Science.gov

Sample records for intestinal microbial ecology

  1. Enteric defensins are essential regulators of intestinal microbial ecology.

    PubMed

    Salzman, Nita H; Hung, Kuiechun; Haribhai, Dipica; Chu, Hiutung; Karlsson-Sjöberg, Jenny; Amir, Elad; Teggatz, Paul; Barman, Melissa; Hayward, Michael; Eastwood, Daniel; Stoel, Maaike; Zhou, Yanjiao; Sodergren, Erica; Weinstock, George M; Bevins, Charles L; Williams, Calvin B; Bos, Nicolaas A

    2010-01-01

    Antimicrobial peptides are important effectors of innate immunity throughout the plant and animal kingdoms. In the mammalian small intestine, Paneth cell alpha-defensins are antimicrobial peptides that contribute to host defense against enteric pathogens. To determine if alpha-defensins also govern intestinal microbial ecology, we analyzed the intestinal microbiota of mice expressing a human alpha-defensin gene (DEFA5) and in mice lacking an enzyme required for the processing of mouse alpha-defensins. In these complementary models, we detected significant alpha-defensin-dependent changes in microbiota composition, but not in total bacterial numbers. Furthermore, DEFA5-expressing mice had striking losses of segmented filamentous bacteria and fewer interleukin 17 (IL-17)-producing lamina propria T cells. Our data ascribe a new homeostatic role to alpha-defensins in regulating the makeup of the commensal microbiota. PMID:19855381

  2. Yeast culture supplement during nursing and transport affects immunity and intestinal microbial ecology of weanling pigs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Weaning and transport stress can have a negative impact on the piglet's immune system and intestinal microbiota. The objective of this study was to determine the influence of a yeast product on innate immunity and microbial ecology of the gastrointestinal tract following stress of weaning and trans...

  3. Sampling of intestinal microbiota and targeted amplification of bacterial 16S rRNA genes for microbial ecologic analysis.

    PubMed

    Tong, Maomeng; Jacobs, Jonathan P; McHardy, Ian H; Braun, Jonathan

    2014-11-03

    Dysbiosis of host-associated commensal microbiota is emerging as an important factor in risk and phenotype of immunologic, metabolic, and behavioral diseases. Accurate analysis of microbial composition and functional state in humans or mice requires appropriate collection and pre-processing of biospecimens. Methods to sample luminal and mucosal microbiota from human or mouse intestines and to profile microbial phylogenetic composition using 16S rRNA sequencing are presented here. Data generated using the methods in this unit can be used for downstream quantitative analysis of microbial ecology.

  4. Sampling of intestinal microbiota and targeted amplification of bacterial 16S rRNA genes for microbial ecologic analysis

    PubMed Central

    Tong, Maomeng; Jacobs, Jonathan P.; McHardy, Ian H.; Braun, Jonathan

    2015-01-01

    Dysbiosis of host-associated commensal microbiota is emerging as an important factor in risk and phenotype of immunologic, metabolic, and behavioral diseases. Appropriate collection and pre-processing of biospecimens from humans or mice is necessary for accurate analysis of microbial composition and functional state. Methods to sample intestinal luminal and mucosal microbiota from humans and mice, and to profile microbial phylogenetic composition using 16S rRNA sequencing are presented here. Data generated using this protocol can be used for downstream quantitative analysis of microbial ecology. PMID:25367129

  5. Ecology, Microbial

    SciTech Connect

    Konopka, Allan

    2009-05-15

    Microbial ecology is a relatively young discipline within the field of microbiology. Its modern history spans just the past 60 years, and the field is defined by its emphasis on understanding the interactions of microbes with their environment, rather than their behavior under artificial laboratory conditions. Because microbes are ubiquitous, microbial ecologists study a broad diversity of habitats that range from aquatic to terrestrial to plant- or animal-associated. This has made it a challenge to identify unifying principles within the field. One approach is to recognize that although the activity of microbes in nature have effects at the macroscale, they interact with their physical, chemical and biological milieu at a scale of micrometers. At this scale, several different microbial ecosystems can be defined, based upon association with particles, the presence of environmental gradients and the continuous availability of water. Principles applicable to microbial ecology reflect not only their population ecology and physiological ecology, but also their broad versatility and quantitative importance in the biosphere as biogeochemical catalysts and capacity for rapid physiological and evolutionary responses.

  6. Ecology, Microbial

    SciTech Connect

    Konopka, Allan

    2009-03-19

    Microbial ecology is a relatively young discipline within the field of microbiology. Its modern history spans just the past 60 years, and the field is defined by its emphasis on understanding the interactions of microbes with their environment, rather than their behavior under artificial laboratory conditions. Because microbes are ubiquitous, microbial ecologists study a broad diversity of habitats that range from aquatic to terrestrial to plant- or animal-associated. This has made it a challenge to identify unifying principles within the field. One approach is to recognize that although the activity of microbes in nature have effects at the macroscale, they interact with their physical, chemical and biological milieu at a scale of micrometers. At this scale, several different microbial ecosystems can be defined, based upon association with particles, the presence of environmental gradients and the continuous availability of water. Principles applicable to microbial ecology reflect not only their population ecology and physiological ecology, but also their broad versatility and quantitative importance in the biosphere as biogeochemical catalysts and capacity for rapid physiological and evolutionary responses.

  7. Effects of dietary supplementation with fermented ginkgo leaves on antioxidant capacity, intestinal morphology and microbial ecology in broiler chicks.

    PubMed

    Zhang, X H; Sun, Z Y; Cao, F L; Ahmad, H; Yang, X H; Zhao, L G; Wang, T

    2015-01-01

    1. The purpose of this study was to evaluate the effects of supplementing diets with three types of fermented Ginkgo-leaves (FGL) on growth, antioxidant capacity, intestinal morphology and microbial ecology in broiler chicks. 2. A total of 300 d-old broilers were randomly allocated to 4 dietary treatments with 6 replications of 10 birds each. Birds were fed on basal diets (Control) or basal diets supplemented with 0.5% FGL with Candida utilis (CF group), Aspergillus niger (AF group) or their combined fermentation (CAF group), respectively, for a 42 d feeding trial. 3. AF and CAF supplementation improved body weight gain (BWG) (22-42 d) and feed conversion ratio (22-42 d and 1-42 d). Concentrations of serum α-tocopherol in CAF group, as well as hepatic α-tocopherol in the three FGL groups were increased, while hepatic reactive oxygen species (ROS) levels were greatly decreased in group AF and CAF. Chickens in AF and CAF groups had decreased hepatic protein carbonyls and malondialdehyde (MDA), as well as jejunal and ileal protein carbonyls. The total superoxide dismutase (T-SOD) activities and glutathione (GSH) of both jejunum and ileum of the CAF group were higher than the other groups. 4. Duodenal and jejunal villous height of birds fed on the AF and CAF diets were increased, while jejunal crypt depth (CD) was decreased. Furthermore, birds fed on AF and CAF supplemented diets had increased ileal lactobacilli populations. Decreased ileal and caecal Escherichia coli and Salmonellas populations was found for the birds fed on CAF supplemented diets. 5. The present study may indicate that the improved feed efficiency and intestinal functions in the group supplemented with AF and CAF are directly connected with the improved antioxidant capacity and intestinal microbial ecology.

  8. Microbial ecological response of the intestinal flora of Peromyscus maniculatus and P. leucopus to heavy metal contamination.

    PubMed

    Coolon, Joseph D; Jones, Kenneth L; Narayanan, Sanjeev; Wisely, Samantha M

    2010-03-01

    Heavy metal contamination negatively affects natural systems including plants, birds, fish and bacteria by reducing biodiversity at contaminated sites. At the Tri-State Mining District, efforts have been made to remediate sites to mitigate the detrimental effects that contamination has caused on human health. While the remediation effort has returned the site to within federal safety standards, it is unclear if this effort is sufficient to restore floral and faunal communities. Intrinsic to ecosystem and organism health is the biodiversity and composition of microbial communities. We have taken advantage of recent advances in sequencing technology and surveyed the bacterial community of remediated and reference soils as well as the intestinal microbial community of two ubiquitous rodent species to provide insight on the impacts of residual heavy metal contamination on the ecosystem. Rodents found on the remediated site had reduced body mass, smaller body size and lower body fat than animals on reference sites. Using bar-coded, massively parallel sequencing, we found that bacterial communities in both the soil and Peromyscus spp. gastrointestinal tracts had no difference in diversity between reference and remediated sites but assemblages differed in response to contamination. These results suggest that niche voids left by microbial taxa that were unable to deal with the remnant levels of heavy metals on remediated sites were replaced by taxa that could persist in this environment. Whether this replacement provided similar ecosystem services as ancestral bacterial communities is unknown. PMID:20331771

  9. Microbial ecological response of the intestinal flora of Peromyscus maniculatus and P. leucopus to heavy metal contamination.

    PubMed

    Coolon, Joseph D; Jones, Kenneth L; Narayanan, Sanjeev; Wisely, Samantha M

    2010-03-01

    Heavy metal contamination negatively affects natural systems including plants, birds, fish and bacteria by reducing biodiversity at contaminated sites. At the Tri-State Mining District, efforts have been made to remediate sites to mitigate the detrimental effects that contamination has caused on human health. While the remediation effort has returned the site to within federal safety standards, it is unclear if this effort is sufficient to restore floral and faunal communities. Intrinsic to ecosystem and organism health is the biodiversity and composition of microbial communities. We have taken advantage of recent advances in sequencing technology and surveyed the bacterial community of remediated and reference soils as well as the intestinal microbial community of two ubiquitous rodent species to provide insight on the impacts of residual heavy metal contamination on the ecosystem. Rodents found on the remediated site had reduced body mass, smaller body size and lower body fat than animals on reference sites. Using bar-coded, massively parallel sequencing, we found that bacterial communities in both the soil and Peromyscus spp. gastrointestinal tracts had no difference in diversity between reference and remediated sites but assemblages differed in response to contamination. These results suggest that niche voids left by microbial taxa that were unable to deal with the remnant levels of heavy metals on remediated sites were replaced by taxa that could persist in this environment. Whether this replacement provided similar ecosystem services as ancestral bacterial communities is unknown.

  10. Microbial ecology of watery kimchi

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The biochemistry and microbial ecology of 2 similar types of watery (mul) kimchi, containing sliced and unsliced radish and vegetables (nabak and dongchimi, respectively), were investigated. Samples from kimchi were fermented at 4, 10, and 20 °C were analyzed by plating on differential and selective...

  11. Molecular ecology of microbial mats.

    PubMed

    Bolhuis, Henk; Cretoiu, Mariana Silvia; Stal, Lucas J

    2014-11-01

    Phototrophic microbial mats are ideal model systems for ecological and evolutionary analysis of highly diverse microbial communities. Microbial mats are small-scale, nearly closed, and self-sustaining benthic ecosystems that comprise the major element cycles, trophic levels, and food webs. The steep and fluctuating physicochemical microgradients, that are the result of the ever changing environmental conditions and of the microorganisms' own activities, give rise to a plethora of potential niches resulting in the formation of one of the most diverse microbial ecosystems known to date. For several decades, microbial mats have been studied extensively and more recently molecular biological techniques have been introduced that allowed assessing and investigating the diversity and functioning of these systems. These investigations also involved metagenomics analyses using high-throughput DNA and RNA sequencing. Here, we summarize some of the latest developments in metagenomic analysis of three representative phototrophic microbial mat types (coastal, hot spring, and hypersaline). We also present a comparison of the available metagenomic data sets from mats emphasizing the major differences between them as well as elucidating the overlap in overall community composition. PMID:25109247

  12. Molecular ecology of microbial mats.

    PubMed

    Bolhuis, Henk; Cretoiu, Mariana Silvia; Stal, Lucas J

    2014-11-01

    Phototrophic microbial mats are ideal model systems for ecological and evolutionary analysis of highly diverse microbial communities. Microbial mats are small-scale, nearly closed, and self-sustaining benthic ecosystems that comprise the major element cycles, trophic levels, and food webs. The steep and fluctuating physicochemical microgradients, that are the result of the ever changing environmental conditions and of the microorganisms' own activities, give rise to a plethora of potential niches resulting in the formation of one of the most diverse microbial ecosystems known to date. For several decades, microbial mats have been studied extensively and more recently molecular biological techniques have been introduced that allowed assessing and investigating the diversity and functioning of these systems. These investigations also involved metagenomics analyses using high-throughput DNA and RNA sequencing. Here, we summarize some of the latest developments in metagenomic analysis of three representative phototrophic microbial mat types (coastal, hot spring, and hypersaline). We also present a comparison of the available metagenomic data sets from mats emphasizing the major differences between them as well as elucidating the overlap in overall community composition.

  13. Exploring Subglacial Microbial Ecology (Invited)

    NASA Astrophysics Data System (ADS)

    Mikucki, J.; Mitchell, A. C.; Johnson, S. S.; Grzymski, J.

    2009-12-01

    Subglacial environments were long thought to be abiotic. We now know that microbial life exists below glaciers, but know relatively little about the in situ metabolic processes they mediate and how their activity transforms the geochemistry of subglacial efflux. It has been hypothesized that subglacial systems, driven to anoxia in the presence of sufficient organic matter, will follow a continuum of redox chemistries utilizing electron acceptors with decreasing reduction potential (i.e. Fe (III), sulfate, CO2). Indeed, sulfate reduction and methanogenesis have been detected in studies of polythermal glaciers. However, it is unclear whether there is sufficient organic matter to sustain highly reducing conditions below Antarctic ice. Here we present a broad overview of the microbial ecology of subglacial ecosystems and describe the links between microbial diversity and community function in these chemically complex environments. The subglacial environment below the Taylor Glacier, Antarctica provides an example where biogeochemical measurements made on subglacial efflux can inform specific mechanisms of microbial metabolism. We have tested the validity of these mechanisms using environmental genomic surveys and biogeochemical measurements of subglacial fluids to describe an active community that cycles iron and sulfur below Taylor Glacier. Examples include the incorporation of radiolabeled bicarbonate by cells in the outflow and detection of functional genes responsible for CO2-fixation (i.e. RuBisCO), and isotopic composition of sulfate sulfur and oxygen in the outflow indicative of sulfate reduction with the presence of functional genes of the sulfur cycle (i.e. APS reductase). Moving forward in our exploration of subglacial ecosystems, key questions regarding microbial energetics include: 1) How microorganisms cycle mineral substrates below glaciers to gain energy for growth 2) Whether subglacial microorganisms grow syntrophically in order to metabolize iron and

  14. Manipulatiaon of Biofilm Microbial Ecology

    SciTech Connect

    Burkhalter, R.; Macnaughton, S.J.; Palmer, R.J.; Smith, C.A.; Whitaker, K.W.; White, D.C.; Zinn, M.; kirkegaard, R.

    1998-08-09

    The Biofilm mode of growth provides such significant advantages to the members of the consortium that most organisms in important habitats are found in biofilms. The study of factors that allow manipulation of biofilm microbes in the biofilm growth state requires that reproducible biofilms by generated. The most effective monitoring of biofilm formation, succession and desquamation is with on-line monitoring of microbial biofilms with flowcell for direct observation. The biofilm growth state incorporates a second important factor, the heterogeneity in the distribution in time and space of the component members of the biofilm consortium. This heterogeneity is reflected not only in the cellular distribution but in the metabolic activity within a population of cells. Activity and cellular distribution can be mapped in four dimensions with confocal microscopy, and function can be ascertained by genetically manipulated reporter functions for specific genes or by vital stains. The methodology for understanding the microbial ecology of biofilms is now much more readily available and the capacity to manipulate biofilms is becoming an important feature of biotechnology.

  15. Manipulation of Biofilm Microbial Ecology

    SciTech Connect

    White, D.C.; Palmer, R.J., Jr.; Zinn, M.; Smith, C.A.; Burkhalter, R.; Macnaughton, S.J.; Whitaker, K.W.; Kirkegaard, R.D.

    1998-08-15

    The biofilm mode of growth provides such significant advantages to the members of the consortium that most organisms in important habitats are found in biofilms. The study of factors that allow manipulation of biofilm microbes in the biofilm growth state requires that reproducible biofilms be generated. The most effective monitoring of biofilm formation, succession and desaturation is with on-line monitoring of microbial biofilms with flowcell for direct observation. The biofilm growth state incorporates a second important factor, the heterogeneity in distribution in time and space of the component members of the biofilm consortium. This heterogeneity is reflected not only in the cellular distribution but in the metabolic activity within a population of cells. Activity and cellular distribution can be mapped in four dimensions with confocal microscopy, and function can be ascertained by genetically manipulated reporter functions for specific genes or by vital stains. The methodology for understanding the microbial ecology of biofilms is now much more readily available and the capacity to manipulate biofilms is becoming an important feature of biotechnology.

  16. Procedures For Microbial-Ecology Laboratory

    NASA Technical Reports Server (NTRS)

    Huff, Timothy L.

    1993-01-01

    Microbial Ecology Laboratory Procedures Manual provides concise and well-defined instructions on routine technical procedures to be followed in microbiological laboratory to ensure safety, analytical control, and validity of results.

  17. Human microbial ecology: lactobacilli, probiotics, selective decontamination.

    PubMed

    Mikelsaar, Marika

    2011-12-01

    Health care-associated infections are closely associated with different medical interventions which interrupt the balance of human microbiota. The occasional predominance of opportunistic pathogens may lead to their translocation into the lymph nodes and bloodstream, causing endogenous (primary or secondary) hospital infections. The question is raised as to if there is a possibility for prevention of the imbalance of GI microbiota during medical interventions in critically ill patients. Prophylactic selective decontamination of the digestive tract (SDD) simultaneously applies three to four different antimicrobials for the suppression of enteric aerobic microbes, which are potentially pathogenic microorganisms. However, there is no convincing evidence that the indigenous beneficial intestinal microbiota are preserved, resulting in reduced mortality of high-risk patients. In this overview, we have evaluated the antimicrobial treatment guidelines of the Infectious Diseases Society of America (IDSA) for intra-abdominal infections in adults and seniors according to their safety for different Lactobacillus spp. The data from our group and in the literature have shown that all tested lactobacilli strains (nearly one hundred) were insusceptible to metronidazole while different species of lactobacilli of the three fermentation groups expressed particular antibiotic susceptibility to vancomycin, cefoxitin, ciprofloxacin and some new tetracyclines. We have relied on microbial ecology data showing that the GI tracts of adults and the elderly are simultaneously colonised at least with several (four to a maximum of 12) Lactobacillus species expressing variable intrinsic insusceptibility to the aforementioned antimicrobials, according to the provided data in table. This finding offers the possibility of preserving the colonisation of the intestine with some beneficial lactobacilli during antimicrobial treatment in critically ill patients with health care-associated infections

  18. Microbial ecology of drinking water distribution systems.

    PubMed

    Berry, David; Xi, Chuanwu; Raskin, Lutgarde

    2006-06-01

    The supply of clean drinking water is a major, and relatively recent, public health milestone. Control of microbial growth in drinking water distribution systems, often achieved through the addition of disinfectants, is essential to limiting waterborne illness, particularly in immunocompromised subpopulations. Recent inquiries into the microbial ecology of distribution systems have found that pathogen resistance to chlorination is affected by microbial community diversity and interspecies relationships. Research indicates that multispecies biofilms are generally more resistant to disinfection than single-species biofilms. Other recent findings are the increased survival of the bacterial pathogen Legionella pneumophila when present inside its protozoan host Hartmannella vermiformis and the depletion of chloramine disinfectant residuals by nitrifying bacteria, leading to increased overall microbial growth. Interactions such as these are unaccounted for in current disinfection models. An understanding of the microbial ecology of distribution systems is necessary to design innovative and effective control strategies that will ensure safe and high-quality drinking water. PMID:16701992

  19. Microarray Applications in Microbial Ecology Research.

    SciTech Connect

    Gentry, T.; Schadt, C.; Zhou, J.

    2006-04-06

    Microarray technology has the unparalleled potential tosimultaneously determine the dynamics and/or activities of most, if notall, of the microbial populations in complex environments such as soilsand sediments. Researchers have developed several types of arrays thatcharacterize the microbial populations in these samples based on theirphylogenetic relatedness or functional genomic content. Several recentstudies have used these microarrays to investigate ecological issues;however, most have only analyzed a limited number of samples withrelatively few experiments utilizing the full high-throughput potentialof microarray analysis. This is due in part to the unique analyticalchallenges that these samples present with regard to sensitivity,specificity, quantitation, and data analysis. This review discussesspecific applications of microarrays to microbial ecology research alongwith some of the latest studies addressing the difficulties encounteredduring analysis of complex microbial communities within environmentalsamples. With continued development, microarray technology may ultimatelyachieve its potential for comprehensive, high-throughput characterizationof microbial populations in near real-time.

  20. The information science of microbial ecology.

    PubMed

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

    2016-06-01

    A revolution is unfolding in microbial ecology where petabytes of 'multi-omics' data are produced using next generation sequencing and mass spectrometry platforms. This cornucopia of biological information has enormous potential to reveal the hidden metabolic powers of microbial communities in natural and engineered ecosystems. However, to realize this potential, the development of new technologies and interpretative frameworks grounded in ecological design principles are needed to overcome computational and analytical bottlenecks. Here we explore the relationship between microbial ecology and information science in the era of cloud-based computation. We consider microorganisms as individual information processing units implementing a distributed metabolic algorithm and describe developments in ecoinformatics and ubiquitous computing with the potential to eliminate bottlenecks and empower knowledge creation and translation. PMID:27183115

  1. The information science of microbial ecology.

    PubMed

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

    2016-06-01

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

  2. Guiding bioprocess design by microbial ecology.

    PubMed

    Volmer, Jan; Schmid, Andreas; Bühler, Bruno

    2015-06-01

    Industrial bioprocess development is driven by profitability and eco-efficiency. It profits from an early stage definition of process and biocatalyst design objectives. Microbial bioprocess environments can be considered as synthetic technical microbial ecosystems. Natural systems follow Darwinian evolution principles aiming at survival and reproduction. Technical systems objectives are eco-efficiency, productivity, and profitable production. Deciphering technical microbial ecology reveals differences and similarities of natural and technical systems objectives, which are discussed in this review in view of biocatalyst and process design and engineering strategies. Strategies for handling opposing objectives of natural and technical systems and for exploiting and engineering natural properties of microorganisms for technical systems are reviewed based on examples. This illustrates the relevance of considering microbial ecology for bioprocess design and the potential for exploitation by synthetic biology strategies. PMID:25835154

  3. Microfluidics expanding the frontiers of microbial ecology.

    PubMed

    Rusconi, Roberto; Garren, Melissa; Stocker, Roman

    2014-01-01

    Microfluidics has significantly contributed to the expansion of the frontiers of microbial ecology over the past decade by allowing researchers to observe the behaviors of microbes in highly controlled microenvironments, across scales from a single cell to mixed communities. Spatially and temporally varying distributions of organisms and chemical cues that mimic natural microbial habitats can now be established by exploiting physics at the micrometer scale and by incorporating structures with specific geometries and materials. In this article, we review applications of microfluidics that have resulted in insightful discoveries on fundamental aspects of microbial life, ranging from growth and sensing to cell-cell interactions and population dynamics. We anticipate that this flexible multidisciplinary technology will continue to facilitate discoveries regarding the ecology of microorganisms and help uncover strategies to control microbial processes such as biofilm formation and antibiotic resistance.

  4. Guiding bioprocess design by microbial ecology.

    PubMed

    Volmer, Jan; Schmid, Andreas; Bühler, Bruno

    2015-06-01

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

  5. The outer mucus layer hosts a distinct intestinal microbial niche

    PubMed Central

    Li, Hai; Limenitakis, Julien P.; Fuhrer, Tobias; Geuking, Markus B.; Lawson, Melissa A.; Wyss, Madeleine; Brugiroux, Sandrine; Keller, Irene; Macpherson, Jamie A.; Rupp, Sandra; Stolp, Bettina; Stein, Jens V.; Stecher, Bärbel; Sauer, Uwe; McCoy, Kathy D.; Macpherson, Andrew J.

    2015-01-01

    The overall composition of the mammalian intestinal microbiota varies between individuals: within each individual there are differences along the length of the intestinal tract related to host nutrition, intestinal motility and secretions. Mucus is a highly regenerative protective lubricant glycoprotein sheet secreted by host intestinal goblet cells; the inner mucus layer is nearly sterile. Here we show that the outer mucus of the large intestine forms a unique microbial niche with distinct communities, including bacteria without specialized mucolytic capability. Bacterial species present in the mucus show differential proliferation and resource utilization compared with the same species in the intestinal lumen, with high recovery of bioavailable iron and consumption of epithelial-derived carbon sources according to their genome-encoded metabolic repertoire. Functional competition for existence in this intimate layer is likely to be a major determinant of microbiota composition and microbial molecular exchange with the host. PMID:26392213

  6. Microfluidics Expanding the Frontiers of Microbial Ecology

    PubMed Central

    Rusconi, Roberto; Garren, Melissa; Stocker, Roman

    2014-01-01

    The ability afforded by microfluidics to observe the behaviors of microbes in highly controlled and confined microenvironments, across scales from a single cell to mixed communities, has significantly contributed to expand the frontiers of microbial ecology over the last decade. Spatially and temporally varying distributions of organisms and chemical cues that mimic natural microbial habitats can now be established by exploiting physics at the micrometer scale and by incorporating structures with specific geometries and materials. Here we review applications of microfluidics that have resulted in highly insightful discoveries on fundamental aspects of microbial life, ranging from growth and sensing to cell-cell interactions and population dynamics. We anticipate that this flexible, multidisciplinary technology will continue to facilitate discoveries regarding the ecology of microorganisms and help uncover strategies to control phenomena such as biofilm formation and antibiotic resistance. PMID:24773019

  7. Microbial ecology of expanding oxygen minimum zones.

    PubMed

    Wright, Jody J; Konwar, Kishori M; Hallam, Steven J

    2012-06-01

    Dissolved oxygen concentration is a crucial organizing principle in marine ecosystems. As oxygen levels decline, energy is increasingly diverted away from higher trophic levels into microbial metabolism, leading to loss of fixed nitrogen and to production of greenhouse gases, including nitrous oxide and methane. In this Review, we describe current efforts to explore the fundamental factors that control the ecological and microbial biodiversity in oxygen-starved regions of the ocean, termed oxygen minimum zones. We also discuss how recent advances in microbial ecology have provided information about the potential interactions in distributed co-occurrence and metabolic networks in oxygen minimum zones, and we provide new insights into coupled biogeochemical processes in the ocean.

  8. New directions in coral reef microbial ecology.

    PubMed

    Garren, Melissa; Azam, Farooq

    2012-04-01

    Microbial processes largely control the health and resilience of coral reef ecosystems, and new technologies have led to an exciting wave of discovery regarding the mechanisms by which microbial communities support the functioning of these incredibly diverse and valuable systems. There are three questions at the forefront of discovery: What mechanisms underlie coral reef health and resilience? How do environmental and anthropogenic pressures affect ecosystem function? What is the ecology of microbial diseases of corals? The goal is to understand the functioning of coral reefs as integrated systems from microbes and molecules to regional and ocean-basin scale ecosystems to enable accurate predictions of resilience and responses to perturbations such as climate change and eutrophication. This review outlines recent discoveries regarding the microbial ecology of different microenvironments within coral ecosystems, and highlights research directions that take advantage of new technologies to build a quantitative and mechanistic understanding of how coral health is connected through microbial processes to its surrounding environment. The time is ripe for natural resource managers and microbial ecologists to work together to create an integrated understanding of coral reef functioning. In the context of long-term survival and conservation of reefs, the need for this work is immediate. PMID:21955796

  9. Microbial ecology of chlorinated solvent biodegradation.

    PubMed

    David, Maude M; Cecillon, Sebastien; Warne, Brett M; Prestat, Emmanuel; Jansson, Janet K; Vogel, Timothy M

    2015-12-01

    This study focused on the microbial ecology of tetrachloroethene (PCE) degradation to trichloroethene, cis-1,2-dichloroethene and vinyl chloride to evaluate the relationship between the microbial community and the potential accumulation or degradation of these toxic metabolites. Multiple soil microcosms supplied with different organic substrates were artificially contaminated with PCE. A thymidine analogue, bromodeoxyuridine (BrdU), was added to the microcosms and incorporated into the DNA of actively replicating cells. We compared the total and active bacterial communities during the 50-day incubations by using phylogenic microarrays and 454 pyrosequencing to identify microorganisms and functional genes associated with PCE degradation to ethene. By use of this integrative approach, both the key community members and the ecological functions concomitant with complete PCE degradation could be determined, including the presence and activity of microbial community members responsible for producing hydrogen and acetate, which are critical for Dehalococcoides-mediated PCE degradation. In addition, by correlation of chemical data and phylogenic microarray data, we identified several bacteria that could potentially oxidize hydrogen. These results demonstrate that PCE degradation is dependent on some microbial community members for production of appropriate metabolites, while other members of the community compete for hydrogen in soil at low redox potentials.

  10. Microbial contact during pregnancy, intestinal colonization and human disease.

    PubMed

    Rautava, Samuli; Luoto, Raakel; Salminen, Seppo; Isolauri, Erika

    2012-10-01

    Interaction with colonizing intestinal bacteria is essential for healthy intestinal and immunological development in infancy. Advances in understanding early host-microbe interactions indicate that this early microbial programming begins in utero and is substantially modulated by mode of birth, perinatal antibiotics and breastfeeding. Furthermore, it has become evident that this stepwise microbial colonization process, as well as immune and metabolic programming by the microbiota, might have a long-lasting influence on the risk of not only gastrointestinal disease, but also allergic, autoimmune and metabolic disease, in later life. Modulating early host-microbe interaction by maternal probiotic intervention during pregnancy and breastfeeding offers a promising novel tool to reduce the risk of disease. In this Review, we describe the current body of knowledge regarding perinatal microbial contact, initial intestinal colonization and its association with human disease, as well as means of modulating early host-microbe interaction to reduce the risk of disease in the child.

  11. Microbial ecology of Antarctic aquatic systems.

    PubMed

    Cavicchioli, Ricardo

    2015-11-01

    The Earth's biosphere is dominated by cold environments, and the cold biosphere is dominated by microorganisms. Microorganisms in cold Southern Ocean waters are recognized for having crucial roles in global biogeochemical cycles, including carbon sequestration, whereas microorganisms in other Antarctic aquatic biomes are not as well understood. In this Review, I consider what has been learned about Antarctic aquatic microbial ecology from 'omic' studies. I assess the factors that shape the biogeography of Antarctic microorganisms, reflect on some of the unusual biogeochemical cycles that they are associated with and discuss the important roles that viruses have in controlling ecosystem function. PMID:26456925

  12. Microbial ecology of Antarctic aquatic systems.

    PubMed

    Cavicchioli, Ricardo

    2015-11-01

    The Earth's biosphere is dominated by cold environments, and the cold biosphere is dominated by microorganisms. Microorganisms in cold Southern Ocean waters are recognized for having crucial roles in global biogeochemical cycles, including carbon sequestration, whereas microorganisms in other Antarctic aquatic biomes are not as well understood. In this Review, I consider what has been learned about Antarctic aquatic microbial ecology from 'omic' studies. I assess the factors that shape the biogeography of Antarctic microorganisms, reflect on some of the unusual biogeochemical cycles that they are associated with and discuss the important roles that viruses have in controlling ecosystem function.

