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Sample records for microbial community biofabrics

  1. Microbial Community Biofabrics in a Geothermal Mine Adit▿ †

    PubMed Central

    Spear, John R.; Barton, Hazel A.; Robertson, Charles E.; Francis, Christopher A.; Pace, Norman R.

    2007-01-01

    Speleothems such as stalactites and stalagmites are usually considered to be mineralogical in composition and origin; however, microorganisms have been implicated in the development of some speleothems. We have identified and characterized the biological and mineralogical composition of mat-like biofabrics in two novel kinds of speleothems from a 50°C geothermal mine adit near Glenwood Springs, CO. One type of structure consists of 2- to 3-cm-long, 3- to 4-mm-wide, leather-like, hollow, soda straw stalactites. Light and electron microscopy indicated that the stalactites are composed of a mineralized biofabric with several cell morphotypes in a laminated form, with gypsum and sulfur as the dominant mineral components. A small-subunit rRNA gene phylogenetic community analysis along the stalactite length yielded a diverse gradient of organisms, with a relatively simple suite of main constituents: Thermus spp., crenarchaeotes, Chloroflexi, and Gammaproteobacteria. PCR analysis also detected putative crenarchaeal ammonia monooxygenase subunit A (amoA) genes in this community, the majority related to sequences from other geothermal systems. The second type of speleothem, dumpling-like rafts floating on a 50°C pool on the floor of the adit, showed a mat-like fabric of evidently living organisms on the outside of the dumpling, with a multimineral, amorphous, gypsum-based internal composition. These two novel types of biofabrics are examples of the complex roles that microbes can play in mineralization, weathering, and deposition processes in karst environments. PMID:17693567

  2. Microbial community biofabrics in a geothermal mine adit.

    PubMed

    Spear, John R; Barton, Hazel A; Robertson, Charles E; Francis, Christopher A; Pace, Norman R

    2007-10-01

    Speleothems such as stalactites and stalagmites are usually considered to be mineralogical in composition and origin; however, microorganisms have been implicated in the development of some speleothems. We have identified and characterized the biological and mineralogical composition of mat-like biofabrics in two novel kinds of speleothems from a 50 degrees C geothermal mine adit near Glenwood Springs, CO. One type of structure consists of 2- to 3-cm-long, 3- to 4-mm-wide, leather-like, hollow, soda straw stalactites. Light and electron microscopy indicated that the stalactites are composed of a mineralized biofabric with several cell morphotypes in a laminated form, with gypsum and sulfur as the dominant mineral components. A small-subunit rRNA gene phylogenetic community analysis along the stalactite length yielded a diverse gradient of organisms, with a relatively simple suite of main constituents: Thermus spp., crenarchaeotes, Chloroflexi, and Gammaproteobacteria. PCR analysis also detected putative crenarchaeal ammonia monooxygenase subunit A (amoA) genes in this community, the majority related to sequences from other geothermal systems. The second type of speleothem, dumpling-like rafts floating on a 50 degrees C pool on the floor of the adit, showed a mat-like fabric of evidently living organisms on the outside of the dumpling, with a multimineral, amorphous, gypsum-based internal composition. These two novel types of biofabrics are examples of the complex roles that microbes can play in mineralization, weathering, and deposition processes in karst environments.

  3. Biofabrication: a 21st century manufacturing paradigm.

    PubMed

    Mironov, V; Trusk, T; Kasyanov, V; Little, S; Swaja, R; Markwald, R

    2009-06-01

    Biofabrication can be defined as the production of complex living and non-living biological products from raw materials such as living cells, molecules, extracellular matrices, and biomaterials. Cell and developmental biology, biomaterials science, and mechanical engineering are the main disciplines contributing to the emergence of biofabrication technology. The industrial potential of biofabrication technology is far beyond the traditional medically oriented tissue engineering and organ printing and, in the short term, it is essential for developing potentially highly predictive human cell- and tissue-based technologies for drug discovery, drug toxicity, environmental toxicology assays, and complex in vitro models of human development and diseases. In the long term, biofabrication can also contribute to the development of novel biotechnologies for sustainable energy production in the future biofuel industry and dramatically transform traditional animal-based agriculture by inventing 'animal-free' food, leather, and fur products. Thus, the broad spectrum of potential applications and rapidly growing arsenal of biofabrication methods strongly suggests that biofabrication can become a dominant technological platform and new paradigm for 21st century manufacturing. The main objectives of this review are defining biofabrication, outlining the most essential disciplines critical for emergence of this field, analysis of the evolving arsenal of biofabrication technologies and their potential practical applications, as well as a discussion of the common challenges being faced by biofabrication technologies, and the necessary conditions for the development of a global biofabrication research community and commercially successful biofabrication industry. PMID:20811099

  4. Microbial Uptake, Toxicity, and Fate of Biofabricated ZnS:Mn Nanocrystals

    PubMed Central

    Swift, Brian J. F.; Baneyx, Franҫois

    2015-01-01

    Despite their importance in nano-environmental health and safety, interactions between engineered nanomaterials and microbial life remain poorly characterized. Here, we used the model organism E. coli to study the penetration requirements, subcellular localization, induction of stress responses, and long-term fate of luminescent Mn-doped ZnS nanocrystals fabricated under “green” processing conditions with a minimized ZnS-binding protein. We find that such protein-coated quantum dots (QDs) are unable to penetrate the envelope of unmodified E. coli but readily translocate to the cytoplasm of cells that have been made competent by chemical treatment. The process is dose-dependent and reminiscent of bacterial transformation. Cells that have internalized up to 0.5 μg/mL of nanocrystals do not experience a significant activation of the unfolded protein or SOS responses but undergo oxidative stress when exposed to high QD doses (2.5 μg/mL). Finally, although they are stable in quiescent cells over temperatures ranging from 4 to 42°C, internalized QDs are rapidly diluted by cell division in a process that does not involve TolC-dependent efflux. Taken together, our results suggest that biomimetic QDs based on low toxicity inorganic cores capped by a protein shell are unlikely to cause significant damage to the microbial ecosystem. PMID:25902065

  5. Data on biochemical fluxes generated from biofabricated enzyme complexes assembled through engineered tags and microbial transglutaminase.

    PubMed

    Bhokisham, Narendranath; Pakhchanian, Haig; Quan, David; Tschirhart, Tanya; Tsao, Chen-Yu; Payne, Gregory F; Bentley, William E

    2016-09-01

    Data presented is related to an article titled "Modular construction of multi-subunit protein complexes using engineered tags and microbial transglutaminase" (Bhokisham et al., 2016) [1]. In this article, we have presented western blot and flux data associated with assembly of Pfs-LuxS enzyme complexes on beads using uni-tagged and bi-tagged LuxS enzymes. We have also presented biochemical flux following changes in enzyme stoichiometries. We covalently coupled a Pfs-LuxS complex with Protein G, an antibody binding non-enzyme component and directed these complexes to the surfaces of bacterial cells via anti-Escherichia coli antibodies. Fluorescence microscopy images represented the altered behavior of bacterial cells in response to the autoinducer-2 that is synthesized by the Protein G-enzyme complexes.

  6. Data on biochemical fluxes generated from biofabricated enzyme complexes assembled through engineered tags and microbial transglutaminase.

    PubMed

    Bhokisham, Narendranath; Pakhchanian, Haig; Quan, David; Tschirhart, Tanya; Tsao, Chen-Yu; Payne, Gregory F; Bentley, William E

    2016-09-01

    Data presented is related to an article titled "Modular construction of multi-subunit protein complexes using engineered tags and microbial transglutaminase" (Bhokisham et al., 2016) [1]. In this article, we have presented western blot and flux data associated with assembly of Pfs-LuxS enzyme complexes on beads using uni-tagged and bi-tagged LuxS enzymes. We have also presented biochemical flux following changes in enzyme stoichiometries. We covalently coupled a Pfs-LuxS complex with Protein G, an antibody binding non-enzyme component and directed these complexes to the surfaces of bacterial cells via anti-Escherichia coli antibodies. Fluorescence microscopy images represented the altered behavior of bacterial cells in response to the autoinducer-2 that is synthesized by the Protein G-enzyme complexes. PMID:27508259

  7. Why Microbial Communities?

    ScienceCinema

    Fredrickson, Jim (PNNL)

    2016-07-12

    The Microbial Communities Initiative is a 5-year investment by Pacific Northwest National Laboratory that integrates biological/ecological experimentation, analytical chemistry, and simulation modeling. The objective is to create transforming technologies, elucidate mechanistic forces, and develop theoretical frameworks for the analysis and predictive understanding of microbial communities. Dr. Fredrickson introduces the symposium by defining microbial communities and describing their scientific relevance as they relate to solving problems in energy, climate, and sustainability.

  8. SEAGRASS RHIZOSPHERE MICROBIAL COMMUNITIES

    EPA Science Inventory

    Devereux, Richard. 2005. Seagrass Rhizosphere Microbial Communities. In: Interactions Between Macro- and Microorganisms in Marine Sediments. E. Kristense, J.E. Kostka and R.H. Haese, Editors. American Geophysical Union, Washington, DC. p199-216. (ERL,GB 1213).

    Seagrasses ...

  9. Microbial Communities as Experimental Units.

    PubMed

    Day, Mitch D; Beck, Daniel; Foster, James A

    2011-05-01

    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.

  10. Archean Microbial Mat Communities

    NASA Astrophysics Data System (ADS)

    Tice, Michael M.; Thornton, Daniel C. O.; Pope, Michael C.; Olszewski, Thomas D.; Gong, Jian

    2011-05-01

    Much of the Archean record of microbial communities consists of fossil mats and stromatolites. Critical physical emergent properties governing the evolution of large-scale (centimeters to meters) topographic relief on the mat landscape are (a) mat surface roughness relative to the laminar sublayer and (b) cohesion. These properties can be estimated for fossil samples under many circumstances. A preliminary analysis of Archean mat cohesion suggests that mats growing in shallow marine environments from throughout this time had cohesions similar to those of modern shallow marine mats. There may have been a significant increase in mat strength at the end of the Archean.

  11. In-vitro bio-fabrication of silver nanoparticle using Adhathoda vasica leaf extract and its anti-microbial activity

    NASA Astrophysics Data System (ADS)

    Nazeruddin, G. M.; Prasad, N. R.; Prasad, S. R.; Garadkar, K. M.; Nayak, Arpan Kumar

    2014-07-01

    It is well known that on treating the metallic salt solution with some plant extracts, a rapid reduction occurs leading to the formation of highly stable metal nanoparticles. Extracellular synthesis of metal nanoparticles using extracts of plants like Azadirachta indica (Neem), and Zingiber officinale (Ginger) has been reported to be successfully carried out. In this study we have developed a novel method to synthesize silver nanoparticles by mixing silver salt solution with leaf extract of Adhathoda vasica (Adulsa) without using any surfactant or external energy. By this method physiologically stable, bio-compatible Ag nanoparticles were formed which could be used for a variety of applications such as targeted drug delivery which ensures enhanced therapeutic efficacy and minimal side effects. With this method rapid synthesis of nanoparticles was observed to occur; i.e. reaction time was 1-2 h as compared to 2-4 days required by microorganisms. These nanoparticles were analyzed by various characterization techniques to reveal their morphology, chemical composition, and antimicrobial activity. TEM image of these NPs indicated the formation of spherical, non-uniform, poly-dispersed nanoparticles. A detailed study of anti-microbial activity of nanoparticles was carried out.

  12. Interchange of entire communities: microbial community coalescence.

    PubMed

    Rillig, Matthias C; Antonovics, Janis; Caruso, Tancredi; Lehmann, Anika; Powell, Jeff R; Veresoglou, Stavros D; Verbruggen, Erik

    2015-08-01

    Microbial communities are enigmatically diverse. We propose a novel view of processes likely affecting microbial assemblages, which could be viewed as the Great American Interchange en miniature: the wholesale exchange among microbial communities resulting from moving pieces of the environment containing entire assemblages. Incidental evidence for such 'community coalescence' is accumulating, but such processes are rarely studied, likely because of the absence of suitable terminology or a conceptual framework. We provide the nucleus for such a conceptual foundation for the study of community coalescence, examining factors shaping these events, links to bodies of ecological theory, and we suggest modeling approaches for understanding coalescent communities. We argue for the systematic study of community coalescence because of important functional and applied consequences.

  13. In-Drift Microbial Communities

    SciTech Connect

    D. Jolley

    2000-11-09

    As directed by written work direction (CRWMS M and O 1999f), Performance Assessment (PA) developed a model for microbial communities in the engineered barrier system (EBS) as documented here. The purpose of this model is to assist Performance Assessment and its Engineered Barrier Performance Section in modeling the geochemical environment within a potential repository drift for TSPA-SR/LA, thus allowing PA to provide a more detailed and complete near-field geochemical model and to answer the key technical issues (KTI) raised in the NRC Issue Resolution Status Report (IRSR) for the Evolution of the Near Field Environment (NFE) Revision 2 (NRC 1999). This model and its predecessor (the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document, CRWMS M and O 1998a) was developed to respond to the applicable KTIs. Additionally, because of the previous development of the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a), the M and O was effectively able to resolve a previous KTI concern regarding the effects of microbial processes on seepage and flow (NRC 1998). This document supercedes the in-drift microbial communities model as documented in Chapter 4 of the TSPA-VA Technical Basis Document (CRWMS M and O 1998a). This document provides the conceptual framework of the revised in-drift microbial communities model to be used in subsequent performance assessment (PA) analyses.

  14. Systems biology of Microbial Communities

    SciTech Connect

    Navid, A; Ghim, C; Fenley, A; Yoon, S; Lee, S; Almaas, E

    2008-04-11

    Microbes exist naturally in a wide range of environments, spanning the extremes of high acidity and high temperature to soil and the ocean, in communities where their interactions are significant. We present a practical discussion of three different approaches for modeling microbial communities: rate equations, individual-based modeling, and population dynamics. We illustrate the approaches with detailed examples. Each approach is best fit to different levels of system representation, and they have different needs for detailed biological input. Thus, this set of approaches is able to address the operation and function of microbial communities on a wide range of organizational levels.

  15. The influence of soluble microbial products on microbial community composition: hypothesis of microbial community succession.

    PubMed

    Chipasa, Kangala B; Medrzycka, Krystyna

    2008-01-01

    Soluble microbial products (SMP) are organic compounds produced by activated sludge microorganisms as they degrade substrates. They include by-products of microbial activity, death and lysis. The available literature does not reveal how SMP influence microbial community composition. In this regard, we microscopically studied changes in composition of microbial communities, especially protozoa and metazoa, under the influence of increased as well as reduced levels of SMP. The presence of SMP at high level significantly caused changes in microbial community composition. Microbial species shifted from attached ciliates (12-175 microm) to free-swimming and crawling ciliates (35-330 microm) and then invertebrates, which included rotifers (0.2-1 mm) and nematodes (1-50 mm). The shift of small-size microorganisms to large ones was observed as one of the most significant influences of SMP. Attached ciliates reappeared when we removed the SMP that had accumulated in the bioreactors - we have called this as the resurrection phenomenon of microorganisms. Such rapid changes in microbial community composition were not observed in the experiment with low concentration of SMP. Overall, the results suggest that accumulation of SMP is one of the intrinsic regulatory mechanisms that control viability and dormancy of microbial communities in activated sludge. PMID:18610657

  16. Flat laminated microbial mat communities

    NASA Astrophysics Data System (ADS)

    Franks, Jonathan; Stolz, John F.

    2009-10-01

    Flat laminated microbial mats are complex microbial ecosystems that inhabit a wide range of environments (e.g., caves, iron springs, thermal springs and pools, salt marshes, hypersaline ponds and lagoons, methane and petroleum seeps, sea mounts, deep sea vents, arctic dry valleys). Their community structure is defined by physical (e.g., light quantity and quality, temperature, density and pressure) and chemical (e.g., oxygen, oxidation/reduction potential, salinity, pH, available electron acceptors and donors, chemical species) parameters as well as species interactions. The main primary producers may be photoautotrophs (e.g., cyanobacteria, purple phototrophs, green phototrophs) or chemolithoautophs (e.g., colorless sulfur oxidizing bacteria). Anaerobic phototrophy may predominate in organic rich environments that support high rates of respiration. These communities are dynamic systems exhibiting both spatial and temporal heterogeneity. They are characterized by steep gradients with microenvironments on the submillimeter scale. Diel oscillations in the physical-chemical profile (e.g., oxygen, hydrogen sulfide, pH) and species distribution are typical for phototroph-dominated communities. Flat laminated microbial mats are often sites of robust biogeochemical cycling. In addition to well-established modes of metabolism for phototrophy (oxygenic and non-oxygenic), respiration (both aerobic and anaerobic), and fermentation, novel energetic pathways have been discovered (e.g., nitrate reduction couple to the oxidation of ammonia, sulfur, or arsenite). The application of culture-independent techniques (e.g., 16S rRNA clonal libraries, metagenomics), continue to expand our understanding of species composition and metabolic functions of these complex ecosystems.

  17. Fundamentals of microbial community resistance and resilience.

    PubMed

    Shade, Ashley; Peter, Hannes; Allison, Steven D; Baho, Didier L; Berga, Mercè; Bürgmann, Helmut; Huber, David H; Langenheder, Silke; Lennon, Jay T; Martiny, Jennifer B H; Matulich, Kristin L; Schmidt, Thomas M; Handelsman, Jo

    2012-01-01

    Microbial communities are at the heart of all ecosystems, and yet microbial community behavior in disturbed environments remains difficult to measure and predict. Understanding the drivers of microbial community stability, including resistance (insensitivity to disturbance) and resilience (the rate of recovery after disturbance) is important for predicting community response to disturbance. Here, we provide an overview of the concepts of stability that are relevant for microbial communities. First, we highlight insights from ecology that are useful for defining and measuring stability. To determine whether general disturbance responses exist for microbial communities, we next examine representative studies from the literature that investigated community responses to press (long-term) and pulse (short-term) disturbances in a variety of habitats. Then we discuss the biological features of individual microorganisms, of microbial populations, and of microbial communities that may govern overall community stability. We conclude with thoughts about the unique insights that systems perspectives - informed by meta-omics data - may provide about microbial community stability.

  18. Molecular Survey of Concrete Biofilm Microbial Communities

    EPA Science Inventory

    Although several studies have shown that bacteria can deteriorate concrete structures, there is very little information on the composition of concrete microbial communities. To this end, we studied different microbial communities associated with concrete biofilms using 16S rRNA g...

  19. Modeling microbial communities: current, developing, and future technologies for predicting microbial community interaction.

    PubMed

    Larsen, Peter; Hamada, Yuki; Gilbert, Jack

    2012-07-31

    Never has there been a greater opportunity for investigating microbial communities. Not only are the profound effects of microbial ecology on every aspect of Earth's geochemical cycles beginning to be understood, but also the analytical and computational tools for investigating microbial Earth are undergoing a rapid revolution. This environmental microbial interactome, the system of interactions between the microbiome and the environment, has shaped the planet's past and will undoubtedly continue to do so in the future. We review recent approaches for modeling microbial community structures and the interactions of microbial populations with their environments. Different modeling approaches consider the environmental microbial interactome from different aspects, and each provides insights to different facets of microbial ecology. We discuss the challenges and opportunities for the future of microbial modeling and describe recent advances in microbial community modeling that are extending current descriptive technologies into a predictive science.

  20. Modeling microbial communities: current, developing, and future technologies for predicting microbial community interaction.

    PubMed

    Larsen, Peter; Hamada, Yuki; Gilbert, Jack

    2012-07-31

    Never has there been a greater opportunity for investigating microbial communities. Not only are the profound effects of microbial ecology on every aspect of Earth's geochemical cycles beginning to be understood, but also the analytical and computational tools for investigating microbial Earth are undergoing a rapid revolution. This environmental microbial interactome, the system of interactions between the microbiome and the environment, has shaped the planet's past and will undoubtedly continue to do so in the future. We review recent approaches for modeling microbial community structures and the interactions of microbial populations with their environments. Different modeling approaches consider the environmental microbial interactome from different aspects, and each provides insights to different facets of microbial ecology. We discuss the challenges and opportunities for the future of microbial modeling and describe recent advances in microbial community modeling that are extending current descriptive technologies into a predictive science. PMID:22465599

  1. Patterns and Processes of Microbial Community Assembly

    PubMed Central

    Schmidt, Steven K.; Fukami, Tadashi; O'Neill, Sean P.; Bilinski, Teresa M.; Stanish, Lee F.; Knelman, Joseph E.; Darcy, John L.; Lynch, Ryan C.; Wickey, Phillip; Ferrenberg, Scott

    2013-01-01

    SUMMARY Recent research has expanded our understanding of microbial community assembly. However, the field of community ecology is inaccessible to many microbial ecologists because of inconsistent and often confusing terminology as well as unnecessarily polarizing debates. Thus, we review recent literature on microbial community assembly, using the framework of Vellend (Q. Rev. Biol. 85:183–206, 2010) in an effort to synthesize and unify these contributions. We begin by discussing patterns in microbial biogeography and then describe four basic processes (diversification, dispersal, selection, and drift) that contribute to community assembly. We also discuss different combinations of these processes and where and when they may be most important for shaping microbial communities. The spatial and temporal scales of microbial community assembly are also discussed in relation to assembly processes. Throughout this review paper, we highlight differences between microbes and macroorganisms and generate hypotheses describing how these differences may be important for community assembly. We end by discussing the implications of microbial assembly processes for ecosystem function and biodiversity. PMID:24006468

  2. Resistance, resilience, and redundancy in microbial communities

    PubMed Central

    Allison, Steven D.; Martiny, Jennifer B. H.

    2008-01-01

    Although it is generally accepted that plant community composition is key for predicting rates of ecosystem processes in the face of global change, microbial community composition is often ignored in ecosystem modeling. To address this issue, we review recent experiments and assess whether microbial community composition is resistant, resilient, or functionally redundant in response to four different disturbances. We find that the composition of most microbial groups is sensitive and not immediately resilient to disturbance, regardless of taxonomic breadth of the group or the type of disturbance. Other studies demonstrate that changes in composition are often associated with changes in ecosystem process rates. Thus, changes in microbial communities due to disturbance may directly affect ecosystem processes. Based on these relationships, we propose a simple framework to incorporate microbial community composition into ecosystem process models. We conclude that this effort would benefit from more empirical data on the links among microbial phylogeny, physiological traits, and disturbance responses. These relationships will determine how readily microbial community composition can be used to predict the responses of ecosystem processes to global change. PMID:18695234

  3. Comparative molecular analysis of endoevaporitic microbial communities.

    PubMed

    Sahl, Jason W; Pace, Norman R; Spear, John R

    2008-10-01

    A phylogenetic comparison of microbial communities in hypersaline evaporites was conducted on crusts from Guerrero Negro, Mexico, and Lindsey Lake, New Mexico, using culture-independent rRNA gene sequence analysis. Many sequences were shared between evaporites, which suggests that similar environments select for specific microbial lineages from a global metacommunity. PMID:18757573

  4. Comparative molecular analysis of endoevaporitic microbial communities.

    PubMed

    Sahl, Jason W; Pace, Norman R; Spear, John R

    2008-10-01

    A phylogenetic comparison of microbial communities in hypersaline evaporites was conducted on crusts from Guerrero Negro, Mexico, and Lindsey Lake, New Mexico, using culture-independent rRNA gene sequence analysis. Many sequences were shared between evaporites, which suggests that similar environments select for specific microbial lineages from a global metacommunity.

  5. Metabolic Network Modeling of Microbial Communities

    PubMed Central

    Biggs, Matthew B.; Medlock, Gregory L.; Kolling, Glynis L.

    2015-01-01

    Genome-scale metabolic network reconstructions and constraint-based analysis are powerful methods that have the potential to make functional predictions about microbial communities. Current use of genome-scale metabolic networks to characterize the metabolic functions of microbial communities includes species compartmentalization, separating species-level and community-level objectives, dynamic analysis, the “enzyme-soup” approach, multi-scale modeling, and others. There are many challenges inherent to the field, including a need for tools that accurately assign high-level omics signals to individual community members, new automated reconstruction methods that rival manual curation, and novel algorithms for integrating omics data and engineering communities. As technologies and modeling frameworks improve, we expect that there will be proportional advances in the fields of ecology, health science, and microbial community engineering. PMID:26109480

  6. Two-stage microbial community experimental design.

    PubMed

    Tickle, Timothy L; Segata, Nicola; Waldron, Levi; Weingart, Uri; Huttenhower, Curtis

    2013-12-01

    Microbial community samples can be efficiently surveyed in high throughput by sequencing markers such as the 16S ribosomal RNA gene. Often, a collection of samples is then selected for subsequent metagenomic, metabolomic or other follow-up. Two-stage study design has long been used in ecology but has not yet been studied in-depth for high-throughput microbial community investigations. To avoid ad hoc sample selection, we developed and validated several purposive sample selection methods for two-stage studies (that is, biological criteria) targeting differing types of microbial communities. These methods select follow-up samples from large community surveys, with criteria including samples typical of the initially surveyed population, targeting specific microbial clades or rare species, maximizing diversity, representing extreme or deviant communities, or identifying communities distinct or discriminating among environment or host phenotypes. The accuracies of each sampling technique and their influences on the characteristics of the resulting selected microbial community were evaluated using both simulated and experimental data. Specifically, all criteria were able to identify samples whose properties were accurately retained in 318 paired 16S amplicon and whole-community metagenomic (follow-up) samples from the Human Microbiome Project. Some selection criteria resulted in follow-up samples that were strongly non-representative of the original survey population; diversity maximization particularly undersampled community configurations. Only selection of intentionally representative samples minimized differences in the selected sample set from the original microbial survey. An implementation is provided as the microPITA (Microbiomes: Picking Interesting Taxa for Analysis) software for two-stage study design of microbial communities.

  7. 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.

  8. Microbial community modeling using reliability theory.

    PubMed

    Zilles, Julie L; Rodríguez, Luis F; Bartolerio, Nicholas A; Kent, Angela D

    2016-08-01

    Linking microbial community composition with the corresponding ecosystem functions remains challenging. Because microbial communities can differ in their functional responses, this knowledge gap limits ecosystem assessment, design and management. To develop models that explicitly incorporate microbial populations and guide efforts to characterize their functional differences, we propose a novel approach derived from reliability engineering. This reliability modeling approach is illustrated here using a microbial ecology dataset from denitrifying bioreactors. Reliability modeling is well-suited for analyzing the stability of complex networks composed of many microbial populations. It could also be applied to evaluate the redundancy within a particular biochemical pathway in a microbial community. Reliability modeling allows characterization of the system's resilience and identification of failure-prone functional groups or biochemical steps, which can then be targeted for monitoring or enhancement. The reliability engineering approach provides a new perspective for unraveling the interactions between microbial community diversity, functional redundancy and ecosystem services, as well as practical tools for the design and management of engineered ecosystems.

  9. High-resolution phylogenetic microbial community profiling

    PubMed Central

    Singer, Esther; Bushnell, Brian; Coleman-Derr, Devin; Bowman, Brett; Bowers, Robert M; Levy, Asaf; Gies, Esther A; Cheng, Jan-Fang; Copeland, Alex; Klenk, Hans-Peter; Hallam, Steven J; Hugenholtz, Philip; Tringe, Susannah G; Woyke, Tanja

    2016-01-01

    Over the past decade, high-throughput short-read 16S rRNA gene amplicon sequencing has eclipsed clone-dependent long-read Sanger sequencing for microbial community profiling. The transition to new technologies has provided more quantitative information at the expense of taxonomic resolution with implications for inferring metabolic traits in various ecosystems. We applied single-molecule real-time sequencing for microbial community profiling, generating full-length 16S rRNA gene sequences at high throughput, which we propose to name PhyloTags. We benchmarked and validated this approach using a defined microbial community. When further applied to samples from the water column of meromictic Sakinaw Lake, we show that while community structures at the phylum level are comparable between PhyloTags and Illumina V4 16S rRNA gene sequences (iTags), variance increases with community complexity at greater water depths. PhyloTags moreover allowed less ambiguous classification. Last, a platform-independent comparison of PhyloTags and in silico generated partial 16S rRNA gene sequences demonstrated significant differences in community structure and phylogenetic resolution across multiple taxonomic levels, including a severe underestimation in the abundance of specific microbial genera involved in nitrogen and methane cycling across the Lake's water column. Thus, PhyloTags provide a reliable adjunct or alternative to cost-effective iTags, enabling more accurate phylogenetic resolution of microbial communities and predictions on their metabolic potential. PMID:26859772

  10. Surface reflectance degradation by microbial communities

    SciTech Connect

    Cheng, Meng -Dawn; Allman, Steve L.; Graham, David E.; Cheng, Karen R.; Pfiffner, Susan Marie; Vishnivetskaya, Tatiana A.; Desjarlais, Andre Omer

    2015-11-05

    Building envelope, such as a roof, is the interface between a building structure and the environment. Understanding of the physics of microbial interactions with the building envelope is limited. In addition to the natural weathering, microorganisms and airborne particulate matter that attach to a cool roof tend to reduce the roof reflectance over time, compromising the energy efficiency advantages of the reflective coating designs. We applied microbial ecology analysis to identify the natural communities present on the exposed coatings and investigated the reduction kinetics of the surface reflectance upon the introduction of a defined mixture of both photoautotrophic and heterotrophic microorganisms representing the natural communities. The result are (1) reflectance degradation by microbial communities follows a first-order kinetic relationship and (2) more than 50% of degradation from the initial reflectance value can be caused by microbial species alone in much less time than 3 years required by the current standard ENERGY STAR® test methods.

  11. Surface reflectance degradation by microbial communities

    DOE PAGES

    Cheng, Meng -Dawn; Allman, Steve L.; Graham, David E.; Cheng, Karen R.; Pfiffner, Susan Marie; Vishnivetskaya, Tatiana A.; Desjarlais, Andre Omer

    2015-11-05

    Building envelope, such as a roof, is the interface between a building structure and the environment. Understanding of the physics of microbial interactions with the building envelope is limited. In addition to the natural weathering, microorganisms and airborne particulate matter that attach to a cool roof tend to reduce the roof reflectance over time, compromising the energy efficiency advantages of the reflective coating designs. We applied microbial ecology analysis to identify the natural communities present on the exposed coatings and investigated the reduction kinetics of the surface reflectance upon the introduction of a defined mixture of both photoautotrophic and heterotrophicmore » microorganisms representing the natural communities. The result are (1) reflectance degradation by microbial communities follows a first-order kinetic relationship and (2) more than 50% of degradation from the initial reflectance value can be caused by microbial species alone in much less time than 3 years required by the current standard ENERGY STAR® test methods.« less

  12. Nutrient Addition Dramatically Accelerates Microbial Community Succession

    PubMed Central

    Knelman, Joseph E.; Schmidt, Steven K.; Lynch, Ryan C.; Darcy, John L.; Castle, Sarah C.; Cleveland, Cory C.; Nemergut, Diana R.

    2014-01-01

    The ecological mechanisms driving community succession are widely debated, particularly for microorganisms. While successional soil microbial communities are known to undergo predictable changes in structure concomitant with shifts in a variety of edaphic properties, the causal mechanisms underlying these patterns are poorly understood. Thus, to specifically isolate how nutrients – important drivers of plant succession – affect soil microbial succession, we established a full factorial nitrogen (N) and phosphorus (P) fertilization plot experiment in recently deglaciated (∼3 years since exposure), unvegetated soils of the Puca Glacier forefield in Southeastern Peru. We evaluated soil properties and examined bacterial community composition in plots before and one year after fertilization. Fertilized soils were then compared to samples from three reference successional transects representing advancing stages of soil development ranging from 5 years to 85 years since exposure. We found that a single application of +NP fertilizer caused the soil bacterial community structure of the three-year old soils to most resemble the 85-year old soils after one year. Despite differences in a variety of soil edaphic properties between fertilizer plots and late successional soils, bacterial community composition of +NP plots converged with late successional communities. Thus, our work suggests a mechanism for microbial succession whereby changes in resource availability drive shifts in community composition, supporting a role for nutrient colimitation in primary succession. These results suggest that nutrients alone, independent of other edaphic factors that change with succession, act as an important control over soil microbial community development, greatly accelerating the rate of succession. PMID:25050551

  13. Metabolic interactions and dynamics in microbial communities

    NASA Astrophysics Data System (ADS)

    Segre', Daniel

    Metabolism, in addition to being the engine of every living cell, plays a major role in the cell-cell and cell-environment relations that shape the dynamics and evolution of microbial communities, e.g. by mediating competition and cross-feeding interactions between different species. Despite the increasing availability of metagenomic sequencing data for numerous microbial ecosystems, fundamental aspects of these communities, such as the unculturability of many isolates, and the conditions necessary for taxonomic or functional stability, are still poorly understood. We are developing mechanistic computational approaches for studying the interactions between different organisms based on the knowledge of their entire metabolic networks. In particular, we have recently built an open source platform for the Computation of Microbial Ecosystems in Time and Space (COMETS), which combines metabolic models with convection-diffusion equations to simulate the spatio-temporal dynamics of metabolism in microbial communities. COMETS has been experimentally tested on small artificial communities, and is scalable to hundreds of species in complex environments. I will discuss recent developments and challenges towards the implementation of models for microbiomes and synthetic microbial communities.

  14. Desert Varnish - Preservation of Biofabrics/Implcations for Mars

    NASA Technical Reports Server (NTRS)

    Probst, Luke W.; Allen, Carlton C.; Thomas-Keprta, Kathie L.; Clemett, Simon J.; Longazo, Teresa G.; Nelman-Gonzalez, Mayra A.; Sams, Clarence

    2002-01-01

    Desert varnish is the orange to dark brown rind that accumulates on exposed rock surfaces in many arid environments. Samples from the Sonoran Desert of Arizona are composed predominantly of clays (illite, smectite) and Mn- and Fe- oxides (birnessite, hematite). Features that appear to be single organisms are found within the varnish and at the rock-varnish interface. Many of these features are embedded in films that strongly resemble the water-rich extracellular polysaccharides produced by diverse microorganisms. Most common are rod-shaped celllike objects, 0.5-2 microns in the longest dimension, located within the varnish coatings. Some of these objects are shown to contain amines by fluorescence microscopy. The rod-shaped objects are observed in various states of degradation, as indicated by C and S abundances. Rods with higher C and S abundances appear less degraded than those with lower concentrations of these two elements. Regions rich in apparent microbes are present, while other regions display Mn- and Fe-rich mineral fabrics with microbe-sized voids and no obvious cells. These textures are interpreted as biofabrics, preserved by the precipitation of Mn and Fe minerals. We are researching the preservation of biofabrics by desert varnish in Earth's geological record. Rock coatings may similarly preserve evidence of microbial life on the hyper-arid surface of Mars.

  15. Does iron inhibit cryptoendolithic microbial communities?

    NASA Technical Reports Server (NTRS)

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

    1988-01-01

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

  16. Does iron inhibit cryptoendolithic microbial communities?

    PubMed

    Johnston, C G; Vestal, J R

    1988-01-01

    Photosynthetic activity of three cryptoendolithic microbial communities was studied under controlled conditions in the laboratory. In two of these communities, the dominant organisms were lichens, collected from Linnaeus Terrace and from Battleship Promontory. The third community, dominated by cyanobacteria, was collected from Battleship Promontory. Both sites are in the ice-free valleys of southern Victoria Land. Previous efforts have shown how physical conditions can influence metabolic activity in endolithic communities (Kappen and Friedmann 1983; Kappen, Friedmann, and Garty 1981; Vestal, Federle, and Friedmann 1984). Biological activity can also be strongly influenced by the chemical environment. Inorganic nutrients such as nitrate, ammonia, and phosphate are often limiting factors, so their effects on photosynthetic carbon-14 bicarbonate incorporation were investigated. Iron and manganese are two metals present in Linnaeus Terrace and Battleship Promontory sandstones, and their effects on photosynthesis were also studied. The results may add to our understanding of biogeochemical interactions within this unique microbial community. PMID:11538332

  17. Microbial astronauts: assembling microbial communities for advanced life support systems

    NASA Technical Reports Server (NTRS)

    Roberts, M. S.; Garland, J. L.; Mills, A. L.

    2004-01-01

    Extension of human habitation into space requires that humans carry with them many of the microorganisms with which they coexist on Earth. The ubiquity of microorganisms in close association with all living things and biogeochemical processes on Earth predicates that they must also play a critical role in maintaining the viability of human life in space. Even though bacterial populations exist as locally adapted ecotypes, the abundance of individuals in microbial species is so large that dispersal is unlikely to be limited by geographical barriers on Earth (i.e., for most environments "everything is everywhere" given enough time). This will not be true for microbial communities in space where local species richness will be relatively low because of sterilization protocols prior to launch and physical barriers between Earth and spacecraft after launch. Although community diversity will be sufficient to sustain ecosystem function at the onset, richness and evenness may decline over time such that biological systems either lose functional potential (e.g., bioreactors may fail to reduce BOD or nitrogen load) or become susceptible to invasion by human-associated microorganisms (pathogens) over time. Research at the John F. Kennedy Space Center has evaluated fundamental properties of microbial diversity and community assembly in prototype bioregenerative systems for NASA Advanced Life Support. Successional trends related to increased niche specialization, including an apparent increase in the proportion of nonculturable types of organisms, have been consistently observed. In addition, the stability of the microbial communities, as defined by their resistance to invasion by human-associated microorganisms, has been correlated to their diversity. Overall, these results reflect the significant challenges ahead for the assembly of stable, functional communities using gnotobiotic approaches, and the need to better define the basic biological principles that define ecosystem

  18. Microbial astronauts: assembling microbial communities for advanced life support systems.

    PubMed

    Roberts, M S; Garland, J L; Mills, A L

    2004-02-01

    Extension of human habitation into space requires that humans carry with them many of the microorganisms with which they coexist on Earth. The ubiquity of microorganisms in close association with all living things and biogeochemical processes on Earth predicates that they must also play a critical role in maintaining the viability of human life in space. Even though bacterial populations exist as locally adapted ecotypes, the abundance of individuals in microbial species is so large that dispersal is unlikely to be limited by geographical barriers on Earth (i.e., for most environments "everything is everywhere" given enough time). This will not be true for microbial communities in space where local species richness will be relatively low because of sterilization protocols prior to launch and physical barriers between Earth and spacecraft after launch. Although community diversity will be sufficient to sustain ecosystem function at the onset, richness and evenness may decline over time such that biological systems either lose functional potential (e.g., bioreactors may fail to reduce BOD or nitrogen load) or become susceptible to invasion by human-associated microorganisms (pathogens) over time. Research at the John F. Kennedy Space Center has evaluated fundamental properties of microbial diversity and community assembly in prototype bioregenerative systems for NASA Advanced Life Support. Successional trends related to increased niche specialization, including an apparent increase in the proportion of nonculturable types of organisms, have been consistently observed. In addition, the stability of the microbial communities, as defined by their resistance to invasion by human-associated microorganisms, has been correlated to their diversity. Overall, these results reflect the significant challenges ahead for the assembly of stable, functional communities using gnotobiotic approaches, and the need to better define the basic biological principles that define ecosystem

  19. High-resolution phylogenetic microbial community profiling

    SciTech Connect

    Singer, Esther; Coleman-Derr, Devin; Bowman, Brett; Schwientek, Patrick; Clum, Alicia; Copeland, Alex; Ciobanu, Doina; Cheng, Jan-Fang; Gies, Esther; Hallam, Steve; Tringe, Susannah; Woyke, Tanja

    2014-03-17

    The representation of bacterial and archaeal genome sequences is strongly biased towards cultivated organisms, which belong to merely four phylogenetic groups. Functional information and inter-phylum level relationships are still largely underexplored for candidate phyla, which are often referred to as microbial dark matter. Furthermore, a large portion of the 16S rRNA gene records in the GenBank database are labeled as environmental samples and unclassified, which is in part due to low read accuracy, potential chimeric sequences produced during PCR amplifications and the low resolution of short amplicons. In order to improve the phylogenetic classification of novel species and advance our knowledge of the ecosystem function of uncultivated microorganisms, high-throughput full length 16S rRNA gene sequencing methodologies with reduced biases are needed. We evaluated the performance of PacBio single-molecule real-time (SMRT) sequencing in high-resolution phylogenetic microbial community profiling. For this purpose, we compared PacBio and Illumina metagenomic shotgun and 16S rRNA gene sequencing of a mock community as well as of an environmental sample from Sakinaw Lake, British Columbia. Sakinaw Lake is known to contain a large age of microbial species from candidate phyla. Sequencing results show that community structure based on PacBio shotgun and 16S rRNA gene sequences is highly similar in both the mock and the environmental communities. Resolution power and community representation accuracy from SMRT sequencing data appeared to be independent of GC content of microbial genomes and was higher when compared to Illumina-based metagenome shotgun and 16S rRNA gene (iTag) sequences, e.g. full-length sequencing resolved all 23 OTUs in the mock community, while iTags did not resolve closely related species. SMRT sequencing hence offers various potential benefits when characterizing uncharted microbial communities.

  20. [Biofabrication with chitosan and its application progress].

    PubMed

    Meng, Fanping; Zhang, Aijing

    2009-05-01

    Chitosan is a polymer with good biocompatibility, unique pH-responsive solubility, convenient modification and easier film-formability. Chitosan could serve as an active mediator between biological components and microfabricated devices to prepare biological micro electro mechanical systems (BioMEMS) with high selectivity and sensitivity. Recently, there has been a growing interest in BioMEMS based on biofabrication of chitosan. We reviewed the mechanisms and processes of three biofabrication methods based on chitosan, including directed assembly, enzymatic assembly and self-assembly. Current applications and research progress in biological, medical and environmental fields are also discussed. Finally, future research directions are prospected.

  1. Bioprinting is coming of age: Report from the International Conference on Bioprinting and Biofabrication in Bordeaux (3B'09).

    PubMed

    Guillemot, Fabien; Mironov, Vladimir; Nakamura, Makoto

    2010-03-01

    The International Conference on Bioprinting and Biofabrication in Bordeaux (3B'09) demonstrated that the field of bioprinting and biofabrication continues to evolve. The increasing number and broadening geography of participants, the emergence of new exciting bioprinting technologies, and the attraction of young investigators indicates the strong growth potential of this emerging field. Bioprinting can be defined as the use of computer-aided transfer processes for patterning and assembling living and non-living materials with a prescribed 2D or 3D organization in order to produce bio-engineered structures serving in regenerative medicine, pharmacokinetic and basic cell biology studies. The use of bioprinting technology for biofabrication of in vitro assay has been shown to be a realistic short-term application. At the same time, the principal feasibility of bioprinting vascularized human organs as well as in vivo bioprinting has been demonstrated. The bioprinting of complex 3D human tissues and constructs in vitro and especially in vivo are exciting, but long-term, applications. It was decided that the 5th International Conference on Bioprinting and Biofabrication would be held in Philadelphia, USA in October 2010. The specially appointed 'Eploratory Committee' will consider the possibility of turning the growing bioprinting community into a more organized entity by creating a new bioprinting and biofabrication society. The new journal Biofabrication was also presented at 3B'09. This is an important milestone per se which provides additional objective evidence that the bioprinting and biofabrication field is consolidating and maturing. Thus, it is safe to state that bioprinting technology is coming of age.

  2. Microbial communities evolve faster in extreme environments

    PubMed Central

    Li, Sheng-Jin; Hua, Zheng-Shuang; Huang, Li-Nan; Li, Jie; Shi, Su-Hua; Chen, Lin-Xing; Kuang, Jia-Liang; Liu, Jun; Hu, Min; Shu, Wen-Sheng

    2014-01-01

    Evolutionary analysis of microbes at the community level represents a new research avenue linking ecological patterns to evolutionary processes, but remains insufficiently studied. Here we report a relative evolutionary rates (rERs) analysis of microbial communities from six diverse natural environments based on 40 metagenomic samples. We show that the rERs of microbial communities are mainly shaped by environmental conditions, and the microbes inhabiting extreme habitats (acid mine drainage, saline lake and hot spring) evolve faster than those populating benign environments (surface ocean, fresh water and soil). These findings were supported by the observation of more relaxed purifying selection and potentially frequent horizontal gene transfers in communities from extreme habitats. The mechanism of high rERs was proposed as high mutation rates imposed by stressful conditions during the evolutionary processes. This study brings us one stage closer to an understanding of the evolutionary mechanisms underlying the adaptation of microbes to extreme environments. PMID:25158668

  3. Method for analyzing microbial communities

    SciTech Connect

    Zhou, Jizhong; Wu, Liyou

    2010-07-20

    The present invention provides a method for quantitatively analyzing microbial genes, species, or strains in a sample that contains at least two species or strains of microorganisms. The method involves using an isothermal DNA polymerase to randomly and representatively amplify genomic DNA of the microorganisms in the sample, hybridizing the resultant polynucleotide amplification product to a polynucleotide microarray that can differentiate different genes, species, or strains of microorganisms of interest, and measuring hybridization signals on the microarray to quantify the genes, species, or strains of interest.

  4. Microbial Communities of Pavilion Lake Microbialites

    NASA Astrophysics Data System (ADS)

    Russell, J. A.; Biddle, J.; Pointing, S.; Cardman, Z.; Brady, A. L.; Slater, G. F.; Lim, D. S.

    2011-12-01

    Fossilized remnants of microbial mat growth, called stromatolites, are found in the rock record and are thought to be some of the earliest evidence for life on Earth. On the modern Earth, living versions of these stromatolites, called microbialites, are found in few environments across the globe. Pavilion Lake in British Columbia was found to host these microbialites, even though conditions are not extreme in the lake and grazers exist amongst the microbial growths. The Pavilion Lake Research Project, funded by NASA, the CSA and others, has developed the lake into an analog research site for the exploration of extraplanetary bodies since 2004. Pavilion Lake began to be explored for microbial ecology in 2007 to attempt to determine how the microbial communities change over time, location and depth to build these microbialite structures. DNA extracted from microbialites at two different locations and 3 depths at each location were analyzed by T-RFLP patterns. Significant differences were seen in the total communities from each location. Additional samples were taken in the summer and budding seasons, and significant differences were seen by season. A survey performed on just the cyanobacterial populations show less differences between taxa between sites, but significant differences with depth above and below the chemocline and between mineralized and non-mineralized mats. Differences were also examined between purple and green nodules, which are thought to be the growth forms of the microbialites. Detailed sequence analysis shows that Pavilion Lake microorganisms are similar, yet different, from microbial communities seen in other microbialite systems. In 2011, the research project moved to Kelly Lake, a lake nearby Pavilion Lake, that also contain microbialite structures. Similar morphologies were seen in Kelly Lake with an approximate 20 ft. offset in the typical depths where morphologies were seen. Continued analysis of Kelly Lake microbialites will be performed

  5. Environmental Microbial Community Proteomics: Status, Challenges and Perspectives

    PubMed Central

    Wang, Da-Zhi; Kong, Ling-Fen; Li, Yuan-Yuan; Xie, Zhang-Xian

    2016-01-01

    Microbial community proteomics, also termed metaproteomics, is an emerging field within the area of microbiology, which studies the entire protein complement recovered directly from a complex environmental microbial community at a given point in time. Although it is still in its infancy, microbial community proteomics has shown its powerful potential in exploring microbial diversity, metabolic potential, ecological function and microbe-environment interactions. In this paper, we review recent advances achieved in microbial community proteomics conducted in diverse environments, such as marine and freshwater, sediment and soil, activated sludge, acid mine drainage biofilms and symbiotic communities. The challenges facing microbial community proteomics are also discussed, and we believe that microbial community proteomics will greatly enhance our understanding of the microbial world and its interactions with the environment. PMID:27527164

  6. Environmental Microbial Community Proteomics: Status, Challenges and Perspectives.

    PubMed

    Wang, Da-Zhi; Kong, Ling-Fen; Li, Yuan-Yuan; Xie, Zhang-Xian

    2016-01-01

    Microbial community proteomics, also termed metaproteomics, is an emerging field within the area of microbiology, which studies the entire protein complement recovered directly from a complex environmental microbial community at a given point in time. Although it is still in its infancy, microbial community proteomics has shown its powerful potential in exploring microbial diversity, metabolic potential, ecological function and microbe-environment interactions. In this paper, we review recent advances achieved in microbial community proteomics conducted in diverse environments, such as marine and freshwater, sediment and soil, activated sludge, acid mine drainage biofilms and symbiotic communities. The challenges facing microbial community proteomics are also discussed, and we believe that microbial community proteomics will greatly enhance our understanding of the microbial world and its interactions with the environment. PMID:27527164

  7. Wetland Microbial Community Response to Restoration

    NASA Astrophysics Data System (ADS)

    Theroux, S.; Hartman, W.; Tringe, S. G.

    2015-12-01

    Wetland restoration has been proposed as a potential long-term carbon storage solution, with a goal of engineering geochemical dynamics to accelerate peat accretion and encourage greenhouse gas (GHG) sequestration. However, wetland microbial community composition and metabolic rates are poorly understood and their predicted response to wetland restoration is a veritable unknown. In an effort to better understand the underlying factors that shape the balance of carbon flux in wetland soils, we targeted the microbial communities along a salinity gradient ranging from freshwater tidal marshes to hypersaline ponds in the San Francisco Bay-Delta region. Using 16S rRNA gene sequencing and shotgun metagenomics, coupled with greenhouse gas measurements, we sampled sixteen sites capturing a range in salinity and restoration status. Seawater delivers sulfate to wetland ecosystems, encouraging sulfate reduction and discouraging methane production. As expected, we observed the highest rates of methane production in the freshwater wetlands. Recently restored wetlands had significantly higher rates of methane production compared to their historic counterparts that could be attributed to variations in trace metal and organic carbon content in younger wetlands. In contrast, our sequencing results revealed an almost immediate return of the indigenous microbial communities following seasonal flooding and full tidal restoration in saline and hypersaline wetlands and managed ponds. Notably, we found elevated methane production rates in hypersaline ponds, the result of methylotrophic methane production confirmed by sequence data and lab incubations. Our study links belowground microbial communities and their aboveground greenhouse gas production and highlights the inherent complexity in predicting wetland microbial response in the face of both natural and unnatural disturbances.

  8. From microbial communities to cells

    NASA Technical Reports Server (NTRS)

    Margulis, L.

    1985-01-01

    The eukraotic cell, the unit of structure of protoctists, plants, fungi, and animals, is not at all homologous to prokaryotic cells. Instead the eukaryotic cell is homologous to communities of microorganisms such as those of the sulfuretum. This research is based on the hypothesis that at least four different interacting community members entered the original associations that, when stabilized, led to the emergence of eukaryotic cells. These are: (1) host nucleocytoplasm (thermoplasma like archaebacteria); (2) mitochrondria (paracoccus or bdellovibryo like respiring bacteria; and (3) plastids (cyanobacteria) and undulipodia. Tubulin like protein was found in the free living spirochete Spirochaeta bajacaliforniensis and in several other spirochetes. The amino acid sequence was to see if the spirochete protein is homologous to the tubulin of undulipodial and mitotic spindle microtubules.

  9. Can transgenic maize affect soil microbial communities?

    PubMed

    Mulder, Christian; Wouterse, Marja; Raubuch, Markus; Roelofs, Willem; Rutgers, Michiel

    2006-09-29

    The aim of the experiment was to determine if temporal variations of belowground activity reflect the influence of the Cry1Ab protein from transgenic maize on soil bacteria and, hence, on a regulatory change of the microbial community (ability to metabolize sources belonging to different chemical guilds) and/or a change in numerical abundance of their cells. Litter placement is known for its strong influence on the soil decomposer communities. The effects of the addition of crop residues on respiration and catabolic activities of the bacterial community were examined in microcosm experiments. Four cultivars of Zea mays L. of two different isolines (each one including the conventional crop and its Bacillus thuringiensis cultivar) and one control of bulk soil were included in the experimental design. The growth models suggest a dichotomy between soils amended with either conventional or transgenic maize residues. The Cry1Ab protein appeared to influence the composition of the microbial community. The highly enhanced soil respiration observed during the first 72 h after the addition of Bt-maize residues can be interpreted as being related to the presence of the transgenic crop residues. This result was confirmed by agar plate counting, as the averages of the colony-forming units of soils in conventional treatments were about one-third of those treated with transgenic straw. Furthermore, the addition of Bt-maize appeared to induce increased microbial consumption of carbohydrates in BIOLOG EcoPlates. Three weeks after the addition of maize residues to the soils, no differences between the consumption rate of specific chemical guilds by bacteria in soils amended with transgenic maize and bacteria in soils amended with conventional maize were detectable. Reaped crop residues, comparable to post-harvest maize straw (a common practice in current agriculture), rapidly influence the soil bacterial cells at a functional level. Overall, these data support the existence of short

  10. Characterizing microbial communities through space and time

    PubMed Central

    Gonzalez, Antonio; King, Andrew; Robeson, Michael S.; Song, Sejin; Shade, Ashley; Metcalf, Jessica; Knight, Rob

    2011-01-01

    Until recently, the study of microbial diversity has mainly been limited to descriptive approaches, rather than predictive model-based analyses. The development of advanced analytical tools and decreasing cost of high-throughput multi-omics technologies has made the later approach more feasible. However, consensus is lacking as to which spatial and temporal scales best facilitate understanding of the role of microbial diversity in determining both public and environmental health. Here, we review the potential for combining these new technologies with both traditional and nascent spatio-temporal analysis methods. The fusion of proper spatio-temporal sampling, combined with modern multi-omics and computational tools, will provide insight into the tracking, development and manipulation of microbial communities. PMID:22154467

  11. The dynamic genetic repertoire of microbial communities

    PubMed Central

    Wilmes, Paul; Simmons, Sheri L; Denef, Vincent J; Banfield, Jillian F

    2009-01-01

    Community genomic data have revealed multiple levels of variation between and within microbial consortia. This variation includes large-scale differences in gene content between ecosystems as well as within-population sequence heterogeneity. In the present review, we focus specifically on how fine-scale variation within microbial and viral populations is apparent from community genomic data. A major unresolved question is how much of the observed variation is due to neutral vs. adaptive processes. Limited experimental data hint that some of this fine-scale variation may be in part functionally relevant, whereas sequence-based and modeling analyses suggest that much of it may be neutral. While methods for interpreting population genomic data are still in their infancy, we discuss current interpretations of existing datasets in the light of evolutionary processes and models. Finally, we highlight the importance of virus–host dynamics in generating and shaping within-population diversity. PMID:19054116

  12. Microbial Community Composition Affects Soil Fungistasis†

    PubMed Central

    de Boer, Wietse; Verheggen, Patrick; Klein Gunnewiek, Paulien J. A.; Kowalchuk, George A.; van Veen, Johannes A.

    2003-01-01

    Most soils inhibit fungal germination and growth to a certain extent, a phenomenon known as soil fungistasis. Previous observations have implicated microorganisms as the causal agents of fungistasis, with their action mediated either by available carbon limitation (nutrient deprivation hypothesis) or production of antifungal compounds (antibiosis hypothesis). To obtain evidence for either of these hypotheses, we measured soil respiration and microbial numbers (as indicators of nutrient stress) and bacterial community composition (as an indicator of potential differences in the composition of antifungal components) during the development of fungistasis. This was done for two fungistatic dune soils in which fungistasis was initially fully or partly relieved by partial sterilization treatment or nutrient addition. Fungistasis development was measured as restriction of the ability of the fungi Chaetomium globosum, Fusarium culmorum, Fusarium oxysporum, and Trichoderma harzianum to colonize soils. Fungistasis did not always reappear after soil treatments despite intense competition for carbon, suggesting that microbial community composition is important in the development of fungistasis. Both microbial community analysis and in vitro antagonism tests indicated that the presence of pseudomonads might be essential for the development of fungistasis. Overall, the results lend support to the antibiosis hypothesis. PMID:12571002

  13. Hydrolytic microbial communities in terrestrial ecosystems

    NASA Astrophysics Data System (ADS)

    Manucharova, Natalia; Chernov, Timofey; Kolcova, Ekaterina; Zelezova, Alena; Lukacheva, Euhenia; Zenova, Galina

    2014-05-01

    Hydrolytic microbial communities in terrestrial ecosystems Manucharova N.A., Chernov T.I., Kolcova E.M., Zelezova A.D., Lukacheva E.G. Lomonosov Moscow State University, Russia Vertical differentiation of terrestrial biogeocenoses is conditioned by the formation of vertical tiers that differ considerably in the composition and structure of microbial communities. All the three tiers, phylloplane, litter and soil, are united by a single flow of organic matter, and are spatially separated successional stages of decomposition of organic substances. Decomposition of organic matter is mainly due to the activity of microorganisms producing enzymes - hydrolase and lyase - which destroy complex organic compounds. Application of molecular biological techniques (FISH) in environmental studies provides a more complete information concerning the taxonomic diversity and potential hydrolytic activity of microbial complexes of terrestrial ecosystems that exist in a wide range of environmental factors (moisture, temperature, redox potential, organic matter). The combination of two molecular biological techniques (FISH and DGGE-analysis of fragments of gene 16S rRNA total amplificate) enables an informative assessment of the differences in the structure of dominant and minor components of hydrolytic complexes formed in different tiers of terrestrial ecosystems. The functional activity of hydrolytic microbial complexes of terrestrial ecosystems is determined by the activity of dominant and minor components, which also have a high gross enzymatic activity. Degradation of biopolymers in the phylloplane is mainly due to the representatives of the Proteobacteria phylogenetic group (classes alpha and beta). In mineral soil horizons, the role of hydrolytic representatives of Firmicutes and Actinobacteria increases. Among the key environmental parameters that determine the functional activity of the hydrolytic (chitinolytic) complex of soil layer (moisture, nutrient supply, successional

  14. ANALYSIS OF AQUATIC MICROBIAL COMMUNITIES IMPACTED BY LARGE POULTRY FORMS

    EPA Science Inventory

    Microbial communities often respond more rapidly and extensively to environmental change than communities of higher organisms. Thus, characterizing shifts in the structure of native bacterial communities as a response to changes in nutrients, antimicrobials, and invading pathogen...

  15. Microbial Communities in Pre-Columbian Coprolites

    PubMed Central

    Santiago-Rodriguez, Tasha M.; Narganes-Storde, Yvonne M.; Chanlatte, Luis; Crespo-Torres, Edwin; Toranzos, Gary A.; Jimenez-Flores, Rafael; Hamrick, Alice; Cano, Raul J.

    2013-01-01

    The study of coprolites from earlier cultures represents a great opportunity to study an “unaltered” composition of the intestinal microbiota. To test this, pre-Columbian coprolites from two cultures, the Huecoid and Saladoid, were evaluated for the presence of DNA, proteins and lipids by cytochemical staining, human and/or dog-specific Bacteroides spp. by PCR, as well as bacteria, fungi and archaea using Terminal Restriction Fragment analyses. DNA, proteins and lipids, and human-specific Bacteroides DNA were detected in all coprolites. Multidimensional scaling analyses resulted in spatial arrangements of microbial profiles by culture, further supported by cluster analysis and ANOSIM. Differences between the microbial communities were positively correlated with culture, and SIMPER analysis indicated 68.8% dissimilarity between the Huecoid and Saladoid. Proteobacteria, Bacteroidetes and methanogens were found in all coprolite samples. Propionebacteria, Shewanella and lactic acid bacteria dominated in the Huecoid samples, while Acidobacteria, and peptococci were dominant in Saladoid samples. Yeasts, including Candida albicans and Crypotococcus spp. were found in all samples. Basidiomycetes were the most notable fungi in Huecoid samples while Ascomycetes predominated in Saladoid samples, suggesting differences in dietary habits. Our study provides an approach for the study of the microbial communities of coprolite samples from various cultures. PMID:23755194

  16. Decoding molecular interactions in microbial communities.

    PubMed

    Abreu, Nicole A; Taga, Michiko E

    2016-09-01

    Microbial communities govern numerous fundamental processes on earth. Discovering and tracking molecular interactions among microbes is critical for understanding how single species and complex communities impact their associated host or natural environment. While recent technological developments in DNA sequencing and functional imaging have led to new and deeper levels of understanding, we are limited now by our inability to predict and interpret the intricate relationships and interspecies dependencies within these communities. In this review, we highlight the multifaceted approaches investigators have taken within their areas of research to decode interspecies molecular interactions that occur between microbes. Understanding these principles can give us greater insight into ecological interactions in natural environments and within synthetic consortia. PMID:27417261

  17. Evolutionary limits to cooperation in microbial communities

    PubMed Central

    Oliveira, Nuno M.; Niehus, Rene; Foster, Kevin R.

    2014-01-01

    Microbes produce many compounds that are costly to a focal cell but promote the survival and reproduction of neighboring cells. This observation has led to the suggestion that microbial strains and species will commonly cooperate by exchanging compounds. Here, we examine this idea with an ecoevolutionary model where microbes make multiple secretions, which can be exchanged among genotypes. We show that cooperation between genotypes only evolves under specific demographic regimes characterized by intermediate genetic mixing. The key constraint on cooperative exchanges is a loss of autonomy: strains become reliant on complementary genotypes that may not be reliably encountered. Moreover, the form of cooperation that we observe arises through mutual exploitation that is related to cheating and “Black Queen” evolution for a single secretion. A major corollary is that the evolution of cooperative exchanges reduces community productivity relative to an autonomous strain that makes everything it needs. This prediction finds support in recent work from synthetic communities. Overall, our work suggests that natural selection will often limit cooperative exchanges in microbial communities and that, when exchanges do occur, they can be an inefficient solution to group living. PMID:25453102

  18. Defining seasonal marine microbial community dynamics.

    PubMed

    Gilbert, Jack A; Steele, Joshua A; Caporaso, J Gregory; Steinbrück, Lars; Reeder, Jens; Temperton, Ben; Huse, Susan; McHardy, Alice C; Knight, Rob; Joint, Ian; Somerfield, Paul; Fuhrman, Jed A; Field, Dawn

    2012-02-01

    Here we describe, the longest microbial time-series analyzed to date using high-resolution 16S rRNA tag pyrosequencing of samples taken monthly over 6 years at a temperate marine coastal site off Plymouth, UK. Data treatment effected the estimation of community richness over a 6-year period, whereby 8794 operational taxonomic units (OTUs) were identified using single-linkage preclustering and 21 130 OTUs were identified by denoising the data. The Alphaproteobacteria were the most abundant Class, and the most frequently recorded OTUs were members of the Rickettsiales (SAR 11) and Rhodobacteriales. This near-surface ocean bacterial community showed strong repeatable seasonal patterns, which were defined by winter peaks in diversity across all years. Environmental variables explained far more variation in seasonally predictable bacteria than did data on protists or metazoan biomass. Change in day length alone explains >65% of the variance in community diversity. The results suggested that seasonal changes in environmental variables are more important than trophic interactions. Interestingly, microbial association network analysis showed that correlations in abundance were stronger within bacterial taxa rather than between bacteria and eukaryotes, or between bacteria and environmental variables.

  19. Microbial community composition in sediments resists perturbation by nutrient enrichment.

    PubMed

    Bowen, Jennifer L; Ward, Bess B; Morrison, Hilary G; Hobbie, John E; Valiela, Ivan; Deegan, Linda A; Sogin, Mitchell L

    2011-09-01

    Functional redundancy in bacterial communities is expected to allow microbial assemblages to survive perturbation by allowing continuity in function despite compositional changes in communities. Recent evidence suggests, however, that microbial communities change both composition and function as a result of disturbance. We present evidence for a third response: resistance. We examined microbial community response to perturbation caused by nutrient enrichment in salt marsh sediments using deep pyrosequencing of 16S rRNA and functional gene microarrays targeting the nirS gene. Composition of the microbial community, as demonstrated by both genes, was unaffected by significant variations in external nutrient supply in our sampling locations, despite demonstrable and diverse nutrient-induced changes in many aspects of marsh ecology. The lack of response to external forcing demonstrates a remarkable uncoupling between microbial composition and ecosystem-level biogeochemical processes and suggests that sediment microbial communities are able to resist some forms of perturbation. PMID:21412346

  20. Microbial community composition in sediments resists perturbation by nutrient enrichment

    PubMed Central

    Bowen, Jennifer L; Ward, Bess B; Morrison, Hilary G; Hobbie, John E; Valiela, Ivan; Deegan, Linda A; Sogin, Mitchell L

    2011-01-01

    Functional redundancy in bacterial communities is expected to allow microbial assemblages to survive perturbation by allowing continuity in function despite compositional changes in communities. Recent evidence suggests, however, that microbial communities change both composition and function as a result of disturbance. We present evidence for a third response: resistance. We examined microbial community response to perturbation caused by nutrient enrichment in salt marsh sediments using deep pyrosequencing of 16S rRNA and functional gene microarrays targeting the nirS gene. Composition of the microbial community, as demonstrated by both genes, was unaffected by significant variations in external nutrient supply in our sampling locations, despite demonstrable and diverse nutrient-induced changes in many aspects of marsh ecology. The lack of response to external forcing demonstrates a remarkable uncoupling between microbial composition and ecosystem-level biogeochemical processes and suggests that sediment microbial communities are able to resist some forms of perturbation. PMID:21412346

  1. Microbial community assembly, theory and rare functions

    PubMed Central

    Pholchan, Mujalin K.; Baptista, Joana de C.; Davenport, Russell J.; Sloan, William T.; Curtis, Thomas P.

    2013-01-01

    Views of community assembly have traditionally been based on the contrasting perspectives of the deterministic niche paradigm and stochastic neutral models. This study sought to determine if we could use empirical interventions conceived from a niche and neutral perspective to change the diversity and evenness of the microbial community within a reactor treating wastewater and to see if there was any associated change in the removal of endocrine disrupting compounds (EDCs). The systematic removal of EDCs and micropollutants from biological treatment systems is a major challenge for environmental engineers. We manipulated pairs of bioreactors in an experiment in which “niche” (temporal variation in resource concentration and resource complexity) and “neutral” (community size and immigration) attributes were changed and the effect on the detectable diversity and the removal of steroidal estrogens was evaluated. The effects of manipulations on diversity suggested that both niche and neutral processes are important in community assembly. We found that temporal variation in environmental conditions increased diversity but resource complexity did not. Larger communities had greater diversity but attempting to increase immigration by adding soil had the opposite effect. The effects of the manipulations on EDC removal efficiency were complex. Decreases in diversity, which were associated with a decrease in evenness, were associated with an increase in EDC removal. A simple generalized neutral model (calibrated with parameters typical of wastewater treatment plants) showed that decreases in diversity should lead to the increase in abundance of some ostensibly taxa rare. We conclude that neither niche and neutral perspectives nor the effect of diversity on putative rare functions can be properly understood by naïve qualitative observations. Instead, the relative importance of the key microbial mechanisms must be determined and, ideally, expressed mathematically

  2. Microbial community assembly, theory and rare functions.

    PubMed

    Pholchan, Mujalin K; Baptista, Joana de C; Davenport, Russell J; Sloan, William T; Curtis, Thomas P

    2013-01-01

    Views of community assembly have traditionally been based on the contrasting perspectives of the deterministic niche paradigm and stochastic neutral models. This study sought to determine if we could use empirical interventions conceived from a niche and neutral perspective to change the diversity and evenness of the microbial community within a reactor treating wastewater and to see if there was any associated change in the removal of endocrine disrupting compounds (EDCs). The systematic removal of EDCs and micropollutants from biological treatment systems is a major challenge for environmental engineers. We manipulated pairs of bioreactors in an experiment in which "niche" (temporal variation in resource concentration and resource complexity) and "neutral" (community size and immigration) attributes were changed and the effect on the detectable diversity and the removal of steroidal estrogens was evaluated. The effects of manipulations on diversity suggested that both niche and neutral processes are important in community assembly. We found that temporal variation in environmental conditions increased diversity but resource complexity did not. Larger communities had greater diversity but attempting to increase immigration by adding soil had the opposite effect. The effects of the manipulations on EDC removal efficiency were complex. Decreases in diversity, which were associated with a decrease in evenness, were associated with an increase in EDC removal. A simple generalized neutral model (calibrated with parameters typical of wastewater treatment plants) showed that decreases in diversity should lead to the increase in abundance of some ostensibly taxa rare. We conclude that neither niche and neutral perspectives nor the effect of diversity on putative rare functions can be properly understood by naïve qualitative observations. Instead, the relative importance of the key microbial mechanisms must be determined and, ideally, expressed mathematically. PMID

  3. Microbial communities in the deep subsurface

    NASA Astrophysics Data System (ADS)

    Krumholz, Lee R.

    The diversity of microbial populations and microbial communities within the earth's subsurface is summarized in this review. Scientists are currently exploring the subsurface and addressing questions of microbial diversity, the interactions among microorganisms, and mechanisms for maintenance of subsurface microbial communities. Heterotrophic anaerobic microbial communities exist in relatively permeable sandstone or sandy sediments, located adjacent to organic-rich deposits. These microorganisms appear to be maintained by the consumption of organic compounds derived from adjacent deposits. Sources of organic material serving as electron donors include lignite-rich Eocene sediments beneath the Texas coastal plain, organic-rich Cretaceous shales from the southwestern US, as well as Cretaceous clays containing organic materials and fermentative bacteria from the Atlantic Coastal Plain. Additionally, highly diverse microbial communities occur in regions where a source of organic matter is not apparent but where igneous rock is present. Examples include the basalt-rich subsurface of the Columbia River valley and the granitic subsurface regions of Sweden and Canada. These subsurface microbial communities appear to be maintained by the action of lithotrophic bacteria growing on H2 that is chemically generated within the subsurface. Other deep-dwelling microbial communities exist within the deep sediments of oceans. These systems often rely on anaerobic metabolism and sulfate reduction. Microbial colonization extends to the depths below which high temperatures limit the ability of microbes to survive. Energy sources for the organisms living in the oceanic subsurface may originate as oceanic sedimentary deposits. In this review, each of these microbial communities is discussed in detail with specific reference to their energy sources, their observed growth patterns, and their diverse composition. This information is critical to develop further understanding of subsurface

  4. Biochar addition impacts soil microbial community in tropical soils

    NASA Astrophysics Data System (ADS)

    Paz-Ferreiro, Jorge; Fu, Shenglei; Méndez, Ana; Gascó, Gabriel

    2014-05-01

    Studies on the effect of biochar on soil microbial activity and community structure in tropical areas are scarce. In this study we report the effect of several types of biochar (sewage sludge biochar, paper mill waste biochar, miscanthus biochar and pinewood biochar) in the soil microbial community of two tropical soils, an Acrisol and an Oxisol. In addition we study the effect of the presence or absence of earthworms in soil microbial community. Soil microbial community was more strongly affected by biochar than by the presence or absence of macrofauna.

  5. Microbial Communities Initiative: Melding Technology, Experimentation, and Theory

    ScienceCinema

    Konopka, Allan

    2016-07-12

    The Microbial Communities Initiative is a 5-year investment by Pacific Northwest National Laboratory that integrates biological/ecological experimentation, analytical chemistry, and simulation modeling. The objective is to create transforming technologies, elucidate mechanistic forces, and develop theoretical frameworks for the analysis and predictive understanding of microbial communities. Dr. Konopka describes PNNLs Microbial Communities Initiative. The MCI will integrate biological/ecological experimentation, analytical chemistry, and simulation modeling to create transforming technologies, elucidate mechanistic forces, and develop theoretical frameworks for the analysis and predictive understanding of microbial communities.

  6. Microbial communities in the deep subsurface

    NASA Astrophysics Data System (ADS)

    Krumholz, Lee R.

    The diversity of microbial populations and microbial communities within the earth's subsurface is summarized in this review. Scientists are currently exploring the subsurface and addressing questions of microbial diversity, the interactions among microorganisms, and mechanisms for maintenance of subsurface microbial communities. Heterotrophic anaerobic microbial communities exist in relatively permeable sandstone or sandy sediments, located adjacent to organic-rich deposits. These microorganisms appear to be maintained by the consumption of organic compounds derived from adjacent deposits. Sources of organic material serving as electron donors include lignite-rich Eocene sediments beneath the Texas coastal plain, organic-rich Cretaceous shales from the southwestern US, as well as Cretaceous clays containing organic materials and fermentative bacteria from the Atlantic Coastal Plain. Additionally, highly diverse microbial communities occur in regions where a source of organic matter is not apparent but where igneous rock is present. Examples include the basalt-rich subsurface of the Columbia River valley and the granitic subsurface regions of Sweden and Canada. These subsurface microbial communities appear to be maintained by the action of lithotrophic bacteria growing on H2 that is chemically generated within the subsurface. Other deep-dwelling microbial communities exist within the deep sediments of oceans. These systems often rely on anaerobic metabolism and sulfate reduction. Microbial colonization extends to the depths below which high temperatures limit the ability of microbes to survive. Energy sources for the organisms living in the oceanic subsurface may originate as oceanic sedimentary deposits. In this review, each of these microbial communities is discussed in detail with specific reference to their energy sources, their observed growth patterns, and their diverse composition. This information is critical to develop further understanding of subsurface

  7. Community history affects the predictability of microbial ecosystem development

    PubMed Central

    Pagaling, Eulyn; Strathdee, Fiona; Spears, Bryan M; Cates, Michael E; Allen, Rosalind J; Free, Andrew

    2014-01-01

    Microbial communities mediate crucial biogeochemical, biomedical and biotechnological processes, yet our understanding of their assembly, and our ability to control its outcome, remain poor. Existing evidence presents conflicting views on whether microbial ecosystem assembly is predictable, or inherently unpredictable. We address this issue using a well-controlled laboratory model system, in which source microbial communities colonize a pristine environment to form complex, nutrient-cycling ecosystems. When the source communities colonize a novel environment, final community composition and function (as measured by redox potential) are unpredictable, although a signature of the community's previous history is maintained. However, when the source communities are pre-conditioned to their new habitat, community development is more reproducible. This situation contrasts with some studies of communities of macro-organisms, where strong selection under novel environmental conditions leads to reproducible community structure, whereas communities under weaker selection show more variability. Our results suggest that the microbial rare biosphere may have an important role in the predictability of microbial community development, and that pre-conditioning may help to reduce unpredictability in the design of microbial communities for biotechnological applications. PMID:23985743

  8. Response of soil microbial communities during changes in land management

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The response of soil microbial communities to restoration following disturbances is poorly understood. We studied the soil microbial communities in a forest disturbance-restoration series comprising a native deciduous forest (DF), conventionally tilled cropland (CT) and mid-succession forest (SF) re...

  9. Soil amendments yield persisting changes in the microbial communities

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soil microbial communities are sensitive to carbon amendments and largely control the decomposition and accumulation of soil organic matter. In this study, we evaluated whether the type of carbon amendment applied to wheat-cropped or fallow soil imparted lasting effects on the microbial community w...

  10. Microbial biomass, activity and community composition in constructed wetlands.

    PubMed

    Truu, Marika; Juhanson, Jaanis; Truu, Jaak

    2009-06-15

    The aim of the current article is to give an overview about microbial communities and their functioning but also about factors affecting microbial activity in the three most common types (surface flow and two types of sub-surface flow) of constructed wetlands. The paper reviews the community composition and structural diversity of the microbial biomass, analyzing different aspects of microbial activity with respect to wastewater properties, specific wetland type, and environmental parameters. A brief introduction about the application of different novel molecular techniques for the assessment of microbial communities in constructed wetlands is also given. Microbially mediated processes in constructed wetlands are mainly dependent on hydraulic conditions, wastewater properties, including substrate and nutrient quality and availability, filter material or soil type, plants, and different environmental factors. Microbial biomass is within similar ranges in both horizontal and vertical subsurface flow and surface flow constructed wetlands. Stratification of the biomass but also a stratified structural pattern of the bacterial community can be seen in subsurface flow systems. Microbial biomass C/N ratio is higher in horizontal flow systems compared to vertical flow systems, indicating the structural differences in microbial communities between those two constructed wetland types. The total activity of the microbial community is in the same range, but heterotrophic growth is higher in the subsurface (vertical flow) system compared to the surface flow systems. Available species-specific data about microbial communities in different types of wetlands is scarce and therefore it is impossible make any general conclusions about the dynamics of microbial community structure in wetlands, its relationship to removal processes and operational parameters.

  11. Characterization Of Sponge-Associated Microbial Communities

    NASA Astrophysics Data System (ADS)

    Bailey, K. L.; Weisz, J.; Lindquist, N.

    2004-12-01

    To more fully understand the endosymbiotic relationship between sponges and microorganisms, it is necessary to characterize the microbial communities of the sponges. In this study, DNA was extracted from each of three individual sponges from four sponge species collected in a shallow mangrove cut in Florida Bay near Key Largo, Florida. A fragment of the 16S rRNA gene from sponge-associated bacteria was amplified using the polymerase chain reaction (PCR). The resulting PCR products were analyzed by denaturing gradient gel electrophoresis (DGGE), which separates DNA fragments based on their sequence differences. Some 16S sequences appeared to be shared by each of the four sponge species, while other fragments found in only particular species likely represent unique bacterial strains that play a role in sponge nutrition.

  12. Community Proteomics of a Natural Microbial Biofilm

    SciTech Connect

    Ram, Rachna J.; Verberkmoes, Nathan C; Thelen, Michael P.; Tyson, Gene W.; Baker, Brett J.; Shah, Manesh B; BlakeII, Robert C.; Hettich, Robert {Bob} L; Banfield, Jillian F.

    2005-06-01

    Using genomic and mass spectrometry-based proteomic methods, we evaluated gene expression, identified key activities, and examined partitioning of metabolic functions in a natural acid mine drainage (AMD) microbial biofilm community. We detected 2033 proteins from the five most abundant species in the biofilm, including 48% of the predicted proteins from the dominant biofilm organism, Leptospirillum group II. Proteins involved in protein refolding and response to oxidative stress appeared to be highly expressed, which suggests that damage to biomolecules is a key challenge for survival. We validated and estimated the relative abundance and cellular localization of 357 unique and 215 conserved novel proteins and determined that one abundant novel protein is a cytochrome central to iron oxidation and AMD formation.

  13. Microbial Community Functional Change during Vertebrate Carrion Decomposition

    PubMed Central

    Pechal, Jennifer L.; Crippen, Tawni L.; Tarone, Aaron M.; Lewis, Andrew J.; Tomberlin, Jeffery K.; Benbow, M. Eric

    2013-01-01

    Microorganisms play a critical role in the decomposition of organic matter, which contributes to energy and nutrient transformation in every ecosystem. Yet, little is known about the functional activity of epinecrotic microbial communities associated with carrion. The objective of this study was to provide a description of the carrion associated microbial community functional activity using differential carbon source use throughout decomposition over seasons, between years and when microbial communities were isolated from eukaryotic colonizers (e.g., necrophagous insects). Additionally, microbial communities were identified at the phyletic level using high throughput sequencing during a single study. We hypothesized that carrion microbial community functional profiles would change over the duration of decomposition, and that this change would depend on season, year and presence of necrophagous insect colonization. Biolog EcoPlates™ were used to measure the variation in epinecrotic microbial community function by the differential use of 29 carbon sources throughout vertebrate carrion decomposition. Pyrosequencing was used to describe the bacterial community composition in one experiment to identify key phyla associated with community functional changes. Overall, microbial functional activity increased throughout decomposition in spring, summer and winter while it decreased in autumn. Additionally, microbial functional activity was higher in 2011 when necrophagous arthropod colonizer effects were tested. There were inconsistent trends in the microbial function of communities isolated from remains colonized by necrophagous insects between 2010 and 2011, suggesting a greater need for a mechanistic understanding of the process. These data indicate that functional analyses can be implemented in carrion studies and will be important in understanding the influence of microbial communities on an essential ecosystem process, carrion decomposition. PMID:24265741

  14. Microbial community functional change during vertebrate carrion decomposition.

    PubMed

    Pechal, Jennifer L; Crippen, Tawni L; Tarone, Aaron M; Lewis, Andrew J; Tomberlin, Jeffery K; Benbow, M Eric

    2013-01-01

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

  15. Reciprocal influences of microbial community and hydrogeomorphology in sandy streambeds

    NASA Astrophysics Data System (ADS)

    Mendoza-Lera, C.; Federlein, L. L.; Frossard, A.; Gessner, M. O.; Knie, M.; Mutz, M.

    2015-12-01

    Stream hydrogeomorphology is a strong determinant of streambed microbial community activity, which in turn influences stream biogeochemistry. Whether this influence is unidirectional or whether microbial communities can also modulate biogeochemical processes by affecting hydrogeomorphology is an emerging question in research on sediment-water interfaces. Using experimental flumes simulating sandy streams, we tested whether such influences can occur through altered water exchange across the sediment-water interface. Results show that microbial communities in sandy streambeds can indeed affect hydrogeomorphology by producing gas bubbles. Specifically, gas bubbles accumulating in microbial biofilms can alter the water exchange by (i) reducing sediment pore space or (ii) provoking the detachment of the microbial biofilm detachment and thus altering streambed topography. Additionally, results indicate that water exchange is the major for the structure and activity of the microbial community. Our data also indicate that the potential of microbial communities to influence water exchange can be modulated by factors such as light intensity and discharge fluctuations. These biological-physical interactions and their effects on the influence of microbial communities on hydrogeomorphology is a source of spatiotemporal variability in water exchange across the sediment-water interface. Heterogeneity in water exchange is known to increase biogeochemical pathways and, thus, ecosystem functions. These results suggest that a holistic understanding of vertical connectivity in running waters requires consideration of biological-physical interactions at the water-sediment interface.

  16. Substrate-induced changes in microbial community-level physiological profiles and their application to discriminate soil microbial communities.

    PubMed

    Chen, Jian; Xie, Huijun; Zhuang, Xuliangli; Zhuang, Guoqiang; Bai, Zhihui; Zhang, Hongxun

    2008-01-01

    The addition of simple substrates could affect the microbial respiration in soils. This substrate-induced respiration is widely used to estimate the soil microbial biomass, but little attention has been paid to its influence on the changes of community-level physiological profiles. In this study, the process of microbial communities responding to the added substrate using sole-carbon-source utilization (BIOLOG) was investigated. BIOLOG is biased toward fast-growing bacteria; this advantage was taken to detect the prompt response of the active microbial communities to the added substrate. Four soil samples from agricultural fields adjacent to heavy metal mines were amended with L-arginine, citric acid, or D-glucose. Substrate amendments could, generally, not only increase the metabolic activity of the microbial communities, but also change the metabolic diverse patterns compared with no-substrate control. By tracking the process, it was found that the variance between substrate-induced treatment and control fluctuated greatly during the incubation course, and the influences of these three substrates were different. In addition, the application of these induced changes to discriminate soil microbial communities was tested. The distance among all samples was greatly increased, which further showed the functional variance among microbial communities in soils. This can be very useful in the discrimination of microbial communities even with high similarity.

  17. Organ printing: from bioprinter to organ biofabrication line.

    PubMed

    Mironov, Vladimir; Kasyanov, Vladimir; Markwald, Roger R

    2011-10-01

    Organ printing, or the layer by layer additive robotic biofabrication of functional three-dimensional tissue and organ constructs using self-assembling tissue spheroid building blocks, is a rapidly emerging technology that promises to transform tissue engineering into a commercially successful biomedical industry. It is increasingly obvious that similar well-established industries implement automated robotic systems on the path to commercial translation and economic success. The use of robotic bioprinters alone however is not sufficient for the development of large industrial scale organ biofabrication. The design and development of a fully integrated organ biofabrication line is imperative for the commercial translation of organ printing technology. This paper presents recent progress and challenges in the development of the essential components of an organ biofabrication line.

  18. Desert Varnish -- Preservation of Biofabrics and Implications for Mars

    NASA Astrophysics Data System (ADS)

    Probst, L. W.; Allen, C. C.; Thomas-Keprta, K. L.; Clemett, S. J.; Longazo, T. G.; Nelman-Gonzalez, M. A.; Sams, C.

    2002-03-01

    Preliminary data suggest that biofabrics are preserved by Mn and Fe minerals (birnessite and hematite) in desert varnish. A martian hematite-rich deposit with indications of biological activity may prove to be a prime site for future sample return.

  19. Comparative Metagenomics of Freshwater Microbial Communities

    SciTech Connect

    Hemme, Chris; Deng, Ye; Tu, Qichao; Fields, Matthew; Gentry, Terry; Wu, Liyou; Tringe, Susannah; Watson, David; He, Zhili; Hazen, Terry; Tiedje, James; Rubin, Eddy; Zhou, Jizhong

    2010-05-17

    Previous analyses of a microbial metagenome from uranium and nitric-acid contaminated groundwater (FW106) showed significant environmental effects resulting from the rapid introduction of multiple contaminants. Effects include a massive loss of species and strain biodiversity, accumulation of toxin resistant genes in the metagenome and lateral transfer of toxin resistance genes between community members. To better understand these results in an ecological context, a second metagenome from a pristine groundwater system located along the same geological strike was sequenced and analyzed (FW301). It is hypothesized that FW301 approximates the ancestral FW106 community based on phylogenetic profiles and common geological parameters; however, even if is not the case, the datasets still permit comparisons between healthy and stressed groundwater ecosystems. Complex carbohydrate metabolism has been almost entirely lost in the stressed ecosystem. In contrast, the pristine system encodes a wide diversity of complex carbohydrate metabolism systems, suggesting that carbon turnover is very rapid and less leaky in the healthy groundwater system. FW301 encodes many (~;;160+) carbon monoxide dehydrogenase genes while FW106 encodes none. This result suggests that the community is frequently exposed to oxygen from aerated rainwater percolating into the subsurface, with a resulting high rate of carbon metabolism and CO production. When oxygen levels fall, the CO then serves as a major carbon source for the community. FW301 appears to be capable of CO2 fixation via the reductive carboxylase (reverse TCA) cycle and possibly acetogenesis, activities; these activities are lacking in the heterotrophic FW106 system which relies exclusively on respiration of nitrate and/or oxygen for energy production. FW301 encodes a complete set of B12 biosynthesis pathway at high abundance suggesting the use of sodium gradients for energy production in the healthy groundwater community. Overall

  20. Mangrove succession enriches the sediment microbial community in South China.

    PubMed

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

    2016-01-01

    Sediment microorganisms help create and maintain mangrove ecosystems. Although the changes in vegetation during mangrove forest succession have been well studied, the changes in the sediment microbial community during mangrove succession are poorly understood. To investigate the changes in the sediment microbial community during succession of mangroves at Zhanjiang, South China, we used phospholipid fatty acid (PLFA) analysis and the following chronosequence from primary to climax community: unvegetated shoal; Avicennia marina community; Aegiceras corniculatum community; and Bruguiera gymnorrhiza + Rhizophora stylosa community. The PLFA concentrations of all sediment microbial groups (total microorganisms, fungi, gram-positive bacteria, gram-negative bacteria, and actinomycetes) increased significantly with each stage of mangrove succession. Microbial PLFA concentrations in the sediment were significantly lower in the wet season than in the dry season. Regression and ordination analyses indicated that the changes in the microbial community with mangrove succession were mainly associated with properties of the aboveground vegetation (mainly plant height) and the sediment (mainly sediment organic matter and total nitrogen). The changes in the sediment microbial community can probably be explained by increases in nutrients and microhabitat heterogeneity during mangrove succession. PMID:27265262

  1. Integrating Ecological and Engineering Concepts of Resilience in Microbial Communities

    PubMed Central

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

    2015-01-01

    Many definitions of resilience have been proffered for natural and engineered ecosystems, but a conceptual consensus on resilience in microbial communities is still lacking. We argue that the disconnect largely results from the wide variance in microbial community complexity, which range from compositionally 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 that undergo both recoverable and unrecoverable transitions, 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 two 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 and suggest that state changes in response to environmental variation may be a key mechanism driving functional resilience in microbial communities. PMID:26648912

  2. Mangrove succession enriches the sediment microbial community in South China

    PubMed Central

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

    2016-01-01

    Sediment microorganisms help create and maintain mangrove ecosystems. Although the changes in vegetation during mangrove forest succession have been well studied, the changes in the sediment microbial community during mangrove succession are poorly understood. To investigate the changes in the sediment microbial community during succession of mangroves at Zhanjiang, South China, we used phospholipid fatty acid (PLFA) analysis and the following chronosequence from primary to climax community: unvegetated shoal; Avicennia marina community; Aegiceras corniculatum community; and Bruguiera gymnorrhiza + Rhizophora stylosa community. The PLFA concentrations of all sediment microbial groups (total microorganisms, fungi, gram-positive bacteria, gram-negative bacteria, and actinomycetes) increased significantly with each stage of mangrove succession. Microbial PLFA concentrations in the sediment were significantly lower in the wet season than in the dry season. Regression and ordination analyses indicated that the changes in the microbial community with mangrove succession were mainly associated with properties of the aboveground vegetation (mainly plant height) and the sediment (mainly sediment organic matter and total nitrogen). The changes in the sediment microbial community can probably be explained by increases in nutrients and microhabitat heterogeneity during mangrove succession. PMID:27265262

  3. Integrating Ecological and Engineering Concepts of Resilience in Microbial Communities.

    PubMed

    Song, Hyun-Seob; Renslow, Ryan S; Fredrickson, Jim K; Lindemann, Stephen R

    2015-01-01

    Many definitions of resilience have been proffered for natural and engineered ecosystems, but a conceptual consensus on resilience in microbial communities is still lacking. We argue that the disconnect largely results from the wide variance in microbial community complexity, which range from compositionally 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 that undergo both recoverable and unrecoverable transitions, 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 two 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 and suggest that state changes in response to environmental variation may be a key mechanism driving functional resilience in microbial communities.

  4. Mangrove succession enriches the sediment microbial community in South China.

    PubMed

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

    2016-06-06

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

  5. A trait-based approach for examining microbial community assembly

    NASA Astrophysics Data System (ADS)

    Prest, T. L.; Nemergut, D.

    2015-12-01

    Microorganisms regulate all of Earth's major biogeochemical cycles and an understanding of how microbial communities assemble is a key part in evaluating controls over many types of ecosystem processes. Rapid advances in technology and bioinformatics have led to a better appreciation for the variation in microbial community structure in time and space. Yet, advances in theory are necessary to make sense of these data and allow us to generate unifying hypotheses about the causes and consequences of patterns in microbial biodiversity and what they mean for ecosystem function. Here, I will present a metaanalysis of microbial community assembly from a variety of successional and post-disturbance systems. Our analysis shows various distinct patterns in community assembly, and the potential importance of nutrients and dispersal in shaping microbial community beta diversity in these systems. We also used a trait-based approach to generate hypotheses about the mechanisms driving patterns of microbial community assembly and the implications for function. Our work reveals the importance of rRNA operon copy number as a community aggregated trait in helping to reconcile differences in community dynamics between distinct types of successional and disturbed systems. Specifically, our results demonstrate that decreases in average copy number can be a common feature of communities across various drivers of ecological succession, supporting a transition from an r-selected to a K-selected community. Importantly, our work supports the scaling of the copy number trait over multiple levels of biological organization, from cells to populations and communities, and has implications for both ecology and evolution. Trait-based approaches are an important next step to generate and test hypotheses about the forces structuring microbial communities and the subsequent consequences for ecosystem function.

  6. Microbial community dynamics alleviate stoichiometric constraints during litter decay.

    PubMed

    Kaiser, Christina; Franklin, Oskar; Dieckmann, Ulf; Richter, Andreas

    2014-06-01

    Under the current paradigm, organic matter decomposition and nutrient cycling rates are a function of the imbalance between substrate and microbial biomass stoichiometry. Challenging this view, we demonstrate that in an individual-based model, microbial community dynamics alter relative C and N limitation during litter decomposition, leading to a system behaviour not predictable from stoichiometric theory alone. Rather, the dynamics of interacting functional groups lead to an adaptation at the community level, which accelerates nitrogen recycling in litter with high initial C : N ratios and thus alleviates microbial N limitation. This mechanism allows microbial decomposers to overcome large imbalances between resource and biomass stoichiometry without the need to decrease carbon use efficiency (CUE), which is in contrast to predictions of traditional stoichiometric mass balance equations. We conclude that identifying and implementing microbial community-driven mechanisms in biogeochemical models are necessary for accurately predicting terrestrial C fluxes in response to changing environmental conditions. PMID:24628731

  7. Microbial community dynamics alleviate stoichiometric constraints during litter decay.

    PubMed

    Kaiser, Christina; Franklin, Oskar; Dieckmann, Ulf; Richter, Andreas

    2014-06-01

    Under the current paradigm, organic matter decomposition and nutrient cycling rates are a function of the imbalance between substrate and microbial biomass stoichiometry. Challenging this view, we demonstrate that in an individual-based model, microbial community dynamics alter relative C and N limitation during litter decomposition, leading to a system behaviour not predictable from stoichiometric theory alone. Rather, the dynamics of interacting functional groups lead to an adaptation at the community level, which accelerates nitrogen recycling in litter with high initial C : N ratios and thus alleviates microbial N limitation. This mechanism allows microbial decomposers to overcome large imbalances between resource and biomass stoichiometry without the need to decrease carbon use efficiency (CUE), which is in contrast to predictions of traditional stoichiometric mass balance equations. We conclude that identifying and implementing microbial community-driven mechanisms in biogeochemical models are necessary for accurately predicting terrestrial C fluxes in response to changing environmental conditions.

  8. Microbial community dynamics alleviate stoichiometric constraints during litter decay

    PubMed Central

    Kaiser, Christina; Franklin, Oskar; Dieckmann, Ulf; Richter, Andreas

    2014-01-01

    Under the current paradigm, organic matter decomposition and nutrient cycling rates are a function of the imbalance between substrate and microbial biomass stoichiometry. Challenging this view, we demonstrate that in an individual-based model, microbial community dynamics alter relative C and N limitation during litter decomposition, leading to a system behaviour not predictable from stoichiometric theory alone. Rather, the dynamics of interacting functional groups lead to an adaptation at the community level, which accelerates nitrogen recycling in litter with high initial C : N ratios and thus alleviates microbial N limitation. This mechanism allows microbial decomposers to overcome large imbalances between resource and biomass stoichiometry without the need to decrease carbon use efficiency (CUE), which is in contrast to predictions of traditional stoichiometric mass balance equations. We conclude that identifying and implementing microbial community-driven mechanisms in biogeochemical models are necessary for accurately predicting terrestrial C fluxes in response to changing environmental conditions. PMID:24628731

  9. Cultivation and quantitative proteomic analyses of acidophilic microbial communities

    SciTech Connect

    Belnap, Christopher P.; Pan, Chongle; Verberkmoes, Nathan C; Power, Mary E.; Samatova, Nagiza F; Carver, Rudolf L.; Hettich, Robert {Bob} L; Banfield, Jillian F.

    2010-01-01

    Acid mine drainage (AMD), an extreme environment characterized by low pH and high metal concentrations, can support dense acidophilic microbial biofilm communities that rely on chemoautotrophic production based on iron oxidation. Field determined production rates indicate that, despite the extreme conditions, these communities are sufficiently well adapted to their habitats to achieve primary production rates comparable to those of microbial communities occurring in some non-extreme environments. To enable laboratory studies of growth, production and ecology of AMD microbial communities, a culturing system was designed to reproduce natural biofilms, including organisms recalcitrant to cultivation. A comprehensive metabolic labeling-based quantitative proteomic analysis was used to verify that natural and laboratory communities were comparable at the functional level. Results confirmed that the composition and core metabolic activities of laboratory-grown communities were similar to a natural community, including the presence of active, low abundance bacteria and archaea that have not yet been isolated. However, laboratory growth rates were slow compared with natural communities, and this correlated with increased abundance of stress response proteins for the dominant bacteria in laboratory communities. Modification of cultivation conditions reduced the abundance of stress response proteins and increased laboratory community growth rates. The research presented here represents the first description of the application of a metabolic labeling-based quantitative proteomic analysis at the community level and resulted in a model microbial community system ideal for testing physiological and ecological hypotheses.

  10. Microbial communities involved in electricity generation from sulfide oxidation in a microbial fuel cell.

    PubMed

    Sun, Min; Tong, Zhong-Hua; Sheng, Guo-Ping; Chen, Yong-Zhen; Zhang, Feng; Mu, Zhe-Xuan; Wang, Hua-Lin; Zeng, Raymond J; Liu, Xian-Wei; Yu, Han-Qing; Wei, Li; Ma, Fang

    2010-10-15

    Simultaneous electricity generation and sulfide removal can be achieved in a microbial fuel cell (MFC). In electricity harvesting from sulfide oxidation in such an MFC, various microbial communities are involved. It is essential to elucidate the microbial communities and their roles in the sulfide conversion and electricity generation. In this work, an MFC was constructed to enrich a microbial consortium, which could harvest electricity from sulfide oxidation. Electrochemical analysis demonstrated that microbial catalysis was involved in electricity output in the sulfide-fed MFC. The anode-attached and planktonic communities could perform catalysis independently, and synergistic interactions occurred when the two communities worked together. A 16S rRNA clone library analysis was employed to characterize the microbial communities in the MFC. The anode-attached and planktonic communities shared similar richness and diversity, while the LIBSHUFF analysis revealed that the two community structures were significantly different. The exoelectrogenic, sulfur-oxidizing and sulfate-reducing bacteria were found in the MFC anodic chamber. The discovery of these bacteria was consistent with the community characteristics for electricity generation from sulfide oxidation. The exoelectrogenic bacteria were found both on the anode and in the solution. The sulfur-oxidizing bacteria were present in greater abundance on the anode than in the solution, while the sulfate-reducing bacteria preferably lived in the solution.

  11. Integrating ecological and engineering concepts of resilience in microbial communities

    DOE PAGES

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

    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

  12. Integrating ecological and engineering concepts of resilience in microbial communities

    SciTech Connect

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

    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 two 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.

  13. Which Microbial Communities Are Present? Sequence-Based Metagenomics

    NASA Astrophysics Data System (ADS)

    Caffrey, Sean M.

    The use of metagenomic methods that directly sequence environmental samples has revealed the extraordinary microbial diversity missed by traditional culture-based methodologies. Therefore, to develop a complete and representative model of an environment's microbial community and activities, metagenomic analysis is an essential tool.

  14. Microbial Community Analysis of a Single Chamber Microbial Fuel Cell Using Potato Wastewater

    SciTech Connect

    Zhen Li; Rishika Haynes; Eugene Sato; Malcolm Shields; Yoshiko Fujita; Chikashi Sato

    2014-04-01

    Microbial fuel cells (MFCs) convert chemical energy to electrical energy via bioelectrochemical reactions mediated by microorganisms. We investigated the diversity of the microbial community in an air cathode single chamber MFC that utilized potato-process wastewater as substrate. Terminal Restriction Fragment Length Polymorphism (T-RFLP) results indicated that the bacterial communities on the anode, cathode, control electrode, and MFC bulk fluid were similar, but differed dramatically from that of the anaerobic domestic sludge and potato wastewater inoculum. The 16S rDNA sequencing results showed that microbial species detected on the anode were predominantly within the phyla of Proteobacteria, Firmicutes, and Bacteroidetes. Fluorescent microscopy results indicated that there was a clear enhancement of biofilm formation on the anode. Results of this study could help improve understanding of the complexity of microbial communities and optimize the microbial composition for generating electricity by MFCs that utilize potato wastewater.

  15. A hydrogen-based subsurface microbial community dominated by methanogens

    USGS Publications Warehouse

    Chapelle, F.H.; O'Neill, K.; Bradley, P.M.; Methe, B.A.; Ciufo, S.A.; Knobel, L.L.; Lovley, D.R.

    2002-01-01

    The search for extraterrestrial life may be facilitated if ecosystems can be found on Earth that exist under conditions analogous to those present on other planets or moons. It has been proposed, on the basis of geochemical and thermodynamic considerations, that geologically derived hydrogen might support subsurface microbial communities on Mars and Europa in which methanogens form the base of the ecosystem1-5. Here we describe a unique subsurface microbial community in which hydrogen-consuming, methane-producing Archaea far outnumber the Bacteria. More than 90% of the 16s ribosomal DNA sequences recovered from hydrothermal waters circulating through deeply buried igneous rocks in Idaho are related to hydrogen-using methanogenic microorganisms. Geochemical characterization indicates that geothermal hydrogen, not organic carbon, is the primary energy source for this methanogen-dominated microbial community. These results demonstrate that hydrogen-based methanogenic communities do occur in Earth's subsurface, providing an analogue for possible subsurface microbial ecosystems on other planets.

  16. A hydrogen-based subsurface microbial community dominated by methanogens.

    PubMed

    Chapelle, Francis H; O'Neill, Kathleen; Bradley, Paul M; Methé, Barbara A; Ciufo, Stacy A; Knobel, LeRoy L; Lovley, Derek R

    2002-01-17

    The search for extraterrestrial life may be facilitated if ecosystems can be found on Earth that exist under conditions analogous to those present on other planets or moons. It has been proposed, on the basis of geochemical and thermodynamic considerations, that geologically derived hydrogen might support subsurface microbial communities on Mars and Europa in which methanogens form the base of the ecosystem. Here we describe a unique subsurface microbial community in which hydrogen-consuming, methane-producing Archaea far outnumber the Bacteria. More than 90% of the 16S ribosomal DNA sequences recovered from hydrothermal waters circulating through deeply buried igneous rocks in Idaho are related to hydrogen-using methanogenic microorganisms. Geochemical characterization indicates that geothermal hydrogen, not organic carbon, is the primary energy source for this methanogen-dominated microbial community. These results demonstrate that hydrogen-based methanogenic communities do occur in Earth's subsurface, providing an analogue for possible subsurface microbial ecosystems on other planets.

  17. Sequencing, Assembly and Analysis of Human Microbial Communities

    SciTech Connect

    Petrosino, Joe

    2010-06-04

    Joe Petrosino of Baylor College of Medicine discusses using next generation sequencing technologies to study human microbial communities associated with health and disease on June 4, 2010 at the "Sequencing, Finishing, Analysis in the Future" meeting in Santa Fe, NM

  18. Microbial communities respond to experimental warming, but site matters.

    PubMed

    Cregger, Melissa A; Sanders, Nathan J; Dunn, Robert R; Classen, Aimée T

    2014-01-01

    Because microorganisms are sensitive to temperature, ongoing global warming is predicted to influence microbial community structure and function. We used large-scale warming experiments established at two sites near the northern and southern boundaries of US eastern deciduous forests to explore how microbial communities and their function respond to warming at sites with differing climatic regimes. Soil microbial community structure and function responded to warming at the southern but not the northern site. However, changes in microbial community structure and function at the southern site did not result in changes in cellulose decomposition rates. While most global change models rest on the assumption that taxa will respond similarly to warming across sites and their ranges, these results suggest that the responses of microorganisms to warming may be mediated by differences across the geographic boundaries of ecosystems.

  19. Perspective for Aquaponic Systems: "Omic" Technologies for Microbial Community Analysis.

    PubMed

    Munguia-Fragozo, Perla; Alatorre-Jacome, Oscar; Rico-Garcia, Enrique; Torres-Pacheco, Irineo; Cruz-Hernandez, Andres; Ocampo-Velazquez, Rosalia V; Garcia-Trejo, Juan F; Guevara-Gonzalez, Ramon G

    2015-01-01

    Aquaponics is the combined production of aquaculture and hydroponics, connected by a water recirculation system. In this productive system, the microbial community is responsible for carrying out the nutrient dynamics between the components. The nutrimental transformations mainly consist in the transformation of chemical species from toxic compounds into available nutrients. In this particular field, the microbial research, the "Omic" technologies will allow a broader scope of studies about a current microbial profile inside aquaponics community, even in those species that currently are unculturable. This approach can also be useful to understand complex interactions of living components in the system. Until now, the analog studies were made to set up the microbial characterization on recirculation aquaculture systems (RAS). However, microbial community composition of aquaponics is still unknown. "Omic" technologies like metagenomic can help to reveal taxonomic diversity. The perspectives are also to begin the first attempts to sketch the functional diversity inside aquaponic systems and its ecological relationships. The knowledge of the emergent properties inside the microbial community, as well as the understanding of the biosynthesis pathways, can derive in future biotechnological applications. Thus, the aim of this review is to show potential applications of current "Omic" tools to characterize the microbial community in aquaponic systems.

  20. Perspective for Aquaponic Systems: "Omic" Technologies for Microbial Community Analysis.

    PubMed

    Munguia-Fragozo, Perla; Alatorre-Jacome, Oscar; Rico-Garcia, Enrique; Torres-Pacheco, Irineo; Cruz-Hernandez, Andres; Ocampo-Velazquez, Rosalia V; Garcia-Trejo, Juan F; Guevara-Gonzalez, Ramon G

    2015-01-01

    Aquaponics is the combined production of aquaculture and hydroponics, connected by a water recirculation system. In this productive system, the microbial community is responsible for carrying out the nutrient dynamics between the components. The nutrimental transformations mainly consist in the transformation of chemical species from toxic compounds into available nutrients. In this particular field, the microbial research, the "Omic" technologies will allow a broader scope of studies about a current microbial profile inside aquaponics community, even in those species that currently are unculturable. This approach can also be useful to understand complex interactions of living components in the system. Until now, the analog studies were made to set up the microbial characterization on recirculation aquaculture systems (RAS). However, microbial community composition of aquaponics is still unknown. "Omic" technologies like metagenomic can help to reveal taxonomic diversity. The perspectives are also to begin the first attempts to sketch the functional diversity inside aquaponic systems and its ecological relationships. The knowledge of the emergent properties inside the microbial community, as well as the understanding of the biosynthesis pathways, can derive in future biotechnological applications. Thus, the aim of this review is to show potential applications of current "Omic" tools to characterize the microbial community in aquaponic systems. PMID:26509157

  1. Microbial community transitions across the deep sediment-basement interface

    NASA Astrophysics Data System (ADS)

    Labonté, J.; Lever, M. A.; Orcutt, B.

    2015-12-01

    Previous studies of microbial abundance and geochemistry in deep marine sediments indicate a stimulation of microbial activity near the sediment-basement interface; yet, the extent to which microbial communities in bottom sediments and underlying crustal habitats interact is unclear. We conducted tag pyrosequencing on DNA extracted from a spectrum of deep sediment-basement samples to try to identify patterns in microbial community shifts across sediment-basement interfaces, focusing on samples from the subsurface of the Juan de Fuca Ridge flank (IODP Expedition 327). Our results demonstrate that sediment and the basaltic crust harbor microbial communities that are phylogenetically connected, but the eveness is characteristic of the environment. We will discuss the microbial community transitions that occur horizontally along fluid flow pathways and vertically across the sediment basement interface, as well as the possible implications regarding the controls of microbial community composition along deep sediment-basement interfaces in hydrothermal systems. We will also highlight efforts to overcome sample contamination in crustal subsurface samples.

  2. Elevated Carbon Dioxide Alters the Structure of Soil Microbial Communities

    PubMed Central

    Deng, Ye; He, Zhili; Xu, Meiying; Qin, Yujia; Van Nostrand, Joy D.; Wu, Liyou; Roe, Bruce A.; Wiley, Graham; Hobbie, Sarah E.; Reich, Peter B.

    2012-01-01

    Pyrosequencing analysis of 16S rRNA genes was used to examine impacts of elevated CO2 (eCO2) on soil microbial communities from 12 replicates each from ambient CO2 (aCO2) and eCO2 settings. The results suggest that the soil microbial community composition and structure significantly altered under conditions of eCO2, which was closely associated with soil and plant properties. PMID:22307288

  3. Community Analysis of Dynamic Microbial Mat Communities from Actively Erupting Seamounts (Invited)

    NASA Astrophysics Data System (ADS)

    Davis, R.; Tebo, B.; Moyer, C. L.

    2009-12-01

    The actively erupting deep-sea volcanoes NW Rota-1 and W Mata have multiple diffuse low-temperature (Tmax= 20-30 degrees) vent sites which harbor dense populations of microbial mat communities driven by chemoautotrophy. These microbial mats were often composed of white filamentous bacteria growing in close proximity to focused hydrothermal flow. Eight microbial mats were sampled from discrete hydrothermal vents on NW Rota-1 and W Mata volcanoes in 2009. The microbial mat communities were analyzed with quantitative PCR (Q-PCR) and terminal-restriction fragment length polymorphism (T-RFLP) community fingerprinting. All of the sampled microbial mats were dominated by the class Epsilonproteobacteria. The microbial mat at Iceberg Vent contained 13.5% Archaea, while all other microbial mats contained less than 1% Archaea. Bacterial community fingerprints from NW Rota-1 and W Mata formed distinct clusters that were well separated from clusters formed by hydrothermal communities from Axial and Eifuku Seamounts that were also dominated by Epsilonproteobacteria. Iceberg vent communities from NW Rota-1 have transitioned from being dominated by Caminibacter phylotypes to Sulfuimonas group phylotypes since 2004. These data suggest that microbial communities found on actively erupting volcanoes are geographically distinct and provide a natural laboratory to study microbial colonization and community succession at hydrothermal systems.

  4. Soil microbial communities following bush removal in a Namibian savanna

    NASA Astrophysics Data System (ADS)

    Buyer, J. S.; Schmidt-Küntzel, A.; Nghikembua, M.; Maul, J. E.; Marker, L.

    2015-12-01

    Savanna ecosystems are subject to desertification and bush encroachment, which reduce the carrying capacity for wildlife and livestock. Bush thinning is a management approach that can, at least temporarily, restore grasslands and raise the grazing value of the land. In this study we examined the soil microbial communities under bush and grass in Namibia. We analyzed the soil through a chronosequence where bush was thinned at 9, 5, or 3 years before sampling. Soil microbial biomass, the biomass of specific taxonomic groups, and overall microbial community structure was determined by phospholipid fatty acid analysis, while the community structure of Bacteria, Archaea, and fungi was determined by multiplex terminal restriction fragment length polymorphism analysis. Soil under bush had higher pH, C, N, and microbial biomass than under grass, and the microbial community structure was also altered under bush compared to grass. A major disturbance to the ecosystem, bush thinning, resulted in an altered microbial community structure compared to control plots, but the magnitude of this perturbation gradually declined with time. Community structure was primarily driven by pH, C, and N, while vegetation type, bush thinning, and time since bush thinning were of secondary importance.

  5. Soil microbial communities following bush removal in a Namibian savanna

    NASA Astrophysics Data System (ADS)

    Buyer, Jeffrey S.; Schmidt-Küntzel, Anne; Nghikembua, Matti; Maul, Jude E.; Marker, Laurie

    2016-03-01

    Savanna ecosystems are subject to desertification and bush encroachment, which reduce the carrying capacity for wildlife and livestock. Bush thinning is a management approach that can, at least temporarily, restore grasslands and raise the grazing value of the land. In this study we examined the soil microbial communities under bush and grass in Namibia. We analyzed the soil through a chronosequence where bush was thinned at 9, 5, or 3 years before sampling. Soil microbial biomass, the biomass of specific taxonomic groups, and overall microbial community structure was determined by phospholipid fatty acid analysis, while the community structure of Bacteria, Archaea, and fungi was determined by multiplex terminal restriction fragment length polymorphism analysis. Soil under bush had higher pH, C, N, and microbial biomass than under grass, and the microbial community structure was also altered under bush compared to grass. A major disturbance to the ecosystem, bush thinning, resulted in an altered microbial community structure compared to control plots, but the magnitude of this perturbation gradually declined with time. Community structure was primarily driven by pH, C, and N, while vegetation type, bush thinning, and time since bush thinning were of secondary importance.

  6. 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

  7. Succession in a microbial mat community - A Gaian perspective

    NASA Technical Reports Server (NTRS)

    Stolz, J. F.

    1984-01-01

    The contribution of prokaryotes to Gaian control systems is discussed. The survival of the Microcoleus-dominated stratified microbial community at Laguna Figueroa, after heavy rains flooded the evaporite flat with up to 3 m of water and deposited 5-10 cm of allocthonous sediment, demonstrates the resiliency of these communities to short-term perturbations while the microbial fossil record attests to their persistence over geologic time. It is shown that the great diversity of microbial species and their short generation time make them uniquely suited for Gaian mechanisms.

  8. Microbial community assembly and metabolic function during mammalian corpse decomposition

    USGS Publications Warehouse

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

    2016-01-01

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

  9. Relating Anaerobic Digestion Microbial Community and Process Function

    PubMed Central

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

    2015-01-01

    Anaerobic digestion (AD) involves a consortium of microorganisms that convert substrates into biogas containing methane for renewable energy. The technology has suffered from the perception of being periodically unstable due to limited understanding of the relationship between microbial community structure and function. The emphasis of this review is to describe microbial communities in digesters and quantitative and qualitative relationships between community structure and digester function. Progress has been made in the past few decades to identify key microorganisms influencing AD. Yet, more work is required to realize robust, quantitative relationships between microbial community structure and functions such as methane production rate and resilience after perturbations. Other promising areas of research for improved AD may include methods to increase/control (1) hydrolysis rate, (2) direct interspecies electron transfer to methanogens, (3) community structure–function relationships of methanogens, (4) methanogenesis via acetate oxidation, and (5) bioaugmentation to study community–activity relationships or improve engineered bioprocesses. PMID:27127410

  10. Microbial community assembly and metabolic function during mammalian corpse decomposition.

    PubMed

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

    2016-01-01

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

  11. Microbial community assembly and metabolic function during mammalian corpse decomposition.

    PubMed

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

    2016-01-01

    Vertebrate corpse decomposition provides an important stage in nutrient cycling in most terrestrial habitats, yet microbially mediated processes are poorly understood. Here we combine deep microbial community characterization, community-level metabolic reconstruction, and soil biogeochemical assessment to understand the principles governing microbial community assembly during decomposition of mouse and human corpses on different soil substrates. We find a suite of bacterial and fungal groups that contribute to nitrogen cycling and a reproducible network of decomposers that emerge on predictable time scales. Our results show that this decomposer community is derived primarily from bulk soil, but key decomposers are ubiquitous in low abundance. Soil type was not a dominant factor driving community development, and the process of decomposition is sufficiently reproducible to offer new opportunities for forensic investigations. PMID:26657285

  12. Composition and physiological profiling of sprout-associated microbial communities

    NASA Technical Reports Server (NTRS)

    Matos, Anabelle; Garland, Jay L.; Fett, William F.

    2002-01-01

    The native microfloras of various types of sprouts (alfalfa, clover, sunflower, mung bean, and broccoli sprouts) were examined to assess the relative effects of sprout type and inoculum factors (i.e., sprout-growing facility, seed lot, and inoculation with sprout-derived inocula) on the microbial community structure of sprouts. Sprouts were sonicated for 7 min or hand shaken with glass beads for 2 min to recover native microfloras from the surface, and the resulting suspensions were diluted and plated. The culturable fraction was characterized by the density (log CFU/g), richness (e.g., number of types of bacteria), and diversity (e.g., microbial richness and evenness) of colonies on tryptic soy agar plates incubated for 48 h at 30 degrees C. The relative similarity between sprout-associated microbial communities was assessed with the use of community-level physiological profiles (CLPPs) based on patterns of utilization of 95 separate carbon sources. Aerobic plate counts of 7.96 +/- 0.91 log CFU/g of sprout tissue (fresh weight) were observed, with no statistically significant differences in microbial cell density, richness, or diversity due to sprout type, sprout-growing facility, or seed lot. CLPP analyses revealed that the microbial communities associated with alfalfa and clover sprouts are more similar than those associated with the other sprout types tested. Variability among sprout types was more extensive than any differences between microbial communities associated with alfalfa and clover sprouts from different sprout-growing facilities and seed lots. These results indicate that the subsequent testing of biocontrol agents should focus on similar organisms for alfalfa and clover, but alternative types may be most suitable for the other sprout types tested. The inoculation of alfalfa sprouts with communities derived from various sprout types had a significant, source-independent effect on microbial community structure, indicating that the process of

  13. Metagenomics meets time series analysis: unraveling microbial community dynamics.

    PubMed

    Faust, Karoline; Lahti, Leo; Gonze, Didier; de Vos, Willem M; Raes, Jeroen

    2015-06-01

    The recent increase in the number of microbial time series studies offers new insights into the stability and dynamics of microbial communities, from the world's oceans to human microbiota. Dedicated time series analysis tools allow taking full advantage of these data. Such tools can reveal periodic patterns, help to build predictive models or, on the contrary, quantify irregularities that make community behavior unpredictable. Microbial communities can change abruptly in response to small perturbations, linked to changing conditions or the presence of multiple stable states. With sufficient samples or time points, such alternative states can be detected. In addition, temporal variation of microbial interactions can be captured with time-varying networks. Here, we apply these techniques on multiple longitudinal datasets to illustrate their potential for microbiome research.

  14. Microbial communities associated with wet flue gas desulfurization systems.

    PubMed

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

    2012-01-01

    Flue gas desulfurization (FGD) systems are employed to remove SO(x) 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.

  15. 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

  16. Microbial communities associated with wet flue gas desulfurization systems.

    PubMed

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

    2012-01-01

    Flue gas desulfurization (FGD) systems are employed to remove SO(x) 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

  17. Segregation of the Anodic Microbial Communities in a Microbial Fuel Cell Cascade.

    PubMed

    Hodgson, Douglas M; Smith, Ann; Dahale, Sonal; Stratford, James P; Li, Jia V; Grüning, André; Bushell, Michael E; Marchesi, Julian R; Avignone Rossa, C

    2016-01-01

    Metabolic interactions within microbial communities are essential for the efficient degradation of complex organic compounds, and underpin natural phenomena driven by microorganisms, such as the recycling of carbon-, nitrogen-, and sulfur-containing molecules. These metabolic interactions ultimately determine the function, activity and stability of the community, and therefore their understanding would be essential to steer processes where microbial communities are involved. This is exploited in the design of microbial fuel cells (MFCs), bioelectrochemical devices that convert the chemical energy present in substrates into electrical energy through the metabolic activity of microorganisms, either single species or communities. In this work, we analyzed the evolution of the microbial community structure in a cascade of MFCs inoculated with an anaerobic microbial community and continuously fed with a complex medium. The analysis of the composition of the anodic communities revealed the establishment of different communities in the anodes of the hydraulically connected MFCs, with a decrease in the abundance of fermentative taxa and a concurrent increase in respiratory taxa along the cascade. The analysis of the metabolites in the anodic suspension showed a metabolic shift between the first and last MFC, confirming the segregation of the anodic communities. Those results suggest a metabolic interaction mechanism between the predominant fermentative bacteria at the first stages of the cascade and the anaerobic respiratory electrogenic population in the latter stages, which is reflected in the observed increase in power output. We show that our experimental system represents an ideal platform for optimization of processes where the degradation of complex substrates is involved, as well as a potential tool for the study of metabolic interactions in complex microbial communities.

  18. Segregation of the Anodic Microbial Communities in a Microbial Fuel Cell Cascade

    PubMed Central

    Hodgson, Douglas M.; Smith, Ann; Dahale, Sonal; Stratford, James P.; Li, Jia V.; Grüning, André; Bushell, Michael E.; Marchesi, Julian R.; Avignone Rossa, C.

    2016-01-01

    Metabolic interactions within microbial communities are essential for the efficient degradation of complex organic compounds, and underpin natural phenomena driven by microorganisms, such as the recycling of carbon-, nitrogen-, and sulfur-containing molecules. These metabolic interactions ultimately determine the function, activity and stability of the community, and therefore their understanding would be essential to steer processes where microbial communities are involved. This is exploited in the design of microbial fuel cells (MFCs), bioelectrochemical devices that convert the chemical energy present in substrates into electrical energy through the metabolic activity of microorganisms, either single species or communities. In this work, we analyzed the evolution of the microbial community structure in a cascade of MFCs inoculated with an anaerobic microbial community and continuously fed with a complex medium. The analysis of the composition of the anodic communities revealed the establishment of different communities in the anodes of the hydraulically connected MFCs, with a decrease in the abundance of fermentative taxa and a concurrent increase in respiratory taxa along the cascade. The analysis of the metabolites in the anodic suspension showed a metabolic shift between the first and last MFC, confirming the segregation of the anodic communities. Those results suggest a metabolic interaction mechanism between the predominant fermentative bacteria at the first stages of the cascade and the anaerobic respiratory electrogenic population in the latter stages, which is reflected in the observed increase in power output. We show that our experimental system represents an ideal platform for optimization of processes where the degradation of complex substrates is involved, as well as a potential tool for the study of metabolic interactions in complex microbial communities. PMID:27242723

  19. Coupling among Microbial Communities, Biogeochemistry, and Mineralogy across Biogeochemical Facies.

    PubMed

    Stegen, James C; Konopka, Allan; McKinley, James P; Murray, Chris; Lin, Xueju; Miller, Micah D; Kennedy, David W; Miller, Erin A; Resch, Charles T; Fredrickson, Jim K

    2016-01-01

    Physical properties of sediments are commonly used to define subsurface lithofacies and these same physical properties influence subsurface microbial communities. This suggests an (unexploited) opportunity to use the spatial distribution of facies to predict spatial variation in biogeochemically relevant microbial attributes. Here, we characterize three biogeochemical facies-oxidized, reduced, and transition-within one lithofacies and elucidate relationships among facies features and microbial community biomass, richness, and composition. Consistent with previous observations of biogeochemical hotspots at environmental transition zones, we find elevated biomass within a biogeochemical facies that occurred at the transition between oxidized and reduced biogeochemical facies. Microbial richness-the number of microbial taxa-was lower within the reduced facies and was well-explained by a combination of pH and mineralogy. Null modeling revealed that microbial community composition was influenced by ecological selection imposed by redox state and mineralogy, possibly due to effects on nutrient availability or transport. As an illustrative case, we predict microbial biomass concentration across a three-dimensional spatial domain by coupling the spatial distribution of subsurface biogeochemical facies with biomass-facies relationships revealed here. We expect that merging such an approach with hydro-biogeochemical models will provide important constraints on simulated dynamics, thereby reducing uncertainty in model predictions. PMID:27469056

  20. Coupling among Microbial Communities, Biogeochemistry, and Mineralogy across Biogeochemical Facies

    PubMed Central

    Stegen, James C.; Konopka, Allan; McKinley, James P.; Murray, Chris; Lin, Xueju; Miller, Micah D.; Kennedy, David W.; Miller, Erin A.; Resch, Charles T.; Fredrickson, Jim K.

    2016-01-01

    Physical properties of sediments are commonly used to define subsurface lithofacies and these same physical properties influence subsurface microbial communities. This suggests an (unexploited) opportunity to use the spatial distribution of facies to predict spatial variation in biogeochemically relevant microbial attributes. Here, we characterize three biogeochemical facies—oxidized, reduced, and transition—within one lithofacies and elucidate relationships among facies features and microbial community biomass, richness, and composition. Consistent with previous observations of biogeochemical hotspots at environmental transition zones, we find elevated biomass within a biogeochemical facies that occurred at the transition between oxidized and reduced biogeochemical facies. Microbial richness—the number of microbial taxa—was lower within the reduced facies and was well-explained by a combination of pH and mineralogy. Null modeling revealed that microbial community composition was influenced by ecological selection imposed by redox state and mineralogy, possibly due to effects on nutrient availability or transport. As an illustrative case, we predict microbial biomass concentration across a three-dimensional spatial domain by coupling the spatial distribution of subsurface biogeochemical facies with biomass-facies relationships revealed here. We expect that merging such an approach with hydro-biogeochemical models will provide important constraints on simulated dynamics, thereby reducing uncertainty in model predictions. PMID:27469056

  1. 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.

  2. Coupling among Microbial Communities, Biogeochemistry, and Mineralogy across Biogeochemical Facies

    NASA Astrophysics Data System (ADS)

    Stegen, James C.; Konopka, Allan; McKinley, James P.; Murray, Chris; Lin, Xueju; Miller, Micah D.; Kennedy, David W.; Miller, Erin A.; Resch, Charles T.; Fredrickson, Jim K.

    2016-07-01

    Physical properties of sediments are commonly used to define subsurface lithofacies and these same physical properties influence subsurface microbial communities. This suggests an (unexploited) opportunity to use the spatial distribution of facies to predict spatial variation in biogeochemically relevant microbial attributes. Here, we characterize three biogeochemical facies—oxidized, reduced, and transition—within one lithofacies and elucidate relationships among facies features and microbial community biomass, richness, and composition. Consistent with previous observations of biogeochemical hotspots at environmental transition zones, we find elevated biomass within a biogeochemical facies that occurred at the transition between oxidized and reduced biogeochemical facies. Microbial richness—the number of microbial taxa—was lower within the reduced facies and was well-explained by a combination of pH and mineralogy. Null modeling revealed that microbial community composition was influenced by ecological selection imposed by redox state and mineralogy, possibly due to effects on nutrient availability or transport. As an illustrative case, we predict microbial biomass concentration across a three-dimensional spatial domain by coupling the spatial distribution of subsurface biogeochemical facies with biomass-facies relationships revealed here. We expect that merging such an approach with hydro-biogeochemical models will provide important constraints on simulated dynamics, thereby reducing uncertainty in model predictions.

  3. Soil water fluctuations: microbial community responses and CO2 production

    NASA Astrophysics Data System (ADS)

    Placella, S.; Brodie, E. L.; Firestone, M. K.; Lennon, J. T.

    2012-12-01

    Water availability is one of the primary controllers of microbial activity in soils. Likely even more important to microbial activity than static values of soil water potential are changes in soil water potential; changes in soil water potential may trigger pulses of or cross thresholds for microbial activity. How do increases and declines in soil water potential affect microbial activity and rates of carbon dioxide (CO2) production from soil? While extremely dry soils have very low rates of CO2 production, wetting of dry soil is known to initiate a large CO2 pulse known as the Birch effect. We studied this pulse in two California annual grassland soils while concurrently monitoring microbial resuscitation. We also examined the impacts of reduced rainfall in a successional grassland in Michigan, with a focus on changes in microbial activity during a dry down period. In both systems we used relative RNA quantity to identify when different microorganisms were relatively more active. Upon wetting of dry soil, we found that the large CO2 pulse occurred during the resuscitation of the microbial community. We identified three resuscitation strategies (rapid, intermediate and delayed responders) and found that they are phylogenetically conserved, with related organisms displaying the same strategy. During a soil dry down event, we found a decline in the rate of CO2 production from soils and examined the concurrent change in the microbial community during this 7-day period. We also investigated how a summer of greater water potential fluctuation, due to reduced rainfall, impacted the stability of the microbial community. Our results demonstrate that changes in water potential can drive changes in microbial activity, leading to serious implications for soil CO2 production.

  4. Mathematical Modeling of Microbial Community Dynamics: A Methodological Review

    SciTech Connect

    Song, Hyun-Seob; Cannon, William R.; Beliaev, Alex S.; Konopka, Allan

    2014-10-17

    Microorganisms in nature form diverse communities that dynamically change in structure and function in response to environmental variations. As a complex adaptive system, microbial communities show higher-order properties that are not present in individual microbes, but arise from their interactions. Predictive mathematical models not only help to understand the underlying principles of the dynamics and emergent properties of natural and synthetic microbial communities, but also provide key knowledge required for engineering them. In this article, we provide an overview of mathematical tools that include not only current mainstream approaches, but also less traditional approaches that, in our opinion, can be potentially useful. We discuss a broad range of methods ranging from low-resolution supra-organismal to high-resolution individual-based modeling. Particularly, we highlight the integrative approaches that synergistically combine disparate methods. In conclusion, we provide our outlook for the key aspects that should be further developed to move microbial community modeling towards greater predictive power.

  5. Response of a salt marsh microbial community to metal contamination

    NASA Astrophysics Data System (ADS)

    Mucha, Ana P.; Teixeira, Catarina; Reis, Izabela; Magalhães, Catarina; Bordalo, Adriano A.; Almeida, C. Marisa R.

    2013-09-01

    Salt marshes are important sinks for contaminants, namely metals that tend to accumulate around plant roots and could eventually be taken up in a process known as phytoremediation. On the other hand, microbial communities display important roles in the salt marsh ecosystems, such as recycling of nutrients and/or degradation of organic contaminants. Thus, plants can benefit from the microbial activity in the phytoremediation process. Nevertheless, above certain levels, metals are known to be toxic to microorganisms, fact that can eventually compromise their ecological functions. In this vein, the aim of present study was to investigate, in the laboratory, the effect of selected metals (Cd, Cu and Pb) on the microbial communities associated to the roots of two salt marsh plants. Sediments colonized by Juncus maritimus and Phragmites australis were collected in the River Lima estuary (NW Portugal), and spiked with each of the metals at three different Effects Range-Median (ERM) concentrations (1, 10×, 50×), being ERM the sediment quality guideline that indicates the concentration above which adverse biological effects may frequently occur. Spiked sediments were incubated with a nutritive saline solution, being left in the dark under constant agitation for 7 days. The results showed that, despite the initial sediments colonized by J. maritimus and P. australis displayed significant (p < 0.05) differences in terms of microbial community structure (evaluated by ARISA), they presented similar microbial abundances (estimated by DAPI). Also, in terms of microbial abundance, both sediments showed a similar response to metal addition, with a decrease in number of cells only observed for the higher addition of Cu. Nevertheless, both Cu and Pb, at intermediate metals levels promote a shift in the microbial community structure, with possibly effect on the ecological function of these microbial communities in salt marshes. These changes may affect plants phytoremediation

  6. Ecofunctional enzymes of microbial communities in ground water.

    PubMed

    Fliermans, C B; Franck, M M; Hazen, T C; Gorden, R W

    1997-07-01

    Biolog technology was initially developed as a rapid, broad spectrum method for the biochemical identification of clinical microorganisms. Demand and creative application of this technology has resulted in the development of Biolog plates for Gram-negative and Gram-positive bacteria, for yeast and Lactobacillus sp. Microbial ecologists have extended the use of these plates from the identification of pure culture isolates to a tool for quantifying the metabolic patterns of mixed cultures, consortia and entire microbial communities. Patterns that develop on Biolog microplates are a result of the oxidation of the substrates by microorganisms in the inoculum and the subsequent reduction of the tetrazolium dye to form a color in response to detectable reactions. Depending upon the functional enzymes present in the isolate or community one of a possible 4 x 10(28) patterns can be expressed. The patterns were used to distinguish the physiological ecology of various microbial communities present in remediated groundwater. The data indicate that one can observe differences in the microbial community among treatments of bioventing, 1% and 4% methane injection, and pulse injection of air, methane and nutrients both between and among wells. The investigation indicates that Biolog technology is a useful parameter to measure the physiological response of the microbial community to perturbation and allows one to design enhancement techniques to further the degradation of selected recalcitrant and toxic chemicals. Further it allows one to evaluate the recovery of the microbial subsurface ecosystem after the perturbations have ceased. We propose the term 'ecofunctional enzymes' (EFE) as the most descriptive and useful term for the Biolog plate patterns generated by microbial communities. We offer this designation and provide ecological application in an attempt to standardize the terminology for this relatively new and unique technology.

  7. Microbial communities within saltmarsh sediments: Composition, abundance and pollution constraints

    NASA Astrophysics Data System (ADS)

    Machado, Ana; Magalhães, Catarina; Mucha, Ana P.; Almeida, C. Marisa R.; Bordalo, Adriano A.

    2012-03-01

    The influence of the saltmarsh plant Halimione portucaloides and the level of sediment metal contamination on the distribution of microbial communities were investigated in two Portuguese estuarine systems with different degrees of metal contamination: the Cavado (41.5 N; 8.7 W) and Sado estuaries. In the Sado, two saltmarshes were studied: Lisnave (38.4 N; 8.7 W) and Comporta (38.4 N; 8.8 W). A PCR rDNA-DGGE approach and direct microscopic counts of DAPI-stained cells were applied to study the biodiversity and abundance of prokaryotic communities. Sediment characteristics and metal concentrations (Cd, Cr, Cu, Fe, Pb, Mn, Ni and Zn) were also evaluated to identify possible environmental pollution constraints on spatial and temporal microbial dynamics. Redundancy analysis (RDA) revealed that the Lisnave saltmarsh microbial community was usually associated with a higher degree of metal contamination, especially the metal Pb. In clear contrast, the Cavado estuary microbial assemblage composition was associated with low metal concentrations but higher organic matter content. The Comporta saltmarsh bacterial community clustered in a separate branch, and was associated with higher levels of different metals, such as Ni, Cr and Zn. Additionally, the microbial community structure of the Lisnave and Cavado showed a seasonal pattern. Moreover, microbial abundance correlated negatively with metal concentrations, being higher at the Cavado estuarine site and with general higher counts in the rhizosediment. These findings suggest that increased metal concentrations negatively affect the abundance of prokaryotic cells and that saltmarsh plants may have a pivotal role in shaping the microbial community structure.

  8. Direct Evidence Linking Soil Organic Matter Development to Microbial Communities

    NASA Astrophysics Data System (ADS)

    Kallenbach, C.; Grandy, S.

    2013-12-01

    Despite increasing recognition of microbial contributions to soil organic matter (SOM) formation there is little experimental evidence linking microbial processes to SOM development and the mechanisms responsible remain unclear. Specifically, if stable SOM is largely comprised of microbial products, we need to better understand the soil conditions that influence microbial biomass production and ultimately its stability. Microbial physiology, such as microbial growth efficiency (MGE) and rate (MGR) have direct influences on microbial biomass production and are highly sensitive to resource quality. Therefore, the importance of resource quality on SOM is not necessarily a function of resistance to decay but the degree to which it optimizes microbial biomass production. While resource quality may have an indirect effect on SOM abundance via its influence on microbial physiology, SOM stabilization of labile microbial products may rely heavily on a soil's capacity to form organo-mineral interactions. To examine the relative importance of soil microbial community function, resource quality and mineralogy on direct microbial contributions to SOM formation and stability, an ongoing 15-mo incubation experiment was set up using artificial, initially C- and microbial-free soils. Soil microcosms were constructed by mixing sand with either kaolinite or montmorillonite clays followed with a natural soil microbial inoculum. For both soil mineral treatments, weekly additions of glucose, cellobiose, or syringol are carried out, with an additional treatment of plant leachate to serve as a reference. This simplified system allows us to determine if, in the absence of plant-derived C, microbial products using simple substrates can result in chemically complex SOM similar to natural soils. Over the course of the incubation, MGE, MGR, microbial activity, and SOM accumulation rates are monitored. Pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS) is used to track the microbial

  9. Microbial communities play important roles in modulating paddy soil fertility

    PubMed Central

    Luo, Xuesong; Fu, Xiaoqian; Yang, Yun; Cai, Peng; Peng, Shaobing; Chen, Wenli; Huang, Qiaoyun

    2016-01-01

    We studied microbial communities in two paddy soils, which did not receive nitrogen fertilization and were distinguished by the soil properties. The two microbial communities differed in the relative abundance of gram-negative bacteria and total microbial biomass. Variability in microbial communities between the two fields was related to the levels of phosphorus and soil moisture. Redundancy analysis for individual soils showed that the bacterial community dynamics in the high-yield soil were significantly correlated with total carbon, moisture, available potassium, and pH, and those in the low-yield cores were shaped by pH, and nitrogen factors. Biolog Eco-plate data showed a more active microbial community in the high yield soil. The variations of enzymatic activities in the two soils were significantly explained by total nitrogen, total potassium, and moisture. The enzymatic variability in the low-yield soil was significantly explained by potassium, available nitrogen, pH, and total carbon, and that in the high-yield soil was partially explained by potassium and moisture. We found the relative abundances of Gram-negative bacteria and Actinomycetes partially explained the spatial and temporal variations of soil enzymatic activities, respectively. The high-yield soil microbes are probably more active to modulate soil fertility for rice production. PMID:26841839

  10. Microbial communities play important roles in modulating paddy soil fertility

    NASA Astrophysics Data System (ADS)

    Luo, Xuesong; Fu, Xiaoqian; Yang, Yun; Cai, Peng; Peng, Shaobing; Chen, Wenli; Huang, Qiaoyun

    2016-02-01

    We studied microbial communities in two paddy soils, which did not receive nitrogen fertilization and were distinguished by the soil properties. The two microbial communities differed in the relative abundance of gram-negative bacteria and total microbial biomass. Variability in microbial communities between the two fields was related to the levels of phosphorus and soil moisture. Redundancy analysis for individual soils showed that the bacterial community dynamics in the high-yield soil were significantly correlated with total carbon, moisture, available potassium, and pH, and those in the low-yield cores were shaped by pH, and nitrogen factors. Biolog Eco-plate data showed a more active microbial community in the high yield soil. The variations of enzymatic activities in the two soils were significantly explained by total nitrogen, total potassium, and moisture. The enzymatic variability in the low-yield soil was significantly explained by potassium, available nitrogen, pH, and total carbon, and that in the high-yield soil was partially explained by potassium and moisture. We found the relative abundances of Gram-negative bacteria and Actinomycetes partially explained the spatial and temporal variations of soil enzymatic activities, respectively. The high-yield soil microbes are probably more active to modulate soil fertility for rice production.

  11. Microbial Community Degradation of Widely Used Quaternary Ammonium Disinfectants

    PubMed Central

    Oh, Seungdae; Kurt, Zohre; Tsementzi, Despina; Weigand, Michael R.; Kim, Minjae; Hatt, Janet K.; Tandukar, Madan; Pavlostathis, Spyros G.; Spain, Jim C.

    2014-01-01

    Benzalkonium chlorides (BACs) are disinfectants widely used in a variety of clinical and environmental settings to prevent microbial infections, and they are frequently detected in nontarget environments, such as aquatic and engineered biological systems, even at toxic levels. Therefore, microbial degradation of BACs has important ramifications for alleviating disinfectant toxicity in nontarget environments as well as compromising disinfectant efficacy in target environments. However, how natural microbial communities respond to BAC exposure and what genes underlie BAC biodegradation remain elusive. Our previous metagenomic analysis of a river sediment microbial community revealed that BAC exposure selected for a low-diversity community, dominated by several members of the Pseudomonas genus that quickly degraded BACs. To elucidate the genetic determinants of BAC degradation, we conducted time-series metatranscriptomic analysis of this microbial community during a complete feeding cycle with BACs as the sole carbon and energy source under aerobic conditions. Metatranscriptomic profiles revealed a candidate gene for BAC dealkylation, the first step in BAC biodegradation that results in a product 500 times less toxic. Subsequent biochemical assays and isolate characterization verified that the putative amine oxidase gene product was functionally capable of initiating BAC degradation. Our analysis also revealed cooperative interactions among community members to alleviate BAC toxicity, such as the further degradation of BAC dealkylation by-products by organisms not encoding amine oxidase. Collectively, our results advance the understanding of BAC aerobic biodegradation and provide genetic biomarkers to assess the critical first step of this process in nontarget environments. PMID:24951783

  12. Microbial Inoculants and Their Impact on Soil Microbial Communities: A Review

    PubMed Central

    2013-01-01

    The knowledge of the survival of inoculated fungal and bacterial strains in field and the effects of their release on the indigenous microbial communities has been of great interest since the practical use of selected natural or genetically modified microorganisms has been developed. Soil inoculation or seed bacterization may lead to changes in the structure of the indigenous microbial communities, which is important with regard to the safety of introduction of microbes into the environment. Many reports indicate that application of microbial inoculants can influence, at least temporarily, the resident microbial communities. However, the major concern remains regarding how the impact on taxonomic groups can be related to effects on functional capabilities of the soil microbial communities. These changes could be the result of direct effects resulting from trophic competitions and antagonistic/synergic interactions with the resident microbial populations, or indirect effects mediated by enhanced root growth and exudation. Combination of inoculants will not necessarily produce an additive or synergic effect, but rather a competitive process. The extent of the inoculation impact on the subsequent crops in relation to the buffering capacity of the plant-soil-biota is still not well documented and should be the focus of future research. PMID:23957006

  13. Stable microbial community composition on the Greenland Ice Sheet.

    PubMed

    Musilova, Michaela; Tranter, Martyn; Bennett, Sarah A; Wadham, Jemma; Anesio, Alexandre M

    2015-01-01

    The first molecular-based studies of microbes in snow and on glaciers have only recently been performed on the vast Greenland Ice Sheet (GrIS). Aeolian microbial seeding is hypothesized to impact on glacier surface community compositions. Localized melting of glacier debris (cryoconite) into the surface ice forms cryoconite holes, which are considered 'hot spots' for microbial activity on glaciers. To date, few studies have attempted to assess the origin and evolution of cryoconite and cryoconite hole communities throughout a melt season. In this study, a range of experimental approaches was used for the first time to study the inputs, temporal and structural transformations of GrIS microbial communities over the course of a whole ablation season. Small amounts of aeolian (wind and snow) microbes were potentially seeding the stable communities that were already present on the glacier (composed mainly of Proteobacteria, Cyanobacteria, and Actinobacteria). However, the dominant bacterial taxa in the aeolian samples (Firmicutes) did not establish themselves in local glacier surface communities. Cryoconite and cryoconite hole community composition remained stable throughout the ablation season following the fast community turnover, which accompanied the initial snow melt. The presence of stable communities in cryoconite and cryoconite holes on the GrIS will allow future studies to assess glacier surface microbial diversity at individual study sites from sampling intervals of short duration only. Aeolian inputs also had significantly different organic δ(13)C values (-28.0 to -27.0‰) from the glacier surface values (-25.7 to -23.6‰), indicating that in situ microbial processes are important in fixing new organic matter and transforming aeolian organic carbon. The continuous productivity of stable communities over one melt season makes them important contributors to biogeochemical nutrient cycling on glaciers.

  14. 25th anniversary article: Engineering hydrogels for biofabrication.

    PubMed

    Malda, Jos; Visser, Jetze; Melchels, Ferry P; Jüngst, Tomasz; Hennink, Wim E; Dhert, Wouter J A; Groll, Jürgen; Hutmacher, Dietmar W

    2013-09-25

    With advances in tissue engineering, the possibility of regenerating injured tissue or failing organs has become a realistic prospect for the first time in medical history. Tissue engineering - the combination of bioactive materials with cells to generate engineered constructs that functionally replace lost and/or damaged tissue - is a major strategy to achieve this goal. One facet of tissue engineering is biofabrication, where three-dimensional tissue-like structures composed of biomaterials and cells in a single manufacturing procedure are generated. Cell-laden hydrogels are commonly used in biofabrication and are termed "bioinks". Hydrogels are particularly attractive for biofabrication as they recapitulate several features of the natural extracellular matrix and allow cell encapsulation in a highly hydrated mechanically supportive three-dimensional environment. Additionally, they allow for efficient and homogeneous cell seeding, can provide biologically-relevant chemical and physical signals, and can be formed in various shapes and biomechanical characteristics. However, despite the progress made in modifying hydrogels for enhanced bioactivation, cell survival and tissue formation, little attention has so far been paid to optimize hydrogels for the physico-chemical demands of the biofabrication process. The resulting lack of hydrogel bioinks have been identified as one major hurdle for a more rapid progress of the field. In this review we summarize and focus on the deposition process, the parameters and demands of hydrogels in biofabrication, with special attention to robotic dispensing as an approach that generates constructs of clinically relevant dimensions. We aim to highlight this current lack of effectual hydrogels within biofabrication and initiate new ideas and developments in the design and tailoring of hydrogels. The successful development of a "printable" hydrogel that supports cell adhesion, migration, and differentiation will significantly advance

  15. Attached and suspended microbial communities in a pristine confined aquifer

    NASA Astrophysics Data System (ADS)

    Flynn, Theodore M.; Sanford, Robert A.; Bethke, Craig M.

    2008-07-01

    We compare the community of microbes attached to the sediments in a pristine confined aquifer to the free-floating community suspended in the groundwater there. We sampled the attached microbial community at 19 wells completed in the glacial Mahomet aquifer in east central Illinois using in situ samplers, and we sampled the suspended community by filtering microbes from groundwater. At each well, we profiled the two communities using terminal restriction fragment length polymorphism and compared the profiles we obtained with multivariate statistical analyses. Some populations at a well are detected both in the attached and suspended communities, but the shared populations represent, on average, only one third of each community; the remaining populations are detected exclusively in one community or the other. Clones closely related to the iron-reducing bacteria Geobacter and Geothrix represent more than 20% of the total attached community detected at many wells, but at no well do they make up more than 1% of the suspended community. To fully characterize the microbial community in an aquifer, it may be necessary to sample the attached as well as suspended communities.

  16. Multilevel Samplers to Assess Microbial Community Response to Biostimulation

    NASA Astrophysics Data System (ADS)

    Baldwin, B. R.; McKinley, J. P.; Peacock, A. D.; Park, M.; Ogles, D.; Istok, J. D.; Resch, C. T.; White, D. C.

    2006-05-01

    Passive multilevel samplers (MLS) containing a solid matrix for microbial colonization were used in conjunction with a push-pull biostimulation experiment designed to promote biological U(VI) and Tc(VII) reduction. MLS were deployed at 24 elevations in the injection well and two down gradient wells to investigate the spatial variability in microbial community composition and growth prior to and following biostimulation. The microbial community was characterized by real-time PCR (Q-PCR) quantification of eubacteria, NO3- reducing bacteria (nirS and nirK), δ-proteobacteria, Geobacter sp., and methanogens (mcrA). Pretest cell densities were low overall but varied substantially with significantly greater eubacterial populations detected at circumneutral pH (T-test, α=0.05) suggesting carbon substrate and low pH limitation of microbial activity. Although pretest cell densities were low, denitrifying bacteria were dominant members of the microbial community. Biostimulation with an ethanol amended groundwater resulted in concurrent NO3- and Tc(VII) reduction followed by U(VI) reduction. Q-PCR analysis of MLS revealed significant (1-2 orders of magnitude, T-test, α=0.05) increases in cell densities of eubacteria, denitrifiers, δ- proteobacteria, Geobacter sp., and methanogens in response to biostimulation. Traditionally characterization of sediment samples has been used to investigate the microbial community response to biostimulation, however, collection of sediment samples is expensive and not conducive to deep aquifers or temporal studies. The results presented demonstrate that push-pull tests with passive MLS provide an inexpensive approach to determine the effect of biostimulation on contaminant concentrations, geochemical conditions, and the microbial community composition and function.

  17. Measurements of Microbial Community Activities in Individual Soil Macroaggregates

    SciTech Connect

    Bailey, Vanessa L.; Bilskis, Christina L.; Fansler, Sarah J.; McCue, Lee Ann; Smith, Jeff L.; Konopka, Allan

    2012-05-01

    The functional potential of single soil aggregates may provide insights into the localized distribution of microbial activities better than traditional assays conducted on bulk quantities of soil. Thus, we scaled down enzyme assays for {beta}-glucosidase, N-acetyl-{beta}-D-glucosaminidase, lipase, and leucine aminopeptidase to measure of the enzyme potential of individual aggregates (250-1000 {mu}m diameter). Across all enzymes, the smallest aggregates had the greatest activity and the range of enzyme activities observed in all aggregates supports the hypothesis that functional potential in soil may be distributed in a patchy fashion. Paired analyses of ATP as a surrogate for active microbial biomass and {beta}-glucosidase on the same aggregates suggest the presence of both extracellular {beta}-glucosidase functioning in aggregates with no detectable ATP and also of relatively active microbial communities (high ATP) that have low {beta}-glucosidase potentials. Studying function at a scale more consistent with microbial habitat presents greater opportunity to link microbial community structure to microbial community function.

  18. 3D Printing and Biofabrication for Load Bearing Tissue Engineering.

    PubMed

    Jeong, Claire G; Atala, Anthony

    2015-01-01

    Cell-based direct biofabrication and 3D bioprinting is becoming a dominant technological platform and is suggested as a new paradigm for twenty-first century tissue engineering. These techniques may be our next step in surpassing the hurdles and limitations of conventional scaffold-based tissue engineering, and may offer the industrial potential of tissue engineered products especially for load bearing tissues. Here we present a topically focused review regarding the fundamental concepts, state of the art, and perspectives of this new technology and field of biofabrication and 3D bioprinting, specifically focused on tissue engineering of load bearing tissues such as bone, cartilage, osteochondral and dental tissue engineering.

  19. 3D Printing and Biofabrication for Load Bearing Tissue Engineering.

    PubMed

    Jeong, Claire G; Atala, Anthony

    2015-01-01

    Cell-based direct biofabrication and 3D bioprinting is becoming a dominant technological platform and is suggested as a new paradigm for twenty-first century tissue engineering. These techniques may be our next step in surpassing the hurdles and limitations of conventional scaffold-based tissue engineering, and may offer the industrial potential of tissue engineered products especially for load bearing tissues. Here we present a topically focused review regarding the fundamental concepts, state of the art, and perspectives of this new technology and field of biofabrication and 3D bioprinting, specifically focused on tissue engineering of load bearing tissues such as bone, cartilage, osteochondral and dental tissue engineering. PMID:26545741

  20. Anodic and cathodic microbial communities in single chamber microbial fuel cells.

    PubMed

    Daghio, Matteo; Gandolfi, Isabella; Bestetti, Giuseppina; Franzetti, Andrea; Guerrini, Edoardo; Cristiani, Pierangela

    2015-01-25

    Microbial fuel cells (MFCs) are a rapidly growing technology for energy production from wastewater and biomasses. In a MFC, a microbial biofilm oxidizes organic matter and transfers electrons from reduced compounds to an anode as the electron acceptor by extracellular electron transfer (EET). The aim of this work was to characterize the microbial communities operating in a Single Chamber Microbial Fuel Cell (SCMFC) fed with acetate and inoculated with a biogas digestate in order to gain more insight into anodic and cathodic EET. Taxonomic characterization of the communities was carried out by Illumina sequencing of a fragment of the 16S rRNA gene. Microorganisms belonging to Geovibrio genus and purple non-sulfur (PNS) bacteria were found to be dominant in the anodic biofilm. The alkaliphilic genus Nitrincola and anaerobic microorganisms belonging to Porphyromonadaceae family were the most abundant bacteria in the cathodic biofilm.

  1. Quantitative Tracking of Isotope Flows in Proteomes of Microbial Communities*

    PubMed Central

    Pan, Chongle; Fischer, Curt R.; Hyatt, Doug; Bowen, Benjamin P.; Hettich, Robert L.; Banfield, Jillian F.

    2011-01-01

    Stable isotope probing (SIP) has been used to track nutrient flows in microbial communities, but existing protein-based SIP methods capable of quantifying the degree of label incorporation into peptides and proteins have been demonstrated only by targeting usually less than 100 proteins per sample. Our method automatically (i) identifies the sequence of and (ii) quantifies the degree of heavy atom enrichment for thousands of proteins from microbial community proteome samples. These features make our method suitable for comparing isotopic differences between closely related protein sequences, and for detecting labeling patterns in low-abundance proteins or proteins derived from rare community members. The proteomic SIP method was validated using proteome samples of known stable isotope incorporation levels at 0.4%, ∼50%, and ∼98%. The method was then used to monitor incorporation of 15N into established and regrowing microbial biofilms. The results indicate organism-specific migration patterns from established communities into regrowing communities and provide insights into metabolism during biofilm formation. The proteomic SIP method can be extended to many systems to track fluxes of 13C or 15N in microbial communities. PMID:21285414

  2. Quantitative tracking of isotope flows in proteomes of microbial communities.

    PubMed

    Pan, Chongle; Fischer, Curt R; Hyatt, Doug; Bowen, Benjamin P; Hettich, Robert L; Banfield, Jillian F

    2011-04-01

    Stable isotope probing (SIP) has been used to track nutrient flows in microbial communities, but existing protein-based SIP methods capable of quantifying the degree of label incorporation into peptides and proteins have been demonstrated only by targeting usually less than 100 proteins per sample. Our method automatically (i) identifies the sequence of and (ii) quantifies the degree of heavy atom enrichment for thousands of proteins from microbial community proteome samples. These features make our method suitable for comparing isotopic differences between closely related protein sequences, and for detecting labeling patterns in low-abundance proteins or proteins derived from rare community members. The proteomic SIP method was validated using proteome samples of known stable isotope incorporation levels at 0.4%, ∼50%, and ∼98%. The method was then used to monitor incorporation of (15)N into established and regrowing microbial biofilms. The results indicate organism-specific migration patterns from established communities into regrowing communities and provide insights into metabolism during biofilm formation. The proteomic SIP method can be extended to many systems to track fluxes of (13)C or (15)N in microbial communities.

  3. Microbial ecology of ocean biogeochemistry: a community perspective.

    PubMed

    Strom, Suzanne L

    2008-05-23

    The oceans harbor a tremendous diversity of marine microbes. Different functional groups of bacteria, archaea, and protists arise from this diversity to dominate various habitats and drive globally important biogeochemical cycles. Explanations for the distribution of microbial taxa and their associated activity often focus on resource availability and abiotic conditions. However, the continual reshaping of communities by mortality, allelopathy, symbiosis, and other processes shows that community interactions exert strong selective pressure on marine microbes. Deeper exploration of microbial interactions is now possible via molecular prospecting and taxon-specific experimental approaches. A holistic outlook that encompasses the full array of selective pressures on individuals will help elucidate the maintenance of microbial diversity and the regulation of biogeochemical reactions by planktonic communities.

  4. Evolutionary relationships of wild hominids recapitulated by gut microbial communities.

    PubMed

    Ochman, Howard; Worobey, Michael; Kuo, Chih-Horng; Ndjango, Jean-Bosco N; Peeters, Martine; Hahn, Beatrice H; Hugenholtz, Philip

    2010-11-16

    Multiple factors over the lifetime of an individual, including diet, geography, and physiologic state, will influence the microbial communities within the primate gut. To determine the source of variation in the composition of the microbiota within and among species, we investigated the distal gut microbial communities harbored by great apes, as present in fecal samples recovered within their native ranges. We found that the branching order of host-species phylogenies based on the composition of these microbial communities is completely congruent with the known relationships of the hosts. Although the gut is initially and continuously seeded by bacteria that are acquired from external sources, we establish that over evolutionary timescales, the composition of the gut microbiota among great ape species is phylogenetically conserved and has diverged in a manner consistent with vertical inheritance.

  5. Community structure of a microbial mat: The phylogenetic dimension

    USGS Publications Warehouse

    Risatti, J.B.; Capman, W.C.; Stahl, D.A.

    1994-01-01

    Traditional studies of microbial communities are incomplete because of the inability to identify and quantify all contributing populations. In the present study, we directly determine the abundance and distribution of sulfate-reducing bacterial populations in a microbial mat community by using hybridization probes complementary to the 16S-like rRNAs of major phylogenetic groups. Most of the major groups were found in this single community, distributed for the most part in nonoverlapping depth intervals of the mat. The reflection of the phylogenetic structure in the community structure suggests that those species making up the major phylogenetic groups perform specific interrelated metabolic functions in the community. Comparison of population profiles to previously observed rates of sulfate reduction suggests there are additional populations of sulfate-reducing bacteria both within the photooxic zone and deeper in the mat.

  6. Microbial community composition in soils of Northern Victoria Land, Antarctica.

    PubMed

    Niederberger, Thomas D; McDonald, Ian R; Hacker, Amy L; Soo, Rochelle M; Barrett, John E; Wall, Diana H; Cary, S Craig

    2008-07-01

    Biotic communities and ecosystem dynamics in terrestrial Antarctica are limited by an array of extreme conditions including low temperatures, moisture and organic matter availability, high salinity, and a paucity of biodiversity to facilitate key ecological processes. Recent studies have discovered that the prokaryotic communities in these extreme systems are highly diverse with patchy distributions. Investigating the physical and biological controls over the distribution and activity of microbial biodiversity in Victoria Land is essential to understanding ecological functioning in this region. Currently, little information on the distribution, structure and activity of soil communities anywhere in Victoria Land are available, and their sensitivity to potential climate change remains largely unknown. We investigated soil microbial communities from low- and high-productivity habitats in an isolated Antarctic location to determine how the soil environment impacts microbial community composition and structure. The microbial communities in Luther Vale, Northern Victoria Land were analysed using bacterial 16S rRNA gene clone libraries and were related to soil geochemical parameters and classical morphological analysis of soil metazoan invertebrate communities. A total of 323 16S rRNA gene sequences analysed from four soils spanning a productivity gradient indicated a high diversity (Shannon-Weaver values > 3) of phylotypes within the clone libraries and distinct differences in community structure between the two soil productivity habitats linked to water and nutrient availability. In particular, members of the Deinococcus/Thermus lineage were found exclusively in the drier, low-productivity soils, while Gammaproteobacteria of the genus Xanthomonas were found exclusively in high-productivity soils. However, rarefaction curves indicated that these microbial habitats remain under-sampled. Our results add to the recent literature suggesting that there is a higher

  7. Phylogenetic & Physiological Profiling of Microbial Communities of Contaminated Soils/Sediments: Identifying Microbial consortia...

    SciTech Connect

    Terence L. Marsh

    2004-05-26

    The goals of this study were: (1) survey the microbial community in soil samples from a site contaminated with heavy metals using new rapid molecular techniques that are culture-independent; (2) identify phylogenetic signatures of microbial populations that correlate with metal ion contamination; and (3) cultivate these diagnostic strains using traditional as well as novel cultivation techniques in order to identify organisms that may be of value in site evaluation/management or bioremediation.

  8. Linking Microbial Community Structure to Function in Representative Simulated Systems

    PubMed Central

    Marcus, Ian M.; Wilder, Hailey A.; Quazi, Shanin J.

    2013-01-01

    Pathogenic bacteria are generally studied as a single strain under ideal growing conditions, although these conditions are not the norm in the environments in which pathogens typically proliferate. In this investigation, a representative microbial community along with Escherichia coli O157:H7, a model pathogen, was studied in three environments in which such a pathogen could be found: a human colon, a septic tank, and groundwater. Each of these systems was built in the lab in order to retain the physical/chemical and microbial complexity of the environments while maintaining control of the feed into the models. The microbial community in the colon was found to have a high percentage of bacteriodetes and firmicutes, while the septic tank and groundwater systems were composed mostly of proteobacteria. The introduction of E. coli O157:H7 into the simulated systems elicited a shift in the structures and phenotypic cell characteristics of the microbial communities. The fate and transport of the microbial community with E. coli O157:H7 were found to be significantly different from those of E. coli O157:H7 studied as a single isolate, suggesting that the behavior of the organism in the environment was different from that previously conceived. The findings in this study clearly suggest that to gain insight into the fate of pathogens, cells should be grown and analyzed under conditions simulating those of the environment in which the pathogens are present. PMID:23396331

  9. Microbial Communities Model Parameter Calculation for TSPA/SR

    SciTech Connect

    D. Jolley

    2001-07-16

    This calculation has several purposes. First the calculation reduces the information contained in ''Committed Materials in Repository Drifts'' (BSC 2001a) to useable parameters required as input to MING V1.O (CRWMS M&O 1998, CSCI 30018 V1.O) for calculation of the effects of potential in-drift microbial communities as part of the microbial communities model. The calculation is intended to replace the parameters found in Attachment II of the current In-Drift Microbial Communities Model revision (CRWMS M&O 2000c) with the exception of Section 11-5.3. Second, this calculation provides the information necessary to supercede the following DTN: M09909SPAMING1.003 and replace it with a new qualified dataset (see Table 6.2-1). The purpose of this calculation is to create the revised qualified parameter input for MING that will allow {Delta}G (Gibbs Free Energy) to be corrected for long-term changes to the temperature of the near-field environment. Calculated herein are the quadratic or second order regression relationships that are used in the energy limiting calculations to potential growth of microbial communities in the in-drift geochemical environment. Third, the calculation performs an impact review of a new DTN: M00012MAJIONIS.000 that is intended to replace the currently cited DTN: GS9809083 12322.008 for water chemistry data used in the current ''In-Drift Microbial Communities Model'' revision (CRWMS M&O 2000c). Finally, the calculation updates the material lifetimes reported on Table 32 in section 6.5.2.3 of the ''In-Drift Microbial Communities'' AMR (CRWMS M&O 2000c) based on the inputs reported in BSC (2001a). Changes include adding new specified materials and updating old materials information that has changed.

  10. Taxonomical and functional microbial community selection in soybean rhizosphere

    PubMed Central

    Mendes, Lucas W; Kuramae, Eiko E; Navarrete, Acácio A; van Veen, Johannes A; Tsai, Siu M

    2014-01-01

    This study addressed the selection of the rhizospheric microbial community from the bulk soil reservoir under agricultural management of soybean in Amazon forest soils. We used a shotgun metagenomics approach to investigate the taxonomic and functional diversities of microbial communities in the bulk soil and in the rhizosphere of soybean plants and tested the validity of neutral and niche theories to explain the rhizosphere community assembly processes. Our results showed a clear selection at both taxonomic and functional levels operating in the assembly of the soybean rhizosphere community. The taxonomic analysis revealed that the rhizosphere community is a subset of the bulk soil community. Species abundance in rhizosphere fits the log-normal distribution model, which is an indicator of the occurrence of niche-based processes. In addition, the data indicate that the rhizosphere community is selected based on functional cores related to the metabolisms of nitrogen, iron, phosphorus and potassium, which are related to benefits to the plant, such as growth promotion and nutrition. The network analysis including bacterial groups and functions was less complex in rhizosphere, suggesting the specialization of some specific metabolic pathways. We conclude that the assembly of the microbial community in the rhizosphere is based on niche-based processes as a result of the selection power of the plant and other environmental factors. PMID:24553468

  11. Manipulating soil microbial communities in extensive green roof substrates.

    PubMed

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

    2014-09-15

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

  12. Seasonal dynamics of microbial community composition and function in oak canopy and open grassland soils.

    PubMed

    Waldrop, M P; Firestone, M K

    2006-10-01

    Soil microbial communities are closely associated with aboveground plant communities, with multiple potential drivers of this relationship. Plants can affect available soil carbon, temperature, and water content, which each have the potential to affect microbial community composition and function. These same variables change seasonally, and thus plant control on microbial community composition may be modulated or overshadowed by annual climatic patterns. We examined microbial community composition, C cycling processes, and environmental data in California annual grassland soils from beneath oak canopies and in open grassland areas to distinguish factors controlling microbial community composition and function seasonally and in association with the two plant overstory communities. Every 3 months for up to 2 years, we monitored microbial community composition using phospholipid fatty acid (PLFA) analysis, microbial biomass, respiration rates, microbial enzyme activities, and the activity of microbial groups using isotope labeling of PLFA biomarkers (13C-PLFA). Distinct microbial communities were associated with oak canopy soils and open grassland soils and microbial communities displayed seasonal patterns from year to year. The effects of plant species and seasonal climate on microbial community composition were similar in magnitude. In this Mediterranean ecosystem, plant control of microbial community composition was primarily due to effects on soil water content, whereas the changes in microbial community composition seasonally appeared to be due, in large part, to soil temperature. Available soil carbon was not a significant control on microbial community composition. Microbial community composition (PLFA) and 13C-PLFA ordination values were strongly related to intra-annual variability in soil enzyme activities and soil respiration, but microbial biomass was not. In this Mediterranean climate, soil microclimate appeared to be the master variable controlling

  13. Seasonal dynamics of microbial community composition and function in oak canopy and open grassland soils

    USGS Publications Warehouse

    Waldrop, M.P.; Firestone, M.K.

    2006-01-01

    Soil microbial communities are closely associated with aboveground plant communities, with multiple potential drivers of this relationship. Plants can affect available soil carbon, temperature, and water content, which each have the potential to affect microbial community composition and function. These same variables change seasonally, and thus plant control on microbial community composition may be modulated or overshadowed by annual climatic patterns. We examined microbial community composition, C cycling processes, and environmental data in California annual grassland soils from beneath oak canopies and in open grassland areas to distinguish factors controlling microbial community composition and function seasonally and in association with the two plant overstory communities. Every 3 months for up to 2 years, we monitored microbial community composition using phospholipid fatty acid (PLFA) analysis, microbial biomass, respiration rates, microbial enzyme activities, and the activity of microbial groups using isotope labeling of PLFA biomarkers (13C-PLFA) . Distinct microbial communities were associated with oak canopy soils and open grassland soils and microbial communities displayed seasonal patterns from year to year. The effects of plant species and seasonal climate on microbial community composition were similar in magnitude. In this Mediterranean ecosystem, plant control of microbial community composition was primarily due to effects on soil water content, whereas the changes in microbial community composition seasonally appeared to be due, in large part, to soil temperature. Available soil carbon was not a significant control on microbial community composition. Microbial community composition (PLFA) and 13C-PLFA ordination values were strongly related to intra-annual variability in soil enzyme activities and soil respiration, but microbial biomass was not. In this Mediterranean climate, soil microclimate appeared to be the master variable controlling

  14. Carbon Accumulation and Microbial Community Structure in Reclaimed Mine Soils

    NASA Astrophysics Data System (ADS)

    Pfiffner, S. M.; Palumbo, A. V.; Tarver, J. D.; Fisher, S.; Cantu, J.; Brandt, C. C.

    2002-12-01

    The objective of this study was to investigate the potential for soil amendments to increase accumulation of carbon in reclaimed soils and the relationship between carbon and microbial community structure. Changes in community structure were determined by signature lipid biomarkers (SLBs) or phospholipid fatty acid methyl esters. PLFA provide estimates of the viable biomass, diversity of prokaryotic and eukaryotic diversity, and indications of physiological stress to the microbial community. Artificial neural network (ANN) analysis has been used to examine the relationship between microbial community structure and soil geochemistry. It was hypothesized that (1) soil amendments would cause changes in the structure of the microbial community and carbon content (2) changes in the structure of the microbial community would be vary between the types of amendments, and (3) analysis of the SLB with an artificial neural network (ANN) would distinguish treatment and provide a insight in to the relationship between changes in soil geochemistry and microbial community. Twenty soils samples from different field plots and at different soil horizon depths were analyzed. Biomass as estimated by PLFA analysis, ranged from 1.9 to 265 nmol/g, which corresponded to cell densities of 4.8 x107 to 6.6 x109 cells/g. In the Wall's Farm and Jenkin's Farm samples the microbial biomass decreased with depth. A horizon soils had biomass values of greater or equal to 120 nmol/g, followed by the A2 horizon,(70 to 100 nmol/g) and the weak B horizon at and (40 to 80 nmo/g). The A2 and B horizon samples showed higher relative abundance of mid-chain branched saturates that are indicative of gram positive prokaryotes and actinomycetes. At Well's Farm, the polyunsaturates indicative of eukaryotes were observed at higher abundances. These changes were related to both the prokaryotic and eukaryotic influences in the microbial community in response to the soil amendments. The correlation between

  15. Temperature sensitivity of soil microbial communities: An application of macromolecular rate theory to microbial respiration

    NASA Astrophysics Data System (ADS)

    Alster, Charlotte J.; Koyama, Akihiro; Johnson, Nels G.; Wallenstein, Matthew D.; Fischer, Joseph C.

    2016-06-01

    There is compelling evidence that microbial communities vary widely in their temperature sensitivity and may adapt to warming through time. To date, this sensitivity has been largely characterized using a range of models relying on versions of the Arrhenius equation, which predicts an exponential increase in reaction rate with temperature. However, there is growing evidence from laboratory and field studies that observe nonmonotonic responses of reaction rates to variation in temperature, indicating that Arrhenius is not an appropriate model for quantitatively characterizing temperature sensitivity. Recently, Hobbs et al. (2013) developed macromolecular rate theory (MMRT), which incorporates thermodynamic temperature optima as arising from heat capacity differences between isoenzymes. We applied MMRT to measurements of respiration from soils incubated at different temperatures. These soils were collected from three grassland sites across the U.S. Great Plains and reciprocally transplanted, allowing us to isolate the effects of microbial community type from edaphic factors. We found that microbial community type explained roughly 30% of the variation in the CO2 production rate from the labile C pool but that temperature and soil type were most important in explaining variation in labile and recalcitrant C pool size. For six out of the nine soil × inoculum combinations, MMRT was superior to Arrhenius. The MMRT analysis revealed that microbial communities have distinct heat capacity values and temperature sensitivities sometimes independent of soil type. These results challenge the current paradigm for modeling temperature sensitivity of soil C pools and understanding of microbial enzyme dynamics.

  16. Heterogeneity of Vaginal Microbial Communities within Individuals▿ #

    PubMed Central

    Kim, Tae Kyung; Thomas, Susan M.; Ho, Mengfei; Sharma, Shobha; Reich, Claudia I.; Frank, Jeremy A.; Yeater, Kathleen M.; Biggs, Diana R.; Nakamura, Noriko; Stumpf, Rebecca; Leigh, Steven R.; Tapping, Richard I.; Blanke, Steven R.; Slauch, James M.; Gaskins, H. Rex; Weisbaum, Jon S.; Olsen, Gary J.; Hoyer, Lois L.; Wilson, Brenda A.

    2009-01-01

    Recent culture-independent studies have revealed that a healthy vaginal ecosystem harbors a surprisingly complex assemblage of microorganisms. However, the spatial distribution and composition of vaginal microbial populations have not been investigated using molecular methods. Here, we evaluated site-specific microbial composition within the vaginal ecosystem and examined the influence of sampling technique in detection of the vaginal microbiota. 16S rRNA gene clone libraries were prepared from samples obtained from different locations (cervix, fornix, outer vaginal canal) and by different methods (swabbing, scraping, lavaging) from the vaginal tracts of eight clinically healthy, asymptomatic women. The data reveal that the vaginal microbiota is not homogenous throughout the vaginal tract but differs significantly within an individual with regard to anatomical site and sampling method used. Thus, this study illuminates the complex structure of the vaginal ecosystem and calls for the consideration of microenvironments when sampling vaginal microbiota as a clinical predictor of vaginal health. PMID:19158255

  17. Quantitative tracking of isotope flows in proteomes of microbial communities

    SciTech Connect

    Fisher, Curt; Hyatt, Philip Douglas; Hettich, Robert {Bob} L; Banfield, Jillian F.

    2011-01-01

    Stable isotope probing (SIP) has been used to track nutrient flows in microbial communities, but existing protein-based SIP methods capable of quantifying the degree of label incorporation into peptides and proteins have been demonstrated only by targeting usually less than 100 proteins per sample. Our method automatically (i) identifies the sequence of and (ii) quantifies the degree of heavy atom enrichment for thousands of proteins from microbial community proteome samples. These features make our method suitable for comparing isotopic differences between closely related protein sequences, and for detecting labeling patterns in low-abundance proteins or proteins derived from rare community members. The proteomic stable isotope probing (SIP) method was validated using proteome samples of known stable isotope incorporation levels at 0.4%, {approx}50%, and {approx}98%. The method was then used to monitor incorporation of 15N into established and regrowing microbial biofilms. The results indicate organism-specific migration patterns from established into regrowing communities and provides insight into metabolism during biofilm formation. The SIP-proteomics method can be extended to many systems to track fluxes of 13C or 15N in microbial communities.

  18. Ecological restoration alters microbial communities in mine tailings profiles.

    PubMed

    Li, Yang; Jia, Zhongjun; Sun, Qingye; Zhan, Jing; Yang, Yang; Wang, Dan

    2016-01-01

    Ecological restoration of mine tailings have impact on soil physiochemical properties and microbial communities. The surface soil has been a primary concern in the past decades, however it remains poorly understood about the adaptive response of microbial communities along the profile during ecological restoration of the tailings. In this study, microbial communities along a 60-cm profile were investigated in a mine tailing pond during ecological restoration of the bare waste tailings (BW) with two vegetated soils of Imperata cylindrica (IC) and Chrysopogon zizanioides (CZ) plants. Revegetation of both IC and CZ could retard soil degradation of mine tailing by stimulation of soil pH at 0-30 cm soils and altered the bacterial communities at 0-20 cm depths of the mine tailings. Significant differences existed in the relative abundance of the phyla Alphaproteobacteria, Deltaproteobacteria, Acidobacteria, Firmicutes and Nitrospira. Slight difference of bacterial communities were found at 30-60 cm depths of mine tailings. Abundance and activity analysis of nifH genes also explained the elevated soil nitrogen contents at the surface 0-20 cm of the vegetated soils. These results suggest that microbial succession occurred primarily at surface tailings and vegetation of pioneering plants might have promoted ecological restoration of mine tailings. PMID:27126064

  19. Ecological restoration alters microbial communities in mine tailings profiles

    NASA Astrophysics Data System (ADS)

    Li, Yang; Jia, Zhongjun; Sun, Qingye; Zhan, Jing; Yang, Yang; Wang, Dan

    2016-04-01

    Ecological restoration of mine tailings have impact on soil physiochemical properties and microbial communities. The surface soil has been a primary concern in the past decades, however it remains poorly understood about the adaptive response of microbial communities along the profile during ecological restoration of the tailings. In this study, microbial communities along a 60-cm profile were investigated in a mine tailing pond during ecological restoration of the bare waste tailings (BW) with two vegetated soils of Imperata cylindrica (IC) and Chrysopogon zizanioides (CZ) plants. Revegetation of both IC and CZ could retard soil degradation of mine tailing by stimulation of soil pH at 0–30 cm soils and altered the bacterial communities at 0–20 cm depths of the mine tailings. Significant differences existed in the relative abundance of the phyla Alphaproteobacteria, Deltaproteobacteria, Acidobacteria, Firmicutes and Nitrospira. Slight difference of bacterial communities were found at 30–60 cm depths of mine tailings. Abundance and activity analysis of nifH genes also explained the elevated soil nitrogen contents at the surface 0–20 cm of the vegetated soils. These results suggest that microbial succession occurred primarily at surface tailings and vegetation of pioneering plants might have promoted ecological restoration of mine tailings.

  20. Ecological restoration alters microbial communities in mine tailings profiles

    PubMed Central

    Li, Yang; Jia, Zhongjun; Sun, Qingye; Zhan, Jing; Yang, Yang; Wang, Dan

    2016-01-01

    Ecological restoration of mine tailings have impact on soil physiochemical properties and microbial communities. The surface soil has been a primary concern in the past decades, however it remains poorly understood about the adaptive response of microbial communities along the profile during ecological restoration of the tailings. In this study, microbial communities along a 60-cm profile were investigated in a mine tailing pond during ecological restoration of the bare waste tailings (BW) with two vegetated soils of Imperata cylindrica (IC) and Chrysopogon zizanioides (CZ) plants. Revegetation of both IC and CZ could retard soil degradation of mine tailing by stimulation of soil pH at 0–30 cm soils and altered the bacterial communities at 0–20 cm depths of the mine tailings. Significant differences existed in the relative abundance of the phyla Alphaproteobacteria, Deltaproteobacteria, Acidobacteria, Firmicutes and Nitrospira. Slight difference of bacterial communities were found at 30–60 cm depths of mine tailings. Abundance and activity analysis of nifH genes also explained the elevated soil nitrogen contents at the surface 0–20 cm of the vegetated soils. These results suggest that microbial succession occurred primarily at surface tailings and vegetation of pioneering plants might have promoted ecological restoration of mine tailings. PMID:27126064

  1. Life in the "plastisphere": microbial communities on plastic marine debris.

    PubMed

    Zettler, Erik R; Mincer, Tracy J; Amaral-Zettler, Linda A

    2013-07-01

    Plastics are the most abundant form of marine debris, with global production rising and documented impacts in some marine environments, but the influence of plastic on open ocean ecosystems is poorly understood, particularly for microbial communities. Plastic marine debris (PMD) collected at multiple locations in the North Atlantic was analyzed with scanning electron microscopy (SEM) and next-generation sequencing to characterize the attached microbial communities. We unveiled a diverse microbial community of heterotrophs, autotrophs, predators, and symbionts, a community we refer to as the "Plastisphere". Pits visualized in the PMD surface conformed to bacterial shapes suggesting active hydrolysis of the hydrocarbon polymer. Small-subunit rRNA gene surveys identified several hydrocarbon-degrading bacteria, supporting the possibility that microbes play a role in degrading PMD. Some Plastisphere members may be opportunistic pathogens (the authors, unpublished data) such as specific members of the genus Vibrio that dominated one of our plastic samples. Plastisphere communities are distinct from surrounding surface water, implying that plastic serves as a novel ecological habitat in the open ocean. Plastic has a longer half-life than most natural floating marine substrates, and a hydrophobic surface that promotes microbial colonization and biofilm formation, differing from autochthonous substrates in the upper layers of the ocean. PMID:23745679

  2. Stochastic and Deterministic Assembly Processes in Subsurface Microbial Communities

    SciTech Connect

    Stegen, James C.; Lin, Xueju; Konopka, Allan; Fredrickson, Jim K.

    2012-03-29

    A major goal of microbial community ecology is to understand the forces that structure community composition. Deterministic selection by specific environmental factors is sometimes important, but in other cases stochastic or ecologically neutral processes dominate. Lacking is a unified conceptual framework aiming to understand why deterministic processes dominate in some contexts but not others. Here we work towards such a framework. By testing predictions derived from general ecological theory we aim to uncover factors that govern the relative influences of deterministic and stochastic processes. We couple spatiotemporal data on subsurface microbial communities and environmental parameters with metrics and null models of within and between community phylogenetic composition. Testing for phylogenetic signal in organismal niches showed that more closely related taxa have more similar habitat associations. Community phylogenetic analyses further showed that ecologically similar taxa coexist to a greater degree than expected by chance. Environmental filtering thus deterministically governs subsurface microbial community composition. More importantly, the influence of deterministic environmental filtering relative to stochastic factors was maximized at both ends of an environmental variation gradient. A stronger role of stochastic factors was, however, supported through analyses of phylogenetic temporal turnover. While phylogenetic turnover was on average faster than expected, most pairwise comparisons were not themselves significantly non-random. The relative influence of deterministic environmental filtering over community dynamics was elevated, however, in the most temporally and spatially variable environments. Our results point to general rules governing the relative influences of stochastic and deterministic processes across micro- and macro-organisms.

  3. Assembly-Driven Community Genomics of a Hypersaline Microbial Ecosystem

    PubMed Central

    Podell, Sheila; Ugalde, Juan A.; Narasingarao, Priya; Banfield, Jillian F.; Heidelberg, Karla B.; Allen, Eric E.

    2013-01-01

    Microbial populations inhabiting a natural hypersaline lake ecosystem in Lake Tyrrell, Victoria, Australia, have been characterized using deep metagenomic sampling, iterative de novo assembly, and multidimensional phylogenetic binning. Composite genomes representing habitat-specific microbial populations were reconstructed for eleven different archaea and one bacterium, comprising between 0.6 and 14.1% of the planktonic community. Eight of the eleven archaeal genomes were from microbial species without previously cultured representatives. These new genomes provide habitat-specific reference sequences enabling detailed, lineage-specific compartmentalization of predicted functional capabilities and cellular properties associated with both dominant and less abundant community members, including organisms previously known only by their 16S rRNA sequences. Together, these data provide a comprehensive, culture-independent genomic blueprint for ecosystem-wide analysis of protein functions, population structure, and lifestyles of co-existing, co-evolving microbial groups within the same natural habitat. The “assembly-driven” community genomic approach demonstrated in this study advances our ability to push beyond single gene investigations, and promotes genome-scale reconstructions as a tangible goal in the quest to define the metabolic, ecological, and evolutionary dynamics that underpin environmental microbial diversity. PMID:23637883

  4. Mining the Metabiome: Identifying Novel Natural Products from Microbial Communities

    PubMed Central

    Milshteyn, Aleksandr; Schneider, Jessica S.; Brady, Sean F.

    2014-01-01

    Summary Microbial-derived natural products provide the foundation for most of the chemotherapeutic arsenal available to contemporary medicine. In the face of a dwindling pipeline of new lead structures identified by traditional culturing techniques and an increasing need for new therapeutics, surveys of microbial biosynthetic diversity across environmental metabiomes have revealed enormous reservoirs of as yet untapped natural products chemistry. In this review we touch on the historical context of microbial natural product discovery and discuss innovations and technological advances that are facilitating culture-dependent and culture-independent access to new chemistry from environmental microbiomes with the goal of re-invigorating the small molecule therapeutics discovery pipeline. We highlight the successful strategies that have emerged and some of the challenges that must be overcome to enable the development of high-throughput methods for natural product discovery from complex microbial communities. PMID:25237864

  5. Microbial communities of alluvial soils in the Volga River delta

    NASA Astrophysics Data System (ADS)

    Sal'Nikova, N. A.; Polyanskaya, L. M.; Tyugai, Z. N.; Sal'Nikov, A. N.; Egorov, M. A.

    2009-01-01

    The number and biomass of the microbial community in the upper humus horizon (0-20 cm) were determined in the main types of alluvial soils (mucky gley, desertified soddy calcareous, hydrometamorphic dark-humus soils) in the Volga River delta. Fungal mycelium and alga cells predominate in the biomass of the microorganisms (35-50% and 30-47%, respectively). The proportion of prokaryotes in the microbial biomass of the alluvial soils amounts to 2-6%. No significant seasonal dynamics in the number and biomass of microorganisms were revealed in the alluvial soils. The share of carbon of the microbial biomass in the total carbon content of the soil organic matter is 1.4-2.3% in the spring. High coefficients of microbial mineralization and oligotrophy characterize the processes of organic matter decomposition in the alluvial soils of the mucky gley, desertified soddy calcareous, and hydrometamorphic dark humus soil types.

  6. Microbial Community Responses to Glycine Addition in Kansas Prairie Soils

    NASA Astrophysics Data System (ADS)

    Bottos, E.; Roy Chowdhury, T.; White, R. A., III; Brislawn, C.; Fansler, S.; Kim, Y. M.; Metz, T. O.; McCue, L. A.; Jansson, J.

    2015-12-01

    Advances in sequencing technologies are rapidly expanding our abilities to unravel aspects of microbial community structure and function in complex systems like soil; however, characterizing the highly diverse communities is problematic, due primarily to challenges in data analysis. To tackle this problem, we aimed to constrain the microbial diversity in a soil by enriching for particular functional groups within a community through addition of "trigger substrates". Such trigger substrates, characterized by low molecular weight, readily soluble and diffusible in soil solution, representative of soil organic matter derivatives, would also be rapidly degradable. A relatively small energy investment to maintain the cell in a state of metabolic alertness for such substrates would be a better evolutionary strategy and presumably select for a cohort of microorganisms with the energetics and cellular machinery for utilization and growth. We chose glycine, a free amino acid (AA) known to have short turnover times (in the range of hours) in soil. As such, AAs are a good source of nitrogen and easily degradable, and can serve as building blocks for microbial proteins and other biomass components. We hypothesized that the addition of glycine as a trigger substrate will decrease microbial diversity and evenness, as taxa capable of metabolizing it are enriched in relation to those that are not. We tested this hypothesis by incubating three Kansas native prairie soils with glycine for 24 hours at 21 degree Celsius, and measured community level responses by 16S rRNA gene sequencing, metagenomics, and metatranscriptomics. Preliminary evaluation of 16S rRNA gene sequences revealed minor changes in bacterial community composition in response to glycine addition. We will also present data on functional gene abundance and expression. The results of these analyses will be useful in designing sequencing strategies aimed at dissecting and deciphering complex microbial communities.

  7. Auricular reconstruction using biofabrication-based tissue engineering strategies.

    PubMed

    Otto, I A; Melchels, F P W; Zhao, X; Randolph, M A; Kon, M; Breugem, C C; Malda, J

    2015-07-22

    Auricular malformations, which impose a significant social and psychological burden, are currently treated using ear prostheses, synthetic implants or autologous implants derived from rib cartilage. Advances in the field of regenerative medicine and biofabrication provide the possibility to engineer functional cartilage with intricate architectures and complex shapes using patient-derived or donor cells. However, the development of a successful auricular cartilage implant still faces a number of challenges. These challenges include the generation of a functional biochemical matrix, the fabrication of a customized anatomical shape, and maintenance of that shape. Biofabrication technologies may have the potential to overcome these challenges due to their ability to reproducibly deposit multiple materials in complex geometries in a highly controllable manner. This topical review summarizes this potential of biofabrication technologies for the generation of implants for auricular reconstruction. In particular, it aims to discuss how biofabrication technologies, although still in pre-clinical phase, could overcome the challenges of generating and maintaining the desired auricular shapes. Finally, remaining bottlenecks and future directions are discussed.

  8. 3D Biofabrication Strategies for Tissue Engineering and Regenerative Medicine

    PubMed Central

    Bajaj, Piyush; Schweller, Ryan M.; Khademhosseini, Ali; West, Jennifer L.; Bashir, Rashid

    2014-01-01

    Over the past several decades, there has been an ever-increasing demand for organ transplants. However, there is a severe shortage of donor organs, and as a result of the increasing demand, the gap between supply and demand continues to widen. A potential solution to this problem is to grow or fabricate organs using biomaterial scaffolds and a person’s own cells. Although the realization of this solution has been limited, the development of new biofabrication approaches has made it more realistic. This review provides an overview of natural and synthetic biomaterials that have been used for organ/tissue development. It then discusses past and current biofabrication techniques, with a brief explanation of the state of the art. Finally, the review highlights the need for combining vascularization strategies with current biofabrication techniques. Given the multitude of applications of biofabrication technologies, from organ/tissue development to drug discovery/screening to development of complex in vitro models of human diseases, these manufacturing technologies can have a significant impact on the future of medicine and health care. PMID:24905875

  9. High-resolution microbial community succession of microbially induced concrete corrosion in working sanitary manholes.

    PubMed

    Ling, Alison L; Robertson, Charles E; Harris, J Kirk; Frank, Daniel N; Kotter, Cassandra V; Stevens, Mark J; Pace, Norman R; Hernandez, Mark T

    2015-01-01

    Microbially-induced concrete corrosion in headspaces threatens wastewater infrastructure worldwide. Models for predicting corrosion rates in sewer pipe networks rely largely on information from culture-based investigations. In this study, the succession of microbes associated with corroding concrete was characterized over a one-year monitoring campaign using rRNA sequence-based phylogenetic methods. New concrete specimens were exposed in two highly corrosive manholes (high concentrations of hydrogen sulfide and carbon dioxide gas) on the Colorado Front Range for up to a year. Community succession on corroding surfaces was assessed using Illumina MiSeq sequencing of 16S bacterial rRNA amplicons and Sanger sequencing of 16S universal rRNA clones. Microbial communities associated with corrosion fronts presented distinct succession patterns which converged to markedly low α-diversity levels (< 10 taxa) in conjunction with decreasing pH. The microbial community succession pattern observed in this study agreed with culture-based models that implicate acidophilic sulfur-oxidizer Acidithiobacillus spp. in advanced communities, with two notable exceptions. Early communities exposed to alkaline surface pH presented relatively high α-diversity, including heterotrophic, nitrogen-fixing, and sulfur-oxidizing genera, and one community exposed to neutral surface pH presented a diverse transition community comprised of less than 20% sulfur-oxidizers.

  10. High-resolution microbial community succession of microbially induced concrete corrosion in working sanitary manholes.

    PubMed

    Ling, Alison L; Robertson, Charles E; Harris, J Kirk; Frank, Daniel N; Kotter, Cassandra V; Stevens, Mark J; Pace, Norman R; Hernandez, Mark T

    2015-01-01

    Microbially-induced concrete corrosion in headspaces threatens wastewater infrastructure worldwide. Models for predicting corrosion rates in sewer pipe networks rely largely on information from culture-based investigations. In this study, the succession of microbes associated with corroding concrete was characterized over a one-year monitoring campaign using rRNA sequence-based phylogenetic methods. New concrete specimens were exposed in two highly corrosive manholes (high concentrations of hydrogen sulfide and carbon dioxide gas) on the Colorado Front Range for up to a year. Community succession on corroding surfaces was assessed using Illumina MiSeq sequencing of 16S bacterial rRNA amplicons and Sanger sequencing of 16S universal rRNA clones. Microbial communities associated with corrosion fronts presented distinct succession patterns which converged to markedly low α-diversity levels (< 10 taxa) in conjunction with decreasing pH. The microbial community succession pattern observed in this study agreed with culture-based models that implicate acidophilic sulfur-oxidizer Acidithiobacillus spp. in advanced communities, with two notable exceptions. Early communities exposed to alkaline surface pH presented relatively high α-diversity, including heterotrophic, nitrogen-fixing, and sulfur-oxidizing genera, and one community exposed to neutral surface pH presented a diverse transition community comprised of less than 20% sulfur-oxidizers. PMID:25748024

  11. High-Resolution Microbial Community Succession of Microbially Induced Concrete Corrosion in Working Sanitary Manholes

    PubMed Central

    Ling, Alison L.; Robertson, Charles E.; Harris, J. Kirk; Frank, Daniel N.; Kotter, Cassandra V.; Stevens, Mark J.; Pace, Norman R.; Hernandez, Mark T.

    2015-01-01

    Microbially-induced concrete corrosion in headspaces threatens wastewater infrastructure worldwide. Models for predicting corrosion rates in sewer pipe networks rely largely on information from culture-based investigations. In this study, the succession of microbes associated with corroding concrete was characterized over a one-year monitoring campaign using rRNA sequence-based phylogenetic methods. New concrete specimens were exposed in two highly corrosive manholes (high concentrations of hydrogen sulfide and carbon dioxide gas) on the Colorado Front Range for up to a year. Community succession on corroding surfaces was assessed using Illumina MiSeq sequencing of 16S bacterial rRNA amplicons and Sanger sequencing of 16S universal rRNA clones. Microbial communities associated with corrosion fronts presented distinct succession patterns which converged to markedly low α-diversity levels (< 10 taxa) in conjunction with decreasing pH. The microbial community succession pattern observed in this study agreed with culture-based models that implicate acidophilic sulfur-oxidizer Acidithiobacillus spp. in advanced communities, with two notable exceptions. Early communities exposed to alkaline surface pH presented relatively high α-diversity, including heterotrophic, nitrogen-fixing, and sulfur-oxidizing genera, and one community exposed to neutral surface pH presented a diverse transition community comprised of less than 20% sulfur-oxidizers. PMID:25748024

  12. Oral cavity contains distinct niches with dynamic microbial communities.

    PubMed

    Xu, Xin; He, Jinzhi; Xue, Jing; Wang, Yan; Li, Kun; Zhang, Keke; Guo, Qiang; Liu, Xianghong; Zhou, Yuan; Cheng, Lei; Li, Mingyun; Li, Yuqing; Li, Yan; Shi, Wenyuan; Zhou, Xuedong

    2015-03-01

    Microbes colonize human oral surfaces within hours after delivery. During postnatal development, physiological changes, such as the eruption of primary teeth and replacement of the primary dentition with permanent dentition, greatly alter the microbial habitats, which, in return, may lead to community composition shifts at different phases in people's lives. By profiling saliva, supragingival and mucosal plaque samples from healthy volunteers at different ages and dentition stages, we observed that the oral cavity is a highly heterogeneous ecological system containing distinct niches with significantly different microbial communities. More importantly, the phylogenetic microbial structure varies with ageing. In addition, only a few taxa were present across the whole populations, indicating a core oral microbiome should be defined based on age and oral niches. PMID:24800728

  13. A Comparison of Microbial Communities from Deep Igneous Crust

    NASA Astrophysics Data System (ADS)

    Smith, A. R.; Flores, G. E.; Fisk, M. R.; Colwell, F. S.; Thurber, A. R.; Mason, O. U.; Popa, R.

    2013-12-01

    Recent investigations of life in Earth's crust have revealed common themes in organism function, taxonomy, and diversity. Capacities for hydrogen oxidation, carbon fixation, methanogenesis and methanotrophy, iron and sulfur metabolisms, and hydrocarbon degradation often predominate in deep life communities, and crustal mineralogy has been hypothesized as a driving force for determining deep life community assemblages. Recently, we found that minerals characteristic of the igneous crust harbored unique communities when incubated in the Juan de Fuca Ridge flank borehole IODP 1301A. Here we present attached mineral biofilm morphologies and a comparison of our mineral communities to those from a variety of locations, contamination states, and igneous crustal or mineralogical types. We found that differences in borehole mineral communities were reflected in biofilm morphologies. Olivine biofilms were thick, carbon-rich films with embedded cells of uniform size and shape and often contained secondary minerals. Encrusted cells, spherical and rod-shaped cells, and tubes were indicative of glass surfaces. We also found that the attached communities from incubated borehole minerals were taxonomically more similar to native, attached communities from marine and continental crust than to communities from the aquifer water that seeded it. Our findings further support the hypothesis that mineralogy selects for microbial communities that have distinct phylogenetic, morphological, and potentially functional, signatures. This has important implications for resolving ecosystem function and microbial distributions in igneous crust, the largest deep habitat on Earth.

  14. Microbial communities and exopolysaccharides from Polynesian mats.

    PubMed

    Rougeaux, H; Guezennec, M; Che, L M; Payri, C; Deslandes, E; Guezennec, J

    2001-03-01

    Microbial mats present in two shallow atolls of French Polynesia were characterized by high amounts of exopolysaccharides associated with cyanobacteria as the predominating species. Cyanobacteria were found in the first centimeters of the gelatinous mats, whereas deeper layers showing the occurrence of the sulfate reducers Desulfovibrio and Desulfobacter species as determined by the presence of specific biomarkers. Exopolysaccharides were extracted from these mats and partially characterized. All fractions contained both neutral sugars and uronic acids with a predominance of the former. The large diversity in monosaccharides can be interpreted as the result of exopolymer biosynthesis by either different or unidentified cyanobacterial species. PMID:14961381

  15. Development of a Screening Assay for Microbial Community Profiling

    NASA Astrophysics Data System (ADS)

    Miracle, A. L.; Tilton, F.; Bonheyo, G. T.; McDermott, J.

    2010-12-01

    Remediation of subsurface contaminant plumes has been challenging in the aspects of site characterization, design for treatability, and monitoring of treatment efficacy, to name a few. Characterization of physical and geochemical properties can be achieved through advances in sensor technologies, modeling, and well placement. However, the biotic composition within the subsurface is also an important component that adds an additional biochemical contribution that is not currently being assessed. Changes in the environment have impacts to the composition of microbial communities at this solid/fluid phase interface. The introduction of a remediative treatment may provide an abundant food source for microorganisms in the subsurface and alter the community dynamics. Such changes to the microbial community composition may have dramatic effects on bulk community biochemistry, which in turn may affect the quality of the remediative treatment in terms of effectiveness and transport through alteration of the environment. A screening array is being developed based on DNA sequence information from indigenous microorganisms within target sediments to be used to assess microbial community changes throughout remediative treatments and through time. Integration of physical, chemical, and biotic community information will be assessed to determine efficacy of treatment before, during, and after treatment to assess success of treatment, and measure any post-treatment changes.

  16. Development of soil microbial communities during tallgrass prairie restoration

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soil microbial communities were examined in a chronosequence of four different land-use treatments at the Konza Prairie Biological Station, Kansas. The time series comprised a conventionally tilled cropland (CTC) developed on former prairie soils, two restored grasslands that were initiated on forme...

  17. Post fumigation recovery of soil microbial community structure

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soil fumigants have been extensively used to control target soil-borne pathogens and weeds for the past few decades. It is known that the fumigants with broad biocidal activity can affect both target and non-target soil organisms, but the recovery of soil microbial communities are unknown until rece...

  18. Spatial patterns of microbial community composition within Lake Erie sediments

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Lake Erie is a large freshwater ecosystem with three distinct basins that exhibit an east-west gradient of increasing productivity, as well as allochthonous inputs of nutrients and xenobiotics. To evaluate microbial community composition throughout this ecosystem, 435 16S rDNA environmental clones w...

  19. Microbial community functional change during vertebrate carrion decomposition

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microorganisms play a critical role in the decomposition of organic matter, which contributes to energy and nutrient transformation in every ecosystem, yet little is known about the functional activity of epinecrotic microbial communities associated with carrion. The objective of this study was to ...

  20. Changes in Soil Microbial Community Structure with Flooding

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Flooding disturbs both above- and below-ground ecosystem processes. Although often ignored, changes in below-ground environments are no less important than those that occur above-ground. Shifts in soil microbial community structure are expected when anaerobic conditions develop from flooding. The ...

  1. Effect of Increasing Nitrogen Deposition on Soil Microbial Communities

    SciTech Connect

    Xiao, Shengmu; Xue, Kai; He, Zhili; VanNostrand, Joy D.; Liu, Jianshe; Hobbie, Sarah E.; Reich, Peter B.; Zhou, Jizhong

    2010-05-17

    Increasing nitrogen deposition, increasing atmospheric CO2, and decreasing biodiversity are three main environmental changes occurring on a global scale. The BioCON (Biodiversity, CO2, and Nitrogen) ecological experiment site at the University of Minnesota's Cedar Creek Ecosystem Science Reserve started in 1997, to better understand how these changes would affect soil systems. To understand how increasing nitrogen deposition affects the microbial community diversity, heterogeneity, and functional structure impact soil microbial communities, 12 samples were collected from the BioCON plots in which nitrogenous fertilizer was added to simulate the effect of increasing nitrogen deposition and 12 samples from without added fertilizer. DNA from the 24 samples was extracted using a freeze-grind protocol, amplified, labeled with a fluorescent dye, and then hybridized to GeoChip, a functional gene array containing probes for genes involved in N, S and C cycling, metal resistance and organic contaminant degradation. Detrended correspondence analysis (DCA) of all genes detected was performed to analyze microbial community patterns. The first two axes accounted for 23.5percent of the total variation. The samples fell into two major groups: fertilized and non-fertilized, suggesting that nitrogenous fertilizer had a significant impact on soil microbial community structure and diversity. The functional gene numbers detected in fertilized samples was less that detected in non-fertilizer samples. Functional genes involving in the N cycling were mainly discussed.

  2. Molecular Survey of Concrete Sewer Biofilm Microbial Communities

    EPA Science Inventory

    Although bacteria are implicated in deteriorating concrete structures, there is very little information on the composition of concrete microbial communities. To this end, we studied different concrete biofilms by performing sequence analysis of 16S rDNA concrete clone libraries. ...

  3. Microbial abundance and community structure in a melting alpine snowpack.

    PubMed

    Lazzaro, Anna; Wismer, Andrea; Schneebeli, Martin; Erny, Isolde; Zeyer, Josef

    2015-05-01

    Snowmelt is a crucial period for alpine soil ecosystems, as it is related to inputs of nutrients, particulate matter and microorganisms to the underlying soil. Although snow-inhabiting microbial communities represent an important inoculum for soils, they have thus far received little attention. The distribution and structure of these microorganisms in the snowpack may be linked to the physical properties of the snowpack at snowmelt. Snow samples were taken from snow profiles at four sites (1930-2519 m a.s.l.) in the catchment of the Tiefengletscher, Canton Uri, Switzerland. Microbial (Archaea, Bacteria and Fungi) communities were investigated through T-RFLP profiling of the 16S and 18S rRNA genes, respectively. In parallel, we assessed physical and chemical parameters relevant to the understanding of melting processes. Along the snow profiles, density increased with depth due to compaction, while other physico-chemical parameters, such as temperature and concentrations of DOC and soluble ions, remained in the same range (e.g. <2 mg DOC L(-1), 5-30 μg NH4 (+)-N L(-1)) in all samples at all sites. Along the snow profiles, no major change was observed either in cell abundance or in bacterial and fungal diversity. No Archaea could be detected in the snow. Microbial communities, however, differed significantly between sites. Our results show that meltwater rearranges soluble ions and microbial communities in the snowpack.

  4. Bacterial Invasion Dynamics in Zebrafish Gut Microbial Communities

    NASA Astrophysics Data System (ADS)

    Logan, Savannah; Jemielita, Matthew; Wiles, Travis; Schlomann, Brandon; Hammer, Brian; Guillemin, Karen; Parthasarathy, Raghuveer

    Microbial communities residing in the vertebrate intestine play an important role in host development and health. These communities must be in part shaped by interactions between microbial species as they compete for resources in a physically constrained system. To better understand these interactions, we use light sheet microscopy and zebrafish as a model organism to image established gut microbial communities as they are invaded by robustly-colonizing challengers. We demonstrate that features of the challenger, including motility and spatial distribution, impact success in invasion and in outcompeting the original community. We also show that physical characteristics of the host, such as the motility of the gut, play important roles in mediating inter-species competition. Finally, we examine the influence of the contact-dependent type VI secretion system (T6SS), which is used by specific bacteria to cause cell lysis by injecting toxic effector proteins into competitors. Our findings provide insights into the determinants of microbial success in the complex ecosystems found in the gut.

  5. Microbial Community Structure in the Rhizosphere of Rice Plants.

    PubMed

    Breidenbach, Björn; Pump, Judith; Dumont, Marc G

    2015-01-01

    The microbial community in the rhizosphere environment is critical for the health of land plants and the processing of soil organic matter. The objective of this study was to determine the extent to which rice plants shape the microbial community in rice field soil over the course of a growing season. Rice (Oryza sativa) was cultivated under greenhouse conditions in rice field soil from Vercelli, Italy and the microbial community in the rhizosphere of planted soil microcosms was characterized at four plant growth stages using quantitative PCR and 16S rRNA gene pyrotag analysis and compared to that of unplanted bulk soil. The abundances of 16S rRNA genes in the rice rhizosphere were on average twice that of unplanted bulk soil, indicating a stimulation of microbial growth in the rhizosphere. Soil environment type (i.e., rhizosphere versus bulk soil) had a greater effect on the community structure than did time (e.g., plant growth stage). Numerous phyla were affected by the presence of rice plants, but the strongest effects were observed for Gemmatimonadetes, Proteobacteria, and Verrucomicrobia. With respect to functional groups of microorganisms, potential iron reducers (e.g., Geobacter, Anaeromyxobacter) and fermenters (e.g., Clostridiaceae, Opitutaceae) were notably enriched in the rhizosphere environment. A Herbaspirillum species was always more abundant in the rhizosphere than bulk soil and was enriched in the rhizosphere during the early stage of plant growth. PMID:26793175

  6. Microbial Community Structure in the Rhizosphere of Rice Plants

    PubMed Central

    Breidenbach, Björn; Pump, Judith; Dumont, Marc G.

    2016-01-01

    The microbial community in the rhizosphere environment is critical for the health of land plants and the processing of soil organic matter. The objective of this study was to determine the extent to which rice plants shape the microbial community in rice field soil over the course of a growing season. Rice (Oryza sativa) was cultivated under greenhouse conditions in rice field soil from Vercelli, Italy and the microbial community in the rhizosphere of planted soil microcosms was characterized at four plant growth stages using quantitative PCR and 16S rRNA gene pyrotag analysis and compared to that of unplanted bulk soil. The abundances of 16S rRNA genes in the rice rhizosphere were on average twice that of unplanted bulk soil, indicating a stimulation of microbial growth in the rhizosphere. Soil environment type (i.e., rhizosphere versus bulk soil) had a greater effect on the community structure than did time (e.g., plant growth stage). Numerous phyla were affected by the presence of rice plants, but the strongest effects were observed for Gemmatimonadetes, Proteobacteria, and Verrucomicrobia. With respect to functional groups of microorganisms, potential iron reducers (e.g., Geobacter, Anaeromyxobacter) and fermenters (e.g., Clostridiaceae, Opitutaceae) were notably enriched in the rhizosphere environment. A Herbaspirillum species was always more abundant in the rhizosphere than bulk soil and was enriched in the rhizosphere during the early stage of plant growth. PMID:26793175

  7. Soil microbial communities following bush removal in a Namibian savanna

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Savanna ecosystems are subject to desertification and bush encroachment, which reduce the grazing value of the land and hence the carrying capacity for wildlife and livestock. In this study we examined the soil microbial communities under bush and grass in Namibia. We analyzed the soil at a chronose...

  8. Characterization of fatty acid-producing wastewater microbial communities using next generation sequencing technologies

    EPA Science Inventory

    While wastewater represents a viable source of bacterial biodiesel production, very little is known on the composition of these microbial communities. We studied the taxonomic diversity and succession of microbial communities in bioreactors accumulating fatty acids using 454-pyro...

  9. Effects of biochar blends on microbial community composition in two coastal plain soils

    EPA Science Inventory

    The amendment of soil with biochar has been demonstrated to have an effect not only on the soil physicochemical properties, but also on soil microbial community composition and activity. Previous reports have demonstrated significant impacts on soil microbial community structure....

  10. HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes.

    PubMed

    Forster, Samuel C; Browne, Hilary P; Kumar, Nitin; Hunt, Martin; Denise, Hubert; Mitchell, Alex; Finn, Robert D; Lawley, Trevor D

    2016-01-01

    The Human Pan-Microbe Communities (HPMC) database (http://www.hpmcd.org/) provides a manually curated, searchable, metagenomic resource to facilitate investigation of human gastrointestinal microbiota. Over the past decade, the application of metagenome sequencing to elucidate the microbial composition and functional capacity present in the human microbiome has revolutionized many concepts in our basic biology. When sufficient high quality reference genomes are available, whole genome metagenomic sequencing can provide direct biological insights and high-resolution classification. The HPMC database provides species level, standardized phylogenetic classification of over 1800 human gastrointestinal metagenomic samples. This is achieved by combining a manually curated list of bacterial genomes from human faecal samples with over 21000 additional reference genomes representing bacteria, viruses, archaea and fungi with manually curated species classification and enhanced sample metadata annotation. A user-friendly, web-based interface provides the ability to search for (i) microbial groups associated with health or disease state, (ii) health or disease states and community structure associated with a microbial group, (iii) the enrichment of a microbial gene or sequence and (iv) enrichment of a functional annotation. The HPMC database enables detailed analysis of human microbial communities and supports research from basic microbiology and immunology to therapeutic development in human health and disease. PMID:26578596

  11. MICROBIAL SURVIVAL: The Paleome: A Sedimentary Genetic Record of Past Microbial Communities

    NASA Astrophysics Data System (ADS)

    Inagaki, Fumio; Okada, Hisatake; Tsapin, Alexandre I.; Nealson, Kenneth H.

    2005-06-01

    Molecular genetic methods were used to analyze the remnants of microbial ecosystems contained within an ancient oceanic microbial habitat that was recovered from a continental drilled core of black shale ~100 million years in age. Bacterial ribosomal RNA genes were vertically amplified from the six different depths of a black shale core associated with a phosphate- rich stratum, defined as one of the mid-Cretaceous oceanic anoxic events (OAEs). Although the black shale core was recovered from a terrestrial coring effort, the recovered 16S rRNA gene sequences showed affinity to microbial communities previously seen in deep-sea sedimentary environments (i.e., the microbial assemblage was easily recognizable as a marine community). In particular, a number of 16S rRNA gene clones of oceanic sulfate-reducing bacteria within the δ-Proteobacteria predominated at the OAE layer. The recovered bacterial DNA signatures are consistent with the interpretation that the sequences are derived from the past microbial communities buried in either sea-bottom or subseafloor environments during the sedimentation process and, after ceasing growth, preserved until the present.

  12. HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes.

    PubMed

    Forster, Samuel C; Browne, Hilary P; Kumar, Nitin; Hunt, Martin; Denise, Hubert; Mitchell, Alex; Finn, Robert D; Lawley, Trevor D

    2016-01-01

    The Human Pan-Microbe Communities (HPMC) database (http://www.hpmcd.org/) provides a manually curated, searchable, metagenomic resource to facilitate investigation of human gastrointestinal microbiota. Over the past decade, the application of metagenome sequencing to elucidate the microbial composition and functional capacity present in the human microbiome has revolutionized many concepts in our basic biology. When sufficient high quality reference genomes are available, whole genome metagenomic sequencing can provide direct biological insights and high-resolution classification. The HPMC database provides species level, standardized phylogenetic classification of over 1800 human gastrointestinal metagenomic samples. This is achieved by combining a manually curated list of bacterial genomes from human faecal samples with over 21000 additional reference genomes representing bacteria, viruses, archaea and fungi with manually curated species classification and enhanced sample metadata annotation. A user-friendly, web-based interface provides the ability to search for (i) microbial groups associated with health or disease state, (ii) health or disease states and community structure associated with a microbial group, (iii) the enrichment of a microbial gene or sequence and (iv) enrichment of a functional annotation. The HPMC database enables detailed analysis of human microbial communities and supports research from basic microbiology and immunology to therapeutic development in human health and disease.

  13. Metabarcoding of the kombucha microbial community grown in different microenvironments.

    PubMed

    Reva, Oleg N; Zaets, Iryna E; Ovcharenko, Leonid P; Kukharenko, Olga E; Shpylova, Switlana P; Podolich, Olga V; de Vera, Jean-Pierre; Kozyrovska, Natalia O

    2015-12-01

    Introducing of the DNA metabarcoding analysis of probiotic microbial communities allowed getting insight into their functioning and establishing a better control on safety and efficacy of the probiotic communities. In this work the kombucha poly-microbial probiotic community was analysed to study its flexibility under different growth conditions. Environmental DNA sequencing revealed a complex and flexible composition of the kombucha microbial culture (KMC) constituting more bacterial and fungal organisms in addition to those found by cultural method. The community comprised bacterial and yeast components including cultured and uncultivable microorganisms. Culturing the KMC under different conditions revealed the core part of the community which included acetobacteria of two genera Komagataeibacter (former Gluconacetobacter) and Gluconobacter, and representatives of several yeast genera among which Brettanomyces/Dekkera and Pichia (including former Issatchenkia) were dominant. Herbaspirillum spp. and Halomonas spp., which previously had not been described in KMC, were found to be minor but permanent members of the community. The community composition was dependent on the growth conditions. The bacterial component of KMC was relatively stable, but may include additional member-lactobacilli. The yeast species composition was significantly variable. High-throughput sequencing showed complexity and variability of KMC that may affect the quality of the probiotic drink. It was hypothesized that the kombucha core community might recruit some environmental bacteria, particularly lactobacilli, which potentially may contribute to the fermentative capacity of the probiotic drink. As many KMC-associated microorganisms cannot be cultured out of the community, a robust control for community composition should be provided by using DNA metabarcoding. PMID:26061774

  14. Characterization of the microbial acid mine drainage microbial community using culturing and direct sequencing techniques.

    PubMed

    Auld, Ryan R; Myre, Maxine; Mykytczuk, Nadia C S; Leduc, Leo G; Merritt, Thomas J S

    2013-05-01

    We characterized the bacterial community from an AMD tailings pond using both classical culturing and modern direct sequencing techniques and compared the two methods. Acid mine drainage (AMD) is produced by the environmental and microbial oxidation of minerals dissolved from mining waste. Surprisingly, we know little about the microbial communities associated with AMD, despite the fundamental ecological roles of these organisms and large-scale economic impact of these waste sites. AMD microbial communities have classically been characterized by laboratory culturing-based techniques and more recently by direct sequencing of marker gene sequences, primarily the 16S rRNA gene. In our comparison of the techniques, we find that their results are complementary, overall indicating very similar community structure with similar dominant species, but with each method identifying some species that were missed by the other. We were able to culture the majority of species that our direct sequencing results indicated were present, primarily species within the Acidithiobacillus and Acidiphilium genera, although estimates of relative species abundance were only obtained from direct sequencing. Interestingly, our culture-based methods recovered four species that had been overlooked from our sequencing results because of the rarity of the marker gene sequences, likely members of the rare biosphere. Further, direct sequencing indicated that a single genus, completely missed in our culture-based study, Legionella, was a dominant member of the microbial community. Our results suggest that while either method does a reasonable job of identifying the dominant members of the AMD microbial community, together the methods combine to give a more complete picture of the true diversity of this environment. PMID:23485423

  15. 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.

  16. Environmental microarray analyses of Antarctic soil microbial communities.

    PubMed

    Yergeau, Etienne; Schoondermark-Stolk, Sung A; Brodie, Eoin L; Déjean, Sébastien; DeSantis, Todd Z; Gonçalves, Olivier; Piceno, Yvette M; Andersen, Gary L; Kowalchuk, George A

    2009-03-01

    Antarctic ecosystems are fascinating in their limited trophic complexity, with decomposition and nutrient cycling functions being dominated by microbial activities. Not only are Antarctic habitats exposed to extreme environmental conditions, the Antarctic Peninsula is also experiencing unequalled effects of global warming. Owing to their uniqueness and the potential impact of global warming on these pristine systems, there is considerable interest in determining the structure and function of microbial communities in the Antarctic. We therefore utilized a recently designed 16S rRNA gene microarray, the PhyloChip, which targets 8741 bacterial and archaeal taxa, to interrogate microbial communities inhabiting densely vegetated and bare fell-field soils along a latitudinal gradient ranging from 51 degrees S (Falkland Islands) to 72 degrees S (Coal Nunatak). Results indicated a clear decrease in diversity with increasing latitude, with the two southernmost sites harboring the most distinct Bacterial and Archaeal communities. The microarray approach proved more sensitive in detecting the breadth of microbial diversity than polymerase chain reaction-based bacterial 16S rRNA gene libraries of modest size ( approximately 190 clones per library). Furthermore, the relative signal intensities summed for phyla and families on the PhyloChip were significantly correlated with the relative occurrence of these taxa in clone libraries. PhyloChip data were also compared with functional gene microarray data obtained earlier, highlighting numerous significant relationships and providing evidence for a strong link between community composition and functional gene distribution in Antarctic soils. Integration of these PhyloChip data with other complementary methods provides an unprecedented understanding of the microbial diversity and community structure of terrestrial Antarctic habitats. PMID:19020556

  17. Environmental microarray analyses of Antarctic soil microbial communities.

    PubMed

    Yergeau, Etienne; Schoondermark-Stolk, Sung A; Brodie, Eoin L; Déjean, Sébastien; DeSantis, Todd Z; Gonçalves, Olivier; Piceno, Yvette M; Andersen, Gary L; Kowalchuk, George A

    2009-03-01

    Antarctic ecosystems are fascinating in their limited trophic complexity, with decomposition and nutrient cycling functions being dominated by microbial activities. Not only are Antarctic habitats exposed to extreme environmental conditions, the Antarctic Peninsula is also experiencing unequalled effects of global warming. Owing to their uniqueness and the potential impact of global warming on these pristine systems, there is considerable interest in determining the structure and function of microbial communities in the Antarctic. We therefore utilized a recently designed 16S rRNA gene microarray, the PhyloChip, which targets 8741 bacterial and archaeal taxa, to interrogate microbial communities inhabiting densely vegetated and bare fell-field soils along a latitudinal gradient ranging from 51 degrees S (Falkland Islands) to 72 degrees S (Coal Nunatak). Results indicated a clear decrease in diversity with increasing latitude, with the two southernmost sites harboring the most distinct Bacterial and Archaeal communities. The microarray approach proved more sensitive in detecting the breadth of microbial diversity than polymerase chain reaction-based bacterial 16S rRNA gene libraries of modest size ( approximately 190 clones per library). Furthermore, the relative signal intensities summed for phyla and families on the PhyloChip were significantly correlated with the relative occurrence of these taxa in clone libraries. PhyloChip data were also compared with functional gene microarray data obtained earlier, highlighting numerous significant relationships and providing evidence for a strong link between community composition and functional gene distribution in Antarctic soils. Integration of these PhyloChip data with other complementary methods provides an unprecedented understanding of the microbial diversity and community structure of terrestrial Antarctic habitats.

  18. Effect of electricity on microbial community of microbial fuel cell simultaneously treating sulfide and nitrate

    NASA Astrophysics Data System (ADS)

    Cai, Jing; Zheng, Ping; Xing, Yajuan; Qaisar, Mahmood

    2015-05-01

    The effect of electric current on microbial community is explored in Microbial Fuel Cells (MFCs) simultaneously treating sulfide and nitrate. The MFCs are operated under four different conditions which exhibited different characteristics of electricity generation. In batch mode, MFCs generate intermittently high current pulses in the beginning, and the current density is instable subsequently, while the current density of MFCs in continuous mode is relatively stable. All operational parameters show good capacity for substrate removal, and nitrogen and sulfate were the main reaction products. Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) analysis is employed to obtain profiles of the bacterial communities present in inoculum and suspension of four MFCs. Based on the community diversity indices and Spearman correlation analyses, significant correlation exists between Richness of the community of anode chamber and the electricity generated, while no strong correlation is evident between other indexes (Shannon index, Simpson index and Equitability index) and the electricity. Additionally, the results of Principal Component Analysis (PCA) suggest that MFCs suffering from current shock have similar suspension communities, while the others have diverse microbial communities.

  19. Microbial community dynamics in continuous microbial fuel cells fed with synthetic wastewater and pig slurry.

    PubMed

    Sotres, Ana; Tey, Laura; Bonmatí, August; Viñas, Marc

    2016-10-01

    Two-chambered microbial fuel cells (MFCs) operating with synthetic wastewater and pig slurry were assessed. Additionally, the use of 2-bromoethanesulfonate (BES-Inh) was studied. The synthetic wastewater-fed MFC (MFCSW) showed a maximum power density (PDmax) of 2138mWm(-3), and the addition of BES-Inh (10mM) did not show any improvement in its performance (PDmax=2078mWm(-3)). When pig slurry was used as feed (MFCPS), PDmax increased up to 5623mWm(-3). The microbial community composition was affected by the type of substrate used. While, Pseudomonadaceae and Clostridiaceae were the most representative families within the acetate-based medium, Flavobacteriaceae, Chitinophagaceae, Comamonadaceae and Nitrosomonadaceae were predominant when pig slurry was used as feed. Otherwise, only the Eubacterial microbial community composition was strongly modified when adding BES-Inh, thus leading to an enrichment of the Bacteroidetes phylum. Oppositely, the Archaeal community was less affected by the addition of BES-Inh, and Methanosarcina sp., arose as the predominant family in both situations. Despite all the differences in microbial communities, 6 operational taxonomic units (OTUs) belonging to Bacteroidetes (Porphyromonadaceae and Marinilabiaceae) and Firmicutes (Clostridiales) were found to be common to both MFCs, also for different contents of COD and N-NH4(+), and therefore could be considered as the bioanode core microbiome.

  20. Halophilic microbial communities and their environments.

    PubMed

    Oren, Aharon

    2015-06-01

    Use of culture-independent studies have greatly increased our understanding of the microbiology of hypersaline lakes (the Dead Sea, Great Salt Lake) and saltern ponds in recent years. Exciting new information has become available on the microbial processes in Antarctic lakes and in deep-sea brines. These studies led to the recognition of many new lineages of microorganisms not yet available for study in culture, and their cultivation in the laboratory is now a major challenge. Studies of the metabolic potentials of different halophilic microorganisms, Archaea as well as Bacteria, shed light on the possibilities and the limitations of life at high salt concentrations, and also show their potential for applications in bioremediation. PMID:25727188

  1. Utilization of alternate chirality enantiomers in microbial communities

    NASA Astrophysics Data System (ADS)

    Pikuta, Elena V.; Hoover, Richard B.

    2010-09-01

    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) Growthinhibitory effect of alternate chirality enantiomers; 3) Stickland reaction with alternate chirality amino acids. The results of this research are presented in this paper.

  2. 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.

  3. Relationship between honeybee nutrition and their microbial communities.

    PubMed

    Saraiva, Miriane Acosta; Zemolin, Ana Paula Pegoraro; Franco, Jeferson Luis; Boldo, Juliano Tomazzoni; Stefenon, Valdir Marcos; Triplett, Eric W; de Oliveira Camargo, Flávio Anastácio; Roesch, Luiz Fernando Wurdig

    2015-04-01

    The microbiota and the functional genes actively involved in the process of breakdown and utilization of pollen grains in beebread and bee guts are not yet understood. The aim of this work was to assess the diversity and community structure of bacteria and archaea in Africanized honeybee guts and beebread as well as to predict the genes involved in the microbial bioprocessing of pollen using state of the art 'post-light' based sequencing technology. A total of 11 bacterial phyla were found within bee guts and 10 bacterial phyla were found within beebread. Although the phylum level comparison shows most phyla in common, a deeper phylogenetic analysis showed greater variation of taxonomic composition. The families Enterobacteriaceae, Ricketsiaceae, Spiroplasmataceae and Bacillaceae, were the main groups responsible for the specificity of the bee gut while the main families responsible for the specificity of the beebread were Neisseriaceae, Flavobacteriaceae, Acetobacteraceae and Lactobacillaceae. In terms of microbial community structure, the analysis showed that the communities from the two environments were quite different from each other with only 7 % of species-level taxa shared between bee gut and beebread. The results indicated the presence of a highly specialized and well-adapted microbiota within each bee gut and beebread. The beebread community included a greater relative abundance of genes related to amino acid, carbohydrate, and lipid metabolism, suggesting that pollen biodegradation predominantly occurs in the beebread. These results suggests a complex and important relationship between honeybee nutrition and their microbial communities. PMID:25601048

  4. Microbial communities on Australian modified atmosphere packaged Atlantic salmon.

    PubMed

    Powell, S M; Tamplin, M L

    2012-05-01

    The role of specific spoilage organisms (SSO) in products such as Atlantic salmon has been well documented. However, little is known about what other micro-organisms are present and these organisms may indirectly influence spoilage by their interactions with the SS0. We used a combination of culture-based and DNA-based methods to explore the microbial communities found on Atlantic salmon fillets packed in a modified atmosphere of carbon dioxide and nitrogen. After 15 days the communities were dominated by Shewanella spp. or Carnobacterium spp. and a variety of other genera were present in smaller numbers. Variability in the microbial community composition in packages processed on the same day was also observed. This was mostly due to differences in the presence of minor members of the community including species from genera such as Iodobacter, Serratia, Morganella and Yersinia. The combination of culture-based and culture-independent methods provided greater insight into the development of microbial communities on Atlantic salmon than would have been possible using only one method. This work highlights the potential importance of lactic acid bacteria (LAB) in fresh Atlantic salmon stored under modified atmosphere conditions.

  5. Relationship between honeybee nutrition and their microbial communities.

    PubMed

    Saraiva, Miriane Acosta; Zemolin, Ana Paula Pegoraro; Franco, Jeferson Luis; Boldo, Juliano Tomazzoni; Stefenon, Valdir Marcos; Triplett, Eric W; de Oliveira Camargo, Flávio Anastácio; Roesch, Luiz Fernando Wurdig

    2015-04-01

    The microbiota and the functional genes actively involved in the process of breakdown and utilization of pollen grains in beebread and bee guts are not yet understood. The aim of this work was to assess the diversity and community structure of bacteria and archaea in Africanized honeybee guts and beebread as well as to predict the genes involved in the microbial bioprocessing of pollen using state of the art 'post-light' based sequencing technology. A total of 11 bacterial phyla were found within bee guts and 10 bacterial phyla were found within beebread. Although the phylum level comparison shows most phyla in common, a deeper phylogenetic analysis showed greater variation of taxonomic composition. The families Enterobacteriaceae, Ricketsiaceae, Spiroplasmataceae and Bacillaceae, were the main groups responsible for the specificity of the bee gut while the main families responsible for the specificity of the beebread were Neisseriaceae, Flavobacteriaceae, Acetobacteraceae and Lactobacillaceae. In terms of microbial community structure, the analysis showed that the communities from the two environments were quite different from each other with only 7 % of species-level taxa shared between bee gut and beebread. The results indicated the presence of a highly specialized and well-adapted microbiota within each bee gut and beebread. The beebread community included a greater relative abundance of genes related to amino acid, carbohydrate, and lipid metabolism, suggesting that pollen biodegradation predominantly occurs in the beebread. These results suggests a complex and important relationship between honeybee nutrition and their microbial communities.

  6. Rooting Theories of Plant Community Ecology in Microbial Interactions

    PubMed Central

    Bever, James D.; Dickie, Ian A.; Facelli, Evelina; Facelli, Jose M.; Klironomos, John; Moora, Mari; Rillig, Matthias C.; Stock, William D.; Tibbett, Mark; Zobel, Martin

    2010-01-01

    Predominant frameworks for understanding plant ecology have an aboveground bias that neglects soil micro-organisms. This is inconsistent with recent work illustrating the importance of soil microbes in terrestrial ecology. Microbial effects have been incorporated into plant community dynamics using ideas of niche modification and plant-soil community feedbacks. Here, we expand and integrate qualitative conceptual models of plant niche and feedback to explore implications of microbial interactions for understanding plant community ecology. At the same time we review the empirical evidence for these processes. We also consider common mycorrhizal networks, and suggest these are best interpreted within the feedback framework. Finally, we apply our integrated model of niche and feedback to understanding plant coexistence, monodominance, and invasion ecology. PMID:20557974

  7. Quantitative phylogenetic assessment of microbial communities indiverse environments

    SciTech Connect

    von Mering, C.; Hugenholtz, P.; Raes, J.; Tringe, S.G.; Doerks,T.; Jensen, L.J.; Ward, N.; Bork, P.

    2007-01-01

    The taxonomic composition of environmental communities is an important indicator of their ecology and function. Here, we use a set of protein-coding marker genes, extracted from large-scale environmental shotgun sequencing data, to provide a more direct, quantitative and accurate picture of community composition than traditional rRNA-based approaches using polymerase chain reaction (PCR). By mapping marker genes from four diverse environmental data sets onto a reference species phylogeny, we show that certain communities evolve faster than others, determine preferred habitats for entire microbial clades, and provide evidence that such habitat preferences are often remarkably stable over time.

  8. Characterization of Microbial Communities in Gas Industry Pipelines

    PubMed Central

    Zhu, Xiang Y.; Lubeck, John; Kilbane, John J.

    2003-01-01

    Culture-independent techniques, denaturing gradient gel electrophoresis (DGGE) analysis, and random cloning of 16S rRNA gene sequences amplified from community DNA were used to determine the diversity of microbial communities in gas industry pipelines. Samples obtained from natural gas pipelines were used directly for DNA extraction, inoculated into sulfate-reducing bacterium medium, or used to inoculate a reactor that simulated a natural gas pipeline environment. The variable V2-V3 (average size, 384 bp) and V3-V6 (average size, 648 bp) regions of bacterial and archaeal 16S rRNA genes, respectively, were amplified from genomic DNA isolated from nine natural gas pipeline samples and analyzed. A total of 106 bacterial 16S rDNA sequences were derived from DGGE bands, and these formed three major clusters: beta and gamma subdivisions of Proteobacteria and gram-positive bacteria. The most frequently encountered bacterial species was Comamonas denitrificans, which was not previously reported to be associated with microbial communities found in gas pipelines or with microbially influenced corrosion. The 31 archaeal 16S rDNA sequences obtained in this study were all related to those of methanogens and phylogenetically fall into three clusters: order I, Methanobacteriales; order III, Methanomicrobiales; and order IV, Methanosarcinales. Further microbial ecology studies are needed to better understand the relationship among bacterial and archaeal groups and the involvement of these groups in the process of microbially influenced corrosion in order to develop improved ways of monitoring and controlling microbially influenced corrosion. PMID:12957923

  9. Ecogenomics of microbial communities in bioremediation of chlorinated contaminated sites

    PubMed Central

    Maphosa, Farai; Lieten, Shakti H.; Dinkla, Inez; Stams, Alfons J.; Smidt, Hauke; Fennell, Donna E.

    2012-01-01

    Organohalide compounds such as chloroethenes, chloroethanes, and polychlorinated benzenes are among the most significant pollutants in the world. These compounds are often found in contamination plumes with other pollutants such as solvents, pesticides, and petroleum derivatives. Microbial bioremediation of contaminated sites, has become commonplace whereby key processes involved in bioremediation include anaerobic degradation and transformation of these organohalides by organohalide respiring bacteria and also via hydrolytic, oxygenic, and reductive mechanisms by aerobic bacteria. Microbial ecogenomics has enabled us to not only study the microbiology involved in these complex processes but also develop tools to better monitor and assess these sites during bioremediation. Microbial ecogenomics have capitalized on recent advances in high-throughput and -output genomics technologies in combination with microbial physiology studies to address these complex bioremediation problems at a system level. Advances in environmental metagenomics, transcriptomics, and proteomics have provided insights into key genes and their regulation in the environment. They have also given us clues into microbial community structures, dynamics, and functions at contaminated sites. These techniques have not only aided us in understanding the lifestyles of common organohalide respirers, for example Dehalococcoides, Dehalobacter, and Desulfitobacterium, but also provided insights into novel and yet uncultured microorganisms found in organohalide respiring consortia. In this paper, we look at how ecogenomic studies have aided us to understand the microbial structures and functions in response to environmental stimuli such as the presence of chlorinated pollutants. PMID:23060869

  10. Unique pioneer microbial communities exposed to volcanic sulfur dioxide

    PubMed Central

    Fujimura, Reiko; Kim, Seok-Won; Sato, Yoshinori; Oshima, Kenshiro; Hattori, Masahira; Kamijo, Takashi; Ohta, Hiroyuki

    2016-01-01

    Newly exposed volcanic substrates contain negligible amounts of organic materials. Heterotrophic organisms in newly formed ecosystems require bioavailable carbon and nitrogen that are provided from CO2 and N2 fixation by pioneer microbes. However, the knowledge of initial ecosystem developmental mechanisms, especially the association between microbial succession and environmental change, is still limited. This study reports the unique process of microbial succession in fresh basaltic ash, which was affected by long-term exposure to volcanic sulfur dioxide (SO2). Here we compared the microbial ecosystems among deposits affected by SO2 exposure at different levels. The results of metagenomic analysis suggested the importance of autotrophic iron-oxidizing bacteria, particularly those involved in CO2 and N2 fixation, in the heavily SO2 affected site. Changes in the chemical properties of the deposits after the decline of the SO2 impact led to an apparent decrease in the iron-oxidizer abundance and a possible shift in the microbial community structure. Furthermore, the community structure of the deposits that had experienced lower SO2 gas levels showed higher similarity with that of the control forest soil. Our results implied that the effect of SO2 exposure exerted a selective pressure on the pioneer community structure by changing the surrounding environment of the microbes. PMID:26791101

  11. Microbial community and performance of slaughterhouse wastewater treatment filters.

    PubMed

    Stets, M I; Etto, R M; Galvão, C W; Ayub, R A; Cruz, L M; Steffens, M B R; Barana, A C

    2014-06-16

    The performance of anaerobic filter bioreactors (AFs) is influenced by the composition of the substrate, support medium, and the microbial species present in the sludge. In this study, the efficiency of a slaughterhouse effluent treatment using three AFs containing different support media was tested, and the microbial diversity was investigated by amplified ribosomal DNA restriction analysis and 16S rRNA gene sequencing. The physicochemical analysis of the AF systems tested suggested their feasibility, with rates of chemical oxygen demand removal of 72±8% in hydraulic retention times of 1 day. Analysis of pH, alkalinity, volatile acidity, total solids, total volatile solids, total Kjeldahl nitrogen, and the microbial community structures indicated high similarity among the three AFs. The composition of prokaryotic communities showed a prevalence of Proteobacteria (27.3%) and Bacteroidetes (18.4%) of the Bacteria domain and Methanomicrobiales (36.4%) and Methanosarcinales (35.3%) of the Archaea domain. Despite the high similarity of the microbial communities among the AFs, the reactor containing pieces of clay brick as a support medium presented the highest richness and diversity of bacterial and archaeal operational taxonomic units.

  12. Functional Potential of Soil Microbial Communities in the Maize Rhizosphere

    PubMed Central

    Xiong, Jingbo; Li, Jiabao; He, Zhili; Zhou, Jizhong; Yannarell, Anthony C.; Mackie, Roderick I.

    2014-01-01

    Microbial communities in the rhizosphere make significant contributions to crop health and nutrient cycling. However, their ability to perform important biogeochemical processes remains uncharacterized. Here, we identified important functional genes that characterize the rhizosphere microbial community to understand metabolic capabilities in the maize rhizosphere using the GeoChip-based functional gene array method. Significant differences in functional gene structure were apparent between rhizosphere and bulk soil microbial communities. Approximately half of the detected gene families were significantly (p<0.05) increased in the rhizosphere. Based on the detected gyrB genes, Gammaproteobacteria, Betaproteobacteria, Firmicutes, Bacteroidetes and Cyanobacteria were most enriched in the rhizosphere compared to those in the bulk soil. The rhizosphere niche also supported greater functional diversity in catabolic pathways. The maize rhizosphere had significantly enriched genes involved in carbon fixation and degradation (especially for hemicelluloses, aromatics and lignin), nitrogen fixation, ammonification, denitrification, polyphosphate biosynthesis and degradation, sulfur reduction and oxidation. This research demonstrates that the maize rhizosphere is a hotspot of genes, mostly originating from dominant soil microbial groups such as Proteobacteria, providing functional capacity for the transformation of labile and recalcitrant organic C, N, P and S compounds. PMID:25383887

  13. Unique pioneer microbial communities exposed to volcanic sulfur dioxide

    NASA Astrophysics Data System (ADS)

    Fujimura, Reiko; Kim, Seok-Won; Sato, Yoshinori; Oshima, Kenshiro; Hattori, Masahira; Kamijo, Takashi; Ohta, Hiroyuki

    2016-01-01

    Newly exposed volcanic substrates contain negligible amounts of organic materials. Heterotrophic organisms in newly formed ecosystems require bioavailable carbon and nitrogen that are provided from CO2 and N2 fixation by pioneer microbes. However, the knowledge of initial ecosystem developmental mechanisms, especially the association between microbial succession and environmental change, is still limited. This study reports the unique process of microbial succession in fresh basaltic ash, which was affected by long-term exposure to volcanic sulfur dioxide (SO2). Here we compared the microbial ecosystems among deposits affected by SO2 exposure at different levels. The results of metagenomic analysis suggested the importance of autotrophic iron-oxidizing bacteria, particularly those involved in CO2 and N2 fixation, in the heavily SO2 affected site. Changes in the chemical properties of the deposits after the decline of the SO2 impact led to an apparent decrease in the iron-oxidizer abundance and a possible shift in the microbial community structure. Furthermore, the community structure of the deposits that had experienced lower SO2 gas levels showed higher similarity with that of the control forest soil. Our results implied that the effect of SO2 exposure exerted a selective pressure on the pioneer community structure by changing the surrounding environment of the microbes.

  14. Unravelling Microbial Communities with DNA-Microarrays: Challengesand Future Directions.

    SciTech Connect

    Wagner, Michael; Smidt, Hauke; Loy, Alexander; Zhou, Jizhong

    2007-03-08

    High-throughput technologies are urgently needed formonitoring the formidable biodiversity and functional capabilities ofmicroorganisms in the environment. Ten years ago, DNA microarrays,miniaturized platforms for highly parallel hybridization reactions, foundtheir way into environmental microbiology and raised great expectationsamong researchers in the field. In this article, we briefly summarize thestate-of-the-art of microarray approaches in microbial ecology researchand discuss in more detail crucial problems and promising solutions.Finally, we outline scenarios for an innovative combination ofmicroarrays with other molecular tools for structure-function analysis ofcomplex microbial communities.

  15. Methane dynamics regulated by microbial community response to permafrost thaw.

    PubMed

    McCalley, Carmody K; Woodcroft, Ben J; Hodgkins, Suzanne B; Wehr, Richard A; Kim, Eun-Hae; Mondav, Rhiannon; Crill, Patrick M; Chanton, Jeffrey P; Rich, Virginia I; Tyson, Gene W; Saleska, Scott R

    2014-10-23

    Permafrost contains about 50% of the global soil carbon. It is thought that the thawing of permafrost can lead to a loss of soil carbon in the form of methane and carbon dioxide emissions. The magnitude of the resulting positive climate feedback of such greenhouse gas emissions is still unknown and may to a large extent depend on the poorly understood role of microbial community composition in regulating the metabolic processes that drive such ecosystem-scale greenhouse gas fluxes. Here we show that changes in vegetation and increasing methane emissions with permafrost thaw are associated with a switch from hydrogenotrophic to partly acetoclastic methanogenesis, resulting in a large shift in the δ(13)C signature (10-15‰) of emitted methane. We used a natural landscape gradient of permafrost thaw in northern Sweden as a model to investigate the role of microbial communities in regulating methane cycling, and to test whether a knowledge of community dynamics could improve predictions of carbon emissions under loss of permafrost. Abundance of the methanogen Candidatus 'Methanoflorens stordalenmirensis' is a key predictor of the shifts in methane isotopes, which in turn predicts the proportions of carbon emitted as methane and as carbon dioxide, an important factor for simulating the climate feedback associated with permafrost thaw in global models. By showing that the abundance of key microbial lineages can be used to predict atmospherically relevant patterns in methane isotopes and the proportion of carbon metabolized to methane during permafrost thaw, we establish a basis for scaling changing microbial communities to ecosystem isotope dynamics. Our findings indicate that microbial ecology may be important in ecosystem-scale responses to global change. PMID:25341787

  16. Cecum microbial communities from steers differing in feed efficiency.

    PubMed

    Myer, P R; Wells, J E; Smith, T P L; Kuehn, L A; Freetly, H C

    2015-11-01

    Apart from the rumen, limited knowledge exists regarding the structure and function of bacterial communities within the gastrointestinal tract and their association with beef cattle feed efficiency. The objective of this study was to characterize the microbial communities of the cecum among steers differing in feed efficiency. Within 2 contemporary groups of steers, individual feed intake and BW gain were determined from animals fed the same diet. Within both of 2 contemporary groups, BW was regressed on feed intake and 4 steers within each Cartesian quadrant were sampled ( = 16/group). Bacterial 16S rRNA gene amplicons were sequenced from the cecal content using next-generation sequencing technology. No significant changes in diversity or richness were detected among quadrants, and UniFrac principal coordinate analysis did not show any differences among quadrants for microbial communities within the cecum. The relative abundances of microbial populations and operational taxonomic units revealed significant differences among feed efficiency groups ( < 0.05). Firmicutes was the dominant cecal phylum in all groups and accounted for up to 81% of the populations among samples. Populations were also dominated by families Ruminococcaceae, Lachnospiraceae, and Clostridiaceae, with significant shifts in the relative abundance of taxa among feed efficiency groups, including families Ruminococcaceae ( = 0.040), Lachnospiraceae ( = 0.020), Erysipelotrichaceae ( = 0.046), and Clostridiaceae ( = 0.043) and genera ( = 0.049), ( = 0.044), ( = 0.042), ( = 0.040), ( = 0.042), and ( = 0.042). The study identified cecal microbial associations with feed efficiency, ADG, and ADFI. This study suggests an association of the cecum microbial community with bovine feed efficiency at the 16S level. PMID:26641052

  17. Microbial community composition and function across an arctic tundra landscape.

    PubMed

    Zak, Donald R; Kling, George W

    2006-07-01

    Arctic landscapes are characterized by a diversity of ecosystems, which differ in plant species composition, litter biochemistry, and biogeochemical cycling rates. Tundra ecosystems differing in plant composition should contain compositionally and functionally distinct microbial communities that differentially transform dissolved organic matter as it moves downslope from dry, upland to wet, lowland tundra. To test this idea, we studied soil microbial communities in upland tussock, stream-side birch-willow, and lakeside wet sedge tundra in arctic Alaska, USA. These are a series of ecosystems that differ in topographic position, plant composition, and soil drainage. Phospholipid fatty acid (PLFA) analyses, coupled with compound-specific 13C isotope tracing, were used to quantify microbial community composition and function; we also assayed the activity of extracellular enzymes involved in cellulose, chitin, and lignin degradation. Surface soil from each tundra ecosystem was labeled with 13C-cellobiose,13C-N-acetylglucosamine, or 13C-vanillin. After a five-day incubation, we followed the movement of 13C into bacterial and fungal PLFAs, microbial respiration, dissolved organic carbon, and soil organic matter. Microbial community composition and function were distinct among tundra ecosystems, with tussock tundra containing a significantly greater abundance and activity of soil fungi. Although the majority of 13C-labeled substrates rapidly moved into soil organic matter in all tundra soils (i.e., 50-90% of applied 13C), microbial respiration of labeled substrates in wet sedge tundra soil was lower than in tussock and birch-willow tundra; approximately 8% of 13C-cellobiose and approximately 5% of 13C-vanillin was respired in wet sedge soil vs. 26-38% of 13C-cellobiose and 18-21% of 13C-vanillin in the other tundra ecosystems. Despite these differences, wet sedge tundra exhibited the greatest extracellular enzyme activity. Topographic variation in plant litter biochemistry

  18. The Effect of Dilution on the Structure of Microbial Communities

    NASA Technical Reports Server (NTRS)

    Mills, Aaron L.

    2000-01-01

    To determine how dilution of microbial communities affects the diversity of the diluted assemblage a series of numerical simulations were conducted that determined the theoretical change in diversity, richness, and evenness of the community with serial dilution. The results of the simulation suggested that the effects are non linear with a high degree of dependence on the initial evenness of the community being diluted. A series of incubation experiments using a range of dilutions of raw sewage as an inoculum into sterile sewage was used for comparison to the simulations. The diluted communities were maintained in batch fed reactors (three day retention time) for nine days. The communities were harvested and examined by conventional plating and by molecular analysis of the whole-community DNA using AFLP and T-RFLP. Additional, CLPP analysis was also applied. The effects on richness predicted by the numerical simulations were confirmed by the analyses used. The diluted communities fell into three groups, a low dilution, intermediate dilution, and high dilution group, which corresponded well with the groupings obtained for community richness in simulation. The grouping demonstrated the non-linear nature of dilution of whole communities. Furthermore, the results implied that the undiluted community consisted of a few dominant types accompanied by a number of rare (low abundance) types as is typical in unevenly distributed communities.

  19. Mechanisms Controlling the Plant Diversity Effect on Soil Microbial Community Composition and Soil Microbial Diversity

    NASA Astrophysics Data System (ADS)

    Mellado Vázquez, P. G.; Lange, M.; Griffiths, R.; Malik, A.; Ravenek, J.; Strecker, T.; Eisenhauer, N.; Gleixner, G.

    2015-12-01

    Soil microorganisms are the main drivers of soil organic matter cycling. Organic matter input by living plants is the major energy and matter source for soil microorganisms, higher organic matter inputs are found in highly diverse plant communities. It is therefore relevant to understand how plant diversity alters the soil microbial community and soil organic matter. In a general sense, microbial biomass and microbial diversity increase with increasing plant diversity, however the mechanisms driving these interactions are not fully explored. Working with soils from a long-term biodiversity experiment (The Jena Experiment), we investigated how changes in the soil microbial dynamics related to plant diversity were explained by biotic and abiotic factors. Microbial biomass quantification and differentiation of bacterial and fungal groups was done by phospholipid fatty acid (PLFA) analysis; terminal-restriction fragment length polymorphism was used to determine the bacterial diversity. Gram negative (G-) bacteria predominated in high plant diversity; Gram positive (G+) bacteria were more abundant in low plant diversity and saprotrophic fungi were independent from plant diversity. The separation between G- and G+ bacteria in relation to plant diversity was governed by a difference in carbon-input related factors (e.g. root biomass and soil moisture) between plant diversity levels. Moreover, the bacterial diversity increased with plant diversity and the evenness of the PLFA markers decreased. Our results showed that higher plant diversity favors carbon-input related factors and this in turn favors the development of microbial communities specialized in utilizing new carbon inputs (i.e. G- bacteria), which are contributing to the export of new C from plants to soils.

  20. Microbial Population and Community Dynamics on Plant Roots and Their Feedbacks on Plant Communities

    PubMed Central

    Bever, James D.; Platt, Thomas G.; Morton, Elise R.

    2012-01-01

    The composition of the soil microbial community can be altered dramatically due to association with individual plant species, and these effects on the microbial community can have important feedbacks on plant ecology. Negative plant-soil feedback plays primary roles in maintaining plant community diversity, whereas positive plant-soil feedback may cause community conversion. Host-specific differentiation of the microbial community results from the trade-offs associated with overcoming plant defense and the specific benefits associated with plant rewards. Accumulation of host-specific pathogens likely generates negative feedback on the plant, while changes in the density of microbial mutualists likely generate positive feedback. However, the competitive dynamics among microbes depends on the multidimensional costs of virulence and mutualism, the fine-scale spatial structure within plant roots, and active plant allocation and localized defense. Because of this, incorporating a full view of microbial dynamics is essential to explaining the dynamics of plant-soil feedbacks and therefore plant community ecology. PMID:22726216

  1. Fluvial network imprints on microbial diversity and community network topology

    NASA Astrophysics Data System (ADS)

    Battin, T. J.; Besemer, K.; Widder, S.; Singer, G. A.; Ceola, S.; Bertuzzo, E.; Quince, C.; Sloan, W. T.; Rinaldo, A.

    2013-12-01

    Streams and rivers sculpt continental landscapes and the networks they form carry universal signatures of spatial organization. Biodiversity in fluvial networks ranks among the highest on Earth and microorganisms therein, often enclosed in biofilms, fulfill critical ecosystem functions even with repercussions on the global carbon cycle. We extensively used 454 pyrosequencing on biofilm samples from more than 100 streams from a 5th-order catchment, derived alpha and beta diversity patterns and, using co-occurrence analyses, we studied community network organization. Contrary to current theory and to animal diversity studies, we found microbial alpha diversity in biofilms to decrease downstream with confluences likely acting as filters to biodiversity as it propagates from the smallest headwaters to larger rivers. Along with higher beta diversity in the headwaters, these findings highlight headwaters as critical reservoirs of microbial diversity for entire fluvial networks. Co-occurrence analyses revealed a lower level of fragmentation of community networks in headwaters than in larger rivers downstream and further identified gatekeepers (at family level) as potential architects of the observed network topology. Similarly, fragmentation was higher downstream than upstream of confluences. Consistent with current network theory, simple model simulations suggest that fragmentation patterns are linked to persistence against perturbations. We further explore the role of perturbation for community network topology in the context of fluvial network hydrology. Our findings have deep implications for restoration and conservation. They portrait the imprint of fluvial networks on microbial community networks and thereby expand our knowledge on biodiversity and ecosystem persistence.

  2. Microbial Communities in a High Arctic Polar Desert Landscape

    PubMed Central

    McCann, Clare M.; Wade, Matthew J.; Gray, Neil D.; Roberts, Jennifer A.; Hubert, Casey R. J.; Graham, David W.

    2016-01-01

    The High Arctic is dominated by polar desert habitats whose microbial communities are poorly understood. In this study, we used next generation sequencing to describe the α- and β-diversity of microbial communities in polar desert soils from the Kongsfjorden region of Svalbard. Ten phyla dominated the soils and accounted for 95% of all sequences, with the Proteobacteria, Actinobacteria, and Chloroflexi being the major lineages. In contrast to previous investigations of Arctic soils, relative Acidobacterial abundances were found to be very low as were the Archaea throughout the Kongsfjorden polar desert landscape. Lower Acidobacterial abundances were attributed to characteristic circumneutral soil pHs in this region, which has resulted from the weathering of underlying carbonate bedrock. In addition, we compared previously measured geochemical conditions as possible controls on soil microbial communities. Phosphorus, pH, nitrogen, and calcium levels all significantly correlated with β-diversity, indicating landscape-scale lithological control of available nutrients, which in turn, significantly influenced soil community composition. In addition, soil phosphorus and pH significantly correlated with α-diversity, particularly with the Shannon diversity and Chao 1 richness indices. PMID:27065980

  3. Counteraction of antibiotic production and degradation stabilizes microbial communities

    PubMed Central

    Kelsic, Eric D.; Zhao, Jeffrey; Vetsigian, Kalin; Kishony, Roy

    2015-01-01

    Summary A major challenge in theoretical ecology is understanding how natural microbial communities support species diversity1-8, and in particular how antibiotic producing, sensitive and resistant species coexist9-15. While cyclic “rock-paper-scissors” interactions can stabilize communities in spatial environments9-11, coexistence in unstructured environments remains an enigma12,16. Here, using simulations and analytical models, we show that the opposing actions of antibiotic production and degradation enable coexistence even in well-mixed environments. Coexistence depends on 3-way interactions where an antibiotic degrading species attenuates the inhibitory interactions between two other species. These 3-way interactions enable coexistence that is robust to substantial differences in inherent species growth rates and to invasion by “cheating” species that cease producing or degrading antibiotics. At least two antibiotics are required for stability, with greater numbers of antibiotics enabling more complex communities and diverse dynamical behaviors ranging from stable fixed-points to limit cycles and chaos. Together, these results show how multi-species antibiotic interactions can generate ecological stability in both spatial and mixed microbial communities, suggesting strategies for engineering synthetic ecosystems and highlighting the importance of toxin production and degradation for microbial biodiversity. PMID:25992546

  4. Eukaryotic and prokaryotic microbial communities during microalgal biomass production.

    PubMed

    Lakaniemi, Aino-Maija; Hulatt, Chris J; Wakeman, Kathryn D; Thomas, David N; Puhakka, Jaakko A

    2012-11-01

    Eukaryotic and bacterial communities were characterized and quantified in microalgal photobioreactor cultures of freshwater Chlorella vulgaris and marine Dunaliella tertiolecta. The microalgae exhibited good growth, whilst both cultures contained diverse bacterial communities. Both cultures included Proteobacteria and Bacteroidetes, while C. vulgaris cultures also contained Actinobacteria. The bacterial genera present in the cultures were different due to different growth medium salinities and possibly different extracellular products. Bacterial community profiles were relatively stable in D. tertiolecta cultures but not in C. vulgaris cultures likely due to presence of ciliates (Colpoda sp.) in the latter. The presence of ciliates did not, however, cause decrease in total number of C. vulgaris or bacteria during 14 days of cultivation. Quantitative PCR (qPCR) reliably showed relative microalgal and bacterial cell numbers in the batch cultures with stable microbial communities, but was not effective when bacterial communities varied. Raw culture samples were successfully used as qPCR templates. PMID:22995170

  5. Probabilistic models to describe the dynamics of migrating microbial communities.

    PubMed

    Schroeder, Joanna L; Lunn, Mary; Pinto, Ameet J; Raskin, Lutgarde; Sloan, William T

    2015-01-01

    In all but the most sterile environments bacteria will reside in fluid being transported through conduits and some of these will attach and grow as biofilms on the conduit walls. The concentration and diversity of bacteria in the fluid at the point of delivery will be a mix of those when it entered the conduit and those that have become entrained into the flow due to seeding from biofilms. Examples include fluids through conduits such as drinking water pipe networks, endotracheal tubes, catheters and ventilation systems. Here we present two probabilistic models to describe changes in the composition of bulk fluid microbial communities as they are transported through a conduit whilst exposed to biofilm communities. The first (discrete) model simulates absolute numbers of individual cells, whereas the other (continuous) model simulates the relative abundance of taxa in the bulk fluid. The discrete model is founded on a birth-death process whereby the community changes one individual at a time and the numbers of cells in the system can vary. The continuous model is a stochastic differential equation derived from the discrete model and can also accommodate changes in the carrying capacity of the bulk fluid. These models provide a novel Lagrangian framework to investigate and predict the dynamics of migrating microbial communities. In this paper we compare the two models, discuss their merits, possible applications and present simulation results in the context of drinking water distribution systems. Our results provide novel insight into the effects of stochastic dynamics on the composition of non-stationary microbial communities that are exposed to biofilms and provides a new avenue for modelling microbial dynamics in systems where fluids are being transported.

  6. Probabilistic models to describe the dynamics of migrating microbial communities.

    PubMed

    Schroeder, Joanna L; Lunn, Mary; Pinto, Ameet J; Raskin, Lutgarde; Sloan, William T

    2015-01-01

    In all but the most sterile environments bacteria will reside in fluid being transported through conduits and some of these will attach and grow as biofilms on the conduit walls. The concentration and diversity of bacteria in the fluid at the point of delivery will be a mix of those when it entered the conduit and those that have become entrained into the flow due to seeding from biofilms. Examples include fluids through conduits such as drinking water pipe networks, endotracheal tubes, catheters and ventilation systems. Here we present two probabilistic models to describe changes in the composition of bulk fluid microbial communities as they are transported through a conduit whilst exposed to biofilm communities. The first (discrete) model simulates absolute numbers of individual cells, whereas the other (continuous) model simulates the relative abundance of taxa in the bulk fluid. The discrete model is founded on a birth-death process whereby the community changes one individual at a time and the numbers of cells in the system can vary. The continuous model is a stochastic differential equation derived from the discrete model and can also accommodate changes in the carrying capacity of the bulk fluid. These models provide a novel Lagrangian framework to investigate and predict the dynamics of migrating microbial communities. In this paper we compare the two models, discuss their merits, possible applications and present simulation results in the context of drinking water distribution systems. Our results provide novel insight into the effects of stochastic dynamics on the composition of non-stationary microbial communities that are exposed to biofilms and provides a new avenue for modelling microbial dynamics in systems where fluids are being transported. PMID:25803866

  7. 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

  8. Environmental controls on microbial community cycling in modern marine stromatolites

    NASA Astrophysics Data System (ADS)

    Bowlin, Emily M.; Klaus, James S.; Foster, Jamie S.; Andres, Miriam S.; Custals, Lillian; Reid, R. Pamela

    2012-07-01

    Living stromatolites on the margins of Exuma Sound, Bahamas, are the only examples of modern stromatolites forming in open marine conditions similar to those that may have existed on Precambrian platforms. Six microbial mat types have previously been documented on the surfaces of stromatolites along the eastern side of Highborne Cay (Schizothrix, Solentia, heterotrophic biofilm, stalked diatom, tube diatom and Phormidium mats). Cycling of these communities create laminae with distinct microstructures. Subsurface laminae thus represent a chronology of former surface mats. The present study documents the effects of environmental factors on surface microbial communities of modern marine stromatolites and identifies potential causes of microbial mat cycling. Mat type and burial state at 43 markers along a stromatolitic reef on the margin of Highborne Cay were monitored over a two-year period (2005-2006). Key environmental parameters (i.e., temperature, light, wind, water chemistry) were also monitored. Results indicated that the composition of stromatolite surface mats and transitions from one mat type to another are controlled by both seasonal and stochastic events. All six stromatolite mat communities at Highborne Cay showed significant correlations with water temperature. Heterotrophic biofilms, Solentia, stalked diatom and Phormidium mats showed positive correlations with temperature, whereas Schizothrix and tube diatom communities showed negative correlations. A significant correlation with light (photosynthetically active radiation, PAR) was detected only for the heterotrophic biofilm community. No significant correlations were found between mat type and the monitored wind intensity data, but field observations indicated that wind-related events such as storms and sand abrasion play important roles in the transitions from one mat type to another. An integrated model of stromatolite mat community cycling is developed that includes both predictable seasonal

  9. Reaction Progress and the Changing Diversity of Chemolithotrophic Microbial Communities

    NASA Astrophysics Data System (ADS)

    Shock, E.; Boyd, E.

    2012-12-01

    Is there a correlation between the abundance and diversity of geochemical energy sources and the diversity of chemolithotrophic microbial communities? The available data are suggestive, but not yet conclusive owing to a general lack of models and sampling strategies that integrate microbial, molecular, and geochemical data from microbially dominated ecosystems. While improvements are being made in sampling and analytical strategies, there is an opportunity to examine the underlying thermodynamic framework and generate hypotheses that can lead to quantitate tests of how reaction progress drives microbial diversity. Such quantitative approaches would allow accurate forecasts of the response of microbial communities, the base of all food webs, to environmental change, and development of strategies to deal with shifts in ecosystem function. As a first order consideration, chemolithotrophs require sources of chemical energy, which are provided by oxidation-reduction (redox) reactions that are far from equilibrium. Larger energy supplies can be expected to support larger populations of microbes unless nutrient supply (e.g., phosphate limitation) or other physiological limitations (e.g., thermal limits) are encountered. In geochemical systems, the magnitudes of disequilibria can be evaluated by quantifying how far from equilibrium individual reactions are. As reactions progress, fluctuations in disequilibria can be monitored by explicitly assessing values of reaction-progress variables. Such approaches are commonly used to develop dynamic models of weathering, diagenesis, hydrothermal alteration, and other geochemical processes involving mass transfer. The same framework applied to overall reactions capable of supporting chemolithotrophic populations enables dynamic predictions of changes in the predominant metabolic strategies capable of supporting microbial communities during geochemical processes. These predictions are not limited to changes in microbial biomass and

  10. Metagenome of an Anaerobic Microbial Community Decomposing Poplar Wood Chips

    SciTech Connect

    van der Lelie, D.; Taghavi, S.; McCorkle, S. M.; Li, L. L.; Malfatti, S. A.; Monteleone, D.; Donohoe, B. S.; Ding, S. Y.; Adney, W. S.; Himmel, M. E.; Tringe, S. G.

    2012-05-01

    This study describes the composition and metabolic potential of a lignocellulosic biomass degrading community that decays poplar wood chips under anaerobic conditions. We examined the community that developed on poplar biomass in a non-aerated bioreactor over the course of a year, with no microbial inoculation other than the naturally occurring organisms on the woody material. The composition of this community contrasts in important ways with biomass-degrading communities associated with higher organisms, which have evolved over millions of years into a symbiotic relationship. Both mammalian and insect hosts provide partial size reduction, chemical treatments (low or high pH environments), and complex enzymatic 'secretomes' that improve microbial access to cell wall polymers. We hypothesized that in order to efficiently degrade coarse untreated biomass, a spontaneously assembled free-living community must both employ alternative strategies, such as enzymatic lignin depolymerization, for accessing hemicellulose and cellulose and have a much broader metabolic potential than host-associated communities. This would suggest that such a community would make a valuable resource for finding new catalytic functions involved in biomass decomposition and gaining new insight into the poorly understood process of anaerobic lignin depolymerization. Therefore, in addition to determining the major players in this community, our work specifically aimed at identifying functions potentially involved in the depolymerization of cellulose, hemicelluloses, and lignin, and to assign specific roles to the prevalent community members in the collaborative process of biomass decomposition. A bacterium similar to Magnetospirillum was identified among the dominant community members, which could play a key role in the anaerobic breakdown of aromatic compounds. We suggest that these compounds are released from the lignin fraction in poplar hardwood during the decay process, which would point to

  11. Molecular Analysis of Endolithic Microbial Communities in Volcanic Glasses

    NASA Astrophysics Data System (ADS)

    di Meo, C. A.; Giovannoni, S.; Fisk, M.

    2002-12-01

    Terrestrial and marine volcanic glasses become mineralogically and chemically altered, and in many cases this alteration has been attributed to microbial activity. We have used molecular techniques to study the resident microbial communities from three different volcanic environments that may be responsible for this crustal alteration. Total microbial DNA was extracted from rhyolite glass of the 7 million year old Rattlesnake Tuff in eastern Oregon. The DNA was amplified using the polymerase chain reaction (PCR) with bacterial primers targeting the 16S rRNA gene. This 16S rDNA was cloned and screened with restriction fragment length polymorphism (RFLP). Out of 89 total clones screened, 46 belonged to 13 different clone families containing two or more members, while 43 clones were unique. Sequences of eight clones representing the most dominant clone families in the library were 92 to 97% similar to soil bacterial species. In a separate study, young pillow basalts (<20 yrs old) from six different sites along the ridge axis at 9°N, East Pacific Rise were examined for microbial life. Total DNA was extracted from the basalt glass and screened for the presence of both bacteria and archaea using the PCR. Repeated attempts with different primer sets yielded no bacterial genes, whereas archaeal genes were quite abundant. A genetic fingerprinting technique, terminal restriction fragment length polymorphism (T-RFLP), was used to compare the archaeal community compositions among the six different basalts. Filtered deep-sea water samples (~15 L) were examined in parallel to identify any overlap between rock- and seawater-associated archaea. The six rock community profiles were quite similar to each other, and the background water communities were also similar, respectively. Both the rock and water communities shared the same dominant peak. To identify the T-RFLP peaks corresponding to the individual members of the rock and seawater communities, clone libraries of the archaeal

  12. Community-analyzer: a platform for visualizing and comparing microbial community structure across microbiomes.

    PubMed

    Kuntal, Bhusan K; Ghosh, Tarini Shankar; Mande, Sharmila S

    2013-10-01

    A key goal in comparative metagenomics is to identify microbial group(s) which are responsible for conferring specific characteristics to a given environment. These characteristics are the result of the inter-microbial interactions between the resident microbial groups. We present a new GUI-based comparative metagenomic analysis application called Community-Analyzer which implements a correlation-based graph layout algorithm that not only facilitates a quick visualization of the differences in the analyzed microbial communities (in terms of their taxonomic composition), but also provides insights into the inherent inter-microbial interactions occurring therein. Notably, this layout algorithm also enables grouping of the metagenomes based on the probable inter-microbial interaction patterns rather than simply comparing abundance values of various taxonomic groups. In addition, the tool implements several interactive GUI-based functionalities that enable users to perform standard comparative analyses across microbiomes. For academic and non-profit users, the Community-Analyzer is currently available for download from: http://metagenomics.atc.tcs.com/Community_Analyzer/.

  13. Simulating Microbial Community Patterning Using Biocellion

    SciTech Connect

    Kang, Seung-Hwa; Kahan, Simon H.; Momeni, Babak

    2014-04-17

    Mathematical modeling and computer simulation are important tools for understanding complex interactions between cells and their biotic and abiotic environment: similarities and differences between modeled and observed behavior provide the basis for hypothesis forma- tion. Momeni et al. [5] investigated pattern formation in communities of yeast strains engaging in different types of ecological interactions, comparing the predictions of mathematical modeling and simulation to actual patterns observed in wet-lab experiments. However, simu- lations of millions of cells in a three-dimensional community are ex- tremely time-consuming. One simulation run in MATLAB may take a week or longer, inhibiting exploration of the vast space of parameter combinations and assumptions. Improving the speed, scale, and accu- racy of such simulations facilitates hypothesis formation and expedites discovery. Biocellion is a high performance software framework for ac- celerating discrete agent-based simulation of biological systems with millions to trillions of cells. Simulations of comparable scale and accu- racy to those taking a week of computer time using MATLAB require just hours using Biocellion on a multicore workstation. Biocellion fur- ther accelerates large scale, high resolution simulations using cluster computers by partitioning the work to run on multiple compute nodes. Biocellion targets computational biologists who have mathematical modeling backgrounds and basic C++ programming skills. This chap- ter describes the necessary steps to adapt the original Momeni et al.'s model to the Biocellion framework as a case study.

  14. [Establishment of ARDRA system for Panax ginseng cultivated soil microbial community study].

    PubMed

    Ying, Yixin; Ding, Wanlong; Li, Yong

    2011-02-01

    In this study, ARDRA system was established for Panax ginseng cultivated soil microbial community analysis. In the process of soil analysis we found that, ARDRA can not only distinguish soil microbial communities, proportion of each microbial type in total microorganisms can be calculated based on profiles of restricted enzyme digested 16S rDNA, also. Results indicated that, ARDRA system established was able to analyze microbial communities of P. ginseng cultivated soil samples.

  15. Abiotic drivers and plant traits explain landscape-scale patterns in soil microbial communities.

    PubMed

    de Vries, Franciska T; Manning, Pete; Tallowin, Jerry R B; Mortimer, Simon R; Pilgrim, Emma S; Harrison, Kathryn A; Hobbs, Phil J; Quirk, Helen; Shipley, Bill; Cornelissen, Johannes H C; Kattge, Jens; Bardgett, Richard D

    2012-11-01

    The controls on aboveground community composition and diversity have been extensively studied, but our understanding of the drivers of belowground microbial communities is relatively lacking, despite their importance for ecosystem functioning. In this study, we fitted statistical models to explain landscape-scale variation in soil microbial community composition using data from 180 sites covering a broad range of grassland types, soil and climatic conditions in England. We found that variation in soil microbial communities was explained by abiotic factors like climate, pH and soil properties. Biotic factors, namely community-weighted means (CWM) of plant functional traits, also explained variation in soil microbial communities. In particular, more bacterial-dominated microbial communities were associated with exploitative plant traits versus fungal-dominated communities with resource-conservative traits, showing that plant functional traits and soil microbial communities are closely related at the landscape scale.

  16. Microbial community composition and diversity in Caspian Sea sediments

    PubMed Central

    Mahmoudi, Nagissa; Robeson, Michael S.; Castro, Hector F.; Fortney, Julian L.; Techtmann, Stephen M.; Joyner, Dominique C.; Paradis, Charles J.; Pfiffner, Susan M.; Hazen, Terry C.

    2014-01-01

    The Caspian Sea is heavily polluted due to industrial and agricultural effluents as well as extraction of oil and gas reserves. Microbial communities can influence the fate of contaminants and nutrients. However, insight into the microbial ecology of the Caspian Sea significantly lags behind other marine systems. Here we describe microbial biomass, diversity and composition in sediments collected from three sampling stations in the Caspian Sea. Illumina sequencing of 16S rRNA genes revealed the presence of a number of known bacterial and archaeal heterotrophs suggesting that organic carbon is a primary factor shaping microbial communities. Surface sediments collected from bottom waters with low oxygen levels were dominated by Gammaproteobacteria while surface sediments collected from bottom waters under hypoxic conditions were dominated by Deltaproteobacteria, specifically sulfate-reducing bacteria. Thaumarchaeota was dominant across all surface sediments indicating that nitrogen cycling in this system is strongly influenced by ammonia-oxidizing archaea. This study provides a baseline assessment that may serve as a point of reference as this system changes or as the efficacy of new remediation efforts are implemented. PMID:25764536

  17. Computational meta'omics for microbial community studies

    PubMed Central

    Segata, Nicola; Boernigen, Daniela; Tickle, Timothy L; Morgan, Xochitl C; Garrett, Wendy S; Huttenhower, Curtis

    2013-01-01

    Complex microbial communities are an integral part of the Earth's ecosystem and of our bodies in health and disease. In the last two decades, culture-independent approaches have provided new insights into their structure and function, with the exponentially decreasing cost of high-throughput sequencing resulting in broadly available tools for microbial surveys. However, the field remains far from reaching a technological plateau, as both computational techniques and nucleotide sequencing platforms for microbial genomic and transcriptional content continue to improve. Current microbiome analyses are thus starting to adopt multiple and complementary meta'omic approaches, leading to unprecedented opportunities to comprehensively and accurately characterize microbial communities and their interactions with their environments and hosts. This diversity of available assays, analysis methods, and public data is in turn beginning to enable microbiome-based predictive and modeling tools. We thus review here the technological and computational meta'omics approaches that are already available, those that are under active development, their success in biological discovery, and several outstanding challenges. PMID:23670539

  18. Microbial community composition and diversity in Caspian Sea sediments.

    PubMed

    Mahmoudi, Nagissa; Robeson, Michael S; Castro, Hector F; Fortney, Julian L; Techtmann, Stephen M; Joyner, Dominique C; Paradis, Charles J; Pfiffner, Susan M; Hazen, Terry C

    2015-01-01

    The Caspian Sea is heavily polluted due to industrial and agricultural effluents as well as extraction of oil and gas reserves. Microbial communities can influence the fate of contaminants and nutrients. However, insight into the microbial ecology of the Caspian Sea significantly lags behind other marine systems. Here we describe microbial biomass, diversity and composition in sediments collected from three sampling stations in the Caspian Sea. Illumina sequencing of 16S rRNA genes revealed the presence of a number of known bacterial and archaeal heterotrophs suggesting that organic carbon is a primary factor shaping microbial communities. Surface sediments collected from bottom waters with low oxygen levels were dominated by Gammaproteobacteria while surface sediments collected from bottom waters under hypoxic conditions were dominated by Deltaproteobacteria, specifically sulfate-reducing bacteria. Thaumarchaeota was dominant across all surface sediments indicating that nitrogen cycling in this system is strongly influenced by ammonia-oxidizing archaea. This study provides a baseline assessment that may serve as a point of reference as this system changes or as the efficacy of new remediation efforts are implemented. PMID:25764536

  19. The genotypic view of social interactions in microbial communities.

    PubMed

    Mitri, Sara; Foster, Kevin Richard

    2013-01-01

    Dense and diverse microbial communities are found in many environments. Disentangling the social interactions between strains and species is central to understanding microbes and how they respond to perturbations. However, the study of social evolution in microbes tends to focus on single species. Here, we broaden this perspective and review evolutionary and ecological theory relevant to microbial interactions across all phylogenetic scales. Despite increased complexity, we reduce the theory to a simple null model that we call the genotypic view. This states that cooperation will occur when cells are surrounded by identical genotypes at the loci that drive interactions, with genetic identity coming from recent clonal growth or horizontal gene transfer (HGT). In contrast, because cooperation is only expected to evolve between different genotypes under restrictive ecological conditions, different genotypes will typically compete. Competition between two genotypes includes mutual harm but, importantly, also many interactions that are beneficial to one of the two genotypes, such as predation. The literature offers support for the genotypic view with relatively few examples of cooperation between genotypes. However, the study of microbial interactions is still at an early stage. We outline the logic and methods that help to better evaluate our perspective and move us toward rationally engineering microbial communities to our own advantage.

  20. Bioremediation of petroleum hydrocarbons: catabolic genes, microbial communities, and applications.

    PubMed

    Fuentes, Sebastián; Méndez, Valentina; Aguila, Patricia; Seeger, Michael

    2014-06-01

    Bioremediation is an environmental sustainable and cost-effective technology for the cleanup of hydrocarbon-polluted soils and coasts. In spite of that longer times are usually required compared with physicochemical strategies, complete degradation of the pollutant can be achieved, and no further confinement of polluted matrix is needed. Microbial aerobic degradation is achieved by the incorporation of molecular oxygen into the inert hydrocarbon molecule and funneling intermediates into central catabolic pathways. Several families of alkane monooxygenases and ring hydroxylating dioxygenases are distributed mainly among Proteobacteria, Actinobacteria, Firmicutes and Fungi strains. Catabolic routes, regulatory networks, and tolerance/resistance mechanisms have been characterized in model hydrocarbon-degrading bacteria to understand and optimize their metabolic capabilities, providing the basis to enhance microbial fitness in order to improve hydrocarbon removal. However, microbial communities taken as a whole play a key role in hydrocarbon pollution events. Microbial community dynamics during biodegradation is crucial for understanding how they respond and adapt to pollution and remediation. Several strategies have been applied worldwide for the recovery of sites contaminated with persistent organic pollutants, such as polycyclic aromatic hydrocarbons and petroleum derivatives. Common strategies include controlling environmental variables (e.g., oxygen availability, hydrocarbon solubility, nutrient balance) and managing hydrocarbon-degrading microorganisms, in order to overcome the rate-limiting factors that slow down hydrocarbon biodegradation.

  1. Computational meta'omics for microbial community studies.

    PubMed

    Segata, Nicola; Boernigen, Daniela; Tickle, Timothy L; Morgan, Xochitl C; Garrett, Wendy S; Huttenhower, Curtis

    2013-01-01

    Complex microbial communities are an integral part of the Earth's ecosystem and of our bodies in health and disease. In the last two decades, culture-independent approaches have provided new insights into their structure and function, with the exponentially decreasing cost of high-throughput sequencing resulting in broadly available tools for microbial surveys. However, the field remains far from reaching a technological plateau, as both computational techniques and nucleotide sequencing platforms for microbial genomic and transcriptional content continue to improve. Current microbiome analyses are thus starting to adopt multiple and complementary meta'omic approaches, leading to unprecedented opportunities to comprehensively and accurately characterize microbial communities and their interactions with their environments and hosts. This diversity of available assays, analysis methods, and public data is in turn beginning to enable microbiome-based predictive and modeling tools. We thus review here the technological and computational meta'omics approaches that are already available, those that are under active development, their success in biological discovery, and several outstanding challenges.

  2. Metabolic modeling of a mutualistic microbial community

    SciTech Connect

    Stolyar, Sergey; Van Dien, Steve; Hillesland, Kristina Linnea; Pinel, Nicolas; Lie, Thomas J.; Leigh, John A.; Stahl, David A.

    2007-03-13

    The rate of production of methane in many environmentsdepends upon mutualistic interactions between sulfate-reducing bacteriaand methanogens. To enhance our understanding of these relationships, wetook advantage of the fully sequenced genomes of Desulfovibrio vulgarisand Methanococcus maripaludis to produce and analyze the firstmultispecies stoichiometric metabolic model. Model results were comparedto data on growth of the co-culture on lactate in the absence of sulfate.The model accurately predicted several ecologically relevantcharacteristics, including the flux of metabolites and the ratio of D.vulgaris to M. maripaludis cells during growth. In addition, the modeland our data suggested that it was possible to eliminate formate as aninterspecies electron shuttle, but hydrogen transfer was essential forsyntrophic growth. Our work demonstrated that reconstructed metabolicnetworks and stoichiometric models can serve not only to predictmetabolic fluxes and growth phenotypes of single organisms, but also tocapture growth parameters and community composition of simple bacterialcommunities.

  3. Cheese rind communities provide tractable systems for in situ and in vitro studies of microbial diversity.

    PubMed

    Wolfe, Benjamin E; Button, Julie E; Santarelli, Marcela; Dutton, Rachel J

    2014-07-17

    Tractable microbial communities are needed to bridge the gap between observations of patterns of microbial diversity and mechanisms that can explain these patterns. We developed cheese rinds as model microbial communities by characterizing in situ patterns of diversity and by developing an in vitro system for community reconstruction. Sequencing of 137 different rind communities across 10 countries revealed 24 widely distributed and culturable genera of bacteria and fungi as dominant community members. Reproducible community types formed independent of geographic location of production. Intensive temporal sampling demonstrated that assembly of these communities is highly reproducible. Patterns of community composition and succession observed in situ can be recapitulated in a simple in vitro system. Widespread positive and negative interactions were identified between bacterial and fungal community members. Cheese rind microbial communities represent an experimentally tractable system for defining mechanisms that influence microbial community assembly and function.

  4. Cheese rind communities provide tractable systems for in situ and in vitro studies of microbial diversity

    PubMed Central

    Wolfe, Benjamin E.; Button, Julie E.; Santarelli, Marcela; Dutton, Rachel J.

    2014-01-01

    SUMMARY Tractable microbial communities are needed to bridge the gap between observations of patterns of microbial diversity and mechanisms that can explain these patterns. We developed cheese rinds as model microbial communities by characterizing in situ patterns of diversity and by developing an in vitro system for community reconstruction. Sequencing of 137 different rind communities across 10 countries revealed 24 widely distributed and culturable genera of bacteria and fungi as dominant community members. Reproducible community types formed independent of geographic location of production. Intensive temporal sampling demonstrated that assembly of these communities is highly reproducible. Patterns of community composition and succession observed in situ can be recapitulated in a simple in vitro system. Widespread positive and negative interactions were identified between bacterial and fungal community members. Cheese rind microbial communities represent an experimentally tractable system for defining mechanisms that influence microbial community assembly and function. PMID:25036636

  5. Activated sludge microbial community responses to single-walled carbon nanotubes: community structure does matter.

    PubMed

    Ma, Qiao; Qu, Yuanyuan; Shen, Wenli; Wang, Jingwei; Zhang, Zhaojing; Zhang, Xuwang; Zhou, Hao; Zhou, Jiti

    2015-01-01

    The ecological effects of carbon nanotubes (CNTs) have been a worldwide research focus due to their extensive release and accumulation in environment. Activated sludge acting as an important gathering place will inevitably encounter and interact with CNTs, while the microbial responses have been rarely investigated. Herein, the activated sludges from six wastewater treatment plants were acclimated and treated with single-walled carbon nanotubes (SWCNTs) under identical conditions. Illumina high-throughput sequencing was applied to in-depth analyze microbial changes and results showed SWCNTs differently perturbed the alpha diversity of the six groups (one increase, two decrease, three no change). Furthermore, the microbial community structures were shifted, and specific bacterial performance in each group was different. Since the environmental and operational factors were identical in each group, it could be concluded that microbial responses to SWCNTs were highly depended on the original community structures. PMID:25909735

  6. Microbial community composition of transiently wetted Antarctic Dry Valley soils

    PubMed Central

    Niederberger, Thomas D.; Sohm, Jill A.; Gunderson, Troy E.; Parker, Alexander E.; Tirindelli, Joëlle; Capone, Douglas G.; Carpenter, Edward J.; Cary, Stephen C.

    2015-01-01

    During the summer months, wet (hyporheic) soils associated with ephemeral streams and lake edges in the Antarctic Dry Valleys (DVs) become hotspots of biological activity and are hypothesized to be an important source of carbon and nitrogen for arid DV soils. Recent research in the DV has focused on the geochemistry and microbial ecology of lakes and arid soils, with substantially less information being available on hyporheic soils. Here, we determined the unique properties of hyporheic microbial communities, resolved their relationship to environmental parameters and compared them to archetypal arid DV soils. Generally, pH increased and chlorophyll a concentrations decreased along transects from wet to arid soils (9.0 to ~7.0 for pH and ~0.8 to ~5 μg/cm3 for chlorophyll a, respectively). Soil water content decreased to below ~3% in the arid soils. Community fingerprinting-based principle component analyses revealed that bacterial communities formed distinct clusters specific to arid and wet soils; however, eukaryotic communities that clustered together did not have similar soil moisture content nor did they group together based on sampling location. Collectively, rRNA pyrosequencing indicated a considerably higher abundance of Cyanobacteria in wet soils and a higher abundance of Acidobacterial, Actinobacterial, Deinococcus/Thermus, Bacteroidetes, Firmicutes, Gemmatimonadetes, Nitrospira, and Planctomycetes in arid soils. The two most significant differences at the genus level were Gillisia signatures present in arid soils and chloroplast signatures related to Streptophyta that were common in wet soils. Fungal dominance was observed in arid soils and Viridiplantae were more common in wet soils. This research represents an in-depth characterization of microbial communities inhabiting wet DV soils. Results indicate that the repeated wetting of hyporheic zones has a profound impact on the bacterial and eukaryotic communities inhabiting in these areas. PMID:25674080

  7. Ecotoxicological assessment of soil microbial community tolerance to glyphosate.

    PubMed

    Allegrini, Marco; Zabaloy, María Celina; Gómez, Elena del V

    2015-11-15

    Glyphosate is the most used herbicide worldwide. While contrasting results have been observed related with its impact on soil microbial communities, more studies are necessary to elucidate the potential effects of the herbicide. Differences in tolerance detected by Pollution Induced Community Tolerance (PICT) approach could reflect these effects. The objective of the present study was to assess the tolerance to glyphosate (the active ingredient and a commercial formulation) of contrasting soils with (H) and without (NH) history of exposure. The hypothesis of a higher tolerance in H soils due to a sustained selection pressure on community structure was tested through the PICT approach. Results indicated that tolerance to glyphosate is not consistent with previous history of exposure to the herbicide either for the active ingredient or for a commercial formulation. Soils of H and NH sites were also characterized in order to determine to what extent they differ in their functional diversity and structure of microbial communities. Denaturant Gradient Gel Electrophoresis (DGGE) and Quantitative Real Time PCR (Q-PCR) indicated high similarity of Eubacteria profiles as well as no significant differences in abundance, respectively, between H and NH sites. Community level physiological profiling (CLPP) indicated some differences in respiration of specific sources but functional diversity was very similar as reflected by catabolic evenness (E). These results support PICT assay, which ideally requires soils with differences in their exposure to the contaminant but minor differences in other characteristics. This is, to our knowledge, the first report of PICT approach with glyphosate examining tolerance at soil microbial community level.

  8. Using Artificial Neural Networks to Assess Changes in Microbial Communities

    SciTech Connect

    Brandt, C.C.; Macnaughton, S.; Palumbo, A.V.; Pfiffner, S.M.; Schryver, J.C.

    1999-04-19

    We evaluated artificial neural networks (ANNs) as a technique for assessing changes in soil microbial communities following exposure to metals. We analyzed signature lipid biomarker (SLB) data collected from two soil microcosm experiments using traditional statistical techniques and ANN. Two phases of data analysis were done; pattern recognition and prediction. In general, the ANNs were better able to detect patterns and relationships in the SLB data than were the traditional statistical techniques.

  9. Microbial Community Acquisition of Nutrients from Mineral Surfaces. Final Report

    SciTech Connect

    Hochella, M. F.

    2003-06-03

    Minerals and microbes undergo complex interactions in nature that impact broad aspects of near-surface Earth chemistry. Our primary objective in this project was to gain insight into how microbial species and communities acquire critical but tightly held nutrients residing on or within minerals common in rocks and soils, and to quantitatively study related microbe-mineral interactions including cell adhesion, electron transfer, and siderophore-mineral interaction processes.

  10. Dynamics in microbial communities: Unraveling mechanisms to identify principles

    SciTech Connect

    Konopka, Allan; Lindemann, Stephen R.; Fredrickson, Jim K.

    2015-07-01

    Diversity begets higher order properties such as functional stability and robustness in microbial communities, but principles that inform conceptual (and eventually predictive) models of community dynamics are lacking. Recent work has shown that selection as well as dispersal and drift shape communities, but the mechanistic bases for assembly of communities and the forces that maintain their function in the face of environmental perturbation are not well understood. Conceptually, some interactions among community members could generate endogenous dynamics in composition, even in the absence of environmental changes. These endogenous dynamics are further perturbed by exogenous forcing factors to produce a richer network of community interactions, and it is this “system” that is the basis for higher order community properties. Elucidation of principles that follow from this conceptual model requires identifying the mechanisms that (a) optimize diversity within a community and (b) impart community stability. The network of interactions between organisms can be an important element by providing a buffer against disturbance beyond the effect of functional redundancy, as alternative pathways with different combinations of microbes can be recruited to fulfill specific functions.

  11. Dynamics in microbial communities: unraveling mechanisms to identify principles

    PubMed Central

    Konopka, Allan; Lindemann, Stephen; Fredrickson, Jim

    2015-01-01

    Diversity begets higher-order properties such as functional stability and robustness in microbial communities, but principles that inform conceptual (and eventually predictive) models of community dynamics are lacking. Recent work has shown that selection as well as dispersal and drift shape communities, but the mechanistic bases for assembly of communities and the forces that maintain their function in the face of environmental perturbation are not well understood. Conceptually, some interactions among community members could generate endogenous dynamics in composition, even in the absence of environmental changes. These endogenous dynamics are further perturbed by exogenous forcing factors to produce a richer network of community interactions and it is this ‘system' that is the basis for higher-order community properties. Elucidation of principles that follow from this conceptual model requires identifying the mechanisms that (a) optimize diversity within a community and (b) impart community stability. The network of interactions between organisms can be an important element by providing a buffer against disturbance beyond the effect of functional redundancy, as alternative pathways with different combinations of microbes can be recruited to fulfill specific functions. PMID:25526370

  12. Degradation and impact of phthalate plasticizers on soil microbial communities

    SciTech Connect

    Cartwright, C.D.; Thompson, I.P.; Burns, R.G.

    2000-05-01

    To assess the impact of phthalates on soil microorganisms and to supplement the environmental risk assessment for these xenobiotics, soil was treated with diethyl phthalate (DEP) or di (2-ethyl hexyl) phthalate (DEHP) at 0.1 to 100 mg/g. Bioavailability and membrane disruption were proposed as the characteristics responsible for the observed fate and toxicity of both compounds. Diethyl phthalate was biodegraded rapidly in soil with a half-life of 0.75 d at 20 C, and was not expected to persist in the environment. The DEHP, although biodegradable in aqueous solution, was recalcitrant in soil, because of poor bioavailability and was predicted to account for the majority of phthalate contamination in the environment. Addition of DEP or DEHP to soil at a concentration similar to that detected in nonindustrial environments had no impact on the structural diversity or functional diversity (BIOLOG) of the microbial community. At concentrations representative of a phthalate spill, DEP reduced numbers of both total culturable bacteria and pseudomonads within 1 d. This was due to disruption of membrane fluidity by the lipophilic phthalate, a mechanism not previously attributed to phthalates. However, DEHP had no effect on the microbial community or membrane fluidity, even at 100 mg/g, and was predicted to have no impact on microbial communities in the environment.

  13. Survival of a microbial soil community under Martian conditions

    NASA Astrophysics Data System (ADS)

    Hansen, A. A.; Noernberg, P.; Merrison, J.; Lomstein, B. Aa.; Finster, K. W.

    2003-04-01

    Because of the similarities between Earth and Mars early history the hypothesis was forwarded that Mars is a site where extraterrestrial life might have and/or may still occur(red). Sample-return missions are planned by NASA and ESA to test this hypothesis. The enormous economic costs and the logistic challenges of these missions make earth-based model facilities inevitable. The Mars simulation system at University of Aarhus, Denmark allows microbiological experiments under Mars analogue conditions. Thus detailed studies on the effect of Mars environmental conditions on the survival and the activity of a natural microbial soil community were carried out. Changes in the soil community were determined with a suite of different approaches: 1) total microbial respiration activity was investigated with 14C-glucose, 2) the physiological profile was investigated by the EcoLog-system, 3) colony forming units were determined by plate counts and 4) the microbial diversity on the molecular level was accessed with Denaturing Gradient Gel Electrophoresis. The simulation experiments showed that a part of the bacterial community survived Martian conditions corresponding to 9 Sol. These and future simulation experiments will contribute to our understanding of the possibility for extraterrestrial and terrestrial life on Mars.

  14. Biofouling and microbial communities in membrane distillation and reverse osmosis.

    PubMed

    Zodrow, Katherine R; Bar-Zeev, Edo; Giannetto, Michael J; Elimelech, Menachem

    2014-11-18

    Membrane distillation (MD) is an emerging desalination technology that uses low-grade heat to drive water vapor across a microporous hydrophobic membrane. Currently, little is known about the biofilms that grow on MD membranes. In this study, we use estuarine water collected from Long Island Sound in a bench-scale direct contact MD system to investigate the initial stages of biofilm formation. For comparison, we studied biofilm formation in a bench-scale reverse osmosis (RO) system using the same feedwater. These two membrane desalination systems expose the natural microbial community to vastly different environmental conditions: high temperatures with no hydraulic pressure in MD and low temperature with hydraulic pressure in RO. Over the course of 4 days, we observed a steady decline in bacteria concentration (nearly 2 orders of magnitude) in the MD feed reservoir. Even with this drop in planktonic bacteria, significant biofilm formation was observed. Biofilm morphologies on MD and RO membranes were markedly different. MD membrane biofilms were heterogeneous and contained several colonies, while RO membrane biofilms, although thicker, were a homogeneous mat. Phylogenetic analysis using next-generation sequencing of 16S rDNA showed significant shifts in the microbial communities. Bacteria representing the orders Burkholderiales, Rhodobacterales, and Flavobacteriales were most abundant in the MD biofilms. On the basis of the results, we propose two different regimes for microbial community shifts and biofilm development in RO and MD systems. PMID:25295386

  15. Metaproteomics of complex microbial communities in biogas plants

    PubMed Central

    Heyer, Robert; Kohrs, Fabian; Reichl, Udo; Benndorf, Dirk

    2015-01-01

    Production of biogas from agricultural biomass or organic wastes is an important source of renewable energy. Although thousands of biogas plants (BGPs) are operating in Germany, there is still a significant potential to improve yields, e.g. from fibrous substrates. In addition, process stability should be optimized. Besides evaluating technical measures, improving our understanding of microbial communities involved into the biogas process is considered as key issue to achieve both goals. Microscopic and genetic approaches to analyse community composition provide valuable experimental data, but fail to detect presence of enzymes and overall metabolic activity of microbial communities. Therefore, metaproteomics can significantly contribute to elucidate critical steps in the conversion of biomass to methane as it delivers combined functional and phylogenetic data. Although metaproteomics analyses are challenged by sample impurities, sample complexity and redundant protein identification, and are still limited by the availability of genome sequences, recent studies have shown promising results. In the following, the workflow and potential pitfalls for metaproteomics of samples from full-scale BGP are discussed. In addition, the value of metaproteomics to contribute to the further advancement of microbial ecology is evaluated. Finally, synergistic effects expected when metaproteomics is combined with advanced imaging techniques, metagenomics, metatranscriptomics and metabolomics are addressed. PMID:25874383

  16. Biofouling and microbial communities in membrane distillation and reverse osmosis.

    PubMed

    Zodrow, Katherine R; Bar-Zeev, Edo; Giannetto, Michael J; Elimelech, Menachem

    2014-11-18

    Membrane distillation (MD) is an emerging desalination technology that uses low-grade heat to drive water vapor across a microporous hydrophobic membrane. Currently, little is known about the biofilms that grow on MD membranes. In this study, we use estuarine water collected from Long Island Sound in a bench-scale direct contact MD system to investigate the initial stages of biofilm formation. For comparison, we studied biofilm formation in a bench-scale reverse osmosis (RO) system using the same feedwater. These two membrane desalination systems expose the natural microbial community to vastly different environmental conditions: high temperatures with no hydraulic pressure in MD and low temperature with hydraulic pressure in RO. Over the course of 4 days, we observed a steady decline in bacteria concentration (nearly 2 orders of magnitude) in the MD feed reservoir. Even with this drop in planktonic bacteria, significant biofilm formation was observed. Biofilm morphologies on MD and RO membranes were markedly different. MD membrane biofilms were heterogeneous and contained several colonies, while RO membrane biofilms, although thicker, were a homogeneous mat. Phylogenetic analysis using next-generation sequencing of 16S rDNA showed significant shifts in the microbial communities. Bacteria representing the orders Burkholderiales, Rhodobacterales, and Flavobacteriales were most abundant in the MD biofilms. On the basis of the results, we propose two different regimes for microbial community shifts and biofilm development in RO and MD systems.

  17. Assessing the Unseen Bacterial Diversity in Microbial Communities

    PubMed Central

    Caro-Quintero, Alejandro; Ochman, Howard

    2015-01-01

    For both historical and technical reasons, 16S ribosomal RNA has been the most common molecular marker used to analyze the contents of microbial communities. However, its slow rate of evolution hinders the resolution of closely related bacteria—individual 16S-phylotypes, particularly when clustered at 97% sequence identity, conceal vast amounts of species- and strain-level variation. Protein-coding genes, which evolve more quickly, are useful for differentiating among more recently diverged lineages, but their application is complicated by difficulties in designing low-redundancy primers that amplify homologous regions from distantly related taxa. Given the now-common practice of multiplexing hundreds of samples, adopting new genes usually entails the synthesis of large sets of barcoded primers. To circumvent problems associated with use of protein-coding genes to survey microbial communities, we develop an approach—termed phyloTAGs—that offers an automatic solution for primer design and can be easily adapted to target different taxonomic groups and/or different protein-coding regions. We applied this method to analyze diversity within the gorilla gut microbiome and recovered hundreds of strains that went undetected after deep-sequencing of 16S rDNA amplicons. PhyloTAGs provides a powerful way to recover the fine-level diversity within microbial communities and to study stability and dynamics of bacterial populations. PMID:26615218

  18. Metaproteomics of complex microbial communities in biogas plants.

    PubMed

    Heyer, Robert; Kohrs, Fabian; Reichl, Udo; Benndorf, Dirk

    2015-09-01

    Production of biogas from agricultural biomass or organic wastes is an important source of renewable energy. Although thousands of biogas plants (BGPs) are operating in Germany, there is still a significant potential to improve yields, e.g. from fibrous substrates. In addition, process stability should be optimized. Besides evaluating technical measures, improving our understanding of microbial communities involved into the biogas process is considered as key issue to achieve both goals. Microscopic and genetic approaches to analyse community composition provide valuable experimental data, but fail to detect presence of enzymes and overall metabolic activity of microbial communities. Therefore, metaproteomics can significantly contribute to elucidate critical steps in the conversion of biomass to methane as it delivers combined functional and phylogenetic data. Although metaproteomics analyses are challenged by sample impurities, sample complexity and redundant protein identification, and are still limited by the availability of genome sequences, recent studies have shown promising results. In the following, the workflow and potential pitfalls for metaproteomics of samples from full-scale BGP are discussed. In addition, the value of metaproteomics to contribute to the further advancement of microbial ecology is evaluated. Finally, synergistic effects expected when metaproteomics is combined with advanced imaging techniques, metagenomics, metatranscriptomics and metabolomics are addressed.

  19. Assessing the Unseen Bacterial Diversity in Microbial Communities.

    PubMed

    Caro-Quintero, Alejandro; Ochman, Howard

    2015-12-01

    For both historical and technical reasons, 16S ribosomal RNA has been the most common molecular marker used to analyze the contents of microbial communities. However, its slow rate of evolution hinders the resolution of closely related bacteria--individual 16S-phylotypes, particularly when clustered at 97% sequence identity, conceal vast amounts of species- and strain-level variation. Protein-coding genes, which evolve more quickly, are useful for differentiating among more recently diverged lineages, but their application is complicated by difficulties in designing low-redundancy primers that amplify homologous regions from distantly related taxa. Given the now-common practice of multiplexing hundreds of samples, adopting new genes usually entails the synthesis of large sets of barcoded primers. To circumvent problems associated with use of protein-coding genes to survey microbial communities, we develop an approach--termed phyloTAGs--that offers an automatic solution for primer design and can be easily adapted to target different taxonomic groups and/or different protein-coding regions. We applied this method to analyze diversity within the gorilla gut microbiome and recovered hundreds of strains that went undetected after deep-sequencing of 16S rDNA amplicons. PhyloTAGs provides a powerful way to recover the fine-level diversity within microbial communities and to study stability and dynamics of bacterial populations. PMID:26615218

  20. Linking microbial community structure and microbial processes: An empirical and conceptual overview

    USGS Publications Warehouse

    Bier, R.L.; Bernhardt, E.S.;; Boot, C.M.; Graham, E.B.;; Hall, E.K.; Lennon, J.T.; Nemergut, D.R.; Osborne, B.B.; Ruiz-Gonzalez, C.; Schimel, J.P.; Waldrop, Mark P.; Wallenstein, M.D.

    2015-01-01

    A major goal of microbial ecology is to identify links between microbial community structure and microbial processes. Although this objective seems straightforward, there are conceptual and methodological challenges to designing studies that explicitly evaluate this link. Here, we analyzed literature documenting structure and process responses to manipulations to determine the frequency of structure-process links and whether experimental approaches and techniques influence link detection. We examined nine journals (published 2009–13) and retained 148 experimental studies measuring microbial community structure and processes. Many qualifying papers (112 of 148) documented structure and process responses, but few (38 of 112 papers) reported statistically testing for a link. Of these tested links, 75% were significant and typically used Spearman or Pearson's correlation analysis (68%). No particular approach for characterizing structure or processes was more likely to produce significant links. Process responses were detected earlier on average than responses in structure or both structure and process. Together, our findings suggest that few publications report statistically testing structure-process links. However, when links are tested for they often occur but share few commonalities in the processes or structures that were linked and the techniques used for measuring them.

  1. Anodic microbial community diversity as a predictor of the power output of microbial fuel cells.

    PubMed

    Stratford, James P; Beecroft, Nelli J; Slade, Robert C T; Grüning, André; Avignone-Rossa, Claudio

    2014-03-01

    The relationship between the diversity of mixed-species microbial consortia and their electrogenic potential in the anodes of microbial fuel cells was examined using different diversity measures as predictors. Identical microbial fuel cells were sampled at multiple time-points. Biofilm and suspension communities were analysed by denaturing gradient gel electrophoresis to calculate the number and relative abundance of species. Shannon and Simpson indices and richness were examined for association with power using bivariate and multiple linear regression, with biofilm DNA as an additional variable. In simple bivariate regressions, the correlation of Shannon diversity of the biofilm and power is stronger (r=0.65, p=0.001) than between power and richness (r=0.39, p=0.076), or between power and the Simpson index (r=0.5, p=0.018). Using Shannon diversity and biofilm DNA as predictors of power, a regression model can be constructed (r=0.73, p<0.001). Ecological parameters such as the Shannon index are predictive of the electrogenic potential of microbial communities.

  2. THE EFFECTS OF DIFFERENT SAMPLE CONCENTRATIONS ON THE STRUCTURE OF MICROBIAL COMMUNITIES USING PHOSPHOLIPID FATTY ACID ANALYSIS

    EPA Science Inventory

    Phospholipid fatty acid (PLFA) analysis is a powerful tool for determination of microbial community structures in soils and sediments. However, accurate determination of total microbial biomass and structure of the microbial community may be dependent on the concentration of the...

  3. Gelatin-Methacryloyl Hydrogels: Towards Biofabrication-Based Tissue Repair.

    PubMed

    Klotz, Barbara J; Gawlitta, Debby; Rosenberg, Antoine J W P; Malda, Jos; Melchels, Ferry P W

    2016-05-01

    Research over the past decade on the cell-biomaterial interface has shifted to the third dimension. Besides mimicking the native extracellular environment by 3D cell culture, hydrogels offer the possibility to generate well-defined 3D biofabricated tissue analogs. In this context, gelatin-methacryloyl (gelMA) hydrogels have recently gained increased attention. This interest is sparked by the combination of the inherent bioactivity of gelatin and the physicochemical tailorability of photo-crosslinkable hydrogels. GelMA is a versatile matrix that can be used to engineer tissue analogs ranging from vasculature to cartilage and bone. Convergence of biological and biofabrication approaches is necessary to progress from merely proving cell functionality or construct shape fidelity towards regenerating tissues. GelMA has a critical pioneering role in this process and could be used to accelerate the development of clinically relevant applications. PMID:26867787

  4. Gelatin-Methacryloyl Hydrogels: Towards Biofabrication-Based Tissue Repair.

    PubMed

    Klotz, Barbara J; Gawlitta, Debby; Rosenberg, Antoine J W P; Malda, Jos; Melchels, Ferry P W

    2016-05-01

    Research over the past decade on the cell-biomaterial interface has shifted to the third dimension. Besides mimicking the native extracellular environment by 3D cell culture, hydrogels offer the possibility to generate well-defined 3D biofabricated tissue analogs. In this context, gelatin-methacryloyl (gelMA) hydrogels have recently gained increased attention. This interest is sparked by the combination of the inherent bioactivity of gelatin and the physicochemical tailorability of photo-crosslinkable hydrogels. GelMA is a versatile matrix that can be used to engineer tissue analogs ranging from vasculature to cartilage and bone. Convergence of biological and biofabrication approaches is necessary to progress from merely proving cell functionality or construct shape fidelity towards regenerating tissues. GelMA has a critical pioneering role in this process and could be used to accelerate the development of clinically relevant applications.

  5. Metagenomic analysis of the microbial community in kefir grains.

    PubMed

    Nalbantoglu, Ufuk; Cakar, Atilla; Dogan, Haluk; Abaci, Neslihan; Ustek, Duran; Sayood, Khalid; Can, Handan

    2014-08-01

    Kefir grains as a probiotic have been subject to microbial community identification using culture-dependent and independent methods that target specific strains in the community, or that are based on limited 16S rRNA analysis. We performed whole genome shotgun pyrosequencing using two Turkish Kefir grains. Sequencing generated 3,682,455 high quality reads for a total of ∼1.6 Gbp of data assembled into 6151 contigs with a total length of ∼24 Mbp. Species identification mapped 88.16% and 93.81% of the reads rendering 4 Mpb of assembly that did not show any homology to known bacterial sequences. Identified communities in the two grains showed high concordance where Lactobacillus was the most abundant genus with a mapped abundance of 99.42% and 99.79%. This genus was dominantly represented by three species Lactobacillus kefiranofaciens, Lactobacillus buchneri and Lactobacillus helveticus with a total mapped abundance of 97.63% and 98.74%. We compared and verified our findings with 16S pyrosequencing and model based 16S data analysis. Our results suggest that microbial community profiling using whole genome shotgun data is feasible, can identify novel species data, and has the potential to generate a more accurate and detailed assessment of the underlying bacterial community, especially for low abundance species.

  6. Field Evidence for Magnetite Formation by a Methanogenic Microbial Community

    NASA Astrophysics Data System (ADS)

    Rossbach, S.; Beaver, C. L.; Williams, A.; Atekwana, E. A.; Slater, L. D.; Ntarlagiannis, D.; Lund, A.

    2015-12-01

    The aged, subsurface petroleum spill in Bemidji, Minnesota, has been surveyed with magnetic susceptibility (MS) measurements. High MS values were found in the free-product phase around the fluctuating water table. Although we had hypothesized that high MS values are related to the occurrence of the mineral magnetite resulting from the activity of iron-reducing bacteria, our microbial analysis pointed to the presence of a methanogenic microbial community at the locations and depths of the highest MS values. Here, we report on a more detailed microbial analysis based on high-throughput sequencing of the 16S rRNA gene of sediment samples from four consecutive years. In addition, we provide geochemical data (FeII/FeIII concentrations) to refine our conceptual model of methanogenic hydrocarbon degradation at aged petroleum spills and demonstrate that the microbial induced changes of sediment properties can be monitored with MS. The methanogenic microbial community at the Bemidji site consisted mainly of the syntrophic, hydrocarbon-degrading Smithella and the hydrogenotrophic, methane-generating Methanoregula. There is growing evidence in the literature that not only Bacteria, but also some methanogenic Archaea are able to reduce iron. In fact, a recent study reported that the methanogen Methanosarcina thermophila produced magnetite during the reduction of ferrihydrite in a laboratory experiment when hydrogen was present. Therefore, our finding of high MS values and the presence of magnetite in the methanogenic zone of an aged, subsurface petroleum spill could very well be the first field evidence for magnetite formation during methanogenic hydrocarbon degradation.

  7. Dining local: the microbial diet of a snail that grazes microbial communities is geographically structured.

    PubMed

    O'Rorke, Richard; Cobian, Gerald M; Holland, Brenden S; Price, Melissa R; Costello, Vincent; Amend, Anthony S

    2015-05-01

    Achatinella mustelina is a critically endangered tree snail that subsists entirely by grazing microbes from leaf surfaces of native trees. Little is known about the fundamental aspects of these microbe assemblages: not taxonomic composition, how this varies with host plant or location, nor whether snails selectively consume microbes. To address these questions, we collected 102 snail faecal samples as a proxy for diet, and 102 matched-leaf samples from four locations. We used Illumina amplicon sequencing to determine bacterial and fungal community composition. Microbial community structure was significantly distinct between snail faeces and leaf samples, but the same microbes occurred in both. We conclude that snails are not 'picky' eaters at the microbial level, but graze the surface of whatever plant they are on. In a second experiment, the gut was dissected from non-endangered native tree snails in the same family as Achatinella to confirm that faecal samples reflect gut contents. Over 60% of fungal reads were shared between faeces, gut and leaf samples. Overall, location, sample type (faeces or leaf) and host plant identity all significantly explained the community composition and variation among samples. Understanding the microbial ecology of microbes grazed by tree snails enables effective management when conservation requires captive breeding or field relocation. PMID:25285515

  8. Ohmic resistance affects microbial community and electrochemical kinetics in a multi-anode microbial electrochemical cell

    NASA Astrophysics Data System (ADS)

    Dhar, Bipro Ranjan; Ryu, Hodon; Santo Domingo, Jorge W.; Lee, Hyung-Sool

    2016-11-01

    Multi-anode microbial electrochemical cells (MxCs) are considered as one of the most promising configurations for scale-up of MxCs, but understanding of anode kinetics in multiple anodes is limited in the MxCs. In this study we assessed microbial community and electrochemical kinetic parameters for biofilms on individual anodes in a multi-anode MxC to better comprehend anode fundamentals. Microbial community analysis targeting 16S rRNA Illumina sequencing showed that Geobacter genus was abundant (87%) only on the biofilm anode closest to a reference electrode (low ohmic energy loss) in which current density was the highest among three anodes. In comparison, Geobacter populations were less than 1% for biofilms on other two anodes distant from the reference electrode (high ohmic energy loss), generating small current density. Half-saturation anode potential (EKA) was the lowest at -0.251 to -0.242 V (vs. standard hydrogen electrode) for the closest biofilm anode to the reference electrode, while EKA was as high as -0.134 V for the farthest anode. Our study proves that electric potential of individual anodes changed by ohmic energy loss shifts biofilm communities on individual anodes and consequently influences electron transfer kinetics on each anode in the multi-anode MxC.

  9. Role of vermicompost chemical composition, microbial functional diversity, and fungal community structure in their microbial respiratory response to three pesticides.

    PubMed

    Fernández-Gómez, Manuel J; Nogales, Rogelio; Insam, Heribert; Romero, Esperanza; Goberna, Marta

    2011-10-01

    The relationships between vermicompost chemical features, enzyme activities, community-level physiological profiles (CLPPs), fungal community structures, and its microbial respiratory response to pesticides were investigated. Fungal community structure of vermicomposts produced from damaged tomato fruits (DT), winery wastes (WW), olive-mill waste and biosolids (OB), and cattle manure (CM) were determined by denaturing gradient gel electrophoresis of 18S rDNA. MicroResp™ was used for assessing vermicompost CLPPs and testing the microbial response to metalaxyl, imidacloprid, and diuron. Vermicompost enzyme activities and CLPPs indicated that WW, OB, and DT had higher microbial functional diversity than CM. The microbiota of the former tolerated all three pesticides whereas microbial respiration in CM was negatively affected by metalaxyl and imidacloprid. The response of vermicompost microbiota to the fungicide metalaxyl was correlated to its fungal community structure. The results suggest that vermicomposts with higher microbial functional diversity can be useful for the management of pesticide pollution in agriculture.

  10. Cellular content of biomolecules in sub-seafloor microbial communities

    NASA Astrophysics Data System (ADS)

    Braun, Stefan; Morono, Yuki; Becker, Kevin W.; Hinrichs, Kai-Uwe; Kjeldsen, Kasper U.; Jørgensen, Bo B.; Lomstein, Bente Aa.

    2016-09-01

    Microbial biomolecules, typically from the cell envelope, can provide crucial information about distribution, activity, and adaptations of sub-seafloor microbial communities. However, when cells die these molecules can be preserved in the sediment on timescales that are likely longer than the lifetime of their microbial sources. Here we provide for the first time measurements of the cellular content of biomolecules in sedimentary microbial cells. We separated intact cells from sediment matrices in samples from surficial, deeply buried, organic-rich, and organic-lean marine sediments by density centrifugation. Amino acids, amino sugars, muramic acid, and intact polar lipids were analyzed in both whole sediment and cell extract, and cell separation was optimized and evaluated in terms of purity, separation efficiency, taxonomic resemblance, and compatibility to high-performance liquid chromatography and mass spectrometry for biomolecule analyses. Because cell extracts from density centrifugation still contained considerable amounts of detrital particles and non-cellular biomolecules, we further purified cells from two samples by fluorescence-activated cell sorting (FACS). Cells from these highly purified cell extracts had an average content of amino acids and lipids of 23-28 fg cell-1 and 2.3 fg cell-1, respectively, with an estimated carbon content of 19-24 fg cell-1. In the sediment, the amount of biomolecules associated with vegetative cells was up to 70-fold lower than the total biomolecule content. We find that the cellular content of biomolecules in the marine subsurface is up to four times lower than previous estimates. Our approach will facilitate and improve the use of biomolecules as proxies for microbial abundance in environmental samples and ultimately provide better global estimates of microbial biomass.

  11. Proteogenomic Approaches for the Molecular Characterization of Natural Microbial Communities

    SciTech Connect

    Banfield, Jillian F.; Verberkmoes, Nathan C; Hettich, Robert {Bob} L; Thelen, Michael P.

    2005-01-01

    At the present time we know little about how microbial communities function in their natural habitats. For example, how do microorganisms interact with each other and their physical and chemical surroundings and respond to environmental perturbations? We might begin to answer these questions if we could monitor the ways in which metabolic roles are partitioned amongst members as microbial communities assemble, determine how resources such as carbon, nitrogen, and energy are allocated into metabolic pathways, and understand the mechanisms by which organisms and communities respond to changes in their surroundings. Because many organisms cannot be cultivated, and given that the metabolisms of those growing in monoculture are likely to differ from those of organisms growing as part of consortia, it is vital to develop methods to study microbial communities in situ. Chemoautotrophic biofilms growing in mine tunnels hundreds of meters underground drive pyrite (FeS2) dissolution and acid and metal release, creating habitats that select for a small number of organism types. The geochemical and microbial simplicity of these systems, the significant biomass, and clearly defined biological-inorganic feedbacks make these ecosystem microcosms ideal for development of methods for the study of uncultivated microbial consortia. Our approach begins with the acquisition of genomic data from biofilms that are sampled over time and in different growth conditions. We have demonstrated that it is possible to assemble shotgun sequence data to reveal the gene complement of the dominant community members and to use these data to confidently identify a significant fraction of proteins from the dominant organisms by mass spectrometry (MS)-based proteomics. However, there are technical obstacles currently restricting this type of "proteogenomic" analysis. Composite genomic sequences assembled from environmental data from natural microbial communities do not capture the full range of genetic

  12. Deep-Subterranean Microbial Habitats in the Hishikari Epithermal Gold Mine: Active Thermophilic Microbial Communities and Endolithic Ancient Microbial Relicts.

    NASA Astrophysics Data System (ADS)

    Hirayama, H.; Takai, K.; Inagaki, F.; Horikoshi, K.

    2001-12-01

    Deep subterranean microbial community structures in an epithermal gold-silver deposit, Hishikari gold mine, southern part of Kyusyu Japan, were evaluated through the combined use of enrichment culture methods and culture-independent molecular surveys. The geologic setting of the Hishikari deposit is composed of three lithologies; basement oceanic sediments of the Cretaceous Shimanto Supergroup, Quaternary andesites, and auriferous quartz vein. We studied the drilled core rock of these, and the geothermal hot waters from the basement aquifers collected by means of the dewatering system located at the deepest level in the mining sites. Culture-independent molecular phylogenetic analyses of PCR-amplified ribosomal DNA (rDNA) recovered from drilled cores suggested that the deep-sea oceanic microbial communities were present as ancient indigenous relicts confined in the Shimanto basement. On the other hand, genetic signals of active thermophilic microbial communities, mainly consisting of thermophilic hydrogen-oxidizer within Aquificales, thermophilic methanotroph within g-Proteobacteria and yet-uncultivated bacterium OPB37 within b-Proteobacteria, were detected with these of oceanic relicts from the subterranean geothermal hot aquifers (temp. 70-100ºC). Successful cultivation and FISH analyses strongly supported that these thermophilic lithotrophic microorganisms could be exactly active and they grew using geochemically produced hydrogen and methane gasses as nutrients. Based on these results, the deep-subsurface biosphere occurring in the Hishikari epithermal gold mine was delineated as endolithic ancient microbial relicts and modern habitats raising active lithotrophic thermophiles associated with the geological and geochemical features of the epithermal gold deposit.

  13. Aurelia aurita Ephyrae Reshape a Coastal Microbial Community.

    PubMed

    Zoccarato, Luca; Celussi, Mauro; Pallavicini, Alberto; Fonda Umani, Serena

    2016-01-01

    Over the last two decades, increasing attention has been paid to the impact of jellyfish blooms on marine communities. Aurelia aurita is one of the most studied of the Scyphozoans, and several studies have been carried out to describe its role as a top-down controller within the classical food web. However, little data are available to define the effects of these jellyfish on microbial communities. The aims of this study were to describe the predation impact of A. aurita ephyrae on a natural microplanktonic assemblage, and to determine any reshaping effects on the prokaryote community composition and functioning. Surface coastal water was used to set up a 24-h grazing experiment in microcosms. Samples were collected to determine the variations in prey biomass, heterotrophic carbon production (HCP), extracellular leucine aminopeptidase activity, and grazing pressure. A next-generation sequencing technique was used to investigate biodiversity shifts within the prokaryote and protist communities through the small subunit rRNA tag approach. This study shows that A. aurita ephyrae were responsible for large decreases in the abundances of the more motile microplankton groups, such as tintinnids, Dinophyceae, and aloricate ciliates. Bacillariophyceae and Mediophyceae showed smaller reductions. No evidence of selective predation emerged in the analysis of the community diversity down to the family level. The heterotrophic prokaryote biomass increased significantly (by up to 45%), in parallel with increases in HCP and leucine aminopeptidase activity (40%). Significant modifications were detected in prokaryotic community composition. Some classes of Gammaproteobacteria and Flavobacteriia showed higher relative abundances when exposed to A. aurita ephyrae, while there was a net decrease for Alphaproteobacteria. Overall, this study provides new insight into the effects of A. aurita on microbial communities, underlining their selective predation toward the more motile groups of

  14. Aurelia aurita Ephyrae Reshape a Coastal Microbial Community.

    PubMed

    Zoccarato, Luca; Celussi, Mauro; Pallavicini, Alberto; Fonda Umani, Serena

    2016-01-01

    Over the last two decades, increasing attention has been paid to the impact of jellyfish blooms on marine communities. Aurelia aurita is one of the most studied of the Scyphozoans, and several studies have been carried out to describe its role as a top-down controller within the classical food web. However, little data are available to define the effects of these jellyfish on microbial communities. The aims of this study were to describe the predation impact of A. aurita ephyrae on a natural microplanktonic assemblage, and to determine any reshaping effects on the prokaryote community composition and functioning. Surface coastal water was used to set up a 24-h grazing experiment in microcosms. Samples were collected to determine the variations in prey biomass, heterotrophic carbon production (HCP), extracellular leucine aminopeptidase activity, and grazing pressure. A next-generation sequencing technique was used to investigate biodiversity shifts within the prokaryote and protist communities through the small subunit rRNA tag approach. This study shows that A. aurita ephyrae were responsible for large decreases in the abundances of the more motile microplankton groups, such as tintinnids, Dinophyceae, and aloricate ciliates. Bacillariophyceae and Mediophyceae showed smaller reductions. No evidence of selective predation emerged in the analysis of the community diversity down to the family level. The heterotrophic prokaryote biomass increased significantly (by up to 45%), in parallel with increases in HCP and leucine aminopeptidase activity (40%). Significant modifications were detected in prokaryotic community composition. Some classes of Gammaproteobacteria and Flavobacteriia showed higher relative abundances when exposed to A. aurita ephyrae, while there was a net decrease for Alphaproteobacteria. Overall, this study provides new insight into the effects of A. aurita on microbial communities, underlining their selective predation toward the more motile groups of

  15. Aurelia aurita Ephyrae Reshape a Coastal Microbial Community

    PubMed Central

    Zoccarato, Luca; Celussi, Mauro; Pallavicini, Alberto; Fonda Umani, Serena

    2016-01-01

    Over the last two decades, increasing attention has been paid to the impact of jellyfish blooms on marine communities. Aurelia aurita is one of the most studied of the Scyphozoans, and several studies have been carried out to describe its role as a top-down controller within the classical food web. However, little data are available to define the effects of these jellyfish on microbial communities. The aims of this study were to describe the predation impact of A. aurita ephyrae on a natural microplanktonic assemblage, and to determine any reshaping effects on the prokaryote community composition and functioning. Surface coastal water was used to set up a 24-h grazing experiment in microcosms. Samples were collected to determine the variations in prey biomass, heterotrophic carbon production (HCP), extracellular leucine aminopeptidase activity, and grazing pressure. A next-generation sequencing technique was used to investigate biodiversity shifts within the prokaryote and protist communities through the small subunit rRNA tag approach. This study shows that A. aurita ephyrae were responsible for large decreases in the abundances of the more motile microplankton groups, such as tintinnids, Dinophyceae, and aloricate ciliates. Bacillariophyceae and Mediophyceae showed smaller reductions. No evidence of selective predation emerged in the analysis of the community diversity down to the family level. The heterotrophic prokaryote biomass increased significantly (by up to 45%), in parallel with increases in HCP and leucine aminopeptidase activity (40%). Significant modifications were detected in prokaryotic community composition. Some classes of Gammaproteobacteria and Flavobacteriia showed higher relative abundances when exposed to A. aurita ephyrae, while there was a net decrease for Alphaproteobacteria. Overall, this study provides new insight into the effects of A. aurita on microbial communities, underlining their selective predation toward the more motile groups of

  16. Population dynamics of microbial communities in the zebrafish gut

    NASA Astrophysics Data System (ADS)

    Jemielita, Matthew; Taormina, Michael; Burns, Adam; Hampton, Jennifer; Rolig, Annah; Wiles, Travis; Guillemin, Karen; Parthasarathy, Raghuveer

    2015-03-01

    The vertebrate intestine is home to a diverse microbial community, which plays a crucial role in the development and health of its host. Little is known about the population dynamics and spatial structure of this ecosystem, including mechanisms of growth and interactions between species. We have constructed an experimental model system with which to explore these issues, using initially germ-free larval zebrafish inoculated with defined communities of fluorescently tagged bacteria. Using light sheet fluorescence microscopy combined with computational image analysis we observe and quantify the entire bacterial community of the intestine during the first 24 hours of colonization, during which time the bacterial population grows from tens to tens of thousands of bacteria. We identify both individual bacteria and clusters of bacteria, and quantify the growth rate and spatial distribution of these distinct subpopulations. We find that clusters of bacteria grow considerably faster than individuals and are located in specific regions of the intestine. Imaging colonization by two species reveals spatial segregation and competition. These data and their analysis highlight the importance of spatial organization in the establishment of gut microbial communities, and can provide inputs to physical models of real-world ecological dynamics.

  17. Distinctive Tropical Forest Variants Have Unique Soil Microbial Communities, But Not Always Low Microbial Diversity

    PubMed Central

    Tripathi, Binu M.; Song, Woojin; Slik, J. W. F.; Sukri, Rahayu S.; Jaafar, Salwana; Dong, Ke; Adams, Jonathan M.

    2016-01-01

    There has been little study of whether different variants of tropical rainforest have distinct soil microbial communities and levels of diversity. We compared bacterial and fungal community composition and diversity between primary mixed dipterocarp, secondary mixed dipterocarp, white sand heath, inland heath, and peat swamp forests in Brunei Darussalam, Northwest Borneo by analyzing Illumina Miseq sequence data of 16S rRNA gene and ITS1 region. We hypothesized that white sand heath, inland heath and peat swamp forests would show lower microbial diversity and relatively distinct microbial communities (compared to MDF primary and secondary forests) due to their distinctive environments. We found that soil properties together with bacterial and fungal communities varied significantly between forest types. Alpha and beta-diversity of bacteria was highest in secondary dipterocarp and white sand heath forests. Also, bacterial alpha diversity was strongly structured by pH, adding another instance of this widespread pattern in nature. The alpha diversity of fungi was equally high in all forest types except peat swamp forest, although fungal beta-diversity was highest in primary and secondary mixed dipterocarp forests. The relative abundance of ectomycorrhizal (EcM) fungi varied significantly between forest types, with highest relative abundance observed in MDF primary forest. Overall, our results suggest that the soil bacterial and fungal communities in these forest types are to a certain extent predictable and structured by soil properties, but that diversity is not determined by how distinctive the conditions are. This contrasts with the diversity patterns seen in rainforest trees, where distinctive soil conditions have consistently lower tree diversity. PMID:27092105

  18. Soil microbial communities respond differently to three chemically defined polyphenols.

    PubMed

    Schmidt, Michael A; Kreinberg, Allison J; Gonzalez, Javier M; Halvorson, Jonathan J; French, Elizabeth; Bollmann, Annette; Hagerman, Ann E

    2013-11-01

    High molecular weight polyphenols (e.g. tannins) that enter the soil may affect microbial populations, by serving as substrates for microbial respiration or by selecting for certain microbes. In this study we examined how three phenolic compounds that represent some environmentally widespread tannins or their constituent functional groups were respired by soil microorganisms and how the compounds affected the abundance and diversity of soil bacteria and archaea, including ammonia oxidizers. An acidic, silt loam soil from a pine forest was incubated for two weeks with the monomeric phenol methyl gallate, the small polyphenol epigallocatechin gallate, or the large polyphenol oenothein B. Respiration of the polyphenols during the incubation was measured using the Microresp™ system. After incubation, metabolic diversity was determined by community level physiological profiling (CLPP), and genetic diversity was determined using denaturing gradient gel electrophoresis (DGGE) analysis on DNA extracted from the soil samples. Total microbial populations and ammonia-oxidizing populations were measured using real time quantitative polymerase chain reaction (qPCR). Methyl gallate was respired more efficiently than the higher molecular weight tannins but not as efficiently as glucose. Methyl gallate and epigallocatechin gallate selected for genetically or physiologically unique populations compared to glucose. None of the polyphenols supported microbial growth, and none of the polyphenols affected ammonia-oxidizing bacterial populations or ammonia-oxidizing archaea. Additional studies using both a wider range of polyphenols and a wider range of soils and environments are needed to elucidate the role of polyphenols in determining soil microbiological diversity.

  19. Microbial community succession in alkaline, saline bauxite residue: a cross-refinery study

    NASA Astrophysics Data System (ADS)

    Santini, T.; Malcolm, L. I.; Tyson, G. W.; Warren, L. A.

    2015-12-01

    Bauxite residue, a byproduct of the Bayer process for alumina refining, is an alkaline, saline tailings material that is generally considered to be inhospitable to microbial life. In situ remediation strategies promote soil formation in bauxite residue by enhancing leaching of saline, alkaline pore water, and through incorporation of amendments to boost organic matter content, decrease pH, and improve physical structure. The amelioration of chemical and physical conditions in bauxite residue is assumed to support diversification of microbial communities from narrow, poorly functioning microbial communities towards diverse, well-functioning communities. This study aimed to characterise microbial communities in fresh and remediated bauxite residues from refineries worldwide, to identify (a) whether initial microbial communities differed between refineries; (b) major environmental controls on microbial community composition; and (c) whether remediation successfully shifts the composition of microbial communities in bauxite residue towards those found in reference (desired endpoint) soils. Samples were collected from 16 refineries and characterised using 16S amplicon sequencing to examine microbial community composition and structure, in conjunction with physicochemical analyses. Initial microbial community composition was similar across refineries but partitioned into two major groups. Microbial community composition changes slowly over time and indicates that alkalinity and salinity inhibit diversification. Microbially-based strategies for in situ remediation should consider the initial microbial community composition and whether the pre-treatment of chemical properties would optimise subsequent bioremediation outcomes. During in situ remediation, microbial communities become more diverse and develop wider functional capacity, indicating progression towards communities more commonly observed in natural grassland and forest soils.

  20. 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

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

    PubMed

    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

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

    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.

  3. Sediment microbial communities in Great Boiling Spring are controlled by temperature and distinct from water communities.

    PubMed

    Cole, Jessica K; Peacock, Joseph P; Dodsworth, Jeremy A; Williams, Amanda J; Thompson, Daniel B; Dong, Hailiang; Wu, Geng; Hedlund, Brian P

    2013-04-01

    Great Boiling Spring is a large, circumneutral, geothermal spring in the US Great Basin. Twelve samples were collected from water and four different sediment sites on four different dates. Microbial community composition and diversity were assessed by PCR amplification of a portion of the small subunit rRNA gene using a universal primer set followed by pyrosequencing of the V8 region. Analysis of 164 178 quality-filtered pyrotags clearly distinguished sediment and water microbial communities. Water communities were extremely uneven and dominated by the bacterium Thermocrinis. Sediment microbial communities grouped according to temperature and sampling location, with a strong, negative, linear relationship between temperature and richness at all taxonomic levels. Two sediment locations, Site A (87-80 °C) and Site B (79 °C), were predominantly composed of single phylotypes of the bacterial lineage GAL35 (\\[pmacr]=36.1%), Aeropyrum (\\[pmacr]=16.6%), the archaeal lineage pSL4 (\\[pmacr]=15.9%), the archaeal lineage NAG1 (\\[pmacr]=10.6%) and Thermocrinis (\\[pmacr]=7.6%). The ammonia-oxidizing archaeon 'Candidatus Nitrosocaldus' was relatively abundant in all sediment samples <82 °C (\\[pmacr]=9.51%), delineating the upper temperature limit for chemolithotrophic ammonia oxidation in this spring. This study underscores the distinctness of water and sediment communities in GBS and the importance of temperature in driving microbial diversity, composition and, ultimately, the functioning of biogeochemical cycles.

  4. Microbial Community Structure and Enzyme Activities in Semiarid Agricultural Soils

    NASA Astrophysics Data System (ADS)

    Acosta-Martinez, V. A.; Zobeck, T. M.; Gill, T. E.; Kennedy, A. C.

    2002-12-01

    The effect of agricultural management practices on the microbial community structure and enzyme activities of semiarid soils of different textures in the Southern High Plains of Texas were investigated. The soils (sandy clay loam, fine sandy loam and loam) were under continuous cotton (Gossypium hirsutum L.) or in rotations with peanut (Arachis hypogaea L.), sorghum (Sorghum bicolor L.) or wheat (Triticum aestivum L.), and had different water management (irrigated or dryland) and tillage (conservation or conventional). Microbial community structure was investigated using fatty acid methyl ester (FAME) analysis by gas chromatography and enzyme activities, involved in C, N, P and S cycling of soils, were measured (mg product released per kg soil per h). The activities of b-glucosidase, b-glucosaminidase, alkaline phosphatase, and arylsulfatase were significantly (P<0.05) increased in soils under cotton rotated with sorghum or wheat, and due to conservation tillage in comparison to continuous cotton under conventional tillage. Principal component analysis showed FAME profiles of these soils separated distinctly along PC1 (20 %) and PC2 (13 %) due to their differences in soil texture and management. No significant differences were detected in FAME profiles due to management practices for the same soils in this sampling period. Enzyme activities provide early indications of the benefits in microbial populations and activities and soil organic matter under crop rotations and conservation tillage in comparison to the typical practices in semiarid regions of continuous cotton and conventional tillage.

  5. Carbon use efficiency of microbial communities: stoichiometry, methodology and modelling.

    PubMed

    Sinsabaugh, Robert L; Manzoni, Stefano; Moorhead, Daryl L; Richter, Andreas

    2013-07-01

    Carbon use efficiency (CUE) is a fundamental parameter for ecological models based on the physiology of microorganisms. CUE determines energy and material flows to higher trophic levels, conversion of plant-produced carbon into microbial products and rates of ecosystem carbon storage. Thermodynamic calculations support a maximum CUE value of ~ 0.60 (CUE max). Kinetic and stoichiometric constraints on microbial growth suggest that CUE in multi-resource limited natural systems should approach ~ 0.3 (CUE max /2). However, the mean CUE values reported for aquatic and terrestrial ecosystems differ by twofold (~ 0.26 vs. ~ 0.55) because the methods used to estimate CUE in aquatic and terrestrial systems generally differ and soil estimates are less likely to capture the full maintenance costs of community metabolism given the difficulty of measurements in water-limited environments. Moreover, many simulation models lack adequate representation of energy spilling pathways and stoichiometric constraints on metabolism, which can also lead to overestimates of CUE. We recommend that broad-scale models use a CUE value of 0.30, unless there is evidence for lower values as a result of pervasive nutrient limitations. Ecosystem models operating at finer scales should consider resource composition, stoichiometric constraints and biomass composition, as well as environmental drivers, to predict the CUE of microbial communities.

  6. Microbial Community and Chemical Characteristics of Swine Manure during Maturation.

    PubMed

    Trabue, Steven L; Kerr, Brian J; Bearson, Bradley L; Hur, Manhoi; Parkin, Timothy; Wurtele, Eve S; Ziemer, Cherrie J

    2016-07-01

    Swine diet formulations have the potential to lower animal emissions, including odor and ammonia (NH). The purpose of this study was to determine the impact of manure storage duration on manure chemical and microbial properties in swine feeding trials. Three groups of 12 pigs were fed a standard corn-soybean meal diet over a 13-wk period. Urine and feces were collected at each feeding and transferred to 12 manure storage tanks. Manure chemical characteristics and headspace gas concentrations were monitored for NH, hydrogen sulfide (HS), volatile fatty acids, phenols, and indoles. Microbial analysis of the stored manure included plate counts, community structure (denaturing gradient gel electrophoresis), and metabolic function (Biolog). All odorants in manure and headspace gas concentrations were significantly ( < 0.01) correlated for length of storage using quadratic equations, peaking after Week 5 for all headspace gases and most manure chemical characteristics. Microbial community structure and metabolic utilization patterns showed continued change throughout the 13-wk trial. Denaturing gradient gel electrophoresis species diversity patterns declined significantly ( < 0.01) with time as substrate utilization declined for sugars and certain amino acids, but functionality increased in the utilization of short chain fatty acids as levels of these compounds increased in manure. Studies to assess the effect of swine diet formulations on manure emissions for odor need to be conducted for a minimum of 5 wk. Efforts to determine the impact of diets on greenhouse gas emissions will require longer periods of study (>13 wk). PMID:27380061

  7. Influence of seawater intrusion on microbial communities in groundwater.

    PubMed

    Unno, Tatsuya; Kim, Jungman; Kim, Yumi; Nguyen, Son G; Guevarra, Robin B; Kim, Gee Pyo; Lee, Ji-Hoon; Sadowsky, Michael J

    2015-11-01

    Groundwater is the sole source of potable water on Jeju Island in the Republic of (South) Korea. Groundwater is also used for irrigation and industrial purposes, and it is severely impacted by seawater intrusion in coastal areas. Consequently, monitoring the intrusion of seawater into groundwater on Jeju is very important for health and environmental reasons. A number of studies have used hydrological models to predict the deterioration of groundwater quality caused by seawater intrusion. However, there is conflicting evidence of intrusion due to complicated environmental influences on groundwater quality. Here we investigated the use of next generation sequencing (NGS)-based microbial community analysis as a way to monitor groundwater quality and detect seawater intrusion. Pristine groundwater, groundwater from three coastal areas, and seawater were compared. Analysis of the distribution of bacterial species clearly indicated that the high and low salinity groundwater differed significantly with respect to microbial composition. While members of the family Parvularculaceae were only identified in high salinity water samples, a greater percentage of the phylum Actinobacteria was predominantly observed in pristine groundwater. In addition, we identified 48 shared operational taxonomic units (OTUs) with seawater, among which the high salinity groundwater sample shared a greater number of bacterial species with seawater (6.7%). In contrast, other groundwater samples shared less than 0.5%. Our results suggest that NGS-based microbial community analysis of groundwater may be a useful tool for monitoring groundwater quality and detect seawater intrusion. This technology may also provide additional insights in understanding hydrological dynamics.

  8. Biosafety assessment of GFP transplastomic tobacco to rhizosphere microbial community.

    PubMed

    Lv, Yueping; Cai, Hongsheng; Yu, Jianping; Liu, Jiali; Liu, Qingguo; Guo, Changhong

    2014-05-01

    Green fluorescent protein (GFP) is one of the most widely studied and exploited proteins in biochemistry, and has many applications as a marker, especially in plant transformation system. Although a number of studies have been conducted to assess the toxify of this protein to specific organisms, little is known about GFP on rhizosphere microbial community, which is regarded as good indicator for environmental risk assessment. Chloroplast genetic engineering has shown superiority over traditional nuclear genetic engineering, and has been used in many aspects of plant genetic engineering. High levels of chloroplast-based protein accumulation make this technology as an ideal strategy to evaluate biosafety of transgenes. In the present study, the effects of field-released GFP transplastomic tobacco (Nicotiana tabacum) on rhizosphere microbes over a whole growth cycle were investigated by using both culture-dependent and culture-independent methods. Compared to wild-type control, transplastomic tobacco had no significant influence on the microbial population at the seedling, vegetative, flowering and senescing stages. However, developmental stages had more influence than ecotypes (GFP-transformed and wild-type). This was confirmed by colony forming unit, Biolog Eco(TM) and PCR-DGGE analysis. Thus, these results suggest chloroplast transformation with a GFP reporter gene has no significant influence on rhizosphere microbial community, and will be potential platform for plant biotechnology in future. PMID:24429672

  9. DETERMINATION OF MICROBIAL COMMUNITY STRUCTURE IN UNTREATED WASTEWATER FROM DIFFERENT GEOGRAPHIC LOCALES

    EPA Science Inventory

    Microbial sewage communities consist of a combination of human faecal microorganisms and urban infrastructure-derived microbes originating from infiltration of rainwater and stormwater inputs. Together these different sources of microbial diversity form a unique population struc...

  10. COMPETITIVE METAGENOMIC DNA HYBRIDIZATION IDENTIFIES HOST-SPECIFIC GENETIC MARKERS IN HUMAN FECAL MICROBIAL COMMUNITIES

    EPA Science Inventory

    Although recent technological advances in DNA sequencing and computational biology now allow scientists to compare entire microbial genomes, the use of these approaches to discern key genomic differences between natural microbial communities remains prohibitively expensive for mo...

  11. Electrosynthesis of Commodity Chemicals by an Autotrophic Microbial Community

    PubMed Central

    Marshall, Christopher W.; Ross, Daniel E.; Fichot, Erin B.; Norman, R. Sean

    2012-01-01

    A microbial community originating from brewery waste produced methane, acetate, and hydrogen when selected on a granular graphite cathode poised at −590 mV versus the standard hydrogen electrode (SHE) with CO2 as the only carbon source. This is the first report on the simultaneous electrosynthesis of these commodity chemicals and the first description of electroacetogenesis by a microbial community. Deep sequencing of the active community 16S rRNA revealed a dynamic microbial community composed of an invariant Archaea population of Methanobacterium spp. and a shifting Bacteria population. Acetobacterium spp. were the most abundant Bacteria on the cathode when acetogenesis dominated. Methane was generally the dominant product with rates increasing from <1 to 7 mM day−1 (per cathode liquid volume) and was concomitantly produced with acetate and hydrogen. Acetogenesis increased to >4 mM day−1 (accumulated to 28.5 mM over 12 days), and methanogenesis ceased following the addition of 2-bromoethanesulfonic acid. Traces of hydrogen accumulated during initial selection and subsequently accelerated to >11 mM day−1 (versus 0.045 mM day−1 abiotic production). The hypothesis of electrosynthetic biocatalysis occurring at the microbe-electrode interface was supported by a catalytic wave (midpoint potential of −460 mV versus SHE) in cyclic voltammetry scans of the biocathode, the lack of redox active components in the medium, and the generation of comparatively high amounts of products (even after medium exchange). In addition, the volumetric production rates of these three commodity chemicals are marked improvements for electrosynthesis, advancing the process toward economic feasibility. PMID:23001672

  12. Microbial Communities of the Okinawa Backarc Basin Subvent Biosphere

    NASA Astrophysics Data System (ADS)

    Brandt, L. D.; House, C. H.

    2014-12-01

    IODP Expedition 331 to the Okinawa backarc basin provided an opportunity to study the microbial stratigraphy within the sediments surrounding a hydrothermal vent. The Okinawa backarc basin is a sedimented region of the seafloor located on a continental margin, and also hosts a hydrothermal network within the subsurface. Site C0014 within the Iheya North hydrothermal field is located 450 m east of the active vent and has a surface temperature of 5°C with no evidence of hydrothermal alteration within the top 10 m. Temperature increases with depth at an estimated rate of 3°C/m and transitions from non-hydrothermal margin sediments to a hydrothermally altered regime below 10 m. Site C0014 is a unique location to study changes in microbial communities with depth, as the hydrothermal system generates a thermally and geochemically restrictive subvent biosphere. In this study, we utilized deep 16S rRNA sequencing of DNA from IODP Expedition 331 Site C0014 sediment horizons in order to assess diversity throughout the sediment column as well as determine the potential limits of the biosphere. Analysis of the amplicon data suggests that Archaea represent a significant proportion of the indigenous community throughout the top 15 m of sediment, where Archaea then abruptly disappear. Furthermore, a deeper classification of Archaeal sequences suggests a transition from a mesophilic community to a potentially thermophilic one, where there is an increasingly stronger signal of Miscellaneous Crenarchaeotic Group (MCG) followed by Terrestrial Hot Spring Crenarchaeotic Group (THSCG). Additionally, there are several horizons in which methanotrophy is likely supported, indicated by peaks in anaerobic methanotrophic Archaea. The cessation of Archaea as well as Chloroflexi, a common marine subsurface bacterial phylum, at approximately 15 meters below seafloor (mbsf) is suggestive of a potential boundary within Site C0014 in which the environmental conditions have become too restrictive

  13. Sequencing and beyond: integrating molecular ‘omics for microbial community profiling

    PubMed Central

    Franzosa, Eric A.; Hsu, Tiffany; Sirota-Madi, Alexandra; Shafquat, Afrah; Abu-Ali, Galeb; Morgan, Xochitl C.

    2016-01-01

    High-throughput DNA sequencing has proven invaluable for investigating diverse environmental and host-associated microbial communities. In this Review, we discuss emerging strategies for microbial community analysis that complement and expand traditional metagenomic profiling. These include novel DNA sequencing strategies for identifying strain-level microbial variation and community temporal dynamics; measuring additional multi'omic data types that better capture community functional activity, such as transcriptomics, proteomics, and metabolomics; and combining multiple forms of multi'omic data in an integrated framework. We highlight studies in which the multi'omics approach has led to improved mechanistic models of microbial community structure and function. PMID:25915636

  14. Utilization and control of ecological interactions in polymicrobial infections and community-based microbial cell factories

    PubMed Central

    Wigneswaran, Vinoth; Amador, Cristina Isabel; Jelsbak, Lotte; Sternberg, Claus; Jelsbak, Lars

    2016-01-01

    Microbial activities are most often shaped by interactions between co-existing microbes within mixed-species communities. Dissection of the molecular mechanisms of species interactions within communities is a central issue in microbial ecology, and our ability to engineer and control microbial communities depends, to a large extent, on our knowledge of these interactions. This review highlights the recent advances regarding molecular characterization of microbe-microbe interactions that modulate community structure, activity, and stability, and aims to illustrate how these findings have helped us reach an engineering-level understanding of microbial communities in relation to both human health and industrial biotechnology. PMID:27092245

  15. Redox-driven regulation of microbial community morphogenesis

    PubMed Central

    Okegbe, Chinweike; Price-Whelan, Alexa; Dietrich, Lars E.P.

    2014-01-01

    During growth on surfaces, diverse microbial communities display topographies with captivating patterns. The quality and quantity of matrix excreted by resident cells play major roles in determining community architecture. Two current publications indicate that the cellular redox state and respiratory activity are important parameters affecting matrix output in the divergent bacteria Pseudomonas aeruginosa and Bacillus subtilis. These and related studies have identified regulatory proteins with the potential to respond to changes in redox state and respiratory electron transport and modulate the activity of the signal transduction pathways that control matrix production. These developments hint at the critical mechanistic links between environmental sensing and community behavior, and provide an exciting new context within which to interpret the molecular details of biofilm structure determination. PMID:24607644

  16. Groundwater Microbial Communities, Part 9: Ecological and Hydrological Interactions

    SciTech Connect

    McKinley, James P.; Fredrickson, Jim K.; Colwell, Frederick S.

    2005-12-31

    Microbial communities in aquifers consist of diverse interactive individuals that break down complex organic matter for metabolic energy. Microbes are adapted to function over a large range in environmental conditions, ranging from freezing to boiling acidic to alkaline. They can use oxygen as a reducible metabolite during organic carbon oxidation, but, since oxygen is rapidly depleted in subsurface environments, different groups of organisms may also rely on other compounds such as reducible metals, or on fermentation. Community members are interdependent, but compete for resources, and communities often have predominant groups that rely on recognizable chemical pathways, such as sulfate reduction. The predominant group varies spatially and temporally as the available nutrients change or are depleted.

  17. Effects of pesticides on community composition and activity of sediment microbes--responses at various levels of microbial community organization.

    PubMed

    Widenfalk, Anneli; Bertilsson, Stefan; Sundh, Ingvar; Goedkoop, Willem

    2008-04-01

    A freshwater sediment was exposed to the pesticides captan, glyphosate, isoproturon, and pirimicarb at environmentally relevant and high concentrations. Effects on sediment microorganisms were studied by measuring bacterial activity, fungal and total microbial biomass as community-level endpoints. At the sub-community level, microbial community structure was analysed (PLFA composition and bacterial 16S rRNA genotyping, T-RFLP). Community-level endpoints were not affected by pesticide exposure. At lower levels of microbial community organization, however, molecular methods revealed treatment-induced changes in community composition. Captan and glyphosate exposure caused significant shifts in bacterial community composition (as T-RFLP) at environmentally relevant concentrations. Furthermore, differences in microbial community composition among pesticide treatments were found, indicating that test compounds and exposure concentrations induced multidirectional shifts. Our study showed that community-level end points failed to detect these changes, underpinning the need for application of molecular techniques in aquatic ecotoxicology.

  18. Cheese rind microbial communities: diversity, composition and origin.

    PubMed

    Irlinger, Françoise; Layec, Séverine; Hélinck, Sandra; Dugat-Bony, Eric

    2015-01-01

    Cheese rinds host a specific microbiota composed of both prokaryotes (such as Actinobacteria, Firmicutes and Proteobacteria) and eukaryotes (primarily yeasts and moulds). By combining modern molecular biology tools with conventional, culture-based techniques, it has now become possible to create a catalogue of the biodiversity that inhabits this special environment. Here, we review the microbial genera detected on the cheese surface and highlight the previously unsuspected importance of non-inoculated microflora--raising the question of the latter's environmental sources and their role in shaping microbial communities. There is now a clear need to revise the current view of the cheese rind ecosystem (i.e. that of a well-defined, perfectly controlled ecosystem). Inclusion of these new findings should enable us to better understand the cheese-making process.

  19. Biochar affects soil organic matter cycling and microbial functions but does not alter microbial community structure in a paddy soil.

    PubMed

    Tian, Jing; Wang, Jingyuan; Dippold, Michaela; Gao, Yang; Blagodatskaya, Evgenia; Kuzyakov, Yakov

    2016-06-15

    The application of biochar (BC) in conjunction with mineral fertilizers is one of the most promising management practices recommended to improve soil quality. However, the interactive mechanisms of BC and mineral fertilizer addition affecting microbial communities and functions associated with soil organic matter (SOM) cycling are poorly understood. We investigated the SOM in physical and chemical fractions, microbial community structure (using phospholipid fatty acid analysis, PLFA) and functions (by analyzing enzymes involved in C and N cycling and Biolog) in a 6-year field experiment with BC and NPK amendment. BC application increased total soil C and particulate organic C for 47.4-50.4% and 63.7-74.6%, respectively. The effects of BC on the microbial community and C-cycling enzymes were dependent on fertilization. Addition of BC alone did not change the microbial community compared with the control, but altered the microbial community structure in conjunction with NPK fertilization. SOM fractions accounted for 55% of the variance in the PLFA-related microbial community structure. The particulate organic N explained the largest variation in the microbial community structure. Microbial metabolic activity strongly increased after BC addition, particularly the utilization of amino acids and amines due to an increase in the activity of proteolytic (l-leucine aminopeptidase) enzymes. These results indicate that microorganisms start to mine N from the SOM to compensate for high C:N ratios after BC application, which consequently accelerate cycling of stable N. Concluding, BC in combination with NPK fertilizer application strongly affected microbial community composition and functions, which consequently influenced SOM cycling. PMID:26974565

  20. Biochar affects soil organic matter cycling and microbial functions but does not alter microbial community structure in a paddy soil.

    PubMed

    Tian, Jing; Wang, Jingyuan; Dippold, Michaela; Gao, Yang; Blagodatskaya, Evgenia; Kuzyakov, Yakov

    2016-06-15

    The application of biochar (BC) in conjunction with mineral fertilizers is one of the most promising management practices recommended to improve soil quality. However, the interactive mechanisms of BC and mineral fertilizer addition affecting microbial communities and functions associated with soil organic matter (SOM) cycling are poorly understood. We investigated the SOM in physical and chemical fractions, microbial community structure (using phospholipid fatty acid analysis, PLFA) and functions (by analyzing enzymes involved in C and N cycling and Biolog) in a 6-year field experiment with BC and NPK amendment. BC application increased total soil C and particulate organic C for 47.4-50.4% and 63.7-74.6%, respectively. The effects of BC on the microbial community and C-cycling enzymes were dependent on fertilization. Addition of BC alone did not change the microbial community compared with the control, but altered the microbial community structure in conjunction with NPK fertilization. SOM fractions accounted for 55% of the variance in the PLFA-related microbial community structure. The particulate organic N explained the largest variation in the microbial community structure. Microbial metabolic activity strongly increased after BC addition, particularly the utilization of amino acids and amines due to an increase in the activity of proteolytic (l-leucine aminopeptidase) enzymes. These results indicate that microorganisms start to mine N from the SOM to compensate for high C:N ratios after BC application, which consequently accelerate cycling of stable N. Concluding, BC in combination with NPK fertilizer application strongly affected microbial community composition and functions, which consequently influenced SOM cycling.

  1. The Role of Soil Organic Matter, Nutrients, and Microbial Community Structure on the Performance of Microbial Fuel Cells

    NASA Astrophysics Data System (ADS)

    Rooney-Varga, J. N.; Dunaj, S. J.; Vallino, J. J.; Hines, M. E.; Gay, M.; Kobyljanec, C.

    2011-12-01

    Microbial fuel cells (MFCs) offer the potential for generating electricity, mitigating greenhouse gas emissions, and bioremediating pollutants through utilization of a plentiful, natural, and renewable resource: soil organic carbon. In the current study, we analyzed microbial community structure, MFC performance, and soil characteristics in different microhabitats (bulk soil, anode, and cathode) within MFCs constructed from agricultural or forest soils in order to determine how soil type and microbial dynamics influence MFC performance. MFCs were constructed with soils from agricultural and hardwood forest sites at Harvard Forest (Petersham, MA). The bulk soil characteristics were analyzed, including polyphenols, short chain fatty acids, total organic C and N, abiotic macronutrients, N and P mineralization rates, CO2 respiration rates, and MFC power output. Microbial community structure of the anodes, cathodes, and bulk soils was determined with molecular fingerprinting methods, which included terminal restriction length polymorphism (T-RFLP) analysis and 16S rRNA gene sequencing analysis. Our results indicated that MFCs constructed from agricultural soil had power output about 17 times that of forest soil-based MFCs and respiration rates about 10 times higher than forest soil MFCs. Agricultural soil MFCs had lower C:N ratios, polyphenol content, and acetate concentrations than forest soil MFCs, suggesting that active agricultural MFC microbial communities were supported by higher quality organic carbon. Microbial community profile data indicate that the microbial communities at the anode of the high power MFCs were less diverse than in low power MFCs and were dominated by Deltaproteobacteria, Geobacter, and, to a lesser extent, Clostridia, while low-power MFC anode communities were dominated by Clostridia. These data suggest that the presence of organic carbon substrate (acetate) was not the major limiting factor in selecting for highly electrogenic microbial

  2. Interspecies interactions are an integral determinant of microbial community dynamics.

    PubMed

    Aziz, Fatma A A; Suzuki, Kenshi; Ohtaki, Akihiro; Sagegami, Keita; Hirai, Hidetaka; Seno, Jun; Mizuno, Naoko; Inuzuka, Yuma; Saito, Yasuhisa; Tashiro, Yosuke; Hiraishi, Akira; Futamata, Hiroyuki

    2015-01-01

    This study investigated the factors that determine the dynamics of bacterial communities in a complex system using multidisciplinary methods. Since natural and engineered microbial ecosystems are too complex to study, six types of synthetic microbial ecosystems (SMEs) were constructed under chemostat conditions with phenol as the sole carbon and energy source. Two to four phenol-degrading, phylogenetically and physiologically different bacterial strains were used in each SME. Phylogeny was based on the nucleotide sequence of 16S rRNA genes, while physiologic traits were based on kinetic and growth parameters on phenol. Two indices, J parameter and "interspecies interaction," were compared to predict which strain would become dominant in an SME. The J parameter was calculated from kinetic and growth parameters. On the other hand, "interspecies interaction," a new index proposed in this study, was evaluated by measuring the specific growth activity, which was determined on the basis of relative growth of a strain with or without the supernatant prepared from other bacterial cultures. Population densities of strains used in SMEs were enumerated by real-time quantitative PCR (qPCR) targeting the gene encoding the large subunit of phenol hydroxylase and were compared to predictions made from J parameter and interspecies interaction calculations. In 4 of 6 SEMs tested the final dominant strain shown by real-time qPCR analyses coincided with the strain predicted by both the J parameter and the interspecies interaction. However, in SMEII-2 and SMEII-3 the final dominant Variovorax strains coincided with prediction of the interspecies interaction but not the J parameter. These results demonstrate that the effects of interspecies interactions within microbial communities contribute to determining the dynamics of the microbial ecosystem.

  3. Interspecies interactions are an integral determinant of microbial community dynamics.

    PubMed

    Aziz, Fatma A A; Suzuki, Kenshi; Ohtaki, Akihiro; Sagegami, Keita; Hirai, Hidetaka; Seno, Jun; Mizuno, Naoko; Inuzuka, Yuma; Saito, Yasuhisa; Tashiro, Yosuke; Hiraishi, Akira; Futamata, Hiroyuki

    2015-01-01

    This study investigated the factors that determine the dynamics of bacterial communities in a complex system using multidisciplinary methods. Since natural and engineered microbial ecosystems are too complex to study, six types of synthetic microbial ecosystems (SMEs) were constructed under chemostat conditions with phenol as the sole carbon and energy source. Two to four phenol-degrading, phylogenetically and physiologically different bacterial strains were used in each SME. Phylogeny was based on the nucleotide sequence of 16S rRNA genes, while physiologic traits were based on kinetic and growth parameters on phenol. Two indices, J parameter and "interspecies interaction," were compared to predict which strain would become dominant in an SME. The J parameter was calculated from kinetic and growth parameters. On the other hand, "interspecies interaction," a new index proposed in this study, was evaluated by measuring the specific growth activity, which was determined on the basis of relative growth of a strain with or without the supernatant prepared from other bacterial cultures. Population densities of strains used in SMEs were enumerated by real-time quantitative PCR (qPCR) targeting the gene encoding the large subunit of phenol hydroxylase and were compared to predictions made from J parameter and interspecies interaction calculations. In 4 of 6 SEMs tested the final dominant strain shown by real-time qPCR analyses coincided with the strain predicted by both the J parameter and the interspecies interaction. However, in SMEII-2 and SMEII-3 the final dominant Variovorax strains coincided with prediction of the interspecies interaction but not the J parameter. These results demonstrate that the effects of interspecies interactions within microbial communities contribute to determining the dynamics of the microbial ecosystem. PMID:26539177

  4. Interspecies interactions are an integral determinant of microbial community dynamics

    PubMed Central

    Aziz, Fatma A. A.; Suzuki, Kenshi; Ohtaki, Akihiro; Sagegami, Keita; Hirai, Hidetaka; Seno, Jun; Mizuno, Naoko; Inuzuka, Yuma; Saito, Yasuhisa; Tashiro, Yosuke; Hiraishi, Akira; Futamata, Hiroyuki

    2015-01-01

    This study investigated the factors that determine the dynamics of bacterial communities in a complex system using multidisciplinary methods. Since natural and engineered microbial ecosystems are too complex to study, six types of synthetic microbial ecosystems (SMEs) were constructed under chemostat conditions with phenol as the sole carbon and energy source. Two to four phenol-degrading, phylogenetically and physiologically different bacterial strains were used in each SME. Phylogeny was based on the nucleotide sequence of 16S rRNA genes, while physiologic traits were based on kinetic and growth parameters on phenol. Two indices, J parameter and “interspecies interaction,” were compared to predict which strain would become dominant in an SME. The J parameter was calculated from kinetic and growth parameters. On the other hand, “interspecies interaction,” a new index proposed in this study, was evaluated by measuring the specific growth activity, which was determined on the basis of relative growth of a strain with or without the supernatant prepared from other bacterial cultures. Population densities of strains used in SMEs were enumerated by real-time quantitative PCR (qPCR) targeting the gene encoding the large subunit of phenol hydroxylase and were compared to predictions made from J parameter and interspecies interaction calculations. In 4 of 6 SEMs tested the final dominant strain shown by real-time qPCR analyses coincided with the strain predicted by both the J parameter and the interspecies interaction. However, in SMEII-2 and SMEII-3 the final dominant Variovorax strains coincided with prediction of the interspecies interaction but not the J parameter. These results demonstrate that the effects of interspecies interactions within microbial communities contribute to determining the dynamics of the microbial ecosystem. PMID:26539177

  5. Experimental warming effects on the microbial community of a temperate mountain forest soil.

    PubMed

    Schindlbacher, A; Rodler, A; Kuffner, M; Kitzler, B; Sessitsch, A; Zechmeister-Boltenstern, S

    2011-07-01

    Soil microbial communities mediate the decomposition of soil organic matter (SOM). The amount of carbon (C) that is respired leaves the soil as CO(2) (soil respiration) and causes one of the greatest fluxes in the global carbon cycle. How soil microbial communities will respond to global warming, however, is not well understood. To elucidate the effect of warming on the microbial community we analyzed soil from the soil warming experiment Achenkirch, Austria. Soil of a mature spruce forest was warmed by 4 °C during snow-free seasons since 2004. Repeated soil sampling from control and warmed plots took place from 2008 until 2010. We monitored microbial biomass C and nitrogen (N). Microbial community composition was assessed by phospholipid fatty acid analysis (PLFA) and by quantitative real time polymerase chain reaction (qPCR) of ribosomal RNA genes. Microbial metabolic activity was estimated by soil respiration to biomass ratios and RNA to DNA ratios. Soil warming did not affect microbial biomass, nor did warming affect the abundances of most microbial groups. Warming significantly enhanced microbial metabolic activity in terms of soil respiration per amount of microbial biomass C. Microbial stress biomarkers were elevated in warmed plots. In summary, the 4 °C increase in soil temperature during the snow-free season had no influence on microbial community composition and biomass but strongly increased microbial metabolic activity and hence reduced carbon use efficiency.

  6. Resolution of natural microbial community dynamics by community fingerprinting, flow cytometry, and trend interpretation analysis.

    PubMed

    Bombach, Petra; Hübschmann, Thomas; Fetzer, Ingo; Kleinsteuber, Sabine; Geyer, Roland; Harms, Hauke; Müller, Susann

    2011-01-01

    Natural microbial communities generally have an unknown structure and composition because of their still not yet cultivable members. Therefore, understanding the relationships among the bacterial members, prediction of their behaviour, and controlling their functions are difficult and often only partly successful endeavours to date. This study aims to test a new idea that allows to follow community dynamics on the basis of a simple concept. Terminal restriction fragment length polymorphism (T-RFLP) analysis of bacterial 16S ribosomal RNA genes was used to describe a community profile that we define as composition of a community. Flow cytometry and analysis of DNA contents and forward scatter characteristics of the single cells were used to describe a community profile, which we define as structure of a community. Both approaches were brought together by a non-metric multidimensional scaling (n-MDS) for trend interpretation of changes in the complex community data sets. This was done on the basis of a graphical evaluation of the cytometric data, leading to the newly developed Dalmatian plot tool, which gave an unexpected insight into the dynamics of the unknown bacterial members of the investigated natural microbial community. The approach presented here was compared with other techniques described in the literature. The microbial community investigated in this study was obtained from a BTEX contaminated anoxic aquifer. The indigenous bacteria were allowed to colonise in situ microcosms consisting of activated carbon. These microcosms were amended with benzene and one of the electron acceptors nitrate, sulphate or ferric iron to stimulate microbial growth. The data obtained in this study indicated that the composition (via T-RFLP) and structure (via flow cytometry) of the natural bacterial community were influenced by the hydro-geochemical conditions in the test site, but also by the supplied electron acceptors, which led to distinct shifts in relative abundances of

  7. Microbial community structures differentiated in a single-chamber air-cathode microbial fuel cell fueled with rice straw hydrolysate

    PubMed Central

    2014-01-01

    Background The microbial fuel cell represents a novel technology to simultaneously generate electric power and treat wastewater. Both pure organic matter and real wastewater can be used as fuel to generate electric power and the substrate type can influence the microbial community structure. In the present study, rice straw, an important feedstock source in the world, was used as fuel after pretreatment with diluted acid method for a microbial fuel cell to obtain electric power. Moreover, the microbial community structures of anodic and cathodic biofilm and planktonic culturewere analyzed and compared to reveal the effect of niche on microbial community structure. Results The microbial fuel cell produced a maximum power density of 137.6 ± 15.5 mW/m2 at a COD concentration of 400 mg/L, which was further increased to 293.33 ± 7.89 mW/m2 through adjusting the electrolyte conductivity from 5.6 mS/cm to 17 mS/cm. Microbial community analysis showed reduction of the microbial diversities of the anodic biofilm and planktonic culture, whereas diversity of the cathodic biofilm was increased. Planktonic microbial communities were clustered closer to the anodic microbial communities compared to the cathodic biofilm. The differentiation in microbial community structure of the samples was caused by minor portion of the genus. The three samples shared the same predominant phylum of Proteobacteria. The abundance of exoelectrogenic genus was increased with Desulfobulbus as the shared most abundant genus; while the most abundant exoelectrogenic genus of Clostridium in the inoculum was reduced. Sulfate reducing bacteria accounted for large relative abundance in all the samples, whereas the relative abundance varied in different samples. Conclusion The results demonstrated that rice straw hydrolysate can be used as fuel for microbial fuel cells; microbial community structure differentiated depending on niches after microbial fuel cell operation; exoelectrogens were

  8. 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.

  9. Adaptation of Aquatic Microbial Communities to Quaternary Ammonium Compounds

    PubMed Central

    Ventullo, Roy M.; Larson, Robert J.

    1986-01-01

    The effects of long-chain (C12 to C18) quaternary ammonium compounds (QACs) on the density, heterotrophic activity, and biodegradation capabilities of heterotrophic bacteria were examined in situ in a lake ecosystem. Monoalkyl and dialkyl substituted QACs were tested over a range of concentrations (0.001 to 10 mg/liter) in both acute (3 h) and chronic (21 day) exposures. In general, none of the QACs tested had significant adverse effects on bacterial densities in either acute or chronic studies. However, significant decreases in bacterial heterotrophic activity were noted in acute studies at QAC concentrations from 0.1 to 10 mg/liter. Chronic exposure of lake microbial communities to a specific monoalkyl QAC resulted in an adaptive response and recovery of heterotrophic activity. No-observable-effect level in the adapted populations was >10 mg/liter. Chronic exposure also resulted in significant increases in the number and activity of bacteria capable of biodegrading the material. The increase in biodegradation capability was observed at low (microgram per liter) concentrations which are approximately the same as realistic environmental levels. In general, our studies indicated that exposure of lake microbial communities to QACs results in the development of adapted communities which are less sensitive to potential toxic effects and more active in the biodegradation of these materials. PMID:16346991

  10. Electricity generation from food wastes and microbial community structure in microbial fuel cells.

    PubMed

    Jia, Jianna; Tang, Yu; Liu, Bingfeng; Wu, Di; Ren, Nanqi; Xing, Defeng

    2013-09-01

    Microbial fuel cell (MFC) was studied as an alternate and a novel way to dispose food wastes (FWs) in a waste-to-energy form. Different organic loading rate obviously affected the performance of MFCs fed with FWs. The maximum power density of ~18 W/m(3) (~556 mW/m(2)) was obtained at COD of 3200±400 mg/L and the maximum coulombic efficiency (CE) was ~27.0% at COD of 4900±350 mg/L. The maximum removals of COD, total carbohydrate (TC) and total nitrogen (TN) were ~86.4%, ~95.9% and ~16.1%, respectively. Microbial community analysis using 454 pyrosequencing of 16S rRNA gene demonstrated the combination of the dominant genera of the exoelectrogenic Geobacter and fermentative Bacteroides effectively drove highly efficient and reliable MFC systems with functions of organic matters degradation and electricity generation.

  11. Microbial community structure accompanied with electricity production in a constructed wetland plant microbial fuel cell.

    PubMed

    Lu, Lu; Xing, Defeng; Ren, Zhiyong Jason

    2015-11-01

    This study reveals the complex structure of bacterial and archaeal communities associated with a Canna indica plant microbial fuel cell (PMFC) and its electricity production. The PMFC produced a maximum current of 105 mA/m(2) by utilizing rhizodeposits as the sole electron donor without any external nutrient or buffer supplements, which demonstrates the feasibility of PMFCs in practical oligotrophic conditions with low solution conductivity. The microbial diversity was significantly higher in the PMFC than non-plant controls or sediment-only controls, and pyrosequencing and clone library reveal that rhizodeposits conversion to current were carried out by syntrophic interactions between fermentative bacteria (e.g., Anaerolineaceae) and electrochemically active bacteria (e.g., Geobacter). Denitrifying bacteria and acetotrophic methanogens play a minor role in organics degradation, but abundant hydrogenotrophic methanogens and thermophilic archaea are likely main electron donor competitors.

  12. The viability of native microbial communities in martian environment (model)

    NASA Astrophysics Data System (ADS)

    Vorobyova, Elena; Cheptcov, Vladimir; Pavlov, Anatolyi; Vdovina, Mariya; Lomasov, Vladimir

    For today the important direction in astrobiology is the experimental simulation of extraterrestrial habitats with the assessment of survivability of microorganisms in such conditions. A new task is to investigate the resistance of native microbial ecosystems which are well adapted to the environment and develop unique protection mechanisms that enable to ensure biosphere formation. The purpose of this research was to study the viability of microorganisms as well as viability of native microbial communities of arid soils and permafrost under stress conditions simulating space environment and martian regolith environment, estimation of duration of Earth like life in the Martian soil. The experimental data obtained give the proof of the preservation of high population density, biodiversity, and reproduction activity under favorable conditions in the Earth analogues of Martian soil - arid soils (Deserts of Israel and Morocco) and permafrost (East Siberia, Antarctica), after the treatment of samples by ionizing radiation dose up to 100 kGy at the pressure of 1 torr, temperature (- 50oC) and in the presence of perchlorate (5%). It was shown that in simulated conditions close to the parameters of the Martian regolith, the diversity of natural bacterial communities was not decreased, and in some cases the activation of some bacterial populations occurred in situ. Our results allow suggesting that microbial communities like those that inhabit arid and permafrost ecosystems on the Earth, can survive at least 500 thousand years under conditions of near surface layer of the Martian regolith. Extrapolation of the data according to the intensity of ionizing radiation to the open space conditions allows evaluating the potential lifespan of cells inside meteorites as 20-50 thousand years at least. In this work new experimental data have been obtained confirming the occurrence of liquid water and the formation of wet soil layer due to sublimation of ice when the temperature of the

  13. Using Artificial Neural Networks to Assess Microbial Communities

    SciTech Connect

    Almeida, J.S.; Brand, C.C.; Palumbo, A.V.; Pfiffner, S.M.; Schryver, J.C.

    1998-09-08

    We are evaluating artificial neural networks (ANNs) as tools for assessing changes in soil microbial communities following exposure to metals. We analyzed signature lipid biomarker data collected from two soil microcosm experiments using an autoassociative ANN. In one experiment, the microcosms were exposed to O, 100, or 250 ppm of metals, and in the other experiment the microcosms were exposed to O or 500 ppm of metals. The ANNs were able to distinguish between microcosms exposed and not exposed to metals in both experiments.

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

    PubMed Central

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

    2015-01-01

    The succession of microbial community structure and function is a central ecological topic, as microbes drive the Earth’s biogeochemical cycles. To elucidate the response and mechanistic underpinnings of soil microbial community structure and metabolic potential relevant to natural forest succession, we compared soil microbial communities from three adjacent natural forests: a coniferous forest (CF), a mixed broadleaf forest (MBF) and a deciduous broadleaf forest (DBF) on Shennongjia Mountain in central China. In contrary to plant communities, the microbial taxonomic diversity of the DBF was significantly (P < 0.05) higher than those of CF and MBF, rendering their microbial community compositions markedly different. Consistently, microbial functional diversity was also highest in the DBF. Furthermore, a network analysis of microbial carbon and nitrogen cycling genes showed the network for the DBF samples was relatively large and tight, revealing strong couplings between microbes. Soil temperature, reflective of climate regimes, was important in shaping microbial communities at both taxonomic and functional gene levels. As a first glimpse of both the taxonomic and functional compositions of soil microbial communities, our results suggest that microbial community structure and function potentials will be altered by future environmental changes, which have implications for forest succession. PMID:25943705

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

    PubMed

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

    2015-01-01

    The succession of microbial community structure and function is a central ecological topic, as microbes drive the Earth's biogeochemical cycles. To elucidate the response and mechanistic underpinnings of soil microbial community structure and metabolic potential relevant to natural forest succession, we compared soil microbial communities from three adjacent natural forests: a coniferous forest (CF), a mixed broadleaf forest (MBF) and a deciduous broadleaf forest (DBF) on Shennongjia Mountain in central China. In contrary to plant communities, the microbial taxonomic diversity of the DBF was significantly (P < 0.05) higher than those of CF and MBF, rendering their microbial community compositions markedly different. Consistently, microbial functional diversity was also highest in the DBF. Furthermore, a network analysis of microbial carbon and nitrogen cycling genes showed the network for the DBF samples was relatively large and tight, revealing strong couplings between microbes. Soil temperature, reflective of climate regimes, was important in shaping microbial communities at both taxonomic and functional gene levels. As a first glimpse of both the taxonomic and functional compositions of soil microbial communities, our results suggest that microbial community structure and function potentials will be altered by future environmental changes, which have implications for forest succession. PMID:25943705

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

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

    The succession of microbial community structure and function is a central ecological topic, as microbes drive the Earth’s biogeochemical cycles. To elucidate the response and mechanistic underpinnings of soil microbial community structure and metabolic potential relevant to natural forest succession, we compared soil microbial communities from three adjacent natural forests: a coniferous forest (CF), a mixed broadleaf forest (MBF) and a deciduous broadleaf forest (DBF) on Shennongjia Mountain in central China. In contrary to plant communities, the microbial taxonomic diversity of the DBF was significantly (P < 0.05) higher than those of CF and MBF, rendering their microbial community compositions markedly different. Consistently, microbial functional diversity was also highest in the DBF. Furthermore, a network analysis of microbial carbon and nitrogen cycling genes showed the network for the DBF samples was relatively large and tight, revealing strong couplings between microbes. Soil temperature, reflective of climate regimes, was important in shaping microbial communities at both taxonomic and functional gene levels. As a first glimpse of both the taxonomic and functional compositions of soil microbial communities, our results suggest that microbial community structure and function potentials will be altered by future environmental changes, which have implications for forest succession.

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

    PubMed

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

    2015-05-06

    The succession of microbial community structure and function is a central ecological topic, as microbes drive the Earth's biogeochemical cycles. To elucidate the response and mechanistic underpinnings of soil microbial community structure and metabolic potential relevant to natural forest succession, we compared soil microbial communities from three adjacent natural forests: a coniferous forest (CF), a mixed broadleaf forest (MBF) and a deciduous broadleaf forest (DBF) on Shennongjia Mountain in central China. In contrary to plant communities, the microbial taxonomic diversity of the DBF was significantly (P < 0.05) higher than those of CF and MBF, rendering their microbial community compositions markedly different. Consistently, microbial functional diversity was also highest in the DBF. Furthermore, a network analysis of microbial carbon and nitrogen cycling genes showed the network for the DBF samples was relatively large and tight, revealing strong couplings between microbes. Soil temperature, reflective of climate regimes, was important in shaping microbial communities at both taxonomic and functional gene levels. As a first glimpse of both the taxonomic and functional compositions of soil microbial communities, our results suggest that microbial community structure and function potentials will be altered by future environmental changes, which have implications for forest succession.

  18. EFFECT OF TEMPERATURE ON THE C ISOTOPIC VALUE OF MICROBIAL LIPIDS APPLIED TO DETERMINE C USAGE IN MICROBIAL COMMUNITIES

    EPA Science Inventory

    The combination of compound specific stable isotopic analysis with phospholipid fatty acid (PLFAS) analysis is useful in determining the source of organic carbon used by groups of a microbial community. Determination of the effect of certain environmental parameters is important ...

  19. Evaluation of estuarine sediment communities exposed to pentachlorophenol on the basis of microbial community parameters

    SciTech Connect

    Kurtz, J.C.; Barkay, T.; Devereux, R.; Jonas, R.B.

    1995-12-31

    The effect of pentachlorophenol (PCP), a widely-used wood preserving agent, on natural sediment microbial communities was examined to determine if methods for assessing changes in microbial community structure and function were useful for studies of environmental impact. Current impact assessments predict the potential for environmental impact from data on contaminant bioavailability (partitioning to interstitial water), or on toxicity to benthic infauna, epibenthic species or species that obtain nutrients from the sediment or water column. Since sediment microorganisms are important as terminal oxidizers of organic compounds, providing essential nutrients for support of higher trophic levels, study of the impact of contaminants on microbial communities may add an important dimension to assessments. Estuarine sediment slurries in field-validated microcosms were exposed to PCP at environmentally relevant concentrations (1.0 and 5.0 ug{center_dot}ml{sup {minus}1}). Results indicated that microcosm-contained communities were metabolically impacted by PCP treatment (reduction of sulfate reduction rates to 17.6% of untreated controls, reduction of dark CO{sub 2} fixation rates less pronounced). The structure of sulfate reducing bacterial (SRB) communities changed in response to PCP exposure as revealed by specific 16S ribosomal RNA probes, although direct counts of epifluorescent-stained bacteria remained stable. When compared to untreated microcosms, SRB groups capable of incomplete oxidation of substrates increased in relative abundance when exposed to 5 ug{center_dot}ml{sup {minus}1} PCP, while groups capable of complete oxidation declined in relative abundance. Impacts on the microbial community were produced by PCP exposure and could be detected by the methods employed; therefore, this approach may provide a means for detecting adverse impacts on sediment communities where many recalcitrant pollutants persist.

  20. Systems modeling approaches for microbial community studies: from metagenomics to inference of the community structure

    PubMed Central

    Hanemaaijer, Mark; Röling, Wilfred F. M.; Olivier, Brett G.; Khandelwal, Ruchir A.; Teusink, Bas; Bruggeman, Frank J.

    2015-01-01

    Microbial communities play important roles in health, industrial applications and earth's ecosystems. With current molecular techniques we can characterize these systems in unprecedented detail. However, such methods provide little mechanistic insight into how the genetic properties and the dynamic couplings between individual microorganisms give rise to their dynamic activities. Neither do they give insight into what we call “the community state”, that is the fluxes and concentrations of nutrients within the community. This knowledge is a prerequisite for rational control and intervention in microbial communities. Therefore, the inference of the community structure from experimental data is a major current challenge. We will argue that this inference problem requires mathematical models that can integrate heterogeneous experimental data with existing knowledge. We propose that two types of models are needed. Firstly, mathematical models that integrate existing genomic, physiological, and physicochemical information with metagenomics data so as to maximize information content and predictive power. This can be achieved with the use of constraint-based genome-scale stoichiometric modeling of community metabolism which is ideally suited for this purpose. Next, we propose a simpler coarse-grained model, which is tailored to solve the inference problem from the experimental data. This model unambiguously relate to the more detailed genome-scale stoichiometric models which act as heterogeneous data integrators. The simpler inference models are, in our opinion, key to understanding microbial ecosystems, yet until now, have received remarkably little attention. This has led to the situation where the modeling of microbial communities, using only genome-scale models is currently more a computational, theoretical exercise than a method useful to the experimentalist. PMID:25852671

  1. Estimating and mapping ecological processes influencing microbial community assembly

    SciTech Connect

    Stegen, James C.; Lin, Xueju; Fredrickson, Jim K.; Konopka, Allan E.

    2015-05-01

    Ecological community assembly is governed by a combination of (i) selection resulting from among-taxa differences in performance; (ii) dispersal resulting from organismal movement; and (iii) ecological drift resulting from stochastic changes in population sizes. The relative importance and nature of these processes can vary across environments. Selection can be homogeneous or variable, and while dispersal is a rate, we conceptualize extreme dispersal rates as two categories; dispersal limitation results from limited exchange of organisms among communities, and homogenizing dispersal results from high levels of organism exchange. To estimate the influence and spatial variation of each process we extend a recently developed statistical framework, use a simulation model to evaluate the accuracy of the extended framework, and use the framework to examine subsurface microbial communities over two geologic formations. For each subsurface community we estimate the degree to which it is influenced by homogeneous selection, variable selection, dispersal limitation, and homogenizing dispersal. Our analyses revealed that the relative influences of these ecological processes vary substantially across communities even within a geologic formation. We further identify environmental and spatial features associated with each ecological process, which allowed mapping of spatial variation in ecological-process-influences. The resulting maps provide a new lens through which ecological systems can be understood; in the subsurface system investigated here they revealed that the influence of variable selection was associated with the rate at which redox conditions change with subsurface depth.

  2. Phenotypic plasticity in heterotrophic marine microbial communities in continuous cultures.

    PubMed

    Beier, Sara; Rivers, Adam R; Moran, Mary Ann; Obernosterer, Ingrid

    2015-05-01

    Phenotypic plasticity (PP) is the development of alternate phenotypes of a given taxon as an adaptation to environmental conditions. Methodological limitations have restricted the quantification of PP to the measurement of a few traits in single organisms. We used metatranscriptomic libraries to overcome these challenges and estimate PP using the expressed genes of multiple heterotrophic organisms as a proxy for traits in a microbial community. The metatranscriptomes captured the expression response of natural marine bacterial communities grown on differing carbon resource regimes in continuous cultures. We found that taxa with different magnitudes of PP coexisted in the same cultures, and that members of the order Rhodobacterales had the highest levels of PP. In agreement with previous studies, our results suggest that continuous culturing may have specifically selected for taxa featuring a rather high range of PP. On average, PP and abundance changes within a taxon contributed equally to the organism's change in functional gene abundance, implying that both PP and abundance mediated observed differences in community function. However, not all functional changes due to PP were directly reflected in the bulk community functional response: gene expression changes in individual taxa due to PP were partly masked by counterbalanced expression of the same gene in other taxa. This observation demonstrates that PP had a stabilizing effect on a community's functional response to environmental change.

  3. Estimating and mapping ecological processes influencing microbial community assembly

    PubMed Central

    Stegen, James C.; Lin, Xueju; Fredrickson, Jim K.; Konopka, Allan E.

    2015-01-01

    Ecological community assembly is governed by a combination of (i) selection resulting from among-taxa differences in performance; (ii) dispersal resulting from organismal movement; and (iii) ecological drift resulting from stochastic changes in population sizes. The relative importance and nature of these processes can vary across environments. Selection can be homogeneous or variable, and while dispersal is a rate, we conceptualize extreme dispersal rates as two categories; dispersal limitation results from limited exchange of organisms among communities, and homogenizing dispersal results from high levels of organism exchange. To estimate the influence and spatial variation of each process we extend a recently developed statistical framework, use a simulation model to evaluate the accuracy of the extended framework, and use the framework to examine subsurface microbial communities over two geologic formations. For each subsurface community we estimate the degree to which it is influenced by homogeneous selection, variable selection, dispersal limitation, and homogenizing dispersal. Our analyses revealed that the relative influences of these ecological processes vary substantially across communities even within a geologic formation. We further identify environmental and spatial features associated with each ecological process, which allowed mapping of spatial variation in ecological-process-influences. The resulting maps provide a new lens through which ecological systems can be understood; in the subsurface system investigated here they revealed that the influence of variable selection was associated with the rate at which redox conditions change with subsurface depth. PMID:25983725

  4. Estimating and mapping ecological processes influencing microbial community assembly

    DOE PAGES

    Stegen, James C.; Lin, Xueju; Fredrickson, Jim K.; Konopka, Allan E.

    2015-05-01

    Ecological community assembly is governed by a combination of (i) selection resulting from among-taxa differences in performance; (ii) dispersal resulting from organismal movement; and (iii) ecological drift resulting from stochastic changes in population sizes. The relative importance and nature of these processes can vary across environments. Selection can be homogeneous or variable, and while dispersal is a rate, we conceptualize extreme dispersal rates as two categories; dispersal limitation results from limited exchange of organisms among communities, and homogenizing dispersal results from high levels of organism exchange. To estimate the influence and spatial variation of each process we extend a recentlymore » developed statistical framework, use a simulation model to evaluate the accuracy of the extended framework, and use the framework to examine subsurface microbial communities over two geologic formations. For each subsurface community we estimate the degree to which it is influenced by homogeneous selection, variable selection, dispersal limitation, and homogenizing dispersal. Our analyses revealed that the relative influences of these ecological processes vary substantially across communities even within a geologic formation. We further identify environmental and spatial features associated with each ecological process, which allowed mapping of spatial variation in ecological-process-influences. The resulting maps provide a new lens through which ecological systems can be understood; in the subsurface system investigated here they revealed that the influence of variable selection was associated with the rate at which redox conditions change with subsurface depth.« less

  5. Trajectories of Microbial Community Function in Response to Accelerated Remediation of Subsurface Metal Contaminants

    SciTech Connect

    Firestone, Mary

    2015-01-14

    Objectives of proposed research were to; Determine if the trajectories of microbial community composition and function following organic carbon amendment can be related to, and predicted by, key environmental determinants; Assess the relative importance of the characteristics of the indigenous microbial community, sediment, groundwater, and concentration of organic carbon amendment as the major determinants of microbial community functional response and bioremediation capacity; and Provide a fundamental understanding of the microbial community ecology underlying subsurface metal remediation requisite to successful application of accelerated remediation and long-term stewardship of DOE-IFC sites.

  6. Inter-species interconnections in acid mine drainage microbial communities

    PubMed Central

    Comolli, Luis R.; Banfield, Jill F.

    2014-01-01

    Metagenomic studies are revolutionizing our understanding of microbes in the biosphere. They have uncovered numerous proteins of unknown function in tens of essentially unstudied lineages that lack cultivated representatives. Notably, few of these microorganisms have been visualized, and even fewer have been described ultra-structurally in their essentially intact, physiologically relevant states. Here, we present cryogenic transmission electron microscope (cryo-TEM) 2D images and 3D tomographic datasets for archaeal species from natural acid mine drainage (AMD) microbial communities. Ultrastructural findings indicate the importance of microbial interconnectedness via a range of mechanisms, including direct cytoplasmic bridges and pervasive pili. The data also suggest a variety of biological structures associated with cell-cell interfaces that lack explanation. Some may play roles in inter-species interactions. Interdependences amongst the archaea may have confounded prior isolation efforts. Overall, the findings underline knowledge gaps related to archaeal cell components and highlight the likely importance of co-evolution in shaping microbial lineages. PMID:25120533

  7. Nitrogen Cycling Potential of a Grassland Litter Microbial Community.

    PubMed

    Nelson, Michaeline B; Berlemont, Renaud; Martiny, Adam C; Martiny, Jennifer B H

    2015-10-01

    Because microorganisms have different abilities to utilize nitrogen (N) through various assimilatory and dissimilatory pathways, microbial composition and diversity likely influence N cycling in an ecosystem. Terrestrial plant litter decomposition is often limited by N availability; however, little is known about the microorganisms involved in litter N cycling. In this study, we used metagenomics to characterize the potential N utilization of microbial communities in grassland plant litter. The frequencies of sequences associated with eight N cycling pathways differed by several orders of magnitude. Within a pathway, the distributions of these sequences among bacterial orders differed greatly. Many orders within the Actinobacteria and Proteobacteria appeared to be N cycling generalists, carrying genes from most (five or six) of the pathways. In contrast, orders from the Bacteroidetes were more specialized and carried genes for fewer (two or three) pathways. We also investigated how the abundance and composition of microbial N cycling genes differed over time and in response to two global change manipulations (drought and N addition). For many pathways, the abundance and composition of N cycling taxa differed over time, apparently reflecting precipitation patterns. In contrast to temporal variability, simulated global change had minor effects on N cycling potential. Overall, this study provides a blueprint for the genetic potential of N cycle processes in plant litter and a baseline for comparisons to other ecosystems.

  8. Nitrogen Cycling Potential of a Grassland Litter Microbial Community

    PubMed Central

    Berlemont, Renaud; Martiny, Adam C.; Martiny, Jennifer B. H.

    2015-01-01

    Because microorganisms have different abilities to utilize nitrogen (N) through various assimilatory and dissimilatory pathways, microbial composition and diversity likely influence N cycling in an ecosystem. Terrestrial plant litter decomposition is often limited by N availability; however, little is known about the microorganisms involved in litter N cycling. In this study, we used metagenomics to characterize the potential N utilization of microbial communities in grassland plant litter. The frequencies of sequences associated with eight N cycling pathways differed by several orders of magnitude. Within a pathway, the distributions of these sequences among bacterial orders differed greatly. Many orders within the Actinobacteria and Proteobacteria appeared to be N cycling generalists, carrying genes from most (five or six) of the pathways. In contrast, orders from the Bacteroidetes were more specialized and carried genes for fewer (two or three) pathways. We also investigated how the abundance and composition of microbial N cycling genes differed over time and in response to two global change manipulations (drought and N addition). For many pathways, the abundance and composition of N cycling taxa differed over time, apparently reflecting precipitation patterns. In contrast to temporal variability, simulated global change had minor effects on N cycling potential. Overall, this study provides a blueprint for the genetic potential of N cycle processes in plant litter and a baseline for comparisons to other ecosystems. PMID:26231641

  9. Hypolithic and soil microbial community assembly along an aridity gradient in the Namib Desert.

    PubMed

    Stomeo, Francesca; Valverde, Angel; Pointing, Stephen B; McKay, Christopher P; Warren-Rhodes, Kimberley A; Tuffin, Marla I; Seely, Mary; Cowan, Don A

    2013-03-01

    The Namib Desert is considered the oldest desert in the world and hyperarid for the last 5 million years. However, the environmental buffering provided by quartz and other translucent rocks supports extensive hypolithic microbial communities. In this study, open soil and hypolithic microbial communities have been investigated along an East-West transect characterized by an inverse fog-rainfall gradient. Multivariate analysis showed that structurally different microbial communities occur in soil and in hypolithic zones. Using variation partitioning, we found that hypolithic communities exhibited a fog-related distribution as indicated by the significant East-West clustering. Sodium content was also an important environmental factor affecting the composition of both soil and hypolithic microbial communities. Finally, although null models for patterns in microbial communities were not supported by experimental data, the amount of unexplained variation (68-97 %) suggests that stochastic processes also play a role in the assembly of such communities in the Namib Desert. PMID:23397517

  10. Convergent development of anodic bacterial communities in microbial fuel cells

    PubMed Central

    Yates, Matthew D; Kiely, Patrick D; Call, Douglas F; Rismani-Yazdi, Hamid; Bibby, Kyle; Peccia, Jordan; Regan, John M; Logan, Bruce E

    2012-01-01

    Microbial fuel cells (MFCs) are often inoculated from a single wastewater source. The extent that the inoculum affects community development or power production is unknown. The stable anodic microbial communities in MFCs were examined using three inocula: a wastewater treatment plant sample known to produce consistent power densities, a second wastewater treatment plant sample, and an anaerobic bog sediment. The bog-inoculated MFCs initially produced higher power densities than the wastewater-inoculated MFCs, but after 20 cycles all MFCs on average converged to similar voltages (470±20 mV) and maximum power densities (590±170 mW m−2). The power output from replicate bog-inoculated MFCs was not significantly different, but one wastewater-inoculated MFC (UAJA3 (UAJA, University Area Joint Authority Wastewater Treatment Plant)) produced substantially less power. Denaturing gradient gel electrophoresis profiling showed a stable exoelectrogenic biofilm community in all samples after 11 cycles. After 16 cycles the predominance of Geobacter spp. in anode communities was identified using 16S rRNA gene clone libraries (58±10%), fluorescent in-situ hybridization (FISH) (63±6%) and pyrosequencing (81±4%). While the clone library analysis for the underperforming UAJA3 had a significantly lower percentage of Geobacter spp. sequences (36%), suggesting that a predominance of this microbe was needed for convergent power densities, the lower percentage of this species was not verified by FISH or pyrosequencing analyses. These results show that the predominance of Geobacter spp. in acetate-fed systems was consistent with good MFC performance and independent of the inoculum source. PMID:22572637

  11. Temporal variation in the nitrogen uptake competition between plant community and soil microbial community

    NASA Astrophysics Data System (ADS)

    Legay, N.; Lavorel, S.; Personeni, E.; Bataillé, M. P.; Robson, T. M.; Clément, J. C.

    2012-04-01

    1. Subalpine grasslands are characterized by important seasonal variations and like in others cold environments, the existence of seasonal variations of nitrogen (N) dynamics is strongly plausible. It has been shown that plants and microbes were in competition for nitrogen acquisition mainly during the growing season and particularly at plant biomass peak. During snowmelt, plants could benefit from a decrease in competition potential by microbes given a greater N uptake and freeze-thaw cycles restricting microbial growth. In managed grasslands, these probable interactions are furthermore influenced by recent changes in management, and associated modifications in plant and microbial communities. A previous isotope tracing experiment during the biomass peak suggested that in more intensely managed grasslands, plants exerted a greater control over N cycling than microorganisms, and that soil N availability was stimulated by a greater nitrogen uptake by plants and microbes allowing nutrients to be more readily returned to the soil. 2. A pulse of 15N was added to estimate if the dynamics of N uptake between plants and microbes observed at the biomass peak was applicable at snowmelt. We also asked if the modifications of N dynamics observed depend on management activities across four different grassland types representing decreasing management intensities, from formerly cultivated terraces, either mown or only lightly grazed to unterraced permanent grasslands, either mown or only very lightly grazed. 3. In all grasslands, N pools of aboveground plants were smaller in May than in July while root N pools were greater, and the intrinsic plant uptake was 2 at 5 times weaker in May. N microbial pools were higher in May that in July, while microbial N uptake was 10 to 100 times smaller during snowmelt than at the biomass peak. In spite of the fact that microbial N pools were still larger than the plant N pool, in terms of plants vs microbes competition for N, a microbe N

  12. Similar Microbial Communities Found on Two Distant Seafloor Basalts.

    PubMed

    Singer, Esther; Chong, Lauren S; Heidelberg, John F; Edwards, Katrina J

    2015-01-01

    The oceanic crust forms two thirds of the Earth's surface and hosts a large phylogenetic and functional diversity of microorganisms. While advances have been made in the sedimentary realm, our understanding of the igneous rock portion as a microbial habitat has remained limited. We present the first comparative metagenomic microbial community analysis from ocean floor basalt environments at the Lō'ihi Seamount, Hawai'i, and the East Pacific Rise (EPR; 9°N). Phylogenetic analysis indicates the presence of a total of 43 bacterial and archaeal mono-phyletic groups, dominated by Alpha- and Gammaproteobacteria, as well as Thaumarchaeota. Functional gene analysis suggests that these Thaumarchaeota play an important role in ammonium oxidation on seafloor basalts. In addition to ammonium oxidation, the seafloor basalt habitat reveals a wide spectrum of other metabolic potentials, including CO2 fixation, denitrification, dissimilatory sulfate reduction, and sulfur oxidation. Basalt communities from Lō'ihi and the EPR show considerable metabolic and phylogenetic overlap down to the genus level despite geographic distance and slightly different seafloor basalt mineralogy. PMID:26733957

  13. Microbial community analysis of anaerobic reactors treating soft drink wastewater.

    PubMed

    Narihiro, Takashi; Kim, Na-Kyung; Mei, Ran; Nobu, Masaru K; Liu, Wen-Tso

    2015-01-01

    The anaerobic packed-bed (AP) and hybrid packed-bed (HP) reactors containing methanogenic microbial consortia were applied to treat synthetic soft drink wastewater, which contains polyethylene glycol (PEG) and fructose as the primary constituents. The AP and HP reactors achieved high COD removal efficiency (>95%) after 80 and 33 days of the operation, respectively, and operated stably over 2 years. 16S rRNA gene pyrotag analyses on a total of 25 biofilm samples generated 98,057 reads, which were clustered into 2,882 operational taxonomic units (OTUs). Both AP and HP communities were predominated by Bacteroidetes, Chloroflexi, Firmicutes, and candidate phylum KSB3 that may degrade organic compound in wastewater treatment processes. Other OTUs related to uncharacterized Geobacter and Spirochaetes clades and candidate phylum GN04 were also detected at high abundance; however, their relationship to wastewater treatment has remained unclear. In particular, KSB3, GN04, Bacteroidetes, and Chloroflexi are consistently associated with the organic loading rate (OLR) increase to 1.5 g COD/L-d. Interestingly, KSB3 and GN04 dramatically decrease in both reactors after further OLR increase to 2.0 g COD/L-d. These results indicate that OLR strongly influences microbial community composition. This suggests that specific uncultivated taxa may take central roles in COD removal from soft drink wastewater depending on OLR. PMID:25748027

  14. Similar Microbial Communities Found on Two Distant Seafloor Basalts.

    PubMed

    Singer, Esther; Chong, Lauren S; Heidelberg, John F; Edwards, Katrina J

    2015-01-01

    The oceanic crust forms two thirds of the Earth's surface and hosts a large phylogenetic and functional diversity of microorganisms. While advances have been made in the sedimentary realm, our understanding of the igneous rock portion as a microbial habitat has remained limited. We present the first comparative metagenomic microbial community analysis from ocean floor basalt environments at the Lō'ihi Seamount, Hawai'i, and the East Pacific Rise (EPR; 9°N). Phylogenetic analysis indicates the presence of a total of 43 bacterial and archaeal mono-phyletic groups, dominated by Alpha- and Gammaproteobacteria, as well as Thaumarchaeota. Functional gene analysis suggests that these Thaumarchaeota play an important role in ammonium oxidation on seafloor basalts. In addition to ammonium oxidation, the seafloor basalt habitat reveals a wide spectrum of other metabolic potentials, including CO2 fixation, denitrification, dissimilatory sulfate reduction, and sulfur oxidation. Basalt communities from Lō'ihi and the EPR show considerable metabolic and phylogenetic overlap down to the genus level despite geographic distance and slightly different seafloor basalt mineralogy.

  15. [Microbial community of municipal discharges in a sewage treatment plant].

    PubMed

    Xu, Ai-ling; Ren, Jie; Song, Zhi-wen; Wu, Deng-deng; Xia, Yan

    2014-09-01

    There are numerous microorganisms, especial pathogens, in the discharges. Those microorganisms are discharged into the river and sea through sewage outfalls, which results in possible health risks to coastal populations. And more attention should be paid to municipal discharges in developing countries. This study investigated the microbial community in the discharges by constructing 16S rDNA clones library and using the PCR-RFLP technology. Phylogenetic analysis of bacteria in municipal discharges showed that there were 59 species, which were divided into 11 classes. Proteobacteria accounted for 85% of all the bacteria, of which β-Proteobacteria and γ- Proteobacteria were the dominant classes. Bacteria in the waste water treating process had important influence on microbial community in municipal discharges, therefore, municipal sewage plant should choose the process according to the characteristics and purifying capacity of the receiving water body. Legionella spp. accounted for approximately 10% , the Legionnaires' disease resulted from which might be of top risk for the residents in the surrounding of the municipal discharges outfall and receiving water. Dechloromonas aromatica could make use of chlorite ( CIO - ) , which led to its survival from chlorine disinfection, and it alerted us that several disinfection methods should be used together to ensure the bacterial safety of municipal discharges. Coliform group and other pathogenic bacteria, such as Salmonella spp. , Shigella spp. , Escherichia coli, Vibrio cholerae, Staphylococcus aureus, Arcobacter spp. were not detected in this study, and it indicated that we should do more work and use more methods to investigate the perniciousness of discharges.

  16. Similar Microbial Communities Found on Two Distant Seafloor Basalts

    PubMed Central

    Singer, Esther; Chong, Lauren S.; Heidelberg, John F.; Edwards, Katrina J.

    2015-01-01

    The oceanic crust forms two thirds of the Earth’s surface and hosts a large phylogenetic and functional diversity of microorganisms. While advances have been made in the sedimentary realm, our understanding of the igneous rock portion as a microbial habitat has remained limited. We present the first comparative metagenomic microbial community analysis from ocean floor basalt environments at the Lō’ihi Seamount, Hawai’i, and the East Pacific Rise (EPR; 9°N). Phylogenetic analysis indicates the presence of a total of 43 bacterial and archaeal mono-phyletic groups, dominated by Alpha- and Gammaproteobacteria, as well as Thaumarchaeota. Functional gene analysis suggests that these Thaumarchaeota play an important role in ammonium oxidation on seafloor basalts. In addition to ammonium oxidation, the seafloor basalt habitat reveals a wide spectrum of other metabolic potentials, including CO2 fixation, denitrification, dissimilatory sulfate reduction, and sulfur oxidation. Basalt communities from Lō’ihi and the EPR show considerable metabolic and phylogenetic overlap down to the genus level despite geographic distance and slightly different seafloor basalt mineralogy. PMID:26733957

  17. Microbial Community Analysis of Anaerobic Reactors Treating Soft Drink Wastewater

    PubMed Central

    Narihiro, Takashi; Kim, Na-Kyung; Mei, Ran; Nobu, Masaru K.; Liu, Wen-Tso

    2015-01-01

    The anaerobic packed-bed (AP) and hybrid packed-bed (HP) reactors containing methanogenic microbial consortia were applied to treat synthetic soft drink wastewater, which contains polyethylene glycol (PEG) and fructose as the primary constituents. The AP and HP reactors achieved high COD removal efficiency (>95%) after 80 and 33 days of the operation, respectively, and operated stably over 2 years. 16S rRNA gene pyrotag analyses on a total of 25 biofilm samples generated 98,057 reads, which were clustered into 2,882 operational taxonomic units (OTUs). Both AP and HP communities were predominated by Bacteroidetes, Chloroflexi, Firmicutes, and candidate phylum KSB3 that may degrade organic compound in wastewater treatment processes. Other OTUs related to uncharacterized Geobacter and Spirochaetes clades and candidate phylum GN04 were also detected at high abundance; however, their relationship to wastewater treatment has remained unclear. In particular, KSB3, GN04, Bacteroidetes, and Chloroflexi are consistently associated with the organic loading rate (OLR) increase to 1.5 g COD/L-d. Interestingly, KSB3 and GN04 dramatically decrease in both reactors after further OLR increase to 2.0 g COD/L-d. These results indicate that OLR strongly influences microbial community composition. This suggests that specific uncultivated taxa may take central roles in COD removal from soft drink wastewater depending on OLR. PMID:25748027

  18. Pyrosequencing Based Microbial Community Analysis of Stabilized Mine Soils

    NASA Astrophysics Data System (ADS)

    Park, J. E.; Lee, B. T.; Son, A.

    2015-12-01

    Heavy metals leached from exhausted mines have been causing severe environmental problems in nearby soils and groundwater. Environmental mitigation was performed based on the heavy metal stabilization using Calcite and steel slag in Korea. Since the soil stabilization only temporarily immobilizes the contaminants to soil matrix, the potential risk of re-leaching heavy metal still exists. Therefore the follow-up management of stabilized soils and the corresponding evaluation methods are required to avoid the consequent contamination from the stabilized soils. In this study, microbial community analysis using pyrosequencing was performed for assessing the potential leaching of the stabilized soils. As a result of rarefaction curve and Chao1 and Shannon indices, the stabilized soil has shown lower richness and diversity as compared to non-contaminated negative control. At the phyla level, as the degree of contamination increases, most of phyla decreased with only exception of increased proteobacteria. Among proteobacteria, gamma-proteobacteria increased against the heavy metal contamination. At the species level, Methylobacter tundripaludum of gamma-proteobacteria showed the highest relative portion of microbial community, indicating that methanotrophs may play an important role in either solubilization or immobilization of heavy metals in stabilized soils.

  19. [Microbial community of municipal discharges in a sewage treatment plant].

    PubMed

    Xu, Ai-ling; Ren, Jie; Song, Zhi-wen; Wu, Deng-deng; Xia, Yan

    2014-09-01

    There are numerous microorganisms, especial pathogens, in the discharges. Those microorganisms are discharged into the river and sea through sewage outfalls, which results in possible health risks to coastal populations. And more attention should be paid to municipal discharges in developing countries. This study investigated the microbial community in the discharges by constructing 16S rDNA clones library and using the PCR-RFLP technology. Phylogenetic analysis of bacteria in municipal discharges showed that there were 59 species, which were divided into 11 classes. Proteobacteria accounted for 85% of all the bacteria, of which β-Proteobacteria and γ- Proteobacteria were the dominant classes. Bacteria in the waste water treating process had important influence on microbial community in municipal discharges, therefore, municipal sewage plant should choose the process according to the characteristics and purifying capacity of the receiving water body. Legionella spp. accounted for approximately 10% , the Legionnaires' disease resulted from which might be of top risk for the residents in the surrounding of the municipal discharges outfall and receiving water. Dechloromonas aromatica could make use of chlorite ( CIO - ) , which led to its survival from chlorine disinfection, and it alerted us that several disinfection methods should be used together to ensure the bacterial safety of municipal discharges. Coliform group and other pathogenic bacteria, such as Salmonella spp. , Shigella spp. , Escherichia coli, Vibrio cholerae, Staphylococcus aureus, Arcobacter spp. were not detected in this study, and it indicated that we should do more work and use more methods to investigate the perniciousness of discharges. PMID:25518668

  20. Iron Homeostasis in Yellowstone National Park Hot Spring Microbial Communities

    NASA Technical Reports Server (NTRS)

    Brown, I.; Tringe, S. G.; Franklin, H.; Bryant, D. A.; Klatt, C. G.; Sarkisova, S. A.; Guevara, M.

    2010-01-01

    It has been postulated that life may have originated on Earth, and possibly on Mars, in association with hydrothermal activity and high concentrations of ferrous iron. However, it is not clear how an iron-rich thermal hydrosphere could be hospitable to microbes, since reduced iron appears to stimulate oxidative stress in all domains of life and particularly in oxygenic phototrophs. Therefore, the study of microbial diversity in iron-depositing hot springs (IDHS) and the mechanisms of iron homeostasis and suppression of oxidative stress may help elucidate how Precambrian organisms could withstand the extremely high concentrations of reactive oxygen species (ROS) produced by interaction between environmental Fe(2+) and O2. Proteins and clusters of orthologous groups (COGs) involved in the maintenance of Fe homeostasis found in cyanobacteria (CB) inhabiting environments with high and low [Fe] were main target of this analysis. Preliminary results of the analysis suggest that the Chocolate Pots (CP) microbial community is heavily dominated by phototrophs from the cyanobacteria (CB), Chloroflexi and Chlorobi phyla, while the Mushroom Spring (MS) effluent channel harbors a more diverse community in which Chloroflexi are the dominant phototrophs. It is speculated that CB inhabiting IDHS have an increased tolerance to both high concentrations of Fe(2+) and ROS produced in the Fenton reaction. This hypothesis was explored via a comparative analysis of the diversity of proteins and COGs involved in Fe and redox homeostasis in the CP and MS microbiomes.

  1. Patterns of Endemism and Habitat Selection in Coalbed Microbial Communities

    PubMed Central

    Lawson, Christopher E.; Strachan, Cameron R.; Williams, Dominique D.; Koziel, Susan; Hallam, Steven J.

    2015-01-01

    Microbially produced methane, a versatile, cleaner-burning alternative energy resource to fossil fuels, is sourced from a variety of natural and engineered ecosystems, including marine sediments, anaerobic digesters, shales, and coalbeds. There is a prevailing interest in developing environmental biotechnologies to enhance methane production. Here, we use small-subunit rRNA gene sequencing and metagenomics to better describe the interplay between coalbed methane (CBM) well conditions and microbial communities in the Alberta Basin. Our results show that CBM microbial community structures display patterns of endemism and habitat selection across the Alberta Basin, consistent with observations from other geographical locations. While some phylum-level taxonomic patterns were observed, relative abundances of specific taxonomic groups were localized to discrete wells, likely shaped by local environmental conditions, such as coal rank and depth-dependent physicochemical conditions. To better resolve functional potential within the CBM milieu, a metagenome from a deep volatile-bituminous coal sample was generated. This sample was dominated by Rhodobacteraceae genotypes, resolving a near-complete population genome bin related to Celeribacter sp. that encoded metabolic pathways for the degradation of a wide range of aromatic compounds and the production of methanogenic substrates via acidogenic fermentation. Genomic comparisons between the Celeribacter sp. population genome and related organisms isolated from different environments reflected habitat-specific selection pressures that included nitrogen availability and the ability to utilize diverse carbon substrates. Taken together, our observations reveal that both endemism and metabolic specialization should be considered in the development of biostimulation strategies for nonproductive wells or for those with declining productivity. PMID:26341214

  2. Metagenomic Sequencing of an In Vitro-Simulated Microbial Community

    SciTech Connect

    Morgan, Jenna L.; Darling, Aaron E.; Eisen, Jonathan A.

    2009-12-01

    Background: Microbial life dominates the earth, but many species are difficult or even impossible to study under laboratory conditions. Sequencing DNA directly from the environment, a technique commonly referred to as metagenomics, is an important tool for cataloging microbial life. This culture-independent approach involves collecting samples that include microbes in them, extracting DNA from the samples, and sequencing the DNA. A sample may contain many different microorganisms, macroorganisms, and even free-floating environmental DNA. A fundamental challenge in metagenomics has been estimating the abundance of organisms in a sample based on the frequency with which the organism's DNA was observed in reads generated via DNA sequencing. Methodology/Principal Findings: We created mixtures of ten microbial species for which genome sequences are known. Each mixture contained an equal number of cells of each species. We then extracted DNA from the mixtures, sequenced the DNA, and measured the frequency with which genomic regions from each organism was observed in the sequenced DNA. We found that the observed frequency of reads mapping to each organism did not reflect the equal numbers of cells that were known to be included in each mixture. The relative organism abundances varied significantly depending on the DNA extraction and sequencing protocol utilized. Conclusions/Significance: We describe a new data resource for measuring the accuracy of metagenomic binning methods, created by in vitro-simulation of a metagenomic community. Our in vitro simulation can be used to complement previous in silico benchmark studies. In constructing a synthetic community and sequencing its metagenome, we encountered several sources of observation bias that likely affect most metagenomic experiments to date and present challenges for comparative metagenomic studies. DNA preparation methods have a particularly profound effect in our study, implying that samples prepared with different

  3. Patterns of Endemism and Habitat Selection in Coalbed Microbial Communities.

    PubMed

    Lawson, Christopher E; Strachan, Cameron R; Williams, Dominique D; Koziel, Susan; Hallam, Steven J; Budwill, Karen

    2015-11-01

    Microbially produced methane, a versatile, cleaner-burning alternative energy resource to fossil fuels, is sourced from a variety of natural and engineered ecosystems, including marine sediments, anaerobic digesters, shales, and coalbeds. There is a prevailing interest in developing environmental biotechnologies to enhance methane production. Here, we use small-subunit rRNA gene sequencing and metagenomics to better describe the interplay between coalbed methane (CBM) well conditions and microbial communities in the Alberta Basin. Our results show that CBM microbial community structures display patterns of endemism and habitat selection across the Alberta Basin, consistent with observations from other geographical locations. While some phylum-level taxonomic patterns were observed, relative abundances of specific taxonomic groups were localized to discrete wells, likely shaped by local environmental conditions, such as coal rank and depth-dependent physicochemical conditions. To better resolve functional potential within the CBM milieu, a metagenome from a deep volatile-bituminous coal sample was generated. This sample was dominated by Rhodobacteraceae genotypes, resolving a near-complete population genome bin related to Celeribacter sp. that encoded metabolic pathways for the degradation of a wide range of aromatic compounds and the production of methanogenic substrates via acidogenic fermentation. Genomic comparisons between the Celeribacter sp. population genome and related organisms isolated from different environments reflected habitat-specific selection pressures that included nitrogen availability and the ability to utilize diverse carbon substrates. Taken together, our observations reveal that both endemism and metabolic specialization should be considered in the development of biostimulation strategies for nonproductive wells or for those with declining productivity. PMID:26341214

  4. Profiling in situ microbial community structure with an amplification microarray.

    PubMed

    Chandler, Darrell P; Knickerbocker, Christopher; Bryant, Lexi; Golova, Julia; Wiles, Cory; Williams, Kenneth H; Peacock, Aaron D; Long, Philip E

    2013-02-01

    The objectives of this study were to unify amplification, labeling, and microarray hybridization chemistries within a single, closed microfluidic chamber (an amplification microarray) and verify technology performance on a series of groundwater samples from an in situ field experiment designed to compare U(VI) mobility under conditions of various alkalinities (as HCO(3)(-)) during stimulated microbial activity accompanying acetate amendment. Analytical limits of detection were between 2 and 200 cell equivalents of purified DNA. Amplification microarray signatures were well correlated with 16S rRNA-targeted quantitative PCR results and hybridization microarray signatures. The succession of the microbial community was evident with and consistent between the two microarray platforms. Amplification microarray analysis of acetate-treated groundwater showed elevated levels of iron-reducing bacteria (Flexibacter, Geobacter, Rhodoferax, and Shewanella) relative to the average background profile, as expected. Identical molecular signatures were evident in the transect treated with acetate plus NaHCO(3), but at much lower signal intensities and with a much more rapid decline (to nondetection). Azoarcus, Thaurea, and Methylobacterium were responsive in the acetate-only transect but not in the presence of bicarbonate. Observed differences in microbial community composition or response to bicarbonate amendment likely had an effect on measured rates of U reduction, with higher rates probable in the part of the field experiment that was amended with bicarbonate. The simplification in microarray-based work flow is a significant technological advance toward entirely closed-amplicon microarray-based tests and is generally extensible to any number of environmental monitoring applications.

  5. Profiling In Situ Microbial Community Structure with an Amplification Microarray

    PubMed Central

    Knickerbocker, Christopher; Bryant, Lexi; Golova, Julia; Wiles, Cory; Williams, Kenneth H.; Peacock, Aaron D.; Long, Philip E.

    2013-01-01

    The objectives of this study were to unify amplification, labeling, and microarray hybridization chemistries within a single, closed microfluidic chamber (an amplification microarray) and verify technology performance on a series of groundwater samples from an in situ field experiment designed to compare U(VI) mobility under conditions of various alkalinities (as HCO3−) during stimulated microbial activity accompanying acetate amendment. Analytical limits of detection were between 2 and 200 cell equivalents of purified DNA. Amplification microarray signatures were well correlated with 16S rRNA-targeted quantitative PCR results and hybridization microarray signatures. The succession of the microbial community was evident with and consistent between the two microarray platforms. Amplification microarray analysis of acetate-treated groundwater showed elevated levels of iron-reducing bacteria (Flexibacter, Geobacter, Rhodoferax, and Shewanella) relative to the average background profile, as expected. Identical molecular signatures were evident in the transect treated with acetate plus NaHCO3, but at much lower signal intensities and with a much more rapid decline (to nondetection). Azoarcus, Thaurea, and Methylobacterium were responsive in the acetate-only transect but not in the presence of bicarbonate. Observed differences in microbial community composition or response to bicarbonate amendment likely had an effect on measured rates of U reduction, with higher rates probable in the part of the field experiment that was amended with bicarbonate. The simplification in microarray-based work flow is a significant technological advance toward entirely closed-amplicon microarray-based tests and is generally extensible to any number of environmental monitoring applications. PMID:23160129

  6. IN-DRIFT MICROBIAL COMMUNITIES MODEL VALIDATION CALCULATIONS

    SciTech Connect

    D.M. Jolley

    2001-12-18

    The objective and scope of this calculation is to create the appropriate parameter input for MING 1.0 (CSCI 30018 V1.0, CRWMS M&O 1998b) that will allow the testing of the results from the MING software code with both scientific measurements of microbial populations at the site and laboratory and with natural analogs to the site. This set of calculations provides results that will be used in model validation for the ''In-Drift Microbial Communities'' model (CRWMS M&O 2000) which is part of the Engineered Barrier System Department (EBS) process modeling effort that eventually will feed future Total System Performance Assessment (TSPA) models. This calculation is being produced to replace MING model validation output that is effected by the supersession of DTN M09909SPAMINGl.003 using its replacement DTN M00106SPAIDMO 1.034 so that the calculations currently found in the ''In-Drift Microbial Communities'' AMR (CRWMS M&O 2000) will be brought up to date. This set of calculations replaces the calculations contained in sections 6.7.2, 6.7.3 and Attachment I of CRWMS M&O (2000) As all of these calculations are created explicitly for model validation, the data qualification status of all inputs can be considered corroborative in accordance with AP-3.15Q. This work activity has been evaluated in accordance with the AP-2.21 procedure, ''Quality Determinations and Planning for Scientific, Engineering, and Regulatory Compliance Activities'', and is subject to QA controls (BSC 2001). The calculation is developed in accordance with the AP-3.12 procedure, Calculations, and prepared in accordance with the ''Technical Work Plan For EBS Department Modeling FY 01 Work Activities'' (BSC 200 1) which includes controls for the management of electronic data.

  7. In-Drift Microbial Communities Model Validation Calculations

    SciTech Connect

    D. M. Jolley

    2001-09-24

    The objective and scope of this calculation is to create the appropriate parameter input for MING 1.0 (CSCI 30018 V1.0, CRWMS M&O 1998b) that will allow the testing of the results from the MING software code with both scientific measurements of microbial populations at the site and laboratory and with natural analogs to the site. This set of calculations provides results that will be used in model validation for the ''In-Drift Microbial Communities'' model (CRWMS M&O 2000) which is part of the Engineered Barrier System Department (EBS) process modeling effort that eventually will feed future Total System Performance Assessment (TSPA) models. This calculation is being produced to replace MING model validation output that is effected by the supersession of DTN MO9909SPAMING1.003 using its replacement DTN MO0106SPAIDM01.034 so that the calculations currently found in the ''In-Drift Microbial Communities'' AMR (CRWMS M&O 2000) will be brought up to date. This set of calculations replaces the calculations contained in sections 6.7.2, 6.7.3 and Attachment I of CRWMS M&O (2000) As all of these calculations are created explicitly for model validation, the data qualification status of all inputs can be considered corroborative in accordance with AP-3.15Q. This work activity has been evaluated in accordance with the AP-2.21 procedure, ''Quality Determinations and Planning for Scientific, Engineering, and Regulatory Compliance Activities'', and is subject to QA controls (BSC 2001). The calculation is developed in accordance with the AP-3.12 procedure, Calculations, and prepared in accordance with the ''Technical Work Plan For EBS Department Modeling FY 01 Work Activities'' (BSC 2001) which includes controls for the management of electronic data.

  8. In-Drift Microbial Communities Model Validation Calculation

    SciTech Connect

    D. M. Jolley

    2001-10-31

    The objective and scope of this calculation is to create the appropriate parameter input for MING 1.0 (CSCI 30018 V1.0, CRWMS M&O 1998b) that will allow the testing of the results from the MING software code with both scientific measurements of microbial populations at the site and laboratory and with natural analogs to the site. This set of calculations provides results that will be used in model validation for the ''In-Drift Microbial Communities'' model (CRWMS M&O 2000) which is part of the Engineered Barrier System Department (EBS) process modeling effort that eventually will feed future Total System Performance Assessment (TSPA) models. This calculation is being produced to replace MING model validation output that is effected by the supersession of DTN MO9909SPAMING1.003 using its replacement DTN MO0106SPAIDM01.034 so that the calculations currently found in the ''In-Drift Microbial Communities'' AMR (CRWMS M&O 2000) will be brought up to date. This set of calculations replaces the calculations contained in sections 6.7.2, 6.7.3 and Attachment I of CRWMS M&O (2000) As all of these calculations are created explicitly for model validation, the data qualification status of all inputs can be considered corroborative in accordance with AP-3.15Q. This work activity has been evaluated in accordance with the AP-2.21 procedure, ''Quality Determinations and Planning for Scientific, Engineering, and Regulatory Compliance Activities'', and is subject to QA controls (BSC 2001). The calculation is developed in accordance with the AP-3.12 procedure, Calculations, and prepared in accordance with the ''Technical Work Plan For EBS Department Modeling FY 01 Work Activities'' (BSC 2001) which includes controls for the management of electronic data.

  9. Culturability as an indicator of succession in microbial communities

    NASA Technical Reports Server (NTRS)

    Garland, J. L.; Cook, K. L.; Adams, J. L.; Kerkhof, L.

    2001-01-01

    Successional theory predicts that opportunistic species with high investment of energy in reproduction and wide niche width will be replaced by equilibrium species with relatively higher investment of energy in maintenance and narrower niche width as communities develop. Since the ability to rapidly grow into a detectable colony on nonselective agar medium could be considered as characteristic of opportunistic types of bacteria, the percentage of culturable cells may be an indicator of successional state in microbial communities. The ratios of culturable cells (colony forming units on R2A agar) to total cells (acridine orange direct microscopic counts) and culturable cells to active cells (reduction of 5-cyano-2,3-ditolyl tetrazolium chloride) were measured over time in two types of laboratory microcosms (the rhizosphere of hydroponically grown wheat and aerobic, continuously stirred tank reactors containing plant biomass) to determine the effectiveness of culturabilty as an index of successional state. The culturable cell:total cell ratio in the rhizosphere decreased from approximately 0.25 to less than 0.05 during the first 30-50 days of plant growth, and from 0.65 to 0.14 during the first 7 days of operation of the bioreactor. The culturable cell:active cell ratio followed similar trends, but the values were consistently greater than the culturable cell:total cell ratio, and even exceeded I in early samples. Follow-up studies used a cultivation-independent method, terminal restriction fragment length polymorphisms (TRFLP) from whole community DNA, to assess community structure. The number of TRFLP peaks increased with time, while the number of culturable types did not, indicating that the general decrease in culturability is associated with a shift in community structure. The ratio of respired to assimilated C-14-labeled amino acids increased with the age of rhizosphere communities, supporting the hypothesis that a shift in resource allocation from growth to

  10. Do climate factors govern soil microbial community composition and biomass at a regional scale?

    NASA Astrophysics Data System (ADS)

    Ma, L.; Guo, C.; Lü, X.; Yuan, S.; Wang, R.

    2014-12-01

    Soil microbial communities play important role in organic matter decomposition, nutrient cycling and vegetation dynamic. However, little is known about factors driving soil microbial community composition at large scales. The objective of this study was to determine whether climate dominates among environmental factors governing microbial community composition and biomass at a regional scale. Here, we compared soil microbial communities using phospholipid fatty acid method across 7 land use types from 23 locations in North-East China Transect (850 km x 50 km). The results showed that soil water availability and land use changes exhibited the dominant effects on soil microbial community composition and biomass at the regional scale, while climate factors (expressed as a function of large-scale spatial variation) did not show strong relationships with distribution of microbial community composition. Likewise, factors such as spatial structure, soil texture, nutrient availability and vegetation types were not important. Wetter soils had higher contributions of gram-positive bacteria, whereas drier soils had higher contributions of gram-negative bacteria and fungi. Heavily disturbed soils had lower contributions of gram-negative bacteria and fungi than historically disturbed and undisturbed soils. The lowest microbial biomass appeared in the wettest and driest soils. In conclusion, dominant climate factors, commonly known to structure distribution of macroorganisms, were not the most important drivers governing regional pattern of microbial communities because of inclusion of irrigated and managed practices. In comparison, soil water regime and land use types appear to be primary determinants of microbial community composition and biomass.

  11. Response of microbial community composition and function to soil climate change

    USGS Publications Warehouse

    Waldrop, M.P.; Firestone, M.K.

    2006-01-01

    Soil microbial communities mediate critical ecosystem carbon and nutrient cycles. How microbial communities will respond to changes in vegetation and climate, however, are not well understood. We reciprocally transplanted soil cores from under oak canopies and adjacent open grasslands in a California oak-grassland ecosystem to determine how microbial communities respond to changes in the soil environment and the potential consequences for the cycling of carbon. Every 3 months for up to 2 years, we monitored microbial community composition using phospholipid fatty acid analysis (PLFA), microbial biomass, respiration rates, microbial enzyme activities, and the activity of microbial groups by quantifying 13C uptake from a universal substrate (pyruvate) into PLFA biomarkers. Soil in the open grassland experienced higher maximum temperatures and lower soil water content than soil under the oak canopies. Soil microbial communities in soil under oak canopies were more sensitive to environmental change than those in adjacent soil from the open grassland. Oak canopy soil communities changed rapidly when cores were transplanted into the open grassland soil environment, but grassland soil communities did not change when transplanted into the oak canopy environment. Similarly, microbial biomass, enzyme activities, and microbial respiration decreased when microbial communities were transplanted from the oak canopy soils to the grassland environment, but not when the grassland communities were transplanted to the oak canopy environment. These data support the hypothesis that microbial community composition and function is altered when microbes are exposed to new extremes in environmental conditions; that is, environmental conditions outside of their "life history" envelopes. ?? 2006 Springer Science+Business Media, Inc.

  12. Microbial Community Analysis of Fresh and Old Microbial Biofilms on Bayon Temple Sandstone of Angkor Thom, Cambodia

    PubMed Central

    Lan, Wensheng; Li, Hui; Wang, Wei-Dong; Katayama, Yoko

    2010-01-01

    The temples of Angkor monuments including Angkor Thom and Bayon in Cambodia and surrounding countries were exclusively constructed using sandstone. They are severely threatened by biodeterioration caused by active growth of different microorganisms on the sandstone surfaces, but knowledge on the microbial community and composition of the biofilms on the sandstone is not available from this region. This study investigated the microbial community diversity by examining the fresh and old biofilms of the biodeteriorated bas-relief wall surfaces of the Bayon Temple by analysis of 16S and 18S rRNA gene sequences. The results showed that the retrieved sequences were clustered in 11 bacterial, 11 eukaryotic and two archaeal divisions with disparate communities (Acidobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Proteobacteria; Alveolata, Fungi, Metazoa, Viridiplantae; Crenarchaeote, and Euyarchaeota). A comparison of the microbial communities between the fresh and old biofilms revealed that the bacterial community of old biofilm was very similar to the newly formed fresh biofilm in terms of bacterial composition, but the eukaryotic communities were distinctly different between these two. This information has important implications for understanding the formation process and development of the microbial diversity on the sandstone surfaces, and furthermore to the relationship between the extent of biodeterioration and succession of microbial communities on sandstone in tropic region. Electronic supplementary material The online version of this article (doi:10.1007/s00248-010-9707-5) contains supplementary material, which is available to authorized users. PMID:20593173

  13. Microbial community analysis of fresh and old microbial biofilms on Bayon temple sandstone of Angkor Thom, Cambodia.

    PubMed

    Lan, Wensheng; Li, Hui; Wang, Wei-Dong; Katayama, Yoko; Gu, Ji-Dong

    2010-07-01

    The temples of Angkor monuments including Angkor Thom and Bayon in Cambodia and surrounding countries were exclusively constructed using sandstone. They are severely threatened by biodeterioration caused by active growth of different microorganisms on the sandstone surfaces, but knowledge on the microbial community and composition of the biofilms on the sandstone is not available from this region. This study investigated the microbial community diversity by examining the fresh and old biofilms of the biodeteriorated bas-relief wall surfaces of the Bayon Temple by analysis of 16S and 18S rRNA gene sequences. The results showed that the retrieved sequences were clustered in 11 bacterial, 11 eukaryotic and two archaeal divisions with disparate communities (Acidobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Proteobacteria; Alveolata, Fungi, Metazoa, Viridiplantae; Crenarchaeote, and Euyarchaeota). A comparison of the microbial communities between the fresh and old biofilms revealed that the bacterial community of old biofilm was very similar to the newly formed fresh biofilm in terms of bacterial composition, but the eukaryotic communities were distinctly different between these two. This information has important implications for understanding the formation process and development of the microbial diversity on the sandstone surfaces, and furthermore to the relationship between the extent of biodeterioration and succession of microbial communities on sandstone in tropic region.

  14. Response of Antarctic cryoconite microbial communities to light.

    PubMed

    Bagshaw, Elizabeth A; Wadham, Jemma L; Tranter, Martyn; Perkins, Rupert; Morgan, Alistair; Williamson, Christopher J; Fountain, Andrew G; Fitzsimons, Sean; Dubnick, Ashley

    2016-06-01

    Microbial communities on polar glacier surfaces are found dispersed on the ice surface, or concentrated in cryoconite holes and cryolakes, which are accumulations of debris covered by a layer of ice for some or all of the year. The ice lid limits the penetration of photosynthetically available radiation (PAR) to the sediment layer, since the ice attenuates up to 99% of incoming radiation. This suite of field and laboratory experiments demonstrates that PAR is an important control on primary production in cryoconite and cryolake ecosystems. Increased light intensity increased efficiency of primary production in controlled laboratory incubations of debris from the surface of Joyce Glacier, McMurdo Dry Valleys, Antarctica. However, when light intensity was increased to levels near that received on the ice surface, without the protection of an ice lid, efficiency decreased and measurements of photophysiology showed that the communities suffered light stress. The communities are therefore well adapted to low light levels. Comparison with Arctic cryoconite communities, which are typically not covered by an ice lid for the majority of the ablation season, showed that these organisms were also stressed by high light, so they must employ strategies to protect against photodamage. PMID:27095815

  15. Exploration of community traits as ecological markers in microbial metagenomes.

    PubMed

    Barberán, Albert; Fernández-Guerra, Antoni; Bohannan, Brendan J M; Casamayor, Emilio O

    2012-04-01

    The rate of information collection generated by metagenomics is uncoupled with its meaningful ecological interpretation. New analytical approaches based on functional trait-based ecology may help to bridge this gap and extend the trait approach to the community level in vast and complex environmental genetic data sets. Here, we explored a set of community traits that range from nucleotidic to genomic properties in 53 metagenomic aquatic samples from the Global Ocean Sampling (GOS) expedition. We found significant differences between the community profile derived from the commonly used 16S rRNA gene and from the functional trait set. The traits proved to be valuable ecological markers by discriminating between marine ecosystems (coastal vs. open ocean) and between oceans (Atlantic vs. Indian vs. Pacific). Intertrait relationships were also assessed, and we propose some that could be further used as habitat descriptors or indicators of artefacts during sample processing. Overall, the approach presented here may help to interpret metagenomics data to gain a full understanding of microbial community patterns in a rigorous ecological framework.

  16. Response of Antarctic cryoconite microbial communities to light

    PubMed Central

    Bagshaw, Elizabeth A.; Wadham, Jemma L.; Tranter, Martyn; Perkins, Rupert; Morgan, Alistair; Williamson, Christopher J.; Fountain, Andrew G.; Fitzsimons, Sean; Dubnick, Ashley

    2016-01-01

    Microbial communities on polar glacier surfaces are found dispersed on the ice surface, or concentrated in cryoconite holes and cryolakes, which are accumulations of debris covered by a layer of ice for some or all of the year. The ice lid limits the penetration of photosynthetically available radiation (PAR) to the sediment layer, since the ice attenuates up to 99% of incoming radiation. This suite of field and laboratory experiments demonstrates that PAR is an important control on primary production in cryoconite and cryolake ecosystems. Increased light intensity increased efficiency of primary production in controlled laboratory incubations of debris from the surface of Joyce Glacier, McMurdo Dry Valleys, Antarctica. However, when light intensity was increased to levels near that received on the ice surface, without the protection of an ice lid, efficiency decreased and measurements of photophysiology showed that the communities suffered light stress. The communities are therefore well adapted to low light levels. Comparison with Arctic cryoconite communities, which are typically not covered by an ice lid for the majority of the ablation season, showed that these organisms were also stressed by high light, so they must employ strategies to protect against photodamage. PMID:27095815

  17. Next-generation studies of microbial biofilm communities.

    PubMed

    Rice, Scott A; Wuertz, Stefan; Kjelleberg, Staffan

    2016-09-01

    As we look into the future of microbial biofilm research, there is clearly an emerging focus on communities rather than populations. This represents an essential change in direction to more accurately understand how and why microorganisms assemble into communities, as well as the functional implications for such a life style. For example, current research studies shows that communities display emergent properties or functions that are not predicted from the individual single species populations, including elevated stress tolerance and resistance to antibiotics. Models for mixed species biofilms can be very simple, comprised only a handful of species or can be extremely species rich, with hundreds or thousands of species present. The future holds much promise for this area of research, where investigators will increasingly be able to resolve, at the molecular and biochemical levels, interspecies relationships and mechanisms of interaction. The outcome of these studies will greatly enhance our understanding of the ecological and evolutionary factors that drive community function in natural and engineered systems. PMID:27471123

  18. Microbial Community Dynamics of Lactate Enriched Hanford Groundwaters

    SciTech Connect

    Mosher, Jennifer J.; Drake, Meghan M.; Carroll, Susan L.; Yang, Zamin K.; Schadt, Christopher W.; Brown, Stephen D.; Podar, Mircea; Hazen, Terry C.; Arkin, Adam P.; Phelps, Tommy J.; Palumbo, Anthony V.; Faybishenko, Boris A.; Elias, Dwayne A.

    2010-05-01

    The Department of Energy site at Hanford, WA, has been historically impacted by U and Cr from the nuclear weapons industry. In an attempt to stimulate microbial remediation of these metals, in-situ lactate enrichment experiments are ongoing. In order to bridge the gap from the laboratory to the field, we inoculated triplicate anaerobic, continuous-flow glass reactors with groundwater collected from well Hanford 100-H in order to obtain a stable, enriched community while selecting for metal-reducing bacteria. Each reactor was fed from a single carboy containing defined media with 30 mM lactate at a rate of 0.223 ml/min under continuous nitrogen flow at 9 ml/min. Cell counts, organic acids, gDNA (for qPCR and pyrosequencing) and gases were sampled during the experiment. Cell counts remained low (less than 1x107 cells/ml) during the first two weeks of the experiment, but by day 20, had reached a density greater than 1x108 cells/ml. Metabolite analysis showed a decrease in the lactate concentrations over time. Pyruvate concentrations ranged from 20-40 uM the first week of the experiment then was undetectable after day 10. Likewise, formate appeared in the reactors during the first week with concentrations of 1.48-1.65 mM at day 7 then the concentrations decreased to 0.69-0.95 on day 10 and were undetectable on day 15. Acetate was present in low amounts on day 3 (0.15-0.33 mM) and steadily increased to 3.35-5.22 mM over time. Similarly, carbon dioxide was present in low concentrations early on and increased to 0.28-0.35 mM as the experiment progressed. We also were able to detect low amounts of methane (10-20 uM) during the first week of the experiment, but by day 10 the methane was undetectable. From these results and pyrosequencing analysis, we conclude that a shift in the microbial community dynamics occurred over time to eventually form a stable and enriched microbial community. Comprehensive investigations such as these allow for the examination of not only which

  19. Approaches to analyse dynamic microbial communities such as those seen in cystic fibrosis lung

    PubMed Central

    2009-01-01

    Microbial communities play vital roles in many aspects of our lives, although our understanding of microbial biogeography and community profiles remains unclear. The number of microbes or the diversity of the microbes, even in small environmental niches, is staggering. Current microbiological methods used to analyse these communities are limited, in that many microorganisms cannot be cultured. Even for the isolates that can be cultured, the expense of identifying them definitively is much too high to be practical. Many recent molecular technologies, combined with bioinformatic tools, are raising the bar by improving the sensitivity and reliability of microbial community analysis. These tools and techniques range from those that attempt to understand a microbial community from their length heterogeneity profiles to those that help to identify the strains and species of a random sampling of the microbes in a given sample. These technologies are reviewed here, using the microbial communities present in the lungs of cystic fibrosis patients as a paradigm. PMID:19403459

  20. Functional Diversity of Microbial Communities in Soils in the Vicinity of Wanda Glacier, Antarctic Peninsula

    PubMed Central

    Pessi, Igor Stelmach; de Oliveira Elias, Susana; Simões, Felipe Lorenz; Simões, Jefferson Cardia; Macedo, Alexandre José

    2012-01-01

    Microbial functional diversity in four soils sampled in the vicinity of Wanda Glacier, Antarctic Peninsula, was determined using Biolog EcoPlates at 5°C and 25°C. Comparisons of the patterns of substrate utilization and the diversity index showed differences in community composition, reflecting the heterogeneous distribution of microorganisms in this environment. Differences in microbial diversity may be related to soil chemical properties. Higher incubation temperature influenced the overall microbial diversity, reducing richness due to the selection of psychrotrophic microorganisms. To our knowledge, this is the first study with microbial communities from Wanda Glacier and contributes to understanding the microbial diversity of Antarctic environments. PMID:22791054

  1. Sediment microbial communities in Great Boiling Spring are controlled by temperature and distinct from water communities

    PubMed Central

    Cole, Jessica K; Peacock, Joseph P; Dodsworth, Jeremy A; Williams, Amanda J; Thompson, Daniel B; Dong, Hailiang; Wu, Geng; Hedlund, Brian P

    2013-01-01

    Great Boiling Spring is a large, circumneutral, geothermal spring in the US Great Basin. Twelve samples were collected from water and four different sediment sites on four different dates. Microbial community composition and diversity were assessed by PCR amplification of a portion of the small subunit rRNA gene using a universal primer set followed by pyrosequencing of the V8 region. Analysis of 164 178 quality-filtered pyrotags clearly distinguished sediment and water microbial communities. Water communities were extremely uneven and dominated by the bacterium Thermocrinis. Sediment microbial communities grouped according to temperature and sampling location, with a strong, negative, linear relationship between temperature and richness at all taxonomic levels. Two sediment locations, Site A (87–80 °C) and Site B (79 °C), were predominantly composed of single phylotypes of the bacterial lineage GAL35 (p̂=36.1%), Aeropyrum (p̂=16.6%), the archaeal lineage pSL4 (p̂=15.9%), the archaeal lineage NAG1 (p̂=10.6%) and Thermocrinis (p̂=7.6%). The ammonia-oxidizing archaeon ‘Candidatus Nitrosocaldus' was relatively abundant in all sediment samples <82 °C (p̂=9.51%), delineating the upper temperature limit for chemolithotrophic ammonia oxidation in this spring. This study underscores the distinctness of water and sediment communities in GBS and the importance of temperature in driving microbial diversity, composition and, ultimately, the functioning of biogeochemical cycles. PMID:23235293

  2. Soil microbial communities and metabolic function of a Northern Alabama forest ecosystem

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Thinning, prescribed burning, and their combinations, are common forest management practices to restore degraded forest communities and to prevent uncontrollable wildfires. However, their impacts on soil microbial communities, which are vital to global element cycling, are traditionally overlooked. ...

  3. Changes in Microbial Biofilm Communities during Colonization of Sewer Systems

    PubMed Central

    Auguet, O.; Pijuan, M.; Batista, J.; Gutierrez, O.

    2015-01-01

    The coexistence of sulfate-reducing bacteria (SRB) and methanogenic archaea (MA) in anaerobic biofilms developed in sewer inner pipe surfaces favors the accumulation of sulfide (H2S) and methane (CH4) as metabolic end products, causing severe impacts on sewerage systems. In this study, we investigated the time course of H2S and CH4 production and emission rates during different stages of biofilm development in relation to changes in the composition of microbial biofilm communities. The study was carried out in a laboratory sewer pilot plant that mimics a full-scale anaerobic rising sewer using a combination of process data and molecular techniques (e.g., quantitative PCR [qPCR], denaturing gradient gel electrophoresis [DGGE], and 16S rRNA gene pyrotag sequencing). After 2 weeks of biofilm growth, H2S emission was notably high (290.7 ± 72.3 mg S-H2S liter−1 day−1), whereas emissions of CH4 remained low (17.9 ± 15.9 mg COD-CH4 liter−1 day−1). This contrasting trend coincided with a stable SRB community and an archaeal community composed solely of methanogens derived from the human gut (i.e., Methanobrevibacter and Methanosphaera). In turn, CH4 emissions increased after 1 year of biofilm growth (327.6 ± 16.6 mg COD-CH4 liter−1 day−1), coinciding with the replacement of methanogenic colonizers by species more adapted to sewer conditions (i.e., Methanosaeta spp.). Our study provides data that confirm the capacity of our laboratory experimental system to mimic the functioning of full-scale sewers both microbiologically and operationally in terms of sulfide and methane production, gaining insight into the complex dynamics of key microbial groups during biofilm development. PMID:26253681

  4. Managing microbial communities for sequentially reconstruct genomes from complex metagenomes

    NASA Astrophysics Data System (ADS)

    Delmont, Tom O.; Vogel, Timothy M.; Simonet, Pascal

    2013-04-01

    Global understanding on environmental microbial communities is currently limited by the bottleneck of genome reconstruction. Soil is a typical example where individual cells are currently mostly uncultured and metagenomic datasets unassembled. In this study, the microbial community composition of a natural grassland soil was managed under several controlled selective pressures to experiment a "multi-evenness" stratagem for sequentially attempt to reconstruct genomes from a complex metagenome. While lowly represented in the natural community, several newly dominant genomes (an enrichment attaining 105 in some cases) were successfully reconstructed under various "harsh" tested conditions. These genomes belong to several genera including (but not restricted to) Leifsonia, Rhodanobacter, Bacillus, Ktedonobacter, Xanthomonas, Streptomyces and Burkholderia. So far, from 10 to 78% of generated metagenomic datasets were reconstructed, so providing access to more than 88 000 genes of known or unknown functions and to their genetic environment. Adaptative genes directly related to selective pressures were found, mostly in large plasmids. Functions of potential industrial interest (e.g., novel polyketide synthase modules in Streptomyces) were also discovered. Furthermore, an important phage infection snapshot (>1500X of coverage for the most represented phage) was observed among the Streptomyces population (three distinct genomes reconstructed) of a particular enrichment (mercury, 0.02g/kg) during the fourth month of incubation. This "divide and conquer" strategy could be applied to other environments and using auxiliary sequencing approaches like single cell to detect, connect and mine taxa and functions of interest while creating an extensive set of reference genomes from across the planet. Next limit could turn out to become our imagination defining novel selective pressures to sequentially make dominant the 1030 cells of the biosphere.

  5. Changes in Microbial Biofilm Communities during Colonization of Sewer Systems.

    PubMed

    Auguet, O; Pijuan, M; Batista, J; Borrego, C M; Gutierrez, O

    2015-10-01

    The coexistence of sulfate-reducing bacteria (SRB) and methanogenic archaea (MA) in anaerobic biofilms developed in sewer inner pipe surfaces favors the accumulation of sulfide (H2S) and methane (CH4) as metabolic end products, causing severe impacts on sewerage systems. In this study, we investigated the time course of H2S and CH4 production and emission rates during different stages of biofilm development in relation to changes in the composition of microbial biofilm communities. The study was carried out in a laboratory sewer pilot plant that mimics a full-scale anaerobic rising sewer using a combination of process data and molecular techniques (e.g., quantitative PCR [qPCR], denaturing gradient gel electrophoresis [DGGE], and 16S rRNA gene pyrotag sequencing). After 2 weeks of biofilm growth, H2S emission was notably high (290.7±72.3 mg S-H2S liter(-1) day(-1)), whereas emissions of CH4 remained low (17.9±15.9 mg COD-CH4 liter(-1) day(-1)). This contrasting trend coincided with a stable SRB community and an archaeal community composed solely of methanogens derived from the human gut (i.e., Methanobrevibacter and Methanosphaera). In turn, CH4 emissions increased after 1 year of biofilm growth (327.6±16.6 mg COD-CH4 liter(-1) day(-1)), coinciding with the replacement of methanogenic colonizers by species more adapted to sewer conditions (i.e., Methanosaeta spp.). Our study provides data that confirm the capacity of our laboratory experimental system to mimic the functioning of full-scale sewers both microbiologically and operationally in terms of sulfide and methane production, gaining insight into the complex dynamics of key microbial groups during biofilm development. PMID:26253681

  6. Microbial community structures in a closed raw water distribution system biofilm as revealed by 454-pyrosequencing analysis and the effect of microbial biofilm communities on raw water quality.

    PubMed

    Luo, Jianghan; Liang, Heng; Yan, Lijun; Ma, Jun; Yang, Yanling; Li, Guibai

    2013-11-01

    This is the first report on the characterization of the microbial biofilm community structure and water quality change along a closed and stable raw water distribution system. 454-pyrosequencing was employed to investigate the microbial communities in four biofilm samples. 25,426 optimized sequences were obtained. Results showed Proteobacteria was the dominant phylum in each biofilm sample. The abundance of Nitrospiraes in M6 biofilm, Firmicutes in M8 biofilm, Actinobacteria in M9 biofilm were higher by comparing with other three biofilm samples. The M6 microbial biofilm community structure was similar to that of M7, dissimilar to that of M9. Dissolved oxygen and nitrogen was probably major factors to influence the microbial biofilm communities. Nitrospiraes in M6 biofilm and Firmicutes in M8 biofilm were crucial to remove ammonia nitrogen and nitrate in raw water. How to enrich functional microbes in biofilm to pretreat raw water is an important area of future research. PMID:24055963

  7. Seasonal variation in functional properties of microbial communities in beech forest soil.

    PubMed

    Koranda, Marianne; Kaiser, Christina; Fuchslueger, Lucia; Kitzler, Barbara; Sessitsch, Angela; Zechmeister-Boltenstern, Sophie; Richter, Andreas

    2013-05-01

    Substrate quality and the availability of nutrients are major factors controlling microbial decomposition processes in soils. Seasonal alteration in resource availability, which is driven by plants via belowground C allocation, nutrient uptake and litter fall, also exerts effects on soil microbial community composition. Here we investigate if seasonal and experimentally induced changes in microbial community composition lead to alterations in functional properties of microbial communities and thus microbial processes. Beech forest soils characterized by three distinct microbial communities (winter and summer community, and summer community from a tree girdling plot, in which belowground carbon allocation was interrupted) were incubated with different (13)C-labeled substrates with or without inorganic N supply and analyzed for substrate use and various microbial processes. Our results clearly demonstrate that the three investigated microbial communities differed in their functional response to addition of various substrates. The winter communities revealed a higher capacity for degradation of complex C substrates (cellulose, plant cell walls) than the summer communities, indicated by enhanced cellulase activities and reduced mineralization of soil organic matter. In contrast, utilization of labile C sources (glucose) was lower in winter than in summer, demonstrating that summer and winter community were adapted to the availability of different substrates. The saprotrophic community established in girdled plots exhibited a significantly higher utilization of complex C substrates than the more plant root associated community in control plots if additional nitrogen was provided. In this study we were able to demonstrate experimentally that variation in resource availability as well as seasonality in temperate forest soils cause a seasonal variation in functional properties of soil microorganisms, which is due to shifts in community structure and physiological

  8. Biodiversity and succession of microbial community in a multi-habitat membrane bioreactor.

    PubMed

    Tang, Bing; Zhang, Zi; Chen, Xuan; Bin, Liying; Huang, Shaosong; Fu, Fenglian; Yang, Huiwen; Chen, Cuiqun

    2014-07-01

    The present study focused on establishing a multi-habitat membrane bioreactor, as well as exploring its biodiversity and succession of microbial communities. In a long-term operational period (100 days), the dissolved oxygen level of a local zone within the bioreactor decreased consistently from the original oxic state to the final anaerobic state, which led to a continuous succession of the microbial community in the bioreactor. The results revealed that the biodiversity of the microbial community in different zones simultaneously increased, with a similar microbial composition in their final successional stage. The results also indicated that the dominant species during the whole operation were distributed among 6 major phyla. At the initial operational stages, the dominant species in the anoxic-anaerobic and the oxic zones exhibited distinguished difference, whereas at the final operational stage, both zones presented nearly the same dominant microbial species and a rather similar structure in their microbial communities.

  9. 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.

  10. The influence of tropical plant diversity and composition on soil microbial communities.

    PubMed

    Carney, Karen M; Matson, Pamela A

    2006-08-01

    There is growing interest in understanding the linkages between above- and belowground communities, and very little is known about these linkages in tropical systems. Using an experimental site at La Selva Biological Station, Costa Rica, we examined whether plant diversity, plant community composition, and season influenced microbial communities. We also determined whether soil characteristics were related to differences in microbial communities. Phospholipid fatty acid (PLFA) composition revealed that microbial community composition differed across a plant diversity gradient (plots contained 1, 3, 5, or over 25 species). Plant species identity also was a factor influencing microbial community composition; PLFA composition significantly varied among monocultures, and among three-species combinations that differed in plant species composition. Differences among treatments within each of these comparisons were apparent in all four sampling dates of the study. There was no consistent shift in microbial community composition between wet and dry seasons, although we did see significant changes over time. Of all measured soil characteristics, soil C/N was most often associated with changes in microbial community composition across treatment groups. Our findings provide evidence for human alteration of soil microbial communities via the alteration of plant community composition and diversity and that such changes are mediated in part by changes in soil carbon quality.

  11. Iron cycling microbial communities in sediments of the Baltic Sea

    NASA Astrophysics Data System (ADS)

    Reyes, Carolina; Delwig, Olaf; Noriega-Ortega, Beatriz; Dähnke, Kirstin; Böttcher, Michael E.; Friedrich, Michael W.

    2014-05-01

    The biogeochemical cycling of iron is a key early diagenetic process. However, limited information exists about the diversity and metabolic pathways of microorganisms linked to iron cycling in marine sediments. The goal of this study was to determine the bacterial community diversity in sediments showing ongoing dissimilatory iron reduction using 454-pyrosequencing as a first step in characterizing microorganisms potentially involved in iron reduction. For this purpose, two 35 cm cores were sampled from ferruginous sediments in the Skagerrak (SK) and the Bothnian Bay (BB) from the North-Sea Baltic Sea and the northern Baltic Sea respectively. Pore water profiles showed Fe2+ and Mn2+ levels of ~140-150 µM throughout the core below a 6 cm thick oxidized surface layer in SK sediments and ~300 µM below a 2 cm thick surface layer in BB sediments. Dissolved sulphide levels were below detection in both sediments. No significant depletion of SO42- occurred at both sites, further supported by stable S and O isotope analyses of dissolved sulfate at SK site. Only very minor net sulfate reduction is suggested here from the trend in sulphur isotope signatures, in agreement with previously reported gross microbial sulphate rate measurements (Canfield et al., 1993;GCA). Based on these biogeochemical constraints, Fe reduction in the studied sediments is therefore dominated by microbial dissimilatory iron reduction, while cryptic Fe-S-cycling can be largely excluded. 16S rRNA gene sequences indicate Proteobacteria as the dominating microbial group in these sediments. Potential iron and manganese reducing bacteria included Geobacteraceae, Pelobacteraceae, Shewanellaceae, and Oceanospirillales. Additionally, Actinobacteria and Bacteroidetes were present. Also, Fe-oxidizers were present and their occurrence correlated in depth with a Fe-oxide-rich layer, most likely a former buried Fe-oxidation front. Gene sequences point to the presence of Mariprofundus in SK sediments and

  12. Pyrogenic and Fresh Organic Matter Effects on Soil Microbial Communities

    NASA Astrophysics Data System (ADS)

    Whitman, T.; Buckley, D. H.; Lehmann, J.

    2014-12-01

    Soils hold a globally important stock of carbon (C) and can act as both a C source and sink, depending on management and environmental conditions. Pyrogenic organic matter (PyOM) is produced naturally during fires, and contains relatively stable forms of C. Its intentional production has also been proposed as a mechanism for C management (in such cases PyOM is often referred to as "biochar"). However, the impact of natural or anthropogenic PyOM production on soils is complex and depends on many factors. In particular, PyOM additions to soils may have effects on plant growth and on native soil C cycling. The response of the soil microbial community to PyOM additions is likely key to understanding these interactions, but remains poorly characterized. We studied soil C dynamics and soil microbial communities in a field study with 350°C PyOM from 13C-labelled corn stover, a C3-derived soil, and C4 plants (sudangrass). PyOM additions only temporarily increased total soil CO2 fluxes, dramatically less than the increase associated with the addition of corn stover, which likely increased SOC losses. We used high-throughput sequencing of the 16S region on the MiSeq platform to characterize the initial, 12-day and 82-day soil bacterial communiities. We used three-part stable isotopic partitioning after two months to distinguish 334% higher root-derived CO2 fluxes in the plots with PyOM additions than those without, and 45% lower PyOM-C derived CO2 fluxes in the plots with plants present. The 84% increase in estimated cumulative soil CO2 emissions with stover additions was accompanied by a significant shift in the soil bacterial community on days 12 and 82, while the PyOM additions only resulted in significant changes to the overall community on day 82. We investigate which taxa are driving these community shifts, and how they may relate to the soil CO2 fluxes.

  13. Effects of biochar blends on microbial community composition in two Coastal Plain soils

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The amendment of soil with biochar has been demonstrated to have an effect not only on the soil physicochemical properties, but also on soil microbial community composition and activity. Previous reports have demonstrated both positive and negative effects on soil microbial communities. These effect...

  14. Lateral gene transfer in a heavy metal-contaminated-groundwater microbial community

    DOE PAGES

    Hemme, Christopher L.; Green, Stefan J.; Rishishwar, Lavanya; Prakash, Om; Pettenato, Angelica; Chakraborty, Romy; Deutschbauer, Adam M.; Van Nostrand, Joy D.; Wu, Liyou; He, Zhili; et al

    2016-04-05

    Here, unraveling the drivers controlling the response and adaptation of biological communities to environmental change, especially anthropogenic activities, is a central but poorly understood issue in ecology and evolution. Comparative genomics studies suggest that lateral gene transfer (LGT) is a major force driving microbial genome evolution, but its role in the evolution of microbial communities remains elusive.

  15. Soil microbial community structure and functionality during grassland restoration in the Texas High Plains

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soil microbial communities are an indispensable part of restoration programs due to their significant role in ecosystem functioning and sensitivity to disturbance. We evaluated soil microbial community structure using ester-linked fatty acid (EL-FAME) profiling and metabolic functioning, by measurin...

  16. Microbial community structure and variability in the tropical Pacific

    NASA Astrophysics Data System (ADS)

    Landry, Michael R.; Kirchman, David L.

    The spatially extensive tropical Pacific includes regions that are limited by macronutrients or iron, and is thus broadly representative of open-ocean systems in which microbial communities predominate. Despite strong physical forcing due to the El Niño-Southern Oscillation cycle and the local effects of tropical instability waves, microbial abundances from a variety of JGOFS and related studies show similar, modest levels of variability in the high-nutrient, low-chlorophyll (HNLC) equatorial upwelling region, the oligotrophic, western Pacific Warm Pool, and the North Pacific central gyre. Mean 0-50 m abundances of some of the groups distinguished by flow cytometry are significantly enhanced in the HNLC region, including heterotrophic bacteria (HBACT; 720,000 versus 440,000 cells ml -1), Synechococcus spp. (SYN; 9800 versus 2000 cells ml -1) and pico-eukaryotic algae (PEUK; 6300 versus 800 cells ml -1). However, Prochlorococcus spp. (PRO) are slightly more abundant in the low-nitrate regions (180,000 versus 150,000 cells ml -1). The higher HNLC concentrations of SYN and PEUK are part of a broader expansion of the phytoplankton community over the relatively constant PRO base when the limiting nutrient (iron) pool is increased. Elevated biomass and production of phytoplankton and the greater availability of DOC presumably explain the higher HNLC abundances of HBACT. The mean biomass (±standard deviation) of bacterial populations for cross-equatorial transects (14.1±2.8 μg C l -1) is similar to that in the subtropics (11.6±2.7 μg C l -1), with cruise variations falling generally within a 2-fold range. Heterotrophs comprise a significantly higher mean percentage of total prokaryote biomass (59±9%) in the HNLC region than in the low-nutrient subtropics (42±6%). The biomass production of photosynthetic bacteria (PRO and SYN) in the central equatorial Pacific is conservatively twice that of HBACT, but total carbon flux through bacteria (44-75% of phytoplankton 14C

  17. Effects of octahedral molecular sieve on treatment performance, microbial metabolism, and microbial community in expanded granular sludge bed reactor.

    PubMed

    Pan, Fei; Xu, Aihua; Xia, Dongsheng; Yu, Yang; Chen, Guo; Meyer, Melissa; Zhao, Dongye; Huang, Ching-Hua; Wu, Qihang; Fu, Jie

    2015-12-15

    This study evaluated the effects of synthesized octahedral molecular sieve (OMS-2) nanoparticles on the anaerobic microbial community in a model digester, expanded granular sludge bed (EGSB) reactor. The addition of OMS-2 (0.025 g/L) in the EGSB reactors resulted in an enhanced operational performance, i.e., COD removal and biogas production increased by 4% and 11% respectively, and effluent volatile fatty acid (VFA) decreased by 11% relative to the control group. The Biolog EcoPlate™ test was employed to investigate microbial metabolism in the EGSB reactors. Results showed that OMS-2 not only increased the microbial metabolic level but also significantly changed the community level physiological profiling of the microorganisms. The Illumina MiSeq high-throughput sequencing of 16S rRNA gene indicated OMS-2 enhanced the microbial diversity and altered the community structure. The largest bacterial genus Lactococcus, a lactic acid bacterium, reduced from 29.3% to 20.4% by abundance in the presence of 0.25 g/L OMS-2, which may be conducive to decreasing the VFA production and increasing the microbial diversity. OMS-2 also increased the quantities of acetogenic bacteria and Archaea, and promoted the acetogenesis and methanogenesis. The X-ray photoelectron spectroscopy illustrated that Mn(IV)/Mn(III) with high redox potential in OMS-2 were reduced to Mn(II) in the EGSB reactors; this in turn affected the microbial community. PMID:26397455

  18. Soil microbial substrate properties and microbial community responses under irrigated organic and reduced-tillage crop and forage production systems.

    PubMed

    Ghimire, Rajan; Norton, Jay B; Stahl, Peter D; Norton, Urszula

    2014-01-01

    Changes in soil microbiotic properties such as microbial biomass and community structure in response to alternative management systems are driven by microbial substrate quality and substrate utilization. We evaluated irrigated crop and forage production in two separate four-year experiments for differences in microbial substrate quality, microbial biomass and community structure, and microbial substrate utilization under conventional, organic, and reduced-tillage management systems. The six different management systems were imposed on fields previously under long-term, intensively tilled maize production. Soils under crop and forage production responded to conversion from monocropping to crop rotation, as well as to the three different management systems, but in different ways. Under crop production, four years of organic management resulted in the highest soil organic C (SOC) and microbial biomass concentrations, while under forage production, reduced-tillage management most effectively increased SOC and microbial biomass. There were significant increases in relative abundance of bacteria, fungi, and protozoa, with two- to 36-fold increases in biomarker phospholipid fatty acids (PLFAs). Under crop production, dissolved organic C (DOC) content was higher under organic management than under reduced-tillage and conventional management. Perennial legume crops and organic soil amendments in the organic crop rotation system apparently favored greater soil microbial substrate availability, as well as more microbial biomass compared with other management systems that had fewer legume crops in rotation and synthetic fertilizer applications. Among the forage production management systems with equivalent crop rotations, reduced-tillage management had higher microbial substrate availability and greater microbial biomass than other management systems. Combined crop rotation, tillage management, soil amendments, and legume crops in rotations considerably influenced soil

  19. Soil Microbial Substrate Properties and Microbial Community Responses under Irrigated Organic and Reduced-Tillage Crop and Forage Production Systems

    PubMed Central

    Ghimire, Rajan; Norton, Jay B.; Stahl, Peter D.; Norton, Urszula

    2014-01-01

    Changes in soil microbiotic properties such as microbial biomass and community structure in response to alternative management systems are driven by microbial substrate quality and substrate utilization. We evaluated irrigated crop and forage production in two separate four-year experiments for differences in microbial substrate quality, microbial biomass and community structure, and microbial substrate utilization under conventional, organic, and reduced-tillage management systems. The six different management systems were imposed on fields previously under long-term, intensively tilled maize production. Soils under crop and forage production responded to conversion from monocropping to crop rotation, as well as to the three different management systems, but in different ways. Under crop production, four years of organic management resulted in the highest soil organic C (SOC) and microbial biomass concentrations, while under forage production, reduced-tillage management most effectively increased SOC and microbial biomass. There were significant increases in relative abundance of bacteria, fungi, and protozoa, with two- to 36-fold increases in biomarker phospholipid fatty acids (PLFAs). Under crop production, dissolved organic C (DOC) content was higher under organic management than under reduced-tillage and conventional management. Perennial legume crops and organic soil amendments in the organic crop rotation system apparently favored greater soil microbial substrate availability, as well as more microbial biomass compared with other management systems that had fewer legume crops in rotation and synthetic fertilizer applications. Among the forage production management systems with equivalent crop rotations, reduced-tillage management had higher microbial substrate availability and greater microbial biomass than other management systems. Combined crop rotation, tillage management, soil amendments, and legume crops in rotations considerably influenced soil

  20. Microbial communities involved in Kaşar cheese ripening.

    PubMed

    Aydemir, Oğuz; Harth, Henning; Weckx, Stefan; Dervişoğlu, Muhammet; De Vuyst, Luc

    2015-04-01

    The microbiota of non-starter lactic acid bacteria (NSLAB) and their concomitant community dynamics during cheese ripening were investigated for traditional Turkish Kaşar cheeses made from raw cows' milk. Five batches of 15 Kaşar cheeses produced in different dairy plants located in Kars were analysed during their whole ripening phase up to 180 days. Lactobacilli and lactococci were determined as the prevailing microbial groups. The molecular classification and identification of 594 LAB isolates during Kaşar cheese ripening were performed through (GTG)5-PCR fingerprinting of their genomic DNA followed by verification of the (GTG)5-PCR clusters obtained after numerical analysis through 16S rRNA gene sequencing of representative isolates. Lactobacillus casei (247 isolates, 41.6%), Lactobacillus plantarum (77 isolates, 13.0%), and Pediococcus acidilactici (58 isolates, 9.8%) were the prevailing NSLAB species in all Kaşar cheeses of the different dairy plants investigated throughout cheese ripening. The data of the present study contribute to the inventory of unique cheese varieties to enable the prevention of losses of microbial biodiversity and the selection of starter cultures for controlled cheese manufacturing.

  1. Microbial community dynamics in the forefield of glaciers

    PubMed Central

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

    2014-01-01

    Retreating ice fronts (as a result of a warming climate) expose large expanses of deglaciated forefield, which become colonized by microbes and plants. There has been increasing interest in characterizing the biogeochemical development of these ecosystems using a chronosequence approach. Prior to the establishment of plants, microbes use autochthonously produced and allochthonously delivered nutrients for growth. The microbial community composition is largely made up of heterotrophic microbes (both bacteria and fungi), autotrophic microbes and nitrogen-fixing diazotrophs. Microbial activity is thought to be responsible for the initial build-up of labile nutrient pools, facilitating the growth of higher order plant life in developed soils. However, it is unclear to what extent these ecosystems rely on external sources of nutrients such as ancient carbon pools and periodic nitrogen deposition. Furthermore, the seasonal variation of chronosequence dynamics and the effect of winter are largely unexplored. Modelling this ecosystem will provide a quantitative evaluation of the key processes and could guide the focus of future research. Year-round datasets combined with novel metagenomic techniques will help answer some of the pressing questions in this relatively new but rapidly expanding field, which is of growing interest in the context of future large-scale ice retreat. PMID:25274358

  2. Comparative metagenomics of microbial traits within oceanic viral communities

    PubMed Central

    Sharon, Itai; Battchikova, Natalia; Aro, Eva-Mari; Giglione, Carmela; Meinnel, Thierry; Glaser, Fabian; Pinter, Ron Y; Breitbart, Mya; Rohwer, Forest; Béjà, Oded

    2011-01-01

    Viral genomes often contain genes recently acquired from microbes. In some cases (for example, psbA) the proteins encoded by these genes have been shown to be important for viral replication. In this study, using a unique search strategy on the Global Ocean Survey (GOS) metagenomes in combination with marine virome and microbiome pyrosequencing-based datasets, we characterize previously undetected microbial metabolic capabilities concealed within the genomes of uncultured marine viral communities. A total of 34 microbial gene families were detected on 452 viral GOS scaffolds. The majority of auxiliary metabolic genes found on these scaffolds have never been reported in phages. Host genes detected in viruses were mainly divided between genes encoding for different energy metabolism pathways, such as electron transport and newly identified photosystem genes, or translation and post-translation mechanism related. Our findings suggest previously undetected ways, in which marine phages adapt to their hosts and improve their fitness, including translation and post-translation level control over the host rather than the already known transcription level control. PMID:21307954

  3. Microbial community dynamics in the forefield of glaciers.

    PubMed

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

    2014-11-22

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

  4. Microbial Community Analysis of the Costa Rica Margin from a Metagenomic Perspective

    NASA Astrophysics Data System (ADS)

    Leon Zayas, R. I.; Martino, A. J.; House, C. H.; Biddle, J.

    2015-12-01

    The taxonomic distribution and metabolic capabilities of microbial communities in the subseafloor are poorly understood. In this study we aimed to analyze the microbial community of samples obtained from the Costa Rica margin in two different sites, one where three samples were collected at 2 meters below the sea floor (mbsf), 33 mbsf and 93 mbsf, and another from 22 mbsf to 45 mbsf. Whole community analysis of conserved gene markers show that the microbial community varies with depth, in composition as well as in average genome size. Genome sizes do not increase with depth and metabolic strategies change with streamlined functions at depth. Specific metabolic processes are found to be performed by distinct members of the microbial community. Changes within the microbial populations related to depth, age and geochemistry are able to be investigated.

  5. Metagenomic insights into the dynamics of microbial communities in food.

    PubMed

    Kergourlay, Gilles; Taminiau, Bernard; Daube, Georges; Champomier Vergès, Marie-Christine

    2015-11-20

    Metagenomics has proven to be a powerful tool in exploring a large diversity of natural environments such as air, soil, water, and plants, as well as various human microbiota (e.g. digestive tract, lungs, skin). DNA sequencing techniques are becoming increasingly popular and less and less expensive. Given that high-throughput DNA sequencing approaches have only recently started to be used to decipher food microbial ecosystems, there is a significant growth potential for such technologies in the field of food microbiology. The aim of this review is to present a survey of recent food investigations via metagenomics and to illustrate how this approach can be a valuable tool in the better characterization of foods and their transformation, storage and safety. Traditional food in particular has been thoroughly explored by global approaches in order to provide information on multi-species and multi-organism communities. PMID:26414193

  6. Biocorrosive Thermophilic Microbial Communities in Alaskan North Slope Oil Facilities

    SciTech Connect

    Duncan, Kathleen E.; Gieg, Lisa M.; Parisi, Victoria A.; Tanner, Ralph S.; Green Tringe, Susannah; Bristow, Jim; Suflita, Joseph M.

    2009-09-16

    Corrosion of metallic oilfield pipelines by microorganisms is a costly but poorly understood phenomenon, with standard treatment methods targeting mesophilic sulfatereducing bacteria. In assessing biocorrosion potential at an Alaskan North Slope oil field, we identified thermophilic hydrogen-using methanogens, syntrophic bacteria, peptideand amino acid-fermenting bacteria, iron reducers, sulfur/thiosulfate-reducing bacteria and sulfate-reducing archaea. These microbes can stimulate metal corrosion through production of organic acids, CO2, sulfur species, and via hydrogen oxidation and iron reduction, implicating many more types of organisms than are currently targeted. Micromolar quantities of putative anaerobic metabolites of C1-C4 n-alkanes in pipeline fluids were detected, implying that these low molecular weight hydrocarbons, routinely injected into reservoirs for oil recovery purposes, are biodegraded and provide biocorrosive microbial communities with an important source of nutrients.

  7. Ecology and application of haloalkaliphilic anaerobic microbial communities.

    PubMed

    Sousa, João A B; Sorokin, Dimitry Y; Bijmans, Martijn F M; Plugge, Caroline M; Stams, Alfons J M

    2015-11-01

    Haloalkaliphilic microorganisms that grow optimally at high-pH and high-salinity conditions can be found in natural environments such as soda lakes. These globally spread lakes harbour interesting anaerobic microorganisms that have the potential of being applied in existing technologies or create new opportunities. In this review, we discuss the potential application of haloalkaliphilic anaerobic microbial communities in the fermentation of lignocellulosic feedstocks material subjected to an alkaline pre-treatment, methane production and sulfur removal technology. Also, the general advantages of operation at haloalkaline conditions, such as low volatile fatty acid and sulfide toxicity, are addressed. Finally, an outlook into the main challenges like ammonia toxicity and lack of aggregation is provided. PMID:26359181

  8. Is metagenomics resolving identification of functions in microbial communities?

    PubMed

    Chistoserdova, Ludmila

    2014-01-01

    We are coming up on the tenth anniversary of the broad use of the method involving whole metagenome shotgun sequencing, referred to as metagenomics. The application of this approach has definitely revolutionized microbiology and the related fields, including the realization of the importance of the human microbiome. As such, metagenomics has already provided a novel outlook on the complexity and dynamics of microbial communities that are an important part of the biosphere of the planet. Accumulation of massive amounts of sequence data also caused a surge in the development of bioinformatics tools specially designed to provide pipelines for data analysis and visualization. However, a critical outlook into the field is required to appreciate what could be and what has currently been gained from the massive sequence databases that are being generated with ever-increasing speed.

  9. Metagenomic insights into the dynamics of microbial communities in food.

    PubMed

    Kergourlay, Gilles; Taminiau, Bernard; Daube, Georges; Champomier Vergès, Marie-Christine

    2015-11-20

    Metagenomics has proven to be a powerful tool in exploring a large diversity of natural environments such as air, soil, water, and plants, as well as various human microbiota (e.g. digestive tract, lungs, skin). DNA sequencing techniques are becoming increasingly popular and less and less expensive. Given that high-throughput DNA sequencing approaches have only recently started to be used to decipher food microbial ecosystems, there is a significant growth potential for such technologies in the field of food microbiology. The aim of this review is to present a survey of recent food investigations via metagenomics and to illustrate how this approach can be a valuable tool in the better characterization of foods and their transformation, storage and safety. Traditional food in particular has been thoroughly explored by global approaches in order to provide information on multi-species and multi-organism communities.

  10. Two distinct microbial communities revealed in the sponge Cinachyrella.

    PubMed

    Cuvelier, Marie L; Blake, Emily; Mulheron, Rebecca; McCarthy, Peter J; Blackwelder, Patricia; Thurber, Rebecca L Vega; Lopez, Jose V

    2014-01-01

    Marine sponges are vital components of benthic and coral reef ecosystems, providing shelter and nutrition for many organisms. In addition, sponges act as an essential carbon and nutrient link between the pelagic and benthic environment by filtering large quantities of seawater. Many sponge species harbor a diverse microbial community (including Archaea, Bacteria and Eukaryotes), which can constitute up to 50% of the sponge biomass. Sponges of the genus Cinachyrella are common in Caribbean and Floridian reefs and their archaeal and bacterial microbiomes were explored here using 16S rRNA gene tag pyrosequencing. Cinachyrella specimens and seawater samples were collected from the same South Florida reef at two different times of year. In total, 639 OTUs (12 archaeal and 627 bacterial) belonging to 2 archaeal and 21 bacterial phyla were detected in the sponges. Based on their microbiomes, the six sponge samples formed two distinct groups, namely sponge group 1 (SG1) with lower diversity (Shannon-Weiner index: 3.73 ± 0.22) and SG2 with higher diversity (Shannon-Weiner index: 5.95 ± 0.25). Hosts' 28S rRNA gene sequences further confirmed that the sponge specimens were composed of two taxa closely related to Cinachyrella kuekenthalli. Both sponge groups were dominated by Proteobacteria, but Alphaproteobacteria were significantly more abundant in SG1. SG2 harbored many bacterial phyla (>1% of sequences) present in low abundance or below detection limits (<0.07%) in SG1 including: Acidobacteria, Chloroflexi, Gemmatimonadetes, Nitrospirae, PAUC34f, Poribacteria, and Verrucomicrobia. Furthermore, SG1 and SG2 only had 95 OTUs in common, representing 30.5 and 22.4% of SG1 and SG2's total OTUs, respectively. These results suggest that the sponge host may exert a pivotal influence on the nature and structure of the microbial community and may only be marginally affected by external environment parameters. PMID:25408689

  11. Metagenomic analysis of microbial community in uranium-contaminated soil.

    PubMed

    Yan, Xun; Luo, Xuegang; Zhao, Min

    2016-01-01

    Uranium tailing is a serious pollution challenge for the environment. Based on metagenomic sequencing analysis, we explored the functional and structural diversity of the microbial community in six soil samples taken at different soil depths from uranium-contaminated and uncontaminated areas. Kyoto Encyclopedia of Genes and Genomes Orthology (KO) groups were obtained using a Basic Local Alignment Search Tool search based on the universal protein resource database. The KO-pathway network was then constructed using the selected KOs. Finally, alpha and beta diversity analyses were performed to explore the differences in soil bacterial diversity between the radioactive soil and uncontaminated soil. In total, 30-68 million high-quality reads were obtained. Sequence assembly yielded 286,615 contigs; and these contigs mostly annotated to 1699 KOs. The KO distributions were similar among the six soil samples. Moreover, the proportion of the metabolism of other amino acids (e.g., beta-alanine, taurine, and hypotaurine) and signal transduction was significantly lower in radioactive soil than in uncontaminated soil, whereas the proportion of membrane transport and carbohydrate metabolism was higher. Additionally, KOs were mostly enriched in ATP-binding cassette transporters and two-component systems. According to diversity analyses, Actinobacteria and Proteobacteria were the dominant phyla in radioactive and uncontaminated soil, and Robiginitalea, Microlunatus, and Alicyclobacillus were the dominant genera in radioactive soil. Taken together, these results demonstrate that soil microbial community, structure, and functions show significant changes in uranium-contaminated soil. The dominant categories such as Actinobacteria and Proteobacteria may be applied in environmental governance for uranium-contaminated soil in southern China.

  12. Two distinct microbial communities revealed in the sponge Cinachyrella

    PubMed Central

    Cuvelier, Marie L.; Blake, Emily; Mulheron, Rebecca; McCarthy, Peter J.; Blackwelder, Patricia; Thurber, Rebecca L. Vega; Lopez, Jose V.

    2014-01-01

    Marine sponges are vital components of benthic and coral reef ecosystems, providing shelter and nutrition for many organisms. In addition, sponges act as an essential carbon and nutrient link between the pelagic and benthic environment by filtering large quantities of seawater. Many sponge species harbor a diverse microbial community (including Archaea, Bacteria and Eukaryotes), which can constitute up to 50% of the sponge biomass. Sponges of the genus Cinachyrella are common in Caribbean and Floridian reefs and their archaeal and bacterial microbiomes were explored here using 16S rRNA gene tag pyrosequencing. Cinachyrella specimens and seawater samples were collected from the same South Florida reef at two different times of year. In total, 639 OTUs (12 archaeal and 627 bacterial) belonging to 2 archaeal and 21 bacterial phyla were detected in the sponges. Based on their microbiomes, the six sponge samples formed two distinct groups, namely sponge group 1 (SG1) with lower diversity (Shannon-Weiner index: 3.73 ± 0.22) and SG2 with higher diversity (Shannon-Weiner index: 5.95 ± 0.25). Hosts' 28S rRNA gene sequences further confirmed that the sponge specimens were composed of two taxa closely related to Cinachyrella kuekenthalli. Both sponge groups were dominated by Proteobacteria, but Alphaproteobacteria were significantly more abundant in SG1. SG2 harbored many bacterial phyla (>1% of sequences) present in low abundance or below detection limits (<0.07%) in SG1 including: Acidobacteria, Chloroflexi, Gemmatimonadetes, Nitrospirae, PAUC34f, Poribacteria, and Verrucomicrobia. Furthermore, SG1 and SG2 only had 95 OTUs in common, representing 30.5 and 22.4% of SG1 and SG2's total OTUs, respectively. These results suggest that the sponge host may exert a pivotal influence on the nature and structure of the microbial community and may only be marginally affected by external environment parameters. PMID:25408689

  13. Plant Extract (Bupleurum falcatum) as a Green Factory for Biofabrication of Gold Nanoparticles.

    PubMed

    Lee, You Jeong; Cha, Song-Hyun; Lee, Kyoung Jin; Kim, Yeong Shik; Cho, Seonho; Park, Youmie

    2015-09-01

    This work describes a biofabrication process for gold nanoparticles in which the plant extract (Bupleurum falcatum) is used as a reducing agent to convert gold ions to gold nanoparticles. Biofabricated gold nanoparticles with spherical shapes were observed with an average diameter of 10.5 ± 2.3 nm. The color of the gold nanoparticles was purple, with a surface plasmon resonance peak at 542 nm. The face-centered cubic structure of crystalline gold was confirmed by high-resolution X-ray diffraction patterns. The biofabricated gold nanoparticles demonstrated excellent catalytic activity towards the 4-nitrophenol reduction reaction. The current report suggests that plant extracts are valuable natural sources for the biofabrication of gold nanoparticles with excellent catalytic activities.

  14. Microbial community dynamics and effect of environmental microbial reservoirs on red-backed salamanders (Plethodon cinereus).

    PubMed

    Loudon, Andrew H; Woodhams, Douglas C; Parfrey, Laura Wegener; Archer, Holly; Knight, Rob; McKenzie, Valerie; Harris, Reid N

    2014-04-01

    Beneficial cutaneous bacteria on amphibians can protect against the lethal disease chytridiomycosis, which has devastated many amphibian species and is caused by the fungus Batrachochytrium dendrobatidis. We describe the diversity of bacteria on red-backed salamanders (Plethodon cinereus) in the wild and the stability of these communities through time in captivity using culture-independent Illumina 16S rRNA gene sequencing. After field sampling, salamanders were housed with soil from the field or sterile media. The captive conditions led to different trajectories of bacterial communities. Eight OTUs present on >90% of salamanders in the field, through time, and in both treatments were defined as the core community, suggesting that some bacteria are closely associated with the host and are independent of an environmental reservoir. One of these taxa, a Pseudomonas sp., was previously cultured from amphibians and found to be antifungal. As all host-associated bacteria were found in the soil reservoir, environmental microbes strongly influence host-microbial diversity and likely regulate the core community. Using PICRUSt, an exploratory bioinformatics tool to predict gene functions, we found that core skin bacteria provided similar gene functions to the entire community. We suggest that future experiments focus on testing whether core bacteria on salamander skin contribute to the observed resistance to chytridiomycosis in this species even under hygenic captive conditions. For disease-susceptible hosts, providing an environmental reservoir with defensive bacteria in captive-rearing programs may improve outcomes by increasing bacterial diversity on threatened amphibians or increasing the likelihood that defensive bacteria are available for colonization.

  15. Microbial community dynamics and effect of environmental microbial reservoirs on red-backed salamanders (Plethodon cinereus).

    PubMed

    Loudon, Andrew H; Woodhams, Douglas C; Parfrey, Laura Wegener; Archer, Holly; Knight, Rob; McKenzie, Valerie; Harris, Reid N

    2014-04-01

    Beneficial cutaneous bacteria on amphibians can protect against the lethal disease chytridiomycosis, which has devastated many amphibian species and is caused by the fungus Batrachochytrium dendrobatidis. We describe the diversity of bacteria on red-backed salamanders (Plethodon cinereus) in the wild and the stability of these communities through time in captivity using culture-independent Illumina 16S rRNA gene sequencing. After field sampling, salamanders were housed with soil from the field or sterile media. The captive conditions led to different trajectories of bacterial communities. Eight OTUs present on >90% of salamanders in the field, through time, and in both treatments were defined as the core community, suggesting that some bacteria are closely associated with the host and are independent of an environmental reservoir. One of these taxa, a Pseudomonas sp., was previously cultured from amphibians and found to be antifungal. As all host-associated bacteria were found in the soil reservoir, environmental microbes strongly influence host-microbial diversity and likely regulate the core community. Using PICRUSt, an exploratory bioinformatics tool to predict gene functions, we found that core skin bacteria provided similar gene functions to the entire community. We suggest that future experiments focus on testing whether core bacteria on salamander skin contribute to the observed resistance to chytridiomycosis in this species even under hygenic captive conditions. For disease-susceptible hosts, providing an environmental reservoir with defensive bacteria in captive-rearing programs may improve outcomes by increasing bacterial diversity on threatened amphibians or increasing the likelihood that defensive bacteria are available for colonization. PMID:24335825

  16. Microbial community dynamics and effect of environmental microbial reservoirs on red-backed salamanders (Plethodon cinereus)

    PubMed Central

    Loudon, Andrew H; Woodhams, Douglas C; Parfrey, Laura Wegener; Archer, Holly; Knight, Rob; McKenzie, Valerie; Harris, Reid N

    2014-01-01

    Beneficial cutaneous bacteria on amphibians can protect against the lethal disease chytridiomycosis, which has devastated many amphibian species and is caused by the fungus Batrachochytrium dendrobatidis. We describe the diversity of bacteria on red-backed salamanders (Plethodon cinereus) in the wild and the stability of these communities through time in captivity using culture-independent Illumina 16S rRNA gene sequencing. After field sampling, salamanders were housed with soil from the field or sterile media. The captive conditions led to different trajectories of bacterial communities. Eight OTUs present on >90% of salamanders in the field, through time, and in both treatments were defined as the core community, suggesting that some bacteria are closely associated with the host and are independent of an environmental reservoir. One of these taxa, a Pseudomonas sp., was previously cultured from amphibians and found to be antifungal. As all host-associated bacteria were found in the soil reservoir, environmental microbes strongly influence host–microbial diversity and likely regulate the core community. Using PICRUSt, an exploratory bioinformatics tool to predict gene functions, we found that core skin bacteria provided similar gene functions to the entire community. We suggest that future experiments focus on testing whether core bacteria on salamander skin contribute to the observed resistance to chytridiomycosis in this species even under hygenic captive conditions. For disease-susceptible hosts, providing an environmental reservoir with defensive bacteria in captive-rearing programs may improve outcomes by increasing bacterial diversity on threatened amphibians or increasing the likelihood that defensive bacteria are available for colonization. PMID:24335825

  17. Spatial distribution of viruses associated with planktonic and attached microbial communities in hydrothermal environments.

    PubMed

    Yoshida-Takashima, Yukari; Nunoura, Takuro; Kazama, Hiromi; Noguchi, Takuroh; Inoue, Kazuhiro; Akashi, Hironori; Yamanaka, Toshiro; Toki, Tomohiro; Yamamoto, Masahiro; Furushima, Yasuo; Ueno, Yuichiro; Yamamoto, Hiroyuki; Takai, Ken

    2012-03-01

    Viruses play important roles in marine surface ecosystems, but little is known about viral ecology and virus-mediated processes in deep-sea hydrothermal microbial communities. In this study, we examined virus-like particle (VLP) abundances in planktonic and attached microbial communities, which occur in physical and chemical gradients in both deep and shallow submarine hydrothermal environments (mixing waters between hydrothermal fluids and ambient seawater and dense microbial communities attached to chimney surface areas or macrofaunal bodies and colonies). We found that viruses were widely distributed in a variety of hydrothermal microbial habitats, with the exception of the interior parts of hydrothermal chimney structures. The VLP abundance and VLP-to-prokaryote ratio (VPR) in the planktonic habitats increased as the ratio of hydrothermal fluid to mixing water increased. On the other hand, the VLP abundance in attached microbial communities was significantly and positively correlated with the whole prokaryotic abundance; however, the VPRs were always much lower than those for the surrounding hydrothermal waters. This is the first report to show VLP abundance in the attached microbial communities of submarine hydrothermal environments, which presented VPR values significantly lower than those in planktonic microbial communities reported before. These results suggested that viral lifestyles (e.g., lysogenic prevalence) and virus interactions with prokaryotes are significantly different among the planktonic and attached microbial communities that are developing in the submarine hydrothermal environments. PMID:22210205

  18. Spatial Distribution of Viruses Associated with Planktonic and Attached Microbial Communities in Hydrothermal Environments

    PubMed Central

    Nunoura, Takuro; Kazama, Hiromi; Noguchi, Takuroh; Inoue, Kazuhiro; Akashi, Hironori; Yamanaka, Toshiro; Toki, Tomohiro; Yamamoto, Masahiro; Furushima, Yasuo; Ueno, Yuichiro; Yamamoto, Hiroyuki; Takai, Ken

    2012-01-01

    Viruses play important roles in marine surface ecosystems, but little is known about viral ecology and virus-mediated processes in deep-sea hydrothermal microbial communities. In this study, we examined virus-like particle (VLP) abundances in planktonic and attached microbial communities, which occur in physical and chemical gradients in both deep and shallow submarine hydrothermal environments (mixing waters between hydrothermal fluids and ambient seawater and dense microbial communities attached to chimney surface areas or macrofaunal bodies and colonies). We found that viruses were widely distributed in a variety of hydrothermal microbial habitats, with the exception of the interior parts of hydrothermal chimney structures. The VLP abundance and VLP-to-prokaryote ratio (VPR) in the planktonic habitats increased as the ratio of hydrothermal fluid to mixing water increased. On the other hand, the VLP abundance in attached microbial communities was significantly and positively correlated with the whole prokaryotic abundance; however, the VPRs were always much lower than those for the surrounding hydrothermal waters. This is the first report to show VLP abundance in the attached microbial communities of submarine hydrothermal environments, which presented VPR values significantly lower than those in planktonic microbial communities reported before. These results suggested that viral lifestyles (e.g., lysogenic prevalence) and virus interactions with prokaryotes are significantly different among the planktonic and attached microbial communities that are developing in the submarine hydrothermal environments. PMID:22210205

  19. Microbial Community Metabolic Modeling: A Community Data-Driven Network Reconstruction.

    PubMed

    Henry, Christopher S; Bernstein, Hans C; Weisenhorn, Pamela; Taylor, Ronald C; Lee, Joon-Yong; Zucker, Jeremy; Song, Hyun-Seob

    2016-11-01

    Metabolic network modeling of microbial communities provides an in-depth understanding of community-wide metabolic and regulatory processes. Compared to single organism analyses, community metabolic network modeling is more complex because it needs to account for interspecies interactions. To date, most approaches focus on reconstruction of high-quality individual networks so that, when combined, they can predict community behaviors as a result of interspecies interactions. However, this conventional method becomes ineffective for communities whose members are not well characterized and cannot be experimentally interrogated in isolation. Here, we tested a new approach that uses community-level data as a critical input for the network reconstruction process. This method focuses on directly predicting interspecies metabolic interactions in a community, when axenic information is insufficient. We validated our method through the case study of a bacterial photoautotroph-heterotroph consortium that was used to provide data needed for a community-level metabolic network reconstruction. Resulting simulations provided experimentally validated predictions of how a photoautotrophic cyanobacterium supports the growth of an obligate heterotrophic species by providing organic carbon and nitrogen sources. J. Cell. Physiol. 231: 2339-2345, 2016. © 2016 Wiley Periodicals, Inc. PMID:27186840

  20. Community-Level Physiological Profiling of Microbial Communities in Constructed Wetlands: Effects of Sample Preparation.

    PubMed

    Button, Mark; Weber, Kela; Nivala, Jaime; Aubron, Thomas; Müller, Roland Arno

    2016-03-01

    Community-level physiological profiling (CLPP) using BIOLOG® EcoPlates™ has become a popular method for characterizing and comparing the functional diversity, functional potential, and metabolic activity of heterotrophic microbial communities. The method was originally developed for profiling soil communities; however, its usage has expanded into the fields of ecotoxicology, agronomy, and the monitoring and profiling of microbial communities in various wastewater treatment systems, including constructed wetlands for water pollution control. When performing CLPP on aqueous samples from constructed wetlands, a wide variety of sample characteristics can be encountered and challenges may arise due to excessive solids, color, or turbidity. The aim of this study was to investigate the impacts of different sample preparation methods on CLPP performed on a variety of aqueous samples covering a broad range of physical and chemical characteristics. The results show that using filter paper, centrifugation, or settling helped clarify samples for subsequent CLPP analysis, however did not do so as effectively as dilution for the darkest samples. Dilution was able to provide suitable clarity for the darkest samples; however, 100-fold dilution significantly affected the carbon source utilization patterns (CSUPs), particularly with samples that were already partially or fully clear. Ten-fold dilution also had some effect on the CSUPs of samples which were originally clear; however, the effect was minimal. Based on these findings, for this specific set of samples, a 10-fold dilution provided a good balance between ease of use, sufficient clarity (for dark samples), and limited effect on CSUPs. The process and findings outlined here can hopefully serve future studies looking to utilize CLPP for functional analysis of microbial communities and also assist in comparing data from studies where different sample preparation methods were utilized. PMID:26563413

  1. Community-Level Physiological Profiling of Microbial Communities in Constructed Wetlands: Effects of Sample Preparation.

    PubMed

    Button, Mark; Weber, Kela; Nivala, Jaime; Aubron, Thomas; Müller, Roland Arno

    2016-03-01

    Community-level physiological profiling (CLPP) using BIOLOG® EcoPlates™ has become a popular method for characterizing and comparing the functional diversity, functional potential, and metabolic activity of heterotrophic microbial communities. The method was originally developed for profiling soil communities; however, its usage has expanded into the fields of ecotoxicology, agronomy, and the monitoring and profiling of microbial communities in various wastewater treatment systems, including constructed wetlands for water pollution control. When performing CLPP on aqueous samples from constructed wetlands, a wide variety of sample characteristics can be encountered and challenges may arise due to excessive solids, color, or turbidity. The aim of this study was to investigate the impacts of different sample preparation methods on CLPP performed on a variety of aqueous samples covering a broad range of physical and chemical characteristics. The results show that using filter paper, centrifugation, or settling helped clarify samples for subsequent CLPP analysis, however did not do so as effectively as dilution for the darkest samples. Dilution was able to provide suitable clarity for the darkest samples; however, 100-fold dilution significantly affected the carbon source utilization patterns (CSUPs), particularly with samples that were already partially or fully clear. Ten-fold dilution also had some effect on the CSUPs of samples which were originally clear; however, the effect was minimal. Based on these findings, for this specific set of samples, a 10-fold dilution provided a good balance between ease of use, sufficient clarity (for dark samples), and limited effect on CSUPs. The process and findings outlined here can hopefully serve future studies looking to utilize CLPP for functional analysis of microbial communities and also assist in comparing data from studies where different sample preparation methods were utilized.

  2. Which Members of the Microbial Communities Are Active? Microarrays

    NASA Astrophysics Data System (ADS)

    Morris, Brandon E. L.

    only at the early stages of understanding the microbial processes that occur in petroliferous formations and the surrounding subterranean environment. Important first steps in characterising the microbiology of oilfield systems involve identifying the microbial community structure and determining how population diversity changes are affected by the overall geochemical and biological parameters of the system. This is relatively easy to do today by using general 16S rRNA primers for PCR and building clone libraries. For example, previous studies using molecular methods characterised many dominant prokaryotes in petroleum reservoirs (Orphan et al., 2000) and in two Alaskan North Slope oil facilities (Duncan et al., 2009; Pham et al., 2009). However, the problem is that more traditional molecular biology approaches, such as 16S clone libraries, fail to detect large portions of the community perhaps missing up to half of the biodiversity (see Hong et al., 2009) and require significant laboratory time to construct large libraries necessary to increase the probability of detecting the majority of even bacterial biodiversity. In the energy sector, the overarching desire would be to quickly assess the extent of in situ hydrocarbon biodegradation or to disrupt detrimental processes such as biofouling, and in these cases it may not be necessary to identify specific microbial species. Rather, it would be more critical to evaluate metabolic processes or monitor gene products that are implicated in the specific activity of interest. Research goals such as these are well suited for a tailored application of microarray technology.

  3. Carbon availability structures microbial community composition and function in soil aggregate fractions

    NASA Astrophysics Data System (ADS)

    Hofmockel, K. S.; Bach, E.; Williams, R.; Howe, A.

    2014-12-01

    Identifying the microbial metabolic pathways that most strongly influence ecosystem carbon (C) cycling requires a deeper understanding of the availability and accessibility of microbial substrates. A first step towards this goal is characterizing the relationships between microbial community function and soil C chemistry in a field context. For this perspective, soil aggregate fractions can be used as model systems that scale between microbe-substrate interactions and ecosystem C cycling and storage. The present study addresses how physicochemical variation among soil aggregate fractions influences the composition and functional potential of C cycling microbial communities. We report variation across soil aggregates using plot scale biological replicates from biofuel agroecosystems (fertilized, reconstructed, tallgrass prairie). Our results suggest that C and nitrogen (N) chemistry significantly differ among aggregate fractions. This leads to variation in microbial community composition, which was better characterized among aggregates than by using the whole soil. In fact by considering soil aggregation, we were able to characterize almost 2000 more taxa than whole soil alone, resulting in 65% greater community richness. Availability of C and N strongly influenced the composition of microbial communities among soil aggregate fractions. The normalized abundance of microbial functional guilds among aggregate fractions correlated with C and N chemistry, as did functional potential, measured by extracellular enzyme activity. Metagenomic results suggest that soil aggregate fractions select for functionally distinct microbial communities, which may significantly influence decomposition and soil C storage. Our study provides support for the premise that integration of soil aggregate chemistry, especially microaggregates that have greater microbial richness and occur at spatial scales relevant to microbial community functioning, may be necessary to understand the role of

  4. Colonization patterns of soil microbial communities in the Atacama Desert

    PubMed Central

    2013-01-01

    Background The Atacama Desert is one of the driest deserts in the world and its soil, with extremely low moisture, organic carbon content, and oxidizing conditions, is considered to be at the dry limit for life. Results Analyses of high throughput DNA sequence data revealed that bacterial communities from six geographic locations in the hyper-arid core and along a North-South moisture gradient were structurally and phylogenetically distinct (ANOVA test for observed operating taxonomic units at 97% similarity (OTU0.03), P <0.001) and that communities from locations in the hyper-arid zone displayed the lowest levels of diversity. We found bacterial taxa similar to those found in other arid soil communities with an abundance of Rubrobacterales, Actinomycetales, Acidimicrobiales, and a number of families from the Thermoleophilia. The extremely low abundance of Firmicutes indicated that most bacteria in the soil were in the form of vegetative cells. Integrating molecular data with climate and soil geochemistry, we found that air relative humidity (RH) and soil conductivity significantly correlated with microbial communities’ diversity metrics (least squares linear regression for observed OTU0.03 and air RH and soil conductivity, P <0.001; UniFrac PCoA Spearman’s correlation for air RH and soil conductivity, P <0.0001), indicating that water availability and salt content are key factors in shaping the Atacama soil microbiome. Mineralization studies showed communities actively metabolizing in all soil samples, with increased rates in soils from the southern locations. Conclusions Our results suggest that microorganisms in the driest soils of the Atacama Desert are in a state of stasis for most of the time, but can potentially metabolize if presented with liquid water for a sufficient duration. Over geological time, rare rain events and physicochemical factors potentially played a major role in selecting micro-organisms that are most adapted to extreme desiccating

  5. Oxygen and the spatial structure of microbial communities.

    PubMed

    Fenchel, Tom; Finlay, Bland

    2008-11-01

    Oxygen has two faces. On one side it is the terminal electron acceptor of aerobic respiration - the most efficient engine of energy metabolism. On the other hand, oxygen is toxic because the reduction of molecular O2 creates reactive oxygen species such as the superoxide anion, peroxide, and the hydroxyl radical. Probably most prokaryotes, and virtually all eukaryotes, depend on oxygen respiration, and we show that the ambiguous relation to oxygen is both an evolutionary force and a dominating factor driving functional interactions and the spatial structure of microbial communities.We focus on microbial communities that are specialised for life in concentration gradients of oxygen, where they acquire the full panoply of specific requirements from limited ranges of PO2, which also support the spatial organisation of microbial communities. Marine and lake sediments provide examples of steep O2 gradients, which arise because consumption or production of oxygen exceeds transport rates of molecular diffusion. Deep lakes undergo thermal stratification in warm waters, resulting in seasonal anaerobiosis below the thermocline, and lakes with a permanent pycnocline often have permanent anoxic deep water. The oxycline is here biologically similar to sediments, and it harbours similar microbial biota, the main difference being the spatial scale. In sediments, transport is dominated by molecular diffusion, and in the water column, turbulent mixing dominates vertical transport. Cell size determines the minimum requirement of aerobic organisms. For bacteria (and mitochondria), the half-saturation constant for oxygen uptake ranges within 0.05-0.1% atmospheric saturation; for the amoeba Acanthamoeba castellanii it is 0.2%, and for two ciliate species measuring around 150 microm, it is 1-2 % atmospheric saturation. Protection against O2 toxicity has an energetic cost that increases with increasing ambient O2 tension. Oxygen sensing seems universal in aquatic organisms. Many aspects

  6. [Carbon sources metabolic characteristics of airborne microbial communities in constructed wetlands].

    PubMed

    Song, Zhi-Wen; Wang, Lin; Xu, Ai-Ling; Wu, Deng-Deng; Xia, Yan

    2015-02-01

    Using BIOLOG-GN plates, this article describes the carbon sources metabolic characteristics of airborne microbial communities in a free surface-flow constructed wetland in different seasons and clarify the correlation between airborne microbial metabolic functions and environmental factors. The average well color development (AWCD), carbon metabolic profiles and McIntosh values of airborne microbial communities in different seasons were quite different. Analysis of the variations showed that AWCD in spring and summer differed significantly from that in autumn and winter (P < 0.01). In the same season, the degree of utilization of different types of carbon by airborne microbes was different. Summer had a significant difference from other seasons (P < 0.05). Dominant communities of airborne microbes in four seasons were carboxylic acids metabolic community, carbohydrates metabolic community, polymers metabolic community and carboxylic acids metabolic community respectively. Principal component analysis showed that the carbon metabolic characteristics of airborne microbial community in autumn were similar to those in winter but different from those in spring and summer. The characteristics of carbon metabolism revealed differences between summer and spring, autumn, or winter. These differences were mainly caused by amines or amides while the differences between spring and autumn or winter were mainly caused by carboxylic acids. Environmental factors, including changes in wind speed, temperature, and humidity acted to influence the carbon sources metabolic properties of airborne microbial community. The dominant environmental factors that acted to influence the carbon sources metabolic properties of airborne microbial community varied between different seasons.

  7. Characterization of Microbial Communities Found in Bioreactor Effluent

    NASA Technical Reports Server (NTRS)

    Flowe, Candice

    2013-01-01

    The purpose of this investigation was to examine microbial communities of simulated wastewater effluent from hollow fiber membrane bioreactors collected from the Space Life Science Laboratory and Texas Technical University. Microbes were characterized using quantitative polymerase chain reaction where a total count of bacteria and fungi were determined. The primers that were used to determine the total count of bacteria and fungi were targeted for 16S rDNA genes and the internal transcribed spacer, respectively. PCR products were detected with SYBR Green I fluorescent dye and a melting curve analysis was performed to identify unique melt profiles resulting from DNA sequence variations from each species of the community. Results from both the total bacteria and total fungi count assays showed that distinct populations were present in isolates from these bioreactors. This was exhibited by variation in the number of peaks observed on the melting curve analysis graph. Further analysis of these results using species-specific primers will shed light on exactly which microbes are present in these effluents. Information gained from this study will enable the design of a system that can efficiently monitor microbes that play a role in the biogeochemical cycling of nitrogen in wastewater on the International Space Station to assist in the design of a sustainable system capable of converting this nutrient.

  8. Advances in Quantitative Proteomics of Microbes and Microbial Communities

    NASA Astrophysics Data System (ADS)

    Waldbauer, J.; Zhang, L.; Rizzo, A. I.

    2015-12-01

    Quantitative measurements of gene expression are key to developing a mechanistic, predictive understanding of how microbial metabolism drives many biogeochemical fluxes and responds to environmental change. High-throughput RNA-sequencing can afford a wealth of information about transcript-level expression patterns, but it is becoming clear that expression dynamics are often very different at the protein level where biochemistry actually occurs. These divergent dynamics between levels of biological organization necessitate quantitative proteomic measurements to address many biogeochemical questions. The protein-level expression changes that underlie shifts in the magnitude, or even the direction, of metabolic and biogeochemical fluxes can be quite subtle and test the limits of current quantitative proteomics techniques. Here we describe methodologies for high-precision, whole-proteome quantification that are applicable to both model organisms of biogeochemical interest that may not be genetically tractable, and to complex community samples from natural environments. Employing chemical derivatization of peptides with multiple isotopically-coded tags, this strategy is rapid and inexpensive, can be implemented on a wide range of mass spectrometric instrumentation, and is relatively insensitive to chromatographic variability. We demonstrate the utility of this quantitative proteomics approach in application to both isolates and natural communities of sulfur-metabolizing and photosynthetic microbes.

  9. Arctic microbial community dynamics influenced by elevated CO2 levels

    NASA Astrophysics Data System (ADS)

    Brussaard, C. P. D.; Noordeloos, A. A. M.; Witte, H.; Collenteur, M. C. J.; Schulz, K.; Ludwig, A.; Riebesell, U.

    2012-09-01

    The Arctic Ocean ecosystem is particular vulnerable for ocean acidification (OA) related alterations due to the relatively high CO2 solubility and low carbonate saturation states of its cold surface waters. Thus far, however, there is only little known about the consequences of OA on the base of the food web. In a mesocosm CO2-enrichment experiment (overall CO2 levels ranged from ∼180 to 1100 μatm) in the Kongsfjord off Svalbard, we studied the consequences of OA on a natural pelagic microbial community. The most prominent finding of our study is the profound effect of OA on the composition and growth of the Arctic phytoplankton community, i.e. the picoeukaryotic photoautotrophs and to a lesser extent the nanophytoplankton prospered. A shift towards the smallest phytoplankton as a result of OA will have direct consequences for the structure and functioning of the pelagic food web and thus for the biogeochemical cycles. Furthermore, the dominant pico- and nanophytoplankton groups were found prone to viral lysis, thereby shunting the carbon accumulation in living organisms into the dissolved pools of organic carbon and subsequently affecting the efficiency of the biological pump in these Arctic waters.

  10. Arctic microbial community dynamics influenced by elevated CO2 levels

    NASA Astrophysics Data System (ADS)

    Brussaard, C. P. D.; Noordeloos, A. A. M.; Witte, H.; Collenteur, M. C. J.; Schulz, K.; Ludwig, A.; Riebesell, U.

    2013-02-01

    The Arctic Ocean ecosystem is particularly vulnerable to ocean acidification (OA) related alterations due to the relatively high CO2 solubility and low carbonate saturation states of its cold surface waters. Thus far, however, there is only little known about the consequences of OA on the base of the food web. In a mesocosm CO2-enrichment experiment (overall CO2 levels ranged from ~ 180 to 1100 μatm) in Kongsfjorden off Svalbard, we studied the consequences of OA on a natural pelagic microbial community. OA distinctly affected the composition and growth of the Arctic phytoplankton community, i.e. the picoeukaryotic photoautotrophs and to a lesser extent the nanophytoplankton thrived. A shift towards the smallest phytoplankton as a result of OA will have direct consequences for the structure and functioning of the pelagic food web and thus for the biogeochemical cycles. Besides being grazed, the dominant pico- and nanophytoplankton groups were found prone to viral lysis, thereby shunting the carbon accumulation in living organisms into the dissolved pools of organic carbon and subsequently affecting the efficiency of the biological pump in these Arctic waters.

  11. Microbial community analysis of a full-scale DEMON bioreactor.

    PubMed

    Gonzalez-Martinez, Alejandro; Rodriguez-Sanchez, Alejandro; Muñoz-Palazon, Barbara; Garcia-Ruiz, Maria-Jesus; Osorio, Francisco; van Loosdrecht, Mark C M; Gonzalez-Lopez, Jesus

    2015-03-01

    Full-scale applications of autotrophic nitrogen removal technologies for the treatment of digested sludge liquor have proliferated during the last decade. Among these technologies, the aerobic/anoxic deammonification process (DEMON) is one of the major applied processes. This technology achieves nitrogen removal from wastewater through anammox metabolism inside a single bioreactor due to alternating cycles of aeration. To date, microbial community composition of full-scale DEMON bioreactors have never been reported. In this study, bacterial community structure of a full-scale DEMON bioreactor located at the Apeldoorn wastewater treatment plant was analyzed using pyrosequencing. This technique provided a higher-resolution study of the bacterial assemblage of the system compared to other techniques used in lab-scale DEMON bioreactors. Results showed that the DEMON bioreactor was a complex ecosystem where ammonium oxidizing bacteria, anammox bacteria and many other bacterial phylotypes coexist. The potential ecological role of all phylotypes found was discussed. Thus, metagenomic analysis through pyrosequencing offered new perspectives over the functioning of the DEMON bioreactor by exhaustive identification of microorganisms, which play a key role in the performance of bioreactors. In this way, pyrosequencing has been proven as a helpful tool for the in-depth investigation of the functioning of bioreactors at microbiological scale.

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

    SciTech Connect

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

    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.

  13. 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.

  14. 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. PMID:21608471

  15. Comparison of Anodic Community in Microbial Fuel Cells with Iron Oxide-Reducing Community.

    PubMed

    Yokoyama, Hiroshi; Ishida, Mitsuyoshi; Yamashita, Takahiro

    2016-04-28

    The group of Fe(III) oxide-reducing bacteria includes exoelectrogenic bacteria, and they possess similar properties of transferring electrons to extracellular insoluble-electron acceptors. The exoelectrogenic bacteria can use the anode in microbial fuel cells (MFCs) as the terminal electron acceptor in anaerobic acetate oxidation. In the present study, the anodic community was compared with the community using Fe(III) oxide (ferrihydrite) as the electron acceptor coupled with acetate oxidation. To precisely analyze the structures, the community was established by enrichment cultures using the same inoculum used for the MFCs. High-throughput sequencing of the 16S rRNA gene revealed considerable differences between the structure of the anodic communities and that of the Fe(III) oxide-reducing community. Geobacter species were predominantly detected (>46%) in the anodic communities. In contrast, Pseudomonas (70%) and Desulfosporosinus (16%) were predominant in the Fe(III) oxide-reducing community. These results demonstrated that Geobacter species are the most specialized among Fe(III)-reducing bacteria for electron transfer to the anode in MFCs. In addition, the present study indicates the presence of a novel lineage of bacteria in the genus Pseudomonas that highly prefers ferrihydrite as the terminal electron acceptor in acetate oxidation. PMID:26767577

  16. Biotic and abiotic properties mediating plant diversity effects on soil microbial communities in an experimental grassland.

    PubMed

    Lange, Markus; Habekost, Maike; Eisenhauer, Nico; Roscher, Christiane; Bessler, Holger; Engels, Christof; Oelmann, Yvonne; Scheu, Stefan; Wilcke, Wolfgang; Schulze, Ernst-Detlef; Gleixner, Gerd

    2014-01-01

    Plant diversity drives changes in the soil microbial community which may result in alterations in ecosystem functions. However, the governing factors between the composition of soil microbial communities and plant diversity are not well understood. We investigated the impact of plant diversity (plant species richness and functional group richness) and plant functional group identity on soil microbial biomass and soil microbial community structure in experimental grassland ecosystems. Total microbial biomass and community structure were determined by phospholipid fatty acid (PLFA) analysis. The diversity gradient covered 1, 2, 4, 8, 16 and 60 plant species and 1, 2, 3 and 4 plant functional groups (grasses, legumes, small herbs and tall herbs). In May 2007, soil samples were taken from experimental plots and from nearby fields and meadows. Beside soil texture, plant species richness was the main driver of soil microbial biomass. Structural equation modeling revealed that the positive plant diversity effect was mainly mediated by higher leaf area index resulting in higher soil moisture in the top soil layer. The fungal-to-bacterial biomass ratio was positively affected by plant functional group richness and negatively by the presence of legumes. Bacteria were more closely related to abiotic differences caused by plant diversity, while fungi were more affected by plant-derived organic matter inputs. We found diverse plant communities promoted faster transition of soil microbial communities typical for arable land towards grassland communities. Although some mechanisms underlying the plant diversity effect on soil microorganisms could be identified, future studies have to determine plant traits shaping soil microbial community structure. We suspect differences in root traits among different plant communities, such as root turnover rates and chemical composition of root exudates, to structure soil microbial communities.

  17. Biotic and Abiotic Properties Mediating Plant Diversity Effects on Soil Microbial Communities in an Experimental Grassland

    PubMed Central

    Lange, Markus; Habekost, Maike; Eisenhauer, Nico; Roscher, Christiane; Bessler, Holger; Engels, Christof; Oelmann, Yvonne; Scheu, Stefan; Wilcke, Wolfgang; Schulze, Ernst-Detlef; Gleixner, Gerd

    2014-01-01

    Plant diversity drives changes in the soil microbial community which may result in alterations in ecosystem functions. However, the governing factors between the composition of soil microbial communities and plant diversity are not well understood. We investigated the impact of plant diversity (plant species richness and functional group richness) and plant functional group identity on soil microbial biomass and soil microbial community structure in experimental grassland ecosystems. Total microbial biomass and community structure were determined by phospholipid fatty acid (PLFA) analysis. The diversity gradient covered 1, 2, 4, 8, 16 and 60 plant species and 1, 2, 3 and 4 plant functional groups (grasses, legumes, small herbs and tall herbs). In May 2007, soil samples were taken from experimental plots and from nearby fields and meadows. Beside soil texture, plant species richness was the main driver of soil microbial biomass. Structural equation modeling revealed that the positive plant diversity effect was mainly mediated by higher leaf area index resulting in higher soil moisture in the top soil layer. The fungal-to-bacterial biomass ratio was positively affected by plant functional group richness and negatively by the presence of legumes. Bacteria were more closely related to abiotic differences caused by plant diversity, while fungi were more affected by plant-derived organic matter inputs. We found diverse plant communities promoted faster transition of soil microbial communities typical for arable land towards grassland communities. Although some mechanisms underlying the plant diversity effect on soil microorganisms could be identified, future studies have to determine plant traits shaping soil microbial community structure. We suspect differences in root traits among different plant communities, such as root turnover rates and chemical composition of root exudates, to structure soil microbial communities. PMID:24816860

  18. Microarray-based Analysis of Microbial Community RNAs by Whole Community RNA Amplification (WCRA)

    SciTech Connect

    Gao, Haichun; Yang, Zamin Koo; Gentry, Terry; Wu, Liyou; Schadt, Christopher Warren; Zhou, Jizhong

    2007-01-01

    A new approach, termed whole-community RNA amplification (WCRA), was developed to provide sufficient amounts of mRNAs from environmental samples for microarray analysis. This method employs fusion primers (six to nine random nucleotides with an attached T7 promoter) for the first-strand synthesis. The shortest primer (T7N6S) gave the best results in terms of the yield and representativeness of amplification. About 1,200- to 1,800-fold amplification was obtained with amounts of the RNA templates ranging from 10 to 100 ng, and very representative detection was obtained with 50 to 100 ng total RNA. Evaluation with a Shewanella oneidensis {Delta}fur strain revealed that the amplification method which we developed could preserve the original abundance relationships of mRNAs. In addition, to determine whether representative detection of RNAs can be achieved with mixed community samples, amplification biases were evaluated with a mixture containing equal quantities of RNAs (100 ng each) from four bacterial species, and representative amplification was also obtained. Finally, the method which we developed was applied to the active microbial populations in a denitrifying fluidized bed reactor used for denitrification of contaminated groundwater and ethanol-stimulated groundwater samples for uranium reduction. The genes expressed were consistent with the expected functions of the bioreactor and groundwater system, suggesting that this approach is useful for analyzing the functional activities of microbial communities. This is one of the first demonstrations that microarray-based technology can be used to successfully detect the activities of microbial communities from real environmental samples in a high-throughput fashion.

  19. [Characteristics of microbial community and operation efficiency in biofilter process for drinking water purification].

    PubMed

    Xiang, Hong; Lü, Xi-Wu; Yang, Fei; Yin, Li-Hong; Zhu, Guang-Can

    2011-04-01

    In order to explore characteristics of microbial community and operation efficiency in biofilter (biologically-enhanced active filter and biological activated carbon filter) process for drinking water purification, Biolog and polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) techniques were applied to analyze the metabolic function and structure of microbial community developing in biofilters. Water quality parameters, such as NH; -N, NO; -N, permanganate index, UV254 and BDOC etc, were determined in inflow and outflow of biofilters for investigation of operation efficiency of the biofilters. The results show that metabolic capacity of microbial community of the raw water is reduced after the biofilters, which reflect that metabolically active microbial communities in the raw water can be intercepted by biofilters. After 6 months operation of biofilters, the metabolic profiles of microbial communities are similar between two kinds of biologically-enhanced active filters, and utilization of carbon sources of microbial communities in the two filters are 73.4% and 75.5%, respectively. The metabolic profiles of microbial communities in two biological activated carbon filters showed significant difference. The carbon source utilization rate of microbial community in granule-activated carbon filter is 79.6%, which is obviously higher than 53.8% of the rate in the columnar activated carbon filter (p < 0.01). The analysis results of PCR-SSCP indicate that microbial communities in each biofilter are variety, but the structure of dominant microorganisms is similar among different biofilters. The results also show that the packing materials had little effect on the structure and metabolic function of microbial community in biologically-enhanced active filters, and the difference between two biofilters for the water purification efficiency was not significant (p > 0.05). However, in biological activated carbon filters, granule-activated carbon is

  20. Microbial community structure in three deep-sea carbonate crusts.

    PubMed

    Heijs, S K; Aloisi, G; Bouloubassi, I; Pancost, R D; Pierre, C; Sinninghe Damsté, J S; Gottschal, J C; van Elsas, J D; Forney, L J

    2006-10-01

    Carbonate crusts in marine environments can act as sinks for carbon dioxide. Therefore, understanding carbonate crust formation could be important for understanding global warming. In the present study, the microbial communities of three carbonate crust samples from deep-sea mud volcanoes in the eastern Mediterranean were characterized by sequencing 16S ribosomal RNA (rRNA) genes amplified from DNA directly retrieved from the samples. In combination with the mineralogical composition of the crusts and lipid analyses, sequence data were used to assess the possible role of prokaryotes in crust formation. Collectively, the obtained data showed the presence of highly diverse communities, which were distinct in each of the carbonate crusts studied. Bacterial 16S rRNA gene sequences were found in all crusts and the majority was classified as alpha-, gamma-, and delta- Proteobacteria. Interestingly, sequences of Proteobacteria related to Halomonas and Halovibrio sp., which can play an active role in carbonate mineral formation, were present in all crusts. Archaeal 16S rRNA gene sequences were retrieved from two of the crusts studied. Several of those were closely related to archaeal sequences of organisms that have previously been linked to the anaerobic oxidation of methane (AOM). However, the majority of archaeal sequences were not related to sequences of organisms known to be involved in AOM. In combination with the strongly negative delta 13C values of archaeal lipids, these results open the possibility that organisms with a role in AOM may be more diverse within the Archaea than previously suggested. Different communities found in the crusts could carry out similar processes that might play a role in carbonate crust formation.

  1. Microbial community analysis in biotrickling filters treating isopropanol air emissions.

    PubMed

    Pérez, M Carmen; Alvarez-Hornos, F Javier; San-Valero, Pau; Marzal, Paula; Gabaldón, Carmen

    2013-01-01

    The evolution of the microbial community was analysed over one year in two biotrickling filters operating under intermittent feeding conditions and treating isopropanol emissions, a pollutant typically found in the flexography sector. Each reactor was packed with one media: plastic cross-flow-structured material or polypropylene rings. The communities were monitored by fluorescence in situ hybridization (FISH) and denaturing gradient gel electrophoresis (DGGE) analysis of the 16S rRNA region. After inoculation with activated sludge, the biotrickling filters were operated using inlet loads (ILs) from 20 to 65 g C m(-3) h(-1) and empty-bed residence times (EBRTs) from 14 to 160 s. Removal efficiencies higher than 80% were obtained with ILs up to 35 g C m(-3) h(-1) working at EBRTs as low as 24 s. There was an increase in the total percentage of the target domains of up to around 80% at the end of the experiment. Specifically, the Gammaproteobacteria domain group, which includes the well-known volatile organic compound (VOC)-degrading species such as Pseudomonas putida, showed a noticeable rise in the two biotrickling filters of 26% and 27%, respectively. DGGE pattern band analysis revealed a stable band of Pseudomonas putida in all the samples monitored, even in the lower diversity communities. In addition, at similar operational conditions, the biotrickling filter with a greater relative abundance of Pseudomonas sp. (19.2% vs. 8%) showed higher removal efficiency (90% vs. 79%). Results indicate the importance of undertaking a further in-depth study of the involved species in the biofiltration process and their specific function.

  2. Probabilistic Inference of Biochemical Reactions in Microbial Communities from Metagenomic Sequences

    PubMed Central

    Jiao, Dazhi; Ye, Yuzhen; Tang, Haixu

    2013-01-01

    Shotgun metagenomics has been applied to the studies of the functionality of various microbial communities. As a critical analysis step in these studies, biological pathways are reconstructed based on the genes predicted from metagenomic shotgun sequences. Pathway reconstruction provides insights into the functionality of a microbial community and can be used for comparing multiple microbial communities. The utilization of pathway reconstruction, however, can be jeopardized because of imperfect functional annotation of genes, and ambiguity in the assignment of predicted enzymes to biochemical reactions (e.g., some enzymes are involved in multiple biochemical reactions). Considering that metabolic functions in a microbial community are carried out by many enzymes in a collaborative manner, we present a probabilistic sampling approach to profiling functional content in a metagenomic dataset, by sampling functions of catalytically promiscuous enzymes within the context of the entire metabolic network defined by the annotated metagenome. We test our approach on metagenomic datasets from environmental and human-associated microbial communities. The results show that our approach provides a more accurate representation of the metabolic activities encoded in a metagenome, and thus improves the comparative analysis of multiple microbial communities. In addition, our approach reports likelihood scores of putative reactions, which can be used to identify important reactions and metabolic pathways that reflect the environmental adaptation of the microbial communities. Source code for sampling metabolic networks is available online at http://omics.informatics.indiana.edu/mg/MetaNetSam/. PMID:23555216

  3. Probabilistic inference of biochemical reactions in microbial communities from metagenomic sequences.

    PubMed

    Jiao, Dazhi; Ye, Yuzhen; Tang, Haixu

    2013-01-01

    Shotgun metagenomics has been applied to the studies of the functionality of various microbial communities. As a critical analysis step in these studies, biological pathways are reconstructed based on the genes predicted from metagenomic shotgun sequences. Pathway reconstruction provides insights into the functionality of a microbial community and can be used for comparing multiple microbial communities. The utilization of pathway reconstruction, however, can be jeopardized because of imperfect functional annotation of genes, and ambiguity in the assignment of predicted enzymes to biochemical reactions (e.g., some enzymes are involved in multiple biochemical reactions). Considering that metabolic functions in a microbial community are carried out by many enzymes in a collaborative manner, we present a probabilistic sampling approach to profiling functional content in a metagenomic dataset, by sampling functions of catalytically promiscuous enzymes within the context of the entire metabolic network defined by the annotated metagenome. We test our approach on metagenomic datasets from environmental and human-associated microbial communities. The results show that our approach provides a more accurate representation of the metabolic activities encoded in a metagenome, and thus improves the comparative analysis of multiple microbial communities. In addition, our approach reports likelihood scores of putative reactions, which can be used to identify important reactions and metabolic pathways that reflect the environmental adaptation of the microbial communities. Source code for sampling metabolic networks is available online at http://omics.informatics.indiana.edu/mg/MetaNetSam/. PMID:23555216

  4. Effects of glyphosate on soil microbial communities and its mineralization in a Mississippi soil.

    PubMed

    Weaver, Mark A; Krutz, L Jason; Zablotowicz, Robert M; Reddy, Krishna N

    2007-04-01

    Transgenic glyphosate-resistant (GR) soybean [Glycine max (L.) Merr.] has enabled highly effective and economical weed control. The concomitant increased application of glyphosate could lead to shifts in the soil microbial community. The objective of these experiments was to evaluate the effects of glyphosate on soil microbial community structure, function and activity. Field assessments on soil microbial communities were conducted on a silt loam soil near Stoneville, MS, USA. Surface soil was collected at time of planting, before initial glyphosate application and 14 days after two post-emergence glyphosate applications. Microbial community fatty acid methyl esters (FAMEs) were analyzed from these soil samples and soybean rhizospheres. Principal component analysis of the total FAME profile revealed no differentiation between field treatments, although the relative abundance of several individual fatty acids differed significantly. There was no significant herbicide effect in bulk soil or rhizosphere soils. Collectively, these findings indicate that glyphosate caused no meaningful whole microbial community shifts in this time period, even when applied at greater than label rates. Laboratory experiments, including up to threefold label rates of glyphosate, resulted in up to a 19% reduction in soil hydrolytic activity and small, brief (<7 days) changes in the soil microbial community. After incubation for 42 days, 32-37% of the applied glyphosate was mineralized when applied at threefold field rates, with about 9% forming bound residues. These results indicate that glyphosate has only small and transient effects on the soil microbial community, even when applied at greater than field rates.

  5. Water regime history drives responses of soil Namib Desert microbial communities to wetting events

    PubMed Central

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

    2015-01-01

    Despite the dominance of microorganisms in arid soils, the structures and functional dynamics of microbial communities in hot deserts remain largely unresolved. The effects of wetting event frequency and intensity on Namib Desert microbial communities from two soils with different water-regime histories were tested over 36 days. A total of 168 soil microcosms received wetting events mimicking fog, light rain and heavy rainfall, with a parallel “dry condition” control. T-RFLP data showed that the different wetting events affected desert microbial community structures, but these effects were attenuated by the effects related to the long-term adaptation of both fungal and bacterial communities to soil origins (i.e. soil water regime histories). The intensity of the water pulses (i.e. the amount of water added) rather than the frequency of wetting events had greatest effect in shaping bacterial and fungal community structures. In contrast to microbial diversity, microbial activities (enzyme activities) showed very little response to the wetting events and were mainly driven by soil origin. This experiment clearly demonstrates the complexity of microbial community responses to wetting events in hyperarid hot desert soil ecosystems and underlines the dynamism of their indigenous microbial communities. PMID:26195343

  6. Water regime history drives responses of soil Namib Desert microbial communities to wetting events

    NASA Astrophysics Data System (ADS)

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

    2015-07-01

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

  7. Water regime history drives responses of soil Namib Desert microbial communities to wetting events.

    PubMed

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

    2015-01-01

    Despite the dominance of microorganisms in arid soils, the structures and functional dynamics of microbial communities in hot deserts remain largely unresolved. The effects of wetting event frequency and intensity on Namib Desert microbial communities from two soils with different water-regime histories were tested over 36 days. A total of 168 soil microcosms received wetting events mimicking fog, light rain and heavy rainfall, with a parallel "dry condition" control. T-RFLP data showed that the different wetting events affected desert microbial community structures, but these effects were attenuated by the effects related to the long-term adaptation of both fungal and bacterial communities to soil origins (i.e. soil water regime histories). The intensity of the water pulses (i.e. the amount of water added) rather than the frequency of wetting events had greatest effect in shaping bacterial and fungal community structures. In contrast to microbial diversity, microbial activities (enzyme activities) showed very little response to the wetting events and were mainly driven by soil origin. This experiment clearly demonstrates the complexity of microbial community responses to wetting events in hyperarid hot desert soil ecosystems and underlines the dynamism of their indigenous microbial communities. PMID:26195343

  8. Adaptation of terrestrial microbial communities to elevated CO2 concentrations

    NASA Astrophysics Data System (ADS)

    Krüger, M.; Frerichs, J.; May, F.; Möller, I.

    2009-04-01

    From the IPCC report on global warming, it is clear that large-scale solutions are needed immediately to reduce emissions of greenhouse gases. CO2 capture and storage offers one option for reducing greenhouse gas emissions. Our study aims at investigating the environmental impact of CO2 leakage from deep reservoirs into near-surface terrestrial environments. Therefore, an ecosystem study has been conducted on a natural CO2 leak at the Laacher See, Germany. CO2 is produced below this extinct volcanic caldera. The CO2 releasing vent located on an agricultural field at the western shore of the lake is clearly visible due to a 5m wide core of exposed soil. The determination of environmentally important microbial activities, eg. CO2 and methane production, sulfate reduction and methane oxidation, showed differences between the CO2-rich (>90 % of soil gas) medium (20%) and the control site with background CO2 concentrations. Especially in deeper soil layers, rates of methane production and sulfate reduction increased with increasing CO2 in the soil gas. Methane oxidation activity was highest at the control site. In accordance with the activities, also the microbial communities analysed by DGGE with general bacterial, archaeal and primers for funcitional genes of the C- and N-metabolism showed a shift in species composition between CO2-rich and control sites. However, all results indicate that effects of the gas vent are spatially limited. The ecosystem appears to have adapted to the different conditions through species substitution or adaptation, showing a shift towards anaerobic and acidophilic species under elevated CO2 concentrations.

  9. Mapping and determinism of soil microbial community distribution across an agricultural landscape

    PubMed Central

    Constancias, Florentin; Terrat, Sébastien; Saby, Nicolas P A; Horrigue, Walid; Villerd, Jean; Guillemin, Jean-Philippe; Biju-Duval, Luc; Nowak, Virginie; Dequiedt, Samuel; Ranjard, Lionel; Chemidlin Prévost-Bouré, Nicolas

    2015-01-01

    Despite the relevance of landscape, regarding the spatial patterning of microbial communities and the relative influence of environmental parameters versus human activities, few investigations have been conducted at this scale. Here, we used a systematic grid to characterize the distribution of soil microbial communities at 278 sites across a monitored agricultural landscape of 13 km². Molecular microbial biomass was estimated by soil DNA recovery and bacterial diversity by 16S rRNA gene pyrosequencing. Geostatistics provided the first maps of microbial community at this scale and revealed a heterogeneous but spatially structured distribution of microbial biomass and diversity with patches of several hundreds of meters. Variance partitioning revealed that both microbial abundance and bacterial diversity distribution were highly dependent of soil properties and land use (total variance explained ranged between 55% and 78%). Microbial biomass and bacterial richness distributions were mainly explained by soil pH and texture whereas bacterial evenness distribution was mainly related to land management. Bacterial diversity (richness, evenness, and Shannon index) was positively influenced by cropping intensity and especially by soil tillage, resulting in spots of low microbial diversity in soils under forest management. Spatial descriptors also explained a small but significant portion of the microbial distribution suggesting that landscape configuration also shapes microbial biomass and bacterial diversity. PMID:25833770

  10. Biotic Interactions in Microbial Communities as Modulators of Biogeochemical Processes: Methanotrophy as a Model System

    PubMed Central

    Ho, Adrian; Angel, Roey; Veraart, Annelies J.; Daebeler, Anne; Jia, Zhongjun; Kim, Sang Yoon; Kerckhof, Frederiek-Maarten; Boon, Nico; Bodelier, Paul L. E.

    2016-01-01

    Microbial interaction is an integral component of microbial ecology studies, yet the role, extent, and relevance of microbial interaction in community functioning remains unclear, particularly in the context of global biogeochemical cycles. While many studies have shed light on the physico-chemical cues affecting specific processes, (micro)biotic controls and interactions potentially steering microbial communities leading to altered functioning are less known. Yet, recent accumulating evidence suggests that the concerted actions of a community can be significantly different from the combined effects of individual microorganisms, giving rise to emergent properties. Here, we exemplify the importance of microbial interaction for ecosystem processes by analysis of a reasonably well-understood microbial guild, namely, aerobic methane-oxidizing bacteria (MOB). We reviewed the literature which provided compelling evidence for the relevance of microbial interaction in modulating methane oxidation. Support for microbial associations within methane-fed communities is sought by a re-analysis of literature data derived from stable isotope probing studies of various complex environmental settings. Putative positive interactions between active MOB and other microbes were assessed by a correlation network-based analysis with datasets covering diverse environments where closely interacting members of a consortium can potentially alter the methane oxidation activity. Although, methanotrophy is used as a model system, the fundamentals of our postulations may be applicable to other microbial guilds mediating other biogeochemical processes.

  11. Biotic Interactions in Microbial Communities as Modulators of Biogeochemical Processes: Methanotrophy as a Model System

    PubMed Central

    Ho, Adrian; Angel, Roey; Veraart, Annelies J.; Daebeler, Anne; Jia, Zhongjun; Kim, Sang Yoon; Kerckhof, Frederiek-Maarten; Boon, Nico; Bodelier, Paul L. E.

    2016-01-01

    Microbial interaction is an integral component of microbial ecology studies, yet the role, extent, and relevance of microbial interaction in community functioning remains unclear, particularly in the context of global biogeochemical cycles. While many studies have shed light on the physico-chemical cues affecting specific processes, (micro)biotic controls and interactions potentially steering microbial communities leading to altered functioning are less known. Yet, recent accumulating evidence suggests that the concerted actions of a community can be significantly different from the combined effects of individual microorganisms, giving rise to emergent properties. Here, we exemplify the importance of microbial interaction for ecosystem processes by analysis of a reasonably well-understood microbial guild, namely, aerobic methane-oxidizing bacteria (MOB). We reviewed the literature which provided compelling evidence for the relevance of microbial interaction in modulating methane oxidation. Support for microbial associations within methane-fed communities is sought by a re-analysis of literature data derived from stable isotope probing studies of various complex environmental settings. Putative positive interactions between active MOB and other microbes were assessed by a correlation network-based analysis with datasets covering diverse environments where closely interacting members of a consortium can potentially alter the methane oxidation activity. Although, methanotrophy is used as a model system, the fundamentals of our postulations may be applicable to other microbial guilds mediating other biogeochemical processes. PMID:27602021

  12. Biotic Interactions in Microbial Communities as Modulators of Biogeochemical Processes: Methanotrophy as a Model System.

    PubMed

    Ho, Adrian; Angel, Roey; Veraart, Annelies J; Daebeler, Anne; Jia, Zhongjun; Kim, Sang Yoon; Kerckhof, Frederiek-Maarten; Boon, Nico; Bodelier, Paul L E

    2016-01-01

    Microbial interaction is an integral component of microbial ecology studies, yet the role, extent, and relevance of microbial interaction in community functioning remains unclear, particularly in the context of global biogeochemical cycles. While many studies have shed light on the physico-chemical cues affecting specific processes, (micro)biotic controls and interactions potentially steering microbial communities leading to altered functioning are less known. Yet, recent accumulating evidence suggests that the concerted actions of a community can be significantly different from the combined effects of individual microorganisms, giving rise to emergent properties. Here, we exemplify the importance of microbial interaction for ecosystem processes by analysis of a reasonably well-understood microbial guild, namely, aerobic methane-oxidizing bacteria (MOB). We reviewed the literature which provided compelling evidence for the relevance of microbial interaction in modulating methane oxidation. Support for microbial associations within methane-fed communities is sought by a re-analysis of literature data derived from stable isotope probing studies of various complex environmental settings. Putative positive interactions between active MOB and other microbes were assessed by a correlation network-based analysis with datasets covering diverse environments where closely interacting members of a consortium can potentially alter the methane oxidation activity. Although, methanotrophy is used as a model system, the fundamentals of our postulations may be applicable to other microbial guilds mediating other biogeochemical processes. PMID:27602021

  13. Biotic Interactions in Microbial Communities as Modulators of Biogeochemical Processes: Methanotrophy as a Model System.

    PubMed

    Ho, Adrian; Angel, Roey; Veraart, Annelies J; Daebeler, Anne; Jia, Zhongjun; Kim, Sang Yoon; Kerckhof, Frederiek-Maarten; Boon, Nico; Bodelier, Paul L E

    2016-01-01

    Microbial interaction is an integral component of microbial ecology studies, yet the role, extent, and relevance of microbial interaction in community functioning remains unclear, particularly in the context of global biogeochemical cycles. While many studies have shed light on the physico-chemical cues affecting specific processes, (micro)biotic controls and interactions potentially steering microbial communities leading to altered functioning are less known. Yet, recent accumulating evidence suggests that the concerted actions of a community can be significantly different from the combined effects of individual microorganisms, giving rise to emergent properties. Here, we exemplify the importance of microbial interaction for ecosystem processes by analysis of a reasonably well-understood microbial guild, namely, aerobic methane-oxidizing bacteria (MOB). We reviewed the literature which provided compelling evidence for the relevance of microbial interaction in modulating methane oxidation. Support for microbial associations within methane-fed communities is sought by a re-analysis of literature data derived from stable isotope probing studies of various complex environmental settings. Putative positive interactions between active MOB and other microbes were assessed by a correlation network-based analysis with datasets covering diverse environments where closely interacting members of a consortium can potentially alter the methane oxidation activity. Although, methanotrophy is used as a model system, the fundamentals of our postulations may be applicable to other microbial guilds mediating other biogeochemical processes.

  14. Reactor performances and microbial communities of biogas reactors: effects of inoculum sources.

    PubMed

    Han, Sheng; Liu, Yafeng; Zhang, Shicheng; Luo, Gang

    2016-01-01

    Anaerobic digestion is a very complex process that is mediated by various microorganisms, and the understanding of the microbial community assembly and its corresponding function is critical in order to better control the anaerobic process. The present study investigated the effect of different inocula on the microbial community assembly in biogas reactors treating cellulose with various inocula, and three parallel biogas reactors with the same inoculum were also operated in order to reveal the reproducibility of both microbial communities and functions of the biogas reactors. The results showed that the biogas production, volatile fatty acid (VFA) concentrations, and pH were different for the biogas reactors with different inocula, and different steady-state microbial community patterns were also obtained in different biogas reactors as reflected by Bray-Curtis similarity matrices and taxonomic classification. It indicated that inoculum played an important role in shaping the microbial communities of biogas reactor in the present study, and the microbial community assembly in biogas reactor did not follow the niche-based ecology theory. Furthermore, it was found that the microbial communities and reactor performances of parallel biogas reactors with the same inoculum were different, which could be explained by the neutral-based ecology theory and stochastic factors should played important roles in the microbial community assembly in the biogas reactors. The Bray-Curtis similarity matrices analysis suggested that inoculum affected more on the microbial community assembly compared to stochastic factors, since the samples with different inocula had lower similarity (10-20 %) compared to the samples from the parallel biogas reactors (30 %).

  15. Photochemical Control of Organic Carbon Availability to Coastal Microbial Communities

    NASA Astrophysics Data System (ADS)

    Miller, W. L.; Reader, H. E.; Powers, L. C.

    2010-12-01

    Chromophoric dissolved organic matter (CDOM) is the fraction of dissolved organic matter that absorbs solar radiation. In terrestrially influenced locations high concentrations of CDOM help to shield the biological community from harmful UV radiation. Although CDOM is largely biologically refractory in nature, photochemistry has the potential to transform biologically refractory carbon into more biolabile forms. Studies suggest that in marine systems, the effect of UVR on carbon availability and subsequent bacterial production varies widely, ranging from a +200% increase to a -75% decrease (Mopper and Kieber, 2002). Evidence suggests that the largely negative or “no-effect” samples are from oligotrophic waters and that terrestrially influenced samples experience a more positive effect on the biolability of carbon after irradiation. To quantify the effects of photochemistry on the biolability of DOC in a terrestrially influenced system, a quarterly sampling effort was undertaken at three estuarine locations off the coast of Georgia, USA for a total of 14 apparent quantum yield (AQY) determinations. Large expanses of salt marsh on the coast of Georgia, create a large non-point source of DOC to the coastal ocean. Sapelo Sound, the northernmost sampling site, is dominated by offshore waters and receives little to no freshwater input throughout the year. Altamaha Sound, the southernmost sampling site, is strongly influenced by the Altamaha River, which drains the largest watershed in the state of Georgia. Doboy Sound, situated between these two sites, is largely marine dominated but is influenced by fresh water during periods of high river flow. Each sample was 0.2um filter-sterilized before irradiation in a Suntest Solar Simulator; using optical filters to create 7 distinct radiance spectra in 15 samples for determination of AQY spectra for release of biolabile DOC. Irradiated samples were consequently inoculated with the natural microbial community concentrated

  16. Effect of altitude and season on microbial activity, abundance and community structure in Alpine forest soils.

    PubMed

    Siles, José A; Cajthaml, Tomas; Minerbi, Stefano; Margesin, Rosa

    2016-03-01

    In the current context of climate change, the study of microbial communities along altitudinal gradients is especially useful. Only few studies considered altitude and season at the same time. We characterized four forest sites located in the Italian Alps, along an altitude gradient (545-2000 m a.s.l.), to evaluate the effect of altitude in spring and autumn on soil microbial properties. Each site in each season was characterized with regard to soil temperature, physicochemical properties, microbial activities (respiration, enzymes), community level physiological profiles (CLPP), microbial abundance and community structure (PLFA). Increased levels of soil organic matter (SOM) and nutrients were found at higher altitudes and in autumn, resulting in a significant increase of (soil dry-mass related) microbial activities and abundance at higher altitudes. Significant site- and season-specific effects were found for enzyme production. The significant interaction of the factors site and incubation temperature for soil microbial activities indicated differences in microbial communities and their responses to temperature among sites. CLPP revealed site-specific effects. Microbial community structure was influenced by altitudinal, seasonal and/or site-specific effects. Correlations demonstrated that altitude, and not season, was the main factor determining the changes in abiotic and biotic characteristics at the sites investigated.

  17. The impact of industrial-scale cartridge filtration on the native microbial communities from groundwater.

    PubMed

    Wang, Yingying; Hammes, Frederik; Egli, Thomas

    2008-10-01

    Groundwater is a major source for bottled water, which is increasingly consumed all over the world. Some categories of bottled water can be subjected to treatments such as disinfection prior to bottling. In the current study, we present the quantitative impact of industrial-scale micro-filtration (0.22 microm pore size) on native microbial communities of groundwater and evaluate subsequent microbial growth after bottling. Two separate groundwater aquifers were tested. Flow-cytometric total cell concentration (TCC) and total adenosine tri-phosphate (ATP) analysis were used to quantify microbial abundance. The TCC of the native microbial community in both aquifers was in the range of 10(3)-10(4) cells/ml. Up to 10% of the native microbial community was able to pass through the cartridge filtration units installed at both aquifers. In addition, all samples (either with or without 0.22 microm filtration) showed significant growth after bottling and storage, reaching average final concentrations of 1-3 x 10(5) cells/ml. However, less growth was observed in carbon-free glassware than in standard polyethylene terephthalate (PET) bottles. Furthermore, our results showed that filtration and bottling can alter the microbial community patterns as observed with flow cytometry. The current study established that industrial-scale micro-filtration cannot serve as an absolute barrier for the native microbial community and provided significant insight to the impact of filtration and bottling on microbial concentrations in bottled water.

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

    PubMed Central

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

    2016-01-01

    Investigating microbial response to environmental variables is of great importance for understanding of microbial acclimatization and evolution in natural environments. However, little is known about how microbial communities responded to environmental factors (e.g. salinity, geographic distance) in lake surface sediments of the Qinghai-Tibetan Plateau (QTP). In this study, microbial diversity and community structure in the surface sediments of nine lakes on the QTP were investigated by using the Illumina Miseq sequencing technique and the resulting microbial data were statistically analyzed in combination with environmental variables. The results showed total microbial community of the studied lakes was significantly correlated (r = 0.631, P < 0.001) with lake salinity instead of geographic distance. This suggests that lake salinity is more important than geographic distance in shaping the microbial diversity and community structure in the studied samples. In addition, the abundant and rare taxa (OTUs with relative abundance higher than 1% and lower than 0.01% within one sample, respectively) were significantly (P < 0.05) correlated (r = 0.427 and 0.783, respectively) with salinity, suggesting rare taxa might be more sensitive to salinity than their abundant counterparts, thus cautions should be taken in future when evaluating microbial response (abundant vs. rare sub-communities) to environmental conditions. PMID:27113678

  19. Microbial community dynamics in thermophilic undefined milk starter cultures.

    PubMed

    Parente, Eugenio; Guidone, Angela; Matera, Attilio; De Filippis, Francesca; Mauriello, Gianluigi; Ricciardi, Annamaria

    2016-01-18

    Model undefined thermophilic starter cultures were produced from raw milk of nine pasta-filata cheesemaking plants using a selective procedure based on pasteurization and incubation at high temperature with the objective of studying the microbial community dynamics and the variability in performances under repeated (7-13) reproduction cycles with backslopping. The traditional culture-dependent approach, based on random isolation and molecular characterization of isolates was coupled to the determination of pH and the evaluation of the ability to produce acid and fermentation metabolites. Moreover, a culture-independent approach based on amplicon-targeted next-generation sequencing was employed. The microbial diversity was evaluated by 16S rRNA gene sequencing (V1-V3 regions), while the microdiversity of Streptococcus thermophilus populations was explored by using novel approach based on sequencing of partial amplicons of the phosphoserine phosphatase gene (serB). In addition, the occurrence of bacteriophages was evaluated by qPCR and by multiplex PCR. Although it was relatively easy to select for a community dominated by thermophilic lactic acid bacteria (LAB) within a single reproduction cycle, final pH, LAB populations and acid production activity fluctuated over reproduction cycles. Both culture-dependent and -independent methods showed that the cultures were dominated by either S. thermophilus or Lactobacillus delbrueckii subsp. lactis or by both species. Nevertheless, subdominant mesophilic species, including lactococci and spoilage organisms, persisted at low levels. A limited number of serB sequence types (ST) were present in S. thermophilus populations. L. delbrueckii and Lactococcus lactis bacteriophages were below the detection limit of the method used and high titres of cos type S. thermophilus bacteriophages were detected in only two cases. In one case a high titre of bacteriophages was concurrent with a S. thermophilus biotype shift in the culture

  20. Microbial community dynamics in thermophilic undefined milk starter cultures.

    PubMed

    Parente, Eugenio; Guidone, Angela; Matera, Attilio; De Filippis, Francesca; Mauriello, Gianluigi; Ricciardi, Annamaria

    2016-01-18

    Model undefined thermophilic starter cultures were produced from raw milk of nine pasta-filata cheesemaking plants using a selective procedure based on pasteurization and incubation at high temperature with the objective of studying the microbial community dynamics and the variability in performances under repeated (7-13) reproduction cycles with backslopping. The traditional culture-dependent approach, based on random isolation and molecular characterization of isolates was coupled to the determination of pH and the evaluation of the ability to produce acid and fermentation metabolites. Moreover, a culture-independent approach based on amplicon-targeted next-generation sequencing was employed. The microbial diversity was evaluated by 16S rRNA gene sequencing (V1-V3 regions), while the microdiversity of Streptococcus thermophilus populations was explored by using novel approach based on sequencing of partial amplicons of the phosphoserine phosphatase gene (serB). In addition, the occurrence of bacteriophages was evaluated by qPCR and by multiplex PCR. Although it was relatively easy to select for a community dominated by thermophilic lactic acid bacteria (LAB) within a single reproduction cycle, final pH, LAB populations and acid production activity fluctuated over reproduction cycles. Both culture-dependent and -independent methods showed that the cultures were dominated by either S. thermophilus or Lactobacillus delbrueckii subsp. lactis or by both species. Nevertheless, subdominant mesophilic species, including lactococci and spoilage organisms, persisted at low levels. A limited number