assemblages and geogenic factors were assessed in 187 soil samples collected from four metal-rich provinces across Australia. Field-fresh soils and soils incubated with soluble Au(III) complexes were analysed using three-domain multiplex-terminal restriction fragment length polymorphism, and phylogenetic (PhyloChip) and functional (GeoChip) microarrays. Geogenic factors of soils were determined using lithological-, geomorphological- and soil-mapping combined with analyses of 51 geochemical parameters. Microbial communities differed significantly between landforms, soil horizons, lithologies and also with the occurrence of underlying Au deposits. The strongest responses to these factors, and to amendment with soluble Au(III) complexes, was observed in bacterial communities. PhyloChip analyses revealed a greater abundance and diversity of Alphaproteobacteria (especially Sphingomonas spp.), and Firmicutes (Bacillus spp.) in Au-containing and Au(III)-amended soils. Analyses of potential function (GeoChip) revealed higher abundances of metal-resistance genes in metal-rich soils. For example, genes that hybridised with metal-resistance genes copA, chrA and czcA of a prevalent aurophillic bacterium, Cupriavidus metallidurans CH34, occurred only in auriferous soils. These data help establish key links between geogenic factors and the phylogeny and function within soil microbial communities. In particular, the landform, which is a crucial factor in determining soil geochemistry, strongly affected microbial community structures.

Quantitative microbiome profiling links gut community variation to microbial load.

PubMed

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).

Identifying microbially mediated transformations of DOC across season and tide from simultaneous changes in whole community gene expression and in mass spectra generated by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR-MS)

NASA Astrophysics Data System (ADS)

Ballantyne, F.; Medeiros, P. M.; Moran, M. A.; Song, C.; Whitman, W. B.; Washington, B.; Yu, M.; Lee, J.

2017-12-01

Despite the advent of methods enabling high resolution characterization of metabolic activity and of organic matter, linking microbial metabolism to organic matter transformations remains a challenge. By sequencing metatranscriptomes and using Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR-MS) to characterize organic matter (OM) at the beginning and at the end of incubations of estuarine water across tide and season, we sought to link observed a changes in OM composition to microbial metabolism. We used linear models and K means clustering to identify clusters of genes that responded coherently across season, which accounted for most of the variability in gene expression, over tidal regime, which explained the majority of the remaining variation, and over time during the 24 hour incubations. We used an approach from the field of signal processing, that to our knowledge has not been used to analyze FTICR-MS data, to identify formulae of compounds that changed in concentration during the incubations. This approach, based on the discrete wavelet transform (DWT), allowed us to overcome some of the challenges associated with analyzing FTICR-MS data: variable ionization of organic compounds, signal suppression by high concentration compounds, and uncertainty about how to normalize changes across spectra. We were able to link clusters of metabolic and transporter genes to changes in OM composition, and uniquely identify genes based on their cross correlation with changes in FTICR mass spectra. Our approach for analyzing FTICR- MS data enables more robust inference about OM transformations, and linking high resolution changes in gene expression and in OM data during incubations represents an important step toward formulating models of microbial metabolism relevant for predicting biogeochemically relevant C fluxes.

Deep-Sea Microbes: Linking Biogeochemical Rates to -Omics Approaches

NASA Astrophysics Data System (ADS)

Herndl, G. J.; Sintes, E.; Bayer, B.; Bergauer, K.; Amano, C.; Hansman, R.; Garcia, J.; Reinthaler, T.

2016-02-01

Over the past decade substantial progress has been made in determining deep ocean microbial activity and resolving some of the enigmas in understanding the deep ocean carbon flux. Also, metagenomics approaches have shed light onto the dark ocean's microbes but linking -omics approaches to biogeochemical rate measurements are generally rare in microbial oceanography and even more so for the deep ocean. In this presentation, we will show by combining metagenomics, -proteomics and biogeochemical rate measurements on the bulk and single-cell level that deep-sea microbes exhibit characteristics of generalists with a large genome repertoire, versatile in utilizing substrate as revealed by metaproteomics. This is in striking contrast with the apparently rather uniform dissolved organic matter pool in the deep ocean. Combining the different -omics approaches with metabolic rate measurements, we will highlight some major inconsistencies and enigmas in our understanding of the carbon cycling and microbial food web structure in the dark ocean.

Clinical Implications of Basic Science Discoveries: Immune Homeostasis and the Microbiome-Dietary and Therapeutic Modulation and Implications for Transplantation.

PubMed

Fishman, J A; Thomson, A W

2015-07-01

Links between the human microbiome and the innate and adaptive immune systems and their impact on autoimmune and inflammatory diseases are only beginning to be recognized. Characterization of the complex human microbial community is facilitated by culture-independent nucleic acid sequencing tools and bioinformatics systems. Specific organisms and microbial antigens are linked with initiation of innate immune responses that, depending on the context, may be associated with tolerogenic or effector immune responses. Further complexity is introduced by preclinical data that demonstrate the impacts of dietary manipulation on the prevention of genetically determined, systemic autoimmune disorders and on gastrointestinal microbiota. Investigation of interactions of complex microbial populations with the human immune system may provide new targets for clinical management in allotransplantation. © Copyright 2015 The American Society of Transplantation and the American Society of Transplant Surgeons.

Microbial Enrichment from Six Hydraulic Fracturing Fluids and Biogeochemical Characteristics of Flowback Waters in Oklahoma Shale Formations

NASA Astrophysics Data System (ADS)

Krzmarzick, M. J.; McCutchan, A.; Carroll, J.; Lozano, T.

2017-12-01

Hydraulic fracturing of oil and gas formations has revolutionized the industry, but little is known regarding the interactions of the microbiology in formations and the hydraulic fracturing chemicals used. In the first part of this study, six representative hydraulic fracturing fluids were incubated in bench scale microcosms with surface soils over six months at 1× concentrations used in the field. These fluids differed greatly in terms of biocide, surfactants, corrosion inhibitors and crosslinking agents (if any). The changes in microbial communities were measured by Illumina 16S rRNA gene analysis and quantitative-PCR. As a whole, the microbial communities enriched were significantly varied between fluids, with the magnitude of the difference tightly linked to the total organic carbon of each fluid. Most enriched bacteria heavily grew within just the first couple of weeks, and belonged to genera well-linked to xenobiotic degradation, such as Azospirillum, Ralstonia, and Comamonas. This, combined with bulk parameters such as chemical oxygen demand of the water, indicates that a significant fraction of these fluids are readily degradable, though individual chemicals were not monitored for recalcitrance. In the second component of this work, the flowback waters from sixteen newly completed wells in south-central Oklahoma were monitored over two months for compositions of boron, dissolved solids, BTEX, chloride, and their microbial communities. As expected, dissolved solids increased over time as the flowback waters became more characteristic of the formation waters. In these wells, boron, a carefully measured component of the fracturing fluid for cross-linking applications, was either stable or increased over time. The microbial community characteristics are pending but will be compared between formations, to the chemical data, and to the results in the bench-top degradation study.

Microbiology and potential applications of aerobic methane oxidation coupled to denitrification (AME-D) process: A review.

PubMed

Zhu, Jing; Wang, Qian; Yuan, Mengdong; Tan, Giin-Yu Amy; Sun, Faqian; Wang, Cheng; Wu, Weixiang; Lee, Po-Heng

2016-03-01

Aerobic methane oxidation coupled to denitrification (AME-D) is an important link between the global methane and nitrogen cycles. This mini-review updates discoveries regarding aerobic methanotrophs and denitrifiers, as a prelude to spotlight the microbial mechanism and the potential applications of AME-D. Until recently, AME-D was thought to be accomplished by a microbial consortium where denitrifying bacteria utilize carbon intermediates, which are excreted by aerobic methanotrophs, as energy and carbon sources. Potential carbon intermediates include methanol, citrate and acetate. This mini-review presents microbial thermodynamic estimations and postulates that methanol is the ideal electron donor for denitrification, and may serve as a trophic link between methanotrophic bacteria and denitrifiers. More excitingly, new discoveries have revealed that AME-D is not only confined to the conventional synergism between methanotrophic bacteria and denitrifiers. Specifically, an obligate aerobic methanotrophic bacterium, Methylomonas denitrificans FJG1, has been demonstrated to couple partial denitrification with methane oxidation, under hypoxia conditions, releasing nitrous oxide as a terminal product. This finding not only substantially advances the understanding of AME-D mechanism, but also implies an important but unknown role of aerobic methanotrophs in global climate change through their influence on both the methane and nitrogen cycles in ecosystems. Hence, further investigation on AME-D microbiology and mechanism is essential to better understand global climate issues and to develop niche biotechnological solutions. This mini-review also presents traditional microbial techniques, such as pure cultivation and stable isotope probing, and powerful microbial techniques, such as (meta-) genomics and (meta-) transcriptomics, for deciphering linked methane oxidation and denitrification. Although AME-D has immense potential for nitrogen removal from wastewater, drinking water and groundwater, bottlenecks and potential issues are also discussed. Copyright © 2015 Elsevier Ltd. All rights reserved.

Both the intratumoral immune and microbial microenvironment are linked to recurrence in human colon cancer: results from a prospective, multicenter nodal ultrastaging trial

DOE Office of Scientific and Technical Information (OSTI.GOV)

Noguti, Juliana; Chan, Alfred A.; Bandera, Bradley

Background: Colon cancer (CC) is the third most common cancer diagnosed in the United States and the incidence has been rising among young adults. We and others have shown a relationship between the immune infiltrate and prognosis, with improved disease-free survival (DFS) associated with a higher expression of CD8+ T cells. Additionally, numerous studies indicate the gut microbiota is linked to colon cancer and clinical outcomes. Therefore, we hypothesized a microbial signature might be associated with both the intratumoral immune cells as well as DFS. Results: Ninety-one patients were randomly selected from a prospective NCI-sponsored multicenter trial evaluating ultrastaging inmore » CC to investigate the intratumoral microbiota by 16S rRNA gene amplicon sequencing. Operational taxonomic units (OTUs) were grouped by 97% sequence similarity. A series of clinical, immunohistochemical, and microbiota-related data were first evaluated by univariable cox regression to determine candidate variables associated with DFS. DFS was influenced by three parameters: N-stage, CD8+ labeling, and one microbiota principal component by multivariate analysis (MVA). Not only were the microbiota and CD8 significant contributors to the DFS model, but they were also significantly associated with each other. Alpha diversity showed an inverse correlation to CD8+ T cells (p=0.010, R=-0.278) and beta diversity showed an association with the CD8+ T cells (u-UniFrac p=0.026, w-UniFrac p=0.034). Further analysis at the OTU level with false discovery correction revealed one OTU, OTU_104, belonging to the order Clostridiales to be associated with increased recurrence (HR 1.21, CI 1.08 to 1.36). This OTU_104 was then found to be inversely correlated to CD8+ T cells (p=0.031, R=-0.35). Conclusions: This study is the first to demonstrate an association between the intratumoral microbiota, CD8+ T cells, and recurrence in CC. An increased relative abundance of a specific OTU_104 was inversely associated with CD8+ T cells and increased CC recurrence. The link between this microbe, CD8+ T cells and DFS has not been previously shown. Further studies are warranted to examine the role of infiltrating immune cells and the microbiota on colon cancer.« less

Biogeochemical and Microbial Variation across 5500 km of Antarctic Surface Sediment Implicates Organic Matter as a Driver of Benthic Community Structure

PubMed Central

Learman, Deric R.; Henson, Michael W.; Thrash, J. Cameron; Temperton, Ben; Brannock, Pamela M.; Santos, Scott R.; Mahon, Andrew R.; Halanych, Kenneth M.

2016-01-01

Western Antarctica, one of the fastest warming locations on Earth, is a unique environment that is underexplored with regards to biodiversity. Although pelagic microbial communities in the Southern Ocean and coastal Antarctic waters have been well-studied, there are fewer investigations of benthic communities and most have a focused geographic range. We sampled surface sediment from 24 sites across a 5500 km region of Western Antarctica (covering the Ross Sea to the Weddell Sea) to examine relationships between microbial communities and sediment geochemistry. Sequencing of the 16S and 18S rRNA genes showed microbial communities in sediments from the Antarctic Peninsula (AP) and Western Antarctica (WA), including the Ross, Amundsen, and Bellingshausen Seas, could be distinguished by correlations with organic matter concentrations and stable isotope fractionation (total organic carbon; TOC, total nitrogen; TN, and δ13C). Overall, samples from the AP were higher in nutrient content (TOC, TN, and NH4+) and communities in these samples had higher relative abundances of operational taxonomic units (OTUs) classified as the diatom, Chaetoceros, a marine cercozoan, and four OTUs classified as Flammeovirgaceae or Flavobacteria. As these OTUs were strongly correlated with TOC, the data suggests the diatoms could be a source of organic matter and the Bacteroidetes and cercozoan are grazers that consume the organic matter. Additionally, samples from WA have lower nutrients and were dominated by Thaumarchaeota, which could be related to their known ability to thrive as lithotrophs. This study documents the largest analysis of benthic microbial communities to date in the Southern Ocean, representing almost half the continental shoreline of Antarctica, and documents trophic interactions and coupling of pelagic and benthic communities. Our results indicate potential modifications in carbon sequestration processes related to change in community composition, identifying a prospective mechanism that links climate change to carbon availability. PMID:27047451

Application of RNA Stable Isotope Probing (SIP) to Link Community Activity with Microorganisms Responsible for Autotrophy in the Subseafloor at Axial Seamount

NASA Astrophysics Data System (ADS)

Huber, J. A.; Fortunato, C. S.

2014-12-01

The global ocean comprises the Earth's largest biome, with microorganisms playing a dominant biogeochemical role. However, the potential for production of new microbial biomass within the subseafloor is rarely considered in traditional oceanographic paradigms of carbon cycling or microbial food webs. In this study, we used RNA Stable Isotope Probing (RNA SIP) to determine the microbial community composition and genetic repertoire of active subseafloor autotrophs in warm venting fluids from Axial Seamount. RNA is a responsive biomarker because it is a reflection of cellular activity independent of replication, and RNA SIP thus provides access to both the function of a microbial community and the phylogeny of the organisms accountable for key functions. Diffuse fluids were incubated shipboard at 30°C, 55°C, and 80°C with 13DIC and H2. Metatranscriptomic sequencing of both the enriched and non-enriched RNA was carried out from 13C and 12C controls. In addition, filtered fluid samples were preserved in situ for comparative meta -transcriptomic and -genomic analyses. Diverse lineages of bacteria and archaea and accompanying metabolisms were detected in situ, but RNA SIP results show dominance of three different groups of autotrophs active under each experimental condition. At 30°C, members of the Sulfurimonas genus dominated, with genes for hydrogen oxidation, nitrate reduction, and carbon fixation via the rTCA cycle highly expressed. At 55°C, both Caminibacter and Nautilia transcripts were detected for rTCA cycle, hydrogen oxidation, and nitrate reduction. At 80°C, transcripts for hydrogenotrophic methanogenesis mediated by members of Methanocaldococcus were detected. These results suggest the subseafloor hosts various anaerobic chemolithoautotrophs that span a wide temperature range, with hydrogen playing a key role in microbial metabolism. Complementary experiments are currently being carried out on the seafloor with a novel in situ incubator unit to provide further insights to primary productivity in the subseafloor.

Microbial contamination of the Tzu-Chi Cord Blood Bank from 2005 to 2006.

PubMed

Chen, Shu-Huey; Zheng, Ya-Jun; Yang, Shang-Hsien; Yang, Kuo-Liang; Shyr, Ming-Hwang; Ho, Yu-Huai

2008-01-01

In total, 4502 units of cord blood (CB) were collected during a 2-year period from 2005 to 2006 by the Buddhist Tzu-Chi Stem Cells Center. The aim of this study was to analyze the incidence of microbial contamination and type of organism present in the cord blood. The clinical impact of microbial contamination on hematopoietic progenitor cell (HPC) grafts used for HPC transplantation is also discussed. First and second specimens were obtained for microbial assessment. These were collected in laboratory after cord blood collection and after cord blood unit manipulation, respectively. The samples were cultured and the results reviewed. The overall incidence of microbiological contamination was 1.8% (82/4502). Three CB units were contaminated with two different organisms. Infectious organisms comprised 9.4% (8/85) of total isolated microbes. These infectious microorganisms were beta-Streptococci group B, Candida tropicalis and Staphylococcus aureus which were isolated in 6, 1 and 1 of CB units respectively. Escherichia coli, Bacteroides fragilis, Lactobacillus spp., Enterococcus, beta-Streptococcus Group B, Bacteroides valgatus, Corynebacterium spp., Klebsiella pneumonia and Peptococcus spp. were the most frequently encountered microorganisms. A higher contamination rate of the CB units was noted after vaginal delivery (2.16%) compared to caesarian section (0.85%) (p < 0.01). Extensive training in CB collection, good procedures and good protocols can decrease the rate of microbial contamination. The use of a closed collecting system and an ex utero method have the advantage of a lower contamination rate. In our cord blood bank, we use a closed system but an in utero method. Similar to other studies, most of microorganisms reported here as contaminants are non-pathogenic.

Microbial lime-mud production and its relation to climate change

USGS Publications Warehouse

Yates, K.K.; Robbins, L.L.; Gerhard, L.C.; Harrison, W.E.; Hanson, B.M.B.

2001-01-01

Microbial calcification has been identified as a significant source of carbonate sediment production in modern marine and lacustrine environments around the globe. This process has been linked to the production of modern whitings and large, micritic carbonate deposits throughout the geologic record. Furthermore, carbonate deposits believed to be the result of cyanobacterial and microalgal calcification suggest that the potential exists for long-term preservation of microbial precipitates and storage of carbon dioxide (CO2). Recent research has advanced our understanding of the microbial-calcification mechanism as a photosynthetically driven process. However, little is known of the effects of this process on inorganic carbon cycling or of the effects of changing climate on microbial-calcification mechanisms.Laboratory experiments on microbial cellular physiology demonstrate that cyanobacteria and green algae can utilize different carbon species for metabolism and calcification. Cyanobacterial calcification relies on bicarbonate (HCO3–)utilization while green algae use primarily CO2. Therefore, depending on which carbonate species (HCO3– or CO2) dominates in the ocean or lacustrine environments (a condition ultimately linked to atmospheric partial pressure PCO2), the origin of lime-mud production by cyanobacteria and/or algae may fluctuate through geologic time. Trends of cyanobacteria versus algal dominance in the rock record corroborate this conclusion. These results suggest that relative species abundances of calcareous cyanobacteria and algae in the Phanerozoic may serve as potential proxies for assessing paleoclimatic conditions, including fluctuations in atmospheric PCO2.

Assessment of Anaerobic Metabolic Activity and Microbial Diversity in a Petroleum-Contaminated Aquifer Using Push-Pull Tests in Combination With Molecular Tools and Stable Isotopes

NASA Astrophysics Data System (ADS)

Schroth, M. H.; Kleikemper, J.; Pombo, S. A.; Zeyer, J.

2002-12-01

In the past, studies on microbial communities in natural environments have typically focused on either their structure or on their metabolic function. However, linking structure and function is important for understanding microbial community dynamics, in particular in contaminated environments. We will present results of a novel combination of a hydrogeological field method (push-pull tests) with molecular tools and stable isotope analysis, which was employed to quantify anaerobic activities and associated microbial diversity in a petroleum-contaminated aquifer in Studen, Switzerland. Push-pull tests consisted of the injection of test solution containing a conservative tracer and reactants (electron acceptors, 13C-labeled carbon sources) into the aquifer anoxic zone. Following an incubation period, the test solution/groundwater mixture was extracted from the same location. Metabolic activities were computed from solute concentrations measured during extraction. Simultaneously, microbial diversity in sediment and groundwater was characterized by using fluorescence in situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE), as well as phospholipids fatty acid (PLFA) analysis in combination with 13C isotopic measurements. Results from DGGE analyses provided information on the general community structure before, during and after the tests, while FISH yielded information on active populations. Moreover, using 13C-labeling of microbial PLFA we were able to directly link carbon source assimilation in an aquifer to indigenous microorganisms while providing quantitative information on respective carbon source consumption.

Leaf Litter Mixtures Alter Microbial Community Development: Mechanisms for Non-Additive Effects in Litter Decomposition

PubMed Central

Chapman, Samantha K.; Newman, Gregory S.; Hart, Stephen C.; Schweitzer, Jennifer A.; Koch, George W.

2013-01-01

To what extent microbial community composition can explain variability in ecosystem processes remains an open question in ecology. Microbial decomposer communities can change during litter decomposition due to biotic interactions and shifting substrate availability. Though relative abundance of decomposers may change due to mixing leaf litter, linking these shifts to the non-additive patterns often recorded in mixed species litter decomposition rates has been elusive, and links community composition to ecosystem function. We extracted phospholipid fatty acids (PLFAs) from single species and mixed species leaf litterbags after 10 and 27 months of decomposition in a mixed conifer forest. Total PLFA concentrations were 70% higher on litter mixtures than single litter types after 10 months, but were only 20% higher after 27 months. Similarly, fungal-to-bacterial ratios differed between mixed and single litter types after 10 months of decomposition, but equalized over time. Microbial community composition, as indicated by principal components analyses, differed due to both litter mixing and stage of litter decomposition. PLFA biomarkers a15∶0 and cy17∶0, which indicate gram-positive and gram-negative bacteria respectively, in particular drove these shifts. Total PLFA correlated significantly with single litter mass loss early in decomposition but not at later stages. We conclude that litter mixing alters microbial community development, which can contribute to synergisms in litter decomposition. These findings advance our understanding of how changing forest biodiversity can alter microbial communities and the ecosystem processes they mediate. PMID:23658639

Strong, weak, and missing links in a microbial community of the N.W. Mediterranean Sea.

PubMed

Bettarel, Y; Dolan, J R; Hornak, K; Lemée, R; Masin, M; Pedrotti, M-L; Rochelle-Newall, E; Simek, K; Sime-Ngando, T

2002-12-01

Planktonic microbial communities often appear stable over periods of days and thus tight links are assumed to exist between different functional groups (i.e. producers and consumers). We examined these links by characterizing short-term temporal correspondences in the concentrations and activities of microbial groups sampled from 1 m depth, at a coastal site of the N.W. Mediterranean Sea, in September 2001 every 3 h for 3 days. We estimated the abundance and activity rates of the autotrophic prokaryote Synechococcus, heterotrophic bacteria, viruses, heterotrophic nanoflagellates, as well as dissolved organic carbon concentrations. We found that Synechococcus, heterotrophic bacteria, and viruses displayed distinct patterns. Synechococcus abundance was greatest at midnight and lowest at 21:00 and showed the common pattern of an early evening maximum in dividing cells. In contrast, viral concentrations were minimal at midnight and maximal at 18:00. Viral infection of heterotrophic bacteria was rare (0.5-2.5%) and appeared to peak at 03:00. Heterotrophic bacteria, as % eubacteria-positive cells, peaked at midday, appearing loosely related to relative changes in dissolved organic carbon concentration. Bacterial production as assessed by leucine incorporation showed no consistent temporal pattern but could be related to shifts in the grazing rates of heterotrophic nanoflagellates and viral infection rates. Estimates of virus-induced mortality of heterotrophic bacteria, based on infection frequencies, were only about 10% of cell production. Overall, the dynamics of viruses appeared more closely related to Synechococcus than to heterotrophic bacteria. Thus, we found weak links between dissolved organic carbon concentration, or grazing, and bacterial activity, a possibly strong link between Synechococcus and viruses, and a missing link between light and viruses.

Trait-based approaches for understanding microbial biodiversity and ecosystem functioning

PubMed Central

Krause, Sascha; Le Roux, Xavier; Niklaus, Pascal A.; Van Bodegom, Peter M.; Lennon, Jay T.; Bertilsson, Stefan; Grossart, Hans-Peter; Philippot, Laurent; Bodelier, Paul L. E.

2014-01-01

In ecology, biodiversity-ecosystem functioning (BEF) research has seen a shift in perspective from taxonomy to function in the last two decades, with successful application of trait-based approaches. This shift offers opportunities for a deeper mechanistic understanding of the role of biodiversity in maintaining multiple ecosystem processes and services. In this paper, we highlight studies that have focused on BEF of microbial communities with an emphasis on integrating trait-based approaches to microbial ecology. In doing so, we explore some of the inherent challenges and opportunities of understanding BEF using microbial systems. For example, microbial biologists characterize communities using gene phylogenies that are often unable to resolve functional traits. Additionally, experimental designs of existing microbial BEF studies are often inadequate to unravel BEF relationships. We argue that combining eco-physiological studies with contemporary molecular tools in a trait-based framework can reinforce our ability to link microbial diversity to ecosystem processes. We conclude that such trait-based approaches are a promising framework to increase the understanding of microbial BEF relationships and thus generating systematic principles in microbial ecology and more generally ecology. PMID:24904563

Environmental Selection, Dispersal, and Organism Interactions Shape Community Assembly in High-Throughput Enrichment Culturing

DOE PAGES

Justice, N. B.; Sczesnak, A.; Hazen, T. C.; ...

2017-08-04

A central goal of microbial ecology is to identify and quantify the forces that lead to observed population distributions and dynamics. However, these forces, which include environmental selection, dispersal, and organism interactions, are often difficult to assess in natural environments. Here in this paper, we present a method that links microbial community structures with selective and stochastic forces through highly replicated subsampling and enrichment of a single environmental inoculum. Specifically, groundwater from a well-studied natural aquifer was serially diluted and inoculated into nearly 1,000 aerobic and anaerobic nitrate-reducing cultures, and the final community structures were evaluated with 16S rRNA genemore » amplicon sequencing. We analyzed the frequency and abundance of individual operational taxonomic units (OTUs) to understand how probabilistic immigration, relative fitness differences, environmental factors, and organismal interactions contributed to divergent distributions of community structures. We further used a most probable number (MPN) method to estimate the natural condition-dependent cultivable abundance of each of the nearly 400 OTU cultivated in our study and infer the relative fitness of each. Additionally, we infer condition-specific organism interactions and discuss how this high-replicate culturing approach is essential in dissecting the interplay between overlapping ecological forces and taxon-specific attributes that underpin microbial community assembly. IMPORTANCEThrough highly replicated culturing, in which inocula are subsampled from a single environmental sample, we empirically determine how selective forces, interspecific interactions, relative fitness, and probabilistic dispersal shape bacterial communities. These methods offer a novel approach to untangle not only interspecific interactions but also taxon-specific fitness differences that manifest across different cultivation conditions and lead to the selection and enrichment of specific organisms. Additionally, we provide a method for estimating the number of cultivable units of each OTU in the original sample through the MPN approach.« less

Environmental Selection, Dispersal, and Organism Interactions Shape Community Assembly in High-Throughput Enrichment Culturing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Justice, N. B.; Sczesnak, A.; Hazen, T. C.

A central goal of microbial ecology is to identify and quantify the forces that lead to observed population distributions and dynamics. However, these forces, which include environmental selection, dispersal, and organism interactions, are often difficult to assess in natural environments. Here in this paper, we present a method that links microbial community structures with selective and stochastic forces through highly replicated subsampling and enrichment of a single environmental inoculum. Specifically, groundwater from a well-studied natural aquifer was serially diluted and inoculated into nearly 1,000 aerobic and anaerobic nitrate-reducing cultures, and the final community structures were evaluated with 16S rRNA genemore » amplicon sequencing. We analyzed the frequency and abundance of individual operational taxonomic units (OTUs) to understand how probabilistic immigration, relative fitness differences, environmental factors, and organismal interactions contributed to divergent distributions of community structures. We further used a most probable number (MPN) method to estimate the natural condition-dependent cultivable abundance of each of the nearly 400 OTU cultivated in our study and infer the relative fitness of each. Additionally, we infer condition-specific organism interactions and discuss how this high-replicate culturing approach is essential in dissecting the interplay between overlapping ecological forces and taxon-specific attributes that underpin microbial community assembly. IMPORTANCEThrough highly replicated culturing, in which inocula are subsampled from a single environmental sample, we empirically determine how selective forces, interspecific interactions, relative fitness, and probabilistic dispersal shape bacterial communities. These methods offer a novel approach to untangle not only interspecific interactions but also taxon-specific fitness differences that manifest across different cultivation conditions and lead to the selection and enrichment of specific organisms. Additionally, we provide a method for estimating the number of cultivable units of each OTU in the original sample through the MPN approach.« less

Plant traits related to nitrogen uptake influence plant-microbe competition.

PubMed

Moreau, Delphine; Pivato, Barbara; Bru, David; Busset, Hugues; Deau, Florence; Faivre, Céline; Matejicek, Annick; Strbik, Florence; Philippot, Laurent; Mougel, Christophe

2015-08-01

Plant species are important drivers of soil microbial communities. However, how plant functional traits are shaping these communities has received less attention though linking plant and microbial traits is crucial for better understanding plant-microbe interactions. Our objective was to determine how plant-microbe interactions were affected by plant traits. Specifically we analyzed how interactions between plant species and microbes involved in nitrogen cycling were affected by plant traits related to 'nitrogen nutrition in interaction with soil nitrogen availability. Eleven plant species, selected along an oligotrophic-nitrophilic gradient, were grown individually in a nitrogen-poor soil with two levels of nitrate availability. Plant traits for both carbon and nitrogen nutrition were measured and the genetic structure and abundance of rhizosphere. microbial communities, in particular the ammonia oxidizer and nitrate reducer guilds, were analyzed. The structure of the bacterial community in the rhizosphere differed significantly between plant species and these differences depended on nitrogen availability. The results suggest that the rate of nitrogen uptake per unit of root biomass and per day is a key plant trait, explaining why the effect of nitrogen availability on the structure of the bacterial community depends on the plant species. We also showed that the abundance of nitrate reducing bacteria always decreased with increasing nitrogen uptake per unit of root biomass per day, indicating that there was competition for nitrate between plants and nitrate reducing bacteria. This study demonstrates that nitrate-reducing microorganisms may be adversely affected by plants with a high nitrogen uptake rate. Our work puts forward the role of traits related to nitrogen in plant-microbe interactions, whereas carbon is commonly considered as the main driver. It also suggests that plant traits related to ecophysiological processes, such as nitrogen uptake rates, are more relevant for understanding plant-microbe interactions than composite traits, such as nitrophily, which are related to a number of ecophysiological processes.

Respiration-to-DNA ratio reflects physiological state of microorganisms in root-free and rhizosphere soil

NASA Astrophysics Data System (ADS)

Blagodatskaya, E.; Blagodatsky, S.; Kuzyakov, Y.

2009-04-01

The double-stranded DNA (dsDNA) content in soil can serve as a measure of microbial biomass under near steady-state conditions and quantitatively reflect the exponential microbial growth initiated by substrate addition. The yield of respired CO2 per microbial biomass unit (expressed as DNA content) could be a valuable physiological indicator reflecting state of soil microbial community. Therefore, investigations combining both analyses of DNA content and respiration of soil microorganisms under steady-state and during periods of rapid growth are needed. We studied the relationship between CO2 evolution and microbial dsDNA content in native and glucose-amended samples of root-free and rhizosphere soil under Beta vulgaris (Cambisol, loamy sand from the field experiment of the Institute of Agroecology FAL, Braunschweig, Germany). Quantity of dsDNA was determined by direct DNA isolation from soil with mechanic and enzymatic disruption of microbial cell walls with following spectrofluorimetric detection with PicoGreen (Blagodatskaya et al., 2003). Microbial biomass and the kinetic parameters of microbial growth were estimated by dynamics of the CO2 emission from soil amended with glucose and nutrients (Blagodatsky et al., 2000). The CO2 production rate was measured hourly at 22оС using an automated infrared-gas analyzer system. The overall increase in microbial biomass, DNA content, maximal specific growth rate and therefore, in the fraction of microorganisms with r-strategy were observed in rhizosphere as compared to bulk soil. The rhizosphere effect for microbial respiration, biomass and specific growth rate was more pronounced for plots with half-rate of N fertilizer compared to full N addition. The DNA content was significantly lower in bulk compared to rhizosphere soil both before and during microbial growth initiated by glucose amendment. Addition of glucose to the soil strongly increased the amount of CO2 respired per DNA unit. Without substrate addition the VCO2-to-total DNA ratios were lower than 0.1 µg CO2-C µg-1 total DNA h-1 whereas during exponential microbial growth these values increased consistently and exceeded 1 µg CO2-C µg-1 DNA h-1. Thus, the VCO2-to-total DNA ratio strongly changes along with the physiological state of soil microorganisms and can be used as valuable physiological parameter. In growing microorganisms the quantity of CO2 evolved per unit of newly formed DNA was identical in rhizosphere and root free soil and averaged for 13.5 ± 1.1 µg CO2-C µg-1 newly formed DNA. The CO2 yield per unit of newly formed DNA allows the estimation of microbial growth efficiency and validation of specific growth rates obtained during kinetic analysis of respiration curves. The study was supported by European Commission (Marie Curie IIF program, project MICROSOM) and by Alexander von Humboldt Foundation. References: Blagodatskaya EV, Blagodatskii SA, Anderson TH. 2003. Quantitative Isolation of Microbial DNA from Different Types of Soils of Natural and Agricultural Ecosystems. Microbiology 72(6):744-749. Blagodatsky SA, Heinemeyer O, Richter J. 2000. Estimating the active and total soil microbial biomass by kinetic respiration analysis. Biology and Fertility of Soils 32(1):73-81.

Structure-Function Analysis of a Broad Specificity Populus trichocarpa Endo-β-glucanase Reveals an Evolutionary Link between Bacterial Licheninases and Plant XTH Gene Products*

PubMed Central

Eklöf, Jens M.; Shojania, Shaheen; Okon, Mark; McIntosh, Lawrence P.; Brumer, Harry

2013-01-01

The large xyloglucan endotransglycosylase/hydrolase (XTH) gene family continues to be the focus of much attention in studies of plant cell wall morphogenesis due to the unique catalytic functions of the enzymes it encodes. The XTH gene products compose a subfamily of glycoside hydrolase family 16 (GH16), which also comprises a broad range of microbial endoglucanases and endogalactanases, as well as yeast cell wall chitin/β-glucan transglycosylases. Previous whole-family phylogenetic analyses have suggested that the closest relatives to the XTH gene products are the bacterial licheninases (EC 3.2.1.73), which specifically hydrolyze linear mixed linkage β(1→3)/β(1→4)-glucans. In addition to their specificity for the highly branched xyloglucan polysaccharide, XTH gene products are distinguished from the licheninases and other GH16 enzyme subfamilies by significant active site loop alterations and a large C-terminal extension. Given these differences, the molecular evolution of the XTH gene products in GH16 has remained enigmatic. Here, we present the biochemical and structural analysis of a unique, mixed function endoglucanase from black cottonwood (Populus trichocarpa), which reveals a small, newly recognized subfamily of GH16 members intermediate between the bacterial licheninases and plant XTH gene products. We postulate that this clade comprises an important link in the evolution of the large plant XTH gene families from a putative microbial ancestor. As such, this analysis provides new insights into the diversification of GH16 and further unites the apparently disparate members of this important family of proteins. PMID:23572521

Identification and Characterization of Potential Performance-Related Gut Microbiotas in Broiler Chickens across Various Feeding Trials▿†

PubMed Central

Torok, Valeria A.; Hughes, Robert J.; Mikkelsen, Lene L.; Perez-Maldonado, Rider; Balding, Katherine; MacAlpine, Ron; Percy, Nigel J.; Ophel-Keller, Kathy

2011-01-01

Three broiler feeding trials were investigated in order to identify gut bacteria consistently linked with improvements in bird performance as measured by feed efficiency. Trials were done in various geographic locations and varied in diet composition, broiler breed, and bird age. Gut microbial communities were investigated using microbial profiling. Eight common performance-linked operational taxonomic units (OTUs) were identified within both the ilea (180, 492, and 564–566) and ceca (140–142, 218–220, 284–286, 312, and 482) across trials. OTU 564–566 was associated with lower performance, while OTUs 140–142, 482, and 492 were associated with improved performance. Targeted cloning and sequencing of these eight OTUs revealed that they represented 26 bacterial species or phylotypes which clustered phylogenetically into seven groups related to Lactobacillus spp., Ruminococcaceae, Clostridiales, Gammaproteobacteria, Bacteroidales, Clostridiales/Lachnospiraceae, and unclassified bacteria/clostridia. Where bacteria were identifiable to the phylum level, they belonged predominantly to the Firmicutes, with Bacteroidetes and Proteobacteria also identified. Some of the potential performance-related phylotypes showed high sequence identity with classified bacteria (Lactobacillus salivarius, Lactobacillus aviarius, Lactobacillus crispatus, Faecalibacterium prausnitzii, Escherichia coli, Gallibacterium anatis, Clostridium lactatifermentans, Ruminococcus torques, Bacteroides vulgatus, and Alistipes finegoldii). The 16S rRNA gene sequence information generated will allow quantitative assays to be developed which will enable elucidations of which of these phylotypes are truly performance related. This information could be used to monitor strategies to improve feed efficiency and feed formulation for optimal gut health. PMID:21742925

A Novel Analysis Method for Paired-Sample Microbial Ecology Experiments.

PubMed

Olesen, Scott W; Vora, Suhani; Techtmann, Stephen M; Fortney, Julian L; Bastidas-Oyanedel, Juan R; Rodríguez, Jorge; Hazen, Terry C; Alm, Eric J

2016-01-01

Many microbial ecology experiments use sequencing data to measure a community's response to an experimental treatment. In a common experimental design, two units, one control and one experimental, are sampled before and after the treatment is applied to the experimental unit. The four resulting samples contain information about the dynamics of organisms that respond to the treatment, but there are no analytical methods designed to extract exactly this type of information from this configuration of samples. Here we present an analytical method specifically designed to visualize and generate hypotheses about microbial community dynamics in experiments that have paired samples and few or no replicates. The method is based on the Poisson lognormal distribution, long studied in macroecology, which we found accurately models the abundance distribution of taxa counts from 16S rRNA surveys. To demonstrate the method's validity and potential, we analyzed an experiment that measured the effect of crude oil on ocean microbial communities in microcosm. Our method identified known oil degraders as well as two clades, Maricurvus and Rhodobacteraceae, that responded to amendment with oil but do not include known oil degraders. Our approach is sensitive to organisms that increased in abundance only in the experimental unit but less sensitive to organisms that increased in both control and experimental units, thus mitigating the role of "bottle effects".

Occurrence and diversity of both bacterial and fungal communities in dental unit waterlines subjected to disinfectants.

PubMed

Costa, Damien; Mercier, Anne; Gravouil, Kevin; Lesobre, Jérôme; Verdon, Julien; Imbert, Christine

2016-10-01

Chemical disinfectants are widely advocated to reduce the microbial contamination in dental unit waterlines (DUWL). However, until now their efficacy has been poorly examined after long-term application. In this study, through quantitative PCR and high-throughput sequencing, both bacterial and fungal communities were profiled from 8- to 12-year-old DUWL treated with disinfectants commonly used by European dentists. Water was collected from the tap water supplying units to the output exposure point of the turbine handpiece following a stagnation period and dental care activity. Results showed that (i) the unit itself is the principal source of microbial contamination and (ii) water stagnation, DU maintenance practices and quality of water supplying DU appeared as parameters driving the water quality. Despite disinfecting treatment combined to flushing process, the microbial contamination remained relevant in the studied output water, in association with a high bacterial and fungal diversity. The occurrence of potentially pathogenic microorganisms in these treated DUWL demonstrated a potential infectious risk for both patients and dental staff. A disinfectant shock before a prolonged stagnation period could limit the microbial proliferation inside DUWL. Necessity to proceed to regular water quality control of DUWL was highlighted. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Microbial diversity of an oil-water processing site and its associated oil field: the possible role of microorganisms as information carriers from oil-associated environments.

PubMed

van der Kraan, Geert M; Bruining, Johannes; Lomans, Bart P; van Loosdrecht, Mark C M; Muyzer, Gerard

2010-03-01

The phylogenetic diversity of Bacteria and Archaea in water retrieved from a Dutch oil field and units of the associated oil-water separation site were determined using two culture-independent methods. Denaturing gradient gel electrophoresis of PCR-amplified 16S rRNA gene fragments was used to scan the microbial diversity in (1) the oil-water emulsion produced, (2) two different oil-water separator tanks, (3) a wash tank and (4) a water injector. Longer 16S rRNA gene fragments were amplified, cloned and sequenced to determine the diversity in more detail. One of the questions addressed was whether the detected microorganisms could serve as indicators for the environments from which they were retrieved. It was observed that the community found in the production water resembled those reported previously in oil reservoirs, indicating that these ecosystems harbor specific microbial communities. It was shown that changes, like a decrease in temperature, cause a distinctive shift in these communities. The addition of SO(3)(2-) to the wash tank as ammonium bisulphite, used in the oil industry to scavenge oxygen, resulted in a complete community change, giving rise to an unwanted sulphate-reducing community. The fact that these changes in the community can be linked to changes in their environment might indicate that these tools can be used for the monitoring of changing conditions in oil reservoirs upon, for example, water flooding.

Dysbiosis of gut microbiota and microbial metabolites in Parkinson's Disease.

PubMed

Sun, Meng-Fei; Shen, Yan-Qin

2018-04-26

Gut microbial dysbiosis and alteration of microbial metabolites in Parkinson's disease (PD) have been increasingly reported. Dysbiosis in the composition and abundance of gut microbiota can affect both the enteric nervous system and the central nervous system (CNS), indicating the existence of a microbiota-gut-brain axis and thereby causing CNS diseases. Disturbance of the microbiota-gut-brain axis has been linked to specific microbial products that are related to gut inflammation and neuroinflammation. Future directions should therefore focus on the exploration of specific gut microbes or microbial metabolites that contribute to the development of PD. Microbiota-targeted interventions, such as antibiotics, probiotics and fecal microbiota transplantation, have been shown to favorably affect host health. In this review, recent findings regarding alterations and the role of gut microbiota and microbial metabolites in PD are summarized, and potential molecular mechanisms and microbiota-targeted interventions in PD are discussed. Copyright © 2018. Published by Elsevier B.V.

Breaking the Chain of Infection: Dental Unit Water Quality Control

PubMed Central

Pawar, Amrita; Mehta, Sonia; Dang, Rajat

2016-01-01

Introduction The air–water syringes, ultrasonic scalers, high speed air turbine handpieces are connected to dental units by a network of small-bore plastic tubes through which water and air travel to activate or cool the instruments and it had been shown that this system is extensively contaminated with microbial biofilms and pose a potential risk of infection for patients as well as dental professionals. Aim To evaluate and compare the efficacy of various disinfectants in reducing the microbial colony count in water derived from Dental Unit Waterlines. Materials and Methods Five random dental units were selected and samples were collected before and after intervention with 5 disinfectants (0.02% H2O2 continuously, 0.02% H2O2 continuously with shock treatment with 0.25% H2O2 weekly, 0.12% Chlorohexidine and 12% Ethanol overnight, 1:50 Original Listerine overnight, 2% Sodium Perborate and 2% EDTA 5 minutes in morning) using different disinfection methods for 4 weeks. Samples were cultured on Reasoner’s 2A (R2A) agar for microbial counting. Results Results were recorded as Colony forming units/ml (cfu/ml) and were evaluated statistically. Results showed that all the dental unit waterlines were heavily contaminated with microbes before any intervention. After 1 day of disinfection regime the counts reduced significantly and showed progressive reduction in consecutive weeks. Goals set by ADA & CDC were ultimately achieved at the end of 4 weeks. Conclusion All the disinfectants were equally effective in reducing the microbial colony count of DUWLs, irrespective of their concentration and method of disinfection. PMID:27630960

Breaking the Chain of Infection: Dental Unit Water Quality Control.

PubMed

Pawar, Amrita; Garg, Sandeep; Mehta, Sonia; Dang, Rajat

2016-07-01

The air-water syringes, ultrasonic scalers, high speed air turbine handpieces are connected to dental units by a network of small-bore plastic tubes through which water and air travel to activate or cool the instruments and it had been shown that this system is extensively contaminated with microbial biofilms and pose a potential risk of infection for patients as well as dental professionals. To evaluate and compare the efficacy of various disinfectants in reducing the microbial colony count in water derived from Dental Unit Waterlines. Five random dental units were selected and samples were collected before and after intervention with 5 disinfectants (0.02% H2O2 continuously, 0.02% H2O2 continuously with shock treatment with 0.25% H2O2 weekly, 0.12% Chlorohexidine and 12% Ethanol overnight, 1:50 Original Listerine overnight, 2% Sodium Perborate and 2% EDTA 5 minutes in morning) using different disinfection methods for 4 weeks. Samples were cultured on Reasoner's 2A (R2A) agar for microbial counting. Results were recorded as Colony forming units/ml (cfu/ml) and were evaluated statistically. Results showed that all the dental unit waterlines were heavily contaminated with microbes before any intervention. After 1 day of disinfection regime the counts reduced significantly and showed progressive reduction in consecutive weeks. Goals set by ADA & CDC were ultimately achieved at the end of 4 weeks. All the disinfectants were equally effective in reducing the microbial colony count of DUWLs, irrespective of their concentration and method of disinfection.

Response of soil microbial communities and microbial interactions to long-term heavy metal contamination.

PubMed

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

2017-12-01

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

Linking N2O emissions from biochar-amended soil to the structure and function of the N-cycling microbial community

PubMed Central

Harter, Johannes; Krause, Hans-Martin; Schuettler, Stefanie; Ruser, Reiner; Fromme, Markus; Scholten, Thomas; Kappler, Andreas; Behrens, Sebastian

2014-01-01

Nitrous oxide (N2O) contributes 8% to global greenhouse gas emissions. Agricultural sources represent about 60% of anthropogenic N2O emissions. Most agricultural N2O emissions are due to increased fertilizer application. A considerable fraction of nitrogen fertilizers are converted to N2O by microbiological processes (that is, nitrification and denitrification). Soil amended with biochar (charcoal created by pyrolysis of biomass) has been demonstrated to increase crop yield, improve soil quality and affect greenhouse gas emissions, for example, reduce N2O emissions. Despite several studies on variations in the general microbial community structure due to soil biochar amendment, hitherto the specific role of the nitrogen cycling microbial community in mitigating soil N2O emissions has not been subject of systematic investigation. We performed a microcosm study with a water-saturated soil amended with different amounts (0%, 2% and 10% (w/w)) of high-temperature biochar. By quantifying the abundance and activity of functional marker genes of microbial nitrogen fixation (nifH), nitrification (amoA) and denitrification (nirK, nirS and nosZ) using quantitative PCR we found that biochar addition enhanced microbial nitrous oxide reduction and increased the abundance of microorganisms capable of N2-fixation. Soil biochar amendment increased the relative gene and transcript copy numbers of the nosZ-encoded bacterial N2O reductase, suggesting a mechanistic link to the observed reduction in N2O emissions. Our findings contribute to a better understanding of the impact of biochar on the nitrogen cycling microbial community and the consequences of soil biochar amendment for microbial nitrogen transformation processes and N2O emissions from soil. PMID:24067258

Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics [Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics and NanoSIMS.

DOE PAGES

Burow, Luke C.; Woebken, Dagmar; Marshall, Ian PG; ...

2012-11-29

Photosynthetic microbial mats possess extraordinary phylogenetic and functional diversity that makes linking specific pathways with individual microbial populations a daunting task. Close metabolic and spatial relationships between Cyanobacteria and Chloroflexi have previously been observed in diverse microbial mats. Here in this paper, we report that an expressed metabolic pathway for the anoxic catabolism of photosynthate involving Cyanobacteria and Chloroflexi in microbial mats can be reconstructed through metatranscriptomic sequencing of mats collected at Elkhorn Slough, Monterey Bay, CA, USA. In this reconstruction, Microcoleus spp., the most abundant cyanobacterial group in the mats, ferment photosynthate to organic acids, CO 2 and Hmore » 2 through multiple pathways, and an uncultivated lineage of the Chloroflexi take up these organic acids to store carbon as polyhydroxyalkanoates. The metabolic reconstruction is consistent with metabolite measurements and single cell microbial imaging with fluorescence in situ hybridization and NanoSIMS.« less

Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics [Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics and NanoSIMS.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Burow, Luke C.; Woebken, Dagmar; Marshall, Ian PG

Photosynthetic microbial mats possess extraordinary phylogenetic and functional diversity that makes linking specific pathways with individual microbial populations a daunting task. Close metabolic and spatial relationships between Cyanobacteria and Chloroflexi have previously been observed in diverse microbial mats. Here in this paper, we report that an expressed metabolic pathway for the anoxic catabolism of photosynthate involving Cyanobacteria and Chloroflexi in microbial mats can be reconstructed through metatranscriptomic sequencing of mats collected at Elkhorn Slough, Monterey Bay, CA, USA. In this reconstruction, Microcoleus spp., the most abundant cyanobacterial group in the mats, ferment photosynthate to organic acids, CO 2 and Hmore » 2 through multiple pathways, and an uncultivated lineage of the Chloroflexi take up these organic acids to store carbon as polyhydroxyalkanoates. The metabolic reconstruction is consistent with metabolite measurements and single cell microbial imaging with fluorescence in situ hybridization and NanoSIMS.« less

NATURAL ARSENIC CONTAMINATION OF HOLOCENE ALLUVIAL AQUIFERS BY LINKED TECTONIC, WEATHERING, AND MICROBIAL PROCESSES

EPA Science Inventory

Linked tectonic, geochemical, and biologic processes lead to natural arsenic contamination of groundwater in Holocene alluvial aquifers, which are the main threat to human health around the world. These groundwaters are commonly found a long distance from their ultimate source of...

Conditional effect of selenium on the mammalian hind gut microbiota

USDA-ARS?s Scientific Manuscript database

Selenium (Se) status is linked to cancer risk in humans and other mammals. Because Se is used by certain microbial species which contain selenoproteins, and because hind gut microfloral composition is linked to cancer development, we proposed that supranutritional Se could reduce tumorigenisis by af...

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Minjing; Qian, Wei-jun; Gao, Yuqian

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

Linking Microbial Community Structure to β-Glucosidic Function in Soil Aggregates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bailey, Vanessa L.; Fansler, Sarah J.; Stegen, James C.

2013-10-01

To link microbial community 16S structure to a measured function in a natural soil we have scaled both DNA and β-glucosidase assays down to a volume of soil that may approach a unique microbial community. β-glucosidase activity was assayed in 450 individual aggregates which were then sorted into classes of high or low activities, from which groups of 10 or 11 aggregates were identified and grouped for DNA extraction and pyrosequencing. Tandem assays of ATP were conducted for each aggregate in order to normalize these small groups of aggregates for biomass size. In spite of there being no significant differencesmore » in the richness or diversity of the microbial communities associated with high β-glucosidase activities compared with the communities associated with low β-glucosidase communities, several analyses of variance clearly show that the communities of these two groups differ. The separation of these groups is partially driven by the differential abundances of members of the Chitinophagaceae family. It may be that observed functional differences in otherwise similar soil aggregates can be largely attributed to differences in resource availability, rather than to presence or absence of particular taxonomic groups.« less

Competition between roots and microorganisms for phosphorus: A novel 33P labeling approach

NASA Astrophysics Data System (ADS)

Zilla, Thomas; Kuzyakov, Yakov; Zavišiæ, Aljoša; Polle, Andrea

2015-04-01

While organic N mineralization exhibits clear seasonal uptake dynamics, knowledge about seasonal variation in microbial P uptake and mineralization is scarce. We hypothesize that the dynamics of P uptake and mineralization by microorganisms in temperate forest soils exhibit a seasonality anti-cyclic to plant P uptake. Therefore, the ratio of microbial P to labile P increases by the transition from acquiring ecosystems (in spring) to recycling ones (in fall). To investigate this, intact soil-plant mesocosms containing Ah horizon with 1 year old F. sylvatica were removed from the P-rich field site Bad Brueckenau and the P-depleted field site Luess in Germany. During incubation under controlled conditions, seasonal pulse labeling by 33P-orthophosphate was performed at 5 time points over the course of one year. 33P recovery in microbial compounds of organic and mineral soil horizons was determined 7 and 30 days after the labeling. This procedure will account for temporal changes in P allocation and also considers the rather slow P transport from the mycorrhiza into the plants and other microorganisms. For the first time we analyzed the 33P incorporation into total PLFA and consequently provide a new technique for the analysis of P uptake by microorganisms, which has clear advantages compared to P quantification after chloroform fumigation. Polar lipids are hereby extracted with a Frostegård-modified Bligh-and-Dyer buffer, i.e. a single phase mixture of chloroform, methanol and citrate buffer (0.8:1:2, v:v:v). Phospholipids (PLFA) are isolated and purified by solid phase extraction via a silica gel column chromatography. Subsequently, PLFA are hydrolyzed and the resulting fatty acids derivatized by methylation. The fatty acid methyl esters were extracted with n-hexane and measured by GC/MS to investigate the composition of the microbial community. The remaining extract, containing head groups, phosphate units and glycerol backbones, was used to determine 33P activity and recovery in the microbial membrane lipids with a multi-purpose scintillation counter. This approach offers the unique possibility to quantify P fluxes through the microbial network. For the first time, P cycling can be linked to changes in microbial community structure and activity in soils in situ.

Effect of Malathion on the Microbial Ecology of Activated Sludge

DTIC Science & Technology

2015-03-26

EFFECT OF MALATHION ON THE MICROBIAL ECOLOGY OF ACTIVATED SLUDGE THESIS Seth K. Martin, Senior Master Sergeant, USAF AFIT-ENV-MS-15-M-095 DEPARTMENT...Government and is not subject to copyright protection in the United States. AFIT-ENV-MS-15-M-095 EFFECT OF MALATHION ON THE MICROBIAL ECOLOGY OF ACTIVATED...UNLIMITED. AFIT-ENV-MS-15-M-095 EFFECT OF MALATHION ON THE MICROBIAL ECOLOGY OF ACTIVATED SLUDGE THESIS Seth K. Martin, B.S. Senior Master Sergeant

Linking soil biology and chemistry in biological soil crust using isolate exometabolomics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Swenson, Tami L.; Karaoz, Ulas; Swenson, Joel M.

Metagenomic sequencing provides a window into microbial community structure and metabolic potential; however, linking these data to exogenous metabolites that microorganisms process and produce (the exometabolome) remains challenging. Previously, we observed strong exometabolite niche partitioning among bacterial isolates from biological soil crust (biocrust). For this study, we examine native biocrust to determine if these patterns are reproduced in the environment. Overall, most soil metabolites display the expected relationship (positive or negative correlation) with four dominant bacteria following a wetting event and across biocrust developmental stages. For metabolites that were previously found to be consumed by an isolate, 70% are negativelymore » correlated with the abundance of the isolate's closest matching environmental relative in situ, whereas for released metabolites, 67% were positively correlated. Our results demonstrate that metabolite profiling, shotgun sequencing and exometabolomics may be successfully integrated to functionally link microbial community structure with environmental chemistry in biocrust.« less

Linking soil biology and chemistry in biological soil crust using isolate exometabolomics

DOE PAGES

Swenson, Tami L.; Karaoz, Ulas; Swenson, Joel M.; ...

2018-01-02

Metagenomic sequencing provides a window into microbial community structure and metabolic potential; however, linking these data to exogenous metabolites that microorganisms process and produce (the exometabolome) remains challenging. Previously, we observed strong exometabolite niche partitioning among bacterial isolates from biological soil crust (biocrust). For this study, we examine native biocrust to determine if these patterns are reproduced in the environment. Overall, most soil metabolites display the expected relationship (positive or negative correlation) with four dominant bacteria following a wetting event and across biocrust developmental stages. For metabolites that were previously found to be consumed by an isolate, 70% are negativelymore » correlated with the abundance of the isolate's closest matching environmental relative in situ, whereas for released metabolites, 67% were positively correlated. Our results demonstrate that metabolite profiling, shotgun sequencing and exometabolomics may be successfully integrated to functionally link microbial community structure with environmental chemistry in biocrust.« less

Linking soil biology and chemistry in biological soil crust using isolate exometabolomics.

PubMed

Swenson, Tami L; Karaoz, Ulas; Swenson, Joel M; Bowen, Benjamin P; Northen, Trent R

2018-01-02

Metagenomic sequencing provides a window into microbial community structure and metabolic potential; however, linking these data to exogenous metabolites that microorganisms process and produce (the exometabolome) remains challenging. Previously, we observed strong exometabolite niche partitioning among bacterial isolates from biological soil crust (biocrust). Here we examine native biocrust to determine if these patterns are reproduced in the environment. Overall, most soil metabolites display the expected relationship (positive or negative correlation) with four dominant bacteria following a wetting event and across biocrust developmental stages. For metabolites that were previously found to be consumed by an isolate, 70% are negatively correlated with the abundance of the isolate's closest matching environmental relative in situ, whereas for released metabolites, 67% were positively correlated. Our results demonstrate that metabolite profiling, shotgun sequencing and exometabolomics may be successfully integrated to functionally link microbial community structure with environmental chemistry in biocrust.

A novel series of N-acyl substituted indole-linked benzimidazoles and naphthoimidazoles as potential anti inflammatory, anti biofilm and anti microbial agents.

PubMed

Abraham, Rajan; Prakash, Periakaruppan; Mahendran, Karthikeyan; Ramanathan, Murugappan

2018-01-01

A novel N-acyl substituted indole-linked benzimidazoles and naphthoimidazoles were synthesized. Their chemical structures were confirmed using spectroscopic tools including 1 H NMR, 13 C NMR and CHN-elemental analyses. Anti inflammatory activity for all target compounds was evaluated in-vitro. The synthesized compounds hinder the biofilm formation and control the growth of the pathogen, Staphylococcus epidermis. Anti microbial activity of the compounds was evaluated against both Gram negative and Gram positive bacteria such as Staphylococcus aureus (MTCC 2940), Pseudomonas aeruginosa (MTCC424), Escherchia coli (MTCC 443) and Enterococcus fecalis. Copyright © 2017 Elsevier Ltd. All rights reserved.

Linking microbial community structure to membrane biofouling associated with varying dissolved oxygen concentrations.

PubMed

Gao, Da-wen; Fu, Yuan; Tao, Yu; Li, Xin-xin; Xing, Min; Gao, Xiu-hong; Ren, Nan-qi

2011-05-01

In order to elucidate how dissolved oxygen (DO) concentration influenced the generation of extracellular polymeric substance (EPS) and soluble microbial products (SMP) in mixed liquor and biocake, 16S rDNA fingerprinting analyses were performed to investigate the variation of the microbial community in an aerobic membrane bioreactor (MBR). The function of microbial community structure was proved to be ultimately responsible for biofouling. Obvious microbial community succession from the subphylum of Betaproteobacteria to Deltaproteobacteria was observed in biocake. High concentration of EPS in biocake under the low DO concentration (0.5 mg L(-1)) caused severe biofouling. The correlation coefficient of membrane fouling rate with EPS content in biocake (0.9941-0.9964) was much higher than that in mixed liquor (0.6689-0.8004). Copyright © 2011 Elsevier Ltd. All rights reserved.

Anoxia stimulates microbially catalyzed metal release from Animas River sediments.

PubMed

Saup, Casey M; Williams, Kenneth H; Rodríguez-Freire, Lucía; Cerrato, José M; Johnston, Michael D; Wilkins, Michael J

2017-04-19

The Gold King Mine spill in August 2015 released 11 million liters of metal-rich mine waste to the Animas River watershed, an area that has been previously exposed to historical mining activity spanning more than a century. Although adsorption onto fluvial sediments was responsible for rapid immobilization of a significant fraction of the spill-associated metals, patterns of longer-term mobility are poorly constrained. Metals associated with river sediments collected downstream of the Gold King Mine in August 2015 exhibited distinct presence and abundance patterns linked to location and mineralogy. Simulating riverbed burial and development of anoxic conditions, sediment microcosm experiments amended with Animas River dissolved organic carbon revealed the release of specific metal pools coupled to microbial Fe- and SO 4 2- -reduction. Results suggest that future sedimentation and burial of riverbed materials may drive longer-term changes in patterns of metal remobilization linked to anaerobic microbial metabolism, potentially driving decreases in downstream water quality. Such patterns emphasize the need for long-term water monitoring efforts in metal-impacted watersheds.

Lipids as paleomarkers to constrain the marine nitrogen cycle

PubMed Central

Rush, Darci

2017-01-01

Summary Global climate is, in part, regulated by the effect of microbial processes on biogeochemical cycling. The nitrogen cycle, in particular, is driven by microorganisms responsible for the fixation and loss of nitrogen, and the reduction‐oxidation transformations of bio‐available nitrogen. Within marine systems, nitrogen availability is often the limiting factor in the growth of autotrophic organisms, intrinsically linking the nitrogen and carbon cycles. In order to elucidate the state of these cycles in the past, and help envisage present and future variability, it is essential to understand the specific microbial processes responsible for transforming bio‐available nitrogen species. As most microorganisms are soft‐bodied and seldom leave behind physical fossils in the sedimentary record, recalcitrant lipid biomarkers are used to unravel microbial processes in the geological past. This review emphasises the recent advances in marine nitrogen cycle lipid biomarkers, underlines the missing links still needed to fully elucidate past shifts in this biogeochemically‐important cycle, and provides examples of biomarker applications in the geological past. PMID:28142226

Development and validation of a citrate synthase directed quantitative PCR marker for soil bacterial communities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Castro Gonzalez, Hector F; Classen, Aimee T; Austin, Emily E

2012-01-01

Molecular innovations in microbial ecology are allowing scientists to correlate microbial community characteristics to a variety of ecosystem functions. However, to date the majority of soil microbial ecology studies target phylogenetic rRNA markers, while a smaller number target functional markers linked to soil processes. We validated a new primer set targeting citrate synthase (gtlA), a central enzyme in the citric acid cycle linked to aerobic respiration. Primers for a 225 bp fragment suitable for qPCR were tested for specificity and assay performance verified on multiple soils. Clone libraries of the PCR-amplified gtlA gene exhibited high diversity and recovered most majormore » groups identified in a previous 16S rRNA gene study. Comparisons among bacterial communities based on gtlA sequencing using UniFrac revealed differences among the experimental soils studied. Conditions for gtlA qPCR were optimized and calibration curves were highly linear (R2 > 0.99) over six orders of magnitude (4.56 10^5 to 4.56 10^11 copies), with high amplification efficiencies (>1.7). We examined the performance of the gtlA qPCR across a variety of soils and ecosystems, spanning forests, old fields and agricultural areas. We were able to amplify gtlA genes in all tested soils, and detected differences in gtlA abundance within and among environments. These results indicate that a fully developed gtlA-targeted qPCR approach may have potential to link microbial community characteristics with changes in soil respiration.« less

A novel analysis method for paired-sample microbial ecology experiments

DOE PAGES

Olesen, Scott W.; Vora, Suhani; Techtmann, Stephen M.; ...

2016-05-06

Many microbial ecology experiments use sequencing data to measure a community s response to an experimental treatment. In a common experimental design, two units, one control and one experimental, are sampled before and after the treatment is applied to the experimental unit. The four resulting samples contain information about the dynamics of organisms that respond to the treatment, but there are no analytical methods designed to extract exactly this type of information from this configuration of samples. Here we present an analytical method specifically designed to visualize and generate hypotheses about microbial community dynamics in experiments that have paired samplesmore » and few or no replicates. The method is based on the Poisson lognormal distribution, long studied in macroecology, which we found accurately models the abundance distribution of taxa counts from 16S rRNA surveys. To demonstrate the method s validity and potential, we analyzed an experiment that measured the effect of crude oil on ocean microbial communities in microcosm. Our method identified known oil degraders as well as two clades, Maricurvus and Rhodobacteraceae, that responded to amendment with oil but do not include known oil degraders. Furthermore, our approach is sensitive to organisms that increased in abundance only in the experimental unit but less sensitive to organisms that increased in both control and experimental units, thus mitigating the role of bottle effects .« less

A novel analysis method for paired-sample microbial ecology experiments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Olesen, Scott W.; Vora, Suhani; Techtmann, Stephen M.

Many microbial ecology experiments use sequencing data to measure a community s response to an experimental treatment. In a common experimental design, two units, one control and one experimental, are sampled before and after the treatment is applied to the experimental unit. The four resulting samples contain information about the dynamics of organisms that respond to the treatment, but there are no analytical methods designed to extract exactly this type of information from this configuration of samples. Here we present an analytical method specifically designed to visualize and generate hypotheses about microbial community dynamics in experiments that have paired samplesmore » and few or no replicates. The method is based on the Poisson lognormal distribution, long studied in macroecology, which we found accurately models the abundance distribution of taxa counts from 16S rRNA surveys. To demonstrate the method s validity and potential, we analyzed an experiment that measured the effect of crude oil on ocean microbial communities in microcosm. Our method identified known oil degraders as well as two clades, Maricurvus and Rhodobacteraceae, that responded to amendment with oil but do not include known oil degraders. Furthermore, our approach is sensitive to organisms that increased in abundance only in the experimental unit but less sensitive to organisms that increased in both control and experimental units, thus mitigating the role of bottle effects .« less

Host gene-microbiome interactions: molecular mechanisms in inflammatory bowel disease.

PubMed

Chu, Hiutung

2017-07-24

Recent studies have identified links between host genetic variants and microbial recognition of the microbiome. Defects in host-microbiome interactions in individuals harboring inflammatory bowel disease risk alleles may result in imbalances of the microbial community, impaired pathogen clearance, and failure to sense beneficial commensal microbes. These findings highlight the importance of maintaining bi-directional communication at the mucosal interface during intestinal homeostasis.

Shifts among Eukaryota, Bacteria, and Archaea define the vertical organization of a lake sediment.

PubMed

Wurzbacher, Christian; Fuchs, Andrea; Attermeyer, Katrin; Frindte, Katharina; Grossart, Hans-Peter; Hupfer, Michael; Casper, Peter; Monaghan, Michael T

2017-04-08

Lake sediments harbor diverse microbial communities that cycle carbon and nutrients while being constantly colonized and potentially buried by organic matter sinking from the water column. The interaction of activity and burial remained largely unexplored in aquatic sediments. We aimed to relate taxonomic composition to sediment biogeochemical parameters, test whether community turnover with depth resulted from taxonomic replacement or from richness effects, and to provide a basic model for the vertical community structure in sediments. We analyzed four replicate sediment cores taken from 30-m depth in oligo-mesotrophic Lake Stechlin in northern Germany. Each 30-cm core spanned ca. 170 years of sediment accumulation according to 137 Cs dating and was sectioned into layers 1-4 cm thick. We examined a full suite of biogeochemical parameters and used DNA metabarcoding to examine community composition of microbial Archaea, Bacteria, and Eukaryota. Community β-diversity indicated nearly complete turnover within the uppermost 30 cm. We observed a pronounced shift from Eukaryota- and Bacteria-dominated upper layers (<5 cm) to Bacteria-dominated intermediate layers (5-14 cm) and to deep layers (>14 cm) dominated by enigmatic Archaea that typically occur in deep-sea sediments. Taxonomic replacement was the prevalent mechanism in structuring the community composition and was linked to parameters indicative of microbial activity (e.g., CO 2 and CH 4 concentration, bacterial protein production). Richness loss played a lesser role but was linked to conservative parameters (e.g., C, N, P) indicative of past conditions. By including all three domains, we were able to directly link the exponential decay of eukaryotes with the active sediment microbial community. The dominance of Archaea in deeper layers confirms earlier findings from marine systems and establishes freshwater sediments as a potential low-energy environment, similar to deep sea sediments. We propose a general model of sediment structure and function based on microbial characteristics and burial processes. An upper "replacement horizon" is dominated by rapid taxonomic turnover with depth, high microbial activity, and biotic interactions. A lower "depauperate horizon" is characterized by low taxonomic richness, more stable "low-energy" conditions, and a dominance of enigmatic Archaea.

A microbial biogeochemistry network for soil carbon and nitrogen cycling and methane flux: model structure and application to Asia

NASA Astrophysics Data System (ADS)

Xu, X.; Song, C.; Wang, Y.; Ricciuto, D. M.; Lipson, D.; Shi, X.; Zona, D.; Song, X.; Yuan, F.; Oechel, W. C.; Thornton, P. E.

2017-12-01

A microbial model is introduced for simulating microbial mechanisms controlling soil carbon and nitrogen biogeochemical cycling and methane fluxes. The model is built within the CN (carbon-nitrogen) framework of Community Land Model 4.5, named as CLM-Microbe to emphasize its explicit representation of microbial mechanisms to biogeochemistry. Based on the CLM4.5, three new pools were added: bacteria, fungi, and dissolved organic matter. It has 11 pools and 34 transitional processes, compared with 8 pools and 9 transitional flow in the CLM4.5. The dissolve organic carbon was linked with a new microbial functional group based methane module to explicitly simulate methane production, oxidation, transport and their microbial controls. Comparing with CLM4.5-CN, the CLM-Microbe model has a number of new features, (1) microbial control on carbon and nitrogen flows between soil carbon/nitrogen pools; (2) an implicit representation of microbial community structure as bacteria and fungi; (3) a microbial functional-group based methane module. The model sensitivity analysis suggests the importance of microbial carbon allocation parameters on soil biogeochemistry and microbial controls on methane dynamics. Preliminary simulations validate the model's capability for simulating carbon and nitrogen dynamics and methane at a number of sites across the globe. The regional application to Asia has verified the model in simulating microbial mechanisms in controlling methane dynamics at multiple scales.

Taxonomic and Functional Differences between Microbial Communities in Qinghai Lake and Its Input Streams

PubMed Central

Ren, Ze; Wang, Fang; Qu, Xiaodong; Elser, James J.; Liu, Yang; Chu, Limin

2017-01-01

Understanding microbial communities in terms of taxon and function is essential to decipher the biogeochemical cycling in aquatic ecosystems. Lakes and their input streams are highly linked. However, the differences between microbial assemblages in streams and lakes are still unclear. In this study, we conducted an intensive field sampling of microbial communities from lake water and stream biofilms in the Qinghai Lake watershed, the largest lake in China. We determined bacterial communities using high-throughput 16S rRNA gene sequencing and predicted functional profiles using PICRUSt to determine the taxonomic and functional differences between microbial communities in stream biofilms and lake water. The results showed that stream biofilms and lake water harbored distinct microbial communities. The microbial communities were different taxonomically and functionally between stream and lake. Moreover, streams biofilms had a microbial network with higher connectivity and modularity than lake water. Functional beta diversity was strongly correlated with taxonomic beta diversity in both the stream and lake microbial communities. Lake microbial assemblages displayed greater predicted metabolic potentials of many metabolism pathways while the microbial assemblages in stream biofilms were more abundant in xenobiotic biodegradation and metabolism and lipid metabolism. Furthermore, lake microbial assemblages had stronger predicted metabolic potentials in amino acid metabolism, carbon fixation, and photosynthesis while stream microbial assemblages were higher in carbohydrate metabolism, oxidative phosphorylation, and nitrogen metabolism. This study adds to our knowledge of stream-lake linkages from the functional and taxonomic composition of microbial assemblages. PMID:29213266

The potentiality of cross-linked fungal chitosan to control water contamination through bioactive filtration.

PubMed

Tayel, Ahmed A; El-Tras, Wael F; Elguindy, Nihal M

2016-07-01

Water contamination, with heavy metals and microbial pathogens, is among the most dangerous challenges that confront human health worldwide. Chitosan is a bioactive biopolymer that could be produced from fungal mycelia to be utilized in various applied fields. An attempt to apply fungal chitosan for heavy metals chelation and microbial pathogens inhibition, in contaminated water, was performed in current study. Chitosan was produced from the mycelia of Aspergillus niger, Cunninghamella elegans, Mucor rouxii and from shrimp shells, using unified production conditions. The FT-IR spectra of produced chitosans were closely comparable. M. rouxii chitosan had the highest deacetylation degree (91.3%) and the lowest molecular weight (33.2kDa). All chitosan types had potent antibacterial activities against Escherichia coli and Staphylococcus aureus; the most forceful type was C. elegans chitosan. Chitosan beads were cross-linked with glutaraldehyde (GLA) and ethylene-glycol-diglycidyl ether (EGDE); linked beads became insoluble in water, acidic and alkaline solutions and could effectively adsorb heavy metals ions, e.g. copper, lead and zinc, in aqueous solution. The bioactive filter, loaded with EGDE- A. niger chitosan beads, was able to reduce heavy metals' concentration with >68%, and microbial load with >81%, after 6h of continuous water flow in the experimentally designed filter. Copyright © 2016 Elsevier B.V. All rights reserved.

The P/N (Positive-to-Negative Links) Ratio in Complex Networks-A Promising In Silico Biomarker for Detecting Changes Occurring in the Human Microbiome.

PubMed

Ma, Zhanshan Sam

2018-05-01

Relatively little progress in the methodology for differentiating between the healthy and diseased microbiomes, beyond comparing microbial community diversities with traditional species richness or Shannon index, has been made. Network analysis has increasingly been called for the task, but most currently available microbiome datasets only allows for the construction of simple species correlation networks (SCNs). The main results from SCN analysis are a series of network properties such as network degree and modularity, but the metrics for these network properties often produce inconsistent evidence. We propose a simple new network property, the P/N ratio, defined as the ratio of positive links to the number of negative links in the microbial SCN. We postulate that the P/N ratio should reflect the balance between facilitative and inhibitive interactions among microbial species, possibly one of the most important changes occurring in diseased microbiome. We tested our hypothesis with five datasets representing five major human microbiome sites and discovered that the P/N ratio exhibits contrasting differences between healthy and diseased microbiomes and may be harnessed as an in silico biomarker for detecting disease-associated changes in the human microbiome, and may play an important role in personalized diagnosis of the human microbiome-associated diseases.

Rapid culture-independent microbial analysis aboard the international space station (ISS) stage two: quantifying three microbial biomarkers.

PubMed

Morris, Heather C; Damon, Michael; Maule, Jake; Monaco, Lisa A; Wainwright, Norm

2012-09-01

Abstract A portable, rapid, microbial detection unit, the Lab-On-a-Chip Application Development Portable Test System (LOCAD-PTS), was launched to the International Space Station (ISS) as a technology demonstration unit in December 2006. Results from the first series of experiments designed to detect Gram-negative bacteria on ISS surfaces by quantifying a single microbial biomarker lipopolysaccharide (LPS) were reported in a previous article. Herein, we report additional technology demonstration experiments expanding the on-orbit capabilities of the LOCAD-PTS to detecting three different microbial biomarkers on ISS surfaces. Six different astronauts on more than 20 occasions participated in these experiments, which were designed to test the new beta-glucan (fungal cell wall molecule) and lipoteichoic acid (LTA; Gram-positive bacterial cell wall component) cartridges individually and in tandem with the existing Limulus Amebocyte Lysate (LAL; Gram-negative bacterial LPS detection) cartridges. Additionally, we conducted the sampling side by side with the standard culture-based detection method currently used on the ISS. Therefore, we present data on the distribution of three microbial biomarkers collected from various surfaces in every module present on the ISS at the time of sampling. In accordance with our previous experiments, we determined that spacecraft surfaces known to be frequently in contact with crew members demonstrated higher values of all three microbial molecules. Key Words: Planetary protection-Spaceflight-Microbiology-Biosensor. Astrobiology 12, 830-840.

Anaerobic Methane Oxidation Driven by Microbial Reduction of Natural Organic Matter in a Tropical Wetland

PubMed Central

Valenzuela, Edgardo I.; Prieto-Davó, Alejandra; López-Lozano, Nguyen E.; Hernández-Eligio, Alberto; Vega-Alvarado, Leticia; Juárez, Katy; García-González, Ana Sarahí; López, Mercedes G.

2017-01-01

ABSTRACT Wetlands constitute the main natural source of methane on Earth due to their high content of natural organic matter (NOM), but key drivers, such as electron acceptors, supporting methanotrophic activities in these habitats are poorly understood. We performed anoxic incubations using freshly collected sediment, along with water samples harvested from a tropical wetland, amended with 13C-methane (0.67 atm) to test the capacity of its microbial community to perform anaerobic oxidation of methane (AOM) linked to the reduction of the humic fraction of its NOM. Collected evidence demonstrates that electron-accepting functional groups (e.g., quinones) present in NOM fueled AOM by serving as a terminal electron acceptor. Indeed, while sulfate reduction was the predominant process, accounting for up to 42.5% of the AOM activities, the microbial reduction of NOM concomitantly occurred. Furthermore, enrichment of wetland sediment with external NOM provided a complementary electron-accepting capacity, of which reduction accounted for ∼100 nmol 13CH4 oxidized · cm−3 · day−1. Spectroscopic evidence showed that quinone moieties were heterogeneously distributed in the wetland sediment, and their reduction occurred during the course of AOM. Moreover, an enrichment derived from wetland sediments performing AOM linked to NOM reduction stoichiometrically oxidized methane coupled to the reduction of the humic analogue anthraquinone-2,6-disulfonate. Microbial populations potentially involved in AOM coupled to microbial reduction of NOM were dominated by divergent biota from putative AOM-associated archaea. We estimate that this microbial process potentially contributes to the suppression of up to 114 teragrams (Tg) of CH4 · year−1 in coastal wetlands and more than 1,300 Tg · year−1, considering the global wetland area. IMPORTANCE The identification of key processes governing methane emissions from natural systems is of major importance considering the global warming effects triggered by this greenhouse gas. Anaerobic oxidation of methane (AOM) coupled to the microbial reduction of distinct electron acceptors plays a pivotal role in mitigating methane emissions from ecosystems. Given their high organic content, wetlands constitute the largest natural source of atmospheric methane. Nevertheless, processes controlling methane emissions in these environments are poorly understood. Here, we provide tracer analysis with 13CH4 and spectroscopic evidence revealing that AOM linked to the microbial reduction of redox functional groups in natural organic matter (NOM) prevails in a tropical wetland. We suggest that microbial reduction of NOM may largely contribute to the suppression of methane emissions from tropical wetlands. This is a novel avenue within the carbon cycle in which slowly decaying NOM (e.g., humic fraction) in organotrophic environments fuels AOM by serving as a terminal electron acceptor. PMID:28341676

Anaerobic Methane Oxidation Driven by Microbial Reduction of Natural Organic Matter in a Tropical Wetland.

PubMed

Valenzuela, Edgardo I; Prieto-Davó, Alejandra; López-Lozano, Nguyen E; Hernández-Eligio, Alberto; Vega-Alvarado, Leticia; Juárez, Katy; García-González, Ana Sarahí; López, Mercedes G; Cervantes, Francisco J

2017-06-01

Wetlands constitute the main natural source of methane on Earth due to their high content of natural organic matter (NOM), but key drivers, such as electron acceptors, supporting methanotrophic activities in these habitats are poorly understood. We performed anoxic incubations using freshly collected sediment, along with water samples harvested from a tropical wetland, amended with 13 C-methane (0.67 atm) to test the capacity of its microbial community to perform anaerobic oxidation of methane (AOM) linked to the reduction of the humic fraction of its NOM. Collected evidence demonstrates that electron-accepting functional groups (e.g., quinones) present in NOM fueled AOM by serving as a terminal electron acceptor. Indeed, while sulfate reduction was the predominant process, accounting for up to 42.5% of the AOM activities, the microbial reduction of NOM concomitantly occurred. Furthermore, enrichment of wetland sediment with external NOM provided a complementary electron-accepting capacity, of which reduction accounted for ∼100 nmol 13 CH 4 oxidized · cm -3 · day -1 Spectroscopic evidence showed that quinone moieties were heterogeneously distributed in the wetland sediment, and their reduction occurred during the course of AOM. Moreover, an enrichment derived from wetland sediments performing AOM linked to NOM reduction stoichiometrically oxidized methane coupled to the reduction of the humic analogue anthraquinone-2,6-disulfonate. Microbial populations potentially involved in AOM coupled to microbial reduction of NOM were dominated by divergent biota from putative AOM-associated archaea. We estimate that this microbial process potentially contributes to the suppression of up to 114 teragrams (Tg) of CH 4 · year -1 in coastal wetlands and more than 1,300 Tg · year -1 , considering the global wetland area. IMPORTANCE The identification of key processes governing methane emissions from natural systems is of major importance considering the global warming effects triggered by this greenhouse gas. Anaerobic oxidation of methane (AOM) coupled to the microbial reduction of distinct electron acceptors plays a pivotal role in mitigating methane emissions from ecosystems. Given their high organic content, wetlands constitute the largest natural source of atmospheric methane. Nevertheless, processes controlling methane emissions in these environments are poorly understood. Here, we provide tracer analysis with 13 CH 4 and spectroscopic evidence revealing that AOM linked to the microbial reduction of redox functional groups in natural organic matter (NOM) prevails in a tropical wetland. We suggest that microbial reduction of NOM may largely contribute to the suppression of methane emissions from tropical wetlands. This is a novel avenue within the carbon cycle in which slowly decaying NOM (e.g., humic fraction) in organotrophic environments fuels AOM by serving as a terminal electron acceptor. Copyright © 2017 American Society for Microbiology.

2500 high-quality genomes reveal that the biogeochemical cycles of C, N, S and H are cross-linked by metabolic handoffs in the terrestrial subsurface

NASA Astrophysics Data System (ADS)

Anantharaman, K.; Brown, C. T.; Hug, L. A.; Sharon, I.; Castelle, C. J.; Shelton, A.; Bonet, B.; Probst, A. J.; Thomas, B. C.; Singh, A.; Wilkins, M.; Williams, K. H.; Tringe, S. G.; Beller, H. R.; Brodie, E.; Hubbard, S. S.; Banfield, J. F.

2015-12-01

Microorganisms drive the transformations of carbon compounds in the terrestrial subsurface, a key reservoir of carbon on earth, and impact other linked biogeochemical cycles. Our current knowledge of the microbial ecology in this environment is primarily based on 16S rRNA gene sequences that paint a biased picture of microbial community composition and provide no reliable information on microbial metabolism. Consequently, little is known about the identity and metabolic roles of the uncultivated microbial majority in the subsurface. In turn, this lack of understanding of the microbial processes that impact the turnover of carbon in the subsurface has restricted the scope and ability of biogeochemical models to capture key aspects of the carbon cycle. In this study, we used a culture-independent, genome-resolved metagenomic approach to decipher the metabolic capabilities of microorganisms in an aquifer adjacent to the Colorado River, near Rifle, CO, USA. We sequenced groundwater and sediment samples collected across fifteen different geochemical regimes. Sequence assembly, binning and manual curation resulted in the recovery of 2,542 high-quality genomes, 27 of which are complete. These genomes represent 1,300 non-redundant organisms comprising both abundant and rare community members. Phylogenetic analyses involving ribosomal proteins and 16S rRNA genes revealed the presence of up to 34 new phyla that were hitherto unknown. Less than 11% of all genomes belonged to the 4 most commonly represented phyla that constitute 93% of all currently available genomes. Genome-specific analyses of metabolic potential revealed the co-occurrence of important functional traits such as carbon fixation, nitrogen fixation and use of electron donors and electron acceptors. Finally, we predict that multiple organisms are often required to complete redox pathways through a complex network of metabolic handoffs that extensively cross-link subsurface biogeochemical cycles.

Introducing SONS, a tool for operational taxonomic unit-based comparisons of microbial community memberships and structures.

PubMed

Schloss, Patrick D; Handelsman, Jo

2006-10-01

The recent advent of tools enabling statistical inferences to be drawn from comparisons of microbial communities has enabled the focus of microbial ecology to move from characterizing biodiversity to describing the distribution of that biodiversity. Although statistical tools have been developed to compare community structures across a phylogenetic tree, we lack tools to compare the memberships and structures of two communities at a particular operational taxonomic unit (OTU) definition. Furthermore, current tests of community structure do not indicate the similarity of the communities but only report the probability of a statistical hypothesis. Here we present a computer program, SONS, which implements nonparametric estimators for the fraction and richness of OTUs shared between two communities.

Synthetic Microbial Ecology: Engineering Habitats for Modular Consortia

PubMed Central

Ben Said, Sami; Or, Dani

2017-01-01

The metabolic diversity present in microbial communities enables cooperation toward accomplishing more complex tasks than possible by a single organism. Members of a consortium communicate by exchanging metabolites or signals that allow them to coordinate their activity through division of labor. In contrast with monocultures, evidence suggests that microbial consortia self-organize to form spatial patterns, such as observed in biofilms or in soil aggregates, that enable them to respond to gradient, to improve resource interception and to exchange metabolites more effectively. Current biotechnological applications of microorganisms remain rudimentary, often relying on genetically engineered monocultures (e.g., pharmaceuticals) or mixed-cultures of partially known composition (e.g., wastewater treatment), yet the vast potential of “microbial ecological power” observed in most natural environments, remains largely underused. In line with the Unified Microbiome Initiative (UMI) which aims to “discover and advance tools to understand and harness the capabilities of Earth's microbial ecosystems,” we propose in this concept paper to capitalize on ecological insights into the spatial and modular design of interlinked microbial consortia that would overcome limitations of natural systems and attempt to optimize the functionality of the members and the performance of the engineered consortium. The topology of the spatial connections linking the various members and the regulated fluxes of media between those modules, while representing a major engineering challenge, would allow the microbial species to interact. The modularity of such spatially linked microbial consortia (SLMC) could facilitate the design of scalable bioprocesses that can be incorporated as parts of a larger biochemical network. By reducing the need for a compatible growth environment for all species simultaneously, SLMC will dramatically expand the range of possible combinations of microorganisms and their potential applications. We briefly review existing tools to engineer such assemblies and optimize potential benefits resulting from the collective activity of their members. Prospective microbial consortia and proposed spatial configurations will be illustrated and preliminary calculations highlighting the advantages of SLMC over co-cultures will be presented, followed by a discussion of challenges and opportunities for moving forward with some designs. PMID:28670307

Synthetic Microbial Ecology: Engineering Habitats for Modular Consortia.

PubMed

Ben Said, Sami; Or, Dani

2017-01-01

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

Capturing the genetic makeup of the active microbiome in situ.

PubMed

Singer, Esther; Wagner, Michael; Woyke, Tanja

2017-09-01

More than any other technology, nucleic acid sequencing has enabled microbial ecology studies to be complemented with the data volumes necessary to capture the extent of microbial diversity and dynamics in a wide range of environments. In order to truly understand and predict environmental processes, however, the distinction between active, inactive and dead microbial cells is critical. Also, experimental designs need to be sensitive toward varying population complexity and activity, and temporal as well as spatial scales of process rates. There are a number of approaches, including single-cell techniques, which were designed to study in situ microbial activity and that have been successively coupled to nucleic acid sequencing. The exciting new discoveries regarding in situ microbial activity provide evidence that future microbial ecology studies will indispensably rely on techniques that specifically capture members of the microbiome active in the environment. Herein, we review those currently used activity-based approaches that can be directly linked to shotgun nucleic acid sequencing, evaluate their relevance to ecology studies, and discuss future directions.

Capturing the genetic makeup of the active microbiome in situ

PubMed Central

Singer, Esther; Wagner, Michael; Woyke, Tanja

2017-01-01

More than any other technology, nucleic acid sequencing has enabled microbial ecology studies to be complemented with the data volumes necessary to capture the extent of microbial diversity and dynamics in a wide range of environments. In order to truly understand and predict environmental processes, however, the distinction between active, inactive and dead microbial cells is critical. Also, experimental designs need to be sensitive toward varying population complexity and activity, and temporal as well as spatial scales of process rates. There are a number of approaches, including single-cell techniques, which were designed to study in situ microbial activity and that have been successively coupled to nucleic acid sequencing. The exciting new discoveries regarding in situ microbial activity provide evidence that future microbial ecology studies will indispensably rely on techniques that specifically capture members of the microbiome active in the environment. Herein, we review those currently used activity-based approaches that can be directly linked to shotgun nucleic acid sequencing, evaluate their relevance to ecology studies, and discuss future directions. PMID:28574490

Microbial Threats to Health. Emerging Infections: Microbial Threats to Health in the United States.

DTIC Science & Technology

1992-10-01

enzootic in much of the rodent population in the western United States, Mexico , and Canada. Thanks to modem sanitation and the availability of...pandemic, as explorers, soldiers, and others ini acted by the smallpox virus traveled to all parts of the globe. Smallpox was introduced into Mexico 6y...Caribbean and on the Yucatan Peninsula of Mexico . Although the disease is concentrated in a small number of areas, world- wide incidence rates for DHF

Microbial fuel cells as pollutant treatment units: Research updates.

PubMed

Zhang, Quanguo; Hu, Jianjun; Lee, Duu-Jong

2016-10-01

Microbial fuel cells (MFC) are a device that can convert chemical energy in influent substances to electricity via biological pathways. Based on the consent that MFC technology should be applied as a waste/wastewater treatment unit rather than a renewable energy source, this mini-review discussed recent R&D efforts on MFC technologies for pollutant treatments and highlighted the challenges and research and development needs. Owing to the low power density levels achievable by larger-scale MFC, the MFC should be used as a device other than energy source such as being a pollutant treatment unit. Copyright © 2016 Elsevier Ltd. All rights reserved.

Composition of Hydrothermal Vent Microbial Communities as Revealed by Analyses of Signature Lipids, Stable Carbon Isotopes and Aquificales Cultures

NASA Technical Reports Server (NTRS)

Jahnke, Linda L.; Eder, Wolfgang; Huber, Robert; Hinrichs, Kai-Uwe; Hayes, John M.; Cady, Sherry L.; DesMarais, David J.; Hope, Janet M.; Summons, Roger E.

2001-01-01

Extremely thermophilic microbial communities associated with the siliceous vent walls and outflow channel of Octopus Spring, Yellowstone National Park, have been examined for lipid biomarker and carbon isotopic signatures. These data were compared with that obtained from representatives of three Aquificales genera. Thermocrinis ruber, Thermocrinis sp. HI, Hydrogenobacter thermophilus, Aquifex pyrophilus and Aquifex aeolicus all contained phospholipids composed not only of the usual ester-linked fatty acids, but also ether-linked alkyl moieties. The fatty acids of all cultured organisms were dominated by very distinct pattern of n-C-20:1 and cy-C-21 compounds. The alkyl glycerol ethers were present primarily as C-18:0 monoethers with the exception of the Aquifex spp. in which dialkyl glycerol ethers with a boarder carbon-number distribution were also present. These Aquificales biomarker lipids were the major constituents in the lipid extracts of the Octopus Spring microbial samples. Two natural samples, a microbial biofilm growing in association with deposition of amorphous silica on the vent walls at 92 C, and the well-known "pink-streamer community" (PSC), siliceous filaments of a microbial consortia growing in the outflow channel at 87 C were analyzed. Both the biofilm and PSC samples contained mono- and dialkyl glycerol ethers with a prevalence of C-18 and C-20 alkyls. Phospholipid fatty acids were comprised of both the characteristic. Additional information is contained in the original extended abstract.

Antibiotic-induced changes in the microbiota disrupt redox dynamics in the gut

PubMed Central

Reese, Aspen T; Cho, Eugenia H; Klitzman, Bruce; Nichols, Scott P; Wisniewski, Natalie A; Villa, Max M; Durand, Heather K; Jiang, Sharon; Midani, Firas S; Nimmagadda, Sai N; O'Connell, Thomas M; Wright, Justin P; Deshusses, Marc A

2018-01-01

How host and microbial factors combine to structure gut microbial communities remains incompletely understood. Redox potential is an important environmental feature affected by both host and microbial actions. We assessed how antibiotics, which can impact host and microbial function, change redox state and how this contributes to post-antibiotic succession. We showed gut redox potential increased within hours of an antibiotic dose in mice. Host and microbial functioning changed under treatment, but shifts in redox potentials could be attributed specifically to bacterial suppression in a host-free ex vivo human gut microbiota model. Redox dynamics were linked to blooms of the bacterial family Enterobacteriaceae. Ecological succession to pre-treatment composition was associated with recovery of gut redox, but also required dispersal from unaffected gut communities. As bacterial competition for electron acceptors can be a key ecological factor structuring gut communities, these results support the potential for manipulating gut microbiota through managing bacterial respiration. PMID:29916366

Methods for understanding microbial community structures and functions in microbial fuel cells: a review.

PubMed

Zhi, Wei; Ge, Zheng; He, Zhen; Zhang, Husen

2014-11-01

Microbial fuel cells (MFCs) employ microorganisms to recover electric energy from organic matter. However, fundamental knowledge of electrochemically active bacteria is still required to maximize MFCs power output for practical applications. This review presents microbiological and electrochemical techniques to help researchers choose the appropriate methods for the MFCs study. Pre-genomic and genomic techniques such as 16S rRNA based phylogeny and metagenomics have provided important information in the structure and genetic potential of electrode-colonizing microbial communities. Post-genomic techniques such as metatranscriptomics allow functional characterizations of electrode biofilm communities by quantifying gene expression levels. Isotope-assisted phylogenetic analysis can further link taxonomic information to microbial metabolisms. A combination of electrochemical, phylogenetic, metagenomic, and post-metagenomic techniques offers opportunities to a better understanding of the extracellular electron transfer process, which in turn can lead to process optimization for power output. Copyright © 2014 Elsevier Ltd. All rights reserved.

Hydration status and diurnal trophic interactions shape microbial community function in desert biocrusts

NASA Astrophysics Data System (ADS)

Kim, Minsu; Or, Dani

2017-12-01

Biological soil crusts (biocrusts) are self-organised thin assemblies of microbes, lichens, and mosses that are ubiquitous in arid regions and serve as important ecological and biogeochemical hotspots. Biocrust ecological function is intricately shaped by strong gradients of water, light, oxygen, and dynamics in the abundance and spatial organisation of the microbial community within a few millimetres of the soil surface. We report a mechanistic model that links the biophysical and chemical processes that shape the functioning of biocrust representative microbial communities that interact trophically and respond dynamically to cycles of hydration, light, and temperature. The model captures key features of carbon and nitrogen cycling within biocrusts, such as microbial activity and distribution (during early stages of biocrust establishment) under diurnal cycles and the associated dynamics of biogeochemical fluxes at different hydration conditions. The study offers new insights into the highly dynamic and localised processes performed by microbial communities within thin desert biocrusts.

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

PubMed

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.

Earth's Earliest Ecosystems in the Classroom: The Use of Microbial Mats to Teach General Principles in Microbial Ecology, and Scientific Inquiry

NASA Technical Reports Server (NTRS)

Beboutl, Brad M.; Bucaria, Robin

2004-01-01

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

Microbial diversity arising from thermodynamic constraints

PubMed Central

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 Community Profile of a Lead Service Line Removed from a Drinking Water Distribution System▿

PubMed Central

White, Colin; Tancos, Matthew; Lytle, Darren A.

2011-01-01

A corroded lead service line was removed from a drinking water distribution system, and the microbial community was profiled using 16S rRNA gene techniques. This is the first report of the characterization of a biofilm on the surface of a corroded lead drinking water service line. The majority of phylotypes have been linked to heavy-metal-contaminated environments. PMID:21652741

Mercury methylation by novel microorganisms from new environments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gilmour, C C; Podar, Mircea; Bullock, Allyson L

2013-01-01

Microbial mercury (Hg) methylation transforms a toxic trace metal into the highly bioaccumulated neurotoxin methylmercury (MeHg). The lack of a genetic marker for microbial MeHg production has prevented a clear understanding of Hg-methylating organism distribution in nature. Recently, a specific gene cluster (hgcAB) was linked to Hg methylation in two bacteria.1 Here we test if the presence of hgcAB orthologues is a reliable predictor of Hg methylation capability in microorganisms, a necessary confirmation for the development of molecular probes for Hg-methylation in nature. Although hgcAB orthologues are rare among all available microbial genomes, organisms are much more phylogenetically and environmentallymore » diverse than previously thought. By directly measuring MeHg production in several bacterial and archaeal strains encoding hgcAB, we confirmed that possessing hgcAB predicts Hg methylation capability. For the first time, we demonstrated Hg methylation in a number of species other than sulfate- (SRB) and iron- (FeRB) reducing bacteria, including methanogens, and syntrophic, acetogenic, and fermentative Firmicutes. Several of these species occupy novel environmental niches for Hg methylation, including methanogenic habitats such as rice paddies, the animal gut, and extremes of pH and salinity. Identification of these organisms as Hg methylators now links methylation to discrete gene markers in microbial communities.« less

Mercury methylation by novel microorganisms from new environments.

PubMed

Gilmour, Cynthia C; Podar, Mircea; Bullock, Allyson L; Graham, Andrew M; Brown, Steven D; Somenahally, Anil C; Johs, Alex; Hurt, Richard A; Bailey, Kathryn L; Elias, Dwayne A

2013-10-15

Microbial mercury (Hg) methylation transforms a toxic trace metal into the highly bioaccumulated neurotoxin methylmercury (MeHg). The lack of a genetic marker for microbial MeHg production has prevented a clear understanding of Hg-methylating organism distribution in nature. Recently, a specific gene cluster (hgcAB) was linked to Hg methylation in two bacteria.1 Here we test if the presence of hgcAB orthologues is a reliable predictor of Hg methylation capability in microorganisms, a necessary confirmation for the development of molecular probes for Hg-methylation in nature. Although hgcAB orthologues are rare among all available microbial genomes, organisms are much more phylogenetically and environmentally diverse than previously thought. By directly measuring MeHg production in several bacterial and archaeal strains encoding hgcAB, we confirmed that possessing hgcAB predicts Hg methylation capability. For the first time, we demonstrated Hg methylation in a number of species other than sulfate- (SRB) and iron- (FeRB) reducing bacteria, including methanogens, and syntrophic, acetogenic, and fermentative Firmicutes. Several of these species occupy novel environmental niches for Hg methylation, including methanogenic habitats such as rice paddies, the animal gut, and extremes of pH and salinity. Identification of these organisms as Hg methylators now links methylation to discrete gene markers in microbial communities.

Deriving site-specific soil clean-up values for metals and metalloids: Rationale for including protection of soil microbial processes

PubMed Central

Kuperman, Roman G; Siciliano, Steven D; Römbke, Jörg; Oorts, Koen

2014-01-01

Although it is widely recognized that microorganisms are essential for sustaining soil fertility, structure, nutrient cycling, groundwater purification, and other soil functions, soil microbial toxicity data were excluded from the derivation of Ecological Soil Screening Levels (Eco-SSL) in the United States. Among the reasons for such exclusion were claims that microbial toxicity tests were too difficult to interpret because of the high variability of microbial responses, uncertainty regarding the relevance of the various endpoints, and functional redundancy. Since the release of the first draft of the Eco-SSL Guidance document by the US Environmental Protection Agency in 2003, soil microbial toxicity testing and its use in ecological risk assessments have substantially improved. A wide range of standardized and nonstandardized methods became available for testing chemical toxicity to microbial functions in soil. Regulatory frameworks in the European Union and Australia have successfully incorporated microbial toxicity data into the derivation of soil threshold concentrations for ecological risk assessments. This article provides the 3-part rationale for including soil microbial processes in the development of soil clean-up values (SCVs): 1) presenting a brief overview of relevant test methods for assessing microbial functions in soil, 2) examining data sets for Cu, Ni, Zn, and Mo that incorporated soil microbial toxicity data into regulatory frameworks, and 3) offering recommendations on how to integrate the best available science into the method development for deriving site-specific SCVs that account for bioavailability of metals and metalloids in soil. Although the primary focus of this article is on the development of the approach for deriving SCVs for metals and metalloids in the United States, the recommendations provided in this article may also be applicable in other jurisdictions that aim at developing ecological soil threshold values for protection of microbial processes in contaminated soils. PMID:24376192

Biophysical processes supporting the diversity of microbial life in soil

PubMed Central

Tecon, Robin

2017-01-01

Abstract Soil, the living terrestrial skin of the Earth, plays a central role in supporting life and is home to an unimaginable diversity of microorganisms. This review explores key drivers for microbial life in soils under different climates and land-use practices at scales ranging from soil pores to landscapes. We delineate special features of soil as a microbial habitat (focusing on bacteria) and the consequences for microbial communities. This review covers recent modeling advances that link soil physical processes with microbial life (termed biophysical processes). Readers are introduced to concepts governing water organization in soil pores and associated transport properties and microbial dispersion ranges often determined by the spatial organization of a highly dynamic soil aqueous phase. The narrow hydrological windows of wetting and aqueous phase connectedness are crucial for resource distribution and longer range transport of microorganisms. Feedbacks between microbial activity and their immediate environment are responsible for emergence and stabilization of soil structure—the scaffolding for soil ecological functioning. We synthesize insights from historical and contemporary studies to provide an outlook for the challenges and opportunities for developing a quantitative ecological framework to delineate and predict the microbial component of soil functioning. PMID:28961933

Evidence of Microbial Regulation of Biogeochemical Cycles from a Study on Methane Flux and Land Use Change

PubMed Central

Nazaries, Loïc; Pan, Yao; Bodrossy, Levente; Baggs, Elizabeth M.; Millard, Peter; Murrell, J. Colin

2013-01-01

Microbes play an essential role in ecosystem functions, including carrying out biogeochemical cycles, but are currently considered a black box in predictive models and all global biodiversity debates. This is due to (i) perceived temporal and spatial variations in microbial communities and (ii) lack of ecological theory explaining how microbes regulate ecosystem functions. Providing evidence of the microbial regulation of biogeochemical cycles is key for predicting ecosystem functions, including greenhouse gas fluxes, under current and future climate scenarios. Using functional measures, stable-isotope probing, and molecular methods, we show that microbial (community diversity and function) response to land use change is stable over time. We investigated the change in net methane flux and associated microbial communities due to afforestation of bog, grassland, and moorland. Afforestation resulted in the stable and consistent enhancement in sink of atmospheric methane at all sites. This change in function was linked to a niche-specific separation of microbial communities (methanotrophs). The results suggest that ecological theories developed for macroecology may explain the microbial regulation of the methane cycle. Our findings provide support for the explicit consideration of microbial data in ecosystem/climate models to improve predictions of biogeochemical cycles. PMID:23624469

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

PubMed

Barberán, Albert; Casamayor, Emilio O

2014-12-01

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

Microbial profiling of South African acid mine water samples using next generation sequencing platform.

PubMed

Kamika, I; Azizi, S; Tekere, M

2016-07-01

This study monitored changes in bacterial and fungal structure in a mine water in a monthly basis over 4 months. Over the 4-month study period, mine water samples contained more bacteria (91.06 %) compared to fungi (8.94 %). For bacteria, mine water samples were dominated by Proteobacteria (39.14 to 65.06 %) followed by Firmicutes (26.34 to 28.9 %) in summer, and Cyanobacteria (27.05 %) in winter. In the collected samples, 18 % of bacteria could not be assigned to a phylum and remained unclassified suggesting hitherto vast untapped microbial diversity especially during winter. The fungal domain was the sole eukaryotic microorganism found in the mine water samples with unclassified fungi (68.2 to 91 %) as the predominant group, followed by Basidiomycota (6.9 to 27.8 %). The time of collection, which was linked to the weather, had higher impact on bacterial community than fungal community. The bacterial operational taxonomic units (OTUs) ranged from 865 to 4052 over the 4-month sampling period, while fungal OTUs varied from 73 to 249. The diversity indices suggested that the bacterial community inhabiting the mine water samples were more diverse than the fungal community. The canonical correspondence analysis (CCA) results highlighted that the bacterial community variance had the strongest relationship with water temperature, conductivity, pH, and dissolved oxygen (DO) content, as compared to fungi and water characteristics, had the greatest contribution to both bacterial and fungal community variance. The results provided the relationships between microbial community and environmental variables in the studied mining sites.

Hemolymph microbiome of Pacific oysters in response to temperature, temperature stress and infection

PubMed Central

Lokmer, Ana; Mathias Wegner, Karl

2015-01-01

Microbiota provide their hosts with a range of beneficial services, including defense from external pathogens. However, host-associated microbial communities themselves can act as a source of opportunistic pathogens depending on the environment. Marine poikilotherms and their microbiota are strongly influenced by temperature, but experimental studies exploring how temperature affects the interactions between both parties are rare. To assess the effects of temperature, temperature stress and infection on diversity, composition and dynamics of the hemolymph microbiota of Pacific oysters (Crassostrea gigas), we conducted an experiment in a fully-crossed, three-factorial design, in which the temperature acclimated oysters (8 or 22 °C) were exposed to temperature stress and to experimental challenge with a virulent Vibrio sp. strain. We monitored oyster survival and repeatedly collected hemolymph of dead and alive animals to determine the microbiome composition by 16s rRNA gene amplicon pyrosequencing. We found that the microbial dynamics and composition of communities in healthy animals (including infection survivors) were significantly affected by temperature and temperature stress, but not by infection. The response was mediated by changes in the incidence and abundance of operational taxonomic units (OTUs) and accompanied by little change at higher taxonomic levels, indicating dynamic stability of the hemolymph microbiome. Dead and moribund oysters, on the contrary, displayed signs of community structure disruption, characterized by very low diversity and proliferation of few OTUs. We can therefore link short-term responses of host-associated microbial communities to abiotic and biotic factors and assess the potential feedback between microbiota dynamics and host survival during disease. PMID:25180968

Linking Archaeal Molecular Diversity and Lipid Biomarker Composition in a Hypersaline Microbial Mat Community

NASA Technical Reports Server (NTRS)

Jahnke, Linda; Orphan, Victoria; Turk, Kendra; Embaye, Tsegereda; Kubo, Mike; Summons, Roger

2005-01-01

Lipid biomarkers for discrete microbial groups are a valuable tool for establishing links to ancient microbial ecosystems. Lipid biomarkers can establish organism source and function in contemporary microbial ecosystems (membrane lipids) and by analogy, potential relevance to the fossilized carbon skeletons (geolipids) extracted from ancient sedimentary rock. The Mars Exploration Rovers have provided clear evidence for an early wet Mars and the presence of hypersaline evaporitic basins. Ongoing work on an early Earth analog, the hypersaline benthic mats in Guerrero Negro, Baja California Sur, may provide clues to what may have evolved and flourished on an early wet Mars, if only for a short period. Cyanobacterial mats are a pertinent early Earth analog for consideration of evolutionary and microbial processes within the aerobic photosynthetic and adjacent anoxic layers. Fluctuations in physio-chemical parameters associated with spatial and temporal scales are expressed through vast microbial metabolic diversity. Our recent work hopes to establish the dynamic of archaeal diversity, particularly as it relates to methane production in this high sulfate environment, through the use of lipid biomarker and phylogenetic analyses. Archaeal 16s rRNA and mcrA gene assemblages, demonstrated distinct spatial separation over the 130 mm core of at least three distinct genera within the order Methanosarcinales, as well as an abundance of uncultured members of the Thermoplasmales and Crenarchaeota. Ether-bound lipid analysis identified abundant 0-alkyl and 0-isopranyl chains throughout the core, and the presence of sn-2 hydroxyarchaeol, a biomarker for methylotrophic methanogens. A unique ether isoprenoid chain, a C30:1 , possibly related to the geolipid squalane, a paleobiomarker associated with hypersaline environments, was most abundant within the oxic-anoxic transition zone.

Microbial Community Structure and Activity Linked to Contrasting Biogeochemical Gradients in Bog and Fen Environments of the Glacial Lake Agassiz Peatland

PubMed Central

Lin, X.; Green, S.; Tfaily, M. M.; Prakash, O.; Konstantinidis, K. T.; Corbett, J. E.; Chanton, J. P.; Cooper, W. T.

2012-01-01

The abundances, compositions, and activities of microbial communities were investigated at bog and fen sites in the Glacial Lake Agassiz Peatland of northwestern Minnesota. These sites contrast in the reactivity of dissolved organic matter (DOM) and the presence or absence of groundwater inputs. Microbial community composition was characterized using pyrosequencing and clone library construction of phylogenetic marker genes. Microbial distribution patterns were linked to pH, concentrations of dissolved organic carbon and nitrogen, C/N ratios, optical properties of DOM, and activities of laccase and peroxidase enzymes. Both bacterial and archaeal richness and rRNA gene abundance were >2 times higher on average in the fen than in the bog, in agreement with a higher pH, labile DOM content, and enhanced enzyme activities in the fen. Fungi were equivalent to an average of 1.4% of total prokaryotes in gene abundance assayed by quantitative PCR. Results revealed statistically distinct spatial patterns between bacterial and fungal communities. Fungal distribution did not covary with pH and DOM optical properties and was vertically stratified, with a prevalence of Ascomycota and Basidiomycota near the surface and much higher representation of Zygomycota in the subsurface. In contrast, bacterial community composition largely varied between environments, with the bog dominated by Acidobacteria (61% of total sequences), while the Firmicutes (52%) dominated in the fen. Acetoclastic Methanosarcinales showed a much higher relative abundance in the bog, in contrast to the dominance of diverse hydrogenotrophic methanogens in the fen. This is the first quantitative and compositional analysis of three microbial domains in peatlands and demonstrates that the microbial abundance, diversity, and activity parallel with the pronounced differences in environmental variables between bog and fen sites. PMID:22843538

Impacts of Microbial Growth on the Air Quality of the International Space Station

NASA Technical Reports Server (NTRS)

Macatangay, Ariel V.; Bruce, Rebekah J.

2009-01-01

An understanding of the various sources of non-methane volatile organic compounds (NMVOCs) is one facet to ensuring the habitability of crewed spacecraft. Even though the International Space Station (ISS) atmosphere is relatively well characterized in terms of what is in the atmosphere and approximately how much, linking the majority of these trace contaminants detected to their source is virtually impossible. Albeit a few of can be associated to a single source, the majority of these trace contaminants have their origins from multiple sources. On crewed spacecraft such as ISS, trace contaminants are broadly categorized as either coming from equipment, which includes systems and payloads, or from the metabolic processes of the crew members. Such widely encompassing categories clearly illustrate the difficulty in linking air contaminants to their source(s). It is well known that microbial growth in ISS can flourish if left unchecked. Although processes are in place to limit microbial growth, in reality, microbial growth has pervaded the habitable environment of ISS. This is simply a consequence of having crewed spacecraft, as humans are the largest contributor to the bioload. As with crew members, microbes also have metabolic processes which, in many ways, are comparable to human metabolism. As such, it can be expected that microbial growth can lead to the release of volatile organic compounds into the ISS atmosphere. Given a large enough microbial population, the impact to the air quality of ISS can be potentially large. A survey of the microbiology found in ISS will be presented as well as the possible types of volatile organic compounds that can result from such organisms. This will be correlated to the observations provided by ground-based analysis of ISS atmosphere samples.

Microbial activity promotes carbon storage in temperate soils

NASA Astrophysics Data System (ADS)

Lange, Markus; Eisenhauer, Nico; Sierra, Carlos; Gleixner, Gerd

2014-05-01

Soils are one of the most important carbon sink and sources. Soils contain up to 3/4 of all terrestrial carbon. Beside physical aspects of soil properties (e.g. soil moisture and texture) plants play an important role in carbon sequestration. The positive effect of plant diversity on carbon storage is already known, though the underlying mechanisms remain still unclear. In the frame of the Jena Experiment, a long term biodiversity experiment, we are able to identify these processes. Nine years after an land use change from an arable field to managed grassland the mean soil carbon concentrations increased towards the concentrations of permanent meadows. The increase was positively linked to a plant diversity gradient. High diverse plant communities produce more biomass, which in turn results in higher amounts of litter inputs. The plant litter is transferred to the soil organic matter by the soil microbial community. However, higher plant diversity also causes changes in micro-climatic condition. For instance, more diverse plant communities have a more dense vegetation structure, which reduced the evaporation of soils surface and thus, increases soil moisture in the top layer. Higher inputs and higher soil moisture lead to an enlarged respiration of the soil microbial community. Most interestingly, the carbon storage in the Jena Experiment was much more related to microbial respiration than to plant root inputs. Moreover, using radiocarbon, we found a significant younger carbon age in soils of more diverse plant communities than in soils of lower diversity, indicating that more fresh carbon is integrated into the carbon pool. Putting these findings together, we could show, that the positive link between plant diversity and carbon storage is due to a higher microbial decomposition of plant litter, pointing out that carbon storage in soils is a function of the microbial community.

Impacts of Microbial Growth on the Air Quality of the International Space Station

NASA Technical Reports Server (NTRS)

Macatangay, Ariel V.; Bruce, Rebekah J.

2010-01-01

An understanding of the various sources of non-methane volatile organic compounds (NMVOCs) is one facet to ensuring the habitability of crewed spacecraft. Even though the International Space Station (ISS) atmosphere is relatively well characterized in terms of what is in the atmosphere and approximately how much, linking the majority of these trace contaminants detected to their source is virtually impossible. Albeit a few of can be associated to a single source, the majority of these trace contaminants have their origins from multiple sources. On crewed spacecraft such as ISS, trace contaminants are broadly categorized as either coming from equipment, which includes systems and payloads, or from the metabolic processes of the crew members. Such widely encompassing categories clearly illustrate the difficulty in linking air contaminants to their source(s). It is well known that microbial growth in ISS can flourish if left unchecked. Although processes are in place to limit microbial growth, in reality, microbial growth has pervaded the habitable environment of ISS. This is simply a consequence of having crewed spacecraft, as humans are the largest contributor to the bioload. As with crew members, microbes also have metabolic processes which, in many ways, are comparable to human metabolism. As such, it can be expected that microbial growth can lead to the release of volatile organic compounds into the ISS atmosphere. Given a large enough microbial population, the impact to the air quality of ISS can be potentially large. A survey of the microbiology found in ISS will be presented as well as the possible types of volatile organic compounds that can result from such organisms. This will be correlated to the observations provided by ground-based analysis of ISS atmosphere samples

Microbes as engines of ecosystem function: When does community structure enhance predictions of ecosystem processes?

DOE PAGES

Graham, Emily B.; Knelman, Joseph E.; Schindlbacher, Andreas; ...

2016-02-24

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

Microbes as engines of ecosystem function: When does community structure enhance predictions of ecosystem processes?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Graham, Emily B.; Knelman, Joseph E.; Schindlbacher, Andreas

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

Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?

PubMed Central

Graham, Emily B.; Knelman, Joseph E.; Schindlbacher, Andreas; Siciliano, Steven; Breulmann, Marc; Yannarell, Anthony; Beman, J. M.; Abell, Guy; Philippot, Laurent; Prosser, James; Foulquier, Arnaud; Yuste, Jorge C.; Glanville, Helen C.; Jones, Davey L.; Angel, Roey; Salminen, Janne; Newton, Ryan J.; Bürgmann, Helmut; Ingram, Lachlan J.; Hamer, Ute; Siljanen, Henri M. P.; Peltoniemi, Krista; Potthast, Karin; Bañeras, Lluís; Hartmann, Martin; Banerjee, Samiran; Yu, Ri-Qing; Nogaro, Geraldine; Richter, Andreas; Koranda, Marianne; Castle, Sarah C.; Goberna, Marta; Song, Bongkeun; Chatterjee, Amitava; Nunes, Olga C.; Lopes, Ana R.; Cao, Yiping; Kaisermann, Aurore; Hallin, Sara; Strickland, Michael S.; Garcia-Pausas, Jordi; Barba, Josep; Kang, Hojeong; Isobe, Kazuo; Papaspyrou, Sokratis; Pastorelli, Roberta; Lagomarsino, Alessandra; Lindström, Eva S.; Basiliko, Nathan; Nemergut, Diana R.

2016-01-01

Microorganisms are vital in mediating the earth’s biogeochemical cycles; yet, despite our rapidly increasing ability to explore complex environmental microbial communities, the relationship between microbial community structure and ecosystem processes remains poorly understood. Here, we address a fundamental and unanswered question in microbial ecology: ‘When do we need to understand microbial community structure to accurately predict function?’ We present a statistical analysis investigating the value of environmental data and microbial community structure independently and in combination for explaining rates of carbon and nitrogen cycling processes within 82 global datasets. Environmental variables were the strongest predictors of process rates but left 44% of variation unexplained on average, suggesting the potential for microbial data to increase model accuracy. Although only 29% of our datasets were significantly improved by adding information on microbial community structure, we observed improvement in models of processes mediated by narrow phylogenetic guilds via functional gene data, and conversely, improvement in models of facultative microbial processes via community diversity metrics. Our results also suggest that microbial diversity can strengthen predictions of respiration rates beyond microbial biomass parameters, as 53% of models were improved by incorporating both sets of predictors compared to 35% by microbial biomass alone. Our analysis represents the first comprehensive analysis of research examining links between microbial community structure and ecosystem function. Taken together, our results indicate that a greater understanding of microbial communities informed by ecological principles may enhance our ability to predict ecosystem process rates relative to assessments based on environmental variables and microbial physiology. PMID:26941732

Microbes as Engines of Ecosystem Function: When Does Community Structure Enhance Predictions of Ecosystem Processes?

PubMed

Graham, Emily B; Knelman, Joseph E; Schindlbacher, Andreas; Siciliano, Steven; Breulmann, Marc; Yannarell, Anthony; Beman, J M; Abell, Guy; Philippot, Laurent; Prosser, James; Foulquier, Arnaud; Yuste, Jorge C; Glanville, Helen C; Jones, Davey L; Angel, Roey; Salminen, Janne; Newton, Ryan J; Bürgmann, Helmut; Ingram, Lachlan J; Hamer, Ute; Siljanen, Henri M P; Peltoniemi, Krista; Potthast, Karin; Bañeras, Lluís; Hartmann, Martin; Banerjee, Samiran; Yu, Ri-Qing; Nogaro, Geraldine; Richter, Andreas; Koranda, Marianne; Castle, Sarah C; Goberna, Marta; Song, Bongkeun; Chatterjee, Amitava; Nunes, Olga C; Lopes, Ana R; Cao, Yiping; Kaisermann, Aurore; Hallin, Sara; Strickland, Michael S; Garcia-Pausas, Jordi; Barba, Josep; Kang, Hojeong; Isobe, Kazuo; Papaspyrou, Sokratis; Pastorelli, Roberta; Lagomarsino, Alessandra; Lindström, Eva S; Basiliko, Nathan; Nemergut, Diana R

2016-01-01

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

A quantitative microbial risk assessment for center pivot irrigation of dairy wastewaters

USDA-ARS?s Scientific Manuscript database

In the western United States where livestock wastewaters are commonly land applied, there are concerns over individuals being exposed to airborne pathogens. In response, a quantitative microbial risk assessment (QMRA) was performed to estimate infectious risks from inhaling pathogens aerosolized dur...

Effects and mechanisms of biochar-microbe interactions in soil improvement and pollution remediation: A review.

PubMed

Zhu, Xiaomin; Chen, Baoliang; Zhu, Lizhong; Xing, Baoshan

2017-08-01

Biochars have attracted tremendous attention due to their effects on soil improvement; they enhance carbon storage, soil fertility and quality, and contaminant (organic and heavy metal) immobilization and transformation. These effects could be achieved by modifying soil microbial habitats and (or) directly influencing microbial metabolisms, which together induce changes in microbial activity and microbial community structures. This review links microbial responses, including microbial activity, community structures and soil enzyme activities, with changes in soil properties caused by biochars. In particular, we summarized possible mechanisms that are involved in the effects that biochar-microbe interactions have on soil carbon sequestration and pollution remediation. Special attention has been paid to biochar effects on the formation and protection of soil aggregates, biochar adsorption of contaminants, biochar-mediated transformation of soil contaminants by microorganisms, and biochar-facilitated electron transfer between microbial cells and contaminants and soil organic matter. Certain reactive organic compounds and heavy metals in biochar may induce toxicity to soil microorganisms. Adsorption and hydrolysis of signaling molecules by biochar interrupts microbial interspecific communications, potentially altering soil microbial community structures. Further research is urged to verify the proposed mechanisms involved in biochar-microbiota interactions for soil remediation and improvement. Copyright © 2017 Elsevier Ltd. All rights reserved.

Functional diversity of microbial communities in pristine aquifers inferred by PLFA- and sequencing-based approaches

NASA Astrophysics Data System (ADS)

Schwab, Valérie F.; Herrmann, Martina; Roth, Vanessa-Nina; Gleixner, Gerd; Lehmann, Robert; Pohnert, Georg; Trumbore, Susan; Küsel, Kirsten; Totsche, Kai U.

2017-05-01

Microorganisms in groundwater play an important role in aquifer biogeochemical cycles and water quality. However, the mechanisms linking the functional diversity of microbial populations and the groundwater physico-chemistry are still not well understood due to the complexity of interactions between surface and subsurface. Within the framework of Hainich (north-western Thuringia, central Germany) Critical Zone Exploratory of the Collaborative Research Centre AquaDiva, we used the relative abundances of phospholipid-derived fatty acids (PLFAs) to link specific biochemical markers within the microbial communities to the spatio-temporal changes of the groundwater physico-chemistry. The functional diversities of the microbial communities were mainly correlated with groundwater chemistry, including dissolved O2, Fet and NH4+ concentrations. Abundances of PLFAs derived from eukaryotes and potential nitrite-oxidizing bacteria (11Me16:0 as biomarker for Nitrospira moscoviensis) were high at sites with elevated O2 concentration where groundwater recharge supplies bioavailable substrates. In anoxic groundwaters more rich in Fet, PLFAs abundant in sulfate-reducing bacteria (SRB), iron-reducing bacteria and fungi increased with Fet and HCO3- concentrations, suggesting the occurrence of active iron reduction and the possible role of fungi in meditating iron solubilization and transport in those aquifer domains. In more NH4+-rich anoxic groundwaters, anammox bacteria and SRB-derived PLFAs increased with NH4+ concentration, further evidencing the dependence of the anammox process on ammonium concentration and potential links between SRB and anammox bacteria. Additional support of the PLFA-based bacterial communities was found in DNA- and RNA-based Illumina MiSeq amplicon sequencing of bacterial 16S rRNA genes, which showed high predominance of nitrite-oxidizing bacteria Nitrospira, e.g. Nitrospira moscoviensis, in oxic aquifer zones and of anammox bacteria in more NH4+-rich anoxic groundwater. Higher relative abundances of sequence reads in the RNA-based datasets affiliated with iron-reducing bacteria in more Fet-rich groundwater supported the occurrence of active dissimilatory iron reduction. The functional diversity of the microbial communities in the biogeochemically distinct groundwater assemblages can be largely attributed to the redox conditions linked to changes in bioavailable substrates and input of substrates with the seepage. Our results demonstrate the power of complementary information derived from PLFA-based and sequencing-based approaches.

Phylogenetic analysis of bacterial isolates from man-made high-pH, high-salt environments and identification of gene-cassette-associated open reading frames.

PubMed

Ghauri, Muhammad A; Khalid, Ahmad M; Grant, Susan; Grant, William D; Heaphy, Shaun

2006-06-01

Environmental samples were collected from high-pH sites in Pakistan, including a uranium heap set up for carbonate leaching, the lime unit of a tannery, and the Khewra salt mine. Another sample was collected from a hot spring on the shore of the soda lake, Magadi, in Kenya. Microbial cultures were enriched from Pakistani samples. Phylogenetic analysis of isolates was carried out by sequencing 16S rRNA genes. Genomic DNA was amplified by polymerase chain reaction using integron gene-cassette-specific primers. Different gene-cassette-linked genes were recovered from the cultured strains related to Halomonas magadiensis, Virgibacillus halodenitrificans, and Yania flava and from the uncultured environmental DNA sample. The usefulness of this technique as a tool for gene mining is indicated.

A logical data representation framework for electricity-driven bioproduction processes.

PubMed

Patil, Sunil A; Gildemyn, Sylvia; Pant, Deepak; Zengler, Karsten; Logan, Bruce E; Rabaey, Korneel

2015-11-01

Microbial electrosynthesis (MES) is a process that uses electricity as an energy source for driving the production of chemicals and fuels using microorganisms and CO2 or organics as carbon sources. The development of this highly interdisciplinary technology on the interface between biotechnology and electrochemistry requires knowledge and expertise in a variety of scientific and technical areas. The rational development and commercialization of MES can be achieved at a faster pace if the research data and findings are reported in appropriate and uniformly accepted ways. Here we provide a framework for reporting on MES research and propose several pivotal performance indicators to describe these processes. Linked to this study is an online tool to perform necessary calculations and identify data gaps. A key consideration is the calculation of effective energy expenditure per unit product in a manner enabling cross comparison of studies irrespective of reactor design. We anticipate that the information provided here on different aspects of MES ranging from reactor and process parameters to chemical, electrochemical, and microbial functionality indicators will assist researchers in data presentation and ease data interpretation. Furthermore, a discussion on secondary MES aspects such as downstream processing, process economics and life cycle analysis is included. Copyright © 2015 Elsevier Inc. All rights reserved.

Gut microbial markers are associated with diabetes onset, regulatory imbalance, and IFN-γ level in NOD mice.

PubMed

Krych, Ł; Nielsen, D S; Hansen, A K; Hansen, C H F

2015-01-01

Gut microbiota regulated imbalances in the host's immune profile seem to be an important factor in the etiology of type 1 diabetes (T1D), and identifying bacterial markers for T1D may therefore be useful in diagnosis and prevention of T1D. The aim of the present study was to investigate the link between the early gut microbiota and immune parameters of non-obese diabetic (NOD) mice in order to select alleged bacterial markers of T1D. Gut microbial composition in feces was analyzed with 454/FLX Titanium (Roche) pyro-sequencing and correlated with diabetes onset age and immune cell populations measured in diabetic and non-diabetic mice at 30 weeks of age. The early gut microbiota composition was found to be different between NOD mice that later in life were classified as diabetic or non-diabetic. Those differences were further associated with changes in FoxP3(+) regulatory T cells, CD11b(+) dendritic cells, and IFN-γ production. The model proposed in this work suggests that operational taxonomic units classified to S24-7, Prevotella, and an unknown Bacteriodales (all Bacteroidetes) act in favor of diabetes protection whereas members of Lachnospiraceae, Ruminococcus, and Oscillospira (all Firmicutes) promote pathogenesis.

The Microbiome and Complement Activation: A Mechanistic Model for Preterm Birth

PubMed Central

Dunn, Alexis B.; Dunlop, Anne L.; Hogue, Carol J.; Miller, Andrew; Corwin, Elizabeth J.

2018-01-01

Preterm Birth (PTB, < 37 completed weeks' gestation) is one of the leading obstetrical problems in the United States affecting approximately 1 of every 9 births. Even more concerning are the persistent racial disparities in PTB with particularly high rates in African Americans. There are several recognized pathophysiologic pathways to PTB, including infection and/or exaggerated systemic or local inflammation. Intrauterine infection is a causal factor linked to PTB, thought to result most commonly from inflammatory processes triggered by microbial invasion of bacteria ascending from the vaginal microbiome. Trials to treat various infections have shown limited efficacy in reducing PTB risk, suggesting that other complex mechanisms, including those associated with inflammation, may be involved in the relationship between microbes, infection, and PTB. A key mediator of the inflammatory response, and recently shown to be associated with PTB, is the complement system, an innate defense mechanism involved in both normal physiologic processes that occur during pregnancy implantation, as well as processes that promote the elimination of pathogenic microbes. The purpose of this paper is to present a mechanistic model of inflammation-associated PTB, which hypothesizes a relationship between the microbiome and dysregulation of the complement system. Exploring the relationships between the microbial environment and complement biomarkers may elucidate a potentially modifiable biological pathway to preterm birth. PMID:28073296

Emerging roles for the gut microbiome in autism spectrum disorder

PubMed Central

Vuong, Helen E.; Hsiao, Elaine Y.

2016-01-01

Autism spectrum disorder (ASD) is a serious neurodevelopmental disorder that affects one in 45 children in the United States, with a similarly striking prevalence in countries around the world. However, mechanisms underlying its etiology and manifestations remain poorly understood. While ASD is diagnosed based on the presence and severity of impaired social communication and repetitive behavior, immune dysregulation and gastrointestinal issues are common co-morbidities. The microbiome is an integral part of human physiology; recent studies show that changes in the gut microbiota can modulate gastrointestinal physiology, immune function and even behavior. Links between particular bacteria from the indigenous gut microbiota and phenotypes relevant to ASD raise the important question of whether microbial dysbiosis plays a role in the development or presentation of ASD symptoms. Here we review reports of microbial dysbiosis in ASD. We further discuss potential effects of the microbiota on ASD-associated symptoms, drawing upon signaling mechanisms for reciprocal interactions between the microbiota, immunity, gut function and behavior. In addition, we discuss recent findings supporting a role for the microbiome as an interface between environmental and genetic risk factors that are associated with ASD. These studies highlight the integration of pathways across multiple body systems that together can impact brain and behavior and suggest that changes in the microbiome may contribute to symptoms of neurodevelopmental disease. PMID:27773355

Differences in fecal microbial metabolites and microbiota of children with autism spectrum disorders

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kang, Dae-Wook; Ilhan, Zehra Esra; Isern, Nancy G.

Evidence supporting that gut problems are linked to ASD symptoms has been accumulating both in humans and animal models of ASD. Gut microbes and their metabolites may be linked not only to GI problems but also to ASD behavior symptoms. Despite this high interest, most previous studies have looked mainly at microbial structure, and studies on fecal metabolites are rare in the context of ASD. Thus, we aimed to detect fecal metabolites that may be present at significantly different concentrations between 21 children with ASD and 23 neurotypical children and to investigate its possible link to human gut microbiome. Usingmore » NMR spectroscopy and 16S rRNA gene amplicon sequencing, we examined metabolite profiles and microbial compositions in fecal samples, respectively. Of the 59 metabolites detected, isopropanol concentrations were significantly higher in feces of children with ASD after multiple testing corrections. We also observed similar trends of fecal metabolites to previous studies; children with ASD have higher fecal p-cresol and possibly lower GABA concentrations. In addition, Fisher Discriminant Analysis (FDA) with leave-out-validation suggested that a group of metabolites- caprate, nicotinate, glutamine, thymine, and aspartate- may potentially function as a biomarker to separate ASD participants from the neurotypical group (78% sensitivity and 81% specificity). Consistent with our previous Arizona cohort study, we also confirmed lower gut microbial diversity and reduced relative abundances of Prevotella copri in children with ASD. After multiple testing corrections, we also learned that relative abundances of Feacalibacterium prausnitzii and Haemophilus parainfluenzae were lower in feces of children with ASD. Despite a relatively short list of fecal metabolites, the data in this study support that children with ASD have altered metabolite profiles in feces when compared with neurotypical children and warrant further investigation of metabolites in larger cohorts.« less

Effects of dairy manure management in annual and perennial cropping systems on soil microbial communities associated with in situ N2O fluxes

NASA Astrophysics Data System (ADS)

Dunfield, Kari; Thompson, Karen; Bent, Elizabeth; Abalos, Diego; Wagner-Riddle, Claudia

2016-04-01

Liquid dairy manure (LDM) application and ploughing events may affect soil microbial community functioning differently between perennial and annual cropping systems due to plant-specific characteristics stimulating changes in microbial community structure. Understanding how these microbial communities change in response to varied management, and how these changes relate to in situ N2O fluxes may allow the creation of predictive models for use in the development of best management practices (BMPs) to decrease nitrogen (N) losses through choice of crop, plough, and LDM practices. Our objectives were to contrast changes in the population sizes and community structures of genes associated with nitrifier (amoA, crenamoA) and denitrifier (nirK, nirS, nosZ) communities in differently managed annual and perennial fields demonstrating variation in N2O flux, and to determine if differences in these microbial communities were linked to the observed variation in N2O fluxes. Soil was sampled in 2012 and in 2014 in a 4-ha spring-applied LDM grass-legume (perennial) plot and two 4-ha corn (annual) treatments under fall or spring LDM application. Soil DNA was extracted and used to target N-cycling genes via qPCR (n=6) and for next-generation sequencing (Illumina Miseq) (n=3). Significantly higher field-scale N2O fluxes were observed in the annual plots compared to the perennial system; however N2O fluxes increased after plough down of the perennial plot. Nonmetric multidimensional scaling (NMS) indicated differences in N-cycling communities between annual and perennial cropping systems, and some communities became similar between annual and perennial plots after ploughing. Shifts in these communities demonstrated relationships with agricultural management, which were associated with differences in N2O flux. Indicator species analysis was used to identify operational taxonomic units (OTUs) most responsible for community shifts related to management. Nitrifying and denitrifying soil bacterial communities are sensitive to agricultural management (annual or perennial crop type, LDM management, and ploughing) and communities will respond to variations in management, affecting field N2O fluxes.

Microbial contamination of dental unit waterlines and effect on quality of indoor air.

PubMed

Kadaifciler, Duygu Göksay; Cotuk, Aysin

2014-06-01

The microbiological quality in dental unit waterlines (DUWLs) is considered to be important because patients and dental staff with suppressed immune systems are regularly exposed to water and aerosols generated from dental units (DUs). Opportunistic pathogens like Pseudomonas, Legionella, Candida, and Aspergillus can be present in DUWLs, while during consultations, bioaerosols can be dispersed in the air, thus resulting in effects on microbiological quality of indoor air. This present study represents microbiological air and water quality in dental offices (DOs) and also concerns the relationship between the quality of DO air and dental unit water. This study aimed to assess both the microbial quality of dental unit water and the indoor air in 20 DOs and to survey the effect on the quality of the indoor air with the existing microorganisms in dental unit water. Fourteen out of 20 (70 %) DUWLs were found to be contaminated with a high number of aerobic mesophilic heterotrophic bacteria. In terms of bacterial air contamination levels, in 90 % of DOs, a medium level (<500 colony-forming units (CFU)/m(3)) of contamination was determined, while in terms of microfungal air contamination, in all DOs, a low level (<100 CFU/m(3)) of contamination was determined. Potential infection or allergen agents, such as Pseudomonas, Micrococcus, Staphylococcus, Alternaria, Cladosporium, Penicillium, Aspergillus, and Paecilomyces were isolated from water and air samples. This study's determination of contamination sources and evaluation of microbial load in DOs could contribute to the development of quality control methods in the future.

SigTree: A Microbial Community Analysis Tool to Identify and Visualize Significantly Responsive Branches in a Phylogenetic Tree.

PubMed

Stevens, John R; Jones, Todd R; Lefevre, Michael; Ganesan, Balasubramanian; Weimer, Bart C

2017-01-01

Microbial community analysis experiments to assess the effect of a treatment intervention (or environmental change) on the relative abundance levels of multiple related microbial species (or operational taxonomic units) simultaneously using high throughput genomics are becoming increasingly common. Within the framework of the evolutionary phylogeny of all species considered in the experiment, this translates to a statistical need to identify the phylogenetic branches that exhibit a significant consensus response (in terms of operational taxonomic unit abundance) to the intervention. We present the R software package SigTree , a collection of flexible tools that make use of meta-analysis methods and regular expressions to identify and visualize significantly responsive branches in a phylogenetic tree, while appropriately adjusting for multiple comparisons.

Back to the future of soil metagenomics

DOE PAGES

Nesme, Joseph; Achouak, Wafa; Agathos, Spiros N.; ...

2016-02-10

Here, direct extraction and characterization of microbial community DNA through PCR amplicon surveys and metagenomics has revolutionized the study of environmental microbiology and microbial ecology. In particular, metagenomic analysis of nucleic acids provides direct access to the genomes of the “uncultivated majority.” Accelerated by advances in sequencing technology, microbiologists have discovered more novel phyla, classes, genera, and genes from microorganisms in the first decade and a half of the twenty-first century than since these “many very little living animalcules” were first discovered by van Leeuwenhoek (Table 1). The unsurpassed diversity of soils promises continued exploration of a range of industrial,more » agricultural, and environmental functions. The ability to explore soil microbial communities with increasing capacity offers the highest promise for answering many outstanding who, what, where, when, why, and with whom questions such as: Which microorganisms are linked to which soil habitats? How do microbial abundances change with changing edaphic conditions? How do microbial assemblages interact and influence one another synergistically or antagonistically? What is the full extent of soil microbial diversity, both functionally and phylogenetically? What are the dynamics of microbial communities in space and time? How sensitive are microbial communities to a changing climate? What is the role of horizontal gene transfer in the stability of microbial communities? Do highly diverse microbial communities confer resistance and resilience in soils?« less

Back to the future of soil metagenomics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nesme, Joseph; Achouak, Wafa; Agathos, Spiros N.

Here, direct extraction and characterization of microbial community DNA through PCR amplicon surveys and metagenomics has revolutionized the study of environmental microbiology and microbial ecology. In particular, metagenomic analysis of nucleic acids provides direct access to the genomes of the “uncultivated majority.” Accelerated by advances in sequencing technology, microbiologists have discovered more novel phyla, classes, genera, and genes from microorganisms in the first decade and a half of the twenty-first century than since these “many very little living animalcules” were first discovered by van Leeuwenhoek (Table 1). The unsurpassed diversity of soils promises continued exploration of a range of industrial,more » agricultural, and environmental functions. The ability to explore soil microbial communities with increasing capacity offers the highest promise for answering many outstanding who, what, where, when, why, and with whom questions such as: Which microorganisms are linked to which soil habitats? How do microbial abundances change with changing edaphic conditions? How do microbial assemblages interact and influence one another synergistically or antagonistically? What is the full extent of soil microbial diversity, both functionally and phylogenetically? What are the dynamics of microbial communities in space and time? How sensitive are microbial communities to a changing climate? What is the role of horizontal gene transfer in the stability of microbial communities? Do highly diverse microbial communities confer resistance and resilience in soils?« less

Rapid System to Quantitatively Characterize the Airborne Microbial Community

NASA Technical Reports Server (NTRS)

Macnaughton, Sarah J.

1998-01-01

Bioaerosols have been linked to a wide range of different allergies and respiratory illnesses. Currently, microorganism culture is the most commonly used method for exposure assessment. Such culture techniques, however, generally fail to detect between 90-99% of the actual viable biomass. Consequently, an unbiased technique for detecting airborne microorganisms is essential. In this Phase II proposal, a portable air sampling device his been developed for the collection of airborne microbial biomass from indoor (and outdoor) environments. Methods were evaluated for extracting and identifying lipids that provide information on indoor air microbial biomass, and automation of these procedures was investigated. Also, techniques to automate the extraction of DNA were explored.

Termites and flooding affect microbial communities in decomposing wood

Treesearch

Michael D. Ulyshen; Susan V. Diehl; Dragica Jeremic

2016-01-01

Wood properties and microbial community characteristics were compared between loblolly pine (Pinus taeda L.) logs protected or unprotected from termites (Blattodea: Rhinotermitidae: Reticulitermes spp.) and other arthropods for two years in seasonally flooded and unflooded forests in the southeastern United States. Significant compositional differences were observed...

Microbial Survey of a Full-Scale, Biologically Active Filter for Treatment of Drinking Water

EPA Science Inventory

Biological nitrification has been used as a reliable technology in wastewater treatment for decades. Implementing biological approaches to drinking water treatment has faced resistance in the United States due in part to the lack of understanding of microbial processes and conce...

Use of Quantitative Microbial Risk Assessment to Improve Interpretation of a Recreational Water Epidemiological Study

EPA Science Inventory

We conducted a supplemental water quality monitoring study and quantitative microbial risk assessment (QMRA) to complement the United States Environmental Protection Agency’s (U.S. EPA) National Epidemiological and Environmental Assessment of Recreational Water study at Boquerón ...

A Customized DNA Microarray for Microbial Source Tracking in Environmental Systems

EPA Science Inventory

It is estimated that more than 160, 000 miles of rivers and streams in the United States are impaired due to the presence of waterborne pathogens. These pathogens typically originate from human and other animal fecal pollution sources; therefore, a rapid microbial source tracking...

WATERBORNE DISEASES AND MICROBIAL QUALITY MONITORING FOR RECREATIONAL WATER BODIES USING REGULATORY METHODS

EPA Science Inventory

This chapter will provide the reader with a historical perspective of microbial water quality and monitoring of recreational waters, with special attention to marine environments. It will review the regulations that are currently in effect in the United States and discuss critic...

Microbial enhanced oil recovery: Entering the log phase

DOE Office of Scientific and Technical Information (OSTI.GOV)

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 andmore » 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.« less

Portable Immune-Assessment System

NASA Technical Reports Server (NTRS)

Pierson, Duane L.; Stowe, Raymond P.; Mishra, Saroj K.

1995-01-01

Portable immune-assessment system developed for use in rapidly identifying infections or contaminated environment. System combines few specific fluorescent reagents for identifying immune-cell dysfunction, toxic substances, buildup of microbial antigens or microbial growth, and potential identification of pathogenic microorganisms using fluorescent microplate reader linked to laptop computer. By using few specific dyes for cell metabolism, DNA/RNA conjugation, specific enzyme activity, or cell constituents, one makes immediate, onsite determination of person's health or of contamination of environment.

Anoxia stimulates microbially catalyzed metal release from Animas River sediments

DOE PAGES

Saup, Casey M.; Williams, Kenneth H.; Rodríguez-Freire, Lucía; ...

2017-03-06

The Gold King Mine spill in August 2015 released 11 million liters of metal-rich mine waste to the Animas River watershed, an area that has been previously exposed to historical mining activity spanning more than a century. Although adsorption onto fluvial sediments was responsible for rapid immobilization of a significant fraction of the spill-associated metals, patterns of longer-term mobility are poorly constrained. Metals associated with river sediments collected downstream of the Gold King Mine in August 2015 exhibited distinct presence and abundance patterns linked to location and mineralogy. Simulating riverbed burial and development of anoxic conditions, sediment microcosm experiments amendedmore » with Animas River dissolved organic carbon revealed the release of specific metal pools coupled to microbial Fe- and SO 4 2-reduction. Results suggest that future sedimentation and burial of riverbed materials may drive longer-term changes in patterns of metal remobilization linked to anaerobic microbial metabolism, potentially driving decreases in downstream water quality. Such patterns emphasize the need for long-term water monitoring efforts in metal-impacted watersheds.« less

Anoxia stimulates microbially catalyzed metal release from Animas River sediments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saup, Casey M.; Williams, Kenneth H.; Rodríguez-Freire, Lucía

The Gold King Mine spill in August 2015 released 11 million liters of metal-rich mine waste to the Animas River watershed, an area that has been previously exposed to historical mining activity spanning more than a century. Although adsorption onto fluvial sediments was responsible for rapid immobilization of a significant fraction of the spill-associated metals, patterns of longer-term mobility are poorly constrained. Metals associated with river sediments collected downstream of the Gold King Mine in August 2015 exhibited distinct presence and abundance patterns linked to location and mineralogy. Simulating riverbed burial and development of anoxic conditions, sediment microcosm experiments amendedmore » with Animas River dissolved organic carbon revealed the release of specific metal pools coupled to microbial Fe- and SO 4 2-reduction. Results suggest that future sedimentation and burial of riverbed materials may drive longer-term changes in patterns of metal remobilization linked to anaerobic microbial metabolism, potentially driving decreases in downstream water quality. Such patterns emphasize the need for long-term water monitoring efforts in metal-impacted watersheds.« less

Lipids as paleomarkers to constrain the marine nitrogen cycle.

PubMed

Rush, Darci; Sinninghe Damsté, Jaap S

2017-06-01

Global climate is, in part, regulated by the effect of microbial processes on biogeochemical cycling. The nitrogen cycle, in particular, is driven by microorganisms responsible for the fixation and loss of nitrogen, and the reduction-oxidation transformations of bio-available nitrogen. Within marine systems, nitrogen availability is often the limiting factor in the growth of autotrophic organisms, intrinsically linking the nitrogen and carbon cycles. In order to elucidate the state of these cycles in the past, and help envisage present and future variability, it is essential to understand the specific microbial processes responsible for transforming bio-available nitrogen species. As most microorganisms are soft-bodied and seldom leave behind physical fossils in the sedimentary record, recalcitrant lipid biomarkers are used to unravel microbial processes in the geological past. This review emphasises the recent advances in marine nitrogen cycle lipid biomarkers, underlines the missing links still needed to fully elucidate past shifts in this biogeochemically-important cycle, and provides examples of biomarker applications in the geological past. © 2017 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Comparative study on protein cross-linking and gel enhancing effect of microbial transglutaminase on surimi from different fish.

PubMed

Chanarat, Sochaya; Benjakul, Soottawat; H-Kittikun, Aran

2012-03-15

Microbial transglutaminase (MTGase) has been used to increase the gel strength of surimi. Nevertheless, its effectiveness varies with fish species. The aim of this study was to elucidate the effect of MTGase at different levels on protein cross-linking and gel property of surimi from threadfin bream, Indian mackerel and sardine in the presence and absence of endogenous transglutaminase. Breaking force of all surimi gels increased as MTGase levels (0-0.6 U g⁻¹) increased except for threadfin bream surimi gel, where the breaking force decreased at 0.6 U g⁻¹ (P < 0.05). In the presence of EDTA, the gel strengthening effect was lower, suggesting the combined effect of endogenous transglutaminase with MTGase. With the addition of MTGase, the gel with the highest increase in breaking force showed highest decrease in myosin heavy chain. When cross-linking activity of MTGase on natural actomyosin (NAM) was determined, the highest decreasing rate in ε-amino group content with the concomitant increased formation of cross-linked proteins was found in NAM from threadfin bream. The reactivity of muscle proteins toward MTGase-induced cross-linking was in agreement with surimi gel strengthening. The composition and properties of muscle proteins of varying fish species more likely determined protein cross-linking induced by MTGase, thereby affecting their gel properties.

Simultaneous wastewater treatment and bioelectricity production in microbial fuel cells using cross-linked chitosan-graphene oxide mixed-matrix membranes.

PubMed

Holder, Shima L; Lee, Ching-Hwa; Popuri, Srinivasa R

2017-05-01

Microbial fuel cells (MFCs) are emerging technology for wastewater treatment by chemical oxygen demand (COD) reduction and simultaneous bioelectricity production. Fabrication of an effective proton exchange membrane (PEM) is a vital component for MFC performance. In this work, green chitosan-based (CS) PEMs were fabricated with graphene oxide (GO) as filler material (CS-GO) and cross-linked with phosphoric acid (CS-GO-P(24)) or sulfuric acid (CS-GO-S(24)) to determine their effect on PEM properties. Interrogation of the physicochemical, thermal, and mechanical properties of the cross-linked CS-GO PEMs demonstrated that ionic cross-linking based on the incorporation of PO 4 3- groups in the CS-GO mixed-matrix composites, when compared with sulfuric acid cross-linking commonly used in proton exchange membrane fuel cell (PEMFC) studies, generated additional density of ionic cluster domains, rendered enhanced sorption properties, and augmented the thermal and mechanical stability of the composite structure. Consequently, bioelectricity performance analysis in MFC application showed that CS-GO-P(24) membrane produced 135% higher power density than the CS-GO-S(24) MFC system. Simultaneously, 89.52% COD removal of primary clarifier municipal wastewater was achieved in the MFC operated with the CS-GO-P(24) membrane.

Effect of curcumin caged silver nanoparticle on collagen stabilization for biomedical applications.

PubMed

Srivatsan, Kunnavakkam Vinjimur; Duraipandy, N; Begum, Shajitha; Lakra, Rachita; Ramamurthy, Usha; Korrapati, Purna Sai; Kiran, Manikantan Syamala

2015-04-01

The current study aims at understanding the influence of curcumin caged silver nanoparticle (CCSNP) on stability of collagen. The results indicated that curcumin caged silver nanoparticles efficiently stabilize collagen, indicated by enhanced tensile strength, fibril formation and viscosity. The tensile strength of curcumin caged silver nanoparticle cross-linked collagen and elongation at break was also found to be higher than glutaraldehyde cross-linked collagen. The physicochemical characteristics of curcumin caged nanoparticle cross-linked collagen exhibited enhanced strength. The thermal properties were also good with both thermal degradation temperature and hydrothermal stability higher than native collagen. CD analysis showed no structural disparity in spite of superior physicochemical properties suggesting the significance of curcumin caged nanoparticle mediated cross-linking. The additional enhancement in the stabilization of collagen could be attributed to multiple sites for interaction with collagen molecule provided by curcumin caged silver nanoparticles. The results of cell proliferation and anti-microbial activity assays indicated that curcumin caged silver nanoparticles promoted cell proliferation and inhibited microbial growth making it an excellent biomaterial for wound dressing application. The study opens scope for nano-biotechnological strategies for the development of alternate non-toxic cross-linking agents facilitating multiple site interaction thereby improving therapeutic values to the collagen for biomedical application. Copyright © 2015 Elsevier B.V. All rights reserved.

Potential Mechanisms for Microbial Energy Acquisition in Oxic Deep-Sea Sediments

PubMed Central

Heidelberg, John F.

2016-01-01

ABSTRACT The South Pacific Gyre (SPG) possesses the lowest rates of sedimentation, surface chlorophyll concentration, and primary productivity in the global oceans. As a direct result, deep-sea sediments are thin and contain small amounts of labile organic carbon. It was recently shown that the entire SPG sediment column is oxygenated and may be representative of up to a third of the global marine environment. To understand the microbial processes that contribute to the removal of the labile organic matter at the water-sediment interface, a sediment sample was collected and subjected to metagenomic sequencing and analyses. Analysis of nine partially reconstructed environmental genomes, which represent approximately one-third of the microbial community, revealed that the members of the SPG surface sediment microbial community are phylogenetically distinct from surface/upper-ocean organisms. These genomes represent a wide distribution of novel organisms, including deep-branching Alphaproteobacteria, two novel organisms within the Proteobacteria, and new members of the Nitrospirae, Nitrospinae, and candidate phylum NC10. These genomes contain evidence for microbially mediated metal (iron/manganese) oxidation and carbon fixation linked to nitrification. Additionally, despite hypothesized energy limitation, members of the SPG microbial community had motility and chemotaxis genes and possessed mechanisms for the degradation of high-molecular-weight organic matter. This study contributes to our understanding of the metabolic potential of microorganisms in deep-sea oligotrophic sediments and their impact on local carbon geochemistry. IMPORTANCE This research provides insight into the microbial metabolic potential of organisms inhabiting oxygenated deep-sea marine sediments. Current estimates suggest that these environments account for up to a third of the global marine sediment habitat. Nine novel deep-sea microbial genomes were reconstructed from a metagenomic data set and expand the limited number of environmental genomes from deep-sea sediment environments. This research provides phylogeny-linked insight into critical metabolisms, including carbon fixation associated with nitrification, which is assignable to members of the marine group 1 Thaumarchaeota, Nitrospinae, and Nitrospirae and neutrophilic metal (iron/manganese) oxidation assignable to a novel proteobacterium. PMID:27208118

Potential Mechanisms for Microbial Energy Acquisition in Oxic Deep-Sea Sediments.

PubMed

Tully, Benjamin J; Heidelberg, John F

2016-07-15

The South Pacific Gyre (SPG) possesses the lowest rates of sedimentation, surface chlorophyll concentration, and primary productivity in the global oceans. As a direct result, deep-sea sediments are thin and contain small amounts of labile organic carbon. It was recently shown that the entire SPG sediment column is oxygenated and may be representative of up to a third of the global marine environment. To understand the microbial processes that contribute to the removal of the labile organic matter at the water-sediment interface, a sediment sample was collected and subjected to metagenomic sequencing and analyses. Analysis of nine partially reconstructed environmental genomes, which represent approximately one-third of the microbial community, revealed that the members of the SPG surface sediment microbial community are phylogenetically distinct from surface/upper-ocean organisms. These genomes represent a wide distribution of novel organisms, including deep-branching Alphaproteobacteria, two novel organisms within the Proteobacteria, and new members of the Nitrospirae, Nitrospinae, and candidate phylum NC10. These genomes contain evidence for microbially mediated metal (iron/manganese) oxidation and carbon fixation linked to nitrification. Additionally, despite hypothesized energy limitation, members of the SPG microbial community had motility and chemotaxis genes and possessed mechanisms for the degradation of high-molecular-weight organic matter. This study contributes to our understanding of the metabolic potential of microorganisms in deep-sea oligotrophic sediments and their impact on local carbon geochemistry. This research provides insight into the microbial metabolic potential of organisms inhabiting oxygenated deep-sea marine sediments. Current estimates suggest that these environments account for up to a third of the global marine sediment habitat. Nine novel deep-sea microbial genomes were reconstructed from a metagenomic data set and expand the limited number of environmental genomes from deep-sea sediment environments. This research provides phylogeny-linked insight into critical metabolisms, including carbon fixation associated with nitrification, which is assignable to members of the marine group 1 Thaumarchaeota, Nitrospinae, and Nitrospirae and neutrophilic metal (iron/manganese) oxidation assignable to a novel proteobacterium. Copyright © 2016 Tully and Heidelberg.

Seasonal induced changes in spinach rhizosphere microbial community structure with varying salinity and drought

USDA-ARS?s Scientific Manuscript database

Salinity is a common problem under irrigated agriculture, especially in low rainfall and high evaporative demand areas of southwestern United States and other semi-arid regions around the world. However, studies on salinity effects on soil microbial communities are relatively few while the effects o...

Soil and public health: invisible bridges

NASA Astrophysics Data System (ADS)

Pachepsky, Yakov

2017-04-01

Public health institutions, as ancient as civilizations itself, are intrinsically connected with soils. The massive body of the empirical knowledge about this connection has been accumulated. Recently unraveling the underlying mechanisms of this link has begun, and many of them appear to have the microbiological origin. The impressive progress in understanding the nexus between soil and health has been achieved by experimentation with preserved soil microbial systems functioning along with the metagenomic characterization. The objective of this work is to present an overview of some recent onsets. In the food safety arena, survival of human pathogens in soils has been related to the degree of soil eutrophication and/or related structure of soil microbial communities. Soil microbial systems affect the affinity of plants to internalizing pathogenic organisms. Pharmaceutical arsenals benefit from using field soil environment for developing antibiotics. Enzyme production by soil bacteria is used as the signal source for drug activation. Sanitary functions of sols are dependent on soil microbial system workings. The healthy living can be enhanced by the human immune system training received from direct contact with soils. The hygiene hypothesis considers the microbial input due to exposure to soil as the essential ecosystem service. The invisible links between soil and public health result in large-scale consequences. Examples of concurrent degradation of soil and public health are worth scrutinizing. Public health records can provide valuable sources of 'soil-public health' interactions. It may be worthwhile to examine current assessments of soil health from the public health standpoint. Soil management can be an efficient instrument of public health control.

When micro meets macro: microbial lipid analysis and ecosystem ecology

NASA Astrophysics Data System (ADS)

Balser, T.; Gutknecht, J.

2008-12-01

There is growing interest in linking soil microbial community composition and activity with large-scale field studies of nutrient cycling or plant community response to disturbances. And while analysis of microbial communities has moved rapidly in the past decade from culture-based to non-culture based techniques, still it must be asked what have we gained from the move? How well does the necessarily micro-scale of microbial analysis allow us to address questions of interest at the macro-scale? Several challenges exist in bridging the scales, and foremost is the question of methodological feasibility. Past microbiological methodologies have not been readily adaptable to the large sample sizes necessary for ecosystem-scale research. As a result, it has been difficult to generate compatible microbial and ecosystem data sets. We describe the use of a modified lipid extraction method to generate microbial community data sets that allow us to match landscape-scale or long-term ecological studies with microbial community data. We briefly discuss the challenges and advantages associated with lipid analysis as an approach to addressing ecosystem ecological studies, and provide examples from our research in ecosystem restoration and recovery following disturbance and climate change.

Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate

PubMed Central

Bokulich, Nicholas A.; Thorngate, John H.; Richardson, Paul M.; Mills, David A.

2014-01-01

Wine grapes present a unique biogeography model, wherein microbial biodiversity patterns across viticultural zones not only answer questions of dispersal and community maintenance, they are also an inherent component of the quality, consumer acceptance, and economic appreciation of a culturally important food product. On their journey from the vineyard to the wine bottle, grapes are transformed to wine through microbial activity, with indisputable consequences for wine quality parameters. Wine grapes harbor a wide range of microbes originating from the surrounding environment, many of which are recognized for their role in grapevine health and wine quality. However, determinants of regional wine characteristics have not been identified, but are frequently assumed to stem from viticultural or geological factors alone. This study used a high-throughput, short-amplicon sequencing approach to demonstrate that regional, site-specific, and grape-variety factors shape the fungal and bacterial consortia inhabiting wine-grape surfaces. Furthermore, these microbial assemblages are correlated to specific climatic features, suggesting a link between vineyard environmental conditions and microbial inhabitation patterns. Taken together, these factors shape the unique microbial inputs to regional wine fermentations, posing the existence of nonrandom “microbial terroir” as a determining factor in regional variation among wine grapes. PMID:24277822

Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate.

PubMed

Bokulich, Nicholas A; Thorngate, John H; Richardson, Paul M; Mills, David A

2014-01-07

Wine grapes present a unique biogeography model, wherein microbial biodiversity patterns across viticultural zones not only answer questions of dispersal and community maintenance, they are also an inherent component of the quality, consumer acceptance, and economic appreciation of a culturally important food product. On their journey from the vineyard to the wine bottle, grapes are transformed to wine through microbial activity, with indisputable consequences for wine quality parameters. Wine grapes harbor a wide range of microbes originating from the surrounding environment, many of which are recognized for their role in grapevine health and wine quality. However, determinants of regional wine characteristics have not been identified, but are frequently assumed to stem from viticultural or geological factors alone. This study used a high-throughput, short-amplicon sequencing approach to demonstrate that regional, site-specific, and grape-variety factors shape the fungal and bacterial consortia inhabiting wine-grape surfaces. Furthermore, these microbial assemblages are correlated to specific climatic features, suggesting a link between vineyard environmental conditions and microbial inhabitation patterns. Taken together, these factors shape the unique microbial inputs to regional wine fermentations, posing the existence of nonrandom "microbial terroir" as a determining factor in regional variation among wine grapes.

Direct and indirect influence of parental bedrock on streambed microbial community structure in forested streams.

PubMed

Mosher, Jennifer J; Findlay, Robert H

2011-11-01

A correlative study was performed to determine if variation in streambed microbial community structure in low-order forested streams can be directly or indirectly linked to the chemical nature of the parental bedrock of the environments through which the streams flow. Total microbial and photosynthetic biomass (phospholipid phosphate [PLP] and chlorophyll a), community structure (phospholipid fatty acid analysis), and physical and chemical parameters were measured in six streams, three located in sandstone and three in limestone regions of the Bankhead National Forest in northern Alabama. Although stream water flowing through the two different bedrock types differed significantly in chemical composition, there were no significant differences in total microbial and photosynthetic biomass in the sediments. In contrast, sedimentary microbial community structure differed between the bedrock types and was significantly correlated with stream water ion concentrations. A pattern of seasonal variation in microbial community structure was also observed. Further statistical analysis indicated dissolved organic matter (DOM) quality, which was previously shown to be influenced by geological variation, correlated with variation in bacterial community structure. These results indicate that the geology of underlying bedrock influences benthic microbial communities directly via changes in water chemistry and also indirectly via stream water DOM quality.

Microorganisms in Confined Habitats: Microbial Monitoring and Control of Intensive Care Units, Operating Rooms, Cleanrooms and the International Space Station

PubMed Central

Mora, Maximilian; Mahnert, Alexander; Koskinen, Kaisa; Pausan, Manuela R.; Oberauner-Wappis, Lisa; Krause, Robert; Perras, Alexandra K.; Gorkiewicz, Gregor; Berg, Gabriele; Moissl-Eichinger, Christine

2016-01-01

Indoor environments, where people spend most of their time, are characterized by a specific microbial community, the indoor microbiome. Most indoor environments are connected to the natural environment by high ventilation, but some habitats are more confined: intensive care units, operating rooms, cleanrooms and the international space station (ISS) are extraordinary living and working areas for humans, with a limited exchange with the environment. The purposes for confinement are different: a patient has to be protected from infections (intensive care unit, operating room), product quality has to be assured (cleanrooms), or confinement is necessary due to extreme, health-threatening outer conditions, as on the ISS. The ISS represents the most secluded man-made habitat, constantly inhabited by humans since November 2000 – and, inevitably, also by microorganisms. All of these man-made confined habitats need to be microbiologically monitored and controlled, by e.g., microbial cleaning and disinfection. However, these measures apply constant selective pressures, which support microbes with resistance capacities against antibiotics or chemical and physical stresses and thus facilitate the rise of survival specialists and multi-resistant strains. In this article, we summarize the available data on the microbiome of aforementioned confined habitats. By comparing the different operating, maintenance and monitoring procedures as well as microbial communities therein, we emphasize the importance to properly understand the effects of confinement on the microbial diversity, the possible risks represented by some of these microorganisms and by the evolution of (antibiotic) resistances in such environments – and the need to reassess the current hygiene standards. PMID:27790191

Microorganisms in Confined Habitats: Microbial Monitoring and Control of Intensive Care Units, Operating Rooms, Cleanrooms and the International Space Station.

PubMed

Mora, Maximilian; Mahnert, Alexander; Koskinen, Kaisa; Pausan, Manuela R; Oberauner-Wappis, Lisa; Krause, Robert; Perras, Alexandra K; Gorkiewicz, Gregor; Berg, Gabriele; Moissl-Eichinger, Christine

2016-01-01

Indoor environments, where people spend most of their time, are characterized by a specific microbial community, the indoor microbiome. Most indoor environments are connected to the natural environment by high ventilation, but some habitats are more confined: intensive care units, operating rooms, cleanrooms and the international space station (ISS) are extraordinary living and working areas for humans, with a limited exchange with the environment. The purposes for confinement are different: a patient has to be protected from infections (intensive care unit, operating room), product quality has to be assured (cleanrooms), or confinement is necessary due to extreme, health-threatening outer conditions, as on the ISS. The ISS represents the most secluded man-made habitat, constantly inhabited by humans since November 2000 - and, inevitably, also by microorganisms. All of these man-made confined habitats need to be microbiologically monitored and controlled, by e.g., microbial cleaning and disinfection. However, these measures apply constant selective pressures, which support microbes with resistance capacities against antibiotics or chemical and physical stresses and thus facilitate the rise of survival specialists and multi-resistant strains. In this article, we summarize the available data on the microbiome of aforementioned confined habitats. By comparing the different operating, maintenance and monitoring procedures as well as microbial communities therein, we emphasize the importance to properly understand the effects of confinement on the microbial diversity, the possible risks represented by some of these microorganisms and by the evolution of (antibiotic) resistances in such environments - and the need to reassess the current hygiene standards.

Desert Perennial Shrubs Shape the Microbial-Community Miscellany in Laimosphere and Phyllosphere Space.

PubMed

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

2016-10-01

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

Capturing the genetic makeup of the active microbiome in situ

DOE PAGES

Singer, Esther; Wagner, Michael; Woyke, Tanja

2017-06-02

More than any other technology, nucleic acid sequencing has enabled microbial ecology studies to be complemented with the data volumes necessary to capture the extent of microbial diversity and dynamics in a wide range of environments. In order to truly understand and predict environmental processes, however, the distinction between active, inactive and dead microbial cells is critical. Also, experimental designs need to be sensitive toward varying population complexity and activity, and temporal as well as spatial scales of process rates. There are a number of approaches, including single-cell techniques, which were designed to study in situ microbial activity and thatmore » have been successively coupled to nucleic acid sequencing. The exciting new discoveries regarding in situ microbial activity provide evidence that future microbial ecology studies will indispensably rely on techniques that specifically capture members of the microbiome active in the environment. Herein, we review those currently used activity-based approaches that can be directly linked to shotgun nucleic acid sequencing, evaluate their relevance to ecology studies, and discuss future directions.« less

Environmental Regulation of Microbial Community Structure

NASA Technical Reports Server (NTRS)

Bebout, Leslie; DesMarais, D.; Heyenga, G.; Nelson, F.; DeVincenzi, D. (Technical Monitor)

2002-01-01

Most naturally occurring microbes live in complex microbial communities consisting of thousands of phylotypes of microorganisms living in close proximity. Each of these draws nutrients from the environment and releases metabolic waste products, which may in turn serve as substrates for other microbial groups. Gross environmental changes, such as irradiance level, hydrodynamic flow regime, temperature or water chemistry can directly affect the productivity of some community members, which in turn will affect other dependent microbial populations and rate processes. As a first step towards the development of "standard" natural communities of microorganisms for a variety of potential NASA applications, we are measuring biogeochemical cycling in artificially structured communities of microorganisms, created using natural microbial mat communities as inoculum. The responses of these artificially assembled communities of microorganisms to controlled shifts in ecosystem incubation conditions is being determined. This research requires close linking of environmental monitoring, with community composition in a closed and controlled incubation setting. We are developing new incubation chamber designs to allow for this integrated approach to examine the interplay between environmental conditions, microbial community composition and biogeochemical processes.

A Workflow to Model Microbial Loadings in Watersheds ...

EPA Pesticide Factsheets

Many watershed models simulate overland and instream microbial fate and transport, but few actually provide loading rates on land surfaces and point sources to the water body network. This paper describes the underlying general equations for microbial loading rates associated with 1) land-applied manure on undeveloped areas from domestic animals; 2) direct shedding on undeveloped lands by domestic animals and wildlife; 3) urban or engineered areas; and 4) point sources that directly discharge to streams from septic systems and shedding by domestic animals. A microbial source module, which houses these formulations, is linked within a workflow containing eight models and a set of databases that form a loosely configured modeling infrastructure which supports watershed-scale microbial source-to-receptor modeling by focusing on animal-impacted catchments. A hypothetical example application – accessing, retrieving, and using real-world data – demonstrates the ability of the infrastructure to automate many of the manual steps associated with a standard watershed assessment, culminating with calibrated flow and microbial densities at the pour point of a watershed. Presented at 2016 Biennial Conference, International Environmental Modelling & Software Society.

Capturing the genetic makeup of the active microbiome in situ

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singer, Esther; Wagner, Michael; Woyke, Tanja

More than any other technology, nucleic acid sequencing has enabled microbial ecology studies to be complemented with the data volumes necessary to capture the extent of microbial diversity and dynamics in a wide range of environments. In order to truly understand and predict environmental processes, however, the distinction between active, inactive and dead microbial cells is critical. Also, experimental designs need to be sensitive toward varying population complexity and activity, and temporal as well as spatial scales of process rates. There are a number of approaches, including single-cell techniques, which were designed to study in situ microbial activity and thatmore » have been successively coupled to nucleic acid sequencing. The exciting new discoveries regarding in situ microbial activity provide evidence that future microbial ecology studies will indispensably rely on techniques that specifically capture members of the microbiome active in the environment. Herein, we review those currently used activity-based approaches that can be directly linked to shotgun nucleic acid sequencing, evaluate their relevance to ecology studies, and discuss future directions.« less

"FACILS 2014: Microbially-driven facilitation systems in environmental biotechnology" (hereafter "FACILS") presented here by the European Commission (EC)-United States (US) Task Force on Biotechnology Research

DOE Office of Scientific and Technical Information (OSTI.GOV)

Methe, Barbara

As we enter the 21st century, the sustainability of the biosphere is a global challenge that can best be met with a global response. This includes how we train and promote our next generation of research scientists in the emerging arenas of genome-enabled biology and a bio-based economy. It is this fundamental issue that formed the motivation for designing and conducting a shortcourse entitled “FACILIS 2014: Microbially-driven facilitation systems in environmental biotechnology” (hereafter “FACILIS”) presented here by the European Commission (EC)-United States (US) Task Force on Biotechnology Research. This WG was established in 1994 under the umbrella of the US-ECmore » Task Force on Biotechnology Research, a transatlantic collaborative group overseen by the US Office of Science and Technology Policy (OSTP) and the EC. The Environmental Biotechnology Working Group maintains several goals, including establishing research links between scientists in EU countries and the US and fostering the careers of junior scientists from both sides of the Atlantic to the global nature of scientific cooperation. To that end, a shortcourse was held at the University of Milan in Italy on July 12-25 2014 organized around cross-cutting themes of genomic science and designed to attract a stellar group of interdisciplinary early carrier researchers. A total of 22 students, 10 from the US and 12 from the EU participated. The course provided them with hands-on experience with the latest scientific methods in genomics and bioinformatics; using a format that combines lectures, laboratory research and field work with the final goal to enable researchers to finally turn data into knowledge.« less

Functional microbial community response to nutrient pulses by artificial groundwater recharge practice in surface soils and subsoils.

PubMed

Schütz, Kirsten; Kandeler, Ellen; Nagel, Peter; Scheu, Stefan; Ruess, Liliane

2010-06-01

Subsurface microorganisms are essential constituents of the soil purification processes associated with groundwater quality. In particular, soil enzyme activity determines the biodegradation of organic compounds passing through the soil profile. Transects from surface soil to a depth of 3.5 m were investigated for microbial and chemical soil characteristics at two groundwater recharge sites and one control site. The functional diversity of the microbial community was analyzed via the activity of eight enzymes. Acid phosphomonoesterase was dominant across sites and depths, followed by L-leucine aminopeptidase and beta-glucosidase. Structural [e.g. phospholipid fatty acid (PLFA) pattern] and functional microbial diversities were linked to each other at the nonwatered site, whereas amendment with nutrients (DOC, NO(3)(-)) by flooding uncoupled this relationship. Microbial biomass did not differ between sites, whereas microbial respiration was the highest at the watered sites. Hence, excess nutrients available due to artificial groundwater recharge could not compensate for the limitation by others (e.g. phosphorus as assigned by acid phosphomonoesterase activity). Instead, at a similar microbial biomass, waste respiration via overflow metabolism occurred. In summary, ample supply of carbon by flooding led to a separation of decomposition and microbial growth, which may play an important role in regulating purification processes during groundwater recharge.

Recent advances of microbial breeding via heavy-ion mutagenesis at IMP.

PubMed

Hu, W; Li, W; Chen, J

2017-10-01

Nowadays, the value of heavy-ion mutagenesis has been accepted as a novel powerful mutagen technique to generate new microbial mutants due to its high linear energy transfer and high relative biological effectiveness. This paper briefly reviews recent progress in developing a more efficient mutagenesis technique for microbial breeding using heavy-ion mutagenesis, and also presents the outline of the beam line for microbial breeding in Heavy Ion Research Facility of Lanzhou. Then, new insights into microbial biotechnology via heavy-ion mutagenesis are also further explored. We hope that our concerns will give deep insight into microbial breeding biotechnology via heavy-ion mutagenesis. We also believe that heavy-ion mutagenesis breeding will greatly contribute to the progress of a comprehensive study industrial strain engineering for bioindustry in the future. There is currently a great interest in developing rapid and diverse microbial mutation tool for strain modification. Heavy-ion mutagenesis has been proved as a powerful technology for microbial breeding due to its broad spectrum of mutation phenotypes with high efficiency. In order to deeply understand heavy-ion mutagenesis technology, this paper briefly reviews recent progress in microbial breeding using heavy-ion mutagenesis at IMP, and also presents the outline of the beam line for microbial breeding in Heavy Ion Research Facility of Lanzhou (HIRFL) as well as new insights into microbial biotechnology via heavy-ion mutagenesis. Thus, this work can provide the guidelines to promote the development of novel microbial biotechnology cross-linking heavy-ion mutagenesis breeding that could make breeding process more efficiently in the future. © 2017 The Society for Applied Microbiology.

How do microlocal environmental variations affect microbial activities of a Pinus halepensis litter in a Mediterranean coastal area?

PubMed

Qasemian, Leila; Guiral, Daniel; Farnet, Anne-Marie

2014-10-15

Mediterranean coastal ecosystems suffer many different types of natural and anthropogenic environmental pressure. Microbial communities, major conductors of organic matter decomposition are also subject to these environmental constraints. In this study, our aim was to understand how microbial activities vary at a small spatio-temporal scale in a Mediterranean coastal environment. Microbial activities were monitored in a Pinus halepensis litter collected from two areas, one close to (10 m) and one far from (300 m) the French Mediterranean coast. Litters were transferred from one area to the other using litterbags and studied via different microbial indicators after 2, 5 and 13 months. Microbial Basal Respiration, qCO₂, certain enzyme activities (laccase, cellulase, β-glucosidase and acid phosphatase) and functional diversity via Biolog microplates were assayed in litterbags left in the area of origin as well as in litterbags transferred from one area to the other. Results highlight that microbial activities differ significantly in this short spatial scale over time. The influence of microlocal conditions more intensified for litters situated close to the sea, especially during summer seems to have a stressful effect on microbial communities, leading to less efficient functional activities. However, microbial activities were more strongly influenced by temporal variations linked to seasonality than by location. Copyright © 2014 Elsevier B.V. All rights reserved.

Microbial Functional Gene Diversity with a Shift of Subsurface Redox Conditions during In Situ Uranium Reduction

PubMed Central

Liang, Yuting; Van Nostrand, Joy D.; N′Guessan, Lucie A.; Peacock, Aaron D.; Deng, Ye; Long, Philip E.; Resch, C. Tom; Wu, Liyou; He, Zhili; Li, Guanghe; Hazen, Terry C.; Lovley, Derek R.

2012-01-01

To better understand the microbial functional diversity changes with subsurface redox conditions during in situ uranium bioremediation, key functional genes were studied with GeoChip, a comprehensive functional gene microarray, in field experiments at a uranium mill tailings remedial action (UMTRA) site (Rifle, CO). The results indicated that functional microbial communities altered with a shift in the dominant metabolic process, as documented by hierarchical cluster and ordination analyses of all detected functional genes. The abundance of dsrAB genes (dissimilatory sulfite reductase genes) and methane generation-related mcr genes (methyl coenzyme M reductase coding genes) increased when redox conditions shifted from Fe-reducing to sulfate-reducing conditions. The cytochrome genes detected were primarily from Geobacter sp. and decreased with lower subsurface redox conditions. Statistical analysis of environmental parameters and functional genes indicated that acetate, U(VI), and redox potential (Eh) were the most significant geochemical variables linked to microbial functional gene structures, and changes in microbial functional diversity were strongly related to the dominant terminal electron-accepting process following acetate addition. The study indicates that the microbial functional genes clearly reflect the in situ redox conditions and the dominant microbial processes, which in turn influence uranium bioreduction. Microbial functional genes thus could be very useful for tracking microbial community structure and dynamics during bioremediation. PMID:22327592

Cultivation-dependent analysis of the microbial diversity associated with the seagrass meadows in Xincun Bay, South China Sea.

PubMed

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

2015-10-01

Microbial communities have largely existed in the seagrass meadows. A total of 496 strains of the bacteria in the seagrass meadows, which belonged to 50 genera, were obtained by the plate cultivation method from three sites of Xincun Bay, South China Sea. The results showed that Bacillales and Vibrionales accounted for the highest proportions of organisms in all communities. The diversity of the bacteria in the sediment was higher than that associated with seagrass. Thalassia hemperichii possessed the highest abundance of bacteria, followed by Enhalus acoroides and Cymodocea rotundata. Robust seasonal dynamics in microbial community composition were also observed. It was found that microbial activities were closely tied to the growth stage of the seagrass. The microbial distribution was the lowest in site 3. The abundance of the bacteria was linked to the interactions between bacteria and plants, the condition of plant and even the coastal water quality and the nutrition level in the sediment.

[Bacterial contamination of the indoor air in a transplant unit].

PubMed

Matoušková, Ivanka; Holý, Ondřej

2013-12-01

For one year (August 2010 to July 2011), microbial contamination of the indoor air in the Transplant Unit of the Haemato-Oncology Clinic, Olomouc University Hospital was monitored monthly. Twenty sampling sites were singled out and a total of 240 indoor air samples were collected. An MAS-100 air sampler (Merck, GER) was used, air flow rate of 100 liters per minute, 1 minute. The measured values of indoor air temperature were stable. The relative air humidity ranged from 17% to 68%. The highest average value of microbial air contamination was found in the "staff entry room" (1170 CFU/m3). The lowest microbial air contamination (150-250 CFU/m3) was measured in the patient isolation units. The most frequently isolated bacterial strains were coagulase-negative staphylococci (94.3%), followed by Micrococcus spp. (67%) and Bacillus subtilis (11%). It can be assumed that the -source of these airborne bacterial strains are both patients and medical staff. They are classified as -opportunistic pathogens and as such can cause hospital infections among haemato-oncology patients.

SEDIMENT MICROBIAL RESPIRATION IN A SYNOPTIC SURVEY OF MID-ATLANTIC REGION STREAMS

EPA Science Inventory

l. The rate of microbial respiration on fine-grained stream sediments was measured at 196 first-to third-order sites in the mid-Atlantic region of the United States.2. Sample collection took place between April and July in 1993, 1994 and 1995.3. Study streams were randomly sele...

TURKEY FECAL MICROBIAL COMMUNITY STRUCTURE AND ECOLOGICAL FUNCTIONS REVEALED BY 16S RDNA AND METAGENOME SEQUENCES

EPA Science Inventory

Turkey feces are an important source of fecal waste in the United States. With the exception of isolated studies on bacterial pathogens, little is known about the type of bacteria inhabiting the turkey gut. In order to understand the microbial diversity and functional genes assoc...

Reduction of nutrients, microbes, and personal care products in domestic wastewater by a benchtop electrocoagulation unit

PubMed Central

Symonds, E. M.; Cook, M. M.; McQuaig, S. M.; Ulrich, R. M.; Schenck, R. O.; Lukasik, J. O.; Van Vleet, E. S.; Breitbart, M.

2015-01-01

To preserve environmental and human health, improved treatment processes are needed to reduce nutrients, microbes, and emerging chemical contaminants from domestic wastewater prior to discharge into the environment. Electrocoagulation (EC) treatment is increasingly used to treat industrial wastewater; however, this technology has not yet been thoroughly assessed for its potential to reduce concentrations of nutrients, a variety of microbial surrogates, and personal care products found in domestic wastewater. This investigation's objective was to determine the efficiency of a benchtop EC unit with aluminum sacrificial electrodes to reduce concentrations of the aforementioned biological and chemical pollutants from raw and tertiary-treated domestic wastewater. EC treatment resulted in significant reductions (p < 0.05, α = 0.05) in phosphate, all microbial surrogates, and several personal care products from raw and tertiary-treated domestic wastewater. When wastewater was augmented with microbial surrogates representing bacterial, viral, and protozoan pathogens to measure the extent of reduction, EC treatment resulted in up to 7-log10 reduction of microbial surrogates. Future pilot and full-scale investigations are needed to optimize EC treatment for the following: reducing nitrogen species, personal care products, and energy consumption; elucidating the mechanisms behind microbial reductions; and performing life cycle analyses to determine the appropriateness of implementation. PMID:25797885

Reduction of nutrients, microbes, and personal care products in domestic wastewater by a benchtop electrocoagulation unit.

PubMed

Symonds, E M; Cook, M M; McQuaig, S M; Ulrich, R M; Schenck, R O; Lukasik, J O; Van Vleet, E S; Breitbart, M

2015-03-23

To preserve environmental and human health, improved treatment processes are needed to reduce nutrients, microbes, and emerging chemical contaminants from domestic wastewater prior to discharge into the environment. Electrocoagulation (EC) treatment is increasingly used to treat industrial wastewater; however, this technology has not yet been thoroughly assessed for its potential to reduce concentrations of nutrients, a variety of microbial surrogates, and personal care products found in domestic wastewater. This investigation's objective was to determine the efficiency of a benchtop EC unit with aluminum sacrificial electrodes to reduce concentrations of the aforementioned biological and chemical pollutants from raw and tertiary-treated domestic wastewater. EC treatment resulted in significant reductions (p < 0.05, α = 0.05) in phosphate, all microbial surrogates, and several personal care products from raw and tertiary-treated domestic wastewater. When wastewater was augmented with microbial surrogates representing bacterial, viral, and protozoan pathogens to measure the extent of reduction, EC treatment resulted in up to 7-log10 reduction of microbial surrogates. Future pilot and full-scale investigations are needed to optimize EC treatment for the following: reducing nitrogen species, personal care products, and energy consumption; elucidating the mechanisms behind microbial reductions; and performing life cycle analyses to determine the appropriateness of implementation.

Reduction of nutrients, microbes, and personal care products in domestic wastewater by a benchtop electrocoagulation unit

NASA Astrophysics Data System (ADS)

Symonds, E. M.; Cook, M. M.; McQuaig, S. M.; Ulrich, R. M.; Schenck, R. O.; Lukasik, J. O.; van Vleet, E. S.; Breitbart, M.

2015-03-01

To preserve environmental and human health, improved treatment processes are needed to reduce nutrients, microbes, and emerging chemical contaminants from domestic wastewater prior to discharge into the environment. Electrocoagulation (EC) treatment is increasingly used to treat industrial wastewater; however, this technology has not yet been thoroughly assessed for its potential to reduce concentrations of nutrients, a variety of microbial surrogates, and personal care products found in domestic wastewater. This investigation's objective was to determine the efficiency of a benchtop EC unit with aluminum sacrificial electrodes to reduce concentrations of the aforementioned biological and chemical pollutants from raw and tertiary-treated domestic wastewater. EC treatment resulted in significant reductions (p < 0.05, α = 0.05) in phosphate, all microbial surrogates, and several personal care products from raw and tertiary-treated domestic wastewater. When wastewater was augmented with microbial surrogates representing bacterial, viral, and protozoan pathogens to measure the extent of reduction, EC treatment resulted in up to 7-log10 reduction of microbial surrogates. Future pilot and full-scale investigations are needed to optimize EC treatment for the following: reducing nitrogen species, personal care products, and energy consumption; elucidating the mechanisms behind microbial reductions; and performing life cycle analyses to determine the appropriateness of implementation.

Using NEON Data to Test and Refine Conceptual and Numerical Models of Soil Biogeochemical and Microbial Dynamics

NASA Astrophysics Data System (ADS)

Weintraub, S. R.; Stanish, L.; Ayers, E.

2017-12-01

Recent conceptual and numerical models have proposed new mechanisms that underpin key biogeochemical phenomena, including soil organic matter storage and ecosystem response to nitrogen deposition. These models seek to explicitly capture the ecological links among biota, especially microbes, and their physical and chemical environment to represent belowground pools and fluxes and how they respond to perturbation. While these models put forth exciting new concepts, their broad predictive abilities are unclear as some have been developed and tested against only small or regional datasets. The National Ecological Observatory Network (NEON) presents new opportunities to test and validate these models with multi-site data that span wide climatic, edaphic, and ecological gradients. NEON is measuring surface soil biogeochemical pools and fluxes along with diversity, abundance, and functional potential of soil microbiota at 47 sites distributed across the United States. This includes co-located measurements of soil carbon and nitrogen concentrations and stable isotopes, net nitrogen mineralization and nitrification rates, soil moisture, pH, microbial biomass, and community composition via 16S and ITS rRNA sequencing and shotgun metagenomic analyses. Early NEON data demonstrates that these wide edaphic and climatic gradients are related to changes in microbial community structure and functional potential, as well as element pools and process rates. Going forward, NEON's suite of standardized soil data has the potential to advance our understanding of soil communities and processes by allowing us to test the predictions of new soil biogeochemical frameworks and models. Here, we highlight several recently developed models that are ripe for this kind of data validation, and discuss key insights that may result. Further, we explore synergies with other networks, such as (i)LTER and (i)CZO, which may increase our ability to advance the frontiers of soil biogeochemical modeling.

Protein Stable Isotope Fingerprinting (P-SIF): A New Tool to Understand Natural Isotopic Heterogeneity of Mixed Microbial Ecosystems

NASA Astrophysics Data System (ADS)

Pearson, A.; Mohr, W.; Tang, T.; Sattin, S.; Bovee, R.

2014-12-01

Protein stable isotope fingerprinting (P-SIF) is a method to measure the carbon isotope ratios of whole proteins separated from complex mixtures, including cultures and environmental samples. The goal of P-SIF is to expose the links between identity and function in microbial ecosystems by (i) determining the ratios of 13C/12C (values of δ13C) for different taxonomic divisions, and (ii) using those values as clues to the metabolic pathways employed by the respective organisms, while (iii) not perturbing the system, i.e., not adding exogenous substrates or isotope labels. To accomplish this, we employ two-dimensional HPLC to resolve a sample containing ca. 5-10 mg of mixed proteins into 960-1440 fractions. Each fraction then is split in two aliquots: The first is digested with trypsin for peptide sequencing, while the second is measured in triplicate using an isotope-ratio mass spectrometer interfaced with a spooling wire microcombustion device. Data from pure cultures show that bacteria have a narrow distribution of protein δ13C values within individual taxa (±0.7-1.2‰, 1σ). This is moderately larger than the mean precision of the triplicate isotope measurements (±0.5‰, 1σ) and may reflect heterogeneous distribution of 13C among the amino acids. When cells from different species are mixed together prior to protein extraction and separation, the results can predict accurately (to within ±1σ) the δ13C values of the original taxa. The number of data points required for this endmember prediction is ≥20/taxon, yielding a theoretical resolution of ca. 10 taxonomic units/sample. Initial tests on environmental samples suggest the approach will be useful to determine the overall trophic breadth of mixed microbial ecosystems.

A 100-Year Review: Microbiology and safety of milk handling.

PubMed

Boor, Kathryn J; Wiedmann, Martin; Murphy, Sarah; Alcaine, Sam

2017-12-01

Microbes that may be present in milk can include pathogens, spoilage organisms, organisms that may be conditionally beneficial (e.g., lactic acid bacteria), and those that have not been linked to either beneficial or detrimental effects on product quality or human health. Although milk can contain a full range of organisms classified as microbes (i.e., bacteria, viruses, fungi, and protozoans), with few exceptions (e.g., phages that affect fermentations, fungal spoilage organisms, and, to a lesser extent, the protozoan pathogens Cryptosporidium and Giardia) dairy microbiology to date has focused predominantly on bacteria. Between 1917 and 2017, our understanding of the microbes present in milk and the tools available for studying those microbes have changed dramatically. Improved microbiological tools have enabled enhanced detection of known microbes in milk and dairy products and have facilitated better identification of pathogens and spoilage organisms that were not known or well recognized in the early 20th century. Starting before 1917, gradual introduction and refinement of pasteurization methods throughout the United States and many other parts of the world have improved the safety and quality of milk and dairy products. In parallel to pasteurization, others strategies for reducing microbial contamination throughout the dairy chain (e.g., improved dairy herd health, raw milk tests, clean-in-place technologies) also played an important role in improving microbial milk quality and safety. Despite tremendous advances in reducing microbial food safety hazards and spoilage issues, the dairy industry still faces important challenges, including but not limited to the need for improved science-based strategies for safety of raw milk cheeses, control of postprocessing contamination, and control of sporeforming pathogens and spoilage organisms. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Listeria monocytogenes cross-contamination of cheese: risk throughout the food supply chain.

PubMed

Sauders, B D; D'Amico, D J

2016-10-01

Listeria monocytogenes has been the most common microbial cause of cheese-related recalls in both the United States and Canada in recent years. Since L. monocytogenes is inactivated by pasteurization, the majority of these cases have been linked to environmental and cross-contamination of fresh-soft, soft-ripened, and semi-soft cheeses. Cross-contamination of foods with L. monocytogenes is a continuous risk throughout the food supply chain and presents unique challenges for subsequent illness and outbreak investigations. Reports on outbreaks of listeriosis attributed to cross-contamination downstream from primary processing help highlight the critical role of epidemiological investigation coupled with coordinated molecular subtyping and surveillance in the recognition and investigation of complex foodborne outbreaks. Despite their complexity, environmental sampling throughout the supply chain coupled with improved genotyping approaches and concomitant analysis of foodborne illness epidemiological exposure data are needed to help resolve these and similar cases more rapidly and with greater confidence.

The Effect of a Reduction in Microbial Diversity on Greenhouse Gas Production in Alaskan Tundra Soils.

NASA Astrophysics Data System (ADS)

Wagner, R.; Oechel, W. C.; Lipson, D.

2017-12-01

Atmospheric methane accounts for 20% of the warming potential of all greenhouse gases, has increased by 150% since pre-industrial times, and has the potential to double again over the next century. Microbially mediated CH4 emissions from natural wetlands represent the highest uncertainty in relative contributions to atmospheric CH4 levels of all CH4 sources, with Arctic wetlands currently experiencing twice the rate of warming as the rest of the planet. Notwithstanding the central role that the soil microbial community plays, and the high uncertainty in CH4 emissions from this ecosystem, surprisingly little research has been done to directly connect the microbial community structure to methane production rates. This is especially disconcerting given that most current CH4 emission models completely neglect microbial characteristics, despite the fact that the soil microbial community is predicted to be heavily impacted by a changing climate. Here, the effect of an artificial reduction in soil microbial α-diversity was investigated with regard to methane production and respiration rates. The microbial community was serially diluted followed by re-inoculation of sterilized Arctic soils in a mesocosm experiment. Methane production and respiration rates were measured, metagenomic sequencing was performed to determine microbial community diversity measures, and the effect of the oxidation state of iron was investigated. Preliminary results indicate that microbial communities with reduced α-diversity have lowered respiration rates in these soils. Analyses are ongoing and are expected to provide critical observations linking the role of soil microbial community diversity and greenhouse gas production in Arctic tundra ecosystems.

Effect of mobile unidirectional air flow unit on microbial contamination of air in standard urologic procedures.

PubMed

Ferretti, Stefania; Pasquarella, Cesira; Fornia, Samanta; Saccani, Elisa; Signorelli, Carlo; Vitali, Pietro; Sansebastiano, Giuliano Ezio

2009-12-01

Infection is one of the most feared complications of surgery. New instrumentation is being developed to reduce deposition of bacteria. We investigated 45 major surgical procedures (21 radical nephrectomies [RN] and 24 radical retropubic prostatectomies [RRP]) in our urology department during 2007. In about one-half of the interventions, an ultraclean air flow mobile (UAF) unit was used. Bacterial sedimentation was evaluated by nitrocellulose membranes placed on the instrument tray and by settle plates positioned at four points in the operating room. In 27 operations, an additional membrane was located near the incision. Bacterial counts on the nitrocellulose membranes during RN were 230 colony-forming units (cfu)/m(2)/h with the UAF unit and 2,254 cfu/m(2)/h without the unit (p = 0.001). During RRP, the values were 288 cfu/m(2)/h and 3,126 cfu/m(2)/h respectively (p = 0.001). The membrane placed near the incision during RN showed a microbial count of 1,235 cfu/m(2)/h with the UAF unit and 5,093 cfu/m(2)/h without the unit (p = 0.002); during RRP, the values were 1,845 cfu/m(2)/h and 3,790 cfu/m(2)/h, respectively (difference not significant). Bacterial contamination detected by settle plates during RN showed a mean value of 2,273 cfu/m(2)/h when the UAF unit was used and 2,054 cfu/m(2)/h without the unit; during RRP, the values were 2,332 cfu/m(2)/h and 2,629 cfu/m(2)/h with and without the UAF unit, respectively (NS). No statistically significant differences were detected in the clinical data registered in patients operated on under standard conditions and while the UAF unit was functioning. The UAF appears able to reduce microbial contamination at the operating table, reaching a bacterial number obtained in ultraclean operating theatres.

Integrating ecological and engineering concepts of resilience in microbial communities

DOE PAGES

Song, Hyun -Seob; Renslow, Ryan S.; Fredrickson, Jim K.; ...

2015-12-01

We note that many definitions of resilience have been proffered for natural and engineered ecosystems, but a conceptual consensus on resilience in microbial communities is still lacking. Here, we argue that the disconnect largely results from the wide variance in microbial community complexity, which range from simple synthetic consortia to complex natural communities, and divergence between the typical practical outcomes emphasized by ecologists and engineers. Viewing microbial communities as elasto-plastic systems, we argue that this gap between the engineering and ecological definitions of resilience stems from their respective emphases on elastic and plastic deformation, respectively. We propose that the twomore » concepts may be fundamentally united around the resilience of function rather than state in microbial communities and the regularity in the relationship between environmental variation and a community’s functional response. Furthermore, we posit that functional resilience is an intrinsic property of microbial communities, suggesting that state changes in response to environmental variation may be a key mechanism driving resilience in microbial communities.« less

Changes in coral microbial communities in response to a natural pH gradient.

PubMed

Meron, Dalit; Rodolfo-Metalpa, Riccardo; Cunning, Ross; Baker, Andrew C; Fine, Maoz; Banin, Ehud

2012-09-01

Surface seawater pH is currently 0.1 units lower than pre-industrial values and is projected to decrease by up to 0.4 units by the end of the century. This acidification has the potential to cause significant perturbations to the physiology of ocean organisms, particularly those such as corals that build their skeletons/shells from calcium carbonate. Reduced ocean pH could also have an impact on the coral microbial community, and thus may affect coral physiology and health. Most of the studies to date have examined the impact of ocean acidification on corals and/or associated microbiota under controlled laboratory conditions. Here we report the first study that examines the changes in coral microbial communities in response to a natural pH gradient (mean pH(T) 7.3-8.1) caused by volcanic CO(2) vents off Ischia, Gulf of Naples, Italy. Two Mediterranean coral species, Balanophyllia europaea and Cladocora caespitosa, were examined. The microbial community diversity and the physiological parameters of the endosymbiotic dinoflagellates (Symbiodinium spp.) were monitored. We found that pH did not have a significant impact on the composition of associated microbial communities in both coral species. In contrast to some earlier studies, we found that corals present at the lower pH sites exhibited only minor physiological changes and no microbial pathogens were detected. Together, these results provide new insights into the impact of ocean acidification on the coral holobiont.

Complex Host Genetics Influence the Microbiome in Inflammatory Bowel Disease

DTIC Science & Technology

2016-09-09

specific bacterial taxa. Methods Ethics and consent This study was approved by the Partners Human Re- search Committee, 116 Huntington Avenue, Boston, MA...microbial ecology . Proc Natl Acad Sci U S A 2005, 102:11070–11075. 17. Hashimoto T, Perlot T, Rehman A, Trichereau J, Ishiguro H, Paolino M, Sigl V...JM: ACE2 links amino acid malnutrition to microbial ecology and intestinal inflammation. Nature 2012, 487:477–481. 18. Cortes A, Brown MA: Promise and

Genetics Home Reference: familial Mediterranean fever

MedlinePlus

... a site of injury or disease to fight microbial invaders and facilitate tissue repair. When this process ... fever Additional NIH Resources (2 links) National Human Genome Research Institute National Institute of Diabetes and Digestive ...

The microbial community in decaying fallen logs varies with critical period in an alpine forest.

PubMed

Chang, Chenhui; Wu, Fuzhong; Yang, Wanqin; Xu, Zhenfeng; Cao, Rui; He, Wei; Tan, Bo; Justine, Meta Francis

2017-01-01

Little information has been available on the shifts in the microbial community in decaying fallen logs during critical periods in cold forests. Minjiang fir (Abies faxoniana) fallen logs in decay classes I-V were in situ incubated on the forest floor of an alpine forest in the eastern Tibet Plateau. The microbial community was investigated during the seasonal snow cover period (SP), snow thawing period (TP), early growing season (EG) and late growing season (LG) using Phosphorous Lipid Fatty Acid (PLFA) analysis. Total microbial biomass and microbial diversity in fallen logs were much more affected by critical period than decay class, whereas decay class had a stronger effect on microbial diversity than on microbial biomass. Abundant microbial biomass and microbial diversity in logs even without the cover of snow were observed in winter, which could not be linked to thermal insulation by snow cover. The freshly decayed logs functioned as an excellent buffer of environmental variation for microbial organisms during the sharp fluctuations in temperature in winter. We also found distinct decay patterns along with seasonality for heartwood, sapwood and bark, which requires further detailed research. Gram- bacteria mainly dominated the shifts in microbial community composition from SP to EG, while fungi and Gram+ bacteria mainly dominated it from SP to TP. Based on previous work and the present study, we conclude that fallen logs on the forest floor alter ecological processes by influencing microbial communities on woody debris and beneath the soil and litter. Our study also emphasizes the need to maintain a number of fallen logs, especially fresh ones, on the forest floor.

The microbial community in decaying fallen logs varies with critical period in an alpine forest

PubMed Central

Chang, Chenhui; Wu, Fuzhong; Xu, Zhenfeng; Cao, Rui; He, Wei; Tan, Bo; Justine, Meta Francis

2017-01-01

Little information has been available on the shifts in the microbial community in decaying fallen logs during critical periods in cold forests. Minjiang fir (Abies faxoniana) fallen logs in decay classes I-V were in situ incubated on the forest floor of an alpine forest in the eastern Tibet Plateau. The microbial community was investigated during the seasonal snow cover period (SP), snow thawing period (TP), early growing season (EG) and late growing season (LG) using Phosphorous Lipid Fatty Acid (PLFA) analysis. Total microbial biomass and microbial diversity in fallen logs were much more affected by critical period than decay class, whereas decay class had a stronger effect on microbial diversity than on microbial biomass. Abundant microbial biomass and microbial diversity in logs even without the cover of snow were observed in winter, which could not be linked to thermal insulation by snow cover. The freshly decayed logs functioned as an excellent buffer of environmental variation for microbial organisms during the sharp fluctuations in temperature in winter. We also found distinct decay patterns along with seasonality for heartwood, sapwood and bark, which requires further detailed research. Gram- bacteria mainly dominated the shifts in microbial community composition from SP to EG, while fungi and Gram+ bacteria mainly dominated it from SP to TP. Based on previous work and the present study, we conclude that fallen logs on the forest floor alter ecological processes by influencing microbial communities on woody debris and beneath the soil and litter. Our study also emphasizes the need to maintain a number of fallen logs, especially fresh ones, on the forest floor. PMID:28787465

Distinct microbiological signatures associated with triple negative breast cancer.

PubMed

Banerjee, Sagarika; Wei, Zhi; Tan, Fei; Peck, Kristen N; Shih, Natalie; Feldman, Michael; Rebbeck, Timothy R; Alwine, James C; Robertson, Erle S

2015-10-15

Infectious agents are the third highest human cancer risk factor and may have a greater role in the origin and/or progression of cancers, and related pathogenesis. Thus, knowing the specific viruses and microbial agents associated with a cancer type may provide insights into cause, diagnosis and treatment. We utilized a pan-pathogen array technology to identify the microbial signatures associated with triple negative breast cancer (TNBC). This technology detects low copy number and fragmented genomes extracted from formalin-fixed paraffin embedded archival tissues. The results, validated by PCR and sequencing, define a microbial signature present in TNBC tissue which was underrepresented in normal tissue. Hierarchical clustering analysis displayed two broad microbial signatures, one prevalent in bacteria and parasites and one prevalent in viruses. These signatures demonstrate a new paradigm in our understanding of the link between microorganisms and cancer, as causative or commensal in the tumor microenvironment and provide new diagnostic potential.

Landscape topography structures the soil microbiome in arctic polygonal tundra.

PubMed

Taş, Neslihan; Prestat, Emmanuel; Wang, Shi; Wu, Yuxin; Ulrich, Craig; Kneafsey, Timothy; Tringe, Susannah G; Torn, Margaret S; Hubbard, Susan S; Jansson, Janet K

2018-02-22

In the Arctic, environmental factors governing microbial degradation of soil carbon (C) in active layer and permafrost are poorly understood. Here we determined the functional potential of soil microbiomes horizontally and vertically across a cryoperturbed polygonal landscape in Alaska. With comparative metagenomics, genome binning of novel microbes, and gas flux measurements we show that microbial greenhouse gas (GHG) production is strongly correlated to landscape topography. Active layer and permafrost harbor contrasting microbiomes, with increasing amounts of Actinobacteria correlating with decreasing soil C in permafrost. While microbial functions such as fermentation and methanogenesis were dominant in wetter polygons, in drier polygons genes for C mineralization and CH 4 oxidation were abundant. The active layer microbiome was poised to assimilate N and not to release N 2 O, reflecting low N 2 O flux measurements. These results provide mechanistic links of microbial metabolism to GHG fluxes that are needed for the refinement of model predictions.

Metagenomic analyses of drinking water receiving different disinfection treatments.

PubMed

Gomez-Alvarez, Vicente; Revetta, Randy P; Santo Domingo, Jorge W

2012-09-01

A metagenome-based approach was used to assess the taxonomic affiliation and function potential of microbial populations in free-chlorine-treated (CHL) and monochloramine-treated (CHM) drinking water (DW). In all, 362,640 (averaging 544 bp) and 155,593 (averaging 554 bp) pyrosequencing reads were analyzed for the CHL and CHM samples, respectively. Most annotated proteins were found to be of bacterial origin, although eukaryotic, archaeal, and viral proteins were also identified. Differences in community structure and function were noted. Most notably, Legionella-like genes were more abundant in the CHL samples while mycobacterial genes were more abundant in CHM samples. Genes associated with multiple disinfectant mechanisms were identified in both communities. Moreover, sequences linked to virulence factors, such as antibiotic resistance mechanisms, were observed in both microbial communities. This study provides new insights into the genetic network and potential biological processes associated with the molecular microbial ecology of DW microbial communities.

Variable-Internal-Stores models of microbial growth and metabolism with dynamic allocation of cellular resources.

PubMed

Nev, Olga A; van den Berg, Hugo A

2017-01-01

Variable-Internal-Stores models of microbial metabolism and growth have proven to be invaluable in accounting for changes in cellular composition as microbial cells adapt to varying conditions of nutrient availability. Here, such a model is extended with explicit allocation of molecular building blocks among various types of catalytic machinery. Such an extension allows a reconstruction of the regulatory rules employed by the cell as it adapts its physiology to changing environmental conditions. Moreover, the extension proposed here creates a link between classic models of microbial growth and analyses based on detailed transcriptomics and proteomics data sets. We ascertain the compatibility between the extended Variable-Internal-Stores model and the classic models, demonstrate its behaviour by means of simulations, and provide a detailed treatment of the uniqueness and the stability of its equilibrium point as a function of the availabilities of the various nutrients.

Metagenomic Analyses of Drinking Water Receiving Different Disinfection Treatments

PubMed Central

Gomez-Alvarez, Vicente; Revetta, Randy P.

2012-01-01

A metagenome-based approach was used to assess the taxonomic affiliation and function potential of microbial populations in free-chlorine-treated (CHL) and monochloramine-treated (CHM) drinking water (DW). In all, 362,640 (averaging 544 bp) and 155,593 (averaging 554 bp) pyrosequencing reads were analyzed for the CHL and CHM samples, respectively. Most annotated proteins were found to be of bacterial origin, although eukaryotic, archaeal, and viral proteins were also identified. Differences in community structure and function were noted. Most notably, Legionella-like genes were more abundant in the CHL samples while mycobacterial genes were more abundant in CHM samples. Genes associated with multiple disinfectant mechanisms were identified in both communities. Moreover, sequences linked to virulence factors, such as antibiotic resistance mechanisms, were observed in both microbial communities. This study provides new insights into the genetic network and potential biological processes associated with the molecular microbial ecology of DW microbial communities. PMID:22729545

Exploring the Association between Alzheimer's Disease, Oral Health, Microbial Endocrinology and Nutrition.

PubMed

Harding, Alice; Gonder, Ulrike; Robinson, Sarita J; Crean, StJohn; Singhrao, Sim K

2017-01-01

Longitudinal monitoring of patients suggests a causal link between chronic periodontitis and the development of Alzheimer's disease (AD). However, the explanation of how periodontitis can lead to dementia remains unclear. A working hypothesis links extrinsic inflammation as a secondary cause of AD. This hypothesis suggests a compromised oral hygiene leads to a dysbiotic oral microbiome whereby Porphyromonas gingivalis , a keystone periodontal pathogen, with its companion species, orchestrates immune subversion in the host. Brushing and chewing on teeth supported by already injured soft tissues leads to bacteremias. As a result, a persistent systemic inflammatory response develops to periodontal pathogens. The pathogens, and the host's inflammatory response, subsequently lead to the initiation and progression of multiple metabolic and inflammatory co-morbidities, including AD. Insufficient levels of essential micronutrients can lead to microbial dysbiosis through the growth of periodontal pathogens such as demonstrated for P. gingivalis under low hemin bioavailability. An individual's diet also defines the consortium of microbial communities that take up residency in the oral and gastrointestinal (GI) tract microbiomes. Their imbalance can lead to behavioral changes. For example, probiotics enriched in Lactobacillus genus of bacteria, when ingested, exert some anti-inflammatory influence through common host/bacterial neurochemicals, both locally, and through sensory signaling back to the brain. Early life dietary behaviors may cause an imbalance in the host/microbial endocrinology through a dietary intake incompatible with a healthy GI tract microbiome later in life. This imbalance in host/microbial endocrinology may have a lasting impact on mental health. This observation opens up an opportunity to explore the mechanisms, which may underlie the previously detected relationship between diet, oral/GI microbial communities, to anxiety, cognition and sleep patterns. This review suggests healthy diet based interventions that together with improved life style/behavioral changes may reduce and/or delay the incidence of AD.

Exploring the Association between Alzheimer’s Disease, Oral Health, Microbial Endocrinology and Nutrition

PubMed Central

Harding, Alice; Gonder, Ulrike; Robinson, Sarita J.; Crean, StJohn; Singhrao, Sim K.

2017-01-01

Longitudinal monitoring of patients suggests a causal link between chronic periodontitis and the development of Alzheimer’s disease (AD). However, the explanation of how periodontitis can lead to dementia remains unclear. A working hypothesis links extrinsic inflammation as a secondary cause of AD. This hypothesis suggests a compromised oral hygiene leads to a dysbiotic oral microbiome whereby Porphyromonas gingivalis, a keystone periodontal pathogen, with its companion species, orchestrates immune subversion in the host. Brushing and chewing on teeth supported by already injured soft tissues leads to bacteremias. As a result, a persistent systemic inflammatory response develops to periodontal pathogens. The pathogens, and the host’s inflammatory response, subsequently lead to the initiation and progression of multiple metabolic and inflammatory co-morbidities, including AD. Insufficient levels of essential micronutrients can lead to microbial dysbiosis through the growth of periodontal pathogens such as demonstrated for P. gingivalis under low hemin bioavailability. An individual’s diet also defines the consortium of microbial communities that take up residency in the oral and gastrointestinal (GI) tract microbiomes. Their imbalance can lead to behavioral changes. For example, probiotics enriched in Lactobacillus genus of bacteria, when ingested, exert some anti-inflammatory influence through common host/bacterial neurochemicals, both locally, and through sensory signaling back to the brain. Early life dietary behaviors may cause an imbalance in the host/microbial endocrinology through a dietary intake incompatible with a healthy GI tract microbiome later in life. This imbalance in host/microbial endocrinology may have a lasting impact on mental health. This observation opens up an opportunity to explore the mechanisms, which may underlie the previously detected relationship between diet, oral/GI microbial communities, to anxiety, cognition and sleep patterns. This review suggests healthy diet based interventions that together with improved life style/behavioral changes may reduce and/or delay the incidence of AD. PMID:29249963

Exploring the dynamic links between microbial ecology and redox state of the hyporheic zone: insight from flume experiments

NASA Astrophysics Data System (ADS)

Kaufman, M.; Cardenas, M. B.; Stegen, J.; Graham, E.; Cook, P. L. M.; Kessler, A. J.

2016-12-01

The hyporheic zone (HZ) provides key ecosystem services such as heavy metal sequestration, nutrient uptake and consumption, and habitat for a diverse collection of ecologically and commercially important species. Microbes are responsible for many of the chemical transformations in the HZ. These microbe populations are intimately linked to redox conditions, and recent work has shown that redox conditions in the HZ can be highly dynamic. Here we investigate the dynamic coupling between surface flow conditions, hyporheic redox conditions, and the hyporheic microbiome. Our window into this world is a large experimental flume (5m x 0.7m x 0.3m), prepared and incubated in a way that is relatively common to hyporheic zone research, without a strong attempt to impose a specific microbial community structure. We use computer-controlled flow combined with sand bedforms within the flume to generate a pattern of oxic and anoxic sediment zones, from which we collected sediment and water samples. Dissolved oxygen was mapped with a large planar optode. The samples were analyzed for microbial community composition through 16S rRNA gene sequencing. We compare the population structure between oxic and anoxic zones, showing that the presence of oxygen in the HZ is a strong predictor of microbial composition. Additionally, we compare both the oxic and anoxic community structure from the flume to those of samples taken from natural environments, showing both interesting similarities and differences. In the future, we plan to use time-series sampling to observe the response times of microbial communities subjected to dynamic surface channel flow and redox conditions. This work will yield greater understanding of the role that dynamic rivers play in microbe-provided ecosystem services.

Succession of Phenotypic, Genotypic, and Metabolic Community Characteristics during In Vitro Bioslurry Treatment of Polycyclic Aromatic Hydrocarbon-Contaminated Sediments

PubMed Central

Ringelberg, David B.; Talley, Jeffrey W.; Perkins, Edward J.; Tucker, Samuel G.; Luthy, Richard G.; Bouwer, Edward J.; Fredrickson, Herbert L.

2001-01-01

Dredged harbor sediment contaminated with polycyclic aromatic hydrocarbons (PAHs) was removed from the Milwaukee Confined Disposal Facility and examined for in situ biodegradative capacity. Molecular techniques were used to determine the successional characteristics of the indigenous microbiota during a 4-month bioslurry evaluation. Ester-linked phospholipid fatty acids (PLFA), multiplex PCR of targeted genes, and radiorespirometry techniques were used to define in situ microbial phenotypic, genotypic, and metabolic responses, respectively. Soxhlet extractions revealed a loss in total PAH concentrations of 52%. Individual PAHs showed reductions as great as 75% (i.e., acenapthene and fluorene). Rates of 14C-PAH mineralization (percent/day) were greatest for phenanthrene, followed by pyrene and then chrysene. There was no mineralization capacity for benzo[a]pyrene. Ester-linked phospholipid fatty acid analysis revealed a threefold increase in total microbial biomass and a dynamic microbial community composition that showed a strong correlation with observed changes in the PAH chemistry (canonical r2 of 0.999). Nucleic acid analyses showed copies of genes encoding PAH-degrading enzymes (extradiol dioxygenases, hydroxylases, and meta-cleavage enzymes) to increase by as much as 4 orders of magnitude. Shifts in gene copy numbers showed strong correlations with shifts in specific subsets of the extant microbial community. Specifically, declines in the concentrations of three-ring PAH moieties (i.e., phenanthrene) correlated with PLFA indicative of certain gram-negative bacteria (i.e., Rhodococcus spp. and/or actinomycetes) and genes encoding for naphthalene-, biphenyl-, and catechol-2,3-dioxygenase degradative enzymes. The results of this study suggest that the intrinsic biodegradative potential of an environmental site can be derived from the polyphasic characterization of the in situ microbial community. PMID:11282603

Microbial colonization of basaltic glasses in hydrothermal organic-rich sediments at Guaymas Basin

PubMed Central

Callac, Nolwenn; Rommevaux-Jestin, Céline; Rouxel, Olivier; Lesongeur, Françoise; Liorzou, Céline; Bollinger, Claire; Ferrant, Antony; Godfroy, Anne

2013-01-01

Oceanic basalts host diverse microbial communities with various metabolisms involved in C, N, S, and Fe biogeochemical cycles which may contribute to mineral and glass alteration processes at, and below the seafloor. In order to study the microbial colonization on basaltic glasses and their potential biotic/abiotic weathering products, two colonization modules called AISICS (“Autonomous in situ Instrumented Colonization System”) were deployed in hydrothermal deep-sea sediments at the Guaymas Basin for 8 days and 22 days. Each AISICS module contained 18 colonizers (including sterile controls) filled with basaltic glasses of contrasting composition. Chemical analyses of ambient fluids sampled through the colonizers showed a greater contribution of hydrothermal fluids (maximum temperature 57.6°C) for the module deployed during the longer time period. For each colonizer, the phylogenetic diversity and metabolic function of bacterial and archaeal communities were explored using a molecular approach by cloning and sequencing. Results showed large microbial diversity in all colonizers. The bacterial distribution was primarily linked to the deployment duration, as well as the depth for the short deployment time module. Some 16s rRNA sequences formed a new cluster of Epsilonproteobacteria. Within the Archaea the retrieved diversity could not be linked to either duration, depth or substrata. However, mcrA gene sequences belonging to the ANME-1 mcrA-guaymas cluster were found sometimes associated with their putative sulfate-reducers syntrophs depending on the colonizers. Although no specific glass alteration texture was identified, nano-crystals of barite and pyrite were observed in close association with organic matter, suggesting a possible biological mediation. This study gives new insights into the colonization steps of volcanic rock substrates and the capability of microbial communities to exploit new environmental conditions. PMID:23986754

Exploring the dynamic links between microbial ecology and redox state of the hyporheic zone: insight from flume experiments

NASA Astrophysics Data System (ADS)

Kaufman, M.; Cardenas, M. B.; Stegen, J.; Graham, E.; Cook, P. L. M.; Kessler, A. J.

2017-12-01

The hyporheic zone (HZ) provides key ecosystem services such as heavy metal sequestration, nutrient uptake and consumption, and habitat for a diverse collection of ecologically and commercially important species. Microbes are responsible for many of the chemical transformations in the HZ. These microbe populations are intimately linked to redox conditions, and recent work has shown that redox conditions in the HZ can be highly dynamic. Here we investigate the dynamic coupling between surface flow conditions, hyporheic redox conditions, and the hyporheic microbiome. Our window into this world is a large experimental flume (5m x 0.7m x 0.3m), prepared and incubated in a way that is relatively common to hyporheic zone research, without a strong attempt to impose a specific microbial community structure. We use computer-controlled flow combined with sand bedforms within the flume to generate a pattern of oxic and anoxic sediment zones, from which we collected sediment and water samples. Dissolved oxygen was mapped with a large planar optode. The samples were analyzed for microbial community composition through 16S rRNA gene sequencing. We compare the population structure between oxic and anoxic zones, showing that the presence of oxygen in the HZ is a strong predictor of microbial composition. Additionally, we compare both the oxic and anoxic community structure from the flume to those of samples taken from natural environments, showing both interesting similarities and differences. In the future, we plan to use time-series sampling to observe the response times of microbial communities subjected to dynamic surface channel flow and redox conditions. This work will yield greater understanding of the role that dynamic rivers play in microbe-provided ecosystem services.

The maturing of microbial ecology.

PubMed

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.

Mercury in water and biomass of microbial communities in hot springs of Yellowstone National Park, USA

USGS Publications Warehouse

King, S.A.; Behnke, S.; Slack, K.; Krabbenhoft, D.P.; Nordstrom, D. Kirk; Burr, M.D.; Striegl, Robert G.

2006-01-01

Ultra-clean sampling methods and approaches typically used in pristine environments were applied to quantify concentrations of Hg species in water and microbial biomass from hot springs of Yellowstone National Park, features that are geologically enriched with Hg. Microbial populations of chemically-diverse hot springs were also characterized using modern methods in molecular biology as the initial step toward ongoing work linking Hg speciation with microbial processes. Molecular methods (amplification of environmental DNA using 16S rDNA primers, cloning, denatured gradient gel electrophoresis (DGGE) screening of clone libraries, and sequencing of representative clones) were used to examine the dominant members of microbial communities in hot springs. Total Hg (THg), monomethylated Hg (MeHg), pH, temperature, and other parameters influential to Hg speciation and microbial ecology are reported for hot springs water and associated microbial mats. Several hot springs indicate the presence of MeHg in microbial mats with concentrations ranging from 1 to 10 ng g-1 (dry weight). Concentrations of THg in mats ranged from 4.9 to 120,000 ng g-1 (dry weight). Combined data from surveys of geothermal water, lakes, and streams show that aqueous THg concentrations range from l to 600 ng L-1. Species and concentrations of THg in mats and water vary significantly between hot springs, as do the microorganisms found at each site. ?? 2006.

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

NASA Technical Reports Server (NTRS)

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.

Whole-leaf sanitizing wash improves chlorine efficacy for microbial reduction and prevents pathogen cross contamination during fresh-cut lettuce processing

USDA-ARS?s Scientific Manuscript database

Currently, nearly all fresh-cut lettuce processing facilities in the United States use chlorinated water or other sanitizer solutions for microbial reduction after lettuce is cut. It is believed that freshly cut lettuce releases significant amounts of organic matters that negatively impact the effec...

Cheese Microbial Risk Assessments — A Review

PubMed Central

Choi, Kyoung-Hee; Lee, Heeyoung; Lee, Soomin; Kim, Sejeong; Yoon, Yohan

2016-01-01

Cheese is generally considered a safe and nutritious food, but foodborne illnesses linked to cheese consumption have occurred in many countries. Several microbial risk assessments related to Listeria monocytogenes, Staphylococcus aureus, and Escherichia coli infections, causing cheese-related foodborne illnesses, have been conducted. Although the assessments of microbial risk in soft and low moisture cheeses such as semi-hard and hard cheeses have been accomplished, it has been more focused on the correlations between pathogenic bacteria and soft cheese, because cheese-associated foodborne illnesses have been attributed to the consumption of soft cheeses. As a part of this microbial risk assessment, predictive models have been developed to describe the relationship between several factors (pH, Aw, starter culture, and time) and the fates of foodborne pathogens in cheese. Predictions from these studies have been used for microbial risk assessment as a part of exposure assessment. These microbial risk assessments have identified that risk increased in cheese with high moisture content, especially for raw milk cheese, but the risk can be reduced by preharvest and postharvest preventions. For accurate quantitative microbial risk assessment, more data including interventions such as curd cooking conditions (temperature and time) and ripening period should be available for predictive models developed with cheese, cheese consumption amounts and cheese intake frequency data as well as more dose-response models. PMID:26950859

Effect of a temperature gradient on Sphagnum fallax and its associated living microbial communities: a study under controlled conditions.

PubMed

Jassey, Vincent E J; Gilbert, Daniel; Binet, Philippe; Toussaint, Marie-Laure; Chiapusio, Geneviève

2011-03-01

Microbial communities living in Sphagnum are known to constitute early indicators of ecosystem disturbances, but little is known about their response (including their trophic relationships) to climate change. A microcosm experiment was designed to test the effects of a temperature gradient (15, 20, and 25°C) on microbial communities including different trophic groups (primary producers, decomposers, and unicellular predators) in Sphagnum segments (0-3 cm and 3-6 cm of the capitulum). Relationships between microbial communities and abiotic factors (pH, conductivity, temperature, and polyphenols) were also studied. The density and the biomass of testate amoebae in Sphagnum upper segments increased and their community structure changed in heated treatments. The biomass of testate amoebae was linked to the biomass of bacteria and to the total biomass of other groups added and, thus, suggests that indirect effects on the food web structure occurred. Redundancy analysis revealed that microbial assemblages differed strongly in Sphagnum upper segments along a temperature gradient in relation to abiotic factors. The sensitivity of these assemblages made them interesting indicators of climate change. Phenolic compounds represented an important explicative factor in microbial assemblages and outlined the potential direct and (or) indirect effects of phenolics on microbial communities.

Microbial community diversity, structure and assembly across oxygen gradients in meromictic marine lakes, Palau.

PubMed

Meyerhof, Matthew S; Wilson, Jesse M; Dawson, Michael N; Michael Beman, J

2016-12-01

Microbial communities consume oxygen, alter biogeochemistry and compress habitat in aquatic ecosystems, yet our understanding of these microbial-biogeochemical-ecological interactions is limited by a lack of systematic analyses of low-oxygen ecosystems. Marine lakes provide an ideal comparative system, as they range from well-mixed holomictic lakes to stratified, anoxic, meromictic lakes that vary in their vertical extent of anoxia. We examined microbial communities inhabiting six marine lakes and one ocean site using pyrosequencing of 16S rRNA genes. Microbial richness and evenness was typically highest in the anoxic monimolimnion of meromictic lakes, with common marine bacteria present in mixolimnion communities replaced by anoxygenic phototrophs, sulfate-reducing bacteria and SAR406 in the monimolimnion. These sharp changes in community structure were linked to environmental gradients (constrained variation in redundancy analysis = 68%-76%) - particularly oxygen and pH. However, in those lakes with the steepest oxygen gradients, salinity and dissolved nutrients were important secondary constraining variables, indicating that subtle but substantive differences in microbial communities occur within similar low-oxygen habitats. Deterministic processes were a dominant influence on whole community assembly (all nearest taxon index values >4), demonstrating that the strong environmental gradients present in meromictic marine lakes drive microbial community assembly. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

The shift of microbial communities and their roles in sulfur and iron cycling in a copper ore bioleaching system.

PubMed

Niu, Jiaojiao; Deng, Jie; Xiao, Yunhua; He, Zhili; Zhang, Xian; Van Nostrand, J D; Liang, Yili; Deng, Ye; Liu, Xueduan; Yin, Huaqun

2016-10-04

Bioleaching has been employed commercially to recover metals from low grade ores, but the production efficiency remains to be improved due to limited understanding of the system. This study examined the shift of microbial communities and S&Fe cycling in three subsystems within a copper ore bioleaching system: leaching heap (LH), leaching solution (LS) and sediment under LS. Results showed that both LH and LS had higher relative abundance of S and Fe oxidizing bacteria, while S and Fe reducing bacteria were more abundant in the Sediment. GeoChip analysis showed a stronger functional potential for S 0 oxidation in LH microbial communities. These findings were consistent with measured oxidation activities to S 0 and Fe 2+ , which were highest by microbial communities from LH, lower by those from LS and lowest form Sediment. Moreover, phylogenetic molecular ecological network analysis indicated that these differences might be related to interactions among microbial taxa. Last but not the least, a conceptual model was proposed, linking the S&Fe cycling with responsible microbial populations in the bioleaching systems. Collectively, this study revealed the microbial community and functional structures in all three subsystems of the copper ore, and advanced a holistic understanding of the whole bioleaching system.

The shift of microbial communities and their roles in sulfur and iron cycling in a copper ore bioleaching system

NASA Astrophysics Data System (ADS)

Niu, Jiaojiao; Deng, Jie; Xiao, Yunhua; He, Zhili; Zhang, Xian; van Nostrand, J. D.; Liang, Yili; Deng, Ye; Liu, Xueduan; Yin, Huaqun

2016-10-01

Bioleaching has been employed commercially to recover metals from low grade ores, but the production efficiency remains to be improved due to limited understanding of the system. This study examined the shift of microbial communities and S&Fe cycling in three subsystems within a copper ore bioleaching system: leaching heap (LH), leaching solution (LS) and sediment under LS. Results showed that both LH and LS had higher relative abundance of S and Fe oxidizing bacteria, while S and Fe reducing bacteria were more abundant in the Sediment. GeoChip analysis showed a stronger functional potential for S0 oxidation in LH microbial communities. These findings were consistent with measured oxidation activities to S0 and Fe2+, which were highest by microbial communities from LH, lower by those from LS and lowest form Sediment. Moreover, phylogenetic molecular ecological network analysis indicated that these differences might be related to interactions among microbial taxa. Last but not the least, a conceptual model was proposed, linking the S&Fe cycling with responsible microbial populations in the bioleaching systems. Collectively, this study revealed the microbial community and functional structures in all three subsystems of the copper ore, and advanced a holistic understanding of the whole bioleaching system.

The shift of microbial communities and their roles in sulfur and iron cycling in a copper ore bioleaching system

PubMed Central

Niu, Jiaojiao; Deng, Jie; Xiao, Yunhua; He, Zhili; Zhang, Xian; Van Nostrand, J. D.; Liang, Yili; Deng, Ye; Liu, Xueduan; Yin, Huaqun

2016-01-01

Bioleaching has been employed commercially to recover metals from low grade ores, but the production efficiency remains to be improved due to limited understanding of the system. This study examined the shift of microbial communities and S&Fe cycling in three subsystems within a copper ore bioleaching system: leaching heap (LH), leaching solution (LS) and sediment under LS. Results showed that both LH and LS had higher relative abundance of S and Fe oxidizing bacteria, while S and Fe reducing bacteria were more abundant in the Sediment. GeoChip analysis showed a stronger functional potential for S0 oxidation in LH microbial communities. These findings were consistent with measured oxidation activities to S0 and Fe2+, which were highest by microbial communities from LH, lower by those from LS and lowest form Sediment. Moreover, phylogenetic molecular ecological network analysis indicated that these differences might be related to interactions among microbial taxa. Last but not the least, a conceptual model was proposed, linking the S&Fe cycling with responsible microbial populations in the bioleaching systems. Collectively, this study revealed the microbial community and functional structures in all three subsystems of the copper ore, and advanced a holistic understanding of the whole bioleaching system. PMID:27698381

The effect of microbial phytase on ileal phosphorus and amino acid digestibility in the broiler chicken.

PubMed

Rutherfurd, S M; Chung, T K; Moughan, P J

2002-09-01

1. The study aimed to assess the effect of a commercially available microbial phytase on phytate phosphorus and total phosphorus content at the terminal ileum as well as true ileal amino acid digestibility. 2. Five diets, each containing a different plant-based feedstuff, were supplemented with microbial phytase and fed, along with a non-supplemented corresponding diet, to 28-d-old broiler chickens, Chromic oxide was used as an indigestible marker. Ileal contents were collected and analysed, along with the diets, for total phosphorus, phytate phosphorus and amino acids. 3. Endogenous phosphorus determined at the terminal ileum was 272 +/- 108 mg/kg food dry matter (mean +/- SE). Endogenous ileal amino acid flows ranged from 58 +/- 10 mg/kg food dry matter for methionine to 568 +/- 47 mg/kg food dry matter for glutamic acid. 4. Supplementation with microbial phytase resulted in a significantly greater phytate P disappearance from the terminal ileum for rice bran (17% units), but not for soyabean meal, maize, wheat or rapeseed meal. Similarly total phosphorus digestibility was significantly (P < 0.05) higher when microbial phytase was added to the rice-bran-based diet but not for any of the other feedstuffs. 5. Amino acid digestibility was significantly greater in the presence of microbial phytase for all the amino acids examined in wheat, for several of the amino acids each in maize and rapeseed meal and for one amino acid in rice bran and soyabean meal. The average increase in amino acid digestibility for those amino acids affected, was 13, 6, 10, 7 and 12% units for wheat, maize, rapeseed meal, rice bran and soyabean meal, respectively. 6. It appears that microbial phytase improves phosphorus digestibility and amino acid digestibility for certain plant-based feedstuffs.

Italian multicentre study on microbial environmental contamination in dental clinics: a pilot study.

PubMed

Pasquarella, Cesira; Veronesi, Licia; Castiglia, Paolo; Liguori, Giorgio; Montagna, Maria Teresa; Napoli, Christian; Rizzetto, Rolando; Torre, Ida; Masia, Maria Dolores; Di Onofrio, Valeria; Colucci, Maria Eugenia; Tinteri, Carola; Tanzi, Marialuisa

2010-09-01

The dental practice is associated with a high risk of infections, both for patients and healthcare operators, and the environment may play an important role in the transmission of infectious diseases. A microbiological environmental investigation was carried out in six dental clinics as a pilot study for a larger multicentre study that will be performed by the Italian SItI (Society of Hygiene, Preventive Medicine and Public Health) working group "Hygiene in Dentistry". Microbial contamination of water, air and surfaces was assessed in each clinic during the five working days of the week, before and during treatments. Air and surfaces were also examined at the end of the daily activity. A wide variation was found in microbial environmental contamination, both within the participating clinics and relative to the different sampling times. Microbial water contamination in Dental Unit Water Systems (DUWS) reached values of up to 26x10(4)cfu/mL (colony forming units per millilitre). P. aeruginosa was found in 33% of the sampled DUWS and Legionella spp. in 50%. A significant decrease in the Total Viable Count (TVC) was recorded during the activity. Microbial air contamination showed the highest levels during dental treatments and tended to decrease at the end of the working activity (p<0.05). Microbial buildup on surfaces increased significantly during the working hours. As these findings point out, research on microbial environmental contamination and the related risk factors in dental clinics should be expanded and should also be based on larger collections of data, in order to provide the essential knowledge aimed at targeted preventive interventions. Copyright 2010 Elsevier B.V. All rights reserved.

Environmental Filtering Process Has More Important Roles than Dispersal Limitation in Shaping Large-Scale Prokaryotic Beta Diversity Patterns of Grassland Soils.

PubMed

Cao, Peng; Wang, Jun-Tao; Hu, Hang-Wei; Zheng, Yuan-Ming; Ge, Yuan; Shen, Ju-Pei; He, Ji-Zheng

2016-07-01

Despite the utmost importance of microorganisms in maintaining ecosystem functioning and their ubiquitous distribution, our knowledge of the large-scale pattern of microbial diversity is limited, particularly in grassland soils. In this study, the microbial communities of 99 soil samples spanning over 3000 km across grassland ecosystems in northern China were investigated using high-throughput sequencing to analyze the beta diversity pattern and the underlying ecological processes. The microbial communities were dominated by Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, and Planctomycetes across all the soil samples. Spearman's correlation analysis indicated that climatic factors and soil pH were significantly correlated with the dominant microbial taxa, while soil microbial richness was positively linked to annual precipitation. The environmental divergence-dissimilarity relationship was significantly positive, suggesting the importance of environmental filtering processes in shaping soil microbial communities. Structural equation modeling found that the deterministic process played a more important role than the stochastic process on the pattern of soil microbial beta diversity, which supported the predictions of niche theory. Partial mantel test analysis have showed that the contribution of independent environmental variables has a significant effect on beta diversity, while independent spatial distance has no such relationship, confirming that the deterministic process was dominant in structuring soil microbial communities. Overall, environmental filtering process has more important roles than dispersal limitation in shaping microbial beta diversity patterns in the grassland soils.

Natural attenuation of contaminated marine sediments from an old floating dock Part II: changes of sediment microbial community structure and its relationship with environmental variables.

PubMed

Wang, Ya-Fen; Tam, Nora Fung-Yee

2012-04-15

Changes of microbial community structure and its relationship with various environmental variables in surface marine sediments were examined for a one-year period after the removal of an old floating dock in Hong Kong SAR, South China. Temporal variations in the microbial community structure were clearly revealed by principal component analysis (PCA) of the microbial ester-linked fatty acid methyl ester (EL-FAME) profiles. The most obvious shift in microbial community structure was detected 6 months after the removal of the dock, although no significant decline in the levels of pollutants could be detected. As determined by EL-FAME profiles, the microbial diversity recovered and the predominance of gram-negative bacteria was gradually replaced by gram-positive bacteria and fungi in the impacted stations. With redundancy analysis (RDA), the concentration of total polycyclic aromatic hydrocarbons (PAHs) was found to be the second important determinant of microbial community structure, next to Time. The relative abundance of 18:1ω9c and hydroxyl fatty acids enriched in the PAH hot spots, whereas 16:1ω9 and 18:1ω9t were negatively correlated to total PAH concentration. The significant relationships observed between microbial EL-FAME profiles and pollutants, exampled by PAHs in the present study, suggested the potential of microbial community analysis in the assessment of the natural attenuation process in contaminated environments. Copyright © 2012 Elsevier B.V. All rights reserved.

Pricing unit-linked insurance with guaranteed benefit

NASA Astrophysics Data System (ADS)

Iqbal, M.; Novkaniza, F.; Novita, M.

2017-07-01

Unit-linked insurance is an investment-linked insurance, that is, the given benefit is the premium investment out-come. Recently, the most widely marketed insurance in the industry is unit-linked insurance with guaranteed benefit. With guaranteed benefit applied, the insurance benefits form is similar to the payoff form of European call option. Thereby, pricing European call option is involved in pricing unit-linked insurance with guaranteed benefit. The dynamics of investment outcome is assumed to follow stochastic interest rate. Hence, change of measure methods is used in pricing unit-linked insurance. The discount factor with stochastic interest rate needs to be modified as well to be zero coupon bond price. Eventually, the insurance premium is calculated by equivalence principle with guaranteed benefit and insurance period explicitly given.

Relationship between dissolved organic matter quality and microbial community composition across polar glacial environments.

PubMed

Smith, H J; Dieser, M; McKnight, D M; SanClements, M D; Foreman, C M

2018-05-14

Vast expanses of Earth's surface are covered by ice, with microorganisms in these systems affecting local and global biogeochemical cycles. We examined microbial assemblages from habitats fed by glacial meltwater within the McMurdo Dry Valleys, Antarctica, and on the west Greenland Ice Sheet, (GrIS) evaluating potential physicochemical factors explaining trends in community structure. Microbial assemblages present in the different Antarctic dry valley habitats were dominated by Sphingobacteria and Flavobacteria, while Gammaproteobacteria and Sphingobacteria prevailed in west GrIS supraglacial environments. Microbial assemblages clustered by location (Canada Glacier, Cotton Glacier, west GrIS) and were separated by habitat type (i.e. ice, cryoconite holes, supraglacial lakes, sediment, and stream water). Community dissimilarities were strongly correlated with dissolved organic matter (DOM) quality. Microbial meltwater assemblages were most closely associated with different protein-like components of the DOM pool. Microbes in environments with mineral particles (i.e. stream sediments, cryoconite holes) were linked to DOM containing more humic-like fluorescence. Our results demonstrate the establishment of distinct microbial communities within ephemeral glacial meltwater habitats, with DOM-microbe interactions playing an integral role in shaping communities on local and polar spatial scales.

fusionDB: assessing microbial diversity and environmental preferences via functional similarity networks

PubMed Central

Zhu, Chengsheng; Miller, Maximilian

2018-01-01

Abstract Microbial functional diversification is driven by environmental factors, i.e. microorganisms inhabiting the same environmental niche tend to be more functionally similar than those from different environments. In some cases, even closely phylogenetically related microbes differ more across environments than across taxa. While microbial similarities are often reported in terms of taxonomic relationships, no existing databases directly link microbial functions to the environment. We previously developed a method for comparing microbial functional similarities on the basis of proteins translated from their sequenced genomes. Here, we describe fusionDB, a novel database that uses our functional data to represent 1374 taxonomically distinct bacteria annotated with available metadata: habitat/niche, preferred temperature, and oxygen use. Each microbe is encoded as a set of functions represented by its proteome and individual microbes are connected via common functions. Users can search fusionDB via combinations of organism names and metadata. Moreover, the web interface allows mapping new microbial genomes to the functional spectrum of reference bacteria, rendering interactive similarity networks that highlight shared functionality. fusionDB provides a fast means of comparing microbes, identifying potential horizontal gene transfer events, and highlighting key environment-specific functionality. PMID:29112720

A Workflow to Model Microbial Loadings in Watersheds ...

EPA Pesticide Factsheets

Many watershed models simulate overland and instream microbial fate and transport, but few actually provide loading rates on land surfaces and point sources to the water body network. This paper describes the underlying general equations for microbial loading rates associated with 1) land-applied manure on undeveloped areas from domestic animals; 2) direct shedding on undeveloped lands by domestic animals and wildlife; 3) urban or engineered areas; and 4) point sources that directly discharge to streams from septic systems and shedding by domestic animals. A microbial source module, which houses these formulations, is linked within a workflow containing eight models and a set of databases that form a loosely configured modeling infrastructure which supports watershed-scale microbial source-to-receptor modeling by focusing on animal-impacted catchments. A hypothetical example application – accessing, retrieving, and using real-world data – demonstrates the ability of the infrastructure to automate many of the manual steps associated with a standard watershed assessment, culminating with calibrated flow and microbial densities at the pour point of a watershed. In the Proceedings of the International Environmental Modelling and Software Society (iEMSs), 8th International Congress on Environmental Modelling and Software, Toulouse, France

Optimization of biomass composition explains microbial growth-stoichiometry relationships

USGS Publications Warehouse

Franklin, O.; Hall, E.K.; Kaiser, C.; Battin, T.J.; Richter, A.

2011-01-01

Integrating microbial physiology and biomass stoichiometry opens far-reaching possibilities for linking microbial dynamics to ecosystem processes. For example, the growth-rate hypothesis (GRH) predicts positive correlations among growth rate, RNA content, and biomass phosphorus (P) content. Such relationships have been used to infer patterns of microbial activity, resource availability, and nutrient recycling in ecosystems. However, for microorganisms it is unclear under which resource conditions the GRH applies. We developed a model to test whether the response of microbial biomass stoichiometry to variable resource stoichiometry can be explained by a trade-off among cellular components that maximizes growth. The results show mechanistically why the GRH is valid under P limitation but not under N limitation. We also show why variability of growth rate-biomass stoichiometry relationships is lower under P limitation than under N or C limitation. These theoretical results are supported by experimental data on macromolecular composition (RNA, DNA, and protein) and biomass stoichiometry from two different bacteria. In addition, compared to a model with strictly homeostatic biomass, the optimization mechanism we suggest results in increased microbial N and P mineralization during organic-matter decomposition. Therefore, this mechanism may also have important implications for our understanding of nutrient cycling in ecosystems.

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

DOE Office of Scientific and Technical Information (OSTI.GOV)

Taillefert, Martial; Van Cappellen, Philippe

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, competitionmore » 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).« less

The microbiome in PTEN hamartoma tumor syndrome.

PubMed

Byrd, Victoria; Getz, Ted; Padmanabhan, Roshan; Arora, Hans; Eng, Charis

2018-03-01

Germline PTEN mutations defining PTEN hamartoma tumor syndrome (PHTS) confer heritable predisposition to breast, endometrial, thyroid and other cancers with known age-related risks, but it remains impossible to predict if any individual will develop cancer. In the general population, gut microbial dysbiosis has been linked to cancer, yet is unclear whether these are associated in PHTS patients. In this pilot study, we aimed to characterize microbial composition of stool, urine, and oral wash from 32 PTEN mutation-positive individuals using 16S rRNA gene sequencing. PCoA revealed clustering of the fecal microbiome by cancer history ( P  = 0.03, R 2  = 0.04). Fecal samples from PHTS cancer patients had relatively more abundant operational taxonomic units (OTUs) from family Rikenellaceae and unclassified members of Clostridia compared to those from non-cancer patients, whereas families Peptostreptococcaceae, Enterobacteriaceae, and Bifidobacteriaceae represented relatively more abundant OTUs among fecal samples from PHTS non-cancer patients. Functional metagenomic prediction revealed enrichment of the folate biosynthesis, genetic information processing and cell growth and death pathways among fecal samples from PHTS cancer patients compared to non-cancer patients. We found no major shifts in overall diversity and no clustering by cancer history among oral wash or urine samples. Our observations suggest the utility of an expanded study to interrogate gut dysbiosis as a potential cancer risk modifier in PHTS patients. © 2018 The authors.

The activated sludge ecosystem contains a core community of abundant organisms

PubMed Central

Saunders, Aaron M; Albertsen, Mads; Vollertsen, Jes; Nielsen, Per H

2016-01-01

Understanding the microbial ecology of a system requires that the observed population dynamics can be linked to their metabolic functions. However, functional characterization is laborious and the choice of organisms should be prioritized to those that are frequently abundant (core) or transiently abundant, which are therefore putatively make the greatest contribution to carbon turnover in the system. We analyzed the microbial communities in 13 Danish wastewater treatment plants with nutrient removal in consecutive years and a single plant periodically over 6 years, using Illumina sequencing of 16S ribosomal RNA amplicons of the V4 region. The plants contained a core community of 63 abundant genus-level operational taxonomic units (OTUs) that made up 68% of the total reads. A core community consisting of abundant OTUs was also observed within the incoming wastewater to three plants. The net growth rate for individual OTUs was quantified using mass balance, and it was found that 10% of the total reads in the activated sludge were from slow or non-growing OTUs, and that their measured abundance was primarily because of immigration with the wastewater. Transiently abundant organisms were also identified. Among them the genus Nitrotoga (class Betaproteobacteria) was the most abundant putative nitrite oxidizer in a number of activated sludge plants, which challenges previous assumptions that Nitrospira (phylum Nitrospirae) are the primary nitrite-oxidizers in activated sludge systems with nutrient removal. PMID:26262816

Assimilable organic carbon release, chemical migration, and drinking water impacts of multiple brands of plastic pipes available in the USA

NASA Astrophysics Data System (ADS)

Connell, Matthew

Increased installation of polymer potable water pipes in United States plumbing systems has created a need to thoroughly evaluate their water quality impacts. Eleven brands of new polymer drinking water pipe were evaluated for assimilable organic carbon (AOC) release at room temperature for 28 days. They included polyvinyl chloride (PVC), high-density polyethylene (HDPE), polypropylene (PP), and cross-linked polyethylene (PEX) pipes. Three of eight PEX pipe brands exceeded a 100 microg/L AOC threshold for microbial regrowth for the first exposure period and no brands exceeded this value on day 28. No detectable increase in AOC was found for PP and PEX-a1 pipes; the remaining pipe brands contributed marginal AOC levels. Water quality impacts were more fully evaluated for two brands of PEX-b and one brand of PP pipe. PEX pipes released more total organic carbon (TOC), volatile organic compounds (VOC), and semivolatile organic compounds (SVOC) and caused greater odor than the PP pipe. All three materials showed reductions in these water quality parameters over 30 days. Three PEX pipe field studies revealed that aged systems did not display more intense odors than distribution systems. However, the organic releases from polymer pipes may still alter water quality and contribute to rapid microbial growth, even though the aesthetic impacts are temporary.

Successional and seasonal variations in soil and litter microbial community structure and function during tropical postagricultural forest regeneration: a multiyear study.

PubMed

Smith, A Peyton; Marín-Spiotta, Erika; Balser, Teri

2015-09-01

Soil microorganisms regulate fundamental biochemical processes in plant litter decomposition and soil organic matter (SOM) transformations. Understanding how microbial communities respond to changes in vegetation is critical for improving predictions of how land-cover change affects belowground carbon storage and nutrient availability. We measured intra- and interannual variability in soil and forest litter microbial community composition and activity via phospholipid fatty acid analysis (PLFA) and extracellular enzyme activity across a well-replicated, long-term chronosequence of secondary forests growing on abandoned pastures in the wet subtropical forest life zone of Puerto Rico. Microbial community PLFA structure differed between young secondary forests and older secondary and primary forests, following successional shifts in tree species composition. These successional patterns held across seasons, but the microbial groups driving these patterns differed over time. Microbial community composition from the forest litter differed greatly from those in the soil, but did not show the same successional trends. Extracellular enzyme activity did not differ with forest succession, but varied by season with greater rates of potential activity in the dry seasons. We found few robust significant relationships among microbial community parameters and soil pH, moisture, carbon, and nitrogen concentrations. Observed inter- and intrannual variability in microbial community structure and activity reveal the importance of a multiple, temporal sampling strategy when investigating microbial community dynamics with land-use change. Successional control over microbial composition with forest recovery suggests strong links between above and belowground communities. © 2015 John Wiley & Sons Ltd.

Comparison of microbial taxonomic and functional shift pattern along contamination gradient.

PubMed

Ren, Youhua; Niu, Jiaojiao; Huang, Wenkun; Peng, Deliang; Xiao, Yunhua; Zhang, Xian; Liang, Yili; Liu, Xueduan; Yin, Huaqun

2016-06-14

The interaction mechanism between microbial communities and environment is a key issue in microbial ecology. Microbial communities usually change significantly under environmental stress, which has been studied both phylogenetically and functionally, however which method is more effective in assessing the relationship between microbial communities shift and environmental changes still remains controversial. By comparing the microbial taxonomic and functional shift pattern along heavy metal contamination gradient, we found that both sedimentary composition and function shifted significantly along contamination gradient. For example, the relative abundance of Geobacter and Fusibacter decreased along contamination gradient (from high to low), while Janthinobacterium and Arthrobacter increased their abundances. Most genes involved in heavy metal resistance (e.g., metc, aoxb and mer) showed higher intensity in sites with higher concentration of heavy metals. Comparing the two shift patterns, there were correlations between them, because functional and phylogenetic β-diversities were significantly correlated, and many heavy metal resistance genes were derived from Geobacter, explaining their high abundance in heavily contaminated sites. However, there was a stronger link between functional composition and environmental drivers, while stochasticity played an important role in formation and succession of phylogenetic composition demonstrated by null model test. Overall our research suggested that the responses of functional traits depended more on environmental changes, while stochasticity played an important role in formation and succession of phylogenetic composition for microbial communities. So profiling microbial functional composition seems more appropriate to study the relationship between microbial communities and environment, as well as explore the adaptation and remediation mechanism of microbial communities to heavy metal contamination.

Microbial origins of chronic diseases.

PubMed

Gargano, Lisa M; Hughes, James M

2014-01-01

Chronic diseases such as cardiovascular disease and cancer are among the leading causes of death worldwide and have been on the rise over the past decade. Associations between microbial agents and development of chronic diseases have been made in the past, and new connections are currently being assessed. Investigators are examining the relationship between infectious agents and chronic disease using new technologies with more rigor and specificity. This review examines microbial agents' links to and associations with cardiovascular diseases, cancer, neurodegenerative diseases, renal diseases, psychiatric disorders, and obesity and addresses the important role of the human microbiome in maintenance of health and its potential role in chronic diseases. These associations and relationships will impact future research priorities, surveillance approaches, treatment strategies, and prevention programs for chronic diseases.

[Progress in expression and molecular modification of microbial transglutaminase].

PubMed

Liu, Song; Zhang, Dongxu; Du, Guocheng; Chen, Jian

2011-12-01

Microbial transglutaminase, which could catalyze the cross-linking of many proteins or non-protein materials, has been widely used in food, pharmaceutical and textile industry. To enhance the yield of the enzyme and establish corresponding platform for molecular modification, the researchers of Japanese Ajinomoto began to construct the recombinant strain producing transglutaminase in the 1990s. So far, the enzyme has been successfully expressed in different expression systems. Some of the recombinant strains are more productive than wild strains. Recently, progress has been made in the molecular modification of microbial transglutaminase, and the activity, thermo-stability and specificity of the enzyme are improved. This review briefly summarized and analyzed the strategies involved in these studies, and noted its trends.

Microbes versus microbes: control of pathogens in the food chain.

PubMed

Jordan, Kieran; Dalmasso, Marion; Zentek, Juergen; Mader, Anneluise; Bruggeman, Geert; Wallace, John; De Medici, Dario; Fiore, Alfonsina; Prukner-Radovcic, Estella; Lukac, Maja; Axelsson, Lars; Holck, Askild; Ingmer, Hanne; Malakauskas, Mindaugas

2014-12-01

Foodborne illness continues as a considerable threat to public health. Despite improved hygiene management systems and increased regulation, pathogenic bacteria still contaminate food, causing sporadic cases of illness and disease outbreaks worldwide. For many centuries, microbial antagonism has been used in food processing to improve food safety. An understanding of the mode of action of this microbial antagonism has been gained in recent years and potential applications in food and feed safety are now being explored. This review focuses on the potential opportunities presented, and the limitations, of using microbial antagonism as a biocontrol mechanism to reduce contamination along the food chain; including animal feed as its first link. © 2014 Society of Chemical Industry. © 2014 Society of Chemical Industry.

Microbial Eukaryotes: a Missing Link in Gut Microbiome Studies.

PubMed

Laforest-Lapointe, Isabelle; Arrieta, Marie-Claire

2018-01-01

Human-associated microbial communities include prokaryotic and eukaryotic organisms across high-level clades of the tree of life. While advances in high-throughput sequencing technology allow for the study of diverse lineages, the vast majority of studies are limited to bacteria, and very little is known on how eukaryote microbes fit in the overall microbial ecology of the human gut. As recent studies consider eukaryotes in their surveys, it is becoming increasingly clear that eukaryotes play important ecological roles in the microbiome as well as in host health. In this perspective, we discuss new evidence on eukaryotes as fundamental species of the human gut and emphasize that future microbiome studies should characterize the multitrophic interactions between microeukaryotes, other microorganisms, and the host.

Microbial Eukaryotes: a Missing Link in Gut Microbiome Studies

PubMed Central

2018-01-01

ABSTRACT Human-associated microbial communities include prokaryotic and eukaryotic organisms across high-level clades of the tree of life. While advances in high-throughput sequencing technology allow for the study of diverse lineages, the vast majority of studies are limited to bacteria, and very little is known on how eukaryote microbes fit in the overall microbial ecology of the human gut. As recent studies consider eukaryotes in their surveys, it is becoming increasingly clear that eukaryotes play important ecological roles in the microbiome as well as in host health. In this perspective, we discuss new evidence on eukaryotes as fundamental species of the human gut and emphasize that future microbiome studies should characterize the multitrophic interactions between microeukaryotes, other microorganisms, and the host. PMID:29556538

Differences in fecal microbial metabolites and microbiota of children with autism spectrum disorders

DOE PAGES

Kang, Dae-Wook; Ilhan, Zehra Esra; Isern, Nancy G.; ...

2017-12-22

Evidence supporting that gut problems are linked to ASD symptoms has been accumulating both in humans and animal models of ASD. Gut microbes and their metabolites may be linked not only to GI problems but also to ASD behavior symptoms. Despite this high interest, most previous studies have looked mainly at microbial structure, and studies on fecal metabolites are rare in the context of ASD. Thus, we aimed to detect fecal metabolites that may be present at significantly different concentrations between 21 children with ASD and 23 neurotypical children and to investigate its possible link to human gut microbiome. Usingmore » 1H-NMR spectroscopy and 16S rRNA gene amplicon sequencing, we examined metabolite profiles and microbial compositions in fecal samples, respectively. Of the 59 metabolites detected, isopropanol concentrations were significantly higher in feces of children with ASD after multiple testing corrections. We also observed similar trends of fecal metabolites to previous studies; children with ASD have higher fecal p-cresol and possibly lower GABA concentrations. In addition, Fisher Discriminant Analysis (FDA) with leave-out-validation suggested that a group of metabolites-caprate, nicotinate, glutamine, thymine, and aspartate-may potentially function as a modest biomarker to separate ASD participants from the neurotypical group (78% sensitivity and 81% specificity). Consistent with our previous Arizona cohort study, we also confirmed lower gut microbial diversity and reduced relative abundances of phylotypes most closely related to Prevotella copri in children with ASD. After multiple testing corrections, we also learned that relative abundances of Feacalibacterium prausnitzii and Haemophilus parainfluenzae were lower in feces of children with ASD. In conclusion, despite a relatively short list of fecal metabolites, the data in this study support that children with ASD have altered metabolite profiles in feces when compared with neurotypical children and warrant further investigation of metabolites in larger cohorts.« less

Investigating the relationship between peat biogeochemistry and above-ground plant phenology with remote sensing along a gradient of permafrost thaw.

NASA Astrophysics Data System (ADS)

Garnello, A.; Dye, D. G.; Bogle, R.; Hough, M.; Raab, N.; Dominguez, S.; Rich, V. I.; Crill, P. M.; Saleska, S. R.

2016-12-01

Global climate models predict a 50% - 85% decrease in permafrost area in northern regions by 2100 due to increased temperature and precipitation variability, potentially releasing large stores of carbon as greenhouse gases (GHG) due to microbial activity. Linking belowground biogeochemical processes with observable above ground plant dynamics would greatly increase the ability to track and model GHG emissions from permafrost thaw, but current research has yet to satisfactorily develop this link. We hypothesized that seasonal patterns in peatland biogeochemistry manifests itself as observable plant phenology due to the tight coupling resulting from plant-microbial interactions. We tested this by using an automated, tower-based camera to acquire daily composite (red, green, blue) and near infrared (NIR) images of a thawing permafrost peatland site near Abisko, Sweden. The images encompassed a range of exposures which were merged into high-dynamic-range images, a novel application to remote sensing of plant phenology. The 2016 growing season camera images are accompanied by mid-to-late season CH4 and CO2 fluxes measured from soil collars, and by early-mid-late season peat core samples of the composition of microbial communities and key metabolic genes, and of the organic matter and trace gas composition of peat porewater. Additionally, nearby automated gas flux chambers measured sub-hourly fluxes of CO2 and CH4 from the peat, which will also be incorporated into analysis of relationships between seasonal camera-derived vegetation indices and gas fluxes from habitats with different vegetation types. While remote sensing is a proven method in observing plant phenology, this technology has yet to be combined with soil biogeochemical and microbial community data in regions of permafrost thaw. Establishing a high resolution phenology monitoring system linked to soil biogeochemical processes in subarctic peatlands will advance the understanding of how observable patterns in plant phenology can be used to monitor permafrost thaw and ecosystem carbon cycling.

Differences in fecal microbial metabolites and microbiota of children with autism spectrum disorders

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kang, Dae-Wook; Ilhan, Zehra Esra; Isern, Nancy G.

Evidence supporting that gut problems are linked to ASD symptoms has been accumulating both in humans and animal models of ASD. Gut microbes and their metabolites may be linked not only to GI problems but also to ASD behavior symptoms. Despite this high interest, most previous studies have looked mainly at microbial structure, and studies on fecal metabolites are rare in the context of ASD. Thus, we aimed to detect fecal metabolites that may be present at significantly different concentrations between 21 children with ASD and 23 neurotypical children and to investigate its possible link to human gut microbiome. Usingmore » 1H-NMR spectroscopy and 16S rRNA gene amplicon sequencing, we examined metabolite profiles and microbial compositions in fecal samples, respectively. Of the 59 metabolites detected, isopropanol concentrations were significantly higher in feces of children with ASD after multiple testing corrections. We also observed similar trends of fecal metabolites to previous studies; children with ASD have higher fecal p-cresol and possibly lower GABA concentrations. In addition, Fisher Discriminant Analysis (FDA) with leave-out-validation suggested that a group of metabolites-caprate, nicotinate, glutamine, thymine, and aspartate-may potentially function as a modest biomarker to separate ASD participants from the neurotypical group (78% sensitivity and 81% specificity). Consistent with our previous Arizona cohort study, we also confirmed lower gut microbial diversity and reduced relative abundances of phylotypes most closely related to Prevotella copri in children with ASD. After multiple testing corrections, we also learned that relative abundances of Feacalibacterium prausnitzii and Haemophilus parainfluenzae were lower in feces of children with ASD. In conclusion, despite a relatively short list of fecal metabolites, the data in this study support that children with ASD have altered metabolite profiles in feces when compared with neurotypical children and warrant further investigation of metabolites in larger cohorts.« less

The microbial temperature sensitivity to warming is controlled by thermal adaptation and is independent of C-quality across a pan-continental survey

NASA Astrophysics Data System (ADS)

Berglund, Eva; Rousk, Johannes

2017-04-01

Climate models predict that warming will result in an increased loss of soil organic matter (SOM). However, field experiments suggest that although warming results in an immediate increase in SOM turnover, the effect diminishes over time. Although the use and subsequent turnover of SOM is dominated by the soil microbial community, the underlying physiology underpinning warming responses are not considered in current climate models. It has been suggested that a reduction in the perceived quality of SOM to the microbial community, and changes in the microbial thermal adaptation, could be important feed-backs to soil warming. Thus, studies distinguishing between temperature relationships and how substrate quality influences microbial decomposition are a priority. We examined microbial communities and temperature sensitivities along a natural climate gradient including 56 independent samples from across Europe. The gradient included mean annual temperatures (MAT) from ca -4 to 18 ˚ C, along with wide spans of environmental factors known to influence microbial communities, such as pH (4.0 to 8.8), nutrients (C/N from 7 to 50), SOM (from 4 to 94%), and plant communities, etc. The extensive ranges of environmental conditions resulted in wide ranges of substrate quality, indexed as microbial respiration per unit SOM, from 5-150 μg CO2g-1 SOM g-1 h-1. We hypothesised microbial communities to (1) be adapted to the temperature of their climate, leading to warm adapted bacterial communities that were more temperature sensitive (higher Q10s) at higher MAT; (2) have temperature sensitivities affected by the quality of SOM, with higher Q10s for lower quality SOM. To determine the microbial use of SOM and its dependence on temperature, we characterized microbial temperature dependences of bacterial growth (leu inc), fungal growth (ac-in-erg) and soil respiration in all 56 sites. Temperature dependences were determined using brief (ca. 1-2 h at 25˚ C) laboratory incubation experiments including temperatures from 0 to 35˚ C. Temperature relationships were modelled using the Ratkowsky model, and cardinal points including minimum temperature (Tmin) for growth and respiration along with temperature sensitivity (Q10) values were used as indices to compare sites. Microbial communities were cold-adapted in cold sites and warm-adapted in warm sites, as shown by Tmin values ranging from ca. -20 ˚ C to 0 ˚ C. For every 1˚ C rise in MAT, Tmin increased by 0.22˚ C and 0.28˚ C for bacteria and fungi, respectively. Soil respiration was less dependent on MAT, increasing 0.16 ˚ C per 1˚ C. Temperature dependence analyses grew stronger when regressed against summer temperatures, and weaker when regressed against winter temperatures. Hence, microbial communities adjusted their temperature dependence for growth more than for respiration, and higher temperatures had more impact than low temperatures did. The correlation between Tmin and MAT resulted in Q10s increasing with MAT, showing that microorganisms from cold regions were less temperature sensitive than those from warmer regions. For every 1˚ C increase in MAT, Q10 increased with 0.04 and 0.03 units for bacterial and fungal growth respectively, and 0.08 units for soil respiration. In contrast to previous studies, we found no relationship between temperature sensitivity and substrate quality. We demonstrate that the strongest driver of variation in microbial temperatures sensitivities (Q10s) is the microbial adaptation to its thermal environment. Surprisingly, the quality of SOM had no influence on the temperature sensitivity. This calls for a revision of the understanding for how microbial decomposers feed-back to climate warming. Specifically, the thermal adaptation of microbial communities need to be incorporated into climate models to capture responses to warming, while the quality of SOM can be ignored.

Continental-scale distributions of dust-associated bacteria and fungi

PubMed Central

Barberán, Albert; Ladau, Joshua; Pollard, Katherine S.; Menninger, Holly L.; Dunn, Robert R.; Fierer, Noah

2015-01-01

It has been known for centuries that microorganisms are ubiquitous in the atmosphere, where they are capable of long-distance dispersal. Likewise, it is well-established that these airborne bacteria and fungi can have myriad effects on human health, as well as the health of plants and livestock. However, we have a limited understanding of how these airborne communities vary across different geographic regions or the factors that structure the geographic patterns of near-surface microbes across large spatial scales. We collected dust samples from the external surfaces of ∼1,200 households located across the United States to understand the continental-scale distributions of bacteria and fungi in the near-surface atmosphere. The microbial communities were highly variable in composition across the United States, but the geographic patterns could be explained by climatic and soil variables, with coastal regions of the United States sharing similar airborne microbial communities. Although people living in more urbanized areas were not found to be exposed to distinct outdoor air microbial communities compared with those living in more rural areas, our results do suggest that urbanization leads to homogenization of the airborne microbiota, with more urban communities exhibiting less continental-scale geographic variability than more rural areas. These results provide our first insight into the continental-scale distributions of airborne microbes, which is information that could be used to identify likely associations between microbial exposures in outdoor air and incidences of disease in crops, livestock, and humans. PMID:25902536

Aligning the Measurement of Microbial Diversity with Macroecological Theory

DOE PAGES

Stegen, James C.; Hurlbert, Allen H.; Bond-Lamberty, Ben; ...

2016-09-23

The number of microbial operational taxonomic units (OTUs) within a community is akin to species richness within plant/animal (‘macrobial’) systems. A large literature documents OTU richness patterns, drawing comparisons to macrobial theory. There is, however, an unrecognized fundamental disconnect between OTU richness and macrobial theory: OTU richness is commonly estimated on a per-individual basis, while macrobial richness is estimated per-area. Furthermore, the range or extent of sampled environmental conditions can strongly influence a study’s outcomes and conclusions, but this is not commonly addressed when studying OTU richness. Here we (i) propose a new sampling approach that estimates OTU richness per-massmore » of soil, which results in strong support for species energy theory, (ii) use data reduction to show how support for niche conservatism emerges when sampling across a restricted range of environmental conditions, and (iii) show how additional insights into drivers of OTU richness can be generated by combining different sampling methods while simultaneously considering patterns that emerge by restricting the range of environmental conditions. We propose that a more rigorous connection between microbial ecology and macrobial theory can be facilitated by exploring how changes in OTU richness units and environmental extent influence outcomes of data analysis. While fundamental differences between microbial and macrobial systems persist (e.g., species concepts), we suggest that closer attention to units and scale provide tangible and immediate improvements to our understanding of the processes governing OTU richness and how those processes relate to drivers of macrobial species richness.« less

Spartina alterniflora invasion alters soil microbial community composition and microbial respiration following invasion chronosequence in a coastal wetland of China

PubMed Central

Yang, Wen; Jeelani, Nasreen; Leng, Xin; Cheng, Xiaoli; An, Shuqing

2016-01-01

The role of exotic plants in regulating soil microbial community structure and activity following invasion chronosequence remains unclear. We investigated soil microbial community structure and microbial respiration following Spartina alterniflora invasion in a chronosequence of 6-, 10-, 17-, and 20-year-old by comparing with bare flat in a coastal wetland of China. S. alterniflora invasion significantly increased soil moisture and salinity, the concentrations of soil water-soluble organic carbon and microbial biomass carbon (MBC), the quantities of total and various types of phospholipid fatty acids (PLFAs), the fungal:bacterial PLFAs ratio and cumulative microbial respiration compared with bare flat. The highest MBC, gram-negative bacterial and saturated straight-chain PLFAs were found in 10-year-old S. alterniflora soil, while the greatest total PLFAs, bacterial and gram-positive bacterial PLFAs were found in 10- and 17-year-old S. alterniflora soils. The monounsaturated:branched PLFAs ratio declined, and cumulative microbial respiration on a per-unit-PLFAs increased following S. alterniflora invasion in the chronosequence. Our results suggest that S. alterniflora invasion significantly increased the biomass of soil various microbial groups and microbial respiration compared to bare flat soil by increasing soil available substrate, and modifying soil physiochemical properties. Soil microbial community reached the most enriched condition in the 10-year-old S. alterniflora community. PMID:27241173

The players may change but the game remains: network analyses of ruminal microbiomes suggest taxonomic differences mask functional similarity

PubMed Central

Taxis, Tasia M.; Wolff, Sara; Gregg, Sarah J.; Minton, Nicholas O.; Zhang, Chiqian; Dai, Jingjing; Schnabel, Robert D.; Taylor, Jeremy F.; Kerley, Monty S.; Pires, J. Chris; Lamberson, William R.; Conant, Gavin C.

2015-01-01

By mapping translated metagenomic reads to a microbial metabolic network, we show that ruminal ecosystems that are rather dissimilar in their taxonomy can be considerably more similar at the metabolic network level. Using a new network bi-partition approach for linking the microbial network to a bovine metabolic network, we observe that these ruminal metabolic networks exhibit properties consistent with distinct metabolic communities producing similar outputs from common inputs. For instance, the closer in network space that a microbial reaction is to a reaction found in the host, the lower will be the variability of its enzyme copy number across hosts. Similarly, these microbial enzymes that are nearby to host nodes are also higher in copy number than are more distant enzymes. Collectively, these results demonstrate a widely expected pattern that, to our knowledge, has not been explicitly demonstrated in microbial communities: namely that there can exist different community metabolic networks that have the same metabolic inputs and outputs but differ in their internal structure. PMID:26420832

Role of the microbial population on the flavor of the soft-bodied cheese Torta del Casar.

PubMed

Ordiales, Elena; Martín, Alberto; Benito, María José; Hernández, Alejandro; Ruiz-Moyano, Santiago; Córdoba, María de Guía

2013-09-01

The purpose of this work was to investigate the influence of the spontaneous microbial population on the flavor of Torta del Casar cheese. A total of 16 batches of cheeses with different microbial qualities were used. Their physicochemical and microbial characteristics were evaluated during ripening and then related with the volatile compounds, taste, and flavor properties of the finished cheeses. Acids were the most abundant volatile compounds, followed by alcohols and carbonyls. The amount of acetic acid and several alcohols were linked to cheeses with higher counts of lactic acid bacteria (LAB), whereas Enterobacteriaceae counts were associated with semivolatile fatty acids. The gram-positive catalase-positive cocci counts were correlated with esters and methyl ketones. Although the role of the LAB in the flavor development of Torta del Casar is the most relevant, other microbial groups are necessary to impart the flavor of the cheese and to minimize the possible off-flavor derived from excessive concentrations of LAB metabolites, such as acetic acid. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Plant stimulation of soil microbial community succession: how sequential expression mediates soil carbon stabilization and turnover

DOE Office of Scientific and Technical Information (OSTI.GOV)

Firestone, Mary

2015-03-31

It is now understood that most plant C is utilized or transformed by soil microorganisms en route to stabilization. Hence the composition of microbial communities that mediate decomposition and transformation of root C is critical, as are the metabolic capabilities of these communities. The change in composition and function of the C-transforming microbial communities over time in effect defines the biological component of soil C stabilization. Our research was designed to test 2 general hypotheses; the first two hypotheses are discussed first; H1: Root-exudate interactions with soil microbial populations results in the expression of enzymatic capacities for macromolecular, complex carbonmore » decomposition; and H2: Microbial communities surrounding roots undergo taxonomic succession linked to functional gene activities as roots grow, mature, and decompose in soil. Over the term of the project we made significant progress in 1) quantifying the temporal pattern of root interactions with the soil decomposing community and 2) characterizing the role of root exudates in mediating these interactions.« less

Biogeochemical Processes in Microbial Ecosystems

NASA Technical Reports Server (NTRS)

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

2001-01-01

The hierarchical organization of microbial ecosystems determines process rates that shape Earth's environment, create the biomarker sedimentary and atmospheric signatures of life and define the stage upon which major evolutionary events occurred. In order to understand how microorganisms have shaped the global environment of Earth and potentially, other worlds, we must develop an experimental paradigm that links biogeochemical processes with ever-changing temporal and spatial distributions of microbial population, and their metabolic properties. Photosynthetic microbial mats offer an opportunity to define holistic functionality at the millimeter scale. At the same time, their Biogeochemistry contributes to environmental processes on a planetary scale. These mats are possibly direct descendents of the most ancient biological communities; communities in which oxygenic photosynthesis might have been invented. Mats provide one of the best natural systems to study how microbial populations associate to control dynamic biogeochemical gradients. These are self-sustaining, complete ecosystems in which light energy absorbed over a diel (24 hour) cycle drives the synthesis of spatially-organized, diverse biomass. Tightly-coupled microorganisms in the mat have specialized metabolisms that catalyze transformations of carbon, nitrogen. sulfur, and a host of other elements.

Validated measurements of microbial loads on environmental surfaces in intensive care units before and after disinfecting cleaning.

PubMed

Frickmann, H; Bachert, S; Warnke, P; Podbielski, A

2018-03-01

Preanalytic aspects can make results of hygiene studies difficult to compare. Efficacy of surface disinfection was assessed with an evaluated swabbing procedure. A validated microbial screening of surfaces was performed in the patients' environment and from hands of healthcare workers on two intensive care units (ICUs) prior to and after a standardized disinfection procedure. From a pure culture, the recovery rate of the swabs for Staphylococcus aureus was 35%-64% and dropped to 0%-22% from a mixed culture with 10-times more Staphylococcus epidermidis than S. aureus. Microbial surface loads 30 min before and after the cleaning procedures were indistinguishable. The quality-ensured screening procedure proved that adequate hygiene procedures are associated with a low overall colonization of surfaces and skin of healthcare workers. Unchanged microbial loads before and after surface disinfection demonstrated the low additional impact of this procedure in the endemic situation when the pathogen load prior to surface disinfection is already low. Based on a validated screening system ensuring the interpretability and reliability of the results, the study confirms the efficiency of combined hand and surface hygiene procedures to guarantee low rates of bacterial colonization. © 2017 The Society for Applied Microbiology.

Lineage-specific responses of microbial communities to environmental change.

PubMed

Youngblut, Nicholas D; Shade, Ashley; Read, Jordan S; McMahon, Katherine D; Whitaker, Rachel J

2013-01-01

A great challenge facing microbial ecology is how to define ecologically relevant taxonomic units. To address this challenge, we investigated how changing the definition of operational taxonomic units (OTUs) influences the perception of ecological patterns in microbial communities as they respond to a dramatic environmental change. We used pyrosequenced tags of the bacterial V2 16S rRNA region, as well as clone libraries constructed from the cytochrome oxidase C gene ccoN, to provide additional taxonomic resolution for the common freshwater genus Polynucleobacter. At the most highly resolved taxonomic scale, we show that distinct genotypes associated with the abundant Polynucleobacter lineages exhibit divergent spatial patterns and dramatic changes over time, while the also abundant Actinobacteria OTUs are highly coherent. This clearly demonstrates that different bacterial lineages demand different taxonomic definitions to capture ecological patterns. Based on the temporal distribution of highly resolved taxa in the hypolimnion, we demonstrate that change in the population structure of a single genotype can provide additional insight into the mechanisms of community-level responses. These results highlight the importance and feasibility of examining ecological change in microbial communities across taxonomic scales while also providing valuable insight into the ecological characteristics of ecologically coherent groups in this system.

An assessment of microbial communities associated with surface mining-disturbed overburden.

PubMed

Poncelet, Dominique M; Cavender, Nicole; Cutright, Teresa J; Senko, John M

2014-03-01

To assess the microbiological changes that occur during the maturation of overburden that has been disturbed by surface mining of coal, a surface mining-disturbed overburden unit in southeastern Ohio, USA was characterized. Overburden from the same unit that had been disturbed for 37 and 16 years were compared to undisturbed soil from the same region. Overburden and soil samples were collected as shallow subsurface cores from each subregion of the mined area (i.e., land 16 years and 37 years post-mining, and unmined land). Chemical and mineralogical characteristics of overburden samples were determined, as were microbial respiration rates. The composition of microbial communities associated with overburden and soil were determined using culture-independent, nucleic acid-based approaches. Chemical and mineralogical evaluation of overburden suggested that weathering of disturbed overburden gave rise to a setting with lower pH and more oxidized chemical constituents. Overburden-associated microbial biomass and respiration rates increased with time after overburden disturbance. Evaluation of 16S rRNA gene libraries that were produced by "next-generation" sequencing technology revealed that recently disturbed overburden contained an abundance of phylotypes attributable to sulfur-oxidizing Limnobacter spp., but with increasing time post-disturbance, overburden-associated microbial communities developed a structure similar to that of undisturbed soil, but retained characteristics of more recently disturbed overburden. Our results indicate that over time, the biogeochemical weathering of disturbed overburden leads to the development of geochemical conditions and microbial communities that approximate those of undisturbed soil, but that this transition is incomplete after 37 years of overburden maturation.

Linking Metabolic Activity, Microbial Identity, and Microscale Spatial Arrangements in Chemosynthetic Seafloor Habitats

NASA Astrophysics Data System (ADS)

Marlow, J.; Hatzenpichler, R.; Girguis, P.

2018-05-01

With an innovative combination of metabolic tracers, fluorescent probes, and microscopy, we present a novel way to pinpoint the geobiological drivers of metabolic activity at silicate and carbonate-based chemosynthetic seafloor habitats.

Bacterial community dynamics are linked to patterns of coral heat tolerance

NASA Astrophysics Data System (ADS)

Ziegler, Maren; Seneca, Francois O.; Yum, Lauren K.; Palumbi, Stephen R.; Voolstra, Christian R.

2017-02-01

Ocean warming threatens corals and the coral reef ecosystem. Nevertheless, corals can be adapted to their thermal environment and inherit heat tolerance across generations. In addition, the diverse microbes that associate with corals have the capacity for more rapid change, potentially aiding the adaptation of long-lived corals. Here, we show that the microbiome of reef corals is different across thermally variable habitats and changes over time when corals are reciprocally transplanted. Exposing these corals to thermal bleaching conditions changes the microbiome for heat-sensitive corals, but not for heat-tolerant corals growing in habitats with natural high heat extremes. Importantly, particular bacterial taxa predict the coral host response in a short-term heat stress experiment. Such associations could result from parallel responses of the coral and the microbial community to living at high natural temperatures. A competing hypothesis is that the microbial community and coral heat tolerance are causally linked.

Host-microbiota interactions: Epigenomic regulation

PubMed Central

Woo, Vivienne; Alenghat, Theresa

2016-01-01

The coevolution of mammalian hosts and their commensal microbiota has led to the development of complex symbiotic relationships between resident microbes and mammalian cells. Epigenomic modifications enable host cells to alter gene expression without modifying the genetic code, and therefore represent potent mechanisms by which mammalian cells can transcriptionally respond, transiently or stably, to environmental cues. Advances in genome-wide approaches are accelerating our appreciation of microbial influences on host physiology, and increasing evidence highlights that epigenomics represent a level of regulation by which the host integrates and responds to microbial signals. In particular, bacterial-derived short chain fatty acids have emerged as one clear link between how the microbiota intersects with host epigenomic pathways. Here we review recent findings describing crosstalk between the microbiota and epigenomic pathways in multiple mammalian cell populations. Further, we discuss interesting links that suggest that the scope of our understanding of epigenomic regulation in the host-microbiota relationship is still in its infancy. PMID:28103497

Compositional Changes and Baking Performance of Rye Dough As Affected by Microbial Transglutaminase and Xylanase.

PubMed

Grossmann, Isabel; Döring, Clemens; Jekle, Mario; Becker, Thomas; Koehler, Peter

2016-07-20

Doughs supplemented with endoxylanase (XYL) and varying amounts of microbial transglutaminase (TG) were analyzed by sequential protein extraction, quantitation of protein fractions and protein types, and determination of water-extractable arabinoxylans. With increasing TG activity, the concentration of prolamins and glutelins decreased and increased, respectively, and the prolamin-to-glutelin ratio strongly declined. The overall amount of extractable protein decreased with increasing TG level showing that cross-linking by TG provided high-molecular-weight protein aggregates. The decrease of the high-molecular-weight arabinoxylan fraction and the concurrent increase of the medium-molecular-weight fraction confirmed the degradation of arabinoxylans by XYL. However, XYL addition did not lead to significant improved cross-linking of rye proteins by TG. Volume and crumb hardness measurements of bread showed increased protein connectivity induced by XYL and TG. Significant positive effects on the final bread quality were especially obtained by XYL addition.

Complete structure of the cell surface polysaccharide of Streptococcus oralis C104: A 600-MHz NMR study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Abeygunawardana, C.; Bush, C.A.; Cisar, J.O.

1991-09-03

Specific lectin-carbohydrate interactions between certain oral streptococci and actinomyces contribute to the microbial colonization of teeth. The receptor molecules of Streptococcus oralis, 34, ATCC 10557, and Streptococcus mitis J22 for the galactose and N-acetylgalactosamine reactive fimbrial lectins of Actinomyces viscosus and Actinomyces naeslundii are antigenically distinct polysaccharides, each formed by a different phosphodiester-linked oligosaccharide repeating unit. Receptor polysaccharide was isolated form S. oralis C104 cells and was shown to contain galactose, N-acetylgalactosamine, ribitol, and phosphate with molar ratios of 4:1:1:1. The {sup 1}H NMR spectrum of the polysaccharide shows that it contains a repeating structure. The individual sugars in themore » repeating unit were identified by {sup 1}H coupling constants observed in E-COSY and DQF-COSY spectra. NMR methods included complete resonance assignments ({sup 1}H and {sup 13}C) by various homonuclear and heteronuclear correlation experiments that utilize scalar couplings. Sequence and linkage assignments were obtained from the heteronuclear multiple-bond correlation (HMBC) spectrum. This analysis shows that the receptor polysaccharide of S. oralis C104 is a ribitol teichoic acid polymer composed of a linear hexasaccharide repeating unit containing two residues each of galactopyranose and galactofuranose and a residue each of GalNAc and ribitol joined end to end by phosphodiester linkages.« less

Modeling microbial survival in buildup biofilm for complex medical devices

PubMed Central

2009-01-01

Background Flexible endoscopes undergo repeated rounds of patient-use and reprocessing. Some evidence indicates that there is an accumulation or build-up of organic material that occurs over time in endoscope channels. This "buildup biofilm" (BBF) develops as a result of cyclical exposure to wet and dry phases during usage and reprocessing. This study investigated whether the BBF matrix represents a greater challenge to disinfectant efficacy and microbial eradication than traditional biofilm (TBF), which forms when a surface is constantly bathed in fluid. Methods Using the MBEC (Minimum Biofilm Eradication Concentration) system, a unique modelling approach was developed to evaluate microbial survival in BBF formed by repetitive cycles of drying, disinfectant exposure and re-exposure to the test organism. This model mimics the cumulative effect of the reprocessing protocol on flexible endoscopes. Glutaraldehyde (GLUT) and accelerated hydrogen peroxide (AHP) were evaluated to assess the killing of microbes in TBF and BBF. Results The data showed that the combination of an organic matrix and aldehyde disinfection quickly produced a protective BBF that facilitated high levels of organism survival. In cross-linked BBF formed under high nutrient conditions the maximum colony forming units (CFU) reached ~6 Log10 CFU/peg. However, if an oxidizing agent was used for disinfection and if organic levels were kept low, organism survival did not occur. A key finding was that once established, the microbial load of BBF formed by GLUT exposure had a faster rate of accumulation than in TBF. The rate of biofilm survival post high-level disinfection (HLD) determined by the maximum Log10CFU/initial Log10CFU for E. faecalis and P. aeruginosa in BBF was 10 and 8.6 respectively; significantly different compared to a survival rate in TBF of ~2 for each organism. Data from indirect outgrowth testing demonstrated for the first time that there is organism survival in the matrix. Both TBF and BBF had surviving organisms when GLUT was used. For AHP survival was seen less frequently in BBF than in TBF. Conclusion This BBF model demonstrated for the first time that survival of a wide range of microorganisms does occur in BBF, with significantly more rapid outgrowth compared to TBF. This is most pronounced when GLUT is used compared to AHP. The data supports the need for meticulous cleaning of reprocessed endoscopes since the presence of organic material and microorganisms prevents effective disinfection when GLUT and AHP are used. However, cross-linking agents like GLUT are not as effective when there is BBF. The data from the MBEC model of BBF suggest that for flexible endoscopes that are repeatedly used and reprocessed, the assurance of effective high-level disinfection may decrease if BBF develops within the channels. PMID:19426471

DOE Office of Scientific and Technical Information (OSTI.GOV)

Song, Hyun -Seob; Renslow, Ryan S.; Fredrickson, Jim K.

We note that many definitions of resilience have been proffered for natural and engineered ecosystems, but a conceptual consensus on resilience in microbial communities is still lacking. Here, we argue that the disconnect largely results from the wide variance in microbial community complexity, which range from simple synthetic consortia to complex natural communities, and divergence between the typical practical outcomes emphasized by ecologists and engineers. Viewing microbial communities as elasto-plastic systems, we argue that this gap between the engineering and ecological definitions of resilience stems from their respective emphases on elastic and plastic deformation, respectively. We propose that the twomore » concepts may be fundamentally united around the resilience of function rather than state in microbial communities and the regularity in the relationship between environmental variation and a community’s functional response. Furthermore, we posit that functional resilience is an intrinsic property of microbial communities, suggesting that state changes in response to environmental variation may be a key mechanism driving resilience in microbial communities.« less

Alterations in soil microbial community composition and biomass following agricultural land use change.

PubMed

Zhang, Qian; Wu, Junjun; Yang, Fan; Lei, Yao; Zhang, Quanfa; Cheng, Xiaoli

2016-11-04

The effect of agricultural land use change on soil microbial community composition and biomass remains a widely debated topic. Here, we investigated soil microbial community composition and biomass [e.g., bacteria (B), fungi (F), Arbuscular mycorrhizal fungi (AMF) and Actinomycete (ACT)] using phospholipid fatty acids (PLFAs) analysis, and basal microbial respiration in afforested, cropland and adjacent uncultivated soils in central China. We also investigated soil organic carbon and nitrogen (SOC and SON), labile carbon and nitrogen (LC and LN), recalcitrant carbon and nitrogen (RC and RN), pH, moisture, and temperature. Afforestation averaged higher microbial PLFA biomass compared with cropland and uncultivated soils with higher values in top soils than deep soils. The microbial PLFA biomass was strongly correlated with SON and LC. Higher SOC, SON, LC, LN, moisture and lower pH in afforested soils could be explained approximately 87.3% of total variation of higher total PLFAs. Afforestation also enhanced the F: B ratios compared with cropland. The basal microbial respiration was higher while the basal microbial respiration on a per-unit-PLFA basis was lower in afforested land than adjacent cropland and uncultivated land, suggesting afforestation may increase soil C utilization efficiency and decrease respiration loss in afforested soils.

Alterations in soil microbial community composition and biomass following agricultural land use change

NASA Astrophysics Data System (ADS)

Zhang, Qian; Wu, Junjun; Yang, Fan; Lei, Yao; Zhang, Quanfa; Cheng, Xiaoli

2016-11-01

The effect of agricultural land use change on soil microbial community composition and biomass remains a widely debated topic. Here, we investigated soil microbial community composition and biomass [e.g., bacteria (B), fungi (F), Arbuscular mycorrhizal fungi (AMF) and Actinomycete (ACT)] using phospholipid fatty acids (PLFAs) analysis, and basal microbial respiration in afforested, cropland and adjacent uncultivated soils in central China. We also investigated soil organic carbon and nitrogen (SOC and SON), labile carbon and nitrogen (LC and LN), recalcitrant carbon and nitrogen (RC and RN), pH, moisture, and temperature. Afforestation averaged higher microbial PLFA biomass compared with cropland and uncultivated soils with higher values in top soils than deep soils. The microbial PLFA biomass was strongly correlated with SON and LC. Higher SOC, SON, LC, LN, moisture and lower pH in afforested soils could be explained approximately 87.3% of total variation of higher total PLFAs. Afforestation also enhanced the F: B ratios compared with cropland. The basal microbial respiration was higher while the basal microbial respiration on a per-unit-PLFA basis was lower in afforested land than adjacent cropland and uncultivated land, suggesting afforestation may increase soil C utilization efficiency and decrease respiration loss in afforested soils.

Ecological Patterns Among Bacteria and Microbial Eukaryotes Derived from Network Analyses in a Low-Salinity Lake.

PubMed

Jones, Adriane Clark; Hambright, K David; Caron, David A

2018-05-01

Microbial communities are comprised of complex assemblages of highly interactive taxa. We employed network analyses to identify and describe microbial interactions and co-occurrence patterns between microbial eukaryotes and bacteria at two locations within a low salinity (0.5-3.5 ppt) lake over an annual cycle. We previously documented that the microbial diversity and community composition within Lake Texoma, southwest USA, were significantly affected by both seasonal forces and a site-specific bloom of the harmful alga, Prymnesium parvum. We used network analyses to answer ecological questions involving both the bacterial and microbial eukaryotic datasets and to infer ecological relationships within the microbial communities. Patterns of connectivity at both locations reflected the seasonality of the lake including a large rain disturbance in May, while a comparison of the communities between locations revealed a localized response to the algal bloom. A network built from shared nodes (microbial operational taxonomic units and environmental variables) and correlations identified conserved associations at both locations within the lake. Using network analyses, we were able to detect disturbance events, characterize the ecological extent of a harmful algal bloom, and infer ecological relationships not apparent from diversity statistics alone.

Climate shapes the protein abundance of dominant soil bacteria.

PubMed

Bastida, Felipe; Crowther, Tom W; Prieto, Iván; Routh, Devin; García, Carlos; Jehmlich, Nico

2018-05-28

Sensitive models of climate change impacts would require a better integration of multi-omics approaches that connect the abundance and activity of microbial populations. Here, we show that climate is a fundamental driver of the protein abundance of Actinobacteria, Planctomycetes and Proteobacteria, supporting the hypothesis that metabolic activity of some dominant phyla may be closely linked to climate. These results may improve our capacity to construct microbial models that better predict the impact of climate change in ecosystem processes. Copyright © 2018 Elsevier B.V. All rights reserved.

Lipid Biomarkers for a Hypersaline Microbial Mat Community

NASA Technical Reports Server (NTRS)

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

2003-01-01

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

Long-term balanced fertilization increases the soil microbial functional diversity in a phosphorus-limited paddy soil.

PubMed

Su, Jian-Qiang; Ding, Long-Jun; Xue, Kai; Yao, Huai-Ying; Quensen, John; Bai, Shi-Jie; Wei, Wen-Xue; Wu, Jin-Shui; Zhou, Jizhong; Tiedje, James M; Zhu, Yong-Guan

2015-01-01

The influence of long-term chemical fertilization on soil microbial communities has been one of the frontier topics of agricultural and environmental sciences and is critical for linking soil microbial flora with soil functions. In this study, 16S rRNA gene pyrosequencing and a functional gene array, geochip 4.0, were used to investigate the shifts in microbial composition and functional gene structure in paddy soils with different fertilization treatments over a 22-year period. These included a control without fertilizers; chemical nitrogen fertilizer (N); N and phosphate (NP); N and potassium (NK); and N, P and K (NPK). Based on 16S rRNA gene data, both species evenness and key genera were affected by P fertilization. Functional gene array-based analysis revealed that long-term fertilization significantly changed the overall microbial functional structures. Chemical fertilization significantly increased the diversity and abundance of most genes involved in C, N, P and S cycling, especially for the treatments NK and NPK. Significant correlations were found among functional gene structure and abundance, related soil enzymatic activities and rice yield, suggesting that a fertilizer-induced shift in the microbial community may accelerate the nutrient turnover in soil, which in turn influenced rice growth. The effect of N fertilization on soil microbial functional genes was mitigated by the addition of P fertilizer in this P-limited paddy soil, suggesting that balanced chemical fertilization is beneficial to the soil microbial community and its functions. © 2014 John Wiley & Sons Ltd.

The Inter-Valley Soil Comparative Survey: the ecology of Dry Valley edaphic microbial communities

PubMed Central

Lee, Charles K; Barbier, Béatrice A; Bottos, Eric M; McDonald, Ian R; Cary, Stephen Craig

2012-01-01

Recent applications of molecular genetics to edaphic microbial communities of the McMurdo Dry Valleys and elsewhere have rejected a long-held belief that Antarctic soils contain extremely limited microbial diversity. The Inter-Valley Soil Comparative Survey aims to elucidate the factors shaping these unique microbial communities and their biogeography by integrating molecular genetic approaches with biogeochemical analyses. Although the microbial communities of Dry Valley soils may be complex, there is little doubt that the ecosystem's food web is relatively simple, and evidence suggests that physicochemical conditions may have the dominant role in shaping microbial communities. To examine this hypothesis, bacterial communities from representative soil samples collected in four geographically disparate Dry Valleys were analyzed using molecular genetic tools, including pyrosequencing of 16S rRNA gene PCR amplicons. Results show that the four communities are structurally and phylogenetically distinct, and possess significantly different levels of diversity. Strikingly, only 2 of 214 phylotypes were found in all four valleys, challenging a widespread assumption that the microbiota of the Dry Valleys is composed of a few cosmopolitan species. Analysis of soil geochemical properties indicated that salt content, alongside altitude and Cu2+, was significantly correlated with differences in microbial communities. Our results indicate that the microbial ecology of Dry Valley soils is highly localized and that physicochemical factors potentially have major roles in shaping the microbiology of ice-free areas of Antarctica. These findings hint at links between Dry Valley glacial geomorphology and microbial ecology, and raise previously unrecognized issues related to environmental management of this unique ecosystem. PMID:22170424

A communal catalogue reveals Earth's multiscale microbial diversity.

PubMed

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

2017-11-23

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

Microbial succession and stimulation following a test well injection simulating CO2 leakage into shallow Newark Basin aquifers

NASA Astrophysics Data System (ADS)

Dueker, M.; Clauson, K.; Yang, Q.; Umemoto, K.; Seltzer, A. M.; Zakharova, N. V.; Matter, J. M.; Stute, M.; Takahashi, T.; Goldberg, D.; O'Mullan, G. D.

2012-12-01

Despite growing appreciation for the importance of microbes in altering geochemical reactions in the subsurface, the microbial response to geological carbon sequestration injections and the role of microbes in altering metal mobilization following leakage scenarios in shallow aquifers remain poorly constrained. A Newark Basin test well was utilized in field experiments to investigate patterns of microbial succession following injection of CO2 saturated water into isolated aquifer intervals. Additionally, laboratory mesocosm experiments, including microbially-active and inactive (autoclave sterilized) treatments, were used to constrain the microbial role in mineral dissolution, trace metal release, and gas production (e.g. hydrogen and methane). Hydrogen production was detected in both sterilized and unsterilized laboratory mesocosm treatments, indicating abiotic hydrogen production may occur following CO2 leakage, and methane production was detected in unsterilized, microbially active mesocosms. In field experiments, a decrease in pH following injection of CO2 saturated aquifer water was accompanied by mobilization of trace elements (e.g. Fe and Mn), the production of hydrogen gas, and increased bacterial cell concentrations. 16S ribosomal RNA clone libraries, from samples collected before and after the test well injection, were compared in an attempt to link variability in geochemistry to changes in aquifer microbiology. Significant changes in microbial composition, compared to background conditions, were found following the test well injection, including a decrease in Proteobacteria, and an increased presence of Firmicutes, Verrucomicrobia, Acidobacteria and other microbes associated with iron reducing and syntrophic metabolism. The concurrence of increased microbial cell concentration, and rapid microbial community succession, with increased concentrations of hydrogen gas suggests that abiotically produced hydrogen may serve as an ecologically-relevant energy source stimulating changes in aquifer microbial communities immediately following CO2 leakage.

Microbial Life in Soil - Linking Biophysical Models with Observations

NASA Astrophysics Data System (ADS)

Or, Dani; Tecon, Robin; Ebrahimi, Ali; Kleyer, Hannah; Ilie, Olga; Wang, Gang

2015-04-01

Microbial life in soil occurs within fragmented aquatic habitats formed in complex pore spaces where motility is restricted to short hydration windows (e.g., following rainfall). The limited range of self-dispersion and physical confinement promote spatial association among trophically interdepended microbial species. Competition and preferences for different nutrient resources and byproducts and their diffusion require high level of spatial organization to sustain the functioning of multispecies communities. We report mechanistic modeling studies of competing multispecies microbial communities grown on hydrated surfaces and within artificial soil aggregates (represented by 3-D pore network). Results show how trophic dependencies and cell-level interactions within patchy diffusion fields promote spatial self-organization of motile microbial cells. The spontaneously forming patterns of segregated, yet coexisting species were robust to spatial heterogeneities and to temporal perturbations (hydration dynamics), and respond primarily to the type of trophic dependencies. Such spatially self-organized consortia may reflect ecological templates that optimize substrate utilization and could form the basic architecture for more permanent surface-attached microbial colonies. Hydration dynamics affect structure and spatial arrangement of aerobic and anaerobic microbial communities and their biogeochemical functions. Experiments with well-characterized artificial soil microbial assemblies grown on porous surfaces provide access to community dynamics during wetting and drying cycles detected through genetic fingerprinting. Experiments for visual observations of spatial associations of tagged bacterial species with known trophic dependencies on model porous surfaces are underway. Biophysical modeling provide a means for predicting hydration-mediated critical separation distances for activation of spatial self-organization. The study provides new modeling and observational tools that enable new mechanistic insights into how differences in substrate affinities among microbial species and soil micro-hydrological conditions may give rise to a remarkable spatial and functional order in an extremely heterogeneous soil microbial world

Microbial Life in Soil - Linking Biophysical Models with Observations

NASA Astrophysics Data System (ADS)

Or, D.; Tecon, R.; Ebrahimi, A.; Kleyer, H.; Ilie, O.; Wang, G.

2014-12-01

Microbial life in soil occurs within fragmented aquatic habitats in complex pore spaces where motility is restricted to short hydration windows (e.g., following rainfall). The limited range of self-dispersion and physical confinement promote spatial association among trophically interdepended microbial species. Competition and preferences for different nutrient resources and byproducts and their diffusion require high level of spatial organization to sustain the functioning of multispecies communities. We report mechanistic modeling studies of competing multispecies microbial communities grown on hydrated surfaces and within artificial soil aggregates (represented by 3-D pore network). Results show how trophic dependencies and cell-level interactions within patchy diffusion fields promote spatial self-organization of motile microbial cells. The spontaneously forming patterns of segregated, yet coexisting species were robust to spatial heterogeneities and to temporal perturbations (hydration dynamics), and respond primarily to the type of trophic dependencies. Such spatially self-organized consortia may reflect ecological templates that optimize substrate utilization and could form the basic architecture for more permanent surface-attached microbial colonies. Hydration dynamics affect structure and spatial arrangement of aerobic and anaerobic microbial communities and their biogeochemical functions. Experiments with well-characterized artificial soil microbial assemblies grown on porous surfaces provide access to community dynamics during wetting and drying cycles detected through genetic fingerprinting. Experiments for visual observations of spatial associations of tagged bacterial species with known trophic dependencies on model porous surfaces are underway. Biophysical modeling provide a means for predicting hydration-mediated critical separation distances for activation of spatial self-organization. The study provides new modeling and observational tools that enable new mechanistic insights into how differences in substrate affinities among microbial species and soil micro-hydrological conditions may give rise to a remarkable spatial and functional order in an extremely heterogeneous soil microbial world.

Inferring Intra-Community Microbial Interaction Patterns from Metagenomic Datasets Using Associative Rule Mining Techniques

PubMed Central

Mande, Sharmila S.

2016-01-01

The nature of inter-microbial metabolic interactions defines the stability of microbial communities residing in any ecological niche. Deciphering these interaction patterns is crucial for understanding the mode/mechanism(s) through which an individual microbial community transitions from one state to another (e.g. from a healthy to a diseased state). Statistical correlation techniques have been traditionally employed for mining microbial interaction patterns from taxonomic abundance data corresponding to a given microbial community. In spite of their efficiency, these correlation techniques can capture only 'pair-wise interactions'. Moreover, their emphasis on statistical significance can potentially result in missing out on several interactions that are relevant from a biological standpoint. This study explores the applicability of one of the earliest association rule mining algorithm i.e. the 'Apriori algorithm' for deriving 'microbial association rules' from the taxonomic profile of given microbial community. The classical Apriori approach derives association rules by analysing patterns of co-occurrence/co-exclusion between various '(subsets of) features/items' across various samples. Using real-world microbiome data, the efficiency/utility of this rule mining approach in deciphering multiple (biologically meaningful) association patterns between 'subsets/subgroups' of microbes (constituting microbiome samples) is demonstrated. As an example, association rules derived from publicly available gut microbiome datasets indicate an association between a group of microbes (Faecalibacterium, Dorea, and Blautia) that are known to have mutualistic metabolic associations among themselves. Application of the rule mining approach on gut microbiomes (sourced from the Human Microbiome Project) further indicated similar microbial association patterns in gut microbiomes irrespective of the gender of the subjects. A Linux implementation of the Association Rule Mining (ARM) software (customised for deriving 'microbial association rules' from microbiome data) is freely available for download from the following link: http://metagenomics.atc.tcs.com/arm. PMID:27124399

The Impact of Climate Change on Microbial Communities and Carbon Cycling in High Arctic Permafrost Soil from Spitsbergen, Northern Norway

NASA Astrophysics Data System (ADS)

de Leon, K. C.; Schwery, D.; Yoshikawa, K.; Christiansen, H. H.; Pearce, D.

2014-12-01

Permafrost-affected soils are among the most fragile ecosystems in which current microbial controls on organic matter decomposition are changing as a result of climate change. Warmer conditions in the high Arctic will lead to a deepening of the seasonal active layer of permafrost, provoking changes in microbial processes and possibly resulting in exacerbated carbon degradation under increasing anoxic conditions. The viable and non-viable fractions of the microbial community in a permafrost soil from Adventdalen, Spitsbergen, Norway were subjected to a comprehensive investigation using culture-dependent and culture-independent methods. Molecular analyses using FISH (with CTC-DAPI) and amplified rDNA restriction analysis (ARDRA) on a 257cm deep core, revealed the presence of all major microbial soil groups, with the active layer having more viable cells, and a higher microbial community diversity. Carbon dioxide (CO2) and methane (CH4) flux measurements were performed to show the amount of C stored in the sample. We demonstrated that the microbial community composition from the soil in the center of the core was most likely influenced by small scale variations in environmental conditions. Community structure showed distinct shift of presence of bacterial groups along the vertical temperature gradient profile and microbial counts and diversity was found to be highest in the surface layers, decreasing with depth. It was observed that soil properties driving microbial diversity and functional potential varied across the permafrost table. Data on the variability of CO2 and CH4 distribution described in peat structure heterogeneity are important for modeling emissions on a larger scale. Furthermore, linking microbial biomass to gas distribution may elucidate the cause of peak CO2 and CH4 and their changes in relation to environmental change and peat composition.

Cross-Site Soil Microbial Communities under Tillage Regimes: Fungistasis and Microbial Biomarkers

PubMed Central

Yrjälä, Kim; Alakukku, Laura; Palojärvi, Ansa

2012-01-01

The exploitation of soil ecosystem services by agricultural management strategies requires knowledge of microbial communities in different management regimes. Crop cover by no-till management protects the soil surface, reducing the risk of erosion and nutrient leaching, but might increase straw residue-borne and soilborne plant-pathogenic fungi. A cross-site study of soil microbial communities and Fusarium fungistasis was conducted on six long-term agricultural fields with no-till and moldboard-plowed treatments. Microbial communities were studied at the topsoil surface (0 to 5 cm) and bottom (10 to 20 cm) by general bacterial and actinobacterial terminal restriction fragment length polymorphism (T-RFLP) and phospholipid fatty acid (PLFA) analyses. Fusarium culmorum soil fungistasis describing soil receptivity to plant-pathogenic fungi was explored by using the surface layer method. Soil depth had a significant impact on general bacterial as well as actinobacterial communities and PLFA profiles in no-till treatment, with a clear spatial distinction of communities (P < 0.05), whereas the depth-related separation of microbial communities was not observed in plowed fields. The fungal biomass was higher in no-till surface soil than in plowed soil (P < 0.07). Soil total microbial biomass and fungal biomass correlated with fungistasis (P < 0.02 for the sum of PLFAs; P < 0.001 for PLFA 18:2ω6). Our cross-site study demonstrated that agricultural management strategies can have a major impact on soil microbial community structures, indicating that it is possible to influence the soil processes with management decisions. The interactions between plant-pathogenic fungi and soil microbial communities are multifaceted, and a high level of fungistasis could be linked to the high microbial biomass in soil but not to the specific management strategy. PMID:22983972

Inferring Intra-Community Microbial Interaction Patterns from Metagenomic Datasets Using Associative Rule Mining Techniques.

PubMed

Tandon, Disha; Haque, Mohammed Monzoorul; Mande, Sharmila S

2016-01-01

The nature of inter-microbial metabolic interactions defines the stability of microbial communities residing in any ecological niche. Deciphering these interaction patterns is crucial for understanding the mode/mechanism(s) through which an individual microbial community transitions from one state to another (e.g. from a healthy to a diseased state). Statistical correlation techniques have been traditionally employed for mining microbial interaction patterns from taxonomic abundance data corresponding to a given microbial community. In spite of their efficiency, these correlation techniques can capture only 'pair-wise interactions'. Moreover, their emphasis on statistical significance can potentially result in missing out on several interactions that are relevant from a biological standpoint. This study explores the applicability of one of the earliest association rule mining algorithm i.e. the 'Apriori algorithm' for deriving 'microbial association rules' from the taxonomic profile of given microbial community. The classical Apriori approach derives association rules by analysing patterns of co-occurrence/co-exclusion between various '(subsets of) features/items' across various samples. Using real-world microbiome data, the efficiency/utility of this rule mining approach in deciphering multiple (biologically meaningful) association patterns between 'subsets/subgroups' of microbes (constituting microbiome samples) is demonstrated. As an example, association rules derived from publicly available gut microbiome datasets indicate an association between a group of microbes (Faecalibacterium, Dorea, and Blautia) that are known to have mutualistic metabolic associations among themselves. Application of the rule mining approach on gut microbiomes (sourced from the Human Microbiome Project) further indicated similar microbial association patterns in gut microbiomes irrespective of the gender of the subjects. A Linux implementation of the Association Rule Mining (ARM) software (customised for deriving 'microbial association rules' from microbiome data) is freely available for download from the following link: http://metagenomics.atc.tcs.com/arm.

Energy, ecology and the distribution of microbial life.

PubMed

Macalady, Jennifer L; Hamilton, Trinity L; Grettenberger, Christen L; Jones, Daniel S; Tsao, Leah E; Burgos, William D

2013-07-19

Mechanisms that govern the coexistence of multiple biological species have been studied intensively by ecologists since the turn of the nineteenth century. Microbial ecologists in the meantime have faced many fundamental challenges, such as the lack of an ecologically coherent species definition, lack of adequate methods for evaluating population sizes and community composition in nature, and enormous taxonomic and functional diversity. The accessibility of powerful, culture-independent molecular microbiology methods offers an opportunity to close the gap between microbial science and the main stream of ecological theory, with the promise of new insights and tools needed to meet the grand challenges humans face as planetary engineers and galactic explorers. We focus specifically on resources related to energy metabolism because of their direct links to elemental cycling in the Earth's history, engineering applications and astrobiology. To what extent does the availability of energy resources structure microbial communities in nature? Our recent work on sulfur- and iron-oxidizing autotrophs suggests that apparently subtle variations in the concentration ratios of external electron donors and acceptors select for different microbial populations. We show that quantitative knowledge of microbial energy niches (population-specific patterns of energy resource use) can be used to predict variations in the abundance of specific taxa in microbial communities. Furthermore, we propose that resource ratio theory applied to micro-organisms will provide a useful framework for identifying how environmental communities are organized in space and time.

Energy, ecology and the distribution of microbial life

PubMed Central

Macalady, Jennifer L.; Hamilton, Trinity L.; Grettenberger, Christen L.; Jones, Daniel S.; Tsao, Leah E.; Burgos, William D.

2013-01-01

Mechanisms that govern the coexistence of multiple biological species have been studied intensively by ecologists since the turn of the nineteenth century. Microbial ecologists in the meantime have faced many fundamental challenges, such as the lack of an ecologically coherent species definition, lack of adequate methods for evaluating population sizes and community composition in nature, and enormous taxonomic and functional diversity. The accessibility of powerful, culture-independent molecular microbiology methods offers an opportunity to close the gap between microbial science and the main stream of ecological theory, with the promise of new insights and tools needed to meet the grand challenges humans face as planetary engineers and galactic explorers. We focus specifically on resources related to energy metabolism because of their direct links to elemental cycling in the Earth's history, engineering applications and astrobiology. To what extent does the availability of energy resources structure microbial communities in nature? Our recent work on sulfur- and iron-oxidizing autotrophs suggests that apparently subtle variations in the concentration ratios of external electron donors and acceptors select for different microbial populations. We show that quantitative knowledge of microbial energy niches (population-specific patterns of energy resource use) can be used to predict variations in the abundance of specific taxa in microbial communities. Furthermore, we propose that resource ratio theory applied to micro-organisms will provide a useful framework for identifying how environmental communities are organized in space and time. PMID:23754819

Decreased plant productivity resulting from plant group removal experiment constrains soil microbial functional diversity.

PubMed

Zhang, Ximei; Johnston, Eric R; Barberán, Albert; Ren, Yi; Lü, Xiaotao; Han, Xingguo

2017-10-01

Anthropogenic environmental changes are accelerating the rate of biodiversity loss on Earth. Plant diversity loss is predicted to reduce soil microbial diversity primarily due to the decreased variety of carbon/energy resources. However, this intuitive hypothesis is supported by sparse empirical evidence, and most underlying mechanisms remain underexplored or obscure altogether. We constructed four diversity gradients (0-3) in a five-year plant functional group removal experiment in a steppe ecosystem in Inner Mongolia, China, and quantified microbial taxonomic and functional diversity with shotgun metagenome sequencing. The treatments had little effect on microbial taxonomic diversity, but were found to decrease functional gene diversity. However, the observed decrease in functional gene diversity was more attributable to a loss in plant productivity, rather than to the loss of any individual plant functional group per se. Reduced productivity limited fresh plant resources supplied to microorganisms, and thus, intensified the pressure of ecological filtering, favoring genes responsible for energy production/conversion, material transport/metabolism and amino acid recycling, and accordingly disfavored many genes with other functions. Furthermore, microbial respiration was correlated with the variation in functional composition but not taxonomic composition. Overall, the amount of carbon/energy resources driving microbial gene diversity was identified to be the critical linkage between above- and belowground communities, contrary to the traditional framework of linking plant clade/taxonomic diversity to microbial taxonomic diversity. © 2017 John Wiley & Sons Ltd.

Quantitative microbial faecal source tracking with sampling guided by hydrological catchment dynamics.

PubMed

Reischer, G H; Haider, J M; Sommer, R; Stadler, H; Keiblinger, K M; Hornek, R; Zerobin, W; Mach, R L; Farnleitner, A H

2008-10-01

The impairment of water quality by faecal pollution is a global public health concern. Microbial source tracking methods help to identify faecal sources but the few recent quantitative microbial source tracking applications disregarded catchment hydrology and pollution dynamics. This quantitative microbial source tracking study, conducted in a large karstic spring catchment potentially influenced by humans and ruminant animals, was based on a tiered sampling approach: a 31-month water quality monitoring (Monitoring) covering seasonal hydrological dynamics and an investigation of flood events (Events) as periods of the strongest pollution. The detection of a ruminant-specific and a human-specific faecal Bacteroidetes marker by quantitative real-time PCR was complemented by standard microbiological and on-line hydrological parameters. Both quantitative microbial source tracking markers were detected in spring water during Monitoring and Events, with preponderance of the ruminant-specific marker. Applying multiparametric analysis of all data allowed linking the ruminant-specific marker to general faecal pollution indicators, especially during Events. Up to 80% of the variation of faecal indicator levels during Events could be explained by ruminant-specific marker levels proving the dominance of ruminant faecal sources in the catchment. Furthermore, soil was ruled out as a source of quantitative microbial source tracking markers. This study demonstrates the applicability of quantitative microbial source tracking methods and highlights the prerequisite of considering hydrological catchment dynamics in source tracking study design.

Microbial Condition of Water Samples from Foreign Fuel Storage Facilities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Berry, C.J.; Fliermans, C.B.; Santo Domingo, J.

1997-10-30

In order to assess the microbial condition of foreign nuclear fuel storage facilities, fourteen different water samples were received from facilities outside the United States that have sent spent nuclear fuel to SRS for wet storage. Each water sample was analyzed for microbial content and activity as determined by total bacteria, viable aerobic bacteria, viable anaerobic bacteria, viable sulfate- reducing bacteria, viable acid-producing bacteria and enzyme diversity. The results for each water sample were then compared to other foreign samples and to data from the receiving basin for off- site fuel (RBOF) at SRS.

Molecular musings in microbial ecology and evolution

PubMed Central

2011-01-01

A few major discoveries have influenced how ecologists and evolutionists study microbes. Here, in the format of an interview, we answer questions that directly relate to how these discoveries are perceived in these two branches of microbiology, and how they have impacted on both scientific thinking and methodology. The first question is "What has been the influence of the 'Universal Tree of Life' based on molecular markers?" For evolutionists, the tree was a tool to understand the past of known (cultured) organisms, mapping the invention of various physiologies on the evolutionary history of microbes. For ecologists the tree was a guide to discover the current diversity of unknown (uncultured) organisms, without much knowledge of their physiology. The second question we ask is "What was the impact of discovering frequent lateral gene transfer among microbes?" In evolutionary microbiology, frequent lateral gene transfer (LGT) made a simple description of relationships between organisms impossible, and for microbial ecologists, functions could not be easily linked to specific genotypes. Both fields initially resisted LGT, but methods or topics of inquiry were eventually changed in one to incorporate LGT in its theoretical models (evolution) and in the other to achieve its goals despite that phenomenon (ecology). The third and last question we ask is "What are the implications of the unexpected extent of diversity?" The variation in the extent of diversity between organisms invalidated the universality of species definitions based on molecular criteria, a major obstacle to the adaptation of models developed for the study of macroscopic eukaryotes to evolutionary microbiology. This issue has not overtly affected microbial ecology, as it had already abandoned species in favor of the more flexible operational taxonomic units. This field is nonetheless moving away from traditional methods to measure diversity, as they do not provide enough resolution to uncover what lies below the species level. The answers of the evolutionary microbiologist and microbial ecologist to these three questions illustrate differences in their theoretical frameworks. These differences mean that both fields can react quite distinctly to the same discovery, incorporating it with more or less difficulty in their scientific practice. Reviewers This article was reviewed by W. Ford Doolittle, Eugene V. Koonin and Maureen A. O'Malley. PMID:22074255

Molecular musings in microbial ecology and evolution.

PubMed

Case, Rebecca J; Boucher, Yan

2011-11-10

A few major discoveries have influenced how ecologists and evolutionists study microbes. Here, in the format of an interview, we answer questions that directly relate to how these discoveries are perceived in these two branches of microbiology, and how they have impacted on both scientific thinking and methodology.The first question is "What has been the influence of the 'Universal Tree of Life' based on molecular markers?" For evolutionists, the tree was a tool to understand the past of known (cultured) organisms, mapping the invention of various physiologies on the evolutionary history of microbes. For ecologists the tree was a guide to discover the current diversity of unknown (uncultured) organisms, without much knowledge of their physiology.The second question we ask is "What was the impact of discovering frequent lateral gene transfer among microbes?" In evolutionary microbiology, frequent lateral gene transfer (LGT) made a simple description of relationships between organisms impossible, and for microbial ecologists, functions could not be easily linked to specific genotypes. Both fields initially resisted LGT, but methods or topics of inquiry were eventually changed in one to incorporate LGT in its theoretical models (evolution) and in the other to achieve its goals despite that phenomenon (ecology).The third and last question we ask is "What are the implications of the unexpected extent of diversity?" The variation in the extent of diversity between organisms invalidated the universality of species definitions based on molecular criteria, a major obstacle to the adaptation of models developed for the study of macroscopic eukaryotes to evolutionary microbiology. This issue has not overtly affected microbial ecology, as it had already abandoned species in favor of the more flexible operational taxonomic units. This field is nonetheless moving away from traditional methods to measure diversity, as they do not provide enough resolution to uncover what lies below the species level.The answers of the evolutionary microbiologist and microbial ecologist to these three questions illustrate differences in their theoretical frameworks. These differences mean that both fields can react quite distinctly to the same discovery, incorporating it with more or less difficulty in their scientific practice.

Role of the Gastrointestinal Tract Microbiome in the Pathophysiology of Diabetes Mellitus.

PubMed

Sohail, Muhammad U; Althani, Asmaa; Anwar, Haseeb; Rizzi, Roberto; Marei, Hany E

2017-01-01

The incidence of diabetes mellitus is rapidly increasing throughout the world. Although the exact cause of the disease is not fully clear, perhaps, genetics, ethnic origin, obesity, age, and lifestyle are considered as few of many contributory factors for the disease pathogenesis. In recent years, the disease progression is particularly linked with functional and taxonomic alterations in the gastrointestinal tract microbiome. A change in microbial diversity, referred as microbial dysbiosis, alters the gut fermentation profile and intestinal wall integrity and causes metabolic endotoxemia, low-grade inflammation, autoimmunity, and other affiliated metabolic disorders. This article aims to summarize the role of the gut microbiome in the pathogenesis of diabetes. Additionally, we summarize gut microbial dysbiosis in preclinical and clinical diabetes cases reported in literature in the recent years.

Metagenomics: A new horizon in cancer research

PubMed Central

Banerjee, Joyita; Mishra, Neetu; Dhas, Yogita

2015-01-01

Metagenomics has broadened the scope of targeting microbes responsible for inducing various types of cancers. About 16.1% of cancers are associated with microbial infection. Metagenomics is an equitable way of identifying and studying micro-organisms within their habitat. In cancer research, this approach has revolutionized the way of identifying, analyzing and targeting the microbial diversity present in the tissue specimens of cancer patients. The genomic analyses of these micro-organisms through next generation sequencing techniques invariably facilitate in recognizing the microbial population in biopsies and their evolutionary relationships with each other. In this review an attempt has been made to generate current metagenomic view on cancer microbiota. Different types of micro-organisms have been found to be linked to various types of cancers, thus, contributing significantly in understanding the disease at molecular level. PMID:26110115

Stable isotope probing in the metagenomics era: a bridge towards improved bioremediation

PubMed Central

Uhlik, Ondrej; Leewis, Mary-Cathrine; Strejcek, Michal; Musilova, Lucie; Mackova, Martina; Leigh, Mary Beth; Macek, Tomas

2012-01-01

Microbial biodegradation and biotransformation reactions are essential to most bioremediation processes, yet the specific organisms, genes, and mechanisms involved are often not well understood. Stable isotope probing (SIP) enables researchers to directly link microbial metabolic capability to phylogenetic and metagenomic information within a community context by tracking isotopically labeled substances into phylogenetically and functionally informative biomarkers. SIP is thus applicable as a tool for the identification of active members of the microbial community and associated genes integral to the community functional potential, such as biodegradative processes. The rapid evolution of SIP over the last decade and integration with metagenomics provides researchers with a much deeper insight into potential biodegradative genes, processes, and applications, thereby enabling an improved mechanistic understanding that can facilitate advances in the field of bioremediation. PMID:23022353

Low-molecular-weight poly(alpha-methyl beta,L-malate) of microbial origin: synthesis and crystallization.

PubMed

Fernández, Carlos E; Mancera, Manuel; Holler, Eggehard; Bou, Jordi J; Galbis, Juan A; Muñoz-Guerra, Sebastián

2005-02-23

Low-molecular-weight poly(alpha-methyl beta,L-malate) made of approximately 25-30 units was prepared from microbial poly(beta,L-malic acid) by treatment with diazomethane. The thermal characterization of the polymalate methyl ester was carried out and its crystalline structure was preliminary examined. Its ability to crystallize both from solution and from the melt was comparatively evaluated.

Actual measurement, hygrothermal response experiment and growth prediction analysis of microbial contamination of central air conditioning system in Dalian, China

PubMed Central

Lv, Yang; Hu, Guangyao; Wang, Chunyang; Yuan, Wenjie; Wei, Shanshan; Gao, Jiaoqi; Wang, Boyuan; Song, Fangchao

2017-01-01

The microbial contamination of central air conditioning system is one of the important factors that affect the indoor air quality. Actual measurement and analysis were carried out on microbial contamination in central air conditioning system at a venue in Dalian, China. Illumina miseq method was used and three fungal samples of two units were analysed by high throughput sequencing. Results showed that the predominant fungus in air conditioning unit A and B were Candida spp. and Cladosporium spp., and two fungus were further used in the hygrothermal response experiment. Based on the data of Cladosporium in hygrothermal response experiment, this paper used the logistic equation and the Gompertz equation to fit the growth predictive model of Cladosporium genera in different temperature and relative humidity conditions, and the square root model was fitted based on the two environmental factors. In addition, the models were carried on the analysis to verify the accuracy and feasibility of the established model equation. PMID:28367963

Actual measurement, hygrothermal response experiment and growth prediction analysis of microbial contamination of central air conditioning system in Dalian, China.

PubMed

Lv, Yang; Hu, Guangyao; Wang, Chunyang; Yuan, Wenjie; Wei, Shanshan; Gao, Jiaoqi; Wang, Boyuan; Song, Fangchao

2017-04-03

The microbial contamination of central air conditioning system is one of the important factors that affect the indoor air quality. Actual measurement and analysis were carried out on microbial contamination in central air conditioning system at a venue in Dalian, China. Illumina miseq method was used and three fungal samples of two units were analysed by high throughput sequencing. Results showed that the predominant fungus in air conditioning unit A and B were Candida spp. and Cladosporium spp., and two fungus were further used in the hygrothermal response experiment. Based on the data of Cladosporium in hygrothermal response experiment, this paper used the logistic equation and the Gompertz equation to fit the growth predictive model of Cladosporium genera in different temperature and relative humidity conditions, and the square root model was fitted based on the two environmental factors. In addition, the models were carried on the analysis to verify the accuracy and feasibility of the established model equation.

Utilization of Alternate Chirality Enantiomers in Microbial Communities

NASA Technical Reports Server (NTRS)

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.

Reestablishment of recipient-associated microbiota in the lung allograft is linked to reduced risk of bronchiolitis obliterans syndrome.

PubMed

Willner, Dana L; Hugenholtz, Philip; Yerkovich, Stephanie T; Tan, Maxine E; Daly, Joshua N; Lachner, Nancy; Hopkins, Peter M; Chambers, Daniel C

2013-03-15

Bronchiolitis obliterans syndrome (BOS) is the primary limiting factor for long-term survival after lung transplantation, and has previously been associated with microbial infections. To cross-sectionally and longitudinally characterize microbial communities in allografts from transplant recipients with and without BOS using a culture-independent method based on high-throughput sequencing. Allografts were sampled by bronchoalveolar lavage, and microbial communities were profiled using 16S rRNA gene amplicon pyrosequencing. Community profiles were compared using the weighted Unifrac metric and the relationship between microbial populations, BOS, and other covariates was explored using PERMANOVA and logistic regression. Microbial communities in transplant patients fell into two main groups: those dominated by Pseudomonas or those dominated by Streptococcus and Veillonella, which seem to be mutually exclusive lung microbiomes. Aspergillus culture was also negatively correlated with the Pseudomonas-dominated group. The reestablishment of dominant populations present in patients pretransplant, notably Pseudomonas in individuals with cystic fibrosis, was negatively correlated with BOS. Recolonization of the allograft by Pseudomonas in individuals with cystic fibrosis is not associated with BOS. In general, reestablishment of pretransplant lung populations in the allograft seems to have a protective effect against BOS, whereas de novo acquisition of microbial populations often belonging to the same genera may increase the risk of BOS.

Microbial Community Profiles in Wastewaters from Onsite Wastewater Treatment Systems Technology

PubMed Central

Jałowiecki, Łukasz; Chojniak, Joanna Małgorzata; Dorgeloh, Elmar; Hegedusova, Berta; Ejhed, Helene; Magnér, Jörgen; Płaza, Grażyna Anna

2016-01-01

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. PMID:26807728

Microbial production of organic acids in aquitard sediments and its role in aquifer geochemistry

USGS Publications Warehouse

McMahon, P.B.; Chapelle, F.H.

1991-01-01

MICROBIAL activity in aquifers plays an important part in the chemical evolution of ground water1-5. The most important terminal electron-accepting microbial processes in deeply buried anaerobic aquifers are iron reduction, sulphate reduction and methanogenesis5-8, each of which requires simple organic compounds or hydrogen (H2) as electron donors. Until now, the source of these compounds was unknown because the concentrations of dissolved organic carbon and sedimentary organic carbon in aquifers are extremely low9-11. Here we show that rates of microbial fermentation exceed rates of respiration in organic-rich aquitards (low-permeability sediments stratigraphically adjacent to higher-permeability aquifer sediments), resulting in a net accumulation of simple organic acids in pore waters. In aquifers, however, respiration outpaces fermentation, resulting in a net consumption of organic acids. The concentration gradient that develops in response to these two processes drives a net diffusive flux of organic acids from aquitards to aquifers. Diffusion calculations demonstrate that rates of organic acid transport are sufficient to account for observed rates of microbial respiration in aquifers. This overall process effectively links the large pool of sedimentary organic carbon in aquitards to microbial respiration in aquifers, and is a principal mechanism driving groundwater chemistry changes in aquifers.

A Year in the Life of a Contaminated Heater-Cooler Unit With Mycobacterium chimaera?

PubMed

Garvey, Mark I; Bradley, Craig W; Walker, Jimmy

2017-06-01

OBJECTIVE Heater-cooler units (HCUs) have been shown to be a source of Mycobacterium chimaera infections. For the past year, weekly water samples have been taken from HCUs used at University Hospitals Birmingham (UHB) NHS Foundation Trust. We report the microbial contamination of the HCUs over a year detailing the decontamination regimes applied at UHB to reduce the microbial load. DESIGN Observational study SETTING UHB is a tertiary referral teaching hospital in Birmingham, United Kingdom, that provides clinical services to nearly 1 million patients every year. The UHB Cardiac department is one of the largest in the United Kingdom and provides treatment for adult patients with a wide range of cardiac diseases. METHODS Water samples taken from HCUs used at UHB for cardiopulmonary bypass surgery were sampled over a year to determine the number of microorganisms by membrane filtration. Various decontamination processes were employed throughout the year. RESULTS Varying total viable counts containing a wide variety of microorganisms were obtained from water inside the HCUs. No M. chimaera were isolated after replacement of the HCU internal tubing. Stringent decontamination regimes resulted in degradation of the HCUs and increased TVCs after several months. CONCLUSION More work is required to ensure effective decontamination processes to reduce the microbial load within the HCUs. Our studies indicate that weekly water sampling for TVC will be required indefinitely to monitor the water quality in these units as well as regular replacement of the tubing to control the build-up of biofilm. Infect Control Hosp Epidemiol 2017;38:705-711.

Comparative evaluation of microbial diversity and metabolite profiles in doenjang, a fermented soybean paste, during the two different industrial manufacturing processes.

PubMed

Lee, Sunmin; Lee, Sarah; Singh, Digar; Oh, Ji Young; Jeon, Eun Jung; Ryu, Hyung SeoK; Lee, Dong Wan; Kim, Beom Seok; Lee, Choong Hwan

2017-04-15

Two different doenjang manufacturing processes, the industrial process (IP) and the modified industrial process (mIP) with specific microbial assortments, were subjected to metabolite profiling using liquid chromatography-mass spectrometry (LC-MS) and gas chromatography time-of-flight mass spectrometry (GC-TOF-MS). The multivariate analyses indicated that both primary and secondary metabolites exhibited distinct patterns according to the fermentation processes (IP and mIP). Microbial community analysis for doenjang using denaturing gradient gel electrophoresis (DGGE), exhibited that both bacteria and fungi contributed proportionally for each step in the process viz., soybean, steaming, drying, meju fermentation, cooling, brining, and aging. Further, correlation analysis indicated that Aspergillus population was linked to sugar metabolism, Bacillus spp. with that of fatty acids, whereas Tetragenococcus and Zygosaccharomyces were found associated with amino acids. These results suggest that the components and quality of doenjang are critically influenced by the microbial assortments in each process. Copyright © 2016 Elsevier Ltd. All rights reserved.

Community Structure and Function of Amphibian Skin Microbes: An Experiment with Bullfrogs Exposed to a Chytrid Fungus.

PubMed

Walke, Jenifer B; Becker, Matthew H; Loftus, Stephen C; House, Leanna L; Teotonio, Thais L; Minbiole, Kevin P C; Belden, Lisa K

2015-01-01

The vertebrate microbiome contributes to disease resistance, but few experiments have examined the link between microbiome community structure and disease resistance functions. Chytridiomycosis, a major cause of amphibian population declines, is a skin disease caused by the fungus, Batrachochytrium dendrobatidis (Bd). In a factorial experiment, bullfrog skin microbiota was reduced with antibiotics, augmented with an anti-Bd bacterial isolate (Janthinobacterium lividum), or unmanipulated, and individuals were then either exposed or not exposed to Bd. We found that the microbial community structure of individual frogs prior to Bd exposure influenced Bd infection intensity one week following exposure, which, in turn, was negatively correlated with proportional growth during the experiment. Microbial community structure and function differed among unmanipulated, antibiotic-treated, and augmented frogs only when frogs were exposed to Bd. Bd is a selective force on microbial community structure and function, and beneficial states of microbial community structure may serve to limit the impacts of infection.

Community Structure and Function of Amphibian Skin Microbes: An Experiment with Bullfrogs Exposed to a Chytrid Fungus

PubMed Central

Walke, Jenifer B.; Becker, Matthew H.; Loftus, Stephen C.; House, Leanna L.; Teotonio, Thais L.; Minbiole, Kevin P. C.; Belden, Lisa K.

2015-01-01

The vertebrate microbiome contributes to disease resistance, but few experiments have examined the link between microbiome community structure and disease resistance functions. Chytridiomycosis, a major cause of amphibian population declines, is a skin disease caused by the fungus, Batrachochytrium dendrobatidis (Bd). In a factorial experiment, bullfrog skin microbiota was reduced with antibiotics, augmented with an anti-Bd bacterial isolate (Janthinobacterium lividum), or unmanipulated, and individuals were then either exposed or not exposed to Bd. We found that the microbial community structure of individual frogs prior to Bd exposure influenced Bd infection intensity one week following exposure, which, in turn, was negatively correlated with proportional growth during the experiment. Microbial community structure and function differed among unmanipulated, antibiotic-treated, and augmented frogs only when frogs were exposed to Bd. Bd is a selective force on microbial community structure and function, and beneficial states of microbial community structure may serve to limit the impacts of infection. PMID:26445500

Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales.

PubMed

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

2016-09-05

Hydraulic fracturing is the industry standard for extracting hydrocarbons from shale formations. Attention has been paid to the economic benefits and environmental impacts of this process, yet the biogeochemical changes induced in the deep subsurface are poorly understood. Recent single-gene investigations revealed that halotolerant microbial communities were enriched after hydraulic fracturing. Here, the reconstruction of 31 unique genomes coupled to metabolite data from the Marcellus and Utica shales revealed that many of the persisting organisms play roles in methylamine cycling, ultimately supporting methanogenesis in the deep biosphere. Fermentation of injected chemical additives also sustains long-term microbial persistence, while thiosulfate reduction could produce sulfide, contributing to reservoir souring and infrastructure corrosion. Extensive links between viruses and microbial hosts demonstrate active viral predation, which may contribute to the release of labile cellular constituents into the extracellular environment. Our analyses show that hydraulic fracturing provides the organismal and chemical inputs for colonization and persistence in the deep terrestrial subsurface.

Microbial metabolisms in a 2.5-km-deep ecosystem created by hydraulic fracturing in shales

DOE Office of Scientific and Technical Information (OSTI.GOV)

Daly, Rebecca A.; Borton, Mikayla A.; Wilkins, Michael J.

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

Integrating Environmental Genomics and Biogeochemical Models: a Gene-centric Approach

NASA Astrophysics Data System (ADS)

Reed, D. C.; Algar, C. K.; Huber, J. A.; Dick, G.

2013-12-01

Rapid advances in molecular microbial ecology have yielded an unprecedented amount of data about the evolutionary relationships and functional traits of microbial communities that regulate global geochemical cycles. Biogeochemical models, however, are trailing in the wake of the environmental genomics revolution and such models rarely incorporate explicit representations of bacteria and archaea, nor are they compatible with nucleic acid or protein sequence data. Here, we present a functional gene-based framework for describing microbial communities in biogeochemical models that uses genomics data and provides predictions that are readily testable using cutting-edge molecular tools. To demonstrate the approach in practice, nitrogen cycling in the Arabian Sea oxygen minimum zone (OMZ) was modelled to examine key questions about cryptic sulphur cycling and dinitrogen production pathways in OMZs. By directly linking geochemical dynamics to the genetic composition of microbial communities, the method provides mechanistic insights into patterns and biogeochemical consequences of marine microbes. Such an approach is critical for informing our understanding of the key role microbes play in modulating Earth's biogeochemistry.

RNA-based stable isotope probing (RNA-SIP) to unravel intestinal host-microbe interactions.

PubMed

Egert, Markus; Weis, Severin; Schnell, Sylvia

2018-05-30

The RNA-SIP technology, introduced into molecular microbial ecology in 2002, is an elegant technique to link the structure and function of complex microbial communities, i.e. to identify microbial key-players involved in distinct degradation and assimilation processes under in-situ conditions. Due to its dependence of microbial RNA, this technique is particularly suited for environments with high numbers of very active, i.e. significantly RNA-expressing, bacteria. So far, it was mainly used in environmental studies using microbiotas from soil or water habitats. Here we outline and summarize our application of RNA-SIP for the identification of bacteria involved in the degradation and assimilation of prebiotic carbohydrates in intestinal samples of human and animal origin. Following an isotope label from a prebiotic substrate into the RNA of distinct bacterial taxa will help to better understand the functionality of these medically and economically important nutrients in an intestinal environment. Copyright © 2018 Elsevier Inc. All rights reserved.

Diversity and Distribution of Prokaryotes within a Shallow-Water Pockmark Field.

PubMed

Giovannelli, Donato; d'Errico, Giuseppe; Fiorentino, Federica; Fattorini, Daniele; Regoli, Francesco; Angeletti, Lorenzo; Bakran-Petricioli, Tatjana; Vetriani, Costantino; Yücel, Mustafa; Taviani, Marco; Manini, Elena

2016-01-01

Pockmarks are crater-like depression on the seafloor associated with hydrocarbon ascent through muddy sediments in continental shelves around the world. In this study, we examine the diversity and distribution of benthic microbial communities at shallow-water pockmarks adjacent to the Middle Adriatic Ridge. We integrate microbial diversity data with characterization of local hydrocarbons concentrations and sediment geochemistry. Our results suggest these pockmarks are enriched in sedimentary hydrocarbons, and host a microbial community dominated by Bacteria, even in deeper sediment layers. Pockmark sediments showed higher prokaryotic abundance and biomass than surrounding sediments, potentially due to the increased availability of organic matter and higher concentrations of hydrocarbons linked to pockmark activity. Prokaryotic diversity analyses showed that the microbial communities of these shallow-water pockmarks are unique, and comprised phylotypes associated with the cycling of sulfur and nitrate compounds, as well as numerous know hydrocarbon degraders. Altogether, this study suggests that shallow-water pockmark habitats enhance the diversity of the benthic prokaryotic biosphere by providing specialized environmental niches.

Long-term rice cultivation stabilizes soil organic carbon and promotes soil microbial activity in a salt marsh derived soil chronosequence

PubMed Central

Wang, Ping; Liu, Yalong; Li, Lianqing; Cheng, Kun; Zheng, Jufeng; Zhang, Xuhui; Zheng, Jinwei; Joseph, Stephen; Pan, Genxing

2015-01-01

Soil organic carbon (SOC) sequestration with enhanced stable carbon storage has been widely accepted as a very important ecosystem property. Yet, the link between carbon stability and bio-activity for ecosystem functioning with OC accumulation in field soils has not been characterized. We assessed the changes in microbial activity versus carbon stability along a paddy soil chronosequence shifting from salt marsh in East China. We used mean weight diameter, normalized enzyme activity (NEA) and carbon gain from straw amendment for addressing soil aggregation, microbial biochemical activity and potential C sequestration, respectively. In addition, a response ratio was employed to infer the changes in all analyzed parameters with prolonged rice cultivation. While stable carbon pools varied with total SOC accumulation, soil respiration and both bacterial and fungal diversity were relatively constant in the rice soils. Bacterial abundance and NEA were positively but highly correlated to total SOC accumulation, indicating an enhanced bio-activity with carbon stabilization. This could be linked to an enhancement of particulate organic carbon pool due to physical protection with enhanced soil aggregation in the rice soils under long-term rice cultivation. However, the mechanism underpinning these changes should be explored in future studies in rice soils where dynamic redox conditions exist. PMID:26503629

Long-term rice cultivation stabilizes soil organic carbon and promotes soil microbial activity in a salt marsh derived soil chronosequence

NASA Astrophysics Data System (ADS)

Wang, Ping; Liu, Yalong; Li, Lianqing; Cheng, Kun; Zheng, Jufeng; Zhang, Xuhui; Zheng, Jinwei; Joseph, Stephen; Pan, Genxing

2015-10-01

Soil organic carbon (SOC) sequestration with enhanced stable carbon storage has been widely accepted as a very important ecosystem property. Yet, the link between carbon stability and bio-activity for ecosystem functioning with OC accumulation in field soils has not been characterized. We assessed the changes in microbial activity versus carbon stability along a paddy soil chronosequence shifting from salt marsh in East China. We used mean weight diameter, normalized enzyme activity (NEA) and carbon gain from straw amendment for addressing soil aggregation, microbial biochemical activity and potential C sequestration, respectively. In addition, a response ratio was employed to infer the changes in all analyzed parameters with prolonged rice cultivation. While stable carbon pools varied with total SOC accumulation, soil respiration and both bacterial and fungal diversity were relatively constant in the rice soils. Bacterial abundance and NEA were positively but highly correlated to total SOC accumulation, indicating an enhanced bio-activity with carbon stabilization. This could be linked to an enhancement of particulate organic carbon pool due to physical protection with enhanced soil aggregation in the rice soils under long-term rice cultivation. However, the mechanism underpinning these changes should be explored in future studies in rice soils where dynamic redox conditions exist.

Long-term rice cultivation stabilizes soil organic carbon and promotes soil microbial activity in a salt marsh derived soil chronosequence.

PubMed

Wang, Ping; Liu, Yalong; Li, Lianqing; Cheng, Kun; Zheng, Jufeng; Zhang, Xuhui; Zheng, Jinwei; Joseph, Stephen; Pan, Genxing

2015-10-27

Soil organic carbon (SOC) sequestration with enhanced stable carbon storage has been widely accepted as a very important ecosystem property. Yet, the link between carbon stability and bio-activity for ecosystem functioning with OC accumulation in field soils has not been characterized. We assessed the changes in microbial activity versus carbon stability along a paddy soil chronosequence shifting from salt marsh in East China. We used mean weight diameter, normalized enzyme activity (NEA) and carbon gain from straw amendment for addressing soil aggregation, microbial biochemical activity and potential C sequestration, respectively. In addition, a response ratio was employed to infer the changes in all analyzed parameters with prolonged rice cultivation. While stable carbon pools varied with total SOC accumulation, soil respiration and both bacterial and fungal diversity were relatively constant in the rice soils. Bacterial abundance and NEA were positively but highly correlated to total SOC accumulation, indicating an enhanced bio-activity with carbon stabilization. This could be linked to an enhancement of particulate organic carbon pool due to physical protection with enhanced soil aggregation in the rice soils under long-term rice cultivation. However, the mechanism underpinning these changes should be explored in future studies in rice soils where dynamic redox conditions exist.

Impact of anthropogenic activities on the dissemination of antibiotic resistance across ecological boundaries.

PubMed

Tripathi, Vijay; Cytryn, Eddie

2017-02-28

Antibiotics are considered to be one of the major medical breakthroughs in history. Nonetheless, over the past four decades, antibiotic resistance has reached alarming levels worldwide and this trend is expected to continue to increase, leading some experts to forecast the coming of a 'post-antibiotic' era. Although antibiotic resistance in pathogens is traditionally linked to clinical environments, there is a rising concern that the global propagation of antibiotic resistance is also associated with environmental reservoirs that are linked to anthropogenic activities such as animal husbandry, agronomic practices and wastewater treatment. It is hypothesized that the emergence and dissemination of antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes (ARGs) within and between environmental microbial communities can ultimately contribute to the acquisition of antibiotic resistance in human pathogens. Nonetheless, the scope of this phenomenon is not clear due to the complexity of microbial communities in the environment and methodological constraints that limit comprehensive in situ evaluation of microbial genomes. This review summarizes the current state of knowledge regarding antibiotic resistance in non-clinical environments, specifically focusing on the dissemination of antibiotic resistance across ecological boundaries and the contribution of this phenomenon to global antibiotic resistance. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Microbial community assembly patterns under incipient conditions in a basaltic soil system

NASA Astrophysics Data System (ADS)

Sengupta, A.; Stegen, J.; Alves Meira Neto, A.; Wang, Y.; Chorover, J.; Troch, P. A. A.; Maier, R. M.

2017-12-01

In sub-surface environments, the biotic components are critically linked to the abiotic processes. However, there is limited understanding of community establishment, functional associations, and community assembly processes of such microbes in sub-surface environments. This study presents the first analysis of microbial signatures in an incipient terrestrial basalt soil system conducted under controlled conditions. A sub-meter scale sampling of a soil mesocosm revealed the contrasting distribution patterns of simple soil parameters such as bulk density and electrical conductivity. Phylogenetic analysis of 16S rRNA gene indicated the presence of a total 40 bacterial and archaeal phyla, with high relative abundance of Actinobacteria on the surface and highest abundance of Proteobacteria throughout the system. Community diversity patterns were inferred to be dependent on depth profile and average water content in the system. Predicted functional gene analysis suggested mixotrophy lifestyles with both autotrophic and heterotrophic metabolisms, likelihood of a unique salt tolerant methanogenic pathway with links to novel Euryarchea, signatures of an incomplete nitrogen cycle, and predicted enzymes of extracellular iron (II) to iron (III) conversion followed by intracellular uptake, transport and regulation. Null modeling revealed microbial community assembly was predominantly governed by variable selection, but the influence of the variable selection did not show systematic spatial structure. The presence of significant heterogeneity in predicted functions and ecologically deterministic shifts in community composition in a homogeneous incipient basalt highlights the complexity exhibited by microorganisms even in the simplest of environmental systems. This presents an opportunity to further develop our understanding of how microbial communities establish, evolve, impact, and respond in sub-surface environments.

Personal Insect Repellents and Minimum Risk Pesticides

EPA Pesticide Factsheets

An exempt pesticide product may not bear claims to control rodent, insect or microbial pests in a way that links the pests with specific disease. We are considering a proposal to remove personal mosquito and tick repellents from the minimum risk exemption.

EVALUATION OF CHLORPYRIFOS UPTAKE IN STERILIZED AND NON-STERILIZED SEDIMENT

EPA Science Inventory

In order to evaluate chemical interactions in sediment, initial experiments were designed to assess the role of microbial activitiy on chemical fate of chlorpyrifos. In these initial experiments, sediment uptake of chlorpyrifos was evaluated using Enzyme Linked Immunosorbent Assa...

Performance of UV disinfection and the microbial quality of greywater effluent along a reuse system for toilet flushing.

PubMed

Friedler, Eran; Gilboa, Yael

2010-04-01

This paper examines the microbial quality of treated RBC (Rotating Biological Contactor) and MBR (Membrane Bioreactor) light greywater along a continuous pilot-scale reuse system for toilet flushing, quantifies the efficiency of UV disinfection unit, and evaluates the regrowth potential of selected microorganisms along the system. The UV disinfection unit was found to be very efficient in reducing faecal coliforms and Staphylococcus aureus. On the other hand, its efficiency of inactivation of HPC (Heterotrophic Plate Count) and Pseudomonas aeruginosa was lower. Some regrowth occurred in the reuse system as a result of HPC regrowth which included opportunistic pathogens such as P. aeruginosa. Although the membrane (UF) of the MBR system removed all bacteria from the greywater, bacteria were observed in the reuse system due to "hopping phenomenon." The microbial quality of the disinfected greywater was found to be equal or even better than the microbial quality of "clean" water in toilet bowls flushed with potable water (and used for excretion). Thus, the added health risk associated with reusing the UV-disinfected greywater for toilet flushing (regarding P. aeruginosa and S. aureus), was found to be insignificant. The UV disinfection unit totally removed (100%) the viral indicator (F-RNA phage, host: E. coli F(amp)(+)) injected to the treatment systems simulating transient viral contamination. To conclude, this work contributes to better design of UV disinfection reactors and provides an insight into the long-term behavior of selected microorganisms along on-site greywater reuse systems for toilet flushing. (c) 2010 Elsevier B.V. All rights reserved.

Linking metabolite production to taxonomic identity in environmental samples by (MA)LDI-FISH

PubMed Central

Kaltenpoth, Martin; Strupat, Kerstin; Svatoš, Aleš

2016-01-01

One of the greatest challenges in microbial ecology remains to link the metabolic activity of individual cells to their taxonomic identity and localization within environmental samples. Here we combined mass-spectrometric imaging (MSI) through (matrix-assisted) laser desorption ionization time-of-flight MSI ([MA]LDI-TOF/MSI) with fluorescence in situ hybridization (FISH) to monitor antibiotic production in the defensive symbiosis between beewolf wasps and ‘Streptomyces philanthi' bacteria. Our results reveal similar distributions of the different symbiont-produced antibiotics across the surface of beewolf cocoons, which colocalize with the producing cell populations. Whereas FISH achieves single-cell resolution, MSI is currently limited to a step size of 20–50 μm in the combined approach because of the destructive effects of high laser intensities that are associated with tighter laser beam focus at higher lateral resolution. However, on the basis of the applicability of (MA)LDI-MSI to a broad range of small molecules, its combination with FISH provides a powerful tool for studying microbial interactions in situ, and further modifications of this technique could allow for linking metabolic profiling to gene expression. PMID:26172211

Microbial environmental contamination in Italian dental clinics: A multicenter study yielding recommendations for standardized sampling methods and threshold values.

PubMed

Pasquarella, Cesira; Veronesi, Licia; Napoli, Christian; Castiglia, Paolo; Liguori, Giorgio; Rizzetto, Rolando; Torre, Ida; Righi, Elena; Farruggia, Patrizia; Tesauro, Marina; Torregrossa, Maria V; Montagna, Maria T; Colucci, Maria E; Gallè, Francesca; Masia, Maria D; Strohmenger, Laura; Bergomi, Margherita; Tinteri, Carola; Panico, Manuela; Pennino, Francesca; Cannova, Lucia; Tanzi, Marialuisa

2012-03-15

A microbiological environmental investigation was carried out in ten dental clinics in Italy. Microbial contamination of water, air and surfaces was assessed in each clinic during the five working days, for one week per month, for a three-month period. Water and surfaces were sampled before and after clinical activity; air was sampled before, after, and during clinical activity. A wide variation was found in microbial environmental contamination, both within the participating clinics and for the different sampling times. Before clinical activity, microbial water contamination in tap water reached 51,200cfu/mL (colony forming units per milliliter), and that in Dental Unit Water Systems (DUWSs) reached 872,000cfu/mL. After clinical activity, there was a significant decrease in the Total Viable Count (TVC) in tap water and in DUWSs. Pseudomonas aeruginosa was found in 2.38% (7/294) of tap water samples and in 20.06% (59/294) of DUWS samples; Legionella spp. was found in 29.96% (89/297) of tap water samples and 15.82% (47/297) of DUWS samples, with no significant difference between pre- and post-clinical activity. Microbial air contamination was highest during dental treatments, and decreased significantly at the end of the working activity (p<0.05). The microbial buildup on surfaces increased significantly during the working hours. This study provides data for the establishment of standardized sampling methods, and threshold values for contamination monitoring in dentistry. Some very critical situations have been observed which require urgent intervention. Furthermore, the study emphasizes the need for research aimed at defining effective managing strategies for dental clinics. Copyright © 2012 Elsevier B.V. All rights reserved.

Addition of Rubber to soil damages the functional diversity of soil.

PubMed

Goswami, Madhurankhi; Bhattacharyya, Purnita; Tribedi, Prosun

2017-07-01

Rubber is a polymer of isoprene, consisting mainly of cis-1,4-polyisoprene units. The unmanageable production and its irresponsible disposal pose severe threats to environmental ecology. Therefore, the current study focuses extensively on the ill-effects of Rubber disposal on soil microbial functional diversity as it reflects the health of ecosystem by acting as a key component in ecosystem productivity. To investigate the effect of Rubber on soil microbial functional diversity, soil samples were collected from landfill sites and three different soil microcosms (Rubber treated, untreated, and sterile soil) were prepared. The soil enzymatic activity was determined by fluorescein diacetate hydrolysis followed by the determination of the microbial metabolic potential and functional diversity by average well color development and Shannon-Weaver index (H), respectively. BiOLOG ECO plates were used for determining the microbial functional diversity of the soil microcosms. Higher heterotrophic microbial count as well as higher soil microbial activity was observed in Rubber untreated soil than Rubber treated soil microcosm. The result indicated that the addition of Rubber to soil reduced soil heterotrophic microbial count and soil microbial activity considerably. Similarly, soil microbial metabolic potential as well as microbial functional diversity of soil had been decreased by the addition of Rubber gloves in it. Variation in soil microbial metabolic spectrum between Rubber treated and untreated microcosm was confirmed by multivariate analysis. Collectively, all the results demonstrated that the addition of Rubber to soil reduced the soil microbial functional diversity considerably. Therefore, it is necessary for the commission of serious steps regarding Rubber disposal and protection of the environment from serious environmental issues.

The information science of microbial ecology.

PubMed

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.

Central role of the cell in microbial ecology.

PubMed

Zengler, Karsten

2009-12-01

Over the last few decades, advances in cultivation-independent methods have significantly contributed to our understanding of microbial diversity and community composition in the environment. At the same time, cultivation-dependent methods have thrived, and the growing number of organisms obtained thereby have allowed for detailed studies of their physiology and genetics. Still, most microorganisms are recalcitrant to cultivation. This review not only conveys current knowledge about different isolation and cultivation strategies but also discusses what implications can be drawn from pure culture work for studies in microbial ecology. Specifically, in the light of single-cell individuality and genome heterogeneity, it becomes important to evaluate population-wide measurements carefully. An overview of various approaches in microbial ecology is given, and the cell as a central unit for understanding processes on a community level is discussed.

Merging metagenomics and geochemistry reveals environmental controls on biological diversity and evolution.

PubMed

Alsop, Eric B; Boyd, Eric S; Raymond, Jason

2014-05-28

The metabolic strategies employed by microbes inhabiting natural systems are, in large part, dictated by the physical and geochemical properties of the environment. This study sheds light onto the complex relationship between biology and environmental geochemistry using forty-three metagenomes collected from geochemically diverse and globally distributed natural systems. It is widely hypothesized that many uncommonly measured geochemical parameters affect community dynamics and this study leverages the development and application of multidimensional biogeochemical metrics to study correlations between geochemistry and microbial ecology. Analysis techniques such as a Markov cluster-based measure of the evolutionary distance between whole communities and a principal component analysis (PCA) of the geochemical gradients between environments allows for the determination of correlations between microbial community dynamics and environmental geochemistry and provides insight into which geochemical parameters most strongly influence microbial biodiversity. By progressively building from samples taken along well defined geochemical gradients to samples widely dispersed in geochemical space this study reveals strong links between the extent of taxonomic and functional diversification of resident communities and environmental geochemistry and reveals temperature and pH as the primary factors that have shaped the evolution of these communities. Moreover, the inclusion of extensive geochemical data into analyses reveals new links between geochemical parameters (e.g. oxygen and trace element availability) and the distribution and taxonomic diversification of communities at the functional level. Further, an overall geochemical gradient (from multivariate analyses) between natural systems provides one of the most complete predictions of microbial taxonomic and functional composition. Clustering based on the frequency in which orthologous proteins occur among metagenomes facilitated accurate prediction of the ordering of community functional composition along geochemical gradients, despite a lack of geochemical input. The consistency in the results obtained from the application of Markov clustering and multivariate methods to distinct natural systems underscore their utility in predicting the functional potential of microbial communities within a natural system based on system geochemistry alone, allowing geochemical measurements to be used to predict purely biological metrics such as microbial community composition and metabolism.

The United Links for the United States Intermodal Workshop

DOT National Transportation Integrated Search

1993-07-01

On July 14 - 16, 1993, the United States Department of Transportation and The Port Authority of New York and New Jersey co-sponsored an Intermodal Workshop in New York City. The United Links For The United States workshop was the largest of several i...

Soil warming increases metabolic quotients of soil microorganisms without changes in temperature sensitivity of soil respiration

NASA Astrophysics Data System (ADS)

Marañón-Jiménez, Sara; Soong, Jenniffer L.; Leblans, Niki I. W.; Sigurdsson, Bjarni D.; Dauwe, Steven; Fransen, Erik; Janssens, Ivan A.

2017-04-01

Increasing temperatures can accelerate soil organic matter (SOM) decomposition and release large amounts of CO2 to the atmosphere, potentially inducing climate change feedbacks. Alterations to the temperature sensitivity and metabolic pathways of soil microorganisms in response to soil warming can play a key role in these soil carbon (C) losses. Here, we present results of an incubation experiment using soils from a geothermal gradient in Iceland that have been subjected to different intensities of soil warming (+0, +1, +3, +5, +10 and +20 °C above ambient) over seven years. We hypothesized that 7 years of soil warming would led to a depletion of labile organic substrates, with a subsequent decrease of the "apparent" temperature sensitivity of soil respiration. Associated to this C limitation and more sub-optimal conditions for microbial growth, we also hypothesized increased microbial metabolic quotients (soil respiration per unit of microbial biomass), which is associated with increases in the relative amount of C invested into catabolic pathways along the warming gradient. Soil respiration and basal respiration rates decreased with soil warming intensity, in parallel with a decline in soil C availability. Contrasting to our first hypothesis, we did not detect changes in the temperature sensitivity of soil respiration with soil warming or on the availability of nutrients and of labile C substrates at the time of incubation. However, in agreement to our second hypothesis, microbial metabolic quotients (soil respiration per unit of microbial biomass) increased at warmer temperatures, while the C retained in biomass decreased as substrate became limiting. Long-term (7 years) temperature increases thus triggered a change in the metabolic functioning of the soil microbial communities towards increasing energy costs for maintenance or resource acquisition, thereby lowering the capacity of C retention and stabilization of warmed soils. These results highlight the need to incorporate the potential changes in microbial physiological functioning into models, in order to accurately predict future changes in soil C stocks in response to global warming.

Computational analysis for biodegradation of exogenously depolymerizable polymer

NASA Astrophysics Data System (ADS)

Watanabe, M.; Kawai, F.

2018-03-01

This study shows that microbial growth and decay in a biodegradation process of exogenously depolymerizable polymer are controlled by consumption of monomer units. Experimental outcomes for residual polymer were incorporated in inverse analysis for a degradation rate. The Gauss-Newton method was applied to an inverse problem for two parameter values associated with the microbial population. A biodegradation process of polyethylene glycol was analyzed numerically, and numerical outcomes were obtained.

Water system microbial check valve development

NASA Technical Reports Server (NTRS)

Colombo, G. V.; Greenley, D. R.; Putnam, D. F.

1978-01-01

A residual iodine microbial check valve (RIMCV) assembly was developed and tested. The assembly is designed to be used in the space shuttle potable water system. The RIMCV is based on an anion exchange resin that is supersaturated with an iodine solution. This system causes a residual to be present in the effluent water which provides continuing bactericidal action. A flight prototype design was finalized and five units were manufactured and delivered.

Metaproteogenomic Profiling of Microbial Communities Colonizing Actively Venting Hydrothermal Chimneys

PubMed Central

Pjevac, Petra; Meier, Dimitri V.; Markert, Stephanie; Hentschker, Christian; Schweder, Thomas; Becher, Dörte; Gruber-Vodicka, Harald R.; Richter, Michael; Bach, Wolfgang; Amann, Rudolf; Meyerdierks, Anke

2018-01-01

At hydrothermal vent sites, chimneys consisting of sulfides, sulfates, and oxides are formed upon contact of reduced hydrothermal fluids with oxygenated seawater. The walls and surfaces of these chimneys are an important habitat for vent-associated microorganisms. We used community proteogenomics to investigate and compare the composition, metabolic potential and relative in situ protein abundance of microbial communities colonizing two actively venting hydrothermal chimneys from the Manus Basin back-arc spreading center (Papua New Guinea). We identified overlaps in the in situ functional profiles of both chimneys, despite differences in microbial community composition and venting regime. Carbon fixation on both chimneys seems to have been primarily mediated through the reverse tricarboxylic acid cycle and fueled by sulfur-oxidation, while the abundant metabolic potential for hydrogen oxidation and carbon fixation via the Calvin–Benson–Bassham cycle was hardly utilized. Notably, the highly diverse microbial community colonizing the analyzed black smoker chimney had a highly redundant metabolic potential. In contrast, the considerably less diverse community colonizing the diffusely venting chimney displayed a higher metabolic versatility. An increased diversity on the phylogenetic level is thus not directly linked to an increased metabolic diversity in microbial communities that colonize hydrothermal chimneys. PMID:29696004

Lactobacillus plantarum IFPL935 favors the initial metabolism of red wine polyphenols when added to a colonic microbiota.

PubMed

Barroso, Elvira; Sánchez-Patán, Fernando; Martín-Alvarez, Pedro J; Bartolomé, Begoña; Moreno-Arribas, María Victoria; Peláez, Carmen; Requena, Teresa; van de Wiele, Tom; Martínez-Cuesta, M Carmen

2013-10-23

This work aimed to unravel the role of Lactobacillus plantarum IFPL935 strain in the colonic metabolism of a polyphenolic red wine extract, when added to a complex human colonic microbiota from the dynamic simulator of the human intestinal microbial ecosystem (SHIME). The concentration of microbial-derived phenolic metabolites and microbial community changes along with fermentative and proteolytic activities were monitored. The results showed that L. plantarum IFPL935 significantly increased the concentration of the initial microbial ring-fission catabolite of catechins and procyanidins, diphenylpropanol, and, similarly, 4-hydroxy-5-(3'-hydroxyphenyl)valeric acid production. Overall, the addition of L. plantarum IFPL935 did not have an impact on the total concentration of phenolic metabolites, except for batches inoculated with colonic microbiota from the effluent compartment (EC), where the figures were significantly higher when L. plantarum IFPL935 was added (24 h). In summary, the data highlighted that L. plantarum IFPL935 may have an impact on the bioavailability of these dietary polyphenols. Some of the microbial-derived metabolites may play a key role in the protective effects that have been linked to a polyphenol-rich diet.

Controls on development and diversity of Early Archean stromatolites

PubMed Central

Allwood, Abigail C.; Grotzinger, John P.; Knoll, Andrew H.; Burch, Ian W.; Anderson, Mark S.; Coleman, Max L.; Kanik, Isik

2009-01-01

The ≈3,450-million-year-old Strelley Pool Formation in Western Australia contains a reef-like assembly of laminated sedimentary accretion structures (stromatolites) that have macroscale characteristics suggestive of biological influence. However, direct microscale evidence of biology—namely, organic microbial remains or biosedimentary fabrics—has to date eluded discovery in the extensively-recrystallized rocks. Recently-identified outcrops with relatively good textural preservation record microscale evidence of primary sedimentary processes, including some that indicate probable microbial mat formation. Furthermore, we find relict fabrics and organic layers that covary with stromatolite morphology, linking morphologic diversity to changes in sedimentation, seafloor mineral precipitation, and inferred microbial mat development. Thus, the most direct and compelling signatures of life in the Strelley Pool Formation are those observed at the microscopic scale. By examining spatiotemporal changes in microscale characteristics it is possible not only to recognize the presence of probable microbial mats during stromatolite development, but also to infer aspects of the biological inputs to stromatolite morphogenesis. The persistence of an inferred biological signal through changing environmental circumstances and stromatolite types indicates that benthic microbial populations adapted to shifting environmental conditions in early oceans. PMID:19515817

The players may change but the game remains: network analyses of ruminal microbiomes suggest taxonomic differences mask functional similarity.

PubMed

Taxis, Tasia M; Wolff, Sara; Gregg, Sarah J; Minton, Nicholas O; Zhang, Chiqian; Dai, Jingjing; Schnabel, Robert D; Taylor, Jeremy F; Kerley, Monty S; Pires, J Chris; Lamberson, William R; Conant, Gavin C

2015-11-16

By mapping translated metagenomic reads to a microbial metabolic network, we show that ruminal ecosystems that are rather dissimilar in their taxonomy can be considerably more similar at the metabolic network level. Using a new network bi-partition approach for linking the microbial network to a bovine metabolic network, we observe that these ruminal metabolic networks exhibit properties consistent with distinct metabolic communities producing similar outputs from common inputs. For instance, the closer in network space that a microbial reaction is to a reaction found in the host, the lower will be the variability of its enzyme copy number across hosts. Similarly, these microbial enzymes that are nearby to host nodes are also higher in copy number than are more distant enzymes. Collectively, these results demonstrate a widely expected pattern that, to our knowledge, has not been explicitly demonstrated in microbial communities: namely that there can exist different community metabolic networks that have the same metabolic inputs and outputs but differ in their internal structure. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Early microbial contact, the breast milk microbiome and child health.

PubMed

Rautava, S

2016-02-01

The significance of contact with microbes in early life for subsequent health has been the subject of intense research during the last 2 decades. Disturbances in the establishment of the indigenous intestinal microbiome caused by cesarean section delivery or antibiotic exposure in early life have been linked to the risk of immune-mediated and inflammatory conditions such as atopic disorders, inflammatory bowel disease and obesity later in life. Distinct microbial populations have recently been discovered at maternal sites including the amniotic cavity and breast milk, as well as meconium, which have previously been thought to be sterile. Our understanding of the impact of fetal microbial contact on health outcomes is still rudimentary. Breast milk is known to modulate immune and metabolic programming. The breast milk microbiome is hypothesized to guide infant gut colonization and is affected by maternal health status and mode of delivery. Immunomodulatory factors in breast milk interact with the maternal and infant gut microbiome and may mediate some of the health benefits associated with breastfeeding. The intimate connection between the mother and the fetus or the infant is a potential target for microbial therapeutic interventions aiming to support healthy microbial contact and protect against disease.

Citrate and malonate increase microbial activity and alter microbial community composition in uncontaminated and diesel-contaminated soil microcosms

NASA Astrophysics Data System (ADS)

Martin, Belinda C.; George, Suman J.; Price, Charles A.; Shahsavari, Esmaeil; Ball, Andrew S.; Tibbett, Mark; Ryan, Megan H.

2016-09-01

Petroleum hydrocarbons (PHCs) are among the most prevalent sources of environmental contamination. It has been hypothesized that plant root exudation of low molecular weight organic acid anions (carboxylates) may aid degradation of PHCs by stimulating heterotrophic microbial activity. To test their potential implication for bioremediation, we applied two commonly exuded carboxylates (citrate and malonate) to uncontaminated and diesel-contaminated microcosms (10 000 mg kg-1; aged 40 days) and determined their impact on the microbial community and PHC degradation. Every 48 h for 18 days, soil received 5 µmol g-1 of (i) citrate, (ii) malonate, (iii) citrate + malonate or (iv) water. Microbial activity was measured daily as the flux of CO2. After 18 days, changes in the microbial community were assessed by a community-level physiological profile (CLPP) and 16S rRNA bacterial community profiles determined by denaturing gradient gel electrophoresis (DGGE). Saturated PHCs remaining in the soil were assessed by gas chromatography-mass spectrometry (GC-MS). Cumulative soil respiration increased 4- to 6-fold with the addition of carboxylates, while diesel contamination resulted in a small, but similar, increase across all carboxylate treatments. The addition of carboxylates resulted in distinct changes to the microbial community in both contaminated and uncontaminated soils but only a small increase in the biodegradation of saturated PHCs as measured by the n-C17 : pristane biomarker. We conclude that while the addition of citrate and malonate had little direct effect on the biodegradation of saturated hydrocarbons present in diesel, their effect on the microbial community leads us to suggest further studies using a variety of soils and organic acids, and linked to in situ studies of plants, to investigate the role of carboxylates in microbial community dynamics.

Are Microbial Nanowires Responsible for Geoelectrical Changes at Hydrocarbon Contaminated Sites?

NASA Astrophysics Data System (ADS)

Hager, C.; Atekwana, E. A.; Gorby, Y. A.; Duris, J. W.; Allen, J. P.; Atekwana, E. A.; Ownby, C.; Rossbach, S.

2007-05-01

Significant advances in near-surface geophysics and biogeophysics in particular, have clearly established a link between geoelectrical response and the growth and enzymatic activities of microbes in geologic media. Recent studies from hydrocarbon contaminated sites suggest that the activities of distinct microbial populations, specifically syntrophic, sulfate reducing, and dissimilatory iron reducing microbial populations are a contributing factor to elevated sediment conductivity. However, a fundamental mechanistic understanding of the processes and sources resulting in the measured electrical response remains uncertain. The recent discovery of bacterial nanowires and their electron transport capabilities suggest that if bacterial nanowires permeate the subsurface, they may in part be responsible for the anomalous conductivity response. In this study we investigated the microbial population structure, the presence of nanowires, and microbial-induced alterations of a hydrocarbon contaminated environment and relate them to the sediments' geoelectrical response. Our results show that microbial communities varied substantially along the vertical gradient and at depths where hydrocarbons saturated the sediments, ribosomal intergenic spacer analysis (RISA) revealed signatures of microbial communities adapted to hydrocarbon impact. In contrast, RISA profiles from a background location showed little community variations with depth. While all sites showed evidence of microbial activity, a scanning electron microscope (SEM) study of sediment from the contaminated location showed pervasive development of "nanowire-like structures" with morphologies consistent with nanowires from laboratory experiments. SEM analysis suggests extensive alteration of the sediments by microbial Activity. We conclude that, excess organic carbon (electron donor) but limited electron acceptors in these environments cause microorganisms to produce nanowires to shuttle the electrons as they seek for distant electron acceptors. Hence, electron flow via bacterial nanowires may contribute to the geoelectrical response.

Bacterial and Archaeal Lipids Recovered from Subsurface Evaporites of Dalangtan Playa on the Tibetan Plateau and Their Astrobiological Implications

NASA Astrophysics Data System (ADS)

Cheng, Ziye; Xiao, Long; Wang, Hongmei; Yang, Huan; Li, Jingjing; Huang, Ting; Xu, Yi; Ma, Nina

2017-11-01

Qaidam Basin (Tibetan Plateau) is considered an applicable analogue to Mars with regard to sustained extreme aridity and abundant evaporites. To investigate the possibility of the preservation of microbial lipids under these Mars analog conditions, we conducted a mineralogical and organic geochemistry study on samples collected from two Quaternary sections in Dalangtan Playa, northwestern Qaidam Basin, which will enhance our understanding of the potential preservation of molecular biomarkers on Mars. Two sedimentary units were identified along two profiles: one salt unit characterized by a predominance of gypsum and halite, and one detrital unit with a decrease of gypsum and halite and enrichment in siliciclastic minerals. Bacterial fatty acids and archaeal acyclic diether and tetraether membrane lipids were detected, and they varied throughout the sections in concentration and abundance. Bacterial and archaeal biomolecules indicate a dominance of Gram-positive bacteria and halophilic archaea in this hypersaline ecosystem that is similar to those in other hypersaline environments. Furthermore, the abundance of bacterial lipids decreases with the increase of salinity, whereas archaeal lipids showed a reverse trend. The detection of microbial lipids in hypersaline environments would indicate, for example on Mars, a high potential for the detection of microbial biomarkers in evaporites over geological timescales.

Multiplexed chemostat system for quantification of biodiversity and ecosystem functioning in anaerobic digestion

PubMed Central

Plouchart, Diane; Guizard, Guillaume; Latrille, Eric

2018-01-01

Continuous cultures in chemostats have proven their value in microbiology, microbial ecology, systems biology and bioprocess engineering, among others. In these systems, microbial growth and ecosystem performance can be quantified under stable and defined environmental conditions. This is essential when linking microbial diversity to ecosystem function. Here, a new system to test this link in anaerobic, methanogenic microbial communities is introduced. Rigorously replicated experiments or a suitable experimental design typically require operating several chemostats in parallel. However, this is labor intensive, especially when measuring biogas production. Commercial solutions for multiplying reactors performing continuous anaerobic digestion exist but are expensive and use comparably large reactor volumes, requiring the preparation of substantial amounts of media. Here, a flexible system of Lab-scale Automated and Multiplexed Anaerobic Chemostat system (LAMACs) with a working volume of 200 mL is introduced. Sterile feeding, biomass wasting and pressure monitoring are automated. One module containing six reactors fits the typical dimensions of a lab bench. Thanks to automation, time required for reactor operation and maintenance are reduced compared to traditional lab-scale systems. Several modules can be used together, and so far the parallel operation of 30 reactors was demonstrated. The chemostats are autoclavable. Parameters like reactor volume, flow rates and operating temperature can be freely set. The robustness of the system was tested in a two-month long experiment in which three inocula in four replicates, i.e., twelve continuous digesters were monitored. Statistically significant differences in the biogas production between inocula were observed. In anaerobic digestion, biogas production and consequently pressure development in a closed environment is a proxy for ecosystem performance. The precision of the pressure measurement is thus crucial. The measured maximum and minimum rates of gas production could be determined at the same precision. The LAMACs is a tool that enables us to put in practice the often-demanded need for replication and rigorous testing in microbial ecology as well as bioprocess engineering. PMID:29518106

Plant, Microbiome, and Biogeochemistry: Quantifying moss-associated N fixation in Alaska

NASA Astrophysics Data System (ADS)

Stuart, J.; Mack, M. C.; Holland Moritz, H.; Fierer, N.; McDaniels, S.; Lewis, L.

2017-12-01

The future carbon (C) sequestration potential of the Arctic and boreal zones, currently the largest terrestrial C sink globally, is linked to nitrogen (N) cycling and N availability vis-a-vis C accumulation and plant species composition. Pristine environments in Alaska have low anthropogenic N deposition (<1 kg N ha-1 yr-1), and the main source of new N to these ecosystems is through previously overlooked N-fixation from microbial communities on mosses. Despite the importance of moss associated N-fixation, the relationship between moss species, microbial communities, and fixation rates remains ambiguous. In the summer of 2016, the fixation rates of 20 moss species from sites around both Fairbanks and Toolik Lake were quantified using 15N2 incubations. Subsequently, the microbial community and moss genome of the samples were also analyzed by collaborators. The most striking result is that all sampled moss genera fixed N, including well-studied feather mosses such as Hylocomium splendens and Pleurozium schreberi as well as less common but ecologically relevant mosses such as Aulacomnium spp., Dicranum spp., Ptilium crista-castrensis, and Tomentypnum nitens. Across all samples, preliminary fixation rates ranged from 0.004-19.994 µg N g-1 moss d-1. Depending upon percent cover, moss-associated N fixation is the largest input of new N to the ecosystem. Given this, linking variation in N-fixation rates to microbial and moss community structures can be helpful in predicting future trends of C and N cycling in northern latitudes. Vegetation changes, alterations in downstream biogeochemical N processes, and anthropogenic N deposition could all interact with or alter moss associated N-fixation, thereby changing ecosystem N inputs. Further elucidation of the species level signal in N-fixation rates and microbial community will augment our knowledge of N cycling in northern latitudes, both current and future.

High-resolution (SIMS) versus bulk sulfur isotope patterns of pyrite in Proterozoic microbialites with diverse mat textures

NASA Astrophysics Data System (ADS)

Gomes, M. L.; Fike, D. A.; Bergmann, K.; Knoll, A. H.

2015-12-01

Sulfur (S) isotope signatures of sedimentary pyrite preserved in marine rocks provide a rich suite of information about changes in biogeochemical cycling associated with the evolution of microbial metabolisms and oxygenation of Earth surface environments. Conventionally, these S isotope records are based on bulk rock measurements. Yet, in modern microbial mat environments, S isotope compositions of sulfide can vary by up to 40‰ over a spatial range of ~ 1 mm. Similar ranges of S isotope variability have been found in Archean pyrite grains using both Secondary Ion Mass Spectrometry and other micro-analytical techniques. These micron-scale patterns have been linked to changes in rates of microbial sulfate reduction and/or sulfide oxidation, isotopic distillation of the sulfate reservoir due to microbial sulfate reduction, and post-depositional alteration. Fine-scale mapping of S isotope compositions of pyrite can thus be used to differentiate primary environmental signals from post-depositional overprinting - improving our understanding of both. Here, we examine micron-scale S isotope patterns of pyrite in microbialites from the Mesoproterozoic-Neoproterozoic Sukhaya Tunguska Formation and Neoproterozoic Draken Formation in order to explore S isotope variability associated with different mat textures and pyrite grain morphologies. A primary goal is to link modern observations of how sulfide spatial isotope distributions reflect active microbial communities present at given depths in the mats to ancient processes driving fine-sale pyrite variability in microbialites. We find large (up to 60‰) S isotope variability within a spatial range of less than 2.5cm. The micron-scale S isotope measurements converge around the S isotope composition of pyrite extracted from bulk samples of the same microbialites. These micron-scale pyrite S isotope patterns have the potential to reveal important information about ancient biogeochemical cycling in Proterozoic mat environments with implications for interpreting S isotope signatures from the geological record.

Short-term bioavailability of carbon in soil organic matter fractions of different particle sizes and densities in grassland ecosystems.

PubMed

Breulmann, Marc; Masyutenko, Nina Petrovna; Kogut, Boris Maratovich; Schroll, Reiner; Dörfler, Ulrike; Buscot, François; Schulz, Elke

2014-11-01

The quality, stability and availability of organic carbon (OC) in soil organic matter (SOM) can vary widely between differently managed ecosystems. Several approaches have been developed for isolating SOM fractions to examine their ecological roles, but links between the bioavailability of the OC of size-density fractions and soil microbial communities have not been previously explored. Thus, in the presented laboratory study we investigated the potential bioavailability of OC and the structure of associated microbial communities in different particle-size and density fractions of SOM. For this we used samples from four grassland ecosystems with contrasting management intensity regimes and two soil types: a Haplic Cambisol and a typical Chernozem. A combined size-density fractionation protocol was applied to separate clay-associated SOM fractions (CF1, <1 μm; CF2, 1-2 μm) from light SOM fractions (LF1, <1.8 g cm(-3); LF2, 1.8-2.0 g cm(-3)). These fractions were used as carbon sources in a respiration experiment to determine their potential bioavailability. Measured CO2-release was used as an index of substrate accessibility and linked to the soil microbial community structure, as determined by phospholipid fatty acids (PLFA) analysis. Several key factors controlling decomposition processes, and thus the potential bioavailability of OC, were identified: management intensity and the plant community composition of the grasslands (both of which affect the chemical composition and turnover of OC) and specific properties of individual SOM fractions. The PLFA patterns highlighted differences in the composition of microbial communities associated with the examined grasslands, and SOM fractions, providing the first broad insights into their active microbial communities. From observed interactions between abiotic and biotic factors affecting the decomposition of SOM fractions we demonstrate that increasing management intensity could enhance the potential bioavailability of OC, not only in the active and intermediate SOM pools, but also in the passive pool. Copyright © 2014 Elsevier B.V. All rights reserved.

Diet shifts provoke complex and variable changes in the metabolic networks of the ruminal microbiome.

PubMed

Wolff, Sara M; Ellison, Melinda J; Hao, Yue; Cockrum, Rebecca R; Austin, Kathy J; Baraboo, Michael; Burch, Katherine; Lee, Hyuk Jin; Maurer, Taylor; Patil, Rocky; Ravelo, Andrea; Taxis, Tasia M; Truong, Huan; Lamberson, William R; Cammack, Kristi M; Conant, Gavin C

2017-06-08

Grazing mammals rely on their ruminal microbial symbionts to convert plant structural biomass into metabolites they can assimilate. To explore how this complex metabolic system adapts to the host animal's diet, we inferred a microbiome-level metabolic network from shotgun metagenomic data. Using comparative genomics, we then linked this microbial network to that of the host animal using a set of interface metabolites likely to be transferred to the host. When the host sheep were fed a grain-based diet, the induced microbial metabolic network showed several critical differences from those seen on the evolved forage-based diet. Grain-based (e.g., concentrate) diets tend to be dominated by a smaller set of reactions that employ metabolites that are nearer in network space to the host's metabolism. In addition, these reactions are more central in the network and employ substrates with shorter carbon backbones. Despite this apparent lower complexity, the concentrate-associated metabolic networks are actually more dissimilar from each other than are those of forage-fed animals. Because both groups of animals were initially fed on a forage diet, we propose that the diet switch drove the appearance of a number of different microbial networks, including a degenerate network characterized by an inefficient use of dietary nutrients. We used network simulations to show that such disparate networks are not an unexpected result of a diet shift. We argue that network approaches, particularly those that link the microbial network with that of the host, illuminate aspects of the structure of the microbiome not seen from a strictly taxonomic perspective. In particular, different diets induce predictable and significant differences in the enzymes used by the microbiome. Nonetheless, there are clearly a number of microbiomes of differing structure that show similar functional properties. Changes such as a diet shift uncover more of this type of diversity.

A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer.

PubMed

Tully, Benjamin J; Wheat, C Geoff; Glazer, Brain T; Huber, Julie A

2018-01-01

The rock-hosted subseafloor crustal aquifer harbors a reservoir of microbial life that may influence global marine biogeochemical cycles. Here we utilized metagenomic libraries of crustal fluid samples from North Pond, located on the flanks of the Mid-Atlantic Ridge, a site with cold, oxic subseafloor fluid circulation within the upper basement to query microbial diversity. Twenty-one samples were collected during a 2-year period to examine potential microbial metabolism and community dynamics. We observed minor changes in the geochemical signatures over the 2 years, yet the microbial community present in the crustal fluids underwent large shifts in the dominant taxonomic groups. An analysis of 195 metagenome-assembled genomes (MAGs) were generated from the data set and revealed a connection between litho- and autotrophic processes, linking carbon fixation to the oxidation of sulfide, sulfur, thiosulfate, hydrogen, and ferrous iron in members of the Proteobacteria, specifically the Alpha-, Gamma- and Zetaproteobacteria, the Epsilonbacteraeota and the Planctomycetes. Despite oxic conditions, analysis of the MAGs indicated that members of the microbial community were poised to exploit hypoxic or anoxic conditions through the use of microaerobic cytochromes, such as cbb 3 - and bd-type cytochromes, and alternative electron acceptors, like nitrate and sulfate. Temporal and spatial trends from the MAGs revealed a high degree of functional redundancy that did not correlate with the shifting microbial community membership, suggesting functional stability in mediating subseafloor biogeochemical cycles. Collectively, the repeated sampling at multiple sites, together with the successful binning of hundreds of genomes, provides an unprecedented data set for investigation of microbial communities in the cold, oxic crustal aquifer.

Integrated metagenomic analysis of the rumen microbiome of cattle reveals key biological mechanisms associated with methane traits.

PubMed

Wang, Haiying; Zheng, Huiru; Browne, Fiona; Roehe, Rainer; Dewhurst, Richard J; Engel, Felix; Hemmje, Matthias; Lu, Xiangwu; Walsh, Paul

2017-07-15

Methane is one of the major contributors to global warming. The rumen microbiota is directly involved in methane production in cattle. The link between variation in rumen microbial communities and host genetics has important applications and implications in bioscience. Having the potential to reveal the full extent of microbial gene diversity and complex microbial interactions, integrated metagenomics and network analysis holds great promise in this endeavour. This study investigates the rumen microbial community in cattle through the integration of metagenomic and network-based approaches. Based on the relative abundance of 1570 microbial genes identified in a metagenomics analysis, the co-abundance network was constructed and functional modules of microbial genes were identified. One of the main contributions is to develop a random matrix theory-based approach to automatically determining the correlation threshold used to construct the co-abundance network. The resulting network, consisting of 549 microbial genes and 3349 connections, exhibits a clear modular structure with certain trait-specific genes highly over-represented in modules. More specifically, all the 20 genes previously identified to be associated with methane emissions are found in a module (hypergeometric test, p<10 -11 ). One third of genes are involved in methane metabolism pathways. The further examination of abundance profiles across 8 samples of genes highlights that the revealed pattern of metagenomics abundance has a strong association with methane emissions. Furthermore, the module is significantly enriched with microbial genes encoding enzymes that are directly involved in methanogenesis (hypergeometric test, p<10 -9 ). Copyright © 2017 Elsevier Inc. All rights reserved.

The dissipation of three fungicides in a biobed organic substrate and their impact on the structure and activity of the microbial community.

PubMed

Marinozzi, Maria; Coppola, Laura; Monaci, Elga; Karpouzas, Dimitrios G; Papadopoulou, Evangelia; Menkissoglu-Spiroudi, Urania; Vischetti, Costantino

2013-04-01

Biopurification systems (BPS) have been introduced to minimise the risk for point source contamination of natural water resources by pesticides. Their depuration efficiency relies mostly on the high biodegradation of their packing substrate (biomixture). Despite that, little is known regarding the interactions between biomixture microflora and pesticides, especially fungicides which are expected to have a higher impact on the microbial community. This study reports the dissipation of the fungicides azoxystrobin (AZX), fludioxonil (FL) and penconazole (PC), commonly used in vineyards, in a biomixture composed of pruning residues and straw used in vineyard BPS. The impact of fungicides on the microbial community was also studied via microbial biomass carbon, basal respiration and phospholipid fatty acid analysis. AZX dissipated faster (t1/2 = 30.1 days) than PC (t1/2 = 99.0 days) and FL (t1/2 = 115.5 days). Fungicides differently affected the microbial community. PC showed the highest adverse effect on both the size and the activity of the biomixture microflora. A significant change in the structure of the microbial community was noted for PC and FL, and it was attributed to a rapid inhibition of the fungal fraction while bacteria showed a delayed response which was attributed to indirect effects by the late proliferation of fungi. All effects observed were transitory and a full recovery of microbial indices was observed 60 days post-application. Overall, no clear link between pesticide persistence and microbial responses was observed stressing the complex nature of interactions between pesticides in microflora in BPS.

Responses of microbial tolerance to heavy metals along a century-old metal ore pollution gradient in a subarctic birch forest.

PubMed

Rousk, Johannes; Rousk, Kathrin

2018-05-07

Heavy metals are some of the most persistent and potent anthropogenic environmental contaminants. Although heavy metals may compromise microbial communities and soil fertility, it is challenging to causally link microbial responses to heavy metals due to various confounding factors, including correlated soil physicochemistry or nutrient availability. A solution is to investigate whether tolerance to the pollutant has been induced, called Pollution Induced Community Tolerance (PICT). In this study, we investigated soil microbial responses to a century-old gradient of metal ore pollution in an otherwise pristine subarctic birch forest generated by a railway source of iron ore transportation. To do this, we determined microbial biomass, growth, and respiration rates, and bacterial tolerance to Zn and Cu in replicated distance transects (1 m-4 km) perpendicular to the railway. Microbial biomass, growth and respiration rates were stable across the pollution gradient. The microbial community structure could be distinguished between sampled distances, but most of the variation was explained by soil pH differences, and it did not align with distance from the railroad pollution source. Bacterial tolerance to Zn and Cu started from background levels at 4 km distance from the pollution source, and remained at background levels for Cu throughout the gradient. Yet, bacterial tolerance to Zn increased 10-fold 100 m from the railway source. Our results show that the microbial community structure, size and performance remained unaffected by the metal ore exposure, suggesting no impact on ecosystem functioning. Copyright © 2018 Elsevier Ltd. All rights reserved.

High Microbial Diversity Promotes Soil Ecosystem Functioning.

PubMed

Maron, Pierre-Alain; Sarr, Amadou; Kaisermann, Aurore; Lévêque, Jean; Mathieu, Olivier; Guigue, Julien; Karimi, Battle; Bernard, Laetitia; Dequiedt, Samuel; Terrat, Sébastien; Chabbi, Abad; Ranjard, Lionel

2018-05-01

In soil, the link between microbial diversity and carbon transformations is challenged by the concept of functional redundancy. Here, we hypothesized that functional redundancy may decrease with increasing carbon source recalcitrance and that coupling of diversity with C cycling may change accordingly. We manipulated microbial diversity to examine how diversity decrease affects the decomposition of easily degradable (i.e., allochthonous plant residues) versus recalcitrant (i.e., autochthonous organic matter) C sources. We found that a decrease in microbial diversity (i) affected the decomposition of both autochthonous and allochthonous carbon sources, thereby reducing global CO 2 emission by up to 40%, and (ii) shaped the source of CO 2 emission toward preferential decomposition of most degradable C sources. Our results also revealed that the significance of the diversity effect increases with nutrient availability. Altogether, these findings show that C cycling in soil may be more vulnerable to microbial diversity changes than expected from previous studies, particularly in ecosystems exposed to nutrient inputs. Thus, concern about the preservation of microbial diversity may be highly relevant in the current global-change context assumed to impact soil biodiversity and the pulse inputs of plant residues and rhizodeposits into the soil. IMPORTANCE With hundreds of thousands of taxa per gram of soil, microbial diversity dominates soil biodiversity. While numerous studies have established that microbial communities respond rapidly to environmental changes, the relationship between microbial diversity and soil functioning remains controversial. Using a well-controlled laboratory approach, we provide empirical evidence that microbial diversity may be of high significance for organic matter decomposition, a major process on which rely many of the ecosystem services provided by the soil ecosystem. These new findings should be taken into account in future studies aimed at understanding and predicting the functional consequences of changes in microbial diversity on soil ecosystem services and carbon storage in soil. Copyright © 2018 American Society for Microbiology.

Linkages among geophysical facies, microbial composition, biogeochemical rates, and seasonal hydrology in the hyporheic zone

NASA Astrophysics Data System (ADS)

Stegen, J.

2016-12-01

The hyporheic zone is a critical ecosystem transition that links terrestrial, aquatic, and subsurface domains. To understand connections among physical, microbial, and biogeochemical components of the hyporheic zone, we obtained freeze cores along the Columbia River in the Hanford 300 Area and performed geologic, molecular, and microbial assays. Mud and sand content were found to be the primary drivers of microbial community attributes (in particular, of nitrite and carbon oxidizers). Microbial community analysis revealed an abundance of nitrifying Archaea (Thaumarchaea) and an absence of nitrifiying Bacteria. Network analysis revealed significant negative correlations between sand content and some statistical modules of microbial taxa, perhaps indicating the importance of pore water residence time on community composition. A similar set of microbial modules was positively correlated with total organic carbon. One such module that also positively correlated with aerobic metabolic rates was dominated by Thaumarchaea and Nitrospira, suggesting that ammonia oxidation was the dominant aerobic process. We also examined temporal changes in hyporheic microbial structure and activity through repeated sampling of attached and pore water microbes across a spatial gradient. We found that microbial communities remained distinct in river, hyporheic, and inland zones across seasonal variation in hydrologic mixing conditions. One reason was temperature-driven increases in microbial species richness in the hyporheic zone. We show that the relative importance of ecological selection and dispersal varied across environments and across geographic zones. Our results also indicated that while selection imposed short-term constraints on microbial community structure, hyporheic sediment communities did not respond to short-term hydrologic variation. Importantly, we demonstrated that the influence of selective pressures varied with phylogenetic affiliation, which may have been responsible for seasonal increases in Thaumarchaea and aerobic activity. Our results elucidate spatiotemporal shifts in composition and activity of hyporheic microbes across sedimentary and seasonal gradients in pore water environments that correlate with the contribution of Thaumarchaea to aerobic processes.

Natural products: Hunting microbial metabolites

NASA Astrophysics Data System (ADS)

Schmidt, Eric W.

2015-05-01

Symbiotic bacteria synthesize many specialized small molecules; however, establishing the role these chemicals play in human health and disease has been difficult. Now, the chemical structure and mechanism of the Escherichia coli product colibactin provides insight into the link between this secondary metabolite and colorectal cancer.

Identifying the Linkages Between Microbial Activity and Gas Flux of Subaerial Volcanic Environments: A Guide to Exploring Magmatic Planets and Moons

NASA Astrophysics Data System (ADS)

Miller, H. A.; Lopez, T. M.; Fischer, T. P.; Schrenk, M. O.

2017-11-01

Promising contemporary analogs of habitable environments are fumaroles associated with active volcanism. Experimental studies linking sediments, microbes, and volatile outgassing may lead to new bio- or geosignatures of habitability.

Effect of different disinfection protocols on microbial and biofilm contamination of dental unit waterlines in community dental practices.

PubMed

Dallolio, Laura; Scuderi, Amalia; Rini, Maria S; Valente, Sabrina; Farruggia, Patrizia; Sabattini, Maria A Bucci; Pasquinelli, Gianandrea; Acacci, Anna; Roncarati, Greta; Leoni, Erica

2014-02-18

Output water from dental unit waterlines (DUWLs) may be a potential source of infection for both dental healthcare staff and patients. This study compared the efficacy of different disinfection methods with regard to the water quality and the presence of biofilm in DUWLs. Five dental units operating in a public dental health care setting were selected. The control dental unit had no disinfection system; two were disinfected intermittently with peracetic acid/hydrogen peroxide 0.26% and two underwent continuous disinfection with hydrogen peroxide/silver ions (0.02%) and stabilized chlorine dioxide (0.22%), respectively. After three months of applying the disinfection protocols, continuous disinfection systems were more effective than intermittent systems in reducing the microbial contamination of the water, allowing compliance with the CDC guidelines and the European Council regulatory thresholds for drinking water. P. aeruginosa, Legionella spp, sulphite-reducing Clostridium spores, S. aureus and β-haemolytic streptococci were also absent from units treated with continuous disinfection. The biofilm covering the DUWLs was more extensive, thicker and more friable in the intermittent disinfection dental units than in those with continuous disinfection. Overall, the findings showed that the products used for continuous disinfection of dental unit waterlines showed statistically better results than the intermittent treatment products under the study conditions.

Effect of Different Disinfection Protocols on Microbial and Biofilm Contamination of Dental Unit Waterlines in Community Dental Practices

PubMed Central

Dallolio, Laura; Scuderi, Amalia; Rini, Maria S.; Valente, Sabrina; Farruggia, Patrizia; Bucci Sabattini, Maria A.; Pasquinelli, Gianandrea; Acacci, Anna; Roncarati, Greta; Leoni, Erica

2014-01-01

Output water from dental unit waterlines (DUWLs) may be a potential source of infection for both dental healthcare staff and patients. This study compared the efficacy of different disinfection methods with regard to the water quality and the presence of biofilm in DUWLs. Five dental units operating in a public dental health care setting were selected. The control dental unit had no disinfection system; two were disinfected intermittently with peracetic acid/hydrogen peroxide 0.26% and two underwent continuous disinfection with hydrogen peroxide/silver ions (0.02%) and stabilized chlorine dioxide (0.22%), respectively. After three months of applying the disinfection protocols, continuous disinfection systems were more effective than intermittent systems in reducing the microbial contamination of the water, allowing compliance with the CDC guidelines and the European Council regulatory thresholds for drinking water. P. aeruginosa, Legionella spp, sulphite-reducing Clostridium spores, S. aureus and β-haemolytic streptococci were also absent from units treated with continuous disinfection. The biofilm covering the DUWLs was more extensive, thicker and more friable in the intermittent disinfection dental units than in those with continuous disinfection. Overall, the findings showed that the products used for continuous disinfection of dental unit waterlines showed statistically better results than the intermittent treatment products under the study conditions. PMID:24552789

Capturing prokaryotic dark matter genomes.

PubMed

Gasc, Cyrielle; Ribière, Céline; Parisot, Nicolas; Beugnot, Réjane; Defois, Clémence; Petit-Biderre, Corinne; Boucher, Delphine; Peyretaillade, Eric; Peyret, Pierre

2015-12-01

Prokaryotes are the most diverse and abundant cellular life forms on Earth. Most of them, identified by indirect molecular approaches, belong to microbial dark matter. The advent of metagenomic and single-cell genomic approaches has highlighted the metabolic capabilities of numerous members of this dark matter through genome reconstruction. Thus, linking functions back to the species has revolutionized our understanding of how ecosystem function is sustained by the microbial world. This review will present discoveries acquired through the illumination of prokaryotic dark matter genomes by these innovative approaches. Copyright © 2015 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Seasonal microbial and environmental parameters at Crocker Reef, Florida Keys, 2014–2015

USGS Publications Warehouse

Kellogg, Christina A.; Yates, Kimberly K.; Lawler, Stephanie N.; Moore, Christopher S.; Smiley, Nathan A.

2015-11-04

Microbial measurements included enumeration of total bacteria, enumeration of virus-like particles, and plate counts of Vibrio spp. colony-forming units (CFU). These measurements were intended to give a sense of any seasonal changes in the total microbial load and to provide an indication of water quality. Additional environmental parameters measured included water temperature, salinity, dissolved oxygen, and pH. Four sites (table 1) were intensively sampled for periods of approximately 48 hours during summer (July 2014) and winter (January–February 2015), during which water samples were collected every 4 hours for analysis, except when prevented by weather conditions.

Reconnaissance of 47 antibiotics and associated microbial risks in seafood sold in the United States.

PubMed

Done, Hansa Y; Halden, Rolf U

2015-01-23

Aquaculture production has nearly tripled in the last two decades, bringing with it a significant increase in the use of antibiotics. Using liquid chromatography/tandem mass spectrometry (LC-MS/MS), the presence of 47 antibiotics was investigated in U.S. purchased shrimp, salmon, catfish, trout, tilapia, and swai originating from 11 different countries. All samples (n=27) complied with U.S. FDA regulations and five antibiotics were detected above the limits of detection: oxytetracycline (in wild shrimp, 7.7ng/g of fresh weight; farmed tilapia, 2.7; farmed salmon, 8.6; farmed trout with spinal deformities, 3.9), 4-epioxytetracycline (farmed salmon, 4.1), sulfadimethoxine (farmed shrimp, 0.3), ormetoprim (farmed salmon, 0.5), and virginiamycin (farmed salmon marketed as antibiotic-free, 5.2). A literature review showed that sub-regulatory levels of antibiotics, as found here, can promote resistance development; publications linking aquaculture to this have increased more than 8-fold from 1991 to 2013. Although this study was limited in size and employed sample pooling, it represents the largest reconnaissance of antibiotics in U.S. seafood to date, providing data on previously unmonitored antibiotics and on farmed trout with spinal deformities. Results indicate low levels of antibiotic residues and general compliance with U.S. regulations. The potential for development of microbial drug resistance was identified as a key concern and research priority. Copyright © 2014 Elsevier B.V. All rights reserved.

Microwave-assisted cross-linking of milk proteins induced by microbial transglutaminase

NASA Astrophysics Data System (ADS)

Chen, Chun-Chi; Hsieh, Jung-Feng

2016-12-01

We investigated the combined effects of microbial transglutaminase (MTGase, 7.0 units/mL) and microwave irradiation (MI) on the polymerization of milk proteins at 30 °C for 3 h. The addition of MTGase caused the milk proteins to become polymerized, which resulted in the formation of components with a higher molecular-weight (>130 kDa). SDS-PAGE analysis revealed reductions in the protein content of β-lactoglobulin (β-LG), αS-casein (αS-CN), κ-casein (κ-CN) and β-casein (β-CN) to 50.4 ± 2.9, 33.5 ± 3.0, 4.2 ± 0.5 and 1.2 ± 0.1%, respectively. The use of MTGase in conjunction MI with led to a 3-fold increase in the rate of milk protein polymerization, compared to a sample that contained MTGase but did not undergo MI. Results of two-dimensional gel electrophoresis (2-DE) indicated that κ-CN, β-CN, a fraction of serum albumin (SA), β-LG, α-lactalbumin (α-LA), αs1-casein (αs1-CN), and αs2-casein (αs2-CN) were polymerized in the milk, following incubation with MTGase and MI at 30 °C for 1 h. Based on this result, the combined use of MTGase and MI appears to be a better way to polymerize milk proteins.

The role of microbial iron reduction in the formation of Proterozoic molar tooth structures

NASA Astrophysics Data System (ADS)

Hodgskiss, Malcolm S. W.; Kunzmann, Marcus; Poirier, André; Halverson, Galen P.

2018-01-01

Molar tooth structures are poorly understood early diagenetic, microspar-filled voids in clay-rich carbonate sediments. They are a common structure in sedimentary successions dating from 2600-720 Ma, but do not occur in rocks older or younger, with the exception of two isolated Ediacaran occurrences. Despite being locally volumetrically significant in carbonate rocks of this age, their formation and disappearance in the geological record remain enigmatic. Here we present iron isotope data, supported by carbon and oxygen isotopes, major and minor element concentrations, and total organic carbon and sulphur contents for 87 samples from units in ten different basins spanning ca. 1900-635 Ma. The iron isotope composition of molar tooth structures is almost always lighter (modal depletion of 2‰) than the carbonate or residue components in the host sediment. We interpret the isotopically light iron in molar tooth structures to have been produced by dissimilatory iron reduction utilising Fe-rich smectites and Fe-oxyhydroxides in the upper sediment column. The microbial conversion of smectite to illite results in a volume reduction of clay minerals (∼30%) while simultaneously increasing pore water alkalinity. When coupled with wave loading, this biogeochemical process is a viable mechanism to produce voids and subsequently precipitate carbonate minerals. The disappearance of molar tooth structures in the mid-Neoproterozoic is likely linked to a combination of a decrease in smectite abundance, a decline in the marine DIC reservoir, and an increase in the concentration of O2 in shallow seawater.

Characterization of fungi in office dust: Comparing results of microbial secondary metabolites, fungal internal transcribed spacer region sequencing, viable culture and other microbial indices.

PubMed

Park, J-H; Sulyok, M; Lemons, A R; Green, B J; Cox-Ganser, J M

2018-05-04

Recent developments in molecular and chemical methods have enabled the analysis of fungal DNA and secondary metabolites, often produced during fungal growth, in environmental samples. We compared 3 fungal analytical methods by analysing floor dust samples collected from an office building for fungi using viable culture, internal transcribed spacer (ITS) sequencing and secondary metabolites using liquid chromatography-tandem mass spectrometry. Of the 32 metabolites identified, 29 had a potential link to fungi with levels ranging from 0.04 (minimum for alternariol monomethylether) to 5700 ng/g (maximum for neoechinulin A). The number of fungal metabolites quantified per sample ranged from 8 to 16 (average = 13/sample). We identified 216 fungal operational taxonomic units (OTUs) with the number per sample ranging from 6 to 29 (average = 18/sample). We identified 37 fungal species using culture, and the number per sample ranged from 2 to 13 (average = 8/sample). Agreement in identification between ITS sequencing and culturing was weak (kappa = -0.12 to 0.27). The number of cultured fungal species poorly correlated with OTUs, which did not correlate with the number of metabolites. These suggest that using multiple measurement methods may provide an improved understanding of fungal exposures in indoor environments and that secondary metabolites may be considered as an additional source of exposure. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Coupling a continuous watershed-scale microbial fate and transport model with a stochastic dose-response model to estimate risk of illness in an urban watershed.

PubMed

Liao, Hehuan; Krometis, Leigh-Anne H; Kline, Karen

2016-05-01

Within the United States, elevated levels of fecal indicator bacteria (FIB) remain the leading cause of surface water-quality impairments requiring formal remediation plans under the federal Clean Water Act's Total Maximum Daily Load (TMDL) program. The sufficiency of compliance with numerical FIB criteria as the targeted endpoint of TMDL remediation plans may be questionable given poor correlations between FIB and pathogenic microorganisms and varying degrees of risk associated with exposure to different fecal pollution sources (e.g. human vs animal). The present study linked a watershed-scale FIB fate and transport model with a dose-response model to continuously predict human health risks via quantitative microbial risk assessment (QMRA), for comparison to regulatory benchmarks. This process permitted comparison of risks associated with different fecal pollution sources in an impaired urban watershed in order to identify remediation priorities. Results indicate that total human illness risks were consistently higher than the regulatory benchmark of 36 illnesses/1000 people for the study watershed, even when the predicted FIB levels were in compliance with the Escherichia coli geometric mean standard of 126CFU/100mL. Sanitary sewer overflows were associated with the greatest risk of illness. This is of particular concern, given increasing indications that sewer leakage is ubiquitous in urban areas, yet not typically fully accounted for during TMDL development. Uncertainty analysis suggested the accuracy of risk estimates would be improved by more detailed knowledge of site-specific pathogen presence and densities. While previous applications of the QMRA process to impaired waterways have mostly focused on single storm events or hypothetical situations, the continuous modeling framework presented in this study could be integrated into long-term water quality management planning, especially the United States' TMDL program, providing greater clarity to watershed stakeholders and decision-makers. Copyright © 2016 Elsevier B.V. All rights reserved.

Reverse osmosis for wash water recovery in space vehicles.

NASA Technical Reports Server (NTRS)

Lawrence, R. W.; Saltonstall, C. W., Jr.

1973-01-01

Tests were carried out on both synthetic and real wash water derived from clothes laundry to determine the utility of reverse osmosis in recovering the water for recycle use. A blend membrane made from cellulose di- and triacetates, and a cross-linked cellulose acetate/methacrylate were evaluated. Both were found acceptable. A number of detergents were evaluated, including a cationic detergent, sodium dodecyl sulfate, potassium palmitate, and sodium dodecylbenzenesulfonate. The tests were all made at a temperature of 165 F to minimize microbial growth. Long-term (15 to 30 day) runs were made at 600 and 400 psi on laundry water which was pretreated either by alum addition and sand filtration or by filtration only through 0.5 micron filters. A 30-day run was made using a 2-in. diameter by 22-in. long spiral module at 400 psig with filtering as the pretreatment. The membrane fouling by colloidal matter was found to be controllable. The unit produced initially 55 gal/day and 27 gal/day after 30 days.

Nitrogen Cycling in the Mycorrhizosphere: Multipartite Interactions and Plant Nitrogen Uptake Vary with Fertilization Legacy

NASA Astrophysics Data System (ADS)

Hestrin, R.; Lehmann, J.

2017-12-01

Soil microbes play an important role in rhizosphere nutrient cycling and plant productivity. In this study, the contributions of soil microbes to organic matter mineralization and plant nitrogen uptake were investigated using incubation and microcosm experiments. Microbial inocula included arbuscular mycorrhizal fungi and microbial communities sampled across a long-term gradient of nitrogen fertilization. Stable isotopes, nanoSIMS imaging, and phospholipid fatty acid analysis were used to track carbon and nitrogen movement from organic matter into microbes, mycorrhizal fungi, and plants. Results show that multipartite relationships between plants and microbes increased plant growth and access to nitrogen from organic matter, and that nitrogen fertilization history had a lasting effect on microbial contributions to fungal and plant nitrogen uptake. This research links rhizosphere ecology and land management with terrestrial biogeochemistry.

The Functional Impact of the Intestinal Microbiome on Mucosal Immunity and Systemic Autoimmunity

PubMed Central

Longman, Randy S.; Littman, Dan R.

2016-01-01

Purpose of Review This review will highlight recent advances functionally linking the gut microbiome with mucosal and systemic immune cell activation potentially underlying autoimmunity. Recent Findings Dynamic interactions between the gut microbiome and environmental cues (including diet and medicines) shape the effector potential of the microbial organ. Key bacteria and viruses have emerged, that, in defined microenvironments, play a critical role in regulating effector lymphocyte functions. The coordinated interactions between these different microbial kingdoms—including bacteria, helminths, and viruses (termed transkingdom interactions)—play a critical role in shaping immunity. Emerging strategies to identify immunologically-relevant microbes with the potential to regulate immune cell functions both at mucosal sites and systemically will likely define key diagnostic and therapeutic targets. Summary The microbiome constitutes a critical microbial organ with coordinated interactions that shape host immunity. PMID:26002030

Microbially mediated transformations of phosphorus in the sea: new views of an old cycle.

PubMed

Karl, David M

2014-01-01

Phosphorus (P) is a required element for life. Its various chemical forms are found throughout the lithosphere and hydrosphere, where they are acted on by numerous abiotic and biotic processes collectively referred to as the P cycle. In the sea, microorganisms are primarily responsible for P assimilation and remineralization, including recently discovered P reduction-oxidation bioenergetic processes that add new complexity to the marine microbial P cycle. Human-induced enhancement of the global P cycle via mining of phosphate-bearing rock will likely influence the pace of P-cycle dynamics, especially in coastal marine habitats. The inextricable link between the P cycle and cycles of other bioelements predicts future impacts on, for example, nitrogen fixation and carbon dioxide sequestration. Additional laboratory and field research is required to build a comprehensive understanding of the marine microbial P cycle.

Linking social and pathogen transmission networks using microbial genetics in giraffe (Giraffa camelopardalis).

PubMed

VanderWaal, Kimberly L; Atwill, Edward R; Isbell, Lynne A; McCowan, Brenda

2014-03-01

Although network analysis has drawn considerable attention as a promising tool for disease ecology, empirical research has been hindered by limitations in detecting the occurrence of pathogen transmission (who transmitted to whom) within social networks. Using a novel approach, we utilize the genetics of a diverse microbe, Escherichia coli, to infer where direct or indirect transmission has occurred and use these data to construct transmission networks for a wild giraffe population (Giraffe camelopardalis). Individuals were considered to be a part of the same transmission chain and were interlinked in the transmission network if they shared genetic subtypes of E. coli. By using microbial genetics to quantify who transmits to whom independently from the behavioural data on who is in contact with whom, we were able to directly investigate how the structure of contact networks influences the structure of the transmission network. To distinguish between the effects of social and environmental contact on transmission dynamics, the transmission network was compared with two separate contact networks defined from the behavioural data: a social network based on association patterns, and a spatial network based on patterns of home-range overlap among individuals. We found that links in the transmission network were more likely to occur between individuals that were strongly linked in the social network. Furthermore, individuals that had more numerous connections or that occupied 'bottleneck' positions in the social network tended to occupy similar positions in the transmission network. No similar correlations were observed between the spatial and transmission networks. This indicates that an individual's social network position is predictive of transmission network position, which has implications for identifying individuals that function as super-spreaders or transmission bottlenecks in the population. These results emphasize the importance of association patterns in understanding transmission dynamics, even for environmentally transmitted microbes like E. coli. This study is the first to use microbial genetics to construct and analyse transmission networks in a wildlife population and highlights the potential utility of an approach integrating microbial genetics with network analysis. © 2013 The Authors. Journal of Animal Ecology © 2013 British Ecological Society.

Dynamics of soil microbial communities in agroecosystems managed for biofuel production

USDA-ARS?s Scientific Manuscript database

Elevated atmospheric CO2 concentrations and their link to global climate change are stimulating efforts to reduce dependence on fossil fuels and increase use of alternative energy sources. Initial efforts to incorporate significant amounts of cellulosic ethanol into transportation fuels are focused ...

Microbial-driven arsenic cycling in rice paddies amended with monosodium methanearsonate

USDA-ARS?s Scientific Manuscript database

Rice consumption is the second largest contributor to human arsenic exposure worldwide and is linked to many serious diseases. Because rice is uniquely adapted for agricultural production under flooded soils, arsenic species solubilized in such environments can be effectively transported into plant ...

Using an Integrated, Multi-disciplinary Framework to Support Quantitative Microbial Risk Assessments

EPA Science Inventory

The Framework for Risk Analysis in Multimedia Environmental Systems (FRAMES) provides the infrastructure to link disparate models and databases seamlessly, giving an assessor the ability to construct an appropriate conceptual site model from a host of modeling choices, so a numbe...

Comparative performances of microbial capacitive deionization cell and microbial fuel cell fed with produced water from the Bakken shale.

PubMed

Shrestha, Namita; Chilkoor, Govinda; Wilder, Joseph; Ren, Zhiyong Jason; Gadhamshetty, Venkataramana

2018-06-01

This study evaluates and compares the performance of microbial fuel cells (MFCs) and microbial capacitive deionization cells (MCDCs) fed with wastewater produced from the Bakken shale. The produced water was characterized by high levels of dissolved solids and chemical oxygen demand (COD). Two-compartment MFCs and three-compartment MCDCs were evaluated under batch-fed mode using mixed microbial consortia in the anode, ferricyanide in the cathode, and produced water as the electrolyte in the anode and capacitive deionization units. COD removal in the MFCs was 88%, while that in the MCDCs was limited to 76%. The lower performance of the MCDCs was due to the large impedance (6600 Ω cm 2 ) compared with the MFCs (870 Ω cm 2 ). However, the MCDCs achieved two-fold higher removal of dissolved solids. Both the MFCs and MCDCs suffered from a higher impedance induced by fouling in the latter stages of the operation. Copyright © 2018 Elsevier B.V. All rights reserved.

Co-occurrence Networks Among Bacteria and Microbial Eukaryotes of Lake Baikal During a Spring Phytoplankton Bloom.

PubMed

Mikhailov, Ivan S; Zakharova, Yulia R; Bukin, Yuri S; Galachyants, Yuri P; Petrova, Darya P; Sakirko, Maria V; Likhoshway, Yelena V

2018-06-07

The pelagic zone of Lake Baikal is an ecological niche where phytoplankton bloom causes increasing microbial abundance in spring which plays a key role in carbon turnover in the freshwater lake. Co-occurrence patterns revealed among different microbes can be applied to predict interactions between the microbes and environmental conditions in the ecosystem. We used 454 pyrosequencing of 16S rRNA and 18S rRNA genes to study bacterial and microbial eukaryotic communities and their co-occurrence patterns at the pelagic zone of Lake Baikal during a spring phytoplankton bloom. We found that microbes within one domain mostly correlated positively with each other and are highly interconnected. The highly connected taxa in co-occurrence networks were operational taxonomic units (OTUs) of Actinobacteria, Bacteroidetes, Alphaproteobacteria, and autotrophic and unclassified Eukaryota which might be analogous to microbial keystone taxa. Constrained correspondence analysis revealed the relationships of bacterial and microbial eukaryotic communities with geographical location.

Linking TFT-LCD wastewater treatment performance to microbial population abundance of Hyphomicrobium and Thiobacillus spp.

PubMed

Fukushima, Toshikazu; Whang, Liang-Ming; Chen, Po-Chun; Putri, Dyah Wulandari; Chang, Ming-Yu; Wu, Yi-Ju; Lee, Ya-Ching

2013-08-01

This study investigated the linkage between performance of two full-scale membrane bioreactor (MBR) systems treating thin-film transistor liquid crystal display (TFT-LCD) wastewater and the population dynamics of dimethylsulfoxide (DMSO)/dimethylsulfide (DMS) degrading bacteria. High DMSO degradation efficiencies were achieved in both MBRs, while the levels of nitrification inhibition due to DMS production from DMSO degradation were different in the two MBRs. The results of real-time PCR targeting on DMSO/DMS degrading populations, including Hyphomicrobium and Thiobacillus spp., indicated that a higher DMSO oxidation efficiency occurred at a higher Hyphomicrobium spp. abundance in the systems, suggesting that Hyphomicrobium spp. may be more important for complete DMSO oxidation to sulfate compared with Thiobacillus spp. Furthermore, Thiobacillus spp. was more abundant during poor nitrification, while Hyphomicrobium spp. was more abundant during good nitrification. It is suggested that microbial population of DMSO/DMS degrading bacteria is closely linking to both DMSO/DMS degradation efficiency and nitrification performance. Copyright © 2013 Elsevier Ltd. All rights reserved.

Apoptosis in infection.

PubMed

Häcker, Georg

2017-11-04

Apoptosis is one of the principal responses that human cells have at their disposal when faced with changes in their environment. Microbial infection is a massive challenge to a cell, and it is unsurprising that the apoptosis apparatus has been implicated in numerous infections. However, looking at the available data, the impression is one of bewildering complexity. Microbial proteins and other molecules that are often poorly understood interact, with uncertain specificity, with host cell components of varying function, triggering signalling pathways that are ambiguously linked to the apoptotic machinery. Accordingly, many pathogens have been found in different studies both to induce and to inhibit apoptosis. I will here try to present some of the principles of apoptosis and of infection, and to provide a viewpoint on the question how the two are linked. I will further give the reasons for my personal opinion that apoptosis-induction is in most infections beneficial to the host. Copyright © 2017 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Cross-linking of type I collagen with microbial transglutaminase: identification of cross-linking sites.

PubMed

Stachel, Ines; Schwarzenbolz, Uwe; Henle, Thomas; Meyer, Michael

2010-03-08

Collagen is a popular biomaterial. To deal with its lack of thermal stability and its weak resistance to proteolytic degradation, collagen-based materials are stabilized via different cross-linking procedures. Regarding the potential toxicity of residual cross-linking agents, enzyme-mediated cross-linking would provide an alternative and nontoxic method for collagen stabilization. The results of this study show that type I collagen is a substrate for mTG. However, epsilon-(gamma-glutamyl)lysine cross-links are only incorporated at elevated temperatures when the protein is partially or completely denatured. A maximum number of 5.4 cross-links per collagen monomer were found for heat-denatured collagen. Labeling with the primary amine monodansylcadaverine revealed that at least half of the cross-links are located within the triple helical region of the collagen molecule. Because the triple helix is highly ordered in its native state, this finding might explain why the glutamine residues are inaccessible for mTG under nondenaturing conditions.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Penn, Kevin; Jenkins, Caroline; Nett, Markus

Linking functional traits to bacterial phylogeny remains a fundamental but elusive goal of microbial ecology 1. Without this information, it becomes impossible to resolve meaningful units of diversity and the mechanisms by which bacteria interact with each other and adapt to environmental change. Ecological adaptations among bacterial populations have been linked to genomic islands, strain-specific regions of DNA that house functionally adaptive traits 2. In the case of environmental bacteria, these traits are largely inferred from bioinformatic or gene expression analyses 2, thus leaving few examples in which the functions of island genes have been experimentally characterized. Here we reportmore » the complete genome sequences of Salinispora tropica and S. arenicola, the first cultured, obligate marine Actinobacteria 3. These two species inhabit benthic marine environments and dedicate 8-10percent of their genomes to the biosynthesis of secondary metabolites. Despite a close phylogenetic relationship, 25 of 37 secondary metabolic pathways are species-specific and located within 21 genomic islands, thus providing new evidence linking secondary metabolism to ecological adaptation. Species-specific differences are also observed in CRISPR sequences, suggesting that variations in phage immunity provide fitness advantages that contribute to the cosmopolitan distribution of S. arenicola 4. The two Salinispora genomes have evolved by complex processes that include the duplication and acquisition of secondary metabolite genes, the products of which provide immediate opportunities for molecular diversification and ecological adaptation. Evidence that secondary metabolic pathways are exchanged by Horizontal Gene Transfer (HGT) yet are fixed among globally distributed populations 5 supports a functional role for their products and suggests that pathway acquisition represents a previously unrecognized force driving bacterial diversification« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wieder, William R.; Allison, Steven D.; Davidson, Eric A.

Microbes influence soil organic matter (SOM) decomposition and the long-term stabilization of carbon (C) in soils. We contend that by revising the representation of microbial processes and their interactions with the physicochemical soil environment, Earth system models (ESMs) may make more realistic global C cycle projections. Explicit representation of microbial processes presents considerable challenges due to the scale at which these processes occur. Thus, applying microbial theory in ESMs requires a framework to link micro-scale process-level understanding and measurements to macro-scale models used to make decadal- to century-long projections. Here, we review the diversity, advantages, and pitfalls of simulating soilmore » biogeochemical cycles using microbial-explicit modeling approaches. We present a roadmap for how to begin building, applying, and evaluating reliable microbial-explicit model formulations that can be applied in ESMs. Drawing from experience with traditional decomposition models we suggest: (1) guidelines for common model parameters and output that can facilitate future model intercomparisons; (2) development of benchmarking and model-data integration frameworks that can be used to effectively guide, inform, and evaluate model parameterizations with data from well-curated repositories; and (3) the application of scaling methods to integrate microbial-explicit soil biogeochemistry modules within ESMs. With contributions across scientific disciplines, we feel this roadmap can advance our fundamental understanding of soil biogeochemical dynamics and more realistically project likely soil C response to environmental change at global scales.« less

Microbial community composition along a 50 000-year lacustrine sediment sequence

PubMed Central

Ariztegui, Daniel; Horn, Fabian; Kallmeyer, Jens; Orsi, William D

2018-01-01

Abstract For decades, microbial community composition in subseafloor sediments has been the focus of extensive studies. In deep lacustrine sediments, however, the taxonomic composition of microbial communities remains undercharacterized. Greater knowledge on microbial diversity in lacustrine sediments would improve our understanding of how environmental factors, and resulting selective pressures, shape subsurface biospheres in marine and freshwater sediments. Using high-throughput sequencing of 16S rRNA genes across high-resolution climate intervals covering the last 50 000 years in Laguna Potrok Aike, Argentina, we identified changes in microbial populations in response to both past environmental conditions and geochemical changes of the sediment during burial. Microbial communities in Holocene sediments were most diverse, reflecting a layering of taxa linked to electron acceptors availability. In deeper intervals, the data show that salinity, organic matter and the depositional conditions over the Last Glacial-interglacial cycle were all selective pressures in the deep lacustrine assemblage resulting in a genetically distinct biosphere from the surface dominated primarily by Bathyarchaeota and Atribacteria groups. However, similar to marine sediments, some dominant taxa in the shallow subsurface persisted into the subsurface as minor fraction of the community. The subsequent establishment of a deep subsurface community likely results from a combination of paleoenvironmental factors that have shaped the pool of available substrates, together with substrate depletion and/or reworking of organic matter with depth. PMID:29471361

A thiotrophic microbial community in an acidic brine lake in Northern Chile.

PubMed

Escudero, Lorena; Oetiker, Nia; Gallardo, Karem; Tebes-Cayo, Cinthya; Guajardo, Mariela; Nuñez, Claudia; Davis-Belmar, Carol; Pueyo, J J; Chong Díaz, Guillermo; Demergasso, Cecilia

2018-05-10

The endorheic basins of the Northern Chilean Altiplano contain saline lakes and salt flats. Two of the salt flats, Gorbea and Ignorado, have high acidic brines. The causes of the local acidity have been attributed to the occurrence of volcanic native sulfur, the release of sulfuric acid by oxidation, and the low buffering capacity of the rocks in the area. Understanding the microbial community composition and available energy in this pristine ecosystem is relevant in determining the origin of the acidity and in supporting the rationale of conservation policies. Besides, a comparison between similar systems in Australia highlights key microbial components and specific ones associated with geological settings and environmental conditions. Sediment and water samples from the Salar de Gorbea were collected, physicochemical parameters measured and geochemical and molecular biological analyses performed. A low diversity microbial community was observed in brines and sediments dominated by Actinobacteria, Algae, Firmicutes and Proteobacteria. Most of the constituent genera have been reported to be either sulfur oxidizing microorganisms or ones having the potential for sulfur oxidation given available genomic data and information drawn from the literature on cultured relatives. In addition, a link between sulfur oxidation and carbon fixation was observed. In contrast, to acid mine drainage communities, Gorbea microbial diversity is mainly supported by chemolithoheterotrophic, facultative chemolithoautotrophic and oligotrophic sulfur oxidizing populations indicating that microbial activity should also be considered as a causative agent of local acidity.

Soil microbial activities in a constructed soil reed-bed under cheese-dairy farm effluents.

PubMed

Farnet, A M; Prudent, P; Cigna, M; Gros, R

2008-09-01

Soil microbial activities in a reed-bed used for effluent purification of a small cheese-dairy farm under a Mediterranean climate were described and studied. This work aims to demonstrate (i) whether certain enzyme activities used as bioindicators of dairy waste degradation (beta-galactosidase and protease) vary over time, which might influence organic matter degradation and (ii) whether specific microbial communities are selected through contact with the discarded effluent using community level catabolic profiles (CLCPs). beta-galactosidase and protease activities were followed in a 14-month monitoring experiment. These enzyme activities were strongly expressed during the whey-discarding period from February to May. CLCPs using Biolog Ecoplate showed great microbial diversity, as described by Shannon-Weaver index, and no difference was observed in microbial diversity between areas at the receiving end of the reed-bed (where effluent was discarded) and those at the opposite end. This may be explained by successive environmental factors which made enzyme activities vary: whey discarded from February to May and Mediterranean climate conditions (drying-rewetting effects on summer). Microbial enumeration using epifluorescence microscopy also showed a pattern linked to Mediterranean conditions with a drastic decrease in biomass during summer drought. These results on functional biodiversity were correlated with high purification yields: the minimum decrease in Biological Demand in Oxygen was 84% and that in suspended solids was 75%.

Host-associated coral reef microbes respond to the cumulative pressures of ocean warming and ocean acidification.

PubMed

Webster, N S; Negri, A P; Botté, E S; Laffy, P W; Flores, F; Noonan, S; Schmidt, C; Uthicke, S

2016-01-13

Key calcifying reef taxa are currently threatened by thermal stress associated with elevated sea surface temperatures (SST) and reduced calcification linked to ocean acidification (OA). Here we undertook an 8 week experimental exposure to near-future climate change conditions and explored the microbiome response of the corals Acropora millepora and Seriatopora hystrix, the crustose coralline algae Hydrolithon onkodes, the foraminifera Marginopora vertebralis and Heterostegina depressa and the sea urchin Echinometra sp. Microbial communities of all taxa were tolerant of elevated pCO2/reduced pH, exhibiting stable microbial communities between pH 8.1 (pCO2 479-499 μatm) and pH 7.9 (pCO2 738-835 μatm). In contrast, microbial communities of the CCA and foraminifera were sensitive to elevated seawater temperature, with a significant microbial shift involving loss of specific taxa and appearance of novel microbial groups occurring between 28 and 31 °C. An interactive effect between stressors was also identified, with distinct communities developing under different pCO2 conditions only evident at 31 °C. Microbiome analysis of key calcifying coral reef species under near-future climate conditions highlights the importance of assessing impacts from both increased SST and OA, as combinations of these global stressors can amplify microbial shifts which may have concomitant impacts for coral reef structure and function.

A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer

NASA Astrophysics Data System (ADS)

Tully, B. J.; Wheat, C. G.; Glazer, B. T.; Huber, J. A.

2017-12-01

The rock-hosted subseafloor crustal aquifer harbors a reservoir of microbial life that may influence global marine biogeochemical cycles. Here we utilized genomic reconstruction of crustal fluid samples from North Pond, located on the flanks of the Mid-Atlantic Ridge, a site with cold, oxic subseafloor fluid circulation within the upper basement. Twenty-one samples were collected during a two-year period at three different depths and two locations with the basaltic aquifer to examine potential microbial metabolism and community dynamics. We observed minor changes in the geochemical signatures over the two years, yet a dynamic microbial community was present in the crustal fluids that underwent large shifts in the dominant taxonomic groups. An analysis of 195 metagenome-assembled genomes (MAGs) were generated from the dataset and revealed a connection between litho- and autotrophic processes, linking carbon fixation to the oxidation of sulfide, sulfur, thiosulfate, hydrogen, and ferrous iron in a diverse group of microorganisms. Despite oxic conditions, analysis of the MAGs indicated that members of the microbial community were poised to exploit hypoxic or anoxic conditions through the use of microaerobic cytochromes and alternative electron acceptors. Temporal and spatial trends from the MAGs revealed a high degree of functional redundancy that did not correlate with the shifting microbial community membership, suggesting functional stability in mediating subseafloor biogeochemical cycles.

Biocrust-forming mosses mitigate the impact of aridity on soil microbial communities in drylands: observational evidence from three continents.

PubMed

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

2018-04-02

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

Groundwater geochemistry and microbial community structure in the aquifer transition from volcanic to alluvial areas.

PubMed

Amalfitano, S; Del Bon, A; Zoppini, A; Ghergo, S; Fazi, S; Parrone, D; Casella, P; Stano, F; Preziosi, E

2014-11-15

Groundwaters may act as sinks or sources of organic and inorganic solutes, depending on the relative magnitude of biochemical mobilizing processes and groundwater-surface water exchanges. The objective of this study was to link the lithological and hydrogeological gradients to the aquatic microbial community structure in the transition from aquifer recharge (volcanic formations) to discharge areas (alluvial deposits). A field-scale analysis was performed along a water table aquifer in which volcanic products decreased in thickness and areal extension, while alluvial deposits became increasingly important. We measured the main groundwater physical parameters and the concentrations of major and trace elements. In addition, the microbial community structure was assessed by estimating the occurrence of total coliforms and Escherichia coli, the prokaryotic abundance, the cytometric and phylogenetic community composition. The overall biogeochemical asset differed along the aquifer flow path. The concentration of total and live prokaryotic cells significantly increased in alluvial waters, together with the percentages of Beta- and Delta-Proteobacteria. The microbial propagation over a theoretical groundwater travel time allowed for the identification of microbial groups shifting significantly in the transition between the two different hydrogeochemical facies. The microbial community structure was intimately associated with geochemical changes, thus it should be further considered in view of a better understanding of groundwater ecology and sustainable management strategies. Copyright © 2014 Elsevier Ltd. All rights reserved.

A Thermodynamically-consistent FBA-based Approach to Biogeochemical Reaction Modeling

NASA Astrophysics Data System (ADS)

Shapiro, B.; Jin, Q.

2015-12-01

Microbial rates are critical to understanding biogeochemical processes in natural environments. Recently, flux balance analysis (FBA) has been applied to predict microbial rates in aquifers and other settings. FBA is a genome-scale constraint-based modeling approach that computes metabolic rates and other phenotypes of microorganisms. This approach requires a prior knowledge of substrate uptake rates, which is not available for most natural microbes. Here we propose to constrain substrate uptake rates on the basis of microbial kinetics. Specifically, we calculate rates of respiration (and fermentation) using a revised Monod equation; this equation accounts for both the kinetics and thermodynamics of microbial catabolism. Substrate uptake rates are then computed from the rates of respiration, and applied to FBA to predict rates of microbial growth. We implemented this method by linking two software tools, PHREEQC and COBRA Toolbox. We applied this method to acetotrophic methanogenesis by Methanosarcina barkeri, and compared the simulation results to previous laboratory observations. The new method constrains acetate uptake by accounting for the kinetics and thermodynamics of methanogenesis, and predicted well the observations of previous experiments. In comparison, traditional methods of dynamic-FBA constrain acetate uptake on the basis of enzyme kinetics, and failed to reproduce the experimental results. These results show that microbial rate laws may provide a better constraint than enzyme kinetics for applying FBA to biogeochemical reaction modeling.

Surface-Enhanced Raman Scattering (SERS) in Microbiology: Illumination and Enhancement of the Microbial World.

PubMed

Chisanga, Malama; Muhamadali, Howbeer; Ellis, David I; Goodacre, Royston

2018-01-01

The microbial world forms a huge family of organisms that exhibit the greatest phylogenetic diversity on Earth and thus colonize virtually our entire planet. Due to this diversity and subsequent complex interactions, the vast majority of microorganisms are involved in innumerable natural bioprocesses and contribute an absolutely vital role toward the maintenance of life on Earth, whilst a small minority cause various infectious diseases. The ever-increasing demand for environmental monitoring, sustainable ecosystems, food security, and improved healthcare systems drives the continuous search for inexpensive but reproducible, automated and portable techniques for detection of microbial isolates and understanding their interactions for clinical, environmental, and industrial applications and benefits. Surface-enhanced Raman scattering (SERS) is attracting significant attention for the accurate identification, discrimination and characterization and functional assessment of microbial cells at the single cell level. In this review, we briefly discuss the technological advances in Raman and Fourier transform infrared (FT-IR) instrumentation and their application for the analysis of clinically and industrially relevant microorganisms, biofilms, and biological warfare agents. In addition, we summarize the current trends and future prospects of integrating Raman/SERS-isotopic labeling and cell sorting technologies in parallel, to link genotype-to-phenotype in order to define community function of unculturable microbial cells in mixed microbial communities which possess admirable traits such as detoxification of pollutants and recycling of essential metals.

Microbial Functioning and Community Structure Variability in the Mesopelagic and Epipelagic Waters of the Subtropical Northeast Atlantic Ocean

PubMed Central

Arístegui, Javier; Gasol, Josep M.; Herndl, Gerhard J.

2012-01-01

We analyzed the regional distribution of bulk heterotrophic prokaryotic activity (leucine incorporation) and selected single-cell parameters (cell viability and nucleic acid content) as parameters for microbial functioning, as well as bacterial and archaeal community structure in the epipelagic (0 to 200 m) and mesopelagic (200 to 1,000 m) subtropical Northeast Atlantic Ocean. We selectively sampled three contrasting regions covering a wide range of surface productivity and oceanographic properties within the same basin: (i) the eddy field south of the Canary Islands, (ii) the open-ocean NE Atlantic Subtropical Gyre, and (iii) the upwelling filament off Cape Blanc. In the epipelagic waters, a high regional variation in hydrographic parameters and bacterial community structure was detected, accompanied, however, by a low variability in microbial functioning. In contrast, mesopelagic microbial functioning was highly variable between the studied regions despite the homogeneous abiotic conditions found therein. More microbial functioning parameters indicated differences among the three regions within the mesopelagic (i.e., viability of cells, nucleic acid content, cell-specific heterotrophic activity, nanoflagellate abundance, prokaryote-to-nanoflagellate abundance ratio) than within the epipelagic (i.e., bulk activity, nucleic acid content, and nanoflagellate abundance) waters. Our results show that the mesopelagic realm in the Northeast Atlantic is, in terms of microbial activity, more heterogeneous than its epipelagic counterpart, probably linked to mesoscale hydrographical variations. PMID:22344670

Excess labile carbon promotes the expression of virulence factors in coral reef bacterioplankton.

PubMed

Cárdenas, Anny; Neave, Matthew J; Haroon, Mohamed Fauzi; Pogoreutz, Claudia; Rädecker, Nils; Wild, Christian; Gärdes, Astrid; Voolstra, Christian R

2018-01-01

Coastal pollution and algal cover are increasing on many coral reefs, resulting in higher dissolved organic carbon (DOC) concentrations. High DOC concentrations strongly affect microbial activity in reef waters and select for copiotrophic, often potentially virulent microbial populations. High DOC concentrations on coral reefs are also hypothesized to be a determinant for switching microbial lifestyles from commensal to pathogenic, thereby contributing to coral reef degradation, but evidence is missing. In this study, we conducted ex situ incubations to assess gene expression of planktonic microbial populations under elevated concentrations of naturally abundant monosaccharides (glucose, galactose, mannose, and xylose) in algal exudates and sewage inflows. We assembled 27 near-complete (>70%) microbial genomes through metagenomic sequencing and determined associated expression patterns through metatranscriptomic sequencing. Differential gene expression analysis revealed a shift in the central carbohydrate metabolism and the induction of metalloproteases, siderophores, and toxins in Alteromonas, Erythrobacter, Oceanicola, and Alcanivorax populations. Sugar-specific induction of virulence factors suggests a mechanistic link for the switch from a commensal to a pathogenic lifestyle, particularly relevant during increased algal cover and human-derived pollution on coral reefs. Although an explicit test remains to be performed, our data support the hypothesis that increased availability of specific sugars changes net microbial community activity in ways that increase the emergence and abundance of opportunistic pathogens, potentially contributing to coral reef degradation.

2D-Visualization of metabolic activity with planar optical chemical sensors (optodes)

NASA Astrophysics Data System (ADS)

Meier, R. J.; Liebsch, G.

2015-12-01

Microbia plays an outstandingly important role in many hydrologic compartments, such as e.g. the benthic community in sediments, or biologically active microorganisms in the capillary fringe, in ground water, or soil. Oxygen, pH, and CO2 are key factors and indicators for microbial activity. They can be measured using optical chemical sensors. These sensors record changing fluorescence properties of specific indicator dyes. The signals can be measured in a non-contact mode, even through transparent walls, which is important for many lab-experiments. They can measure in closed (transparent) systems, without sampling or intruding into the sample. They do not consume the analytes while measuring, are fully reversible and able to measure in non-stirred solutions. These sensors can be applied as high precision fiberoptic sensors (for profiling), robust sensor spots, or as planar sensors for 2D visualization (imaging). Imaging enables to detect thousands of measurement spots at the same time and generate 2D analyte maps over a region of interest. It allows for comparing different regions within one recorded image, visualizing spatial analyte gradients, or more important to identify hot spots of metabolic activity. We present ready-to-use portable imaging systems for the analytes oxygen, pH, and CO2. They consist of a detector unit, planar sensor foils and a software for easy data recording and evaluation. Sensors foils for various analytes and measurement ranges enable visualizing metabolic activity or analyte changes in the desired range. Dynamics of metabolic activity can be detected in one shot or over long time periods. We demonstrate the potential of this analytical technique by presenting experiments on benthic disturbance-recovery dynamics in sediments and microbial degradation of organic material in the capillary fringe. We think this technique is a new tool to further understand how microbial and geochemical processes are linked in (not solely) hydrologic systems.

Comparison of the Microbial Community Structures of Untreated Wastewaters from Different Geographic Locales

PubMed Central

Shanks, Orin C.; Newton, Ryan J.; Kelty, Catherine A.; Huse, Susan M.; Sogin, Mitchell L.

2013-01-01

Microbial sewage communities consist of a combination of human fecal microorganisms and nonfecal microorganisms, which may be residents of urban sewer infrastructure or flowthrough originating from gray water or rainwater inputs. Together, these different microorganism sources form an identifiable community structure that may serve as a signature for sewage discharges and as candidates for alternative indicators specific for human fecal pollution. However, the structure and variability of this community across geographic space remains uncharacterized. We used massively parallel 454 pyrosequencing of the V6 region in 16S rRNA genes to profile microbial communities from 13 untreated sewage influent samples collected from a wide range of geographic locations in the United States. We obtained a total of 380,175 high-quality sequences for sequence-based clustering, taxonomic analyses, and profile comparisons. The sewage profile included a discernible core human fecal signature made up of several abundant taxonomic groups within Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria. DNA sequences were also classified into fecal, sewage infrastructure (i.e., nonfecal), and transient groups based on data comparisons with fecal samples. Across all sewage samples, an estimated 12.1% of sequences were fecal in origin, while 81.4% were consistently associated with the sewage infrastructure. The composition of feces-derived operational taxonomic units remained congruent across all sewage samples regardless of geographic locale; however, the sewage infrastructure community composition varied among cities, with city latitude best explaining this variation. Together, these results suggest that untreated sewage microbial communities harbor a core group of fecal bacteria across geographically dispersed wastewater sewage lines and that ambient water quality indicators targeting these select core microorganisms may perform well across the United States. PMID:23435885

Methane related changes in prokaryotic activity along geochemical profiles in sediments of Lake Kinneret (Israel)

NASA Astrophysics Data System (ADS)

Bar Or, I.; Ben-Dov, E.; Kushmaro, A.; Eckert, W.; Sivan, O.

2014-06-01

Microbial methane oxidation process (methanotrophy) is the primary control on the emission of the greenhouse gas methane (CH4) to the atmosphere. In terrestrial environments, aerobic methanotrophic bacteria are mainly responsible for oxidizing the methane. In marine sediments the coupling of the anaerobic oxidation of methane (AOM) with sulfate reduction, often by a consortium of anaerobic methanotrophic archaea (ANME) and sulfate reducing bacteria, was found to consume almost all the upward diffusing methane. Recently, we showed geochemical evidence for AOM driven by iron reduction in Lake Kinneret (LK) (Israel) deep sediments and suggested that this process can be an important global methane sink. The goal of the present study was to link the geochemical gradients found in the porewater (chemical and isotope profiles) with possible changes in microbial community structure. Specifically, we examined the possible shift in the microbial community in the deep iron-driven AOM zone and its similarity to known sulfate driven AOM populations. Screening of archaeal 16S rRNA gene sequences revealed Thaumarchaeota and Euryarchaeota as the dominant phyla in the sediment. Thaumarchaeota, which belongs to the family of copper containing membrane-bound monooxgenases, increased with depth while Euryarchaeota decreased. This may indicate the involvement of Thaumarchaeota, which were discovered to be ammonia oxidizers but whose activity could also be linked to methane, in AOM in the deep sediment. ANMEs sequences were not found in the clone libraries, suggesting that iron-driven AOM is not through sulfate. Bacterial 16S rRNA sequences displayed shifts in community diversity with depth. Proteobacteria and Chloroflexi increased with depth, which could be connected with their different dissimilatory anaerobic processes. The observed changes in microbial community structure suggest possible direct and indirect mechanisms for iron-driven AOM in deep sediments.

Alkaline battery containing a separator of a cross-linked copolymer of vinyl alcohol and unsaturated carboxylic acid

NASA Technical Reports Server (NTRS)

Hsu, L. C.; Philipp, W. H.; Sheibley, D. W.; Gonzalez-Sanabria, O. D. (Inventor)

1985-01-01

A battery separator for an alkaline battery is described. The separator comprises a cross linked copolymer of vinyl alcohol units and unsaturated carboxylic acid units. The cross linked copolymer is insoluble in water, has excellent zincate diffusion and oxygen gas barrier properties and a low electrical resistivity. Cross linking with a polyaldehyde cross linking agent is preferred.

Lactic acid concentrations that reduce microbial load yet minimally impact colour and sensory characteristics of beef.

PubMed

Rodríguez-Melcón, Cristina; Alonso-Calleja, Carlos; Capita, Rosa

2017-07-01

Lactic acid (LA) has recently been approved in the EU as beef decontaminant. In order to identify the most appropriate concentration, beef samples were spray-treated with LA (2%, 3%, 4% or 5%) or left untreated (control). Microbial load (aerobic plate counts, psychrotrophs and Enterobacteriaceae), pH, instrumental colour and sensory properties were investigated at 0, 24, 72 and 120h of refrigerated storage. The reductions in bacteria after spraying ranged from 0.57 to 0.95 log units. A residual antimicrobial effect was observed so that at 120h LA reduced microbial load by up to 2 log units compared with the control samples. Samples treated with 5% LA showed the lowest redness value (a*) and hedonic scores at all sampling times. Only for samples treated with 4% LA did the sensorial shelf-life limit extend beyond 120h. It is suggested that treatment of beef with 4% LA not only may improve microbiological quality, but also may enhance sensory properties and shelf-life. Copyright © 2017. Published by Elsevier Ltd.

Fungal endophyte communities reflect environmental structuring across a Hawaiian landscape

PubMed Central

Zimmerman, Naupaka B.; Vitousek, Peter M.

2012-01-01

We surveyed endophytic fungal communities in leaves of a single tree species (Metrosideros polymorpha) across wide environmental gradients (500–5,500 mm of rain/y; 10–22 °C mean annual temperature) spanning short geographic distances on Mauna Loa Volcano, Hawai’i. Using barcoded amplicon pyrosequencing at 13 sites (10 trees/site; 10 leaves/tree), we found very high levels of diversity within sites (a mean of 551 ± 134 taxonomic units per site). However, among-site diversity contributed even more than did within-site diversity to the overall richness of more than 4,200 taxonomic units observed in M. polymorpha, and this among-site variation in endophyte community composition correlated strongly with temperature and rainfall. These results are consistent with suggestions that foliar endophytic fungi are hyperdiverse. They further suggest that microbial diversity may be even greater than has been assumed and that broad-scale environmental controls such as temperature and rainfall can structure eukaryotic microbial diversity. Appropriately constrained study systems across strong environmental gradients present a useful means to understand the environmental factors that structure the diversity of microbial communities. PMID:22837398

Unit Microbes, First Trial Materials, Inspection Set.

ERIC Educational Resources Information Center

Australian Science Education Project, Toorak, Victoria.

The Australian Science Education Project is producing materials designed for use in grades 7-10 of Australian schools. This is the first trial version of a unit investigating microbial action. One of the student booklets contains instructions for the activities demonstrating food decay which all students are expected to complete. The other student…

Microbial pathogens in source and treated waters from drinking water treatment plants in the United States and implications for human health

EPA Science Inventory

An occurrence survey was conducted on selected pathogens in source and treated drinking water collected from 25 drinking water treatment plants (DWTPs) in the United States. Water samples were analyzed for the protozoa Giardia and Cryptosporidium (EPA Method 1623); the fungi Aspe...

Greenhouse gas fluxes of drained organic and flooded mineral agricultural soils in the United States

USDA-ARS?s Scientific Manuscript database

Drained organic soils for agriculture represent less than 1% of the area used for crops in the United States (US). However, emission of carbon dioxide (CO2) from microbial oxidation of drained organic soils offsets almost half of the contributions that carbon sequestration of other cropping systems ...

Ecological effects of nitrogen deposition in the western United States

Treesearch

Mark E. Fenn; Jill S. Baron; Edith B. Allen; Heather M. Rueth; Koren R. Nydick; Linda Geiser; William D. Bowman; James O. Sickman; Thomas Meixner; Dale W. Johnson; Peter Neitlich

2003-01-01

In the western United States vast acreages of land are exposed to low levels of atmospheric nitrogen (N) deposition, with interspersed hotspots of elevated N deposition downwind of large, expanding metropolitan centers or large agricultural operations. Biological response studies in western North America demonstrate that some aquatic and terrestrial plant and microbial...

Influence of corn, switchgrass, and prairie cropping systems on soil microbial communities in the upper Midwest of the United States

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jesus, Ederson da C.; Liang, Chao; Quensen, John F.

Because soil microbes drive many of the processes underpinning ecosystem services provided by soils, understanding how cropping systems affect soil microbial communities is important for productive and sustainable management. We characterized and compared soil microbial communities under restored prairie and three potential cellulosic biomass crops (corn, switchgrass, and mixed prairie grasses) in two spatial experimental designs – side-by-side plots where plant communities were in their second year since establishment (i.e., intensive sites) and regionally distributed fields where plant communities had been in place for at least 10 years (i.e., extensive sites). We assessed microbial community structure and composition using lipidmore » analysis, pyrosequencing of rRNA genes (targeting fungi, bacteria, archaea, and lower eukaryotes), and targeted metagenomics of nifH genes. For the more recently established intensive sites, soil type was more important than plant community in determining microbial community structure, while plant community was the more important driver of soil microbial communities for the older extensive sites where microbial communities under corn were clearly differentiated from those under switchgrass and restored prairie. Here, bacterial and fungal biomasses, especially biomass of arbuscular mycorrhizal fungi, were higher under perennial grasses and restored prairie, suggesting a more active carbon pool and greater microbial processing potential, which should be beneficial for plant acquisition and ecosystem retention of carbon, water, and nutrients.« less

Influence of corn, switchgrass, and prairie cropping systems on soil microbial communities in the upper Midwest of the United States

DOE PAGES

Jesus, Ederson da C.; Liang, Chao; Quensen, John F.; ...

2015-06-28

Because soil microbes drive many of the processes underpinning ecosystem services provided by soils, understanding how cropping systems affect soil microbial communities is important for productive and sustainable management. We characterized and compared soil microbial communities under restored prairie and three potential cellulosic biomass crops (corn, switchgrass, and mixed prairie grasses) in two spatial experimental designs – side-by-side plots where plant communities were in their second year since establishment (i.e., intensive sites) and regionally distributed fields where plant communities had been in place for at least 10 years (i.e., extensive sites). We assessed microbial community structure and composition using lipidmore » analysis, pyrosequencing of rRNA genes (targeting fungi, bacteria, archaea, and lower eukaryotes), and targeted metagenomics of nifH genes. For the more recently established intensive sites, soil type was more important than plant community in determining microbial community structure, while plant community was the more important driver of soil microbial communities for the older extensive sites where microbial communities under corn were clearly differentiated from those under switchgrass and restored prairie. Here, bacterial and fungal biomasses, especially biomass of arbuscular mycorrhizal fungi, were higher under perennial grasses and restored prairie, suggesting a more active carbon pool and greater microbial processing potential, which should be beneficial for plant acquisition and ecosystem retention of carbon, water, and nutrients.« less

Evidence for a soil microbial terroir in the Chianti Classico district in Tuscany (Italy)

NASA Astrophysics Data System (ADS)

Mocali, Stefano; Priori, Simone; Valboa, Giuseppe; Fabiani, Arturo; Pellegrini, Sergio; Puccioni, Sergio; Zombardo, Alessandra; Storchi, Paolo; Costantini, Edoardo

2017-04-01

Originally developed for wine, the terroir concept is becoming popular throughout agri-environmental sciences in many parts of the world, linking the uniqueness and quality of agricultural products to the environment where they are produced. Even thought it is well known that geology, morphology and microclimate influence and diversify the wine characters within a wine district (macro-terroir), recent literature suggests that different soil features can drive wine characters also within the same macro-terroir, at both farm and vineyard scale. However, the drivers beyond these differences remain elusive, and the potential contribution of soil microbes has been ignored until recently. Therefore, in this multidisciplinary work we have tried to assess the possible role of soil microbial communities in vineyards on defining the quality of the wine produced. Soils from 4 different macro-terroir areas located within the Barone Ricasoli farm in Brolio (SI), Tuscany (Central Italy), characterized by different geology and cultivated with the grapevine cultivar Sangiovese, were collected: Fattoio (feldspathic sandstone), Leccio (marine sands), Agresto (limestone), and Ceni (fluvial deposits). Within each terroir, two areas homogeneous for soil features were delimited (Basic terroir unit, BTU) and monitored over 3 years for the soil physico-chemical and biological parameters as well as viticultural parameters. In this work we report the results of the analysis of microbial communities in the 8 BTUs, determined through molecular (PCR-DGGE), metabolic (BIOLOG) and biochemical (microbial respiration, biomass C) techniques. The results showed that each vineyard is characterized by a well defined bacterial community whose structure varies both as a function of different BTUs and terroir areas, depending on soil features. In fact, the vineyards Fattoio 1 and 2 exhibit a very similar bacterial composition between them and stable over time, even for the low total organic matter content. In contrast, Leccio 1 is very different from Leccio 2 (much more than Agresto 1 compared to Agresto 2) and shows values of biological fertility and bacterial diversity always lower than Leccio 2. Ceni 1 and 2, however, even though quite distinct from each other, do not show many similarities with other vineyards. Interesting to note that the values of the Sangiovese performance index, which estimate the quality of the wine produced are well correlated with the bacterial diversity of different BTU. In conclusion, despite soil bacterial community composition was shown to be strictly related to the quality of grapes, further investigation is still required in order to better highlight the effect of such microbial communities on vine physiology and wine quality.

LABORATORY AND FIELD RESULTS LINKING HIGH CONDUCTIVITIES TO THE MICROBIAL DEGRADATION OF PETROLEUM HYDROCARBONS

EPA Science Inventory

The results of a l6-month field and l6-month meso-scale laboratory investigation of unconsolidated sandy environments contaminated by petroleum hydrocarbons that are undergoing natural biodegradation is presented. The purpose was to understand the processes responsible for causin...

GEOCHEMICAL AND BIOLOGICAL ASPECTS OF SULFIDE MINERAL DISSOLUTION: LESSONS FROM IRON MOUNTAIN, CALIFORNIA. (R826189)

EPA Science Inventory

Abstract

The oxidative dissolution of sulfide minerals leading to acid mine drainage (AMD) involves a complex interplay between microorganisms, solutions, and mineral surfaces. Consequently, models that link molecular level reactions and the microbial communities that ...

Marsh soil responses to tidal water nitrogen additions contribute to creek bank fracturing and slumping

EPA Science Inventory

Large-scale dissolved nutrient enrichment can cause a reduction in belowground biomass, increased water content of soils, and increased microbial decomposition, which has been linked with slumping of low marsh Spartina vegetation into creeks, and ultimately marsh loss. Our study ...

Associations among Wine Grape Microbiome, Metabolome, and Fermentation Behavior Suggest Microbial Contribution to Regional Wine Characteristics

PubMed Central

Bokulich, Nicholas A.; Collins, Thomas S.; Masarweh, Chad; Allen, Greg; Heymann, Hildegarde; Ebeler, Susan E.

2016-01-01

ABSTRACT Regionally distinct wine characteristics (terroir) are an important aspect of wine production and consumer appreciation. Microbial activity is an integral part of wine production, and grape and wine microbiota present regionally defined patterns associated with vineyard and climatic conditions, but the degree to which these microbial patterns associate with the chemical composition of wine is unclear. Through a longitudinal survey of over 200 commercial wine fermentations, we demonstrate that both grape microbiota and wine metabolite profiles distinguish viticultural area designations and individual vineyards within Napa and Sonoma Counties, California. Associations among wine microbiota and fermentation characteristics suggest new links between microbiota, fermentation performance, and wine properties. The bacterial and fungal consortia of wine fermentations, composed from vineyard and winery sources, correlate with the chemical composition of the finished wines and predict metabolite abundances in finished wines using machine learning models. The use of postharvest microbiota as an early predictor of wine chemical composition is unprecedented and potentially poses a new paradigm for quality control of agricultural products. These findings add further evidence that microbial activity is associated with wine terroir. PMID:27302757

Microbial diversity and carbon cycling in San Francisco Bay wetlands

DOE Office of Scientific and Technical Information (OSTI.GOV)

Theroux, Susanna; Hartman, Wyatt; He, Shaomei

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

Out of Thin Air: Microbial Utilization of Atmospheric Gaseous Organics in the Surface Ocean

PubMed Central

Arrieta, Jesús M.; Duarte, Carlos M.; Sala, M. Montserrat; Dachs, Jordi

2016-01-01

Volatile and semi-volatile gas-phase organic carbon (GOC) is a largely neglected component of the global carbon cycle, with poorly resolved pools and fluxes of natural and anthropogenic GOC in the biosphere. Substantial amounts of atmospheric GOC are exchanged with the surface ocean, and subsequent utilization of specific GOC compounds by surface ocean microbial communities has been demonstrated. Yet, the final fate of the bulk of the atmospheric GOC entering the surface ocean is unknown. Our data show experimental evidence of efficient use of atmospheric GOC by marine prokaryotes at different locations in the NE Subtropical Atlantic, the Arctic Ocean and the Mediterranean Sea. We estimate that between 2 and 27% of the prokaryotic carbon demand was supported by GOC with a major fraction of GOC inputs being consumed within the mixed layer. The role of the atmosphere as a key vector of organic carbon subsidizing marine microbial metabolism is a novel link yet to be incorporated into the microbial ecology of the surface ocean as well as into the global carbon budget. PMID:26834717

Impact of antiretroviral drugs on the microbiome: unknown answers to important questions

PubMed Central

Pinto-Cardoso, Sandra; Klatt, Nichole R.; Reyes-Terán, Gustavo

2018-01-01

Purpose of review Little is known on how different antiretroviral (ARV) drugs affect the gut microbiome in HIV infection; and conflicting data exists on the effect of ARV drugs on residual inflammation/immune activation and microbial translocation. Recent findings Gut microbiome involvement in the transmission and pathogenesis of HIV infection is increasingly being recognized. Various studies have shown that antiretroviral therapy (ART) is unable to restore gut health despite effective suppression of plasma HIV viremia. Indeed, the resolution of residual inflammation and gut microbial translocation is partial under ART. Very recent studies have provided new evidence that ARV combinations can differentially affect the gut microbiome, immune activation and microbial translocation. Furthermore, a recent article uncovered a link between drug metabolism and specific microbial species indicating that microbes can directly metabolically degrade ARV drugs when administered topically. Summary There are still many unanswered questions regarding ARVs and the gut microbiome. It is, therefore, critical for researchers to address the effect of distinct ARV drugs on the microbiome and vice versa: the effects of the microbiome on ARV drug metabolism, and speculate about possible therapeutic avenues. PMID:29028667

Inorganic polyphosphate in the microbial world. Emerging roles for a multifaceted biopolymer.

PubMed

Albi, Tomás; Serrano, Aurelio

2016-02-01

Inorganic polyphosphates (polyP) are linear polymers of tens to hundreds orthophosphate residues linked by phosphoanhydride bonds. These fairly abundant biopolymers occur in all extant forms of life, from prokaryotes to mammals, and could have played a relevant role in prebiotic evolution. Since the first identification of polyP deposits as metachromatic or volutin granules in yeasts in the nineteenth century, an increasing number of varied physiological functions have been reported. Due to their "high energy" bonds analogous to those in ATP and their properties as polyanions, polyP serve as microbial phosphagens for a variety of biochemical reactions, as a buffer against alkalis, as a storage of Ca(2+) and as a metal-chelating agent. In addition, recent studies have revealed polyP importance in signaling and regulatory processes, cell viability and proliferation, pathogen virulence, as a structural component and chemical chaperone, and as modulator of microbial stress response. This review summarizes the current status of knowledge and future perspectives of polyP functions and their related enzymes in the microbial world.

In Vitro Anti-Oxidant and Anti-Microbial Potentiality Investigation of Different Fractions of Caryota urens Leaves

PubMed Central

Azam, Shofiul; Mahmud, Md. Kayes; Naquib, Md. Hamza; Hossain, Saad Mosharraf; Alam, Mohammad Nazmul; Uddin, Md. Josim; Sajid, Irfan; Hossain, Muhammad Sazzad; Karim, Md. Salimul; Hasan, Md. Ali

2016-01-01

Background: Caryota urens is a member of the Arecaceae family and a common plant in the Southeast Asian region. This plant has been reported as an anti-microbial agent in recent years. Thus, we aimed to find out the MIC (minimum inhibitory concentration) against different pathogenic microorganism. Methods: The leaves of C. urens were extracted and fractioned using different reagents (chloroform, n-hexane and carbon tetrachloride). Disc diffusion method was implemented for the assessment of in vitro anti-microbial potency (500 and 250 µg/disc). Result: The entire fraction showed good effect (with the zone of inhibition 19–25 mm) against both gram positive (Bacillus subtilis, Bacillus megaterium, Bacillus cereus, Sarina lutea) and gram negative (Vibrio mimicus, Shigella boydii, Escherichia coli, Pseudomonas aeruginosa) bacterial pathogens and fungal strains (Aspergillus niger, Saccharomyces cerevisiae). The plants also possess effective free radical scavenging potency with an IC50 of 130.32 µg/mL. Conclusion: This finding reflects a link between the presence of anti-oxidative material and a substantial anti-microbial activity, and substantiates all previous claims against C. urens. PMID:28536384

Out of Thin Air: Microbial Utilization of Atmospheric Gaseous Organics in the Surface Ocean.

PubMed

Arrieta, Jesús M; Duarte, Carlos M; Sala, M Montserrat; Dachs, Jordi

2015-01-01

Volatile and semi-volatile gas-phase organic carbon (GOC) is a largely neglected component of the global carbon cycle, with poorly resolved pools and fluxes of natural and anthropogenic GOC in the biosphere. Substantial amounts of atmospheric GOC are exchanged with the surface ocean, and subsequent utilization of specific GOC compounds by surface ocean microbial communities has been demonstrated. Yet, the final fate of the bulk of the atmospheric GOC entering the surface ocean is unknown. Our data show experimental evidence of efficient use of atmospheric GOC by marine prokaryotes at different locations in the NE Subtropical Atlantic, the Arctic Ocean and the Mediterranean Sea. We estimate that between 2 and 27% of the prokaryotic carbon demand was supported by GOC with a major fraction of GOC inputs being consumed within the mixed layer. The role of the atmosphere as a key vector of organic carbon subsidizing marine microbial metabolism is a novel link yet to be incorporated into the microbial ecology of the surface ocean as well as into the global carbon budget.

In Vitro Anti-Oxidant and Anti-Microbial Potentiality Investigation of Different Fractions of Caryota urens Leaves.

PubMed

Azam, Shofiul; Mahmud, Md Kayes; Naquib, Md Hamza; Hossain, Saad Mosharraf; Alam, Mohammad Nazmul; Uddin, Md Josim; Sajid, Irfan; Hossain, Muhammad Sazzad; Karim, Md Salimul; Hasan, Md Ali

2016-07-27

Caryota urens is a member of the Arecaceae family and a common plant in the Southeast Asian region. This plant has been reported as an anti-microbial agent in recent years. Thus, we aimed to find out the MIC (minimum inhibitory concentration) against different pathogenic microorganism. The leaves of C. urens were extracted and fractioned using different reagents (chloroform, n -hexane and carbon tetrachloride). Disc diffusion method was implemented for the assessment of in vitro anti-microbial potency (500 and 250 µg/disc). The entire fraction showed good effect (with the zone of inhibition 19-25 mm) against both gram positive ( Bacillus subtilis , Bacillus megaterium , Bacillus cereus , Sarina lutea ) and gram negative ( Vibrio mimicus , Shigella boydii , Escherichia coli , Pseudomonas aeruginosa ) bacterial pathogens and fungal strains ( Aspergillus niger , Saccharomyces cerevisiae ). The plants also possess effective free radical scavenging potency with an IC 50 of 130.32 µg/mL. This finding reflects a link between the presence of anti-oxidative material and a substantial anti-microbial activity, and substantiates all previous claims against C. urens .

Environmental factors influencing the structural dynamics of soil microbial communities during assisted phytostabilization of acid-generating mine tailings: a mesocosm experiment.

PubMed

Valentín-Vargas, Alexis; Root, Robert A; Neilson, Julia W; Chorover, Jon; Maier, Raina M

2014-12-01

Compost-assisted phytostabilization has recently emerged as a robust alternative for reclamation of metalliferous mine tailings. Previous studies suggest that root-associated microbes may be important for facilitating plant establishment on the tailings, yet little is known about the long-term dynamics of microbial communities during reclamation. A mechanistic understanding of microbial community dynamics in tailings ecosystems undergoing remediation is critical because these dynamics profoundly influence both the biogeochemical weathering of tailings and the sustainability of a plant cover. Here we monitor the dynamics of soil microbial communities (i.e. bacteria, fungi, archaea) during a 12-month mesocosm study that included 4 treatments: 2 unplanted controls (unamended and compost-amended tailings) and 2 compost-amended seeded tailings treatments. Bacterial, fungal and archaeal communities responded distinctively to the revegetation process and concurrent changes in environmental conditions and pore water chemistry. Compost addition significantly increased microbial diversity and had an immediate and relatively long-lasting buffering-effect on pH, allowing plants to germinate and thrive during the early stages of the experiment. However, the compost buffering capacity diminished after six months and acidification took over as the major factor affecting plant survival and microbial community structure. Immediate changes in bacterial communities were observed following plant establishment, whereas fungal communities showed a delayed response that apparently correlated with the pH decline. Fluctuations in cobalt pore water concentrations, in particular, had a significant effect on the structure of all three microbial groups, which may be linked to the role of cobalt in metal detoxification pathways. The present study represents, to our knowledge, the first documentation of the dynamics of the three major microbial groups during revegetation of compost-amended, metalliferous mine tailings. Copyright © 2014 Elsevier B.V. All rights reserved.

Increasing the Size of the Microbial Biomass Altered Bacterial Community Structure which Enhances Plant Phosphorus Uptake

PubMed Central

Shen, Pu; Murphy, Daniel Vaughan; George, Suman J.; Lapis-Gaza, Hazel; Xu, Minggang

2016-01-01

Agricultural production can be limited by low phosphorus (P) availability, with soil P being constrained by sorption and precipitation reactions making it less available for plant uptake. There are strong links between carbon (C) and nitrogen (N) availability and P cycling within soil P pools, with microorganisms being an integral component of soil P cycling mediating the availability of P to plants. Here we tested a conceptual model that proposes (i) the addition of readily-available organic substrates would increase the size of the microbial biomass thus exhausting the pool of easily-available P and (ii) this would cause the microbial biomass to access P from more recalcitrant pools. In this model it is hypothesised that the size of the microbial population is regulating access to less available P rather than the diversity of organisms contained within this biomass. To test this hypothesis we added mixtures of simple organic compounds that reflect typical root exudates at different C:N ratios to a soil microcosm experiment and assessed changes in soil P pools, microbial biomass and bacterial diversity measures. We report that low C:N ratio (C:N = 12.5:1) artificial root exudates increased the size of the microbial biomass while high C:N ratio (C:N = 50:1) artificial root exudates did not result in a similar increase in microbial biomass. Interestingly, addition of the root exudates did not alter bacterial diversity (measured via univariate diversity indices) but did alter bacterial community structure. Where C, N and P supply was sufficient to support plant growth the increase observed in microbial biomass occurred with a concurrent increase in plant yield. PMID:27893833

Thermophilic bacterial communities inhabiting the microbial mats of "indifferent" and chalybeate (iron-rich) thermal springs: Diversity and biotechnological analysis.

PubMed

Selvarajan, Ramganesh; Sibanda, Timothy; Tekere, Memory

2018-04-01

Microbial mats are occasionally reported in thermal springs and information on such mats is very scarce. In this study, microbial mats were collected from two hot springs (Brandvlei (BV) and Calitzdorp (CA)), South Africa and subjected to scanning electron microscopy (SEM) and targeted 16S rRNA gene amplicon analysis using Next Generation Sequencing (NGS). Spring water temperature was 55°C for Brandvlei and 58°C for Calitzdorp while the pH of both springs was slightly acidic, with an almost identical pH range (6.2-6.3). NGS analysis resulted in a total of 4943 reads, 517 and 736 OTUs for BV and CA at, respectively, a combined total of 14 different phyla in both samples, 88 genera in CA compared to 45 in BV and 37.64% unclassified sequences in CA compared to 27.32% recorded in BV. Dominant bacterial genera in CA microbial mat were Proteobacteria (29.19%), Bacteroidetes (9.41%), Firmicutes (9.01%), Cyanobacteria (6.89%), Actinobacteria (2.65%), Deinococcus-Thermus (2.57%), and Planctomycetes (1.94%) while the BV microbial mat was dominated by Bacteroidetes (47.3%), Deinococcus-Thermus (12.35%), Proteobacteria (7.98%), and Planctomycetes (2.97%). Scanning electron microscopy results showed the presence of microbial filaments possibly resembling cyanobacteria, coccids, rod-shaped bacteria and diatoms in both microbial mats. Dominant genera that were detected in this study have been linked to different biotechnological applications including hydrocarbon degradation, glycerol fermentation, anoxic-fermentation, dehalogenation, and biomining processes. Overall, the results of this study exhibited thermophilic bacterial community structures with high diversity in microbial mats, which have a potential for biotechnological exploitation. © 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Alteration of soil microbial communities and water quality in restored wetlands

USGS Publications Warehouse

Bossio, D.A.; Fleck, J.A.; Scow, K.M.; Fujii, R.

2006-01-01

Land usage is a strong determinant of soil microbial community composition and activity, which in turn determine organic matter decomposition rates and decomposition products in soils. Microbial communities in permanently flooded wetlands, such as those created by wetland restoration on Sacramento-San Joaquin Delta islands in California, function under restricted aeration conditions that result in increasing anaerobiosis with depth. It was hypothesized that the change from agricultural management to permanently flooded wetland would alter microbial community composition, increase the amount and reactivity of dissolved organic carbon (DOC) compounds in Delta waters; and have a predominant impact on microbial communities as compared with the effects of other environmental factors including soil type and agricultural management. Based on phospholipid fatty acid (PLFA) analysis, active microbial communities of the restored wetlands were changed significantly from those of the agricultural fields, and wetland microbial communities varied widely with soil depth. The relative abundance of monounsaturated fatty acids decreased with increasing soil depth in both wetland and agricultural profiles, whereas branched fatty acids were relatively more abundant at all soil depths in wetlands as compared to agricultural fields. Decomposition conditions were linked to DOC quantity and quality using fatty acid functional groups to conclude that restricted aeration conditions found in the wetlands were strongly related to production of reactive carbon compounds. But current vegetation may have had an equally important role in determining DOC quality in restored wetlands. In a larger scale analysis, that included data from wetland and agricultural sites on Delta islands and data from two previous studies from the Sacramento Valley, an aeration gradient was defined as the predominant determinant of active microbial communities across soil types and land usage. ?? 2005 Elsevier Ltd. All rights reserved.

Relating microbial community structure to functioning in forest soil organic carbon transformation and turnover.

PubMed

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

2014-03-01

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

Recovery of microbial communities and carbon cycling processes following drought manipulation in southern California

NASA Astrophysics Data System (ADS)

Allison, S. D.; Martiny, J. B. H.; Martiny, A.; Berlemont, R.; Treseder, K. K.; Goulden, M.; Brodie, E.

2016-12-01

Predicting the functioning of microbial communities under changing environmental conditions remains a key challenge in Earth system science. Metagenomics and other high-throughput molecular approaches can help address this challenge by revealing the functional potential of microbial communities. We coupled metagenomics with models and experimental manipulations to address microbial responses to drought in a California grassland ecosystem along with the consequences for carbon cycling. We developed an approach for extracting trait information from metagenomic data and asked: 1) What is the phylogenetic structure of drought response traits? 2) What is the relationship between these traits and those involved in carbohydrate degradation? 3) How do both classes of traits vary seasonally and with precipitation manipulation? 4) How resilient are these traits in the face of perturbation? We found that drought response traits are phylogenetically conserved at an equivalent of 5-8% ribosomal RNA gene sequence dissimilarity. Experimental drought treatment selected for the genetic potential to degrade starch, xylan, and mixed polysaccharides, suggesting a link between drought response and carbon cycling traits. In addition, microbial communities exposed to experimental drought showed a reduced potential to degrade plant biomass. Particularly among bacteria, seasonal drought had a larger impact on microbial composition, abundance, and carbohydrate-degrading genes compared to experimental drought. Bacterial communities were also more resilient to drought perturbation than fungal communities, which showed legacies of drought perturbation for up to three years. Altogether, these findings imply that microbial communities exhibit trait diversity that facilitates resilience but with substantial time lags and consequences for carbon turnover. This information is being used to inform new trait-based models that address the challenge of predicting microbial functioning under precipitation change.

Modeling the unmeasurable: scaling soil physiology from microns to meters and seconds to centuries (Invited)

NASA Astrophysics Data System (ADS)

Schimel, J.; Xu, X.; Lawrence, C. R.

2013-12-01

Models are essential tools for linking microbial dynamics to their manifestations at large scales. Yet, developing mechanistically accurate models requires data that we often don't have and may not be able to get, such as the functional life-span of an extracellular enzyme. Yet there are approaches to condense complex microbial dynamics into 'workable' models. One example is in describing soil responses to moisture pulses. We developed a family of five separate models to capture microbial dynamics through dry/wet cycles. The simplest was a straight multi-pool, 1st-order decomposition model, with versions adding levels of microbial mechanism, culminating in one that included exoenzyme-breakdown of detritus. However, this identified the critical mechanism, not as exoenzymes, but as the production of a bioavailable C pool that accumulates in dry soil and is rapidly metabolized on rewetting. A final version of the model therefore stripped out explicit enzymes but retained separate polymer breakdown and substrate use; this model was the most robust. A second pervasive question in soil biology has been what controls the size of the microbial biomass across biomes? We approached this through a physiological model that regulated microbial C assimilation into biomass by two processes: initial assimilation followed by ongoing maintenance. Assimilation is a function of substrate quality, while maintenance is regulated by climate--notably the period of the year during which microbes are active. This model was tested against a global dataset of microbial biomass. It explains why, for example, deserts and tundra have relatively high proportions of their organic matter in microbial biomass, while the low substrate quality and long active periods common in temperate conifer forests lead to low biomass levels.

A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer

PubMed Central

Tully, Benjamin J; Wheat, C Geoff; Glazer, Brain T; Huber, Julie A

2018-01-01

The rock-hosted subseafloor crustal aquifer harbors a reservoir of microbial life that may influence global marine biogeochemical cycles. Here we utilized metagenomic libraries of crustal fluid samples from North Pond, located on the flanks of the Mid-Atlantic Ridge, a site with cold, oxic subseafloor fluid circulation within the upper basement to query microbial diversity. Twenty-one samples were collected during a 2-year period to examine potential microbial metabolism and community dynamics. We observed minor changes in the geochemical signatures over the 2 years, yet the microbial community present in the crustal fluids underwent large shifts in the dominant taxonomic groups. An analysis of 195 metagenome-assembled genomes (MAGs) were generated from the data set and revealed a connection between litho- and autotrophic processes, linking carbon fixation to the oxidation of sulfide, sulfur, thiosulfate, hydrogen, and ferrous iron in members of the Proteobacteria, specifically the Alpha-, Gamma- and Zetaproteobacteria, the Epsilonbacteraeota and the Planctomycetes. Despite oxic conditions, analysis of the MAGs indicated that members of the microbial community were poised to exploit hypoxic or anoxic conditions through the use of microaerobic cytochromes, such as cbb3- and bd-type cytochromes, and alternative electron acceptors, like nitrate and sulfate. Temporal and spatial trends from the MAGs revealed a high degree of functional redundancy that did not correlate with the shifting microbial community membership, suggesting functional stability in mediating subseafloor biogeochemical cycles. Collectively, the repeated sampling at multiple sites, together with the successful binning of hundreds of genomes, provides an unprecedented data set for investigation of microbial communities in the cold, oxic crustal aquifer. PMID:29099490

Environmental Factors Influencing the Structural Dynamics of Soil Microbial Communities During Assisted Phytostabilization of Acid-Generating Mine Tailings: a Mesocosm Experiment

PubMed Central

Valentín-Vargas, Alexis; Root, Robert A.; Neilson, Julia W; Chorover, Jon; Maier, Raina M.

2014-01-01

Compost-assisted phytostabilization has recently emerged as a robust alternative for reclamation of metalliferous mine tailings. Previous studies suggest that root-associated microbes may be important for facilitating plant establishment on the tailings, yet little is known about the long-term dynamics of microbial communities during reclamation. A mechanistic understanding of microbial community dynamics in tailings ecosystems undergoing remediation is critical because these dynamics profoundly influence both the biogeochemical weathering of tailings and the sustainability of a plant cover. Here we monitor the dynamics of soil microbial communities (i.e. bacteria, fungi, archaea) during a 12-month mesocosm study that included 4 treatments: 2 unplanted controls (unamended and compost-amended tailings) and 2 compost-amended seeded tailings treatments. Bacterial, fungal and archaeal communities responded distinctively to the revegetation process and concurrent changes in environmental conditions and pore water chemistry. Compost addition significantly increased microbial diversity and had an immediate and relatively long-lasting buffering-effect on pH, allowing plants to germinate and thrive during the early stages of the experiment. However, the compost buffering capacity diminished after six months and acidification took over as the major factor affecting plant survival and microbial community structure. Immediate changes in bacterial communities were observed following plant establishment, whereas fungal communities showed a delayed response that apparently correlated with the pH decline. Fluctuations in cobalt pore water concentrations, in particular, had a significant effect on the structure of all three microbial groups, which may be linked to the role of cobalt in metal detoxification pathways. The present study represents, to our knowledge, the first documentation of the dynamics of the three major microbial groups during revegetation of compost-amended, metalliferous mine tailings. PMID:25237788

Terroir is a key driver of seed-associated microbial assemblages.

PubMed

Klaedtke, Stephanie; Jacques, Marie-Agnès; Raggi, Lorenzo; Préveaux, Anne; Bonneau, Sophie; Negri, Valeria; Chable, Véronique; Barret, Matthieu

2016-06-01

Seeds have evolved in association with diverse microbial assemblages that may influence plant growth and health. However, little is known about the composition of seed-associated microbial assemblages and the ecological processes shaping their structures. In this work, we monitored the relative influence of the host genotypes and terroir on the structure of the seed microbiota through metabarcoding analysis of different microbial assemblages associated to five different bean cultivars harvested in two distinct farms. Overall, few bacterial and fungal operational taxonomic units (OTUs) were conserved across all seed samples. The lack of shared OTUs between samples is explained by a significant effect of the farm site on the structure of microbial assemblage, which explained 12.2% and 39.7% of variance in bacterial and fungal diversity across samples. This site-specific effect is reflected by the significant enrichment of 70 OTUs in Brittany and 88 OTUs in Luxembourg that lead to differences in co-occurrence patterns. In contrast, variance in microbial assemblage structure was not explained by host genotype. Altogether, these results suggest that seed-associated microbial assemblage is determined by niche-based processes and that the terroir is a key driver of these selective forces. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Design of a microbial contamination detector and analysis of error sources in its optical path.

PubMed

Zhang, Chao; Yu, Xiang; Liu, Xingju; Zhang, Lei

2014-05-01

Microbial contamination is a growing concern in the food safety today. To effectively control the types and degree of microbial contamination during food production, this paper introduces a design for a microbial contamination detector that can be used for quick in-situ examination. The designed detector can identify the category of microbial contamination by locating its characteristic absorption peak and then can calculate the concentration of the microbial contamination by fitting the absorbance vs. concentration lines of standard samples with gradient concentrations. Based on traditional scanning grating detection system, this design improves the light splitting unit to expand the scanning range and enhance the accuracy of output wavelength. The motor rotation angle φ is designed to have a linear relationship with the output wavelength angle λ, which simplifies the conversion of output spectral curves into wavelength vs. light intensity curves. In this study, we also derive the relationship between the device's major sources of errors and cumulative error of the output wavelengths, and suggest a simple correction for these errors. The proposed design was applied to test pigments and volatile basic nitrogen (VBN) which evaluated microbial contamination degrees of meats, and the deviations between the measured values and the pre-set values were only in a low range of 1.15% - 1.27%.

Microbial Source Module (MSM): Documenting the Science ...

EPA Pesticide Factsheets

The Microbial Source Module (MSM) estimates microbial loading rates to land surfaces from non-point sources, and to streams from point sources for each subwatershed within a watershed. A subwatershed, the smallest modeling unit, represents the common basis for information consumed and produced by the MSM which is based on the HSPF (Bicknell et al., 1997) Bacterial Indicator Tool (EPA, 2013b, 2013c). Non-point sources include numbers, locations, and shedding rates of domestic agricultural animals (dairy and beef cows, swine, poultry, etc.) and wildlife (deer, duck, raccoon, etc.). Monthly maximum microbial storage and accumulation rates on the land surface, adjusted for die-off, are computed over an entire season for four land-use types (cropland, pasture, forest, and urbanized/mixed-use) for each subwatershed. Monthly point source microbial loadings to instream locations (i.e., stream segments that drain individual sub-watersheds) are combined and determined for septic systems, direct instream shedding by cattle, and POTWs/WWTPs (Publicly Owned Treatment Works/Wastewater Treatment Plants). The MSM functions within a larger modeling system that characterizes human-health risk resulting from ingestion of water contaminated with pathogens. The loading estimates produced by the MSM are input to the HSPF model that simulates flow and microbial fate/transport within a watershed. Microbial counts within recreational waters are then input to the MRA-IT model (Soller et

Searching for links in the biotic characteristics and abiotic parameters of nine different biogas plants

PubMed Central

Walter, Andreas; Knapp, Brigitte A.; Farbmacher, Theresa; Ebner, Christian; Insam, Heribert; Franke‐Whittle, Ingrid H.

2012-01-01

Summary To find links between the biotic characteristics and abiotic process parameters in anaerobic digestion systems, the microbial communities of nine full‐scale biogas plants in South Tyrol (Italy) and Vorarlberg (Austria) were investigated using molecular techniques and the physical and chemical properties were monitored. DNA from sludge samples was subjected to microarray hybridization with the ANAEROCHIP microarray and results indicated that sludge samples grouped into two main clusters, dominated either by Methanosarcina or by Methanosaeta, both aceticlastic methanogens. Hydrogenotrophic methanogens were hardly detected or if detected, gave low hybridization signals. Results obtained using denaturing gradient gel electrophoresis (DGGE) supported the findings of microarray hybridization. Real‐time PCR targeting Methanosarcina and Methanosaeta was conducted to provide quantitative data on the dominating methanogens. Correlation analysis to determine any links between the microbial communities found by microarray analysis, and the physicochemical parameters investigated was conducted. It was shown that the sludge samples dominated by the genus Methanosarcina were positively correlated with higher concentrations of acetate, whereas sludge samples dominated by representatives of the genus Methanosaeta had lower acetate concentrations. No other correlations between biotic characteristics and abiotic parameters were found. Methanogenic communities in each reactor were highly stable and resilient over the whole year. PMID:22950603

What can microbial genetics teach sociobiology?

PubMed Central

Foster, Kevin R.; Parkinson, Katie; Thompson, Christopher R.L.

2009-01-01

Progress in our understanding of sociobiology has occurred with little knowledge of the genetic mechanisms that underlie social traits. However, several recent studies have described microbial genes that affect social traits, thereby bringing genetics to sociobiology. A key finding is that simple genetic changes can have marked social consequences, and mutations that affect cheating and recognition behaviors have been discovered. The study of these mutants confirms a central theoretical prediction of social evolution: that genetic relatedness promotes cooperation. Microbial genetics also provides an important new perspective: that the genome-to-phenome mapping of social organisms might be organized to constrain the evolution of social cheaters. This constraint can occur both through pleiotropic genes that link cheating to a personal cost and through the existence of phoenix genes, which rescue cooperative systems from selfish and destructive strategies. These new insights show the power of studying microorganisms to improve our understanding of the evolution of cooperation. PMID:17207887

IgA Function in Relation to the Intestinal Microbiota.

PubMed

Macpherson, Andrew J; Yilmaz, Bahtiyar; Limenitakis, Julien P; Ganal-Vonarburg, Stephanie C

2018-04-26

IgA is the dominant immunoglobulin isotype produced in mammals, largely secreted across the intestinal mucosal surface. Although induction of IgA has been a hallmark feature of microbiota colonization following colonization in germ-free animals, until recently appreciation of the function of IgA in host-microbial mutualism has depended mainly on indirect evidence of alterations in microbiota composition or penetration of microbes in the absence of somatic mutations in IgA (or compensatory IgM). Highly parallel sequencing techniques that enable high-resolution analysis of either microbial consortia or IgA sequence diversity are now giving us new perspectives on selective targeting of microbial taxa and the trajectory of IgA diversification according to induction mechanisms, between different individuals and over time. The prospects are to link the range of diversified IgA clonotypes to specific antigenic functions in modulating the microbiota composition, position and metabolism to ensure host mutualism.

Biological strategies for enhanced hydrolysis of lignocellulosic biomass during anaerobic digestion: Current status and future perspectives.

PubMed

Shrestha, Shilva; Fonoll, Xavier; Khanal, Samir Kumar; Raskin, Lutgarde

2017-12-01

Lignocellulosic biomass is the most abundant renewable bioresource on earth. In lignocellulosic biomass, the cellulose and hemicellulose are bound with lignin and other molecules to form a complex structure not easily accessible to microbial degradation. Anaerobic digestion (AD) of lignocellulosic biomass with a focus on improving hydrolysis, the rate limiting step in AD of lignocellulosic feedstocks, has received considerable attention. This review highlights challenges with AD of lignocellulosic biomass, factors contributing to its recalcitrance, and natural microbial ecosystems, such as the gastrointestinal tracts of herbivorous animals, capable of performing hydrolysis efficiently. Biological strategies that have been evaluated to enhance hydrolysis of lignocellulosic biomass include biological pretreatment, co-digestion, and inoculum selection. Strategies to further improve these approaches along with future research directions are outlined with a focus on linking studies of microbial communities involved in hydrolysis of lignocellulosics to process engineering. Copyright © 2017 Elsevier Ltd. All rights reserved.

The bacterial skin microbiome in psoriatic arthritis, an unexplored link in pathogenesis: challenges and opportunities offered by recent technological advances.

PubMed

Castelino, Madhura; Eyre, Stephen; Upton, Mathew; Ho, Pauline; Barton, Anne

2014-05-01

The resident microbial community, harboured by humans in sites such as the skin and gastrointestinal tract, is enormous, representing a candidate environmental factor affecting susceptibility to complex diseases, where both genetic and environmental risk factors are important. The potential of microorganisms to influence the human immune system is considerable, given their ubiquity. The impact of the host-gene-microbe interaction on the maintenance of health and the development of disease has not yet been assessed robustly in chronic inflammatory conditions. PsA represents a model inflammatory disease to explore the role of the microbiome because skin involvement and overlap with IBD implicates both the skin and gastrointestinal tract as sources of microbial triggers for PsA. In parallel with genetic studies, characterization of the host microbiota may benefit our understanding of the microbial contribution to disease pathogenesis-knowledge that may eventually inform the development of novel therapeutics.

Molecular approaches for the detection and monitoring of microbial communities in bioaerosols: A review.

PubMed

Yoo, Keunje; Lee, Tae Kwon; Choi, Eun Joo; Yang, Jihoon; Shukla, Sudheer Kumar; Hwang, Sang-Il; Park, Joonhong

2017-01-01

Bioaerosols significantly affect atmospheric processes while they undergo long-range vertical and horizontal transport and influence atmospheric chemistry and physics and climate change. Accumulating evidence suggests that exposure to bioaerosols may cause adverse health effects, including severe disease. Studies of bioaerosols have primarily focused on their chemical composition and largely neglected their biological composition and the negative effects of biological composition on ecosystems and human health. Here, current molecular methods for the identification, quantification, and distribution of bioaerosol agents are reviewed. Modern developments in environmental microbiology technology would be favorable in elucidation of microbial temporal and spatial distribution in the atmosphere at high resolution. In addition, these provide additional supports for growing evidence that microbial diversity or composition in the bioaerosol is an indispensable environmental aspect linking with public health. Copyright © 2016. Published by Elsevier B.V.

Gut microbial metabolite TMAO enhances platelet hyperreactivity and thrombosis risk

PubMed Central

Zhu, Weifei; Gregory, Jill C.; Org, Elin; Buffa, Jennifer A.; Gupta, Nilaksh; Wang, Zeneng; Li, Lin; Fu, Xiaoming; Wu, Yuping; Mehrabian, Margarete; Sartor, R. Balfour; McIntyre, Thomas M.; Silverstein, Roy L.; Tang, W.H. Wilson; DiDonato, Joseph A.; Brown, J. Mark; Lusis, Aldons J.; Hazen, Stanley L.

2016-01-01

SUMMARY Normal platelet function is critical to blood hemostasis and maintenance of a closed circulatory system. Heightened platelet reactivity, however, is associated with cardiometabolic diseases and enhanced potential for thrombotic events. We now show gut microbes, through generation of trimethylamine N-oxide (TMAO), directly contribute to platelet hyperreactivity and enhanced thrombosis potential. Plasma TMAO levels in subjects (N>4000) independently predicted incident (3 yr) thrombosis (heart attack, stroke) risk. Direct exposure of platelets to TMAO enhanced submaximal stimulus-dependent platelet activation from multiple agonists through augmented Ca2+ release from intracellular stores. Animal model studies employing dietary choline or TMAO, germ-free mice, and microbial transplantation, collectively confirm a role for gut microbiota and TMAO in modulating platelet hyperresponsiveness and thrombosis potential, and identify microbial taxa associated with plasma TMAO and thrombosis potential. Collectively, the present results reveal a previously unrecognized mechanistic link between specific dietary nutrients, gut microbes, platelet function, and thrombosis risk. PMID:26972052

Linking Toluene Degradation with Specific Microbial Populations in Soil

PubMed Central

Hanson, Jessica R.; Macalady, Jennifer L.; Harris, David; Scow, Kate M.

1999-01-01

Phospholipid fatty acid (PLFA) analysis of a soil microbial community was coupled with 13C isotope tracer analysis to measure the community’s response to addition of 35 μg of [13C]toluene ml of soil solution−1. After 119 h of incubation with toluene, 96% of the incorporated 13C was detected in only 16 of the total 59 PLFAs (27%) extracted from the soil. Of the total 13C-enriched PLFAs, 85% were identical to the PLFAs contained in a toluene-metabolizing bacterium isolated from the same soil. In contrast, the majority of the soil PLFAs (91%) became labeled when the same soil was incubated with [13C]glucose. Our study showed that coupling 13C tracer analysis with PLFA analysis is an effective technique for distinguishing a specific microbial population involved in metabolism of a labeled substrate in complex environments such as soil. PMID:10583996

Innovative biofilm inhibition and anti-microbial behavior of molybdenum sulfide nanostructures generated by microwave-assisted solvothermal route

NASA Astrophysics Data System (ADS)

Qureshi, Nilam; Patil, Rajendra; Shinde, Manish; Umarji, Govind; Causin, Valerio; Gade, Wasudev; Mulik, Uttam; Bhalerao, Anand; Amalnerkar, Dinesh P.

2015-03-01

The incessant use of antibiotics against infectious diseases has translated into a vicious circle of developing new antibiotic drug and its resistant strains in short period of time due to inherent nature of micro-organisms to alter their genes. Many researchers have been trying to formulate inorganic nanoparticles-based antiseptics that may be linked to broad-spectrum activity and far lower propensity to induce microbial resistance than antibiotics. The way-out approaches in this direction are nanomaterials based (1) bactericidal and (2) bacteriostatic activities. We, herein, present hitherto unreported observations on microbial abatement using non-cytotoxic molybdenum disulfide nanostructures (MSNs) which are synthesized using microwave assisted solvothermal route. Inhibition of biofilm formation using MSNs is a unique feature of our study. Furthermore, this study evinces antimicrobial mechanism of MSNs by reactive oxygen species (ROS) dependent generation of superoxide anion radical via disruption of cellular functions.

Sequential biodegradation of TNT, RDX and HMX in a mixture.

PubMed

Sagi-Ben Moshe, S; Ronen, Z; Dahan, O; Weisbrod, N; Groisman, L; Adar, E; Nativ, R

2009-01-01

We describe TNT's inhibition of RDX and HMX anaerobic degradation in contaminated soil containing indigenous microbial populations. Biodegradation of RDX or HMX alone was markedly faster than their degradation in a mixture with TNT, implying biodegradation inhibition by the latter. The delay caused by the presence of TNT continued even after its disappearance and was linked to the presence of its intermediate, tetranitroazoxytoluene. PCR-DGGE analysis of cultures derived from the soil indicated a clear reduction in microbial biomass and diversity with increasing TNT concentration. At high-TNT concentrations (30 and 90 mg/L), only a single band, related to Clostridium nitrophenolicum, was observed after 3 days of incubation. We propose that the mechanism of TNT inhibition involves a cytotoxic effect on the RDX- and HMX-degrading microbial population. TNT inhibition in the top active soil can therefore initiate rapid transport of RDX and HMX to the less active subsurface and groundwater.

Molecular Ecology of Hypersaline Microbial Mats: Current Insights and New Directions.

PubMed

Wong, Hon Lun; Ahmed-Cox, Aria; Burns, Brendan Paul

2016-01-05

Microbial mats are unique geobiological ecosystems that form as a result of complex communities of microorganisms interacting with each other and their physical environment. Both the microorganisms present and the network of metabolic interactions govern ecosystem function therein. These systems are often found in a range of extreme environments, and those found in elevated salinity have been particularly well studied. The purpose of this review is to briefly describe the molecular ecology of select model hypersaline mat systems (Guerrero Negro, Shark Bay, S'Avall, and Kiritimati Atoll), and any potentially modulating effects caused by salinity to community structure. In addition, we discuss several emerging issues in the field (linking function to newly discovered phyla and microbial dark matter), which illustrate the changing paradigm that is seen as technology has rapidly advanced in the study of these extreme and evolutionally significant ecosystems.

Microbial Monitoring from the Frontlines to Space: A Successful Validation of a Department of Defense (DoD) Funded Small Business Innovation Research (SBIR) Technology on Board the International Space Station (ISS)

NASA Technical Reports Server (NTRS)

Oubre, Cherie; Khodadad, Christina; Castro, Victoria; Ott, Mark; Pollack, Lawrence; Roman, Monsi

2017-01-01

The RAZOR EX (Registered Trademark) PCR unit was initially developed by the DoD as part of an SBIR project to detect and identify biothreats during field deployment. The system was evaluated by NASA as a commercial technology for future microbial monitoring requirements and has been successfully demonstrated in microgravity on-board the International Space Station.

Association of land use and beach closure in the United ...

EPA Pesticide Factsheets

Swimming in natural waters (e.g., oceans, lakes, rivers) is one of most popular recreational activities in the United States. However, exposure to pathogens (e.g., Salmonella spp., Shigella spp., Cryptosporidium, Giardia, adenovirus, norovirus) in recreational waters can lead to a variety of adverse health outcomes. To protect public health and reduce the number of outbreaks associated with recreational waters, the BEACH Act was passed in 2000, which required beach regulators to develop a formal plan to assess beach water quality and to notify the public if recreational waters are unsafe. High levels of microorganisms in water often follow extreme weather events. Besides extreme weather events, the proximity of certain land uses to beaches may also have great influence on beach water quality. Microbial contaminants that lead to beach closures and human illness come mainly from land, either from discrete point sources or from diffuse non-point sources. It is expected that land use will have considerable influence on beach microbial water quality. However, to date, studies on impacts of land use on beach microbial contamination are rare, and few researchers are aware of the relationship between land use and beach closures.In this study, we analyzed beach closure data obtained from 2004 to 2013 for more than 500 beaches in the United States, and examined their associations with land use around beaches in 2006 and 2011. The results show that the number of beach clos

A global comparison of Bactericera cockerelli (Hemiptera: Triozidae) microbial communities.

PubMed

Arp, Alex; Munyaneza, Joseph E; Crosslin, James M; Trumble, John; Bextine, Blake

2014-04-01

The potato psyllid (Bactericera cockerelli Sulc) is an economically important insect pest of solanaceous crops such as potato, tomato, pepper, and tobacco. Historically, the potato psyllid's range included central United States, Mexico, and California; more recently, populations of this insect have been reported in Central America, the Pacific Northwest, and New Zealand. Like most phytophagous insects, potato psyllids require symbiotic bacteria to compensate for nutritional deficiencies in their diet. Potato psyllids harbor the primary symbiont, Candidatus Carsonella ruddii, and may also harbor many secondary symbionts such as Wolbachia sp., Sodalis sp., Pseudomonas sp., and others. These secondary symbionts can have an effect on reproduction, nutrition, immune response, and resistances to heat or pesticides. To identify regional differences in potato psyllid bacterial symbionts, 454 pyrosequencing was performed using generic 16S rRNA gene primers. Analysis was performed using the Qiime 1.6.0 software suite, ARB Silva, and R. Operational taxonomic units were then grouped at 97% identity. Representative sequences were classified to genus using the ARB SILVA database. Potato psyllids collected in California contained a less diverse microbial community than those collected in the central United States and Central America. The crop variety, collection year, and haplotype did not seem to affect the microbial community in potato psyllids. The primary difference between psyllids in different regions was the presence and overall bacterial community composition of Candidatus Carsonella ruddii and Wolbachia.