  13. A Microbial Feed Additive Abates Intestinal Inflammation in Atlantic Salmon

    PubMed Central

    Vasanth, Ghana; Kiron, Viswanath; Kulkarni, Amod; Dahle, Dalia; Lokesh, Jep; Kitani, Yoichiro

    2015-01-01

    The efficacy of a microbial feed additive (Bactocell®) in countering intestinal inflammation in Atlantic salmon was examined in this study. Fish were fed either the additive-coated feed (probiotic) or feed without it (control). After an initial 3-week feeding, an inflammatory condition was induced by anally intubating all the fish with oxazolone. The fish were offered the feeds for 3 more weeks. Distal intestine from the groups was obtained at 4 h, 24 h, and 3 weeks, after oxazolone treatment. Inflammatory responses were prominent in both groups at 24 h, documented by changes in intestinal micromorphology, expression of inflammation-related genes, and intestinal proteome. The control group was characterized by edema, widening of intestinal villi and lamina propria, infiltration of granulocytes and lymphocytes, and higher expression of genes related to inflammatory responses, mul1b, il1b, tnfa, ifng, compared to the probiotic group or other time points of the control group. Further, the protein expression in the probiotic group at 24 h after inducing inflammation revealed five differentially regulated proteins – Calr, Psma5, Trp1, Ctsb, and Naga. At 3 weeks after intubation, the inflammatory responses subsided in the probiotic group. The findings provide evidence that the microbial additive contributes to intestinal homeostasis in Atlantic salmon. PMID:26347738

  14. Manipulating ruminal fermentation: a microbial ecological perspective.

    PubMed

    Weimer, P J

    1998-12-01

    The essential role of ruminal microflora in ruminant nutrition provides the potential for improvement in animal production via altering the numbers or activities of specific classes of microorganisms. Successful alterations will be facilitated by an understanding of the microbial ecology of the rumen based on its mechanistic underpinnings. Demonstrated improvements in ruminal fermentation can be traced to their consonance with well-established principles of microbial ecology (niche occupancy, selective pressure, adaptation, and interactions) and the thermodynamics and kinetics of substrate utilization. Application of these principles to several proposed alterations of the ruminal bacterial population allows a prediction of their relative feasibility. Improving fiber digestion, decreasing protein degradation, and detoxifying feed components that are present in low concentrations will be difficult to achieve in the rumen and are best approached by altering the feed, either genetically or with postharvest treatment. By contrast, the detoxification of feed components present in high concentration, and redirection of electron disposal away from methanogenesis, are more productive targets for microbiological research.

  15. The microbial ecology of wine grape berries.

    PubMed

    Barata, A; Malfeito-Ferreira, M; Loureiro, V

    2012-02-15

    Grapes have a complex microbial ecology including filamentous fungi, yeasts and bacteria with different physiological characteristics and effects upon wine production. Some species are only found in grapes, such as parasitic fungi and environmental bacteria, while others have the ability to survive and grow in wines, constituting the wine microbial consortium. This consortium covers yeast species, lactic acid bacteria and acetic acid bacteria. The proportion of these microorganisms depends on the grape ripening stage and on the availability of nutrients. Grape berries are susceptible to fungal parasites until véraison after which the microbiota of truly intact berries is similar to that of plant leaves, which is dominated by basidiomycetous yeasts (e.g. Cryptococcus spp., Rhodotorula spp. Sporobolomyces spp.) and the yeast-like fungus Aureobasidium pullulans. The cuticle of visually intact berries may bear microfissures and softens with ripening, increasing nutrient availability and explaining the possible dominance by the oxidative or weakly fermentative ascomycetous populations (e.g. Candida spp., Hanseniaspora spp., Metschnikowia spp., Pichia spp.) approaching harvest time. When grape skin is clearly damaged, the availability of high sugar concentrations on the berry surface favours the increase of ascomycetes with higher fermentative activity like Pichia spp. and Zygoascus hellenicus, including dangerous wine spoilage yeasts (e.g. Zygosaccharomyces spp., Torulaspora spp.), and of acetic acid bacteria (e.g. Gluconobacter spp., Acetobacter spp.). The sugar fermenting species Saccharomyces cerevisiae is rarely found on unblemished berries, being favoured by grape damage. Lactic acid bacteria are minor partners of grape microbiota and while being the typical agent of malolactic fermentation, Oenococcus oeni has been seldom isolated from grapes in the vineyard. Environmental ubiquitous bacteria of the genus Enterobacter spp., Enterococcus spp., Bacillus spp

  16. The microbial ecology of wine grape berries.

    PubMed

    Barata, A; Malfeito-Ferreira, M; Loureiro, V

    2012-02-15

    Grapes have a complex microbial ecology including filamentous fungi, yeasts and bacteria with different physiological characteristics and effects upon wine production. Some species are only found in grapes, such as parasitic fungi and environmental bacteria, while others have the ability to survive and grow in wines, constituting the wine microbial consortium. This consortium covers yeast species, lactic acid bacteria and acetic acid bacteria. The proportion of these microorganisms depends on the grape ripening stage and on the availability of nutrients. Grape berries are susceptible to fungal parasites until véraison after which the microbiota of truly intact berries is similar to that of plant leaves, which is dominated by basidiomycetous yeasts (e.g. Cryptococcus spp., Rhodotorula spp. Sporobolomyces spp.) and the yeast-like fungus Aureobasidium pullulans. The cuticle of visually intact berries may bear microfissures and softens with ripening, increasing nutrient availability and explaining the possible dominance by the oxidative or weakly fermentative ascomycetous populations (e.g. Candida spp., Hanseniaspora spp., Metschnikowia spp., Pichia spp.) approaching harvest time. When grape skin is clearly damaged, the availability of high sugar concentrations on the berry surface favours the increase of ascomycetes with higher fermentative activity like Pichia spp. and Zygoascus hellenicus, including dangerous wine spoilage yeasts (e.g. Zygosaccharomyces spp., Torulaspora spp.), and of acetic acid bacteria (e.g. Gluconobacter spp., Acetobacter spp.). The sugar fermenting species Saccharomyces cerevisiae is rarely found on unblemished berries, being favoured by grape damage. Lactic acid bacteria are minor partners of grape microbiota and while being the typical agent of malolactic fermentation, Oenococcus oeni has been seldom isolated from grapes in the vineyard. Environmental ubiquitous bacteria of the genus Enterobacter spp., Enterococcus spp., Bacillus spp

  17. The use of microarrays in microbial ecology

    SciTech Connect

    Andersen, G.L.; He, Z.; DeSantis, T.Z.; Brodie, E.L.; Zhou, J.

    2009-09-15

    Microarrays have proven to be a useful and high-throughput method to provide targeted DNA sequence information for up to many thousands of specific genetic regions in a single test. A microarray consists of multiple DNA oligonucleotide probes that, under high stringency conditions, hybridize only to specific complementary nucleic acid sequences (targets). A fluorescent signal indicates the presence and, in many cases, the abundance of genetic regions of interest. In this chapter we will look at how microarrays are used in microbial ecology, especially with the recent increase in microbial community DNA sequence data. Of particular interest to microbial ecologists, phylogenetic microarrays are used for the analysis of phylotypes in a community and functional gene arrays are used for the analysis of functional genes, and, by inference, phylotypes in environmental samples. A phylogenetic microarray that has been developed by the Andersen laboratory, the PhyloChip, will be discussed as an example of a microarray that targets the known diversity within the 16S rRNA gene to determine microbial community composition. Using multiple, confirmatory probes to increase the confidence of detection and a mismatch probe for every perfect match probe to minimize the effect of cross-hybridization by non-target regions, the PhyloChip is able to simultaneously identify any of thousands of taxa present in an environmental sample. The PhyloChip is shown to reveal greater diversity within a community than rRNA gene sequencing due to the placement of the entire gene product on the microarray compared with the analysis of up to thousands of individual molecules by traditional sequencing methods. A functional gene array that has been developed by the Zhou laboratory, the GeoChip, will be discussed as an example of a microarray that dynamically identifies functional activities of multiple members within a community. The recent version of GeoChip contains more than 24,000 50mer

  18. Oral biofilms: emerging concepts in microbial ecology.

    PubMed

    Filoche, S; Wong, L; Sissons, C H

    2010-01-01

    Oral biofilms develop under a range of different conditions and different environments. This review will discuss emerging concepts in microbial ecology and how they relate to oral biofilm development and the treatment of oral diseases. Clues to how oral biofilms develop may lie in other complex systems, such as interactions between host and gut microbiota, and even in factors that affect biofilm development on leaf surfaces. Most of the conditions under which oral biofilms develop are tightly linked to the overall health and biology of the host. Advances in molecular techniques have led to a greater appreciation of the diversity of human microbiota, the extent of interactions with the human host, and how that relates to inter-individual variation. As a consequence, plaque development may no longer be thought of as a generic process, but rather as a highly individualized process, which has ramifications for the treatment of the diseases it causes.

  19. The Ecology and Evolution of Microbial Competition.

    PubMed

    Ghoul, Melanie; Mitri, Sara

    2016-10-01

    Microbes are typically surrounded by different strains and species with whom they compete for scarce nutrients and limited space. Given such challenging living conditions, microbes have evolved many phenotypes with which they can outcompete and displace their neighbours: secretions to harvest resources, loss of costly genes whose products can be obtained from others, stabbing and poisoning neighbouring cells, or colonising spaces while preventing others from doing so. These competitive phenotypes appear to be common, although evidence suggests that, over time, competition dies down locally, often leading to stable coexistence of genetically distinct lineages. Nevertheless, the selective forces acting on competition and the resulting evolutionary fates of the different players depend on ecological conditions in a way that is not yet well understood. Here, we highlight open questions and theoretical predictions of the long-term dynamics of competition that remain to be tested. Establishing a clearer understanding of microbial competition will allow us to better predict the behaviour of microbes, and to control and manipulate microbial communities for industrial, environmental, and medical purposes.

  20. Microbial Biofilms: from Ecology to Molecular Genetics

    PubMed Central

    Davey, Mary Ellen; O'toole, George A.

    2000-01-01

    Biofilms are complex communities of microorganisms attached to surfaces or associated with interfaces. Despite the focus of modern microbiology research on pure culture, planktonic (free-swimming) bacteria, it is now widely recognized that most bacteria found in natural, clinical, and industrial settings persist in association with surfaces. Furthermore, these microbial communities are often composed of multiple species that interact with each other and their environment. The determination of biofilm architecture, particularly the spatial arrangement of microcolonies (clusters of cells) relative to one another, has profound implications for the function of these complex communities. Numerous new experimental approaches and methodologies have been developed in order to explore metabolic interactions, phylogenetic groupings, and competition among members of the biofilm. To complement this broad view of biofilm ecology, individual organisms have been studied using molecular genetics in order to identify the genes required for biofilm development and to dissect the regulatory pathways that control the plankton-to-biofilm transition. These molecular genetic studies have led to the emergence of the concept of biofilm formation as a novel system for the study of bacterial development. The recent explosion in the field of biofilm research has led to exciting progress in the development of new technologies for studying these communities, advanced our understanding of the ecological significance of surface-attached bacteria, and provided new insights into the molecular genetic basis of biofilm development. PMID:11104821

  1. Ecological modeling from time-series inference: insight into dynamics and stability of intestinal microbiota.

    PubMed

    Stein, Richard R; Bucci, Vanni; Toussaint, Nora C; Buffie, Charlie G; Rätsch, Gunnar; Pamer, Eric G; Sander, Chris; Xavier, João B

    2013-01-01

    The intestinal microbiota is a microbial ecosystem of crucial importance to human health. Understanding how the microbiota confers resistance against enteric pathogens and how antibiotics disrupt that resistance is key to the prevention and cure of intestinal infections. We present a novel method to infer microbial community ecology directly from time-resolved metagenomics. This method extends generalized Lotka-Volterra dynamics to account for external perturbations. Data from recent experiments on antibiotic-mediated Clostridium difficile infection is analyzed to quantify microbial interactions, commensal-pathogen interactions, and the effect of the antibiotic on the community. Stability analysis reveals that the microbiota is intrinsically stable, explaining how antibiotic perturbations and C. difficile inoculation can produce catastrophic shifts that persist even after removal of the perturbations. Importantly, the analysis suggests a subnetwork of bacterial groups implicated in protection against C. difficile. Due to its generality, our method can be applied to any high-resolution ecological time-series data to infer community structure and response to external stimuli. PMID:24348232

  2. Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota

    PubMed Central

    Toussaint, Nora C.; Buffie, Charlie G.; Rätsch, Gunnar; Pamer, Eric G.; Sander, Chris; Xavier, João B.

    2013-01-01

    The intestinal microbiota is a microbial ecosystem of crucial importance to human health. Understanding how the microbiota confers resistance against enteric pathogens and how antibiotics disrupt that resistance is key to the prevention and cure of intestinal infections. We present a novel method to infer microbial community ecology directly from time-resolved metagenomics. This method extends generalized Lotka–Volterra dynamics to account for external perturbations. Data from recent experiments on antibiotic-mediated Clostridium difficile infection is analyzed to quantify microbial interactions, commensal-pathogen interactions, and the effect of the antibiotic on the community. Stability analysis reveals that the microbiota is intrinsically stable, explaining how antibiotic perturbations and C. difficile inoculation can produce catastrophic shifts that persist even after removal of the perturbations. Importantly, the analysis suggests a subnetwork of bacterial groups implicated in protection against C. difficile. Due to its generality, our method can be applied to any high-resolution ecological time-series data to infer community structure and response to external stimuli. PMID:24348232

  3. Molecular musings in microbial ecology and evolution

    PubMed Central

    2011-01-01

    A few major discoveries have influenced how ecologists and evolutionists study microbes. Here, in the format of an interview, we answer questions that directly relate to how these discoveries are perceived in these two branches of microbiology, and how they have impacted on both scientific thinking and methodology. The first question is "What has been the influence of the 'Universal Tree of Life' based on molecular markers?" For evolutionists, the tree was a tool to understand the past of known (cultured) organisms, mapping the invention of various physiologies on the evolutionary history of microbes. For ecologists the tree was a guide to discover the current diversity of unknown (uncultured) organisms, without much knowledge of their physiology. The second question we ask is "What was the impact of discovering frequent lateral gene transfer among microbes?" In evolutionary microbiology, frequent lateral gene transfer (LGT) made a simple description of relationships between organisms impossible, and for microbial ecologists, functions could not be easily linked to specific genotypes. Both fields initially resisted LGT, but methods or topics of inquiry were eventually changed in one to incorporate LGT in its theoretical models (evolution) and in the other to achieve its goals despite that phenomenon (ecology). The third and last question we ask is "What are the implications of the unexpected extent of diversity?" The variation in the extent of diversity between organisms invalidated the universality of species definitions based on molecular criteria, a major obstacle to the adaptation of models developed for the study of macroscopic eukaryotes to evolutionary microbiology. This issue has not overtly affected microbial ecology, as it had already abandoned species in favor of the more flexible operational taxonomic units. This field is nonetheless moving away from traditional methods to measure diversity, as they do not provide enough resolution to uncover what lies

  4. Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond

    PubMed Central

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

    2016-01-01

    Metagenomic approaches are now commonly used in microbial ecology to study microbial communities in more detail, including many strains that cannot be cultivated in the laboratory. Bioinformatic analyses make it possible to mine huge metagenomic datasets and discover general patterns that govern microbial ecosystems. However, the findings of typical metagenomic and bioinformatic analyses still do not completely describe the ecology and evolution of microbes in their environments. Most analyses still depend on straightforward sequence similarity searches against reference databases. We herein review the current state of metagenomics and bioinformatics in microbial ecology and discuss future directions for the field. New techniques will allow us to go beyond routine analyses and broaden our knowledge of microbial ecosystems. We need to enrich reference databases, promote platforms that enable meta- or comprehensive analyses of diverse metagenomic datasets, devise methods that utilize long-read sequence information, and develop more powerful bioinformatic methods to analyze data from diverse perspectives. PMID:27383682

  5. Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond.

    PubMed

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

    2016-09-29

    Metagenomic approaches are now commonly used in microbial ecology to study microbial communities in more detail, including many strains that cannot be cultivated in the laboratory. Bioinformatic analyses make it possible to mine huge metagenomic datasets and discover general patterns that govern microbial ecosystems. However, the findings of typical metagenomic and bioinformatic analyses still do not completely describe the ecology and evolution of microbes in their environments. Most analyses still depend on straightforward sequence similarity searches against reference databases. We herein review the current state of metagenomics and bioinformatics in microbial ecology and discuss future directions for the field. New techniques will allow us to go beyond routine analyses and broaden our knowledge of microbial ecosystems. We need to enrich reference databases, promote platforms that enable meta- or comprehensive analyses of diverse metagenomic datasets, devise methods that utilize long-read sequence information, and develop more powerful bioinformatic methods to analyze data from diverse perspectives. PMID:27383682

  6. Changes in mouse gastrointestinal microbial ecology with ingestion of kale.

    PubMed

    Uyeno, Y; Katayama, S; Nakamura, S

    2014-09-01

    Kale, a cultivar of Brassica oleracea, has attracted a great deal of attention because of its health-promoting effects, which are thought to be exerted through modulation of the intestinal microbiota. The present study was performed to investigate the effects of kale ingestion on the gastrointestinal microbial ecology of mice. 21 male C57BL/6J mice were divided into three groups and housed in a specific pathogen-free facility. The animals were fed either a control diet or experimental diets supplemented with different commercial kale products for 12 weeks. Contents of the caecum and colon of the mice were processed for the determination of active bacterial populations by a bacterial rRNA-based quantification method and short-chain fatty acids by HPLC. rRNAs of Bacteroides-Prevotella, the Clostridium coccoides-Eubacterium rectale group, and Clostridium leptum subgroup constituted the major fraction of microbiota regardless of the composition of the diet. The ratio of Firmicutes to Bacteroidetes was higher in the colon samples of one of the kale diet groups than in the control. The colonic butyrate level was also higher with the kale-supplemented diet. Overall, the ingestion of kale tended to either increase or decrease the activity of specific bacterial groups in the mouse gastrointestinal tract, however, the effect might vary depending on the nutritional composition.

  7. Dietary synbiotic application modulates Atlantic salmon (Salmo salar) intestinal microbial communities and intestinal immunity.

    PubMed

    Abid, A; Davies, S J; Waines, P; Emery, M; Castex, M; Gioacchini, G; Carnevali, O; Bickerdike, R; Romero, J; Merrifield, D L

    2013-12-01

    A feeding trial was conducted to determine the effect of dietary administration of Pediococcus acidilactici MA18/5M and short chain fructooligosaccharides (scFOS) on Atlantic salmon (Salmo salar L.) intestinal health. Salmon (initial average weight 250 g) were allocated into triplicate sea pens and were fed either a control diet (commercial diet: 45% protein, 20% lipid) or a synbiotic treatment diet (control diet + P. acidilactici at 3.5 g kg(-1) and 7 g kg(-1) scFOS) for 63 days. At the end of this period, fish were sampled for intestinal microbiology, intestinal histology and the expression of selected immune-related genes (IL1β, TNFα, IL8, TLR3 and MX-1) in the intestine. Compared to the control fish, the total bacterial levels were significantly lower in the anterior mucosa, posterior mucosa and posterior digesta of the synbiotic fed fish. qPCR revealed good recovery (log 6 bacteria g(-1)) of the probiotic in the intestinal digesta of the synbiotic fed fish and PCR-DGGE revealed that the number of OTUs, as well as the microbial community diversity and richness were significantly higher in the anterior digesta of the synbiotic fed fish than the control. Compared to the control fed fish, the mucosal fold (villi) length and the infiltration of epithelial leucocytes were significantly higher in the anterior and posterior intestine, respectively, in the synbiotic group. Real-time PCR demonstrated that all of the genes investigated were significantly up-regulated in the anterior and posterior intestine of the synbiotic fed salmon, compared to the control group. At the systemic level, serum lysozyme activity was significantly higher in the synbiotic fed fish and growth performance, feed utilisation and biometric measurements (condition factor, gutted weight and gut loss) were not affected. Together these results suggest that the synbiotic modulation of the gut microbiota has a protective action on the intestinal mucosal cells, improving morphology and stimulating

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

    USGS Publications Warehouse

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

    2011-01-01

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

  9. Ordering microbial diversity into ecologically and genetically cohesive units.

    PubMed

    Shapiro, B Jesse; Polz, Martin F

    2014-05-01

    We propose that microbial diversity must be viewed in light of gene flow and selection, which define units of genetic similarity, and of phenotype and ecological function, respectively. We discuss to what extent ecological and genetic units overlap to form cohesive populations in the wild, based on recent evolutionary modeling and on evidence from some of the first microbial populations studied with genomics. These show that if recombination is frequent and selection moderate, ecologically adaptive mutations or genes can spread within populations independently of their original genomic background (gene-specific sweeps). Alternatively, if the effect of recombination is smaller than selection, genome-wide selective sweeps should occur. In both cases, however, distinct units of overlapping ecological and genotypic similarity will form if microgeographic separation, likely involving ecological tradeoffs, induces barriers to gene flow. These predictions are supported by (meta)genomic data, which suggest that a 'reverse ecology' approach, in which genomic and gene flow information is used to make predictions about the nature of ecological units, is a powerful approach to ordering microbial diversity.

  10. Sparse and compositionally robust inference of microbial ecological networks.

    PubMed

    Kurtz, Zachary D; Müller, Christian L; Miraldi, Emily R; Littman, Dan R; Blaser, Martin J; Bonneau, Richard A

    2015-05-01

    16S ribosomal RNA (rRNA) gene and other environmental sequencing techniques provide snapshots of microbial communities, revealing phylogeny and the abundances of microbial populations across diverse ecosystems. While changes in microbial community structure are demonstrably associated with certain environmental conditions (from metabolic and immunological health in mammals to ecological stability in soils and oceans), identification of underlying mechanisms requires new statistical tools, as these datasets present several technical challenges. First, the abundances of microbial operational taxonomic units (OTUs) from amplicon-based datasets are compositional. Counts are normalized to the total number of counts in the sample. Thus, microbial abundances are not independent, and traditional statistical metrics (e.g., correlation) for the detection of OTU-OTU relationships can lead to spurious results. Secondly, microbial sequencing-based studies typically measure hundreds of OTUs on only tens to hundreds of samples; thus, inference of OTU-OTU association networks is severely under-powered, and additional information (or assumptions) are required for accurate inference. Here, we present SPIEC-EASI (SParse InversE Covariance Estimation for Ecological Association Inference), a statistical method for the inference of microbial ecological networks from amplicon sequencing datasets that addresses both of these issues. SPIEC-EASI combines data transformations developed for compositional data analysis with a graphical model inference framework that assumes the underlying ecological association network is sparse. To reconstruct the network, SPIEC-EASI relies on algorithms for sparse neighborhood and inverse covariance selection. To provide a synthetic benchmark in the absence of an experimentally validated gold-standard network, SPIEC-EASI is accompanied by a set of computational tools to generate OTU count data from a set of diverse underlying network topologies. SPIEC

  11. Sparse and Compositionally Robust Inference of Microbial Ecological Networks

    PubMed Central

    Kurtz, Zachary D.; Müller, Christian L.; Miraldi, Emily R.; Littman, Dan R.; Blaser, Martin J.; Bonneau, Richard A.

    2015-01-01

    16S ribosomal RNA (rRNA) gene and other environmental sequencing techniques provide snapshots of microbial communities, revealing phylogeny and the abundances of microbial populations across diverse ecosystems. While changes in microbial community structure are demonstrably associated with certain environmental conditions (from metabolic and immunological health in mammals to ecological stability in soils and oceans), identification of underlying mechanisms requires new statistical tools, as these datasets present several technical challenges. First, the abundances of microbial operational taxonomic units (OTUs) from amplicon-based datasets are compositional. Counts are normalized to the total number of counts in the sample. Thus, microbial abundances are not independent, and traditional statistical metrics (e.g., correlation) for the detection of OTU-OTU relationships can lead to spurious results. Secondly, microbial sequencing-based studies typically measure hundreds of OTUs on only tens to hundreds of samples; thus, inference of OTU-OTU association networks is severely under-powered, and additional information (or assumptions) are required for accurate inference. Here, we present SPIEC-EASI (SParse InversE Covariance Estimation for Ecological Association Inference), a statistical method for the inference of microbial ecological networks from amplicon sequencing datasets that addresses both of these issues. SPIEC-EASI combines data transformations developed for compositional data analysis with a graphical model inference framework that assumes the underlying ecological association network is sparse. To reconstruct the network, SPIEC-EASI relies on algorithms for sparse neighborhood and inverse covariance selection. To provide a synthetic benchmark in the absence of an experimentally validated gold-standard network, SPIEC-EASI is accompanied by a set of computational tools to generate OTU count data from a set of diverse underlying network topologies. SPIEC

  12. Ecological perspectives on synthetic biology: insights from microbial population biology

    PubMed Central

    Escalante, Ana E.; Rebolleda-Gómez, María; Benítez, Mariana; Travisano, Michael

    2015-01-01

    The metabolic capabilities of microbes are the basis for many major biotechnological advances, exploiting microbial diversity by selection or engineering of single strains. However, there are limits to the advances that can be achieved with single strains, and attention has turned toward the metabolic potential of consortia and the field of synthetic ecology. The main challenge for the synthetic ecology is that consortia are frequently unstable, largely because evolution by constituent members affects their interactions, which are the basis of collective metabolic functionality. Current practices in modeling consortia largely consider interactions as fixed circuits of chemical reactions, which greatly increases their tractability. This simplification comes at the cost of essential biological realism, stripping out the ecological context in which the metabolic actions occur and the potential for evolutionary change. In other words, evolutionary stability is not engineered into the system. This realization highlights the necessity to better identify the key components that influence the stable coexistence of microorganisms. Inclusion of ecological and evolutionary principles, in addition to biophysical variables and stoichiometric modeling of metabolism, is critical for microbial consortia design. This review aims to bring ecological and evolutionary concepts to the discussion on the stability of microbial consortia. In particular, we focus on the combined effect of spatial structure (connectivity of molecules and cells within the system) and ecological interactions (reciprocal and non-reciprocal) on the persistence of microbial consortia. We discuss exemplary cases to illustrate these ideas from published studies in evolutionary biology and biotechnology. We conclude by making clear the relevance of incorporating evolutionary and ecological principles to the design of microbial consortia, as a way of achieving evolutionarily stable and sustainable systems. PMID

  13. Ecological perspectives on synthetic biology: insights from microbial population biology.

    PubMed

    Escalante, Ana E; Rebolleda-Gómez, María; Benítez, Mariana; Travisano, Michael

    2015-01-01

    The metabolic capabilities of microbes are the basis for many major biotechnological advances, exploiting microbial diversity by selection or engineering of single strains. However, there are limits to the advances that can be achieved with single strains, and attention has turned toward the metabolic potential of consortia and the field of synthetic ecology. The main challenge for the synthetic ecology is that consortia are frequently unstable, largely because evolution by constituent members affects their interactions, which are the basis of collective metabolic functionality. Current practices in modeling consortia largely consider interactions as fixed circuits of chemical reactions, which greatly increases their tractability. This simplification comes at the cost of essential biological realism, stripping out the ecological context in which the metabolic actions occur and the potential for evolutionary change. In other words, evolutionary stability is not engineered into the system. This realization highlights the necessity to better identify the key components that influence the stable coexistence of microorganisms. Inclusion of ecological and evolutionary principles, in addition to biophysical variables and stoichiometric modeling of metabolism, is critical for microbial consortia design. This review aims to bring ecological and evolutionary concepts to the discussion on the stability of microbial consortia. In particular, we focus on the combined effect of spatial structure (connectivity of molecules and cells within the system) and ecological interactions (reciprocal and non-reciprocal) on the persistence of microbial consortia. We discuss exemplary cases to illustrate these ideas from published studies in evolutionary biology and biotechnology. We conclude by making clear the relevance of incorporating evolutionary and ecological principles to the design of microbial consortia, as a way of achieving evolutionarily stable and sustainable systems. PMID

  14. 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

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

    PubMed

    Kim, Hyeun Bum; Isaacson, Richard E

    2015-06-12

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

  16. Microbial communities in the human small intestine: coupling diversity to metagenomics.

    PubMed

    Booijink, Carien C G M; Zoetendal, Erwin G; Kleerebezem, Michiel; de Vos, Willem M

    2007-06-01

    The gastrointestinal tract is the main site where the conversion and absorption of food components takes place. The host-derived physiological processes and the residing microorganisms, especially in the small intestine, contribute to this nutrient supply. To circumvent sampling problems of the small intestine, several model systems have been developed to study microbial diversity and functionality in the small intestine. In addition, metagenomics offers novel possibilities to gain insight into the genetic potential and functional properties of these microbial communities. Here, an overview is presented of the most recent insights into the diversity and functionality of the microorganisms in the human gastrointestinal tract, with a focus on the small intestine.

  17. [Engineering issues of microbial ecology in space agriculture].

    PubMed

    Yamashita, Masamichi; Ishikawa, Yoji; Oshima, Tairo

    2005-03-01

    Closure of the materials recycle loop for water-foods-oxygen is the primary purpose of space agriculture on Mars and Moon. A microbial ecological system takes a part of agriculture to process our metabolic excreta and inedible biomass and convert them to nutrients and soil substrate for cultivating plants. If we extend the purpose of space agriculture to the creation and control of a healthy and pleasant living environment, we should realize that our human body should not be sterilized but exposed to the appropriate microbial environment. We are proposing a use of hyper-thermophilic aerobic composting microbial ecology in space agriculture. Japan has a broad historical and cultural background on this subject. There had been agriculture that drove a closed loop of materials between consuming cities and farming villages in vicinity. Recent environmental problems regarding garbage collection and processing in towns have motivated home electronics companies to innovate "garbage composting" machines with bacterial technology. Based on those matured technology, together with new insights on microbiology and microbial ecology, we have been developing a conceptual design of space agriculture on Moon and Mars. There are several issues to be answered in order to prove effectiveness of the use of microbial systems in space. 1) Can the recycled nutrients, processed by the hyper-thermal aerobic composting microbial ecology, be formed in the physical and chemical state or configuration, with which plants can uptake those nutrients? A possibility of removing any major components of fertilizer from its recycle loop is another item to be evaluated. 2) What are the merits of forming soil microbial ecology around the root system of plants? This might be the most crucial question. Recent researches exhibit various mutually beneficial relationships among soil microbiota and plants, and symbiotic ecology in composting bacteria. It is essential to understand those features, and define

  18. [Engineering issues of microbial ecology in space agriculture].

    PubMed

    Yamashita, Masamichi; Ishikawa, Yoji; Oshima, Tairo

    2005-03-01

    Closure of the materials recycle loop for water-foods-oxygen is the primary purpose of space agriculture on Mars and Moon. A microbial ecological system takes a part of agriculture to process our metabolic excreta and inedible biomass and convert them to nutrients and soil substrate for cultivating plants. If we extend the purpose of space agriculture to the creation and control of a healthy and pleasant living environment, we should realize that our human body should not be sterilized but exposed to the appropriate microbial environment. We are proposing a use of hyper-thermophilic aerobic composting microbial ecology in space agriculture. Japan has a broad historical and cultural background on this subject. There had been agriculture that drove a closed loop of materials between consuming cities and farming villages in vicinity. Recent environmental problems regarding garbage collection and processing in towns have motivated home electronics companies to innovate "garbage composting" machines with bacterial technology. Based on those matured technology, together with new insights on microbiology and microbial ecology, we have been developing a conceptual design of space agriculture on Moon and Mars. There are several issues to be answered in order to prove effectiveness of the use of microbial systems in space. 1) Can the recycled nutrients, processed by the hyper-thermal aerobic composting microbial ecology, be formed in the physical and chemical state or configuration, with which plants can uptake those nutrients? A possibility of removing any major components of fertilizer from its recycle loop is another item to be evaluated. 2) What are the merits of forming soil microbial ecology around the root system of plants? This might be the most crucial question. Recent researches exhibit various mutually beneficial relationships among soil microbiota and plants, and symbiotic ecology in composting bacteria. It is essential to understand those features, and define

  19. Microbial fuel cells and microbial ecology: applications in ruminant health and production research.

    PubMed

    Bretschger, Orianna; Osterstock, Jason B; Pinchak, William E; Ishii, Shun'ichi; Nelson, Karen E

    2010-04-01

    Microbial fuel cell (MFC) systems employ the catalytic activity of microbes to produce electricity from the oxidation of organic, and in some cases inorganic, substrates. MFC systems have been primarily explored for their use in bioremediation and bioenergy applications; however, these systems also offer a unique strategy for the cultivation of synergistic microbial communities. It has been hypothesized that the mechanism(s) of microbial electron transfer that enable electricity production in MFCs may be a cooperative strategy within mixed microbial consortia that is associated with, or is an alternative to, interspecies hydrogen (H(2)) transfer. Microbial fermentation processes and methanogenesis in ruminant animals are highly dependent on the consumption and production of H(2)in the rumen. Given the crucial role that H(2) plays in ruminant digestion, it is desirable to understand the microbial relationships that control H(2) partial pressures within the rumen; MFCs may serve as unique tools for studying this complex ecological system. Further, MFC systems offer a novel approach to studying biofilms that form under different redox conditions and may be applied to achieve a greater understanding of how microbial biofilms impact animal health. Here, we present a brief summary of the efforts made towards understanding rumen microbial ecology, microbial biofilms related to animal health, and how MFCs may be further applied in ruminant research.

  20. Microbial Fuel Cells and Microbial Ecology: Applications in Ruminant Health and Production Research

    PubMed Central

    Osterstock, Jason B.; Pinchak, William E.; Ishii, Shun’ichi; Nelson, Karen E.

    2009-01-01

    Microbial fuel cell (MFC) systems employ the catalytic activity of microbes to produce electricity from the oxidation of organic, and in some cases inorganic, substrates. MFC systems have been primarily explored for their use in bioremediation and bioenergy applications; however, these systems also offer a unique strategy for the cultivation of synergistic microbial communities. It has been hypothesized that the mechanism(s) of microbial electron transfer that enable electricity production in MFCs may be a cooperative strategy within mixed microbial consortia that is associated with, or is an alternative to, interspecies hydrogen (H2) transfer. Microbial fermentation processes and methanogenesis in ruminant animals are highly dependent on the consumption and production of H2in the rumen. Given the crucial role that H2 plays in ruminant digestion, it is desirable to understand the microbial relationships that control H2 partial pressures within the rumen; MFCs may serve as unique tools for studying this complex ecological system. Further, MFC systems offer a novel approach to studying biofilms that form under different redox conditions and may be applied to achieve a greater understanding of how microbial biofilms impact animal health. Here, we present a brief summary of the efforts made towards understanding rumen microbial ecology, microbial biofilms related to animal health, and how MFCs may be further applied in ruminant research. PMID:20024685

  1. 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

  2. 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.

  3. 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

  4. An Inquiry-Based Laboratory Design for Microbial Ecology

    ERIC Educational Resources Information Center

    Tessier, Jack T.; Penniman, Clayton A.

    2006-01-01

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

  5. Microbial ecology of the cryosphere: sea ice and glacial habitats.

    PubMed

    Boetius, Antje; Anesio, Alexandre M; Deming, Jody W; Mikucki, Jill A; Rapp, Josephine Z

    2015-11-01

    The Earth's cryosphere comprises those regions that are cold enough for water to turn into ice. Recent findings show that the icy realms of polar oceans, glaciers and ice sheets are inhabited by microorganisms of all three domains of life, and that temperatures below 0 °C are an integral force in the diversification of microbial life. Cold-adapted microorganisms maintain key ecological functions in icy habitats: where sunlight penetrates the ice, photoautotrophy is the basis for complex food webs, whereas in dark subglacial habitats, chemoautotrophy reigns. This Review summarizes current knowledge of the microbial ecology of frozen waters, including the diversity of niches, the composition of microbial communities at these sites and their biogeochemical activities. PMID:26344407

  6. Microbial ecology of the cryosphere: sea ice and glacial habitats.

    PubMed

    Boetius, Antje; Anesio, Alexandre M; Deming, Jody W; Mikucki, Jill A; Rapp, Josephine Z

    2015-11-01

    The Earth's cryosphere comprises those regions that are cold enough for water to turn into ice. Recent findings show that the icy realms of polar oceans, glaciers and ice sheets are inhabited by microorganisms of all three domains of life, and that temperatures below 0 °C are an integral force in the diversification of microbial life. Cold-adapted microorganisms maintain key ecological functions in icy habitats: where sunlight penetrates the ice, photoautotrophy is the basis for complex food webs, whereas in dark subglacial habitats, chemoautotrophy reigns. This Review summarizes current knowledge of the microbial ecology of frozen waters, including the diversity of niches, the composition of microbial communities at these sites and their biogeochemical activities.

  7. Energy, ecology and the distribution of microbial life

    PubMed Central

    Macalady, Jennifer L.; Hamilton, Trinity L.; Grettenberger, Christen L.; Jones, Daniel S.; Tsao, Leah E.; Burgos, William D.

    2013-01-01

    Mechanisms that govern the coexistence of multiple biological species have been studied intensively by ecologists since the turn of the nineteenth century. Microbial ecologists in the meantime have faced many fundamental challenges, such as the lack of an ecologically coherent species definition, lack of adequate methods for evaluating population sizes and community composition in nature, and enormous taxonomic and functional diversity. The accessibility of powerful, culture-independent molecular microbiology methods offers an opportunity to close the gap between microbial science and the main stream of ecological theory, with the promise of new insights and tools needed to meet the grand challenges humans face as planetary engineers and galactic explorers. We focus specifically on resources related to energy metabolism because of their direct links to elemental cycling in the Earth's history, engineering applications and astrobiology. To what extent does the availability of energy resources structure microbial communities in nature? Our recent work on sulfur- and iron-oxidizing autotrophs suggests that apparently subtle variations in the concentration ratios of external electron donors and acceptors select for different microbial populations. We show that quantitative knowledge of microbial energy niches (population-specific patterns of energy resource use) can be used to predict variations in the abundance of specific taxa in microbial communities. Furthermore, we propose that resource ratio theory applied to micro-organisms will provide a useful framework for identifying how environmental communities are organized in space and time. PMID:23754819

  8. Analysis of Ancient DNA in Microbial Ecology.

    PubMed

    Gorgé, Olivier; Bennett, E Andrew; Massilani, Diyendo; Daligault, Julien; Pruvost, Melanie; Geigl, Eva-Maria; Grange, Thierry

    2016-01-01

    The development of next-generation sequencing has led to a breakthrough in the analysis of ancient genomes, and the subsequent genomic analyses of the skeletal remains of ancient humans have revolutionized the knowledge of the evolution of our species, including the discovery of a new hominin, and demonstrated admixtures with more distantly related archaic populations such as Neandertals and Denisovans. Moreover, it has also yielded novel insights into the evolution of ancient pathogens. The analysis of ancient microbial genomes allows the study of their recent evolution, presently over the last several millennia. These spectacular results have been attained despite the degradation of DNA after the death of the host, which results in very short DNA molecules that become increasingly damaged, only low quantities of which remain. The low quantity of ancient DNA molecules renders their analysis difficult and prone to contamination with modern DNA molecules, in particular via contamination from the reagents used in DNA purification and downstream analysis steps. Finally, the rare ancient molecules are diluted in environmental DNA originating from the soil microorganisms that colonize bones and teeth. Thus, ancient skeletal remains can share DNA profiles with environmental samples and identifying ancient microbial genomes among the more recent, presently poorly characterized, environmental microbiome is particularly challenging. Here, we describe the methods developed and/or in use in our laboratory to produce reliable and reproducible paleogenomic results from ancient skeletal remains that can be used to identify the presence of ancient microbiota. PMID:26791510

  9. Analysis of Ancient DNA in Microbial Ecology.

    PubMed

    Gorgé, Olivier; Bennett, E Andrew; Massilani, Diyendo; Daligault, Julien; Pruvost, Melanie; Geigl, Eva-Maria; Grange, Thierry

    2016-01-01

    The development of next-generation sequencing has led to a breakthrough in the analysis of ancient genomes, and the subsequent genomic analyses of the skeletal remains of ancient humans have revolutionized the knowledge of the evolution of our species, including the discovery of a new hominin, and demonstrated admixtures with more distantly related archaic populations such as Neandertals and Denisovans. Moreover, it has also yielded novel insights into the evolution of ancient pathogens. The analysis of ancient microbial genomes allows the study of their recent evolution, presently over the last several millennia. These spectacular results have been attained despite the degradation of DNA after the death of the host, which results in very short DNA molecules that become increasingly damaged, only low quantities of which remain. The low quantity of ancient DNA molecules renders their analysis difficult and prone to contamination with modern DNA molecules, in particular via contamination from the reagents used in DNA purification and downstream analysis steps. Finally, the rare ancient molecules are diluted in environmental DNA originating from the soil microorganisms that colonize bones and teeth. Thus, ancient skeletal remains can share DNA profiles with environmental samples and identifying ancient microbial genomes among the more recent, presently poorly characterized, environmental microbiome is particularly challenging. Here, we describe the methods developed and/or in use in our laboratory to produce reliable and reproducible paleogenomic results from ancient skeletal remains that can be used to identify the presence of ancient microbiota.

  10. Colonization resistance and microbial ecophysiology: using gnotobiotic mouse models and single-cell technology to explore the intestinal jungle.

    PubMed

    Stecher, Bärbel; Berry, David; Loy, Alexander

    2013-09-01

    The highly diverse intestinal microbiota forms a structured community engaged in constant communication with itself and its host and is characterized by extensive ecological interactions. A key benefit that the microbiota affords its host is its ability to protect against infections in a process termed colonization resistance (CR), which remains insufficiently understood. In this review, we connect basic concepts of CR with new insights from recent years and highlight key technological advances in the field of microbial ecology. We present a selection of statistical and bioinformatics tools used to generate hypotheses about synergistic and antagonistic interactions in microbial ecosystems from metagenomic datasets. We emphasize the importance of experimentally testing these hypotheses and discuss the value of gnotobiotic mouse models for investigating specific aspects related to microbiota-host-pathogen interactions in a well-defined experimental system. We further introduce new developments in the area of single-cell analysis using fluorescence in situ hybridization in combination with metabolic stable isotope labeling technologies for studying the in vivo activities of complex community members. These approaches promise to yield novel insights into the mechanisms of CR and intestinal ecophysiology in general, and give researchers the means to experimentally test hypotheses in vivo at varying levels of biological and ecological complexity.

  11. Microbial mats: an ecological niche for fungi

    PubMed Central

    Cantrell, Sharon A.; Duval-Pérez, Lisabeth

    2013-01-01

    Fungi were documented in tropical hypersaline microbial mats and their role in the degradation of complex carbohydrates (exopolymeric substance – EPS) was explored. Fungal diversity is higher during the wet season with Acremonium, Aspergillus, Cladosporium, and Penicillium among the more common genera. Diversity is also higher in the oxic layer and in young and transient mats. Enrichments with xanthan (a model EPS) show that without antibiotics (full community) degradation is faster than enrichments with antibacterial (fungal community) and antifungal (bacterial community) agents, suggesting that degradation is performed by a consortium of organisms (bacteria and fungi). The combined evidence from all experiments indicates that bacteria carried out approximately two-third of the xanthan degradation. The pattern of degradation is similar between seasons and layers but degradation is faster in enrichments from the wet season. The research suggests that fungi thrive in these hypersaline consortia and may participate in the carbon cycle through the degradation of complex carbohydrates. PMID:23577004

  12. Microbial ecology of foodborne pathogens associated with produce.

    PubMed

    Critzer, Faith J; Doyle, Michael P

    2010-04-01

    The recent recognition of fresh fruits and vegetables as major vehicles of foodborne illness has led to increased research on mechanisms by which enteric pathogens contaminate and persist on and in this non-host environment. Interactions between foodborne pathogens and plants as well among the naturally occurring microbial communities contribute to endophytic and epiphytic colonization. Scientific findings are just beginning to elucidate the mechanisms that contribute to colonization of produce. This review addresses current knowledge as well as future research needed to increase our understanding of the microbial ecology of enteric pathogens on fruits and vegetables.

  13. A Theoretical Reassessment of Microbial Maintenance and Implications for Microbial Ecology Modeling

    SciTech Connect

    Wang, Gangsheng; Post, Wilfred M

    2012-01-01

    We attempted to reconcile three microbial maintenance models (Herbert, Pirt, and Compromise) through a critical reassessment. We provided a rigorous proof that the true growth yield coefficient (YG) is the ratio of the specific maintenance rate (a in Herbert) to the maintenance coefficient (m in Pirt). Other findings from this study include: (1) the Compromise model is identical to the Herbert for computing microbial growth and substrate consumption, but it expresses the dependence of maintenance on both microbial biomass and substrate; (2) the maximum specific growth rate in the Herbert ( max,H) is higher than those in the other two models ( max,P and max,C), and the difference is the physiological maintenance factor (mq = a); and (3) the overall maintenance coefficient (mT) is more sensitive to mq than to the specific growth rate ( G) and YG. Our critical reassessment of microbial maintenance provides a new approach for quantifying some important components in soil microbial ecology models.

  14. Intestinal microbial flora after feeding phytohemagglutinin lectins (Phaseolus vulgaris) to rats.

    PubMed Central

    Banwell, J G; Howard, R; Cooper, D; Costerton, J W

    1985-01-01

    ., other bacteria, and occasional protozoa. The cecal surfaces of PHA-treated rats retained most of their incomplete overlying mucous layer, which was heavily colonized by the same type of Spirillum sp. seen in untreated animals; intestinal crypts were colonized. These descriptive morphological studies demonstrate that exposure to purified PHA in the diet caused characteristic changes in the microbial ecology of the small intestine. The changes in microbial flora contributed to the malabsorption of nutrients in the small intestines of PHA-fed animals. Images PMID:4026292

  15. Rumen microbial ecology in mule deer.

    PubMed

    Pearson, H A

    1969-06-01

    Mule deer rumen microbial populations from animals in the natural habitat in Utah and from captive deer fed various rations were studied. The microorganisms were characterized on the basis of morphology and Gram reaction. Rumen samples contained 13 identifiable types of bacteria and one genus of ciliate protozoa (Entodinium). Highest rumen bacterial populations were produced on rations containing barley. No differences in proportions of ruminal bacteria in the various morphological groups could be detected when animals were fed either natural browse plants or alfalfa hay. The total numbers of bacteria were similar for animals feeding on controlled diets of browse or hay and those in the natural habitat. Numbers of some bacterial types were directly related to ciliate protozoal numbers, whereas others were inversely related. Highest rumen ciliate protozoal populations were observed on rations containing barley. No differences in protozoal populations were noted between diets containing only browse or hay. Seasonal variations were noted in ciliate protozoal numbers from deer feeding in the natural habitat. The total number of ciliate protozoa decreased in the fall and winter and remained low until spring. There were indications that salt in the deer diet favorably affected rumen ciliate protozoa. Rather than revealing direct deer management applications, this study serves to stimulate and illuminate new approaches to research in range and wildlife nutrition.

  16. Tracking microbial biodiversity through molecular and genomic ecology.

    PubMed

    López-García, Purificación; Moreira, David

    2008-01-01

    Molecular ecology and metagenomics applied to the study of microbial biodiversity are changing our comprehension of the biosphere. An impressive diversity of archaea, bacteria and, more recently, protists has been uncovered by molecular tools. Efforts to couple function to the phylogenetic diversity observed in natural environments are leading to the discovery of novel metabolisms and to a re-evaluation of the global ecological impact of known ones. Interesting questions relating to mechanisms of speciation and evolutionary trends at the smallest and largest phylogenetic scales are emerging.

  17. Microbial ecology and genomics: A crossroads of opportunity

    SciTech Connect

    Stahl, David A.; Tiedje, James M.

    2002-08-30

    Microbes have dominated life on Earth for most of its 4.5 billionyear history. They are the foundation of the biosphere, controlling the biogeochemical cycles and affecting geology, hydrology, and local and global climates. All life is completely dependent upon them. Humans cannot survive without the rich diversity of microbes, but most microbial species can survive without humans. Extraordinary advances in molecular technology have fostered an explosion of information in microbial biology. It is now known that microbial species in culture poorly represent their natural diversity—which dwarfs conventions established for the visible world. This was revealed over the last decade using newer molecular tools to explore environmental diversity and has sparked an explosive growth in microbial ecology and technologies that may profit from the bounty of natural biochemical diversity. Several colloquia and meetings have helped formulate policy recommendations to enable sustained research programs in these areas. One such colloquium organized by the American Academy of Microbiology (“The Microbial World: Foundation of the Biosphere,” 1997) made two key recommendations: (1) develop a more complete inventory of living organisms and the interagency cooperation needed to accomplish this goal, and (2) develop strategies to harvest this remarkable biological diversity for the benefit of science, technology, and society. Complete genome sequence information was identified as an essential part of strategy development, and the recommendation was made to sequence the genome of at least one species of each of the major divisions of microbial life.

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

    DOE PAGESBeta

    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

  19. 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

  20. 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.

  1. 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.

  2. Sialic acid catabolism drives intestinal inflammation and microbial dysbiosis in mice

    PubMed Central

    Huang, Yen-Lin; Chassard, Christophe; Hausmann, Martin; von Itzstein, Mark; Hennet, Thierry

    2015-01-01

    Rapid shifts in microbial composition frequently occur during intestinal inflammation, but the mechanisms underlying such changes remain elusive. Here we demonstrate that an increased caecal sialidase activity is critical in conferring a growth advantage for some bacteria including Escherichia coli (E. coli) during intestinal inflammation in mice. This sialidase activity originates among others from Bacteroides vulgatus, whose intestinal levels expand after dextran sulphate sodium administration. Increased sialidase activity mediates the release of sialic acid from intestinal tissue, which promotes the outgrowth of E. coli during inflammation. The outburst of E. coli likely exacerbates the inflammatory response by stimulating the production of pro-inflammatory cytokines by intestinal dendritic cells. Oral administration of a sialidase inhibitor and low levels of intestinal α2,3-linked sialic acid decrease E. coli outgrowth and the severity of colitis in mice. Regulation of sialic acid catabolism opens new perspectives for the treatment of intestinal inflammation as manifested by E. coli dysbiosis. PMID:26303108

  3. Microbial ecology laboratory procedures manual NASA/MSFC

    NASA Technical Reports Server (NTRS)

    Huff, Timothy L.

    1990-01-01

    An essential part of the efficient operation of any microbiology laboratory involved in sample analysis is a standard procedures manual. The purpose of this manual is to provide concise and well defined instructions on routine technical procedures involving sample analysis and methods for monitoring and maintaining quality control within the laboratory. Of equal importance is the safe operation of the laboratory. This manual outlines detailed procedures to be followed in the microbial ecology laboratory to assure safety, analytical control, and validity of results.

  4. Application of multivariate statistical techniques in microbial ecology.

    PubMed

    Paliy, O; Shankar, V

    2016-03-01

    Recent advances in high-throughput methods of molecular analyses have led to an explosion of studies generating large-scale ecological data sets. In particular, noticeable effect has been attained in the field of microbial ecology, where new experimental approaches provided in-depth assessments of the composition, functions and dynamic changes of complex microbial communities. Because even a single high-throughput experiment produces large amount of data, powerful statistical techniques of multivariate analysis are well suited to analyse and interpret these data sets. Many different multivariate techniques are available, and often it is not clear which method should be applied to a particular data set. In this review, we describe and compare the most widely used multivariate statistical techniques including exploratory, interpretive and discriminatory procedures. We consider several important limitations and assumptions of these methods, and we present examples of how these approaches have been utilized in recent studies to provide insight into the ecology of the microbial world. Finally, we offer suggestions for the selection of appropriate methods based on the research question and data set structure.

  5. Application of multivariate statistical techniques in microbial ecology.

    PubMed

    Paliy, O; Shankar, V

    2016-03-01

    Recent advances in high-throughput methods of molecular analyses have led to an explosion of studies generating large-scale ecological data sets. In particular, noticeable effect has been attained in the field of microbial ecology, where new experimental approaches provided in-depth assessments of the composition, functions and dynamic changes of complex microbial communities. Because even a single high-throughput experiment produces large amount of data, powerful statistical techniques of multivariate analysis are well suited to analyse and interpret these data sets. Many different multivariate techniques are available, and often it is not clear which method should be applied to a particular data set. In this review, we describe and compare the most widely used multivariate statistical techniques including exploratory, interpretive and discriminatory procedures. We consider several important limitations and assumptions of these methods, and we present examples of how these approaches have been utilized in recent studies to provide insight into the ecology of the microbial world. Finally, we offer suggestions for the selection of appropriate methods based on the research question and data set structure. PMID:26786791

  6. The biofilm ecology of microbial biofouling, biocide resistance and corrosion

    SciTech Connect

    White, D.C. |; Kirkegaard, R.D.; Palmer, R.J. Jr.; Flemming, C.A.; Chen, G.; Leung, K.T.; Phiefer, C.B.; Arrage, A.A. |

    1997-06-01

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

  7. Our microbial selves: what ecology can teach us

    PubMed Central

    Gonzalez, Antonio; Clemente, Jose C; Shade, Ashley; Metcalf, Jessica L; Song, Sejin; Prithiviraj, Bharath; Palmer, Brent E; Knight, Rob

    2011-01-01

    Advances in DNA sequencing have allowed us to characterize microbial communities—including those associated with the human body—at a broader range of spatial and temporal scales than ever before. We can now answer fundamental questions that were previously inaccessible and use well-tested ecological theories to gain insight into changes in the microbiome that are associated with normal development and human disease. Perhaps unsurprisingly, the ecosystems associated with our body follow trends identified in communities at other sites and scales, and thus studies of the microbiome benefit from ecological insight. Here, we assess human microbiome research in the context of ecological principles and models, focusing on diversity, biological drivers of community structure, spatial patterning and temporal dynamics, and suggest key directions for future research that will bring us closer to the goal of building predictive models for personalized medicine. PMID:21720391

  8. 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.

  9. 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

  10. Estimating and mapping ecological processes influencing microbial community assembly

    DOE PAGESBeta

    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

  11. Microbial ecology of terrestrial Antarctica: Are microbial systems at risk from human activities?

    SciTech Connect

    White, G.J.

    1996-08-01

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

  12. Aquatic fungi: targeting the forgotten in microbial ecology.

    PubMed

    Grossart, Hans-Peter; Rojas-Jimenez, Keilor

    2016-06-01

    Fungi constitute important and conspicuous components of aquatic microbial communities, but their diversity and functional roles remain poorly characterized. New methods and conceptual frameworks are required to accurately describe their ecological roles, involvement in global cycling processes, and utility for human activities, considering both cultivation-independent techniques as well as experiments in laboratory and in natural ecosystems. Here we highlight recent developments and extant knowledge gaps in aquatic mycology, and provide a conceptual model to expose the importance of fungi in aquatic food webs and related biogeochemical processes.

  13. 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.

  14. Mess management in microbial ecology: Rhetorical processes of disciplinary integration

    NASA Astrophysics Data System (ADS)

    McCracken, Christopher W.

    As interdisciplinary work becomes more common in the sciences, research into the rhetorical processes mediating disciplinary integration becomes more vital. This dissertation, which takes as its subject the integration of microbiology and ecology, combines a postplural approach to rhetoric of science research with Victor Turner's "social drama" analysis and a third-generation activity theory methodological framework to identify conceptual and practical conflicts in interdisciplinary work and describe how, through visual and verbal communication, scientists negotiate these conflicts. First, to understand the conflicting disciplinary principles that might impede integration, the author conducts a Turnerian analysis of a disciplinary conflict that took place in the 1960s and 70s, during which American ecologists and biologists debated whether they should participate in the International Biological Program (IBP). Participation in the IBP ultimately contributed to the emergence of ecology as a discipline distinct from biology, and Turnerian social drama analysis of the debate surrounding participation lays bare the conflicting principles separating biology and ecology. Second, to answer the question of how these conflicting principles are negotiated in practice, the author reports on a yearlong qualitative study of scientists working in a microbial ecology laboratory. Focusing specifically on two case studies from this fieldwork that illustrate the key concept of textually mediated disciplinary integration, the author's analysis demonstrates how scientific objects emerge in differently situated practices, and how these objects manage to cohere despite their multiplicity through textually mediated rhetorical processes of calibration and alignment.

  15. Microbial activities and intestinal homeostasis: A delicate balance between health and disease

    PubMed Central

    Ohland, Christina L.; Jobin, Christian

    2015-01-01

    The concept that the intestinal microbiota modulates numerous physiological processes including immune development and function, nutrition and metabolism as well as pathogen exclusion is relatively well established in the scientific community. The molecular mechanisms driving these various effects and the events leading to the establishment of a “healthy” microbiome are slowly emerging. The objective of this review is to bring into focus important aspects of microbial/host interactions in the intestine and to discuss key molecular mechanisms controlling health and disease states. We will discuss recent evidence on how microbes interact with the host and one another and their impact on intestinal homeostasis. PMID:25729763

  16. Amino acid metabolism in intestinal bacteria: links between gut ecology and host health.

    PubMed

    Dai, Zhao-Lai; Wu, Guoyao; Zhu, Wei-Yun

    2011-01-01

    Bacteria in the gastrointestinal (GI) tract play an important role in the metabolism of dietary substances in the gut and extraintestinal tissues. Amino acids (AA) should be taken into consideration in the development of new strategies to enhance efficiency of nutrient utilization because they are not only major components in the diet and building blocks for protein but also regulate energy and protein homeostasis in organisms. The diversity of the AA-fermenting bacteria and their metabolic redundancy make them easier to survive and interact with their neighboring species or eukaryotic host during transition along GI tract. The outcomes of the interactions have important impacts on gut health and whole-body homeostasis. The AA-derived molecules produced by intestinal bacteria affect host health by regulating either host immunity and cell function or microbial composition and metabolism. Emerging evidence shows that dietary factors, such as protein, non-digestible carbohydrates, probiotics, synbiotics and phytochemicals, modulate AA utilization by gut microorganisms. Interdisciplinary research involving nutritionists and microbiologists is expected to rapidly expand knowledge about crucial roles for AA in gut ecology and host health. PMID:21196263

  17. Quaternary ammonium disinfectants: microbial adaptation, degradation and ecology.

    PubMed

    Tezel, Ulas; Pavlostathis, Spyros G

    2015-06-01

    Disinfectants play an important role in maintaining acceptable health standards by significantly reducing microbial loads as well as reducing, if not eliminating, pathogens. This review focuses on quaternary ammonium compounds (QACs), a widely used class of organic disinfectants. Specifically, it reviews the occurrence, microbial adaptation, and degradation of QACs, focusing on recent reports on the ecology of QAC-degraders, the pathways and mechanisms of microbial adaptation which lead to resistance to QACs, as well as to antibiotics. With the help of culture-dependent and nonculture-dependent tools, as well as advanced analytical techniques, a better understanding of the fate and effect of QACs and their biotransformation products is emerging. Understanding the underlying mechanisms and conditions that result in QAC resistance and biodegradation will be instrumental in the prudent use of existing QAC formulations and foster the development of safer disinfectants. Development and implementation of (bio)technologies for the elimination of QACs from treated wastewater effluents will lessen adverse impacts to both humans and the environment.

  18. The role of hyperparasitism in microbial pathogen ecology and evolution

    PubMed Central

    Parratt, Steven R; Laine, Anna-Liisa

    2016-01-01

    Many micro-organisms employ a parasitic lifestyle and, through their antagonistic interactions with host populations, have major impacts on human, agricultural and natural ecosystems. Most pathogens are likely to host parasites of their own, that is, hyperparasites, but how nested chains of parasites impact on disease dynamics is grossly neglected in the ecological and evolutionary literature. In this minireview we argue that the diversity and dynamics of micro-hyperparasites are an important component of natural host–pathogen systems. We use the current literature from a handful of key systems to show that observed patterns of pathogen virulence and disease dynamics may well be influenced by hyperparasites. Exploring these factors will shed light on many aspects of microbial ecology and disease biology, including resistance–virulence evolution, apparent competition, epidemiology and ecosystem stability. Considering the importance of hyperparasites in natural populations will have applied consequences for the field of biological control and therapeutic science, where hyperparastism is employed as a control mechanism but not necessarily ecologically understood. PMID:26784356

  19. Ecological parameters influencing microbial diversity and stability of traditional sourdough.

    PubMed

    Minervini, Fabio; De Angelis, Maria; Di Cagno, Raffaella; Gobbetti, Marco

    2014-02-01

    The quality of some leavened, sourdough baked goods is not always consistent, unless a well propagated sourdough starter culture is used for the dough fermentation. Among the different types of sourdough used, the traditional sourdough has attracted the interest of researchers, mainly because of its large microbial diversity, especially with respect to lactic acid bacteria. Variation in this diversity and the factors that cause it will impact on quality and is the subject of this review. Sourdough microbial diversity is mainly caused by the following factors: (i) sourdough is obtained through spontaneous, multi-step fermentation; (ii) it is propagated using flour, whose nutrient content may vary according to the batch and to the crop, and which is naturally contaminated by microorganisms; and (iii) it is propagated under peculiar technological parameters, which vary depending on the historical and cultural background and type of baked good. In the population dynamics leading from flour to mature sourdough, lactic acid bacteria (several species of Lactobacillus sp., Leuconostoc sp., and Weissella sp.) and yeasts (mainly Saccharomyces cerevisiae and Candida sp.) outcompete other microbial groups contaminating flour, and interact with each other at different levels. Ecological parameters qualitatively and quantitatively affecting the dominant sourdough microbiota may be classified into specific technological parameters (e.g., percentage of sourdough used as inoculum, time and temperature of fermentation) and parameters that are not fully controlled by those who manage the propagation of sourdough (e.g., chemical, enzyme and microbial composition of flour). Although some sourdoughs have been reported to harbour a persistent dominant microbiota, the stability of sourdough ecosystem during time is debated. Indeed, several factors may interfere with the persistence of species and strains associations that are typical of a given sourdough: metabolic adaptability to the

  20. TLR sorting by Rab11 endosomes maintains intestinal epithelial-microbial homeostasis

    PubMed Central

    Yu, Shiyan; Nie, Yingchao; Knowles, Byron; Sakamori, Ryotaro; Stypulkowski, Ewa; Patel, Chirag; Das, Soumyashree; Douard, Veronique; Ferraris, Ronaldo P; Bonder, Edward M; Goldenring, James R; Ip, Yicktung Tony; Gao, Nan

    2014-01-01

    Compartmentalization of Toll-like receptors (TLRs) in intestinal epithelial cells (IECs) regulates distinct immune responses to microbes; however, the specific cellular machinery that controls this mechanism has not been fully identified. Here we provide genetic evidences that the recycling endosomal compartment in enterocytes maintains a homeostatic TLR9 intracellular distribution, supporting mucosal tolerance to normal microbiota. Genetic ablation of a recycling endosome resident small GTPase, Rab11a, a gene adjacent to a Crohn's disease risk locus, in mouse IECs and in Drosophila midgut caused epithelial cell-intrinsic cytokine production, inflammatory bowel phenotype, and early mortality. Unlike wild-type controls, germ-free Rab11a-deficient mouse intestines failed to tolerate the intraluminal stimulation of microbial agonists. Thus, Rab11a endosome controls intestinal host-microbial homeostasis at least partially via sorting TLRs. PMID:25063677

  1. Recent applications of flow cytometry in aquatic microbial ecology.

    PubMed

    Troussellier, M; Courties, C; Vaquer, A

    1993-01-01

    Microorganisms (unicellular algae, bacteria) constitute fundamental compartments of aquatic ecosystems because of their high concentrations and activities. The evaluation and understanding of their behavior and role raise different problems for which traditional methodologies are often inadequate, whether they refer to global or classical microscopic analyses. Flow cytometry (FCM) has been recently used to study microorganisms in aquatic environments. Although this technology is still applied on a limited scale in our field, a large number of works has been done showing that FCM seems to be a promising tool for aquatic microbial ecology. This paper summarizes, from the literature produced during the last decade and with original data obtained in our laboratory, the main questions related to the cell identification, the evaluation of cell viability, biomasses and productions and the measurements of bacterial and phytoplanktonic activities. The representatives of sampling and observation scales is also discussed within the framework of the FCM measurements. PMID:8220221

  2. Microbial Ecology Dynamics during Rye and Wheat Sourdough Preparation

    PubMed Central

    Ercolini, Danilo; Pontonio, Erica; De Filippis, Francesca; Minervini, Fabio; La Storia, Antonietta; Gobbetti, Marco

    2013-01-01

    The bacterial ecology during rye and wheat sourdough preparation was described by 16S rRNA gene pyrosequencing. Viable plate counts of presumptive lactic acid bacteria, the ratio between lactic acid bacteria and yeasts, the rate of acidification, a permutation analysis based on biochemical and microbial features, the number of operational taxonomic units (OTUs), and diversity indices all together demonstrated the maturity of the sourdoughs during 5 to 7 days of propagation. Flours were mainly contaminated by metabolically active genera (Acinetobacter, Pantoea, Pseudomonas, Comamonas, Enterobacter, Erwinia, and Sphingomonas) belonging to the phylum Proteobacteria or Bacteroidetes (genus Chryseobacterium). Their relative abundances varied with the flour. Soon after 1 day of propagation, this population was almost completely inhibited except for the Enterobacteriaceae. Although members of the phylum Firmicutes were present at very low or intermediate relative abundances in the flours, they became dominant soon after 1 day of propagation. Lactic acid bacteria were almost exclusively representative of the Firmicutes by this time. Weissella spp. were already dominant in rye flour and stably persisted, though they were later flanked by the Lactobacillus sakei group. There was a succession of species during 10 days of propagation of wheat sourdoughs. The fluctuation between dominating and subdominating populations of L. sakei group, Leuconostoc spp., Weissella spp., and Lactococcus lactis was demonstrated. Other subdominant species such as Lactobacillus plantarum were detectable throughout propagation. As shown by PCR-denaturing gradient gel electrophoresis (PCR-DGGE) analysis, Saccharomyces cerevisiae dominated throughout the sourdough propagation. Notwithstanding variations due to environmental and technology determinants, the results of this study represent a clear example of how the microbial ecology evolves during sourdough preparation. PMID:24096427

  3. Perspectives of the microbial carbon pump with special references to microbial respiration and ecological efficiency

    NASA Astrophysics Data System (ADS)

    Dang, H.; Jiao, N.

    2014-01-01

    Although respiration consumes fixed carbon and produce CO2, it provides energy for essential biological processes of an ecosystem, including the microbial carbon pump (MCP). In MCP-driving biotransformation of labile DOC to recalcitrant DOC (RDOC), microbial respiration provides the metabolic energy for environmental organic substrate sensing, cellular enzyme syntheses and catalytic processes such as uptake, secretion, modification, fixation and storage of carbon compounds. The MCP efficiency of a heterotrophic microorganism is thus related to its energy production efficiency and hence to its respiration efficiency. Anaerobically respiring microbes usually have lower energy production efficiency and lower energy-dependent carbon transformation efficiency, and consequently lower MCP efficiency at per cell level. This effect is masked by the phenomena that anoxic environments often store more organic matter. Here we point out that organic carbon preservation and RDOC production is different in mechanisms, and anaerobically respiring ecosystems could also have lower MCP ecological efficiency. Typical cases can be found in large river estuarine ecosystems. Due to strong terrigenous input of nutrients and organic matter, estuarine ecosystems usually experience intense heterotrophic respiration processes that rapidly consume dissolved oxygen, potentially producing hypoxic and anoxic zones in the water column. The lowered availability of dissolved oxygen and the excessive supply of nutrients such as nitrate from river input prompt enhanced anaerobic respiration processes. Thus, some nutrients may be consumed by anaerobically respiring heterotrophic microorganisms, instead of being utilized by phytoplankton for carbon fixation and primary production. In this situation, the ecological functioning of the estuarine ecosystem is altered and the ecological efficiency is lowered, as less carbon is fixed and less energy is produced. Ultimately this would have negatively impacts

  4. Ecology of the rare microbial biosphere of the Arctic Ocean.

    PubMed

    Galand, Pierre E; Casamayor, Emilio O; Kirchman, David L; Lovejoy, Connie

    2009-12-29

    Understanding the role of microbes in the oceans has focused on taxa that occur in high abundance; yet most of the marine microbial diversity is largely determined by a long tail of low-abundance taxa. This rare biosphere may have a cosmopolitan distribution because of high dispersal and low loss rates, and possibly represents a source of phylotypes that become abundant when environmental conditions change. However, the true ecological role of rare marine microorganisms is still not known. Here, we use pyrosequencing to describe the structure and composition of the rare biosphere and to test whether it represents cosmopolitan taxa or whether, similar to abundant phylotypes, the rare community has a biogeography. Our examination of 740,353 16S rRNA gene sequences from 32 bacterial and archaeal communities from various locations of the Arctic Ocean showed that rare phylotypes did not have a cosmopolitan distribution but, rather, followed patterns similar to those of the most abundant members of the community and of the entire community. The abundance distributions of rare and abundant phylotypes were different, following a log-series and log-normal model, respectively, and the taxonomic composition of the rare biosphere was similar to the composition of the abundant phylotypes. We conclude that the rare biosphere has a biogeography and that its tremendous diversity is most likely subjected to ecological processes such as selection, speciation, and extinction.

  5. Ecology of the rare microbial biosphere of the Arctic Ocean

    PubMed Central

    Galand, Pierre E.; Casamayor, Emilio O.; Kirchman, David L.; Lovejoy, Connie

    2009-01-01

    Understanding the role of microbes in the oceans has focused on taxa that occur in high abundance; yet most of the marine microbial diversity is largely determined by a long tail of low-abundance taxa. This rare biosphere may have a cosmopolitan distribution because of high dispersal and low loss rates, and possibly represents a source of phylotypes that become abundant when environmental conditions change. However, the true ecological role of rare marine microorganisms is still not known. Here, we use pyrosequencing to describe the structure and composition of the rare biosphere and to test whether it represents cosmopolitan taxa or whether, similar to abundant phylotypes, the rare community has a biogeography. Our examination of 740,353 16S rRNA gene sequences from 32 bacterial and archaeal communities from various locations of the Arctic Ocean showed that rare phylotypes did not have a cosmopolitan distribution but, rather, followed patterns similar to those of the most abundant members of the community and of the entire community. The abundance distributions of rare and abundant phylotypes were different, following a log-series and log-normal model, respectively, and the taxonomic composition of the rare biosphere was similar to the composition of the abundant phylotypes. We conclude that the rare biosphere has a biogeography and that its tremendous diversity is most likely subjected to ecological processes such as selection, speciation, and extinction. PMID:20018741

  6. PCR-DGGE analysis of intestinal bacteria and effect of Bacillus spp. on intestinal microbial diversity in kuruma shrimp ( Marsupenaeus japonicus)

    NASA Astrophysics Data System (ADS)

    Liu, Huaide; Liu, Mei; Wang, Baojie; Jiang, Keyong; Jiang, Shan); Sun, Shujuan; Wang, Lei

    2010-07-01

    In this study, the intestinal microbiota of kuruma shrimp ( Marsupenaeus japonicus) was examined by molecular analysis of the 16S rDNA to identify the dominant intestinal bacteria and to investigate the effects of Bacillus spp. on intestinal microbial diversity. Samples of the intestines of kuruma shrimp fed normal feed and Bacillus spp. amended feed. PCR and denaturing gradient gel electrophoresis (DGGE) analyses were then performed on DNA extracted directly from the guts. Population fingerprints of the predominant organisms were generated by DGGE analysis of the universal V3 16S rDNA amplicons, and distinct bands in the gels were sequenced. The results suggested that the gut of kuruma shrimp was dominated by Vibrio sp. and uncultured gamma proteobacterium. Overall, the results of this study suggest that PCR-DGGE is a possible method of studying the intestinal microbial diversity of shrimp.

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

    PubMed

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

    2008-04-01

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

  8. Deregulation of intestinal anti-microbial defense by the dietary additive, maltodextrin

    PubMed Central

    Nickerson, Kourtney P; Chanin, Rachael; McDonald, Christine

    2015-01-01

    Inflammatory bowel disease (IBD) is a complex, multi-factorial disease thought to arise from an inappropriate immune response to commensal bacteria in a genetically susceptible person that results in chronic, cyclical, intestinal inflammation. Dietary and environmental factors are implicated in the initiation and perpetuation of IBD; however, a singular causative agent has not been identified. As of now, the role of environmental priming or triggers in IBD onset and pathogenesis are not well understood, but these factors appear to synergize with other disease susceptibility factors. In previous work, we determined that the polysaccharide dietary additive, maltodextrin (MDX), impairs cellular anti-bacterial responses and suppresses intestinal anti-microbial defense mechanisms. In this addendum, we review potential mechanisms for dietary deregulation of intestinal homeostasis, postulate how dietary and genetic risk factors may combine to result in disease pathogenesis, and discuss these ideas in the context of recent findings related to dietary interventions for IBD. PMID:25738413

  9. Deregulation of intestinal anti-microbial defense by the dietary additive, maltodextrin.

    PubMed

    Nickerson, Kourtney P; Chanin, Rachael; McDonald, Christine

    2015-01-01

    Inflammatory bowel disease (IBD) is a complex, multi-factorial disease thought to arise from an inappropriate immune response to commensal bacteria in a genetically susceptible person that results in chronic, cyclical, intestinal inflammation. Dietary and environmental factors are implicated in the initiation and perpetuation of IBD; however, a singular causative agent has not been identified. As of now, the role of environmental priming or triggers in IBD onset and pathogenesis are not well understood, but these factors appear to synergize with other disease susceptibility factors. In previous work, we determined that the polysaccharide dietary additive, maltodextrin (MDX), impairs cellular anti-bacterial responses and suppresses intestinal anti-microbial defense mechanisms. In this addendum, we review potential mechanisms for dietary deregulation of intestinal homeostasis, postulate how dietary and genetic risk factors may combine to result in disease pathogenesis, and discuss these ideas in the context of recent findings related to dietary interventions for IBD.

  10. Oral Microbial Ecology and the Role of Salivary Immunoglobulin A

    PubMed Central

    Marcotte, Harold; Lavoie, Marc C.

    1998-01-01

    In the oral cavity, indigenous bacteria are often associated with two major oral diseases, caries and periodontal diseases. These diseases seem to appear following an inbalance in the oral resident microbiota, leading to the emergence of potentially pathogenic bacteria. To define the process involved in caries and periodontal diseases, it is necessary to understand the ecology of the oral cavity and to identify the factors responsible for the transition of the oral microbiota from a commensal to a pathogenic relationship with the host. The regulatory forces influencing the oral ecosystem can be divided into three major categories: host related, microbe related, and external factors. Among host factors, secretory immunoglobulin A (SIgA) constitutes the main specific immune defense mechanism in saliva and may play an important role in the homeostasis of the oral microbiota. Naturally occurring SIgA antibodies that are reactive against a variety of indigenous bacteria are detectable in saliva. These antibodies may control the oral microbiota by reducing the adherence of bacteria to the oral mucosa and teeth. It is thought that protection against bacterial etiologic agents of caries and periodontal diseases could be conferred by the induction of SIgA antibodies via the stimulation of the mucosal immune system. However, elucidation of the role of the SIgA immune system in controlling the oral indigenous microbiota is a prerequisite for the development of effective vaccines against these diseases. The role of SIgA antibodies in the acquisition and the regulation of the indigenous microbiota is still controversial. Our review discusses the importance of SIgA among the multiple factors that control the oral microbiota. It describes the oral ecosystems, the principal factors that may control the oral microbiota, a basic knowledge of the secretory immune system, the biological functions of SIgA, and, finally, experiments related to the role of SIgA in oral microbial ecology

  11. Decreased microbial diversity and Lactobacillus group in the intestine of geriatric giant pandas (Ailuropoda melanoleuca).

    PubMed

    Peng, Zhirong; Zeng, Dong; Wang, Qiang; Niu, Lili; Ni, Xueqin; Zou, Fuqin; Yang, Mingyue; Sun, Hao; Zhou, Yi; Liu, Qian; Yin, Zhongqiong; Pan, Kangcheng; Jing, Bo

    2016-05-01

    It has been established beyond doubt that giant panda genome lacks lignin-degrading related enzyme, gastrointestinal microbes may play a vital role in digestion of highly fibrous bamboo diet. However, there is not much information available about the intestinal bacteria composition in captive giant pandas with different ages. In this study, we compared the intestinal bacterial community of 12 captive giant pandas from three different age groups (subadults, adults, and geriatrics) through PCR-denaturing gradient gel electrophoresis (DGGE) and real-time PCR analysis. Results indicated that microbial diversity in the intestine of adults was significantly higher than that of the geriatrics (p < 0.05), but not significant compared to the subadults (p > 0.05). The predominant bands in DGGE patterns shared by the twelve pandas were related to Firmicutes and Proteobacteria. Additionally, in comparison to healthy individuals, antibiotic-treated animals showed partial microbial dysbiosis. Real-time PCR analyses confirmed a significantly higher abundance of the Lactobacillus in the fecal microbiota of adults (p < 0.05), while other bacterial groups and species detected did not significantly differ among the three age groups (p > 0.05). This study revealed that captive giant pandas with different ages showed different intestinal bacteria composition. PMID:27038949

  12. Decreased microbial diversity and Lactobacillus group in the intestine of geriatric giant pandas (Ailuropoda melanoleuca).

    PubMed

    Peng, Zhirong; Zeng, Dong; Wang, Qiang; Niu, Lili; Ni, Xueqin; Zou, Fuqin; Yang, Mingyue; Sun, Hao; Zhou, Yi; Liu, Qian; Yin, Zhongqiong; Pan, Kangcheng; Jing, Bo

    2016-05-01

    It has been established beyond doubt that giant panda genome lacks lignin-degrading related enzyme, gastrointestinal microbes may play a vital role in digestion of highly fibrous bamboo diet. However, there is not much information available about the intestinal bacteria composition in captive giant pandas with different ages. In this study, we compared the intestinal bacterial community of 12 captive giant pandas from three different age groups (subadults, adults, and geriatrics) through PCR-denaturing gradient gel electrophoresis (DGGE) and real-time PCR analysis. Results indicated that microbial diversity in the intestine of adults was significantly higher than that of the geriatrics (p < 0.05), but not significant compared to the subadults (p > 0.05). The predominant bands in DGGE patterns shared by the twelve pandas were related to Firmicutes and Proteobacteria. Additionally, in comparison to healthy individuals, antibiotic-treated animals showed partial microbial dysbiosis. Real-time PCR analyses confirmed a significantly higher abundance of the Lactobacillus in the fecal microbiota of adults (p < 0.05), while other bacterial groups and species detected did not significantly differ among the three age groups (p > 0.05). This study revealed that captive giant pandas with different ages showed different intestinal bacteria composition.

  13. Microbial ecology of acid strip mine lakes in southern Indiana

    SciTech Connect

    Gyure, R.A.

    1986-01-01

    In this study, the author examined the limnology and microbial ecology of two acid strip mine lakes in the Greene-Sullivan State Forest near Dugger, Indiana. Reservoir 29 is a larger lake (225 ha) with water column pH of 2.7 and sediment pH of 3.8. Lake B, a smaller (20 ha) lake to the south of Reservoir 29, also has an acidic water column (pH 3.4) but more neutral sediments (pH 6.2). Both have very high sulfate concentrations: 20-30 mM in the water column and as high as 100 mM in the hypolimnion of Lake B. Low allochthonous carbon and nutrient input characterize these lakes as oligotrophic, although algal biomass is higher than would be expected for this trophic status. In both lakes, algal populations are not diverse, with a few species of single-celled Chlorophyta and euglenoids dominating. Algal biomass is concentrated in a thin 10 cm layer at the hypolimnion/metalimnion interface, although light intensity at this depth is low and severely limits productivity. Bacterial activity based on /sup 14/C-glucose incorporation is highest in the hypolimnion of both lakes, and sulfate-reduction is a dominant process in the sediments. Rates of sulfate-reduction compare with those in other freshwater environments, but are not as high as rates measured in high sulfate systems like saltmarsh and marine sediments.

  14. Flagella, flexibility and flow: Physical processes in microbial ecology

    NASA Astrophysics Data System (ADS)

    Brumley, D. R.; Rusconi, R.; Son, K.; Stocker, R.

    2015-12-01

    How microorganisms interact with their environment and with their conspecifics depends strongly on their mechanical properties, on the hydrodynamic signatures they generate while swimming and on fluid flows in their environment. The rich fluid-structure interaction between flagella - the appendages microorganisms use for propulsion - and the surrounding flow, has broad reaching effects for both eukaryotic and prokaryotic microorganisms. Here, we discuss selected recent advances in our understanding of the physical ecology of microorganisms, which have hinged on the ability to directly interrogate the movement of individual cells and their swimming appendages, in precisely controlled fluid environments, and to image them at appropriately fast timescales. We review how a flagellar buckling instability can unexpectedly serve a fundamental function in the motility of bacteria, we elucidate the role of hydrodynamics and flexibility in the emergent properties of groups of eukaryotic flagella, and we show how fluid flows characteristic of microbial habitats can strongly bias the migration and spatial distribution of bacteria. The topics covered here are illustrative of the potential inherent in the adoption of experimental methods and conceptual frameworks from physics in understanding the lives of microorganisms.

  15. MICROBIAL ECOLOGY OF THE SUBSURFACE AT AN ABANDONED CREOSOTE WASTE SITE

    EPA Science Inventory

    The microbial ecology of pristine, slightly contaminated, and heavily contaminated subsurface materials, and four subsurface materials on the periphery of the plume at an abandoned creosote waste site was investigated. Except for the unsaturated zone of the heavily contaminated m...

  16. Novel Polyfermentor Intestinal Model (PolyFermS) for Controlled Ecological Studies: Validation and Effect of pH

    PubMed Central

    Zihler Berner, Annina; Fuentes, Susana; Dostal, Alexandra; Payne, Amanda N.; Vazquez Gutierrez, Pamela; Chassard, Christophe; Grattepanche, Franck; de Vos, Willem M.; Lacroix, Christophe

    2013-01-01

    In vitro gut fermentation modeling offers a useful platform for ecological studies of the intestinal microbiota. In this study we describe a novel Polyfermentor Intestinal Model (PolyFermS) designed to compare the effects of different treatments on the same complex gut microbiota. The model operated in conditions of the proximal colon is composed of a first reactor containing fecal microbiota immobilized in gel beads, and used to continuously inoculate a set of parallel second-stage reactors. The PolyFermS model was validated with three independent intestinal fermentations conducted for 38 days with immobilized human fecal microbiota obtained from three child donors. The microbial diversity of reactor effluents was compared to donor feces using the HITChip, a high-density phylogenetic microarray targeting small subunit rRNA sequences of over 1100 phylotypes of the human gastrointestinal tract. Furthermore, the metabolic response to a decrease of pH from 5.7 to 5.5, applied to balance the high fermentative activity in inoculum reactors, was studied. We observed a reproducible development of stable intestinal communities representing major taxonomic bacterial groups at ratios similar to these in feces of healthy donors, a high similarity of microbiota composition produced in second-stage reactors within a model, and a high time stability of microbiota composition and metabolic activity over 38 day culture. For all tested models, the pH-drop of 0.2 units in inoculum reactors enhanced butyrate production at the expense of acetate, but was accompanied by a donor-specific reorganization of the reactor community, suggesting a concerted metabolic adaptation and trigger of community-specific lactate or acetate cross-feeding pathways in response to varying pH. Our data showed that the PolyFermS model allows the stable cultivation of complex intestinal microbiota akin to the fecal donor and can be developed for the direct comparison of different experimental conditions in

  17. Host-microbial interactions and regulation of intestinal epithelial barrier function: From physiology to pathology

    PubMed Central

    Yu, Linda Chia-Hui; Wang, Jin-Town; Wei, Shu-Chen; Ni, Yen-Hsuan

    2012-01-01

    The gastrointestinal tract is the largest reservoir of commensal bacteria in the human body, providing nutrients and space for the survival of microbes while concurrently operating mucosal barriers to confine the microbial population. The epithelial cells linked by tight junctions not only physically separate the microbiota from the lamina propria, but also secrete proinflammatory cytokines and reactive oxygen species in response to pathogen invasion and metabolic stress and serve as a sentinel to the underlying immune cells. Accumulating evidence indicates that commensal bacteria are involved in various physiological functions in the gut and microbial imbalances (dysbiosis) may cause pathology. Commensal bacteria are involved in the regulation of intestinal epithelial cell turnover, promotion of epithelial restitution and reorganization of tight junctions, all of which are pivotal for fortifying barrier function. Recent studies indicate that aberrant bacterial lipopolysaccharide-mediated signaling in gut mucosa may be involved in the pathogenesis of chronic inflammation and carcinogenesis. Our perception of enteric commensals has now changed from one of opportunistic pathogens to active participants in maintaining intestinal homeostasis. This review attempts to explain the dynamic interaction between the intestinal epithelium and commensal bacteria in disease and health status. PMID:22368784

  18. [Effects of biochar on microbial ecology in agriculture soil: a review].

    PubMed

    Ding, Yan-Li; Liu, Jie; Wang, Ying-Ying

    2013-11-01

    Biochar, as a new type of soil amendment, has been obtained considerable attention in the research field of environmental sciences worldwide. The studies on the effects of biochar in improving soil physical and chemical properties started quite earlier, and already covered the field of soil microbial ecology. However, most of the studies considered the soil physical and chemical properties and the microbial ecology separately, with less consideration of their interactions. This paper summarized and analyzed the interrelationships between the changes of soil physical and chemical properties and of soil microbial community after the addition of biochar. Biochar can not only improve soil pH value, strengthen soil water-holding capacity, increase soil organic matter content, but also affect soil microbial community structure, and alter the abundance of soil bacteria and fungi. After the addition of biochar, the soil environment and soil microorganisms are interacted each other, and promote the improvement of soil microbial ecological system together. This review was to provide a novel perspective for the in-depth studies of the effects of biochar on soil microbial ecology, and to promote the researches on the beneficial effects of biochar to the environment from ecological aspect. The methods to improve the effectiveness of biochar application were discussed, and the potential applications of biochar in soil bioremediation were further analyzed.

  19. Functional Ecological Gene Networks to Reveal the Changes Among Microbial Interactions Under Elevated Carbon Dioxide Conditions

    SciTech Connect

    Deng, Ye; Zhou, Jizhong; Luo, Feng; He, Zhili; Tu, Qichao; Zhi, Xiaoyang

    2010-05-17

    Biodiversity and its responses to environmental changes is a central issue in ecology, and for society. Almost all microbial biodiversity researches focus on species richness and abundance but ignore the interactions among different microbial species/populations. However, determining the interactions and their relationships to environmental changes in microbial communities is a grand challenge, primarily due to the lack of information on the network structure among different microbial species/populations. Here, a novel random matrix theory (RMT)-based conceptual framework for identifying functional ecological gene networks (fEGNs) is developed with the high throughput functional gene array hybridization data from the grassland microbial communities in a long-term FACE (Free Air CO2 Enrichment) experiment. Both fEGNs under elevated CO2 (eCO2) and ambient CO2 (aCO2) possessed general characteristics of many complex systems such as scale-free, small-world, modular and hierarchical. However, the topological structure of the fEGNs is distinctly different between eCO2 and aCO2, suggesting that eCO2 dramatically altered the interactions among different microbial functional groups/populations. In addition, the changes in network structure were significantly correlated with soil carbon and nitrogen dynamics, and plant productivity, indicating the potential importance of network interactions in ecosystem functioning. Elucidating network interactions in microbial communities and their responses to environmental changes are fundamentally important for research in microbial ecology, systems microbiology, and global change.

  20. Effects of alfalfa meal on the intestinal microbial diversity and immunity of growing ducks.

    PubMed

    Jiang, J F; Song, X M; Wu, J L; Jiang, Y Q

    2014-12-01

    This study was conducted to investigate the effects of alfalfa meal diets on the intestinal microbial diversity and immunity of growing egg-type ducks. A total of 128 healthy 7-week-old female egg-type Shaoxing ducks were selected and randomly assigned into four dietary treatments: 0%, 3%, 6% and 9% alfalfa meal for 8 weeks. Each treatment consisted of four replicates of eight ducks each. Polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) was used to characterize the microbiota. The results showed that the DGGE fingerprints of the V6-V8 fragments of the 16S rRNA from the caeca and faeces of ducks fed 3%, 6% and 9% alfalfa meal had significantly higher microbiota species richness than those fed 0% alfalfa meal (p < 0.05). The Shannon-Weiner index of the microbiota from the caeca and faeces of ducks fed 3%, 6% and 9% alfalfa meal was significantly higher than those fed 0% alfalfa meal (p < 0.05). Molecular analysis of the caecal and faecal DNA extracts showed that the alfalfa meal diet promotes the intestinal microbial diversity, as indicated by their higher species richness and Shannon-Weiner index. However, the groups did not significantly differ in terms of average daily gain, feed intake and gain-to-feed ratio (p > 0.05), and the 3-9% alfalfa meal did not affect the growth performance of the growing egg-type ducks. The proliferation of T and B lymphocytes was significantly greater (p < 0.05) in the groups supplemented with 3%, 6% and 9% of alfalfa meal than the unsupplemented control group, and alfalfa meal promoted the lymphocytes proliferation of the growing egg-type ducks. Dietary alfalfa meal supplementation increases intestinal microbial community diversity and improves of the immune response growing egg-type ducks.

  1. Effects of alfalfa meal on the intestinal microbial diversity and immunity of growing ducks.

    PubMed

    Jiang, J F; Song, X M; Wu, J L; Jiang, Y Q

    2014-12-01

    This study was conducted to investigate the effects of alfalfa meal diets on the intestinal microbial diversity and immunity of growing egg-type ducks. A total of 128 healthy 7-week-old female egg-type Shaoxing ducks were selected and randomly assigned into four dietary treatments: 0%, 3%, 6% and 9% alfalfa meal for 8 weeks. Each treatment consisted of four replicates of eight ducks each. Polymerase chain reaction denaturing gradient gel electrophoresis (PCR-DGGE) was used to characterize the microbiota. The results showed that the DGGE fingerprints of the V6-V8 fragments of the 16S rRNA from the caeca and faeces of ducks fed 3%, 6% and 9% alfalfa meal had significantly higher microbiota species richness than those fed 0% alfalfa meal (p < 0.05). The Shannon-Weiner index of the microbiota from the caeca and faeces of ducks fed 3%, 6% and 9% alfalfa meal was significantly higher than those fed 0% alfalfa meal (p < 0.05). Molecular analysis of the caecal and faecal DNA extracts showed that the alfalfa meal diet promotes the intestinal microbial diversity, as indicated by their higher species richness and Shannon-Weiner index. However, the groups did not significantly differ in terms of average daily gain, feed intake and gain-to-feed ratio (p > 0.05), and the 3-9% alfalfa meal did not affect the growth performance of the growing egg-type ducks. The proliferation of T and B lymphocytes was significantly greater (p < 0.05) in the groups supplemented with 3%, 6% and 9% of alfalfa meal than the unsupplemented control group, and alfalfa meal promoted the lymphocytes proliferation of the growing egg-type ducks. Dietary alfalfa meal supplementation increases intestinal microbial community diversity and improves of the immune response growing egg-type ducks. PMID:24460922

  2. 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

  3. Intestine.

    PubMed

    Smith, J M; Skeans, M A; Horslen, S P; Edwards, E B; Harper, A M; Snyder, J J; Israni, A K; Kasiske, B L

    2016-01-01

    Intestine and intestine-liver transplant plays an important role in the treatment of intestinal failure, despite decreased morbidity associated with parenteral nutrition. In 2014, 210 new patients were added to the intestine transplant waiting list. Among prevalent patients on the list at the end of 2014, 65% were waiting for an intestine transplant and 35% were waiting for an intestine-liver transplant. The pretransplant mortality rate decreased dramatically over time for all age groups. Pretransplant mortality was highest for adult candidates, at 22.1 per 100 waitlist years compared with less than 3 per 100 waitlist years for pediatric candidates, and notably higher for candidates for intestine-liver transplant than for candidates for intestine transplant without a liver. Numbers of intestine transplants without a liver increased from a low of 51 in 2013 to 67 in 2014. Intestine-liver transplants increased from a low of 44 in 2012 to 72 in 2014. Short-gut syndrome (congenital and other) was the main cause of disease leading to both intestine and intestine-liver transplant. Graft survival improved over the past decade. Patient survival was lowest for adult intestine-liver recipients and highest for pediatric intestine recipients.

  4. Microbial ecology of Thailand tsunami and non-tsunami affected terrestrials.

    PubMed

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

    2014-01-01

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

  5. Microbial Ecology of Thailand Tsunami and Non-Tsunami Affected Terrestrials

    PubMed Central

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

    2014-01-01

    The effects of tsunamis on microbial ecologies have been ill-defined, especially in Phang Nga province, Thailand. This ecosystem was catastrophically impacted by the 2004 Indian Ocean tsunami as well as the 600 year-old tsunami in Phra Thong island, Phang Nga province. No study has been conducted to elucidate their effects on microbial ecology. This study represents the first to elucidate their effects on microbial ecology. We utilized metagenomics with 16S and 18S rDNA-barcoded pyrosequencing to obtain prokaryotic and eukaryotic profiles for this terrestrial site, tsunami affected (S1), as well as a parallel unaffected terrestrial site, non-tsunami affected (S2). S1 demonstrated unique microbial community patterns than S2. The dendrogram constructed using the prokaryotic profiles supported the unique S1 microbial communities. S1 contained more proportions of archaea and bacteria domains, specifically species belonging to Bacteroidetes became more frequent, in replacing of the other typical floras like Proteobacteria, Acidobacteria and Basidiomycota. Pathogenic microbes, including Acinetobacter haemolyticus, Flavobacterium spp. and Photobacterium spp., were also found frequently in S1. Furthermore, different metabolic potentials highlighted this microbial community change could impact the functional ecology of the site. Moreover, the habitat prediction based on percent of species indicators for marine, brackish, freshwater and terrestrial niches pointed the S1 to largely comprise marine habitat indicating-species. PMID:24710002

  6. Studies of the microbial metabolism of flavonoids extracted from the leaves of Diospyros kaki by intestinal bacteria.

    PubMed

    Zhang, Sheng-hai; Wang, Ying-zi; Meng, Fan-yun; Li, You-lin; Li, Cai-xia; Duan, Fei-peng; Wang, Qing; Zhang, Xiu-ting; Zhang, Chun-ni

    2015-01-01

    Flavonoid glycosides are metabolized by intestinal bacteria, giving rise to a wide range of phenolic acids that may exert systemic effects in the body. The microbial metabolism of flavonoids extracted from the leaves of Diospyros kaki (FLDK) by intestinal bacteria was investigated in vitro. High-performance liquid chromatography/linear trap quadrupole orbitrap mass spectrometry was performed to analyze the metabolites of flavonoids in vivo using Xcalibur2.1 software. The results showed that the levels of flavonoid glycosides and flavonoid aglycones decreased rapidly in the process of microbial metabolism by intestinal bacteria in vitro, and the metabolic rate may be related to the concentration of intestinal bacteria in the culture solution. In vivo metabolites of FLDK were detected in rat plasma and urine after oral administration of FLDK. Eight flavonoids were identified in the urine, and three were identified in the plasma; however, flavonoid aglycones were not found in the plasma.

  7. Methodological approaches for studying the microbial ecology of drinking water distribution systems.

    PubMed

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

    2014-11-15

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

  8. Vitamin B12 as a modulator of gut microbial ecology.

    PubMed

    Degnan, Patrick H; Taga, Michiko E; Goodman, Andrew L

    2014-11-01

    The microbial mechanisms and key metabolites that shape the composition of the human gut microbiota are largely unknown, impeding efforts to manipulate dysbiotic microbial communities toward stability and health. Vitamins, which by definition are not synthesized in sufficient quantities by the host and can mediate fundamental biological processes in microbes, represent an attractive target for reshaping microbial communities. Here, we discuss how vitamin B12 (cobalamin) impacts diverse host-microbe symbioses. Although cobalamin is synthesized by some human gut microbes, it is a precious resource in the gut and is likely not provisioned to the host in significant quantities. However, this vitamin may make an unrecognized contribution in shaping the structure and function of human gut microbial communities. PMID:25440056

  9. Microbial biofilms and wound healing: an ecological hypothesis.

    PubMed

    Krom, Bastiaan P; Oskam, Jacques

    2014-05-19

    Man has lived together with microbes for so long that we have become completely dependent on their presence. Most microbes reside in biofilms; structured communities encased in a protective matrix of biopolymers. Under healthy conditions, the microbial biofilm is in balance with itself (endo-balance) and with the host (exo-balance). Integrity of the skin is an important immunological function. Wounds go through a well-orchestrated series of healing steps. However, if for some reason healing times are extended, serious problems related to infection and homeostasis can develop. Based on recent advances in biofilm research and microbiological identification we discuss two hypotheses describing the role of microbial biofilms in chronic wound biology. The first hypothesis describes microbial biofilms as the cause of extended healing times. The second hypothesis is based on the host as cause of extended healing times and basically treats microbial biofilms as a logical consequence of failure to re-build the integrity of the skin.

  10. Growth performance and intestinal microbial populations of growing pigs fed diets containing sucrose thermal oligosaccharide caramel.

    PubMed

    Orban, J I; Patterson, J A; Adeola, O; Sutton, A L; Richards, G N

    1997-01-01

    Four experiments were conducted to determine growth performance and changes in intestinal microbial populations of growing pigs fed diets containing sucrose thermal oligosaccharide caramel (STOC). Ninety-six barrows and 96 gilts were group-fed experimental nursery diets for 32 d after weaning in both Exp. 1 and 2. For each experiment, pigs were divided into four groups of 48 pigs and were fed either control, antibiotic (Apramycin sulfate, 34 mg/kg), 1% STOC, or 2% STOC diets for 32 d after weaning. Each diet was replicated six times with eight pigs per replication. Pigs were either orally gavaged (Exp 1) with water of STOC (2 g per pig) or pigs were creep-fed (Exp 2) either a control diet or a 2% STOC diet for 5 d before weaning (33 d). At the end of Exp 1 and 2, cecal material was collected for enumeration of total aerobes, total anaerobes, coliforms, lactobacilli, and bifidobacteria. Gilts (96 per experiment) used in Exp. 3 and 4 were weaned at 26 d and fed experimental nursery diets for 32 d. They were fed either a control or 1% STOC diet and were otherwise treated as previously described. There were no significant effects of STOC or antibiotic on ADG, ADFI, feed efficiency, or cecal microbial populations in pigs in this study. Feeding diets containing either antibiotic of STOC did not improve animal performance or change intestinal bacterial populations in the present study. PMID:9027562

  11. Pharmacokinetics, intestinal absorption and microbial metabolism of single platycodin D in comparison to Platycodi radix extract

    PubMed Central

    Shan, Jinjun; Zou, Jiashuang; Xie, Tong; Kang, An; Zhou, Wei; Deng, Haishan; Mao, Yancao; Di, Liuqing; Wang, Shouchuan

    2015-01-01

    Background: Platycodi radix, the dried root of Platycodon grandiflorum A. DC, has been widely used as food and herb medicine for treating cough, cold and other respiratory ailments, and platycodin D (PD) is one of the most important compounds in Platycodi Radix. Objective: The purpose of this study was to compare the pharmacokinetic characteristics, intestinal absorption and microbial metabolism of PD in monomer with that in Platycodi radix extract (PRE). Materials and Methods: In the pharmacokinetic study, the concentrations of PD in rat plasma were determined by ultra-performance liquid chromatography-tandem mass spectrometry and the main pharmacokinetic parameters were calculated by data analysis software (DAS). Besides, in vitro Caco-2 cells and fecal lysate were performed to investigate the intestinal absorption and metabolism, respectively. Results: The results from pharmacokinetics showed that the area under the curve, the peak concentration the time to reach peak concentration and mean residence time of PD in PRE were enhanced significantly compared with that in single PD. Caco-2 cells transport study indicated that the absorption of PD both in monomer and in PRE were poor owning that the permeability of PD were <1/106 cm/s. The hydrolysis degree of PD in PRE was significantly lower than that in monomer PD in fecal lysate, which might be illustrated by the other ingredients in PRE influenced the hydrolysis of PD via gut microbiota. Conclusion: These findings indicated that the difference of microbial metabolism, not apparent absorption in intestine for PD between in monomer and in PRE contributed to their pharmacokinetic difference. PMID:26600720

  12. Intestinal Microbial Metabolites Are Linked to Severity of Myocardial Infarction in Rats.

    PubMed

    Lam, Vy; Su, Jidong; Hsu, Anna; Gross, Garrett J; Salzman, Nita H; Baker, John E

    2016-01-01

    Intestinal microbiota determine severity of myocardial infarction in rats. We determined whether low molecular weight metabolites derived from intestinal microbiota and transported to the systemic circulation are linked to severity of myocardial infarction. Plasma from rats treated for seven days with the non-absorbed antibiotic vancomycin or a mixture of streptomycin, neomycin, polymyxin B and bacitracin was analyzed using mass spectrometry-based metabolite profiling platforms. Antibiotic-induced changes in the abundance of individual groups of intestinal microbiota dramatically altered the host's metabolism. Hierarchical clustering of dissimilarities separated the levels of 284 identified metabolites from treated vs. untreated rats; 193 were altered by the antibiotic treatments with a tendency towards decreased metabolite levels. Catabolism of the aromatic amino acids phenylalanine, tryptophan and tyrosine was the most affected pathway comprising 33 affected metabolites. Both antibiotic treatments decreased the severity of an induced myocardial infarction in vivo by 27% and 29%, respectively. We then determined whether microbial metabolites of the amino acids phenylalanine, tryptophan and tyrosine were linked to decreased severity of myocardial infarction. Vancomycin-treated rats were administered amino acid metabolites prior to ischemia/reperfusion studies. Oral or intravenous pretreatment of rats with these amino acid metabolites abolished the decrease in infarct size conferred by vancomycin. Inhibition of JAK-2 (AG-490, 10 μM), Src kinase (PP1, 20 μM), Akt/PI3 kinase (Wortmannin, 100 nM), p44/42 MAPK (PD98059, 10 μM), p38 MAPK (SB203580, 10 μM), or KATP channels (glibenclamide, 3 μM) abolished cardioprotection by vancomycin, indicating microbial metabolites are interacting with cell surface receptors to transduce their signals through Src kinase, cell survival pathways and KATP channels. These inhibitors have no effect on myocardial infarct size in

  13. Microbial ecology and biogeochemistry of continental Antarctic soils

    PubMed Central

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

    2014-01-01

    The Antarctica Dry Valleys are regarded as the coldest hyperarid desert system on Earth. While a wide variety of environmental stressors including very low minimum temperatures, frequent freeze-thaw cycles and low water availability impose severe limitations to life, suitable niches for abundant microbial colonization exist. Antarctic desert soils contain much higher levels of microbial diversity than previously thought. Edaphic niches, including cryptic and refuge habitats, microbial mats and permafrost soils all harbor microbial communities which drive key biogeochemical cycling processes. For example, lithobionts (hypoliths and endoliths) possess a genetic capacity for nitrogen and carbon cycling, polymer degradation, and other system processes. Nitrogen fixation rates of hypoliths, as assessed through acetylene reduction assays, suggest that these communities are a significant input source for nitrogen into these oligotrophic soils. Here we review aspects of microbial diversity in Antarctic soils with an emphasis on functionality and capacity. We assess current knowledge regarding adaptations to Antarctic soil environments and highlight the current threats to Antarctic desert soil communities. PMID:24782842

  14. 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.

  15. Microbial ecology of deep-water mid-Atlantic canyons

    USGS Publications Warehouse

    Kellogg, Christina A.

    2011-01-01

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

  16. Intestinal Microbial Diversity during Early-Life Colonization Shapes Long-Term IgE Levels

    PubMed Central

    Cahenzli, Julia; Köller, Yasmin; Wyss, Madeleine; Geuking, Markus B.; McCoy, Kathy D.

    2013-01-01

    Summary Microbial exposure following birth profoundly impacts mammalian immune system development. Microbiota alterations are associated with increased incidence of allergic and autoimmune disorders with elevated serum IgE as a hallmark. The previously reported abnormally high serum IgE levels in germ-free mice suggests that immunoregulatory signals from microbiota are required to control basal IgE levels. We report that germ-free mice and those with low-diversity microbiota develop elevated serum IgE levels in early life. B cells in neonatal germ-free mice undergo isotype switching to IgE at mucosal sites in a CD4 T-cell- and IL-4-dependent manner. A critical level of microbial diversity following birth is required in order to inhibit IgE induction. Elevated IgE levels in germ-free mice lead to increased mast-cell-surface-bound IgE and exaggerated oral-induced systemic anaphylaxis. Thus, appropriate intestinal microbial stimuli during early life are critical for inducing an immunoregulatory network that protects from induction of IgE at mucosal sites. PMID:24237701

  17. Evolutionary ecology of microbial wars: within-host competition and (incidental) virulence.

    PubMed

    Brown, Sam P; Fredrik Inglis, R; Taddei, François

    2009-02-01

    Invading an occupied niche is a formidable ecological challenge, and one of particular human importance in the context of food-borne microbial pathogens. We discuss distinct categories of invader-triggered environmental change that facilitate invasion by emptying their niche of competitors. Evidence is reviewed that gut bacteria use such strategies to manipulate their environment (via bacteriocins, temperate phage viruses or immuno-manipulation) at the expense of their competitors are reviewed. The possible virulence implications of microbial warfare among multiple co-infecting strains are diverse. Killing competitors can reduce virulence by reducing overall microbial densities, or increase virulence if for example the allelopathic mechanism involves immuno-manipulation. Finally, we place microbial anti-competitor strategies in a social evolution framework, highlighting how costly anti-competitor strategies can be understood as examples of microbial spite. We conclude by discussing other invasive species that have also developed such proactive strategies of invasion. PMID:25567845

  18. Evolutionary ecology of plant-microbe interactions: soil microbial structure alters selection on plant traits.

    PubMed

    Lau, Jennifer A; Lennon, Jay T

    2011-10-01

    • Below-ground microbial communities influence plant diversity, plant productivity, and plant community composition. Given these strong ecological effects, are interactions with below-ground microbes also important for understanding natural selection on plant traits? • Here, we manipulated below-ground microbial communities and the soil moisture environment on replicated populations of Brassica rapa to examine how microbial community structure influences selection on plant traits and mediates plant responses to abiotic environmental stress. • In soils with experimentally simplified microbial communities, plants were smaller, had reduced chlorophyll content, produced fewer flowers, and were less fecund when compared with plant populations grown in association with more complex soil microbial communities. Selection on plant growth and phenological traits also was stronger when plants were grown in simplified, less diverse soil microbial communities, and these effects typically were consistent across soil moisture treatments. • Our results suggest that microbial community structure affects patterns of natural selection on plant traits. Thus, the below-ground microbial community can influence evolutionary processes, just as recent studies have demonstrated that microbial diversity can influence plant community and ecosystem processes.

  19. Evolutionary ecology of plant-microbe interactions: soil microbial structure alters selection on plant traits.

    PubMed

    Lau, Jennifer A; Lennon, Jay T

    2011-10-01

    • Below-ground microbial communities influence plant diversity, plant productivity, and plant community composition. Given these strong ecological effects, are interactions with below-ground microbes also important for understanding natural selection on plant traits? • Here, we manipulated below-ground microbial communities and the soil moisture environment on replicated populations of Brassica rapa to examine how microbial community structure influences selection on plant traits and mediates plant responses to abiotic environmental stress. • In soils with experimentally simplified microbial communities, plants were smaller, had reduced chlorophyll content, produced fewer flowers, and were less fecund when compared with plant populations grown in association with more complex soil microbial communities. Selection on plant growth and phenological traits also was stronger when plants were grown in simplified, less diverse soil microbial communities, and these effects typically were consistent across soil moisture treatments. • Our results suggest that microbial community structure affects patterns of natural selection on plant traits. Thus, the below-ground microbial community can influence evolutionary processes, just as recent studies have demonstrated that microbial diversity can influence plant community and ecosystem processes. PMID:21658184

  20. Microbial ecology and transformations associated with munitions contaminated soils

    SciTech Connect

    Martin, J.L.; Li, Z.; Kokjohn, T.A.; Shea, P.J.; Comfort, S.D.

    1994-12-31

    Many acres of soil at the former Nebraska Ordnance Plant (NOP) are contaminated with TNT and other munitions residues. In some areas, solid phase TNT is present and controls the concentration of the soil solution. Native microbial populations in uncontaminated soils similar to those at the NOP site were severely reduced when solid phase TNT was allowed to control the soil solution TNT concentration. However, examination of NOP soil revealed an active population of Pseudomonas sp. A single species that could utilize TNT as a sole C source was isolated from the contaminated soil and tentatively identified as Pseudomonas corrugata through the BIOLOG system. Subsequent growth and characterization experiments indicate that the Pseudomonad metabolizes TNT while in the exponential phase of growth in medium containing glucose as a sole N source. Low TNT mineralization rates (measured by CO{sub 2} evolution) in soil and media using the various isolates suggest reduced availability due to sorption and incorporation of transformation intermediates into the organic matrix and microbial biomass. Pretreatment of TNT by acid-metal catalyzed reduction resulted in an initially higher rate of mineralization following addition to TNT-contaminated soil. Observations indicate more rapid microbial utilization of the 2,4,6-triaminotoluene (TAT) reduction product and its spontaneous decay product, methylphloroglucinol (2,4,6-trihydroxytoluene), than TNT. Abiotic pretreatment may be useful in enhancing microbial transformation and detoxification of TNT in highly contaminated soils.

  1. Microbial Ecology Assessment of Mixed Copper Oxide/Sulfide Dump Leach Operation

    SciTech Connect

    Bruhn, D F; Thompson, D N; Noah, K S

    1999-06-01

    Microbial consortia composed of complex mixtures of autotrophic and heterotrophic bacteria are responsible for the dissolution of metals from sulfide minerals. Thus, an efficient copper bioleaching operation depends on the microbial ecology of the system. A microbial ecology study of a mixed oxide/sulfide copper leaching operation was conducted using an "overlay" plating technique to differentiate and identify various bacterial consortium members of the genera Thiobacillus, Leptospirillum, Ferromicrobium, and Acidiphilium. Two temperatures (30C and 45C) were used to select for mesophilic and moderately thermophilic bacteria. Cell numbers varied from 0-106 cells/g dry ore, depending on the sample location and depth. After acid curing for oxide leaching, no viable bacteria were recovered, although inoculation of cells from raffinate re-established a microbial population after three months. Due to the low pH of the operation, very few non-iron-oxidizing acidophilic heterotrophs were recovered. Moderate thermophiles were isolated from the ore samples. Pregnant liquor solutions (PLS) and raffinate both contained a diversity of bacteria. In addition, an intermittently applied waste stream that contained high levels of arsenic and fluoride was tested for toxicity. Twenty vol% waste stream in PLS killed 100% of the cells in 48 hours, indicating substantial toxicity and/or growth inhibition. The data indicate that bacteria populations can recover after acid curing, and that application of the waste stream to the dump should be avoided. Monitoring the microbial ecology of the leaching operation provided significant information that improved copper recovery.

  2. An Open-Ended Investigative Microbial Ecology Laboratory for Introductory Biology

    ERIC Educational Resources Information Center

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

    2010-01-01

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

  3. Effects of biological pit additives on microbial ecology of stored pig manure

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The effects of biological pit additives on microbial ecology in stored pig manure were investigated using a dynamic manure storage system, which allowed for continual addition of swine feces and urine. After 13 weeks of manure collection and storage, four treatments were added to tanks (900 L capaci...

  4. Microbial ecology summer research program, June 20-August 26, 1983

    SciTech Connect

    Not Available

    1983-01-01

    The personnel, lecture topics, and summaries of research reports generated are presented. Research topics include: mutants of Escherichia coli affected in inducer exclusion; anaerobic chitin degradation; feeding relationships of harpacticoid copepods and microbial flora; degradation of ortho phenyl phenol by streptomycetes; biodegradation of dieldrin and aromatic compounds; the effect of neurotoxins on chemotaxis is Spirochaeta aurantia; chemotaxis and algal attachment of caulobacter; pigment formation in Lyngbya aestuari; diel movements of bacteria in a salt marsh; chemotaxis in S. Aurantia; isolation of marine toluate-oxidizing bacteria; growth inhibition of enteric bacteria by methyl-..cap alpha..-D-glucoside; studies of magnetic bacteria in brackish waters; and mechanisms of interaction between two microbial populations in activated sludge. (ACR)

  5. Microbial ecology: human gut microbes associated with obesity.

    PubMed

    Ley, Ruth E; Turnbaugh, Peter J; Klein, Samuel; Gordon, Jeffrey I

    2006-12-21

    Two groups of beneficial bacteria are dominant in the human gut, the Bacteroidetes and the Firmicutes. Here we show that the relative proportion of Bacteroidetes is decreased in obese people by comparison with lean people, and that this proportion increases with weight loss on two types of low-calorie diet. Our findings indicate that obesity has a microbial component, which might have potential therapeutic implications.

  6. Next-generation approaches to the microbial ecology of food fermentations.

    PubMed

    Bokulich, Nicholas A; Mills, David A

    2012-07-01

    Food fermentations have enhanced human health since the dawn of time and remain a prevalent means of food processing and preservation. Due to their cultural and nutritional importance, many of these foods have been studied in detail using molecular tools, leading to enhancements in quality and safety. Furthermore, recent advances in high-throughput sequencing technology are revolutionizing the study of food microbial ecology, deepening insight into complex fermentation systems. This review provides insight into novel applications of select molecular techniques, particularly next-generation sequencing technology, for analysis of microbial communities in fermented foods. We present a guideline for integrated molecular analysis of food microbial ecology and a starting point for implementing next-generation analysis of food systems.

  7. Fermentation by the human large intestine microbial community in an in vitro semicontinuous culture system.

    PubMed Central

    Miller, T L; Wolin, M J

    1981-01-01

    A semicontinuous culture of the microbial community of the human large intestine that was maintained over 81 days is described. The initial inoculum was feces, and about 200 ml of nutrient suspension was fed to 500 ml of fermentor contents once or twice daily. The nutrient suspension contained comminuted fibrous food, sodium deoxycholate, urea, acid-hydrolyzed casein, vitamins, and salts. The fermentation was monitored, and the major products were acetate, propionate, butyrate, methane, hydrogen, and carbon dioxide. The concentration of anaerobic bacteria was 2 X 10(9) per ml of culture contents and was 100 times that of fecal coliforms. When the nutrient suspension contained lettuce, celery, carrots, and unsweetened applesauce, the predominant nonsporeforming anaerobes isolated were Bacteroides species. When carrots and applesauce were omitted, the predominant nonsporeforming isolates were Fusobacterium species. On both diets, clostridia were isolated that resembled Clostridium clostridiiforme. The fermentation and bacteriological analyses indicated that the in vitro ecosystem appears to be a reasonable facsimile of the large intestine ecosystem. Images PMID:7027952

  8. Antibiotic Treatment Affects Intestinal Permeability and Gut Microbial Composition in Wistar Rats Dependent on Antibiotic Class

    PubMed Central

    Tulstrup, Monica Vera-Lise; Christensen, Ellen Gerd; Carvalho, Vera; Linninge, Caroline; Ahrné, Siv; Højberg, Ole; Licht, Tine Rask; Bahl, Martin Iain

    2015-01-01

    Antibiotics are frequently administered orally to treat bacterial infections not necessarily related to the gastrointestinal system. This has adverse effects on the commensal gut microbial community, as it disrupts the intricate balance between specific bacterial groups within this ecosystem, potentially leading to dysbiosis. We hypothesized that modulation of community composition and function induced by antibiotics affects intestinal integrity depending on the antibiotic administered. To address this a total of 60 Wistar rats (housed in pairs with 6 cages per group) were dosed by oral gavage with either amoxicillin (AMX), cefotaxime (CTX), vancomycin (VAN), metronidazole (MTZ), or water (CON) daily for 10–11 days. Bacterial composition, alpha diversity and caecum short chain fatty acid levels were significantly affected by AMX, CTX and VAN, and varied among antibiotic treatments. A general decrease in diversity and an increase in the relative abundance of Proteobacteria was observed for all three antibiotics. Additionally, the relative abundance of Bifidobacteriaceae was increased in the CTX group and both Lactobacillaceae and Verrucomicrobiaceae were increased in the VAN group compared to the CON group. No changes in microbiota composition or function were observed following MTZ treatment. Intestinal permeability to 4 kDa FITC-dextran decreased after CTX and VAN treatment and increased following MTZ treatment. Plasma haptoglobin levels were increased by both AMX and CTX but no changes in expression of host tight junction genes were found in any treatment group. A strong correlation between the level of caecal succinate, the relative abundance of Clostridiaceae 1 family in the caecum, and the level of acute phase protein haptoglobin in blood plasma was observed. In conclusion, antibiotic-induced changes in microbiota may be linked to alterations in intestinal permeability, although the specific interactions remain to be elucidated as changes in permeability did

  9. Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology.

    PubMed

    Gibson, Molly K; Forsberg, Kevin J; Dantas, Gautam

    2015-01-01

    Antibiotic resistance is a dire clinical problem with important ecological dimensions. While antibiotic resistance in human pathogens continues to rise at alarming rates, the impact of environmental resistance on human health is still unclear. To investigate the relationship between human-associated and environmental resistomes, we analyzed functional metagenomic selections for resistance against 18 clinically relevant antibiotics from soil and human gut microbiota as well as a set of multidrug-resistant cultured soil isolates. These analyses were enabled by Resfams, a new curated database of protein families and associated highly precise and accurate profile hidden Markov models, confirmed for antibiotic resistance function and organized by ontology. We demonstrate that the antibiotic resistance functions that give rise to the resistance profiles observed in environmental and human-associated microbial communities significantly differ between ecologies. Antibiotic resistance functions that most discriminate between ecologies provide resistance to β-lactams and tetracyclines, two of the most widely used classes of antibiotics in the clinic and agriculture. We also analyzed the antibiotic resistance gene composition of over 6000 sequenced microbial genomes, revealing significant enrichment of resistance functions by both ecology and phylogeny. Together, our results indicate that environmental and human-associated microbial communities harbor distinct resistance genes, suggesting that antibiotic resistance functions are largely constrained by ecology.

  10. Long-Term Oil Contamination Alters the Molecular Ecological Networks of Soil Microbial Functional Genes.

    PubMed

    Liang, Yuting; Zhao, Huihui; Deng, Ye; Zhou, Jizhong; Li, Guanghe; Sun, Bo

    2016-01-01

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

  11. Long-Term Oil Contamination Alters the Molecular Ecological Networks of Soil Microbial Functional Genes

    PubMed Central

    Liang, Yuting; Zhao, Huihui; Deng, Ye; Zhou, Jizhong; Li, Guanghe; Sun, Bo

    2016-01-01

    With knowledge on microbial composition and diversity, investigation of within-community interactions is a further step to elucidate microbial ecological functions, such as the biodegradation of hazardous contaminants. In this work, microbial functional molecular ecological networks were studied in both contaminated and uncontaminated soils to determine the possible influences of oil contamination on microbial interactions and potential functions. Soil samples were obtained from an oil-exploring site located in South China, and the microbial functional genes were analyzed with GeoChip, a high-throughput functional microarray. By building random networks based on null model, we demonstrated that overall network structures and properties were significantly different between contaminated and uncontaminated soils (P < 0.001). Network connectivity, module numbers, and modularity were all reduced with contamination. Moreover, the topological roles of the genes (module hub and connectors) were altered with oil contamination. Subnetworks of genes involved in alkane and polycyclic aromatic hydrocarbon degradation were also constructed. Negative co-occurrence patterns prevailed among functional genes, thereby indicating probable competition relationships. The potential “keystone” genes, defined as either “hubs” or genes with highest connectivities in the network, were further identified. The network constructed in this study predicted the potential effects of anthropogenic contamination on microbial community co-occurrence interactions. PMID:26870020

  12. Intestinal Microbial Metabolites Are Linked to Severity of Myocardial Infarction in Rats

    PubMed Central

    Lam, Vy; Su, Jidong; Hsu, Anna; Gross, Garrett J.; Salzman, Nita H.

    2016-01-01

    Intestinal microbiota determine severity of myocardial infarction in rats. We determined whether low molecular weight metabolites derived from intestinal microbiota and transported to the systemic circulation are linked to severity of myocardial infarction. Plasma from rats treated for seven days with the non-absorbed antibiotic vancomycin or a mixture of streptomycin, neomycin, polymyxin B and bacitracin was analyzed using mass spectrometry-based metabolite profiling platforms. Antibiotic-induced changes in the abundance of individual groups of intestinal microbiota dramatically altered the host’s metabolism. Hierarchical clustering of dissimilarities separated the levels of 284 identified metabolites from treated vs. untreated rats; 193 were altered by the antibiotic treatments with a tendency towards decreased metabolite levels. Catabolism of the aromatic amino acids phenylalanine, tryptophan and tyrosine was the most affected pathway comprising 33 affected metabolites. Both antibiotic treatments decreased the severity of an induced myocardial infarction in vivo by 27% and 29%, respectively. We then determined whether microbial metabolites of the amino acids phenylalanine, tryptophan and tyrosine were linked to decreased severity of myocardial infarction. Vancomycin-treated rats were administered amino acid metabolites prior to ischemia/reperfusion studies. Oral or intravenous pretreatment of rats with these amino acid metabolites abolished the decrease in infarct size conferred by vancomycin. Inhibition of JAK-2 (AG-490, 10 μM), Src kinase (PP1, 20 μM), Akt/PI3 kinase (Wortmannin, 100 nM), p44/42 MAPK (PD98059, 10 μM), p38 MAPK (SB203580, 10 μM), or KATP channels (glibenclamide, 3 μM) abolished cardioprotection by vancomycin, indicating microbial metabolites are interacting with cell surface receptors to transduce their signals through Src kinase, cell survival pathways and KATP channels. These inhibitors have no effect on myocardial infarct size in

  13. Urban microbial ecology of a freshwater estuary of Lake Michigan

    PubMed Central

    Fisher, Jenny C.; Newton, Ryan J.; Dila, Deborah K.

    2015-01-01

    Freshwater estuaries throughout the Great Lakes region receive stormwater runoff and riverine inputs from heavily urbanized population centers. While human and animal feces contained in this runoff are often the focus of source tracking investigations, non-fecal bacterial loads from soil, aerosols, urban infrastructure, and other sources are also transported to estuaries and lakes. We quantified and characterized this non-fecal urban microbial component using bacterial 16S rRNA gene sequences from sewage, stormwater, rivers, harbor/estuary, and the lake surrounding Milwaukee, WI, USA. Bacterial communities from each of these environments had a distinctive composition, but some community members were shared among environments. We used a statistical biomarker discovery tool to identify the components of the microbial community that were most strongly associated with stormwater and sewage to describe an “urban microbial signature,” and measured the presence and relative abundance of these organisms in the rivers, estuary, and lake. This urban signature increased in magnitude in the estuary and harbor with increasing rainfall levels, and was more apparent in lake samples with closest proximity to the Milwaukee estuary. The dominant bacterial taxa in the urban signature were Acinetobacter, Aeromonas, and Pseudomonas, which are organisms associated with pipe infrastructure and soil and not typically found in pelagic freshwater environments. These taxa were highly abundant in stormwater and sewage, but sewage also contained a high abundance of Arcobacter and Trichococcus that appeared in lower abundance in stormwater outfalls and in trace amounts in aquatic environments. Urban signature organisms comprised 1.7% of estuary and harbor communities under baseflow conditions, 3.5% after rain, and >10% after a combined sewer overflow. With predicted increases in urbanization across the Great Lakes, further alteration of freshwater communities is likely to occur with

  14. The Inter-Valley Soil Comparative Survey: the ecology of Dry Valley edaphic microbial communities.

    PubMed

    Lee, Charles K; Barbier, Béatrice A; Bottos, Eric M; McDonald, Ian R; Cary, Stephen Craig

    2012-05-01

    Recent applications of molecular genetics to edaphic microbial communities of the McMurdo Dry Valleys and elsewhere have rejected a long-held belief that Antarctic soils contain extremely limited microbial diversity. The Inter-Valley Soil Comparative Survey aims to elucidate the factors shaping these unique microbial communities and their biogeography by integrating molecular genetic approaches with biogeochemical analyses. Although the microbial communities of Dry Valley soils may be complex, there is little doubt that the ecosystem's food web is relatively simple, and evidence suggests that physicochemical conditions may have the dominant role in shaping microbial communities. To examine this hypothesis, bacterial communities from representative soil samples collected in four geographically disparate Dry Valleys were analyzed using molecular genetic tools, including pyrosequencing of 16S rRNA gene PCR amplicons. Results show that the four communities are structurally and phylogenetically distinct, and possess significantly different levels of diversity. Strikingly, only 2 of 214 phylotypes were found in all four valleys, challenging a widespread assumption that the microbiota of the Dry Valleys is composed of a few cosmopolitan species. Analysis of soil geochemical properties indicated that salt content, alongside altitude and Cu(2+), was significantly correlated with differences in microbial communities. Our results indicate that the microbial ecology of Dry Valley soils is highly localized and that physicochemical factors potentially have major roles in shaping the microbiology of ice-free areas of Antarctica. These findings hint at links between Dry Valley glacial geomorphology and microbial ecology, and raise previously unrecognized issues related to environmental management of this unique ecosystem. PMID:22170424

  15. The Inter-Valley Soil Comparative Survey: the ecology of Dry Valley edaphic microbial communities

    PubMed Central

    Lee, Charles K; Barbier, Béatrice A; Bottos, Eric M; McDonald, Ian R; Cary, Stephen Craig

    2012-01-01

    Recent applications of molecular genetics to edaphic microbial communities of the McMurdo Dry Valleys and elsewhere have rejected a long-held belief that Antarctic soils contain extremely limited microbial diversity. The Inter-Valley Soil Comparative Survey aims to elucidate the factors shaping these unique microbial communities and their biogeography by integrating molecular genetic approaches with biogeochemical analyses. Although the microbial communities of Dry Valley soils may be complex, there is little doubt that the ecosystem's food web is relatively simple, and evidence suggests that physicochemical conditions may have the dominant role in shaping microbial communities. To examine this hypothesis, bacterial communities from representative soil samples collected in four geographically disparate Dry Valleys were analyzed using molecular genetic tools, including pyrosequencing of 16S rRNA gene PCR amplicons. Results show that the four communities are structurally and phylogenetically distinct, and possess significantly different levels of diversity. Strikingly, only 2 of 214 phylotypes were found in all four valleys, challenging a widespread assumption that the microbiota of the Dry Valleys is composed of a few cosmopolitan species. Analysis of soil geochemical properties indicated that salt content, alongside altitude and Cu2+, was significantly correlated with differences in microbial communities. Our results indicate that the microbial ecology of Dry Valley soils is highly localized and that physicochemical factors potentially have major roles in shaping the microbiology of ice-free areas of Antarctica. These findings hint at links between Dry Valley glacial geomorphology and microbial ecology, and raise previously unrecognized issues related to environmental management of this unique ecosystem. PMID:22170424

  16. The Inter-Valley Soil Comparative Survey: the ecology of Dry Valley edaphic microbial communities.

    PubMed

    Lee, Charles K; Barbier, Béatrice A; Bottos, Eric M; McDonald, Ian R; Cary, Stephen Craig

    2012-05-01

    Recent applications of molecular genetics to edaphic microbial communities of the McMurdo Dry Valleys and elsewhere have rejected a long-held belief that Antarctic soils contain extremely limited microbial diversity. The Inter-Valley Soil Comparative Survey aims to elucidate the factors shaping these unique microbial communities and their biogeography by integrating molecular genetic approaches with biogeochemical analyses. Although the microbial communities of Dry Valley soils may be complex, there is little doubt that the ecosystem's food web is relatively simple, and evidence suggests that physicochemical conditions may have the dominant role in shaping microbial communities. To examine this hypothesis, bacterial communities from representative soil samples collected in four geographically disparate Dry Valleys were analyzed using molecular genetic tools, including pyrosequencing of 16S rRNA gene PCR amplicons. Results show that the four communities are structurally and phylogenetically distinct, and possess significantly different levels of diversity. Strikingly, only 2 of 214 phylotypes were found in all four valleys, challenging a widespread assumption that the microbiota of the Dry Valleys is composed of a few cosmopolitan species. Analysis of soil geochemical properties indicated that salt content, alongside altitude and Cu(2+), was significantly correlated with differences in microbial communities. Our results indicate that the microbial ecology of Dry Valley soils is highly localized and that physicochemical factors potentially have major roles in shaping the microbiology of ice-free areas of Antarctica. These findings hint at links between Dry Valley glacial geomorphology and microbial ecology, and raise previously unrecognized issues related to environmental management of this unique ecosystem.

  17. A guide to statistical analysis in microbial ecology: a community-focused, living review of multivariate data analyses.

    PubMed

    Buttigieg, Pier Luigi; Ramette, Alban

    2014-12-01

    The application of multivariate statistical analyses has become a consistent feature in microbial ecology. However, many microbial ecologists are still in the process of developing a deep understanding of these methods and appreciating their limitations. As a consequence, staying abreast of progress and debate in this arena poses an additional challenge to many microbial ecologists. To address these issues, we present the GUide to STatistical Analysis in Microbial Ecology (GUSTA ME): a dynamic, web-based resource providing accessible descriptions of numerous multivariate techniques relevant to microbial ecologists. A combination of interactive elements allows users to discover and navigate between methods relevant to their needs and examine how they have been used by others in the field. We have designed GUSTA ME to become a community-led and -curated service, which we hope will provide a common reference and forum to discuss and disseminate analytical techniques relevant to the microbial ecology community.

  18. A guide to statistical analysis in microbial ecology: a community-focused, living review of multivariate data analyses.

    PubMed

    Buttigieg, Pier Luigi; Ramette, Alban

    2014-12-01

    The application of multivariate statistical analyses has become a consistent feature in microbial ecology. However, many microbial ecologists are still in the process of developing a deep understanding of these methods and appreciating their limitations. As a consequence, staying abreast of progress and debate in this arena poses an additional challenge to many microbial ecologists. To address these issues, we present the GUide to STatistical Analysis in Microbial Ecology (GUSTA ME): a dynamic, web-based resource providing accessible descriptions of numerous multivariate techniques relevant to microbial ecologists. A combination of interactive elements allows users to discover and navigate between methods relevant to their needs and examine how they have been used by others in the field. We have designed GUSTA ME to become a community-led and -curated service, which we hope will provide a common reference and forum to discuss and disseminate analytical techniques relevant to the microbial ecology community. PMID:25314312

  19. Microbial colonization influences composition and T-cell receptor V beta repertoire of intraepithelial lymphocytes in rat intestine.

    PubMed Central

    Helgeland, L; Vaage, J T; Rolstad, B; Midtvedt, T; Brandtzaeg, P

    1996-01-01

    Studies in mice have shown that the composition of intestinal intraepithelial lymphocytes (IEL) may be markedly altered by gut microbial colonization. Such modulation was studied in a rat model by the use of germ-free and conventionalized animals from which IEL from the small intestine were isolated and analysed by flow cytometry. Conventionalization caused expansion as well as phenotypic alterations of T-cell receptor (TCR) alpha/beta + IEL in that the proportions of CD4+ and CD8 alpha beta + TCR alpha/beta + cells were increased, while the double negative (CD4- CD8-) fraction was reduced. microbial colonization also influenced the TCR V beta repertoire of CD8+ IEL in that the proportions of V beta 8.2+ and V beta 10+ cells were increased, whereas V beta 8.5+ and V beta 16+ cells were relatively decreased. Moreover, conventionalization influenced the levels of TCR cell surface expression in the same V beta subsets. Three-colour flow-cytometric analysis demonstrated that skewing of the V beta repertoire was most pronounced in the CD8 alpha alpha + subset, although the numerical increase of IEL mainly included the CD8 alpha beta + subset. In contrast to IEL, the TCR V beta repertoire in mesenteric lymph nodes was unchanged after intestinal colonization. These results confirm that TCR alpha/beta + IEL subpopulations respond dynamically to the microbial gut flora and suggest that their V beta repertoire can be shaped by luminal microbial antigens. PMID:9014812

  20. 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.

  1. 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

  2. Biogeography and ecology of the rare and abundant microbial lineages in deep-sea hydrothermal vents.

    PubMed

    Anderson, Rika E; Sogin, Mitchell L; Baross, John A

    2015-01-01

    Environmental gradients generate countless ecological niches in deep-sea hydrothermal vent systems, which foster diverse microbial communities. The majority of distinct microbial lineages in these communities occur in very low abundance. However, the ecological role and distribution of rare and abundant lineages, particularly in deep, hot subsurface environments, remain unclear. Here, we use 16S rRNA tag sequencing to describe biogeographic patterning and microbial community structure of both rare and abundant archaea and bacteria in hydrothermal vent systems. We show that while rare archaeal lineages and almost all bacterial lineages displayed geographically restricted community structuring patterns, the abundant lineages of archaeal communities displayed a much more cosmopolitan distribution. Finally, analysis of one high-volume, high-temperature fluid sample representative of the deep hot biosphere described a unique microbial community that differed from microbial populations in diffuse flow fluid or sulfide samples, yet the rare thermophilic archaeal groups showed similarities to those that occur in sulfides. These results suggest that while most archaeal and bacterial lineages in vents are rare and display a highly regional distribution, a small percentage of lineages, particularly within the archaeal domain, are successful at widespread dispersal and colonization. PMID:25764538

  3. Biogeography and ecology of the rare and abundant microbial lineages in deep-sea hydrothermal vents.

    PubMed

    Anderson, Rika E; Sogin, Mitchell L; Baross, John A

    2015-01-01

    Environmental gradients generate countless ecological niches in deep-sea hydrothermal vent systems, which foster diverse microbial communities. The majority of distinct microbial lineages in these communities occur in very low abundance. However, the ecological role and distribution of rare and abundant lineages, particularly in deep, hot subsurface environments, remain unclear. Here, we use 16S rRNA tag sequencing to describe biogeographic patterning and microbial community structure of both rare and abundant archaea and bacteria in hydrothermal vent systems. We show that while rare archaeal lineages and almost all bacterial lineages displayed geographically restricted community structuring patterns, the abundant lineages of archaeal communities displayed a much more cosmopolitan distribution. Finally, analysis of one high-volume, high-temperature fluid sample representative of the deep hot biosphere described a unique microbial community that differed from microbial populations in diffuse flow fluid or sulfide samples, yet the rare thermophilic archaeal groups showed similarities to those that occur in sulfides. These results suggest that while most archaeal and bacterial lineages in vents are rare and display a highly regional distribution, a small percentage of lineages, particularly within the archaeal domain, are successful at widespread dispersal and colonization.

  4. Microbial ecology of sourdough fermentations: diverse or uniform?

    PubMed

    De Vuyst, L; Van Kerrebroeck, S; Harth, H; Huys, G; Daniel, H-M; Weckx, S

    2014-02-01

    Sourdough is a specific and stressful ecosystem inhabited by yeasts and lactic acid bacteria (LAB), mainly heterofermentative lactobacilli. On the basis of their inocula, three types of sourdough fermentation processes can be distinguished, namely backslopped ones, those initiated with starter cultures, and those initiated with a starter culture followed by backslopping. Typical sourdough LAB species are Lactobacillus fermentum, Lactobacillus paralimentarius, Lactobacillus plantarum, and Lactobacillus sanfranciscensis. Typical sourdough yeast species are Candida humilis, Kazachstania exigua, and Saccharomyces cerevisiae. Whereas region specificity is claimed in the case of artisan backslopped sourdoughs, no clear-cut relationship between a typical sourdough and its associated microbiota can be found, as this is dependent on the sampling, isolation, and identification procedures. Both simple and very complex consortia may occur. Moreover, a series of intrinsic and extrinsic factors may influence the composition of the sourdough microbiota. For instance, an influence of the flour (type, quality status, etc.) and the process parameters (temperature, pH, dough yield, backslopping practices, etc.) occurs. In this way, the presence of Lb. sanfranciscensis during sourdough fermentation depends on specific environmental and technological factors. Also, Triticum durum seems to select for obligately heterofermentative LAB species. Finally, there are indications that the sourdough LAB are of intestinal origin.

  5. Intestinal colonization resistance

    PubMed Central

    Lawley, Trevor D; Walker, Alan W

    2013-01-01

    Dense, complex microbial communities, collectively termed the microbiota, occupy a diverse array of niches along the length of the mammalian intestinal tract. During health and in the absence of antibiotic exposure the microbiota can effectively inhibit colonization and overgrowth by invading microbes such as pathogens. This phenomenon is called ‘colonization resistance’ and is associated with a stable and diverse microbiota in tandem with a controlled lack of inflammation, and involves specific interactions between the mucosal immune system and the microbiota. Here we overview the microbial ecology of the healthy mammalian intestinal tract and highlight the microbe–microbe and microbe–host interactions that promote colonization resistance. Emerging themes highlight immunological (T helper type 17/regulatory T-cell balance), microbiota (diverse and abundant) and metabolic (short-chain fatty acid) signatures of intestinal health and colonization resistance. Intestinal pathogens use specific virulence factors or exploit antibiotic use to subvert colonization resistance for their own benefit by triggering inflammation to disrupt the harmony of the intestinal ecosystem. A holistic view that incorporates immunological and microbiological facets of the intestinal ecosystem should facilitate the development of immunomodulatory and microbe-modulatory therapies that promote intestinal homeostasis and colonization resistance. PMID:23240815

  6. Tools and perspectives for a unified approach to understanding microbial ecology in the critical zone

    NASA Astrophysics Data System (ADS)

    Gallery, R. E.; Aronson, E. L.; Fairbanks, D.; Murphy, M. A.; Rich, V. I.; Hart, S. C.

    2015-12-01

    Microbial communities that control nutrient transformation and storage in ecosystems are themselves influenced by landscape topography and vegetative cover. Globally, disturbances such as fires and insect outbreaks are increasing in frequency and severity with enormous impacts on global carbon cycling. The resiliency of soil microbial communities to these heterogeneous disturbances determines rates of nutrient transformations as well as ecosystem structure and recovery. Natural and anthropogenic disturbances are a common thread throughout Critical Zone Observatories and ecosystems in general. Using the 2013 Thompson Ridge Fire in the Jemez River Basin CZO as a case study, we examine the effect of a wildfire disturbance regime on successional changes in soil microbiota and ecosystem fluxes across a landscape with high topographic variation. We find that, layered over the topographic controls of hotspots of biogeochemical activity, fire alters organic substrate quality, microbial biomass, community structure, and activity. For example, fire increases soil pH, which is commonly found as an explanatory variable describing bacterial community structure. Soil microbes excrete exoenzymes to decompose polymers and acquire nutrients, and these activities can indicate changing microbial function or soil quality. In these mixed conifer forests, we find shifts from carbon to nitrogen-dominated exoenzyme activities in burned forests with alkaline soils, suggesting shifts of microbial taxa and function that correspond with recovering soil microbial biomass. More generally we ask - what combination of tools and perspectives is needed to fully understand soil microbial ecology and biogeochemistry of the critical zone? Results from an NSF Science Across Virtual Institutes (SAVI) CZO Network Biogeochemistry Workshop highlight the importance of incorporating a standard suite of microbial activity and community assays along with soil biogeochemical and flux measurements to enable

  7. Microbial Ecology of Anaerobic Digesters: The Key Players of Anaerobiosis

    PubMed Central

    Ali Shah, Fayyaz; Mahmood, Qaisar; Maroof Shah, Mohammad; Pervez, Arshid; Ahmad Asad, Saeed

    2014-01-01

    Anaerobic digestion is the method of wastes treatment aimed at a reduction of their hazardous effects on the biosphere. The mutualistic behavior of various anaerobic microorganisms results in the decomposition of complex organic substances into simple, chemically stabilized compounds, mainly methane and CO2. The conversions of complex organic compounds to CH4 and CO2 are possible due to the cooperation of four different groups of microorganisms, that is, fermentative, syntrophic, acetogenic, and methanogenic bacteria. Microbes adopt various pathways to evade from the unfavorable conditions in the anaerobic digester like competition between sulfate reducing bacteria (SRB) and methane forming bacteria for the same substrate. Methanosarcina are able to use both acetoclastic and hydrogenotrophic pathways for methane production. This review highlights the cellulosic microorganisms, structure of cellulose, inoculum to substrate ratio, and source of inoculum and its effect on methanogenesis. The molecular techniques such as DGGE (denaturing gradient gel electrophoresis) utilized for dynamic changes in microbial communities and FISH (fluorescent in situ hybridization) that deal with taxonomy and interaction and distribution of tropic groups used are also discussed. PMID:24701142

  8. Agent-based model of Fecal Microbial Transplant effect on Bile Acid Metabolism on suppressing Clostridium difficile infection: an example of agent-based modeling of intestinal bacterial infection

    PubMed Central

    Peer, Xavier; An, Gary

    2014-01-01

    Agent-based modeling is a computational modeling method that represents system-level behavior as arising from multiple interactions between the multiple components that make up a system. Biological systems are thus readily described using agent-based models (ABMs), as multi-cellular organisms can be viewed as populations of interacting cells, and microbial systems manifest as colonies of individual microbes. Intersections between these two domains underlie an increasing number of pathophysiological processes, and the intestinal tract represents one of the most significant locations for these inter-domain interactions, so much so that it can be considered an internal ecology of varying robustness and function. Intestinal infections represent significant disturbances of this internal ecology, and one of the most clinically relevant intestinal infections is Clostridium difficile infection (CDI). CDI is precipitated by the use of broad-spectrum antibiotics, involves the depletion of commensal microbiota, and alterations in bile acid composition in the intestinal lumen. We present an example ABM of CDI (the Clostridium difficile Infection ABM, or CDIABM) to examine fundamental dynamics of the pathogenesis of CDI and its response to treatment with anti-CDI antibiotics and a newer treatment therapy, Fecal Microbial Transplant (FMT). The CDIABM focuses on one specific mechanism of potential CDI suppression: commensal modulation of bile acid composition. Even given its abstraction, the CDIABM reproduces essential dynamics of CDI and its response to therapy, and identifies a paradoxical zone of behavior that provides insight into the role of intestinal nutritional status and the efficacy of anti-CDI therapies. It is hoped that this use case example of the CDIABM can demonstrate the usefulness of both agent-based modeling and the application of abstract functional representation as the biomedical community seeks to address the challenges of increasingly complex diseases with

  9. Radiation: microbial evolution, ecology, and relevance to mars missions

    NASA Technical Reports Server (NTRS)

    Rothschild, L. J.; Cockell, C. S.

    1999-01-01

    Ultraviolet (UV) radiation has been an important environmental parameter during the evolution of life on Earth, both in its role as a mutagen and as a selective agent. This was probably especially true during the time from 3.8 to 2.5 billion years ago, when atmospheric ozone levels were less than 1% of present levels. Early Mars may not have had an "ozone shield" either, and it never developed a significant one. Even though Mars is farther away from the Sun than the Earth, a substantial surficial UV flux is present on Mars today. But organisms respond to dose rate, and on Mars, like on Earth, organisms would be exposed to diurnal variations in UV flux. Here we present data on the effect of diurnal patterns of UV flux on microbial ecosystems in nature, with an emphasis on photosynthesis and DNA synthesis effects. These results indicate that diurnal patterns of metabolism occur in nature with a dip in photosynthesis and DNA synthesis in the afternoon, in part regulated by UV flux. Thus, diurnal patterns must be studied in order to understand the effect of UV radiation in nature. The results of this work are significant to the success of human missions to Mars for several reasons. For example, human missions must include photosynthetic organisms for food production and likely oxygen production. An evolutionary approach suggests which organisms might be best suited for high UV fluxes. The diurnal aspect of these studies is critical. Terraforming is a potential goal of Mars exploration, and it will require studies of the effect of Martian UV fluxes, including their diurnal changes, on terrestrial organisms. Such studies may suggest that diurnal changes in UV only require mitigation at some times of day or year.

  10. Radiation: microbial evolution, ecology, and relevance to mars missions.

    PubMed

    Rothschild, L J; Cockell, C S

    1999-12-01

    Ultraviolet (UV) radiation has been an important environmental parameter during the evolution of life on Earth, both in its role as a mutagen and as a selective agent. This was probably especially true during the time from 3.8 to 2.5 billion years ago, when atmospheric ozone levels were less than 1% of present levels. Early Mars may not have had an "ozone shield" either, and it never developed a significant one. Even though Mars is farther away from the Sun than the Earth, a substantial surficial UV flux is present on Mars today. But organisms respond to dose rate, and on Mars, like on Earth, organisms would be exposed to diurnal variations in UV flux. Here we present data on the effect of diurnal patterns of UV flux on microbial ecosystems in nature, with an emphasis on photosynthesis and DNA synthesis effects. These results indicate that diurnal patterns of metabolism occur in nature with a dip in photosynthesis and DNA synthesis in the afternoon, in part regulated by UV flux. Thus, diurnal patterns must be studied in order to understand the effect of UV radiation in nature. The results of this work are significant to the success of human missions to Mars for several reasons. For example, human missions must include photosynthetic organisms for food production and likely oxygen production. An evolutionary approach suggests which organisms might be best suited for high UV fluxes. The diurnal aspect of these studies is critical. Terraforming is a potential goal of Mars exploration, and it will require studies of the effect of Martian UV fluxes, including their diurnal changes, on terrestrial organisms. Such studies may suggest that diurnal changes in UV only require mitigation at some times of day or year.

  11. Microbial Population Differentials between Mucosal and Submucosal Intestinal Tissues in Advanced Crohn's Disease of the Ileum

    PubMed Central

    Chiodini, Rodrick J.; Dowd, Scot E.; Chamberlin, William M.; Galandiuk, Susan; Davis, Brian; Glassing, Angela

    2015-01-01

    Since Crohn's disease is a transmural disease, we hypothesized that examination of deep submucosal tissues directly involved in the inflammatory disease process may provide unique insights into bacterial populations transgressing intestinal barriers and bacterial populations more representative of the causes and agents of the disease. We performed deep 16s microbiota sequencing on isolated ilea mucosal and submucosal tissues on 20 patients with Crohn's disease and 15 non-inflammatory bowel disease controls with a depth of coverage averaging 81,500 sequences in each of the 70 DNA samples yielding an overall resolution down to 0.0001% of the bacterial population. Of the 4,802,328 total sequences generated, 98.9% or 4,749,183 sequences aligned with the Kingdom Bacteria that clustered into 8545 unique sequences with <3% divergence or operational taxonomic units enabling the identification of 401 genera and 698 tentative bacterial species. There were significant differences in all taxonomic levels between the submucosal microbiota in Crohn's disease compared to controls, including organisms of the Order Desulfovibrionales that were present within the submucosal tissues of most Crohn's disease patients but absent in the control group. A variety of organisms of the Phylum Firmicutes were increased in the subjacent submucosa as compared to the parallel mucosal tissue including Ruminococcus spp., Oscillospira spp., Pseudobutyrivibrio spp., and Tumebacillus spp. In addition, Propionibacterium spp. and Cloacibacterium spp. were increased as well as large increases in Proteobacteria including Parasutterella spp. and Methylobacterium spp. This is the first study to examine the microbial populations within submucosal tissues of patients with Crohn's disease and to compare microbial communities found deep within the submucosal tissues with those present on mucosal surfaces. Our data demonstrate the existence of a distinct submucosal microbiome and ecosystem that is not well

  12. Microbial Population Differentials between Mucosal and Submucosal Intestinal Tissues in Advanced Crohn's Disease of the Ileum.

    PubMed

    Chiodini, Rodrick J; Dowd, Scot E; Chamberlin, William M; Galandiuk, Susan; Davis, Brian; Glassing, Angela

    2015-01-01

    Since Crohn's disease is a transmural disease, we hypothesized that examination of deep submucosal tissues directly involved in the inflammatory disease process may provide unique insights into bacterial populations transgressing intestinal barriers and bacterial populations more representative of the causes and agents of the disease. We performed deep 16s microbiota sequencing on isolated ilea mucosal and submucosal tissues on 20 patients with Crohn's disease and 15 non-inflammatory bowel disease controls with a depth of coverage averaging 81,500 sequences in each of the 70 DNA samples yielding an overall resolution down to 0.0001% of the bacterial population. Of the 4,802,328 total sequences generated, 98.9% or 4,749,183 sequences aligned with the Kingdom Bacteria that clustered into 8545 unique sequences with <3% divergence or operational taxonomic units enabling the identification of 401 genera and 698 tentative bacterial species. There were significant differences in all taxonomic levels between the submucosal microbiota in Crohn's disease compared to controls, including organisms of the Order Desulfovibrionales that were present within the submucosal tissues of most Crohn's disease patients but absent in the control group. A variety of organisms of the Phylum Firmicutes were increased in the subjacent submucosa as compared to the parallel mucosal tissue including Ruminococcus spp., Oscillospira spp., Pseudobutyrivibrio spp., and Tumebacillus spp. In addition, Propionibacterium spp. and Cloacibacterium spp. were increased as well as large increases in Proteobacteria including Parasutterella spp. and Methylobacterium spp. This is the first study to examine the microbial populations within submucosal tissues of patients with Crohn's disease and to compare microbial communities found deep within the submucosal tissues with those present on mucosal surfaces. Our data demonstrate the existence of a distinct submucosal microbiome and ecosystem that is not well

  13. Microbial Ecology Assessment of Mixed Copper Oxide/Sulfide Dump Leach Operation

    SciTech Connect

    Bruhn, Debby Fox; Thompson, David Neal; Noah, Karl Scott

    1999-06-01

    Microbial consortia composed of complex mixtures of autotrophic and heterotrophic bacteria are responsible for the dissolution of metals from sulfide minerals. Thus, an efficient copper bioleaching operation depends on the microbial ecology of the system. A microbial ecology study of a mixed oxide/sulfide copper leaching operation was conducted using an "overlay" plating technique to differentiate and identify various bacterial consortium members of the genera Thiobacillus, “Leptospirillum”, “Ferromicrobium”, and Acidiphilium. Two temperatures (30°C and 45°C) were used to select for mesophilic and moderately thermophilic bacteria. Cell numbers varied from 0-106 cells/g dry ore, depending on the sample location and depth. After acid curing for oxide leaching, no viable bacteria were recovered, although inoculation of cells from raffinate re-established a microbial population after three months. Due to low the pH of the operation, very few non-iron-oxidizing acidophilic heterotrophs were recovered. Moderate thermophiles were isolated from the ore samples. Pregnant liquor solutions (PLS) and raffinate both contained a diversity of bacteria. In addition, an intermittently applied waste stream that contained high levels of arsenic and fluoride was tested for toxicity. Twenty vol% waste stream in PLS killed 100% of the cells in 48 hours, indicating substantial toxicity and/or growth inhibition. The data indicate that bacteria populations can recover after acid curing, and that application of the waste stream to the dump should be avoided. Monitoring the microbial ecology of the leaching operation provided significant information that improved copper recovery.

  14. Board-invited review: Rumen microbiology: leading the way in microbial ecology.

    PubMed

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

    2013-01-01

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

  15. Defining DNA-based operational taxonomic units for microbial-eukaryote ecology.

    PubMed

    Caron, David A; Countway, Peter D; Savai, Pratik; Gast, Rebecca J; Schnetzer, Astrid; Moorthi, Stefanie D; Dennett, Mark R; Moran, Dawn M; Jones, Adriane C

    2009-09-01

    DNA sequence information has increasingly been used in ecological research on microbial eukaryotes. Sequence-based approaches have included studies of the total diversity of selected ecosystems, studies of the autecology of ecologically relevant species, and identification and enumeration of species of interest for human health. It is still uncommon, however, to delineate protistan species based on their genetic signatures. The reluctance to assign species-level designations based on DNA sequences is in part a consequence of the limited amount of sequence information presently available for many free-living microbial eukaryotes and in part a consequence of the problematic nature of and debate surrounding the microbial species concept. Despite the difficulties inherent in assigning species names to DNA sequences, there is a growing need to attach meaning to the burgeoning amount of sequence information entering the literature, and there is a growing desire to apply this information in ecological studies. We describe a computer-based tool that assigns DNA sequences from environmental databases to operational taxonomic units at approximately species-level distinctions. This approach provides a practical method for ecological studies of microbial eukaryotes (primarily protists) by enabling semiautomated analysis of large numbers of samples spanning great taxonomic breadth. Derivation of the algorithm was based on an analysis of complete small-subunit (18S) rRNA gene sequences and partial gene sequences obtained from the GenBank database for morphologically described protistan species. The program was tested using environmental 18S rRNA data sets for two oceanic ecosystems. A total of 388 operational taxonomic units were observed for 2,207 sequences obtained from samples collected in the western North Atlantic and eastern North Pacific oceans.

  16. Human gut-on-a-chip inhabited by microbial flora that experiences intestinal peristalsis-like motions and flow.

    PubMed

    Kim, Hyun Jung; Huh, Dongeun; Hamilton, Geraldine; Ingber, Donald E

    2012-06-21

    Development of an in vitro living cell-based model of the intestine that mimics the mechanical, structural, absorptive, transport and pathophysiological properties of the human gut along with its crucial microbial symbionts could accelerate pharmaceutical development, and potentially replace animal testing. Here, we describe a biomimetic 'human gut-on-a-chip' microdevice composed of two microfluidic channels separated by a porous flexible membrane coated with extracellular matrix (ECM) and lined by human intestinal epithelial (Caco-2) cells that mimics the complex structure and physiology of living intestine. The gut microenvironment is recreated by flowing fluid at a low rate (30 μL h(-1)) producing low shear stress (0.02 dyne cm(-2)) over the microchannels, and by exerting cyclic strain (10%; 0.15 Hz) that mimics physiological peristaltic motions. Under these conditions, a columnar epithelium develops that polarizes rapidly, spontaneously grows into folds that recapitulate the structure of intestinal villi, and forms a high integrity barrier to small molecules that better mimics whole intestine than cells in cultured in static Transwell models. In addition, a normal intestinal microbe (Lactobacillus rhamnosus GG) can be successfully co-cultured for extended periods (>1 week) on the luminal surface of the cultured epithelium without compromising epithelial cell viability, and this actually improves barrier function as previously observed in humans. Thus, this gut-on-a-chip recapitulates multiple dynamic physical and functional features of human intestine that are critical for its function within a controlled microfluidic environment that is amenable for transport, absorption, and toxicity studies, and hence it should have great value for drug testing as well as development of novel intestinal disease models. PMID:22434367

  17. Emergence of fecal microbiota transplantation as an approach to repair disrupted microbial gut ecology.

    PubMed

    Khoruts, Alexander; Weingarden, Alexa R

    2014-12-01

    In the recent years fecal microbiota transplantation (FMT) has emerged as an effective therapeutic option for patients with refractory Clostridium difficile infection that is not responding to antibiotic therapy. It results in implantation of donor microbiota into recipients and restoration of normal distal gut microbial community structure. We anticipate that this form of therapy represents merely the first entry into a new class of therapeutics. There is great interest in application of FMT or defined microbial consortia to treatment of many diseases associated with dysbiosis. However, many challenges remain in development as our understanding of microbial ecology within the human body and microbiota-host interactions remain limited. Future advances in this field will be critically depending on detailed mechanistic understanding.

  18. Termite hindguts and the ecology of microbial communities in the sequencing age.

    PubMed

    Tai, Vera; Keeling, Patrick J

    2013-01-01

    Advances in high-throughput nucleic acid sequencing have improved our understanding of microbial communities in a number of ways. Deeper sequence coverage provides the means to assess diversity at the resolution necessary to recover ecological and biogeographic patterns, and at the same time single-cell genomics provides detailed information about the interactions between members of a microbial community. Given the vastness and complexity of microbial ecosystems, such analyses remain challenging for most environments, so greater insight can also be drawn from analysing less dynamic ecosystems. Here, we outline the advantages of one such environment, the wood-digesting hindgut communities of termites and cockroaches, and how it is a model to examine and compare both protist and bacterial communities. Beyond the analysis of diversity, our understanding of protist community ecology will depend on using statistically sound sampling regimes at biologically relevant scales, transitioning from discovery-based to experimental ecology, incorporating single-cell microbiology and other data sources, and continued development of analytical tools. PMID:23710655

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

    PubMed

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

    2016-01-01

    Pharmaceuticals and other micropollutants have been detected in drinking water, groundwater, surface water, and soil around the world. Even in locations where wastewater treatment is required, they can be found in drinking water wells, municipal water supplies, and agricultural soils. It is clear conventional wastewater treatment technologies are not meeting the challenge of the mounting pressures on global freshwater supplies. Cost-effective ecological wastewater treatment technologies have been developed in response. To determine whether the removal of micropollutants in ecological wastewater treatment plants (WWTPs) is promoted by the plant-microbe interactions, as has been reported for other recalcitrant xenobiotics, biofilm microbial communities growing on the surfaces of plant roots were profiled by whole metagenome sequencing and compared to the microbial communities residing in the wastewater. In this study, the concentrations of pharmaceuticals and personal care products (PPCPs) were quantified in each treatment tank of the ecological WWTP treating human wastewater at a highway rest stop and visitor center in Vermont. The concentrations of detected PPCPs were substantially greater than values reported for conventional WWTPs likely due to onsite recirculation of wastewater. The greatest reductions in PPCPs concentrations were observed in the anoxic treatment tank where Bacilli dominated the biofilm community. Benzoate degradation was the most abundant xenobiotic metabolic category identified throughout the system. Collectively, the microbial communities residing in the wastewater were taxonomically and metabolically more diverse than the immersed plant root biofilm. However, greater heterogeneity and higher relative abundances of xenobiotic metabolism genes was observed for the root biofilm. PMID:27610223

  20. Expression of the aryl hydrocarbon receptor contributes to the establishment of intestinal microbial community structure in mice

    PubMed Central

    Murray, Iain A.; Nichols, Robert G.; Zhang, Limin; Patterson, Andrew D.; Perdew, Gary H.

    2016-01-01

    Environmental and genetic factors represent key components in the establishment/maintenance of the intestinal microbiota. The aryl hydrocarbon receptor (AHR) is emerging as a pleiotropic factor, modulating pathways beyond its established role as a xenobiotic sensor. The AHR is known to regulate immune surveillance within the intestine through retention of intraepithelial lymphocytes, functional redistribution of Th17/Treg balance. Consequently, environmental/genetic manipulation of AHR activity likely influences host-microbe homeostasis. Utilizing C57BL6/J Ahr−/+ and Ahr−/− co-housed littermates followed by 18 days of genotypic segregation, we examined the influence of AHR expression upon intestinal microbe composition/functionality and host physiology. 16S sequencing/quantitative PCR (qPCR) revealed significant changes in phyla abundance, particularly Verrucomicrobia together with segmented filamentous bacteria, and an increase in species diversity in Ahr−/− mice following genotypic segregation. Metagenomics/metabolomics indicate microbial composition is associated with functional shifts in bacterial metabolism. Analysis identified Ahr−/−-dependent increases in ileal gene expression, indicating increased inflammatory tone. Transfer of Ahr−/− microbiota to wild-type germ-free mice recapitulated the increase Verrucomicrobia and inflammatory tone, indicating Ahr−/−-microbial dependence. These data suggest a role for the AHR in influencing the community structure of the intestinal microbiota. PMID:27659481

  1. Quantifying the metabolic activities of human-associated microbial communities across multiple ecological scales

    PubMed Central

    Maurice, Corinne Ferrier; Turnbaugh, Peter James

    2013-01-01

    Humans are home to complex microbial communities, whose aggregate genomes and their encoded metabolic activities are referred to as the human microbiome. Recently, researchers have begun to appreciate that different human body habitats and the activities of their resident microorganisms can be better understood in ecological terms, as a range of spatial scales encompassing single cells, guilds of microorganisms responsive to a similar substrate, microbial communities, body habitats, and host populations. However, the bulk of the work to date has focused on studies of culturable microorganisms in isolation or on DNA sequencing-based surveys of microbial diversity in small to moderately sized cohorts of individuals. Here, we discuss recent work that highlights the potential for assessing the human microbiome at a range of spatial scales, and for developing novel techniques that bridge multiple levels: for example, through the combination of single cell methods and metagenomic sequencing. These studies promise to not only provide a much-needed epidemiological and ecological context for mechanistic studies of culturable and genetically tractable microorganisms, but may also lead to the discovery of fundamental rules that govern the assembly and function of host-associated microbial communities. PMID:23550823

  2. Linking geochemistry to microbial ecology in hot springs: examples from southeastern Asia (Invited)

    NASA Astrophysics Data System (ADS)

    Dong, H.; Jiang, H.; Hou, W.; Wang, S.; Huang, Q.; Briggs, B. R.; Huang, L.; Hust, W.; Hedlund, B. P.; Zhang, C.; Hartnett, H. E.; Dijkstra, P.; Hungate, B. A.

    2013-12-01

    Despite recent advances in our understanding of microbial ecology in high temperature environments, important questions remain as to how geochemical conditions shape microbial ecology in hot springs. In the past three years, we have surveyed a large number of hot springs in three regions of southeastern Asia: Tengchong of Yunnan Province, China; Tibet in China; and the Philippines. These springs possess large gradients in pH (2.5-9.4), temperature (22.1-93.6oC), and water and sediment geochemistry. Within each region, these geochemical conditions are important in shaping microbial community structure and diversity. For example, in the Rehai geothermal field of Tengchong, dominant taxa within the dominant bacterial phylum Aquificae and archaeal phylum Crenarchaeota depended on pH (2.5-9.4), temperature (55.1-93.6), Na-Cl-HCO3 water type and silicate rock lithology. In the Ruidian geothermal region, springs with circum-neutral pH (6.71-7.29), moderate temperature (50-82oC), Na-HCO3 water type, and carbonate-dominated lithology, Hydrogenobacter of Aquificae dominated spring water, but the microbial community in sediments was diverse with abundant novel groups. In Tibet springs with low-moderate temperature (22-75oC) and circum-neutral pH (7.2-8.1), temperature appeared to be the most important factor in determining diversity and community structure. In acidic hot springs of the Philippines (Temperature: 60-92°C, pH 3.72-6.58), microbial communities were predominated by those related to sulfur metabolism, which are different from those in acidic springs of Tengchong. When these three regions are considered together, environmental conditions play a major role in controlling microbial community structure, but geographical location appears to be an important factor as well.

  3. Coupled Spatiotemporal Dynamics of Microbial Community Ecology, Biogeochemistry, and Hydrologic Mixing

    NASA Astrophysics Data System (ADS)

    Stegen, J.; Johnson, T. C.; Fredrickson, J.; Wilkins, M.; Konopka, A.; Nelson, W.; Arntzen, E.; Chrisler, W.; Chu, R. K.; Fansler, S.; Kennedy, D.; Resch, T.; Tfaily, M. M.

    2015-12-01

    The hyporheic zone (HZ) is a critical ecosystem component that links terrestrial, surface water, and groundwater ecosystems. A dominant feature of the HZ is groundwater-surface water mixing and the input of terrestrially—as well as aquatically—derived organic carbon. In many systems the HZ has a relatively small spatial extent, but in larger riverine systems groundwater-surface water mixing can occur 100s of meters beyond the surface water shoreline; we consider these more distal locations to be within the 'subsurface interaction zone' (SIZ) as they are beyond the traditional HZ. Microbial communities in the HZ and SIZ drive biogeochemical processes in these system components, yet relatively little is known about the ecological processes that drive HZ and SIZ microbial communities. Here, we applied ecological theory, aqueous biogeochemistry, DNA sequencing, and ultra-high resolution organic carbon profiling to field samples collected through space (400m spatial extent) and time (7 month temporal extent) within the Hanford Site 300 Area. These data streams were integrated to evaluate how the influence of groundwater-surface water mixing on microbial communities changes when moving from the HZ to the broader SIZ. Our results indicate that groundwater-surface water mixing (i) consistently stimulated heterotrophic respiration, but only above a threshold of surface water intrusion, (ii) did not stimulate denitrification, (iii) caused deterministic shifts in HZ microbial communities due to changes in organic carbon composition, and (iv) did not cause shifts in SIZ microbial communities. These results suggest that microbial communities and the biogeochemical processes they drive are impacted by groundwater-surface water mixing primarily in the HZ and to a lesser extent in the SIZ.

  4. Selecting indicators of soil, microbial, and plant conditions to understand ecological changes in Georgia pine forests

    SciTech Connect

    Dale, Virginia H; Garten Jr, Charles T; Wolfe, Amy K; Sobek, Edward A

    2008-11-01

    Characterizing how resource use and management activities affect ecological conditions is necessary to document and understand anthropogenic changes in ecological systems. Resource managers on military installations have the delicate task of balancing the training needs of soldiers effectively with the need to maintain a high quality of ecological conditions. This study considers ways that ecological indicators can provide information on impacts that training has on environmental characteristics that occur at different scales and in different sectors of the environment. The characteristics examined include soil chemistry, soil microbes, and vegetation. A discriminant function analysis was conducted to determine whether ecological indicators could differentiate among different levels of military use. A combination of 10 indicators explained 90% of the variation among plots from five different military use levels. Results indicated that an appropriate suite of ecological indicators for military resource managers includes soil, microbial, and vegetation characteristics. Since many of these indicators are related, managers at this location potentially have freedom to choose indicators that are relatively easy to measure, without sacrificing information.

  5. Microorganisms with a Taste for Vanilla: Microbial Ecology of Traditional Indonesian Vanilla Curing

    PubMed Central

    Röling, Wilfred F. M.; Kerler, Josef; Braster, Martin; Apriyantono, Anton; Stam, Hein; van Verseveld, Henk W.

    2001-01-01

    The microbial ecology of traditional postharvesting processing of vanilla beans (curing) was examined using a polyphasic approach consisting of conventional cultivation, substrate utilization-based and molecular identification of isolates, and cultivation-independent community profiling by 16S ribosomal DNA based PCR-denaturing gradient gel electrophoresis. At two different locations, a batch of curing beans was monitored. In both batches a major shift in microbial communities occurred after short-term scalding of the beans in hot water. Fungi and yeast disappeared, although regrowth of fungi occurred in one batch during a period in which process conditions were temporarily not optimal. Conventional plating showed that microbial communities consisting of thermophilic and thermotolerant bacilli (mainly closely related to Bacillus subtilis, B. licheniformis,, and B. smithii) developed under the high temperatures (up to 65°C) that were maintained for over a week after scalding. Only small changes in the communities of culturable bacteria occurred after this period. Molecular analysis revealed that a proportion of the microbial communities could not be cultured on conventional agar medium, especially during the high-temperature period. Large differences between both batches were observed in the numbers of microorganisms, in species composition, and in the enzymatic abilities of isolated bacteria. These large differences indicate that the effects of microbial activities on the development of vanilla flavor could be different for each batch of cured vanilla beans. PMID:11319073

  6. Contemporary molecular tools in microbial ecology and their application to advancing biotechnology.

    PubMed

    Rashid, Mamoon; Stingl, Ulrich

    2015-12-01

    Novel methods in microbial ecology are revolutionizing our understanding of the structure and function of microbes in the environment, but concomitant advances in applications of these tools to biotechnology are mostly lagging behind. After more than a century of efforts to improve microbial culturing techniques, about 70-80% of microbial diversity - recently called the "microbial dark matter" - remains uncultured. In early attempts to identify and sample these so far uncultured taxonomic lineages, methods that amplify and sequence ribosomal RNA genes were extensively used. Recent developments in cell separation techniques, DNA amplification, and high-throughput DNA sequencing platforms have now made the discovery of genes/genomes of uncultured microorganisms from different environments possible through the use of metagenomic techniques and single-cell genomics. When used synergistically, these metagenomic and single-cell techniques create a powerful tool to study microbial diversity. These genomics techniques have already been successfully exploited to identify sources for i) novel enzymes or natural products for biotechnology applications, ii) novel genes from extremophiles, and iii) whole genomes or operons from uncultured microbes. More can be done to utilize these tools more efficiently in biotechnology.

  7. Microbial ecology and host-microbiota interactions during early life stages.

    PubMed

    Collado, Maria Carmen; Cernada, Maria; Baüerl, Christine; Vento, Máximo; Pérez-Martínez, Gaspar

    2012-01-01

    The role of human microbiota has been redefined during recent years and its physiological role is now much more important than earlier understood. Intestinal microbial colonization is essential for the maturation of immune system and for the developmental regulation of the intestinal physiology. Alterations in this process of colonization have been shown to predispose and increase the risk to disease later in life. The first contact of neonates with microbes is provided by the maternal microbiota. Moreover, mode of delivery, type of infant feeding and other perinatal factors can influence the establishment of the infant microbiota. Taken into consideration all the available information it could be concluded that the exposure to the adequate microbes early in gestation and neonatal period seems to have a relevant role in health. Maternal microbial environment affects maternal and fetal immune physiology and, of relevance, this interaction with microbes at the fetal-maternal interface could be modulated by specific microbes administered to the pregnant mother. Indeed, probiotic interventions aiming to reduce the risk of immune-mediated diseases may appear effective during early life.

  8. Microbial ecology and host-microbiota interactions during early life stages

    PubMed Central

    Collado, Maria Carmen; Cernada, Maria; Baüerl, Christine; Vento, Máximo; Pérez-Martínez, Gaspar

    2012-01-01

    The role of human microbiota has been redefined during recent years and its physiological role is now much more important than earlier understood. Intestinal microbial colonization is essential for the maturation of immune system and for the developmental regulation of the intestinal physiology. Alterations in this process of colonization have been shown to predispose and increase the risk to disease later in life. The first contact of neonates with microbes is provided by the maternal microbiota. Moreover, mode of delivery, type of infant feeding and other perinatal factors can influence the establishment of the infant microbiota. Taken into consideration all the available information it could be concluded that the exposure to the adequate microbes early in gestation and neonatal period seems to have a relevant role in health. Maternal microbial environment affects maternal and fetal immune physiology and, of relevance, this interaction with microbes at the fetal-maternal interface could be modulated by specific microbes administered to the pregnant mother. Indeed, probiotic interventions aiming to reduce the risk of immune-mediated diseases may appear effective during early life. PMID:22743759

  9. Planetary Biology and Microbial Ecology: Molecular Ecology and the Global Nitrogen cycle

    NASA Technical Reports Server (NTRS)

    Nealson, Molly Stone (Editor); Nealson, Kenneth H. (Editor)

    1993-01-01

    This report summarizes the results of the Planetary Biology and Molecular Ecology's summer 1991 program, which was held at the Marine Biological Laboratory in Woods Hole, Massachusetts. The purpose of the interdisciplinary PBME program is to integrate, via lectures and laboratory work, the contributions of university and NASA scientists and student interns. The goals of the 1991 program were to examine several aspects of the biogeochemistry of the nitrogen cycle and to teach the application of modern methods of molecular genetics to field studies of organisms. Descriptions of the laboratory projects and protocols and abstracts and references of the lectures are presented.

  10. Ecological distribution and population physiology defined by proteomics in a natural microbial community

    SciTech Connect

    Muller, R; Denef, Vincent; Kalnejals, Linda; Suttle, K Blake; Thomas, Brian; Wilmes, P; Smith, Richard L.; Nordstrom, D Kirk; McCleskey, R Blaine; Shah, Manesh B; Verberkmoes, Nathan C; Hettich, Robert {Bob} L; Banfield, Jillian F.

    2010-01-01

    An important challenge in microbial ecology is developing methods that simultaneously examine the physiology of organisms at the molecular level and their ecosystem level interactions in complex natural systems.We integrated extensive proteomic, geochemical, and biological information from 28 microbial communities collected from an acid mine drainage environment and representing a range of biofilm development stages and geochemical conditions to evaluate how the physiologies of the dominant and less abundant organisms change along environmental gradients. The initial colonist dominates across all environments, but its proteome changes between two stable states as communities diversify, implying that interspecies interactions affect this organism s metabolism. Its overall physiology is robust to abiotic environmental factors, but strong correlations exist between these factors and certain subsets of proteins, possibly accounting for its wide environmental distribution. Lower abundance populations are patchier in their distribution, and proteomic data indicate that their environmental niches may be constrained by specific sets of abiotic environmental factors. This research establishes an effective strategy to investigate ecological relationships between microbial physiology and the environment for whole communities in situ

  11. Ecological distribution and population physiology defined by proteomics in a natural microbial community

    USGS Publications Warehouse

    Mueller, Ryan S.; Denef, Vincent J.; Kalnejais, Linda H.; Suttle, K. Blake; Thomas, Brian C.; Wilmes, Paul; Smith, Richard L.; Nordstrom, D Kirk; McCleskey, R. Blaine; Shah, Menesh B.; VerBekmoes, Nathan C.; Hettich, Robert L.; Banfield, Jillian F.

    2010-01-01

    An important challenge in microbial ecology is developing methods that simultaneously examine the physiology of organisms at the molecular level and their ecosystem level interactions in complex natural systems. We integrated extensive proteomic, geochemical, and biological information from 28 microbial communities collected from an acid mine drainage environment and representing a range of biofilm development stages and geochemical conditions to evaluate how the physiologies of the dominant and less abundant organisms change along environmental gradients. The initial colonist dominates across all environments, but its proteome changes between two stable states as communities diversify, implying that interspecies interactions affect this organism's metabolism. Its overall physiology is robust to abiotic environmental factors, but strong correlations exist between these factors and certain subsets of proteins, possibly accounting for its wide environmental distribution. Lower abundance populations are patchier in their distribution, and proteomic data indicate that their environmental niches may be constrained by specific sets of abiotic environmental factors. This research establishes an effective strategy to investigate ecological relationships between microbial physiology and the environment for whole communities in situ.

  12. Microbial Eukaryotes in the Human Microbiome: Ecology, Evolution, and Future Directions

    PubMed Central

    Parfrey, Laura Wegener; Walters, William A.; Knight, Rob

    2011-01-01

    High throughput sequencing technology has opened a window into the vast communities of bacteria that live on and in humans, demonstrating tremendous variability, and that they play a large role in health and disease. The eukaryotic component of the human gut microbiome remains relatively unexplored with these methods, but turning these tools toward microbial eukaryotes in the gut will likely yield myriad insights into disease as well as the ecological and evolutionary principles that govern the gut microbiota. Microbial eukaryotes are common inhabitants of the human gut worldwide and parasitic taxa are a major source of morbidity and mortality, especially in developing countries, though there are also taxa that cause no harm or are beneficial. While the role microbial eukaryotes play in healthy individuals is much less clear, there are likely many complex interactions between the bacterial, archaeal, and eukaryotic microbiota that influence human health. Integrating eukaryotic microbes into a broad view of microbiome function requires an integrated ecological approach rather than one focused on specific, disease-causing taxa. Moving forward, we expect broad surveys of the eukaryotic microbiota and associated bacteria from geographically and socioeconomically diverse populations to paint a more complete picture of the human gut microbiome in health and disease. PMID:21808637

  13. The Effect of Diet and Exercise on Intestinal Integrity and Microbial Diversity in Mice

    PubMed Central

    Wisniewski, Paul J.; Noji, Michael; McGuinness, Lora R.; Lightfoot, Stanley A.

    2016-01-01

    Background The gut microbiota is now known to play an important role contributing to inflammatory-based chronic diseases. This study examined intestinal integrity/inflammation and the gut microbial communities in sedentary and exercising mice presented with a normal or high-fat diet. Methods Thirty-six, 6-week old C57BL/6NTac male mice were fed a normal or high-fat diet for 12-weeks and randomly assigned to exercise or sedentary groups. After 12 weeks animals were sacrificed and duodenum/ileum tissues were fixed for immunohistochemistry for occludin, E-cadherin, and cyclooxygenase-2 (COX-2). The bacterial communities were assayed in fecal samples using terminal restriction fragment length polymorphism (TRFLP) analysis and pyrosequencing of 16S rRNA gene amplicons. Results Lean sedentary (LS) mice presented normal histologic villi while obese sedentary (OS) mice had similar villi height with more than twice the width of the LS animals. Both lean (LX) and obese exercise (OX) mice duodenum and ileum were histologically normal. COX-2 expression was the greatest in the OS group, followed by LS, LX and OX. The TRFLP and pyrosequencing indicated that members of the Clostridiales order were predominant in all diet groups. Specific phylotypes were observed with exercise, including Faecalibacterium prausnitzi, Clostridium spp., and Allobaculum spp. Conclusion These data suggest that exercise has a strong influence on gut integrity and host microbiome which points to the necessity for more mechanistic studies of the interactions between specific bacteria in the gut and its host. PMID:26954359

  14. Ecological differentiation in planktonic and sediment-associated chemotrophic microbial populations in Yellowstone hot springs.

    PubMed

    Colman, Daniel R; Feyhl-Buska, Jayme; Robinson, Kirtland J; Fecteau, Kristopher M; Xu, Huifang; Shock, Everett L; Boyd, Eric S

    2016-09-01

    Chemosynthetic sediment and planktonic community composition and sizes, aqueous geochemistry and sediment mineralogy were determined in 15 non-photosynthetic hot springs in Yellowstone National Park (YNP). These data were used to evaluate the hypothesis that differences in the availability of dissolved or mineral substrates in the bulk fluids or sediments within springs coincides with ecologically differentiated microbial communities and their populations. Planktonic and sediment-associated communities exhibited differing ecological characteristics including community sizes, evenness and richness. pH and temperature influenced microbial community composition among springs, but within-spring partitioning of taxa into sediment or planktonic communities was widespread, statistically supported (P < 0.05) and could be best explained by the inferred metabolic strategies of the partitioned taxa. Microaerophilic genera of the Aquificales predominated in many of the planktonic communities. In contrast, taxa capable of mineral-based metabolism such as S(o) oxidation/reduction or Fe-oxide reduction predominated in sediment communities. These results indicate that ecological differentiation within thermal spring habitats is common across a range of spring geochemistry and is influenced by the availability of dissolved nutrients and minerals that can be used in metabolism.

  15. Ecological differentiation in planktonic and sediment-associated chemotrophic microbial populations in Yellowstone hot springs.

    PubMed

    Colman, Daniel R; Feyhl-Buska, Jayme; Robinson, Kirtland J; Fecteau, Kristopher M; Xu, Huifang; Shock, Everett L; Boyd, Eric S

    2016-09-01

    Chemosynthetic sediment and planktonic community composition and sizes, aqueous geochemistry and sediment mineralogy were determined in 15 non-photosynthetic hot springs in Yellowstone National Park (YNP). These data were used to evaluate the hypothesis that differences in the availability of dissolved or mineral substrates in the bulk fluids or sediments within springs coincides with ecologically differentiated microbial communities and their populations. Planktonic and sediment-associated communities exhibited differing ecological characteristics including community sizes, evenness and richness. pH and temperature influenced microbial community composition among springs, but within-spring partitioning of taxa into sediment or planktonic communities was widespread, statistically supported (P < 0.05) and could be best explained by the inferred metabolic strategies of the partitioned taxa. Microaerophilic genera of the Aquificales predominated in many of the planktonic communities. In contrast, taxa capable of mineral-based metabolism such as S(o) oxidation/reduction or Fe-oxide reduction predominated in sediment communities. These results indicate that ecological differentiation within thermal spring habitats is common across a range of spring geochemistry and is influenced by the availability of dissolved nutrients and minerals that can be used in metabolism. PMID:27306555

  16. The Influence of Ecological Isolation on the Structural and Functional Stability of Complex Microbial Communities

    NASA Technical Reports Server (NTRS)

    Franklin, R. B.; Garland, J. L.; Mills, A. L.

    2005-01-01

    To help understand how the behavior of microorganisms and microbial communities in insular space habitats may differ from the behavior of these groups on Earth, long-term incubations (100+ days) were conducting using wastewater bioreactors (batch fed) designed to mimic "closed" and "open" ecological systems. The issue of immigration was considered, and the goal of the research was to determine whether the stability of microbial communities in space is reduced due to their prolonged isolation. Bioreactors were established by inoculating flasks of sterile synthetic wastewater with the microbial community obtained from a local treatment facility; each day, one-third of the medium in the flask was replaced with an equal volume of sterile artificial wastewater. Flasks were divided into two treatments: "closed" and "open" to recruitment of additional microorganisms. "Closed" flasks were maintained as described above, while the medium used to feed the "open" flasks was supplemented daily with a small amount of raw sewage (which provided a continuous source of new potential community members). Significant differences in microbial community structure and function developed in the two sets of communities, and the results suggest that the open community was more stable and better able to adjust to changing environmental conditions. Each community's resistance to environmental (temperature fluctuations) and biological stresses (starvation and invasion by an opportunistic pathogen Pseudomonas aeruginosa) was monitored. Experiments were also conducted to determine whether the effect of isolation changes depending on the microbial communities' initial diversity or composition; communities with a low(er) initial diversity were less stable. Overall, the results indicate that isolation will be an important factor influencing the activity of microbial communities on board spacecraft. A possible way of mitigating these effects would be to include communities with high initial

  17. Using Intact Iron Microbial Mats to Gain Insights Into Mat Ecology and Geochemical Niche at the Microbial Scale

    NASA Astrophysics Data System (ADS)

    Glazer, B. T.; Chan, C. S. Y.; Mcallister, S.; Leavitt, A.; Emerson, D.

    2015-12-01

    Microbial mats are formed by microorganisms working in coordinated symbiosis, often benefitting the community by controlling the local geochemical or physical environment. Thus, the ecology of the mat depends on the individual roles of microbes organized into niches within a larger architecture. Chemolithotrophic Fe-oxidizing bacteria (FeOB) form distinctive Fe oxyhydroxide biominerals which constitute the building blocks of the mat. However, the majority of our progress has been in understanding the overall community structure. Understanding the physical mat structure on the microbial scale is important to unraveling FeOB evolution, the biogeochemistry and ecology of Fe-rich habitats, and ultimately interpreting FeOB biosignatures in the rock record. Mats in freshwater and marine environments contain strikingly similar biomineral morphologies, yet they are formed by phylogenetically distinct microorganisms. This suggests that the overall architecture and underlying genetics of freshwater and marine mats has evolved to serve particular roles specific to Fe oxidation. Thus, we conducted a comparative study of Fe seep freshwater mats and marine hydrothermal mats. We have developed a new approach to sampling Fe mats in order to preserve the delicate structure for analysis by confocal and scanning electron microscopy. Our analyses of these intact mats show that freshwater and marine mats are similarly initiated by a single type of structure-former. These ecosystem engineers form either a hollow sheath or a twisted stalk biomineral during mat formation, with a highly directional structure. These microbes appear to be the vanguard organisms that anchor the community within oxygen/Fe(II) gradients, further allowing for community succession in the mat interior as evidenced by other mineralized morphologies. Patterns in biomineral thickness and directionality were indicative of redox gradients and temporal changes in the geochemical environment. These observations show that

  18. PhyloChip™ microarray comparison of sampling methods used for coral microbial ecology

    USGS Publications Warehouse

    Kellogg, Christina A.; Piceno, Yvette M.; Tom, Lauren M.; DeSantis, Todd Z.; Zawada, David G.; Andersen, Gary L.

    2012-01-01

    Interest in coral microbial ecology has been increasing steadily over the last decade, yet standardized methods of sample collection still have not been defined. Two methods were compared for their ability to sample coral-associated microbial communities: tissue punches and foam swabs, the latter being less invasive and preferred by reef managers. Four colonies of star coral, Montastraea annularis, were sampled in the Dry Tortugas National Park (two healthy and two with white plague disease). The PhyloChip™ G3 microarray was used to assess microbial community structure of amplified 16S rRNA gene sequences. Samples clustered based on methodology rather than coral colony. Punch samples from healthy and diseased corals were distinct. All swab samples clustered closely together with the seawater control and did not group according to the health state of the corals. Although more microbial taxa were detected by the swab method, there is a much larger overlap between the water control and swab samples than punch samples, suggesting some of the additional diversity is due to contamination from water absorbed by the swab. While swabs are useful for noninvasive studies of the coral surface mucus layer, these results show that they are not optimal for studies of coral disease.

  19. Formation of higher plant component microbial community in closed ecological system

    NASA Astrophysics Data System (ADS)

    Tirranen, L. S.

    2001-07-01

    Closed ecological systems (CES) place at the disposal of a researcher unique possibilities to study the role of microbial communities in individual components and of the entire system. The microbial community of the higher plant component has been found to form depending on specific conditions of the closed ecosystem: length of time the solution is reused, introduction of intrasystem waste water into the nutrient medium, effect of other component of the system, and system closure in terms of gas exchange. The higher plant component formed its own microbial complex different from that formed prior to closure. The microbial complex of vegetable polyculture is more diverse and stable than the monoculture of wheat. The composition of the components' microflora changed, species diversity decreased, individual species of bacteria and fungi whose numbers were not so great before the closure prevailed. Special attention should be paid to phytopathogenic and conditionally pathogenic species of microorganisms potentially hazardous to man or plants and the least controlled in CES. This situation can endanger creation of CES and make conjectural existence of preplanned components, man, specifically, and consequently, of CES as it is.

  20. Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system

    PubMed Central

    Speth, Daan R.; in 't Zandt, Michiel H.; Guerrero-Cruz, Simon; Dutilh, Bas E.; Jetten, Mike S. M.

    2016-01-01

    Partial-nitritation anammox (PNA) is a novel wastewater treatment procedure for energy-efficient ammonium removal. Here we use genome-resolved metagenomics to build a genome-based ecological model of the microbial community in a full-scale PNA reactor. Sludge from the bioreactor examined here is used to seed reactors in wastewater treatment plants around the world; however, the role of most of its microbial community in ammonium removal remains unknown. Our analysis yielded 23 near-complete draft genomes that together represent the majority of the microbial community. We assign these genomes to distinct anaerobic and aerobic microbial communities. In the aerobic community, nitrifying organisms and heterotrophs predominate. In the anaerobic community, widespread potential for partial denitrification suggests a nitrite loop increases treatment efficiency. Of our genomes, 19 have no previously cultivated or sequenced close relatives and six belong to bacterial phyla without any cultivated members, including the most complete Omnitrophica (formerly OP3) genome to date. PMID:27029554

  1. Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system.

    PubMed

    Speth, Daan R; In 't Zandt, Michiel H; Guerrero-Cruz, Simon; Dutilh, Bas E; Jetten, Mike S M

    2016-01-01

    Partial-nitritation anammox (PNA) is a novel wastewater treatment procedure for energy-efficient ammonium removal. Here we use genome-resolved metagenomics to build a genome-based ecological model of the microbial community in a full-scale PNA reactor. Sludge from the bioreactor examined here is used to seed reactors in wastewater treatment plants around the world; however, the role of most of its microbial community in ammonium removal remains unknown. Our analysis yielded 23 near-complete draft genomes that together represent the majority of the microbial community. We assign these genomes to distinct anaerobic and aerobic microbial communities. In the aerobic community, nitrifying organisms and heterotrophs predominate. In the anaerobic community, widespread potential for partial denitrification suggests a nitrite loop increases treatment efficiency. Of our genomes, 19 have no previously cultivated or sequenced close relatives and six belong to bacterial phyla without any cultivated members, including the most complete Omnitrophica (formerly OP3) genome to date. PMID:27029554

  2. Molecular Ecology of Hypersaline Microbial Mats: Current Insights and New Directions

    PubMed Central

    Wong, Hon Lun; Ahmed-Cox, Aria; Burns, Brendan Paul

    2016-01-01

    Microbial mats are unique geobiological ecosystems that form as a result of complex communities of microorganisms interacting with each other and their physical environment. Both the microorganisms present and the network of metabolic interactions govern ecosystem function therein. These systems are often found in a range of extreme environments, and those found in elevated salinity have been particularly well studied. The purpose of this review is to briefly describe the molecular ecology of select model hypersaline mat systems (Guerrero Negro, Shark Bay, S’Avall, and Kiritimati Atoll), and any potentially modulating effects caused by salinity to community structure. In addition, we discuss several emerging issues in the field (linking function to newly discovered phyla and microbial dark matter), which illustrate the changing paradigm that is seen as technology has rapidly advanced in the study of these extreme and evolutionally significant ecosystems. PMID:27681900

  3. Molecular Ecology of Hypersaline Microbial Mats: Current Insights and New Directions

    PubMed Central

    Wong, Hon Lun; Ahmed-Cox, Aria; Burns, Brendan Paul

    2016-01-01

    Microbial mats are unique geobiological ecosystems that form as a result of complex communities of microorganisms interacting with each other and their physical environment. Both the microorganisms present and the network of metabolic interactions govern ecosystem function therein. These systems are often found in a range of extreme environments, and those found in elevated salinity have been particularly well studied. The purpose of this review is to briefly describe the molecular ecology of select model hypersaline mat systems (Guerrero Negro, Shark Bay, S’Avall, and Kiritimati Atoll), and any potentially modulating effects caused by salinity to community structure. In addition, we discuss several emerging issues in the field (linking function to newly discovered phyla and microbial dark matter), which illustrate the changing paradigm that is seen as technology has rapidly advanced in the study of these extreme and evolutionally significant ecosystems.

  4. Molecular Ecology of Hypersaline Microbial Mats: Current Insights and New Directions.

    PubMed

    Wong, Hon Lun; Ahmed-Cox, Aria; Burns, Brendan Paul

    2016-01-01

    Microbial mats are unique geobiological ecosystems that form as a result of complex communities of microorganisms interacting with each other and their physical environment. Both the microorganisms present and the network of metabolic interactions govern ecosystem function therein. These systems are often found in a range of extreme environments, and those found in elevated salinity have been particularly well studied. The purpose of this review is to briefly describe the molecular ecology of select model hypersaline mat systems (Guerrero Negro, Shark Bay, S'Avall, and Kiritimati Atoll), and any potentially modulating effects caused by salinity to community structure. In addition, we discuss several emerging issues in the field (linking function to newly discovered phyla and microbial dark matter), which illustrate the changing paradigm that is seen as technology has rapidly advanced in the study of these extreme and evolutionally significant ecosystems. PMID:27681900

  5. Microbial ecology-based methods to characterize the bacterial communities of non-model insects.

    PubMed

    Prosdocimi, Erica M; Mapelli, Francesca; Gonella, Elena; Borin, Sara; Crotti, Elena

    2015-12-01

    Among the animals of the Kingdom Animalia, insects are unparalleled for their widespread diffusion, diversity and number of occupied ecological niches. In recent years they have raised researcher interest not only because of their importance as human and agricultural pests, disease vectors and as useful breeding species (e.g. honeybee and silkworm), but also because of their suitability as animal models. It is now fully recognized that microorganisms form symbiotic relationships with insects, influencing their survival, fitness, development, mating habits and the immune system and other aspects of the biology and ecology of the insect host. Thus, any research aimed at deepening the knowledge of any given insect species (perhaps species of applied interest or species emerging as novel pests or vectors) must consider the characterization of the associated microbiome. The present review critically examines the microbiology and molecular ecology techniques that can be applied to the taxonomical and functional analysis of the microbiome of non-model insects. Our goal is to provide an overview of current approaches and methods addressing the ecology and functions of microorganisms and microbiomes associated with insects. Our focus is on operational details, aiming to provide a concise guide to currently available advanced techniques, in an effort to extend insect microbiome research beyond simple descriptions of microbial communities.

  6. Microbial ecology-based methods to characterize the bacterial communities of non-model insects.

    PubMed

    Prosdocimi, Erica M; Mapelli, Francesca; Gonella, Elena; Borin, Sara; Crotti, Elena

    2015-12-01

    Among the animals of the Kingdom Animalia, insects are unparalleled for their widespread diffusion, diversity and number of occupied ecological niches. In recent years they have raised researcher interest not only because of their importance as human and agricultural pests, disease vectors and as useful breeding species (e.g. honeybee and silkworm), but also because of their suitability as animal models. It is now fully recognized that microorganisms form symbiotic relationships with insects, influencing their survival, fitness, development, mating habits and the immune system and other aspects of the biology and ecology of the insect host. Thus, any research aimed at deepening the knowledge of any given insect species (perhaps species of applied interest or species emerging as novel pests or vectors) must consider the characterization of the associated microbiome. The present review critically examines the microbiology and molecular ecology techniques that can be applied to the taxonomical and functional analysis of the microbiome of non-model insects. Our goal is to provide an overview of current approaches and methods addressing the ecology and functions of microorganisms and microbiomes associated with insects. Our focus is on operational details, aiming to provide a concise guide to currently available advanced techniques, in an effort to extend insect microbiome research beyond simple descriptions of microbial communities. PMID:26476138

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  8. Fc Gamma Receptor Signaling in Mast Cells Links Microbial Stimulation to Mucosal Immune Inflammation in the Intestine

    PubMed Central

    Chen, Xiao; Feng, Bai-Sui; Zheng, Peng-Yuan; Liao, Xue-Qing; Chong, Jasmine; Tang, Shang-Guo; Yang, Ping-Chang

    2008-01-01

    Microbes and microbial products are closely associated with the pathogenesis of inflammatory bowel disease (IBD); however, the mechanisms behind this connection remain unclear. It has been previously reported that flagellin-specific antibodies are increased in IBD patient sera. As mastocytosis is one of the pathological features of IBD, we hypothesized that flagellin-specific immune responses might activate mast cells that then contribute to the initiation and maintenance of intestinal inflammation. Thirty-two colonic biopsy samples were collected from IBD patients. A flagellin/flagellin-specific IgG/Fc gamma receptor I complex was identified on biopsied mast cells using both immunohistochemistry and co-immunoprecipitation experiments; this complex was shown to co-localize on the surfaces of mast cells in the colonic mucosa of patients with IBD. In addition, an ex vivo study showed flagellin-IgG was able to bind to human mast cells. These cells were found to be sensitized to flagellin-specific IgG; re-exposure to flagellin induced the mast cells to release inflammatory mediators. An animal model of IBD was then used to examine flagellin-specific immune responses in the intestine. Mice could be sensitized to flagellin, and repeated challenges with flagellin induced an IBD-like T helper 1 pattern of intestinal inflammation that could be inhibited by pretreatment with anti-Fc gamma receptor I antibodies. Therefore, flagellin-specific immune responses activate mast cells in the intestine and play important roles in the pathogenesis of intestinal immune inflammation. PMID:18974296

  9. Microbial mechanisms of using enhanced ecological floating beds for eutrophic water improvement.

    PubMed

    Wu, Qing; Hu, Yue; Li, Shuqun; Peng, Sen; Zhao, Huabing

    2016-07-01

    Enhanced ecological floating beds were implemented to reduce nutrient quantity and improve the water quality of a eutrophic lake. The results showed that average removal efficiencies of CODCr, total nitrogen, NH3-N and total phosphorus for Canna indica L. set-up were 23.1%, 15.3%, 18.1% and 19.4% higher, respectively, than that of the setup with only substrate, and 14.2%, 12.8%, 7.9% and 11.9% higher than Iris pseudacorus L. ecological floating bed. The microbial community structure had obvious differences between devices and low similarity; bacteria were mainly attached on the fiber filling. The microbial population was abundant at the start and end of the experiment. Shannon index of samples selected ranged from 0.85 to 1.05. The sequencing results showed that fiber filling collected most uncultured bacteria species and the majority of bacteria on the plant roots were β-Proteobacteria and α-Proteobacteria. The co-dominant species attaching to the filling and plant was Nitrosomonadaceae.

  10. CO2 gradient affects on deep subsurface microbial ecology during carbon sequestration

    NASA Astrophysics Data System (ADS)

    Gulliver, D.; Gregory, K.

    2011-12-01

    Geological carbon sequestration is likely to be part of a comprehensive strategy to minimize the release of greenhouse gasses into the atmosphere. Reservoir storage capacities and long-term security of these deposits will be dependent on the trapping mechanisms and mineral transformation in the deep subsurface. Therefore, a critical need exists to understand the evolution of microbial populations that may influence the biogeochemistry in the reservoirs. As the CO2 front moves through the storage aquifer, microbial communities may preside in residual brine left behind in cracks, dead flow zones, and upstream to the front; this brine will have a gradient of dissolved CO2 in which microbial interaction may behave differently, depending on the distance from the CO2 front. The evolution of microbial ecology along this CO2 gradient was investigated using fluid-slurry samples obtained from the prospective carbon sequestration site, the Arbuckle saline aquifer at the Wellington oil field, KS. The native species of these samples were investigated with a series of batch reactors under constant temperature of 40 °C, constant total pressure of 2,000 psi, and varying CO2 partial pressures of 0 psi, 20 psi, 200 psi, and 2,000 psi. After 1 day, 7 days, and 56 days of exposure in the batch reactors, fluid samples were centrifuged and the resulting pellet was biologically analyzed. Clone libraries and quantitative PCR determined that the bacterial diversity and population of the native microbial community was dependant on both the duration of exposure and the CO2 partial pressure. For example, the microbial community of 0 psi CO2 and 20 psi CO2 was predominantly related to the families halomonadaceae and marinilabiaceae while at 2,000 psi CO2 the community was predominantly in the family psychromonadaceae. The population size at 2,000 psi CO2 was also found to decrease by 3 orders of magnitude after only 7 days of CO2 exposure. Although these experiments were relatively short

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

    PubMed Central

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

    2016-01-01

    Many microbial ecology experiments use sequencing data to measure a community’s response to an experimental treatment. In a common experimental design, two units, one control and one experimental, are sampled before and after the treatment is applied to the experimental unit. The four resulting samples contain information about the dynamics of organisms that respond to the treatment, but there are no analytical methods designed to extract exactly this type of information from this configuration of samples. Here we present an analytical method specifically designed to visualize and generate hypotheses about microbial community dynamics in experiments that have paired samples and few or no replicates. The method is based on the Poisson lognormal distribution, long studied in macroecology, which we found accurately models the abundance distribution of taxa counts from 16S rRNA surveys. To demonstrate the method’s validity and potential, we analyzed an experiment that measured the effect of crude oil on ocean microbial communities in microcosm. Our method identified known oil degraders as well as two clades, Maricurvus and Rhodobacteraceae, that responded to amendment with oil but do not include known oil degraders. Our approach is sensitive to organisms that increased in abundance only in the experimental unit but less sensitive to organisms that increased in both control and experimental units, thus mitigating the role of “bottle effects”. PMID:27152415

  12. Ruminal fermentation and microbial ecology of buffaloes and cattle fed the same diet.

    PubMed

    Lwin, Khin-Ohnmar; Kondo, Makoto; Ban-Tokuda, Tomomi; Lapitan, Rosalina M; Del-Barrio, Arnel N; Fujihara, Tsutomu; Matsui, Hiroki

    2012-12-01

    Although buffaloes and cattle are ruminants, their digestive capabilities and rumen microbial compositions are considered to be different. The purpose of this study was to compare the rumen microbial ecology of crossbred water buffaloes and cattle that were fed the same diet. Cattle exhibited a higher fermentation rate than buffaloes. Methane production and methanogen density were lower in buffaloes. Phylogenetic analysis of Fibrobacter succinogenes-specific 16S ribosomal RNA gene clone library showed that the diversity of groups within a species was significantly different (P < 0.05) between buffalo and cattle and most of the clones were affiliated with group 2 of the species. Population densities of F.succinogenes, Ruminococcus albus and R. flavefaciens were higher until 6 h post-feeding in cattle; however, buffaloes exhibited different traits. The population of anaerobic fungi decreased at 3 h in cattle compared to buffaloes and was similar at 0 h and 6 h. The diversity profiles of bacteria and fungi were similar in the two species. The present study showed that the profiles of the fermentation process, microbial population and diversity were similar in crossbred water buffaloes and crossbred cattle.

  13. A novel analysis method for paired-sample microbial ecology experiments

    DOE PAGESBeta

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

    2016-05-06

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

  14. Ecological roles and biotechnological applications of marine and intertidal microbial biofilms.

    PubMed

    Mitra, Sayani; Sana, Barindra; Mukherjee, Joydeep

    2014-01-01

    This review is a retrospective of ecological effects of bioactivities produced by biofilms of surface-dwelling marine/intertidal microbes as well as of the industrial and environmental biotechnologies developed exploiting the knowledge of biofilm formation. Some examples of significant interest pertaining to the ecological aspects of biofilm-forming species belonging to the Roseobacter clade include autochthonous bacteria from turbot larvae-rearing units with potential application as a probiotic as well as production of tropodithietic acid and indigoidine. Species of the Pseudoalteromonas genus are important examples of successful surface colonizers through elaboration of the AlpP protein and antimicrobial agents possessing broad-spectrum antagonistic activity against medical and environmental isolates. Further examples of significance comprise antiprotozoan activity of Pseudoalteromonas tunicata elicited by violacein, inhibition of fungal colonization, antifouling activities, inhibition of algal spore germination, and 2-n-pentyl-4-quinolinol production. Nitrous oxide, an important greenhouse gas, emanates from surface-attached microbial activity of marine animals. Marine and intertidal biofilms have been applied in the biotechnological production of violacein, phenylnannolones, and exopolysaccharides from marine and tropical intertidal environments. More examples of importance encompass production of protease, cellulase, and xylanase, melanin, and riboflavin. Antifouling activity of Bacillus sp. and application of anammox bacterial biofilms in bioremediation are described. Marine biofilms have been used as anodes and cathodes in microbial fuel cells. Some of the reaction vessels for biofilm cultivation reviewed are roller bottle, rotating disc bioreactor, polymethylmethacrylate conico-cylindrical flask, fixed bed reactor, artificial microbial mats, packed-bed bioreactors, and the Tanaka photobioreactor. PMID:24817086

  15. Carbohydrate-Free Peach (Prunus persica) and Plum (Prunus domestica) Juice Affects Fecal Microbial Ecology in an Obese Animal Model

    PubMed Central

    Markel, Melissa; Martino, Hercia S.; Minamoto, Yasushi; Steiner, Jörg M.; Byrne, David; Suchodolski, Jan S.; Mertens-Talcott, Susanne U.

    2014-01-01

    Background Growing evidence shows the potential of nutritional interventions to treat obesity but most investigations have utilized non-digestible carbohydrates only. Peach and plum contain high amounts of polyphenols, compounds with demonstrated anti-obesity effects. The underlying process of successfully treating obesity using polyphenols may involve an alteration of the intestinal microbiota. However, this phenomenon is not well understood. Methodology/Principal Findings Obese Zucker rats were assigned to three groups (peach, plum, and control, n = 10 each), wild-type group was named lean (n = 10). Carbohydrates in the fruit juices were eliminated using enzymatic hydrolysis. Fecal samples were obtained after 11 weeks of fruit or control juice administration. Real-time PCR and 454-pyrosequencing were used to evaluate changes in fecal microbiota. Over 1,500 different Operational Taxonomic Units at 97% similarity were detected in all rats. Several bacterial groups (e.g. Lactobacillus and members of Ruminococcacea) were found to be more abundant in the peach but especially in the plum group (plum juice contained 3 times more total polyphenolics compared to peach juice). Principal coordinate analysis based on Unifrac-based unweighted distance matrices revealed a distinct separation between the microbiota of control and treatment groups. These changes in fecal microbiota occurred simultaneously with differences in fecal short-chain acids concentrations between the control and treatment groups as well as a significant decrease in body weight in the plum group. Conclusions This study suggests that consumption of carbohydrate-free peach and plum juice has the potential to modify fecal microbial ecology in an obese animal model. The separate contribution of polyphenols and non-polyphenols compounds (vitamins and minerals) to the observed changes is unknown. PMID:25007331

  16. Earth's Earliest Ecosystems in the C: The Use of Microbial Mats to Demonstrate General Principles of Scientific Inquiry and Microbial Ecology

    NASA Technical Reports Server (NTRS)

    Bebout, Brad M.; Bucaria, Robin

    2006-01-01

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

  17. Microbial diversity and biogeochemistry in glacier forefields: assessment of ecological stability in high alpine environments

    NASA Astrophysics Data System (ADS)

    Meola, M.; Lazzaro, A.; Zeyer, J.

    2012-04-01

    Microbial communities inhabiting recently deglaciated, unvegetated, high alpine soils (e.g. glacier forefields) need to be adapted to fluctuating environmental conditions, such as strong daily and seasonal humidity and temperature variations. Soil-related characteristics (e.g. oligotrophy, pH, water holding capacity, nutrient concentration) may in addition determine the presence of locally adapted microbial communities. Currently little is known on the ecological stability (resistance and resilience) of such an environment. In this project, we aim at understanding ecological stability of microbial communities of alpine glacier forefields through a reciprocal soil transplantation experiment. The study consists in i) determining bacterial phylotypes that may respond to environmental changes and ii) relating biological, chemical and physical data to observed microbial responses. We selected two different glacier forefields located in the Swiss Alps (approximately at 2500 m.a.s.l.) The Griessen forefield (Canton Obwalden) is characterized by a calcareous bedrock, while the Tiefen forefield (Canton Uri) is of siliceous composition. The sites are well characterized in terms of their geography (e.g. exposure, slope) and climatic fluctuations (Lazzaro et al. 2009, Lazzaro et al. 2011). At each site, we incubated stainless steel pots with four different soil treatments (autochthonous untreated, autochthonous sterilized, allochthonous untreated and allochthonous sterilized). The setup was repeated in quadruplicate. Soil temperature and soil moisture at 10 cm depth were measured every hour by Decagon EM 50 sensors (Decagon Devices Inc.). In July (D0), August (D1) and September (D2) 2011, soil aliquots were sampled from the pots for analysis. We plan to further extend the sampling for at least three snow-free seasons (2011-2013). Chemical analysis of the soil encompassed soluble ions, pH and DOC. Bacterial community analysis included microbial biomass (DAPI cell counts), basal

  18. Phosphoglycerides of Trichophyton terrestre and one phenotype selected from the Apollo 16 microbial ecology evaluation device.

    PubMed

    Sawyer, R T; Deskins, D C; Volz, P A

    1975-05-01

    Total lipid extracted from wild-type Trichophyton terrestre CDC-X285 was found to be 2.0 percent of the dry cell weight. The total lipid contained the following phospholipid components identified by silicic acid-impregnated thin-layer and paper chromatography: phosphatidyl inositol, phosphatidyl choline, phosphatidyl serine, and phosphatidic acid. The total lipid extracted from the phenotype T. terrestre 7048-1 isolated from the Apollo 16 Microbial Ecology Evaluation Device (MEED) was found to vary according to the time at which the phospholipids were extracted. The Trichophyton phenotype was selected from a cuvette housed in the MEED exposed to specific space parameters including ultraviolet light of known wavelengths and energy levels in deep space. The phospholipid components, identified in the phenotype were phosphatidyl ethanolamine and cardiolipin. The major lipid fraction was composed of digalactosyl diglyceride and monogalactosyl diglyceride. An unusual lipid was detected in the phenotype, which appeared to be sterol glycoside.

  19. Mobilifilum chasei: morphology and ecology of a spirochete from an intertidal stratified microbial mat community

    NASA Technical Reports Server (NTRS)

    Margulis, L.; Hinkle, G.; Stolz, J.; Craft, F.; Esteve, I.; Guerrero, R.

    1990-01-01

    Spirochetes were found in the lower anoxiphototrophic layer of a stratified microbial mat (North Pond, Laguna Figueroa, Baja California, Mexico). Ultra-structural analysis of thin sections of field samples revealed spirochetes approximately 0.25 micrometer in diameter with 10 or more periplasmic flagella, leading to the interpretation that these spirochetes bear 10 flagellar insertions on each end. Morphometric study showed these free-living spirochetes greatly resemble certain symbiotic ones, i.e., Borrelia and certain termite spirochetes, the transverse sections of which are presented here. The ultrastructure of this spirochete also resembles Hollandina and Diplocalyx (spirochetes symbiotic in arthropods) more than it does Spirochaeta, the well known genus of mud-dwelling spirochetes. The new spirochete was detected in mat material collected both in 1985 and in 1987. Unique morphology (i.e., conspicuous outer coat of inner membrane, large number of periplasmic flagella) and ecology prompt us to name a new free-living spirochete.

  20. Microbial ecology of muffins baked from cassava and other nonwheat flours.

    PubMed

    Chauhan, S; Lindsay, D; Rey, M E; van Holy, A

    2001-01-01

    Cassava flour was evaluated as a partial substitute for wheat flour in gluten-free muffins. Four replicate test bakes were carried out to evaluate the microbial ecology of two muffin mixes, made with different combinations of cassava, soya, sorghum, sago, and potato flour. The muffins were baked at 180 degrees C for 25 min, stored at 30 degrees C and analysed microbiologically for up to 10 days post-baking. Raw materials were similarly analysed microbiologically on the day of baking. Characterization of predominant bacterial and mould isolates from the raw materials and the muffins was carried out. The rope-free and minimum mould-free shelf life of both muffin types were approximately 1 day and approximately 3 days, respectively. The predominant bacterial isolates from the raw materials and muffins were Bacillus species (83 and 99%, respectively). The moulds predominating in the raw materials were Gloeosporium (42%), Penicillium (13%) and Mucorales (13%), and from muffins Penicillium (37%) and Aspergillus (37%).

  1. Effect of dam parity on litter performance, transfer of passive immunity, and progeny microbial ecology.

    PubMed

    Carney-Hinkle, E E; Tran, H; Bundy, J W; Moreno, R; Miller, P S; Burkey, T E

    2013-06-01

    (P < 0.03) Shannon's diversity index compared with P4 progeny on d 7. Litter performance, passive transfer of immunity, and progeny microbial ecology were affected by dam parity.

  2. Dietary marker effects on fecal microbial ecology, fecal VFA, nutrient digestibility coefficients, and growth performance in finishing pigs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Use of indigestible markers such as Cr2O3, Fe2O3, and TiO2 are commonly used in animal studies to evaluate rate of passage and nutrient digestibility. Yet nothing is known relative to their potential impact on fecal microbial ecology and subsequent VFA generation. Two experiments utilizing a total o...

  3. Dietary Nisin Modulates the Gastrointestinal Microbial Ecology and Enhances Growth Performance of the Broiler Chickens

    PubMed Central

    Józefiak, Damian; Kierończyk, Bartosz; Juśkiewicz, Jerzy; Zduńczyk, Zenon; Rawski, Mateusz; Długosz, Jakub; Sip, Anna; Højberg, Ole

    2013-01-01

    Due to antimicrobial properties, nisin is one of the most commonly used and investigated bacteriocins for food preservation. Surprisingly, nisin has had limited use in animal feed as well as there are only few reports on its influence on microbial ecology of the gastrointestinal tract (GIT). The present study therefore aimed at investigating effects of dietary nisin on broiler chicken GIT microbial ecology and performance in comparison to salinomycin, the widely used ionophore coccidiostat. In total, 720 one-day-old male Ross 308 chicks were randomly distributed to six experimental groups. The positive control (PC) diet was supplemented with salinomycin (60 mg/kg). The nisin (NI) diets were supplemented with increasing levels (100, 300, 900 and 2700 IU nisin/g, respectively) of the bacteriocin. The negative control (NC) diet contained no additives. At slaughter (35 days of age), activity of specific bacterial enzymes (α- and β-glucosidases, α-galactosidases and β-glucuronidase) in crop, ileum and caeca were significantly higher (P<0.05) in the NC group, and nisin supplementation decreased the enzyme activities to levels observed for the PC group. A similar inhibitory influence on bacterial activity was reflected in the levels of short-chain fatty acids (SCFA) and putrefactive SCFA (PSCFA) in digesta from crop and ileum; no effect was observed in caeca. Counts of Bacteroides and Enterobacteriacae in ileum digesta were significantly (P<0.001) decreased by nisin and salinomycin, but no effects were observed on the counts of Clostridium perfringens, Lactobacillus/Enterococcus and total bacteria. Like salinomycin, nisin supplementation improved broiler growth performance in a dose-dependent manner; compared to the NC group, the body weight gain of the NI900 and NI2700 groups was improved by 4.7 and 8.7%, respectively. Our findings suggest that dietary nisin exerts a mode of action similar to salinomycin and could be considered as a dietary supplement for broiler

  4. Dietary nisin modulates the gastrointestinal microbial ecology and enhances growth performance of the broiler chickens.

    PubMed

    Józefiak, Damian; Kierończyk, Bartosz; Juśkiewicz, Jerzy; Zduńczyk, Zenon; Rawski, Mateusz; Długosz, Jakub; Sip, Anna; Højberg, Ole

    2013-01-01

    Due to antimicrobial properties, nisin is one of the most commonly used and investigated bacteriocins for food preservation. Surprisingly, nisin has had limited use in animal feed as well as there are only few reports on its influence on microbial ecology of the gastrointestinal tract (GIT). The present study therefore aimed at investigating effects of dietary nisin on broiler chicken GIT microbial ecology and performance in comparison to salinomycin, the widely used ionophore coccidiostat. In total, 720 one-day-old male Ross 308 chicks were randomly distributed to six experimental groups. The positive control (PC) diet was supplemented with salinomycin (60 mg/kg). The nisin (NI) diets were supplemented with increasing levels (100, 300, 900 and 2700 IU nisin/g, respectively) of the bacteriocin. The negative control (NC) diet contained no additives. At slaughter (35 days of age), activity of specific bacterial enzymes (α- and β-glucosidases, α-galactosidases and β-glucuronidase) in crop, ileum and caeca were significantly higher (P<0.05) in the NC group, and nisin supplementation decreased the enzyme activities to levels observed for the PC group. A similar inhibitory influence on bacterial activity was reflected in the levels of short-chain fatty acids (SCFA) and putrefactive SCFA (PSCFA) in digesta from crop and ileum; no effect was observed in caeca. Counts of Bacteroides and Enterobacteriacae in ileum digesta were significantly (P<0.001) decreased by nisin and salinomycin, but no effects were observed on the counts of Clostridium perfringens, Lactobacillus/Enterococcus and total bacteria. Like salinomycin, nisin supplementation improved broiler growth performance in a dose-dependent manner; compared to the NC group, the body weight gain of the NI₉₀₀ and NI₂₇₀₀ groups was improved by 4.7 and 8.7%, respectively. Our findings suggest that dietary nisin exerts a mode of action similar to salinomycin and could be considered as a dietary supplement

  5. From Structure to Function: the Ecology of Host-Associated Microbial Communities

    PubMed Central

    Robinson, Courtney J.; Bohannan, Brendan J. M.; Young, Vincent B.

    2010-01-01

    Summary: In the past several years, we have witnessed an increased interest in understanding the structure and function of the indigenous microbiota that inhabits the human body. It is hoped that this will yield novel insight into the role of these complex microbial communities in human health and disease. What is less appreciated is that this recent activity owes a great deal to the pioneering efforts of microbial ecologists who have been studying communities in non-host-associated environments. Interactions between environmental microbiologists and human microbiota researchers have already contributed to advances in our understanding of the human microbiome. We review the work that has led to these recent advances and illustrate some of the possible future directions for continued collaboration between these groups of researchers. We discuss how the application of ecological theory to the human-associated microbiota can lead us past descriptions of community structure and toward an understanding of the functions of the human microbiota. Such an approach may lead to a shift in the prevention and treatment of human diseases that involves conservation or restoration of the normal community structure and function of the host-associated microbiota. PMID:20805407

  6. Refinement of biodegradation tests methodologies and the proposed utility of new microbial ecology techniques.

    PubMed

    Kowalczyk, Agnieszka; Martin, Timothy James; Price, Oliver Richard; Snape, Jason Richard; van Egmond, Roger Albert; Finnegan, Christopher James; Schäfer, Hendrik; Davenport, Russell James; Bending, Gary Douglas

    2015-01-01

    Society's reliance upon chemicals over the last few decades has led to their increased production, application and release into the environment. Determination of chemical persistence is crucial for risk assessment and management of chemicals. Current established OECD biodegradation guidelines enable testing of chemicals under laboratory conditions but with an incomplete consideration of factors that can impact on chemical persistence in the environment. The suite of OECD biodegradation tests do not characterise microbial inoculum and often provide little insight into pathways of degradation. The present review considers limitations with the current OECD biodegradation tests and highlights novel scientific approaches to chemical fate studies. We demonstrate how the incorporation of molecular microbial ecology methods (i.e., 'omics') may improve the underlying mechanistic understanding of biodegradation processes, and enable better extrapolation of data from laboratory based test systems to the relevant environment, which would potentially improve chemical risk assessment and decision making. We outline future challenges for relevant stakeholders to modernise OECD biodegradation tests and put the 'bio' back into biodegradation.

  7. Dietary L-glutamine supplementation modulates microbial community and activates innate immunity in the mouse intestine.

    PubMed

    Ren, Wenkai; Duan, Jielin; Yin, Jie; Liu, Gang; Cao, Zhong; Xiong, Xia; Chen, Shuai; Li, Tiejun; Yin, Yulong; Hou, Yongqing; Wu, Guoyao

    2014-10-01

    This study was conducted to determine effects of dietary supplementation with 1 % L-glutamine for 14 days on the abundance of intestinal bacteria and the activation of intestinal innate immunity in mice. The measured variables included (1) the abundance of Bacteroidetes, Firmicutes, Lactobacillus, Streptococcus and Bifidobacterium in the lumen of the small intestine; (2) the expression of toll-like receptors (TLRs), pro-inflammatory cytokines, and antibacterial substances secreted by Paneth cells and goblet cells in the jejunum, ileum and colon; and (3) the activation of TLR4-nuclear factor kappa B (NF-κB), mitogen-activated protein kinases (MAPK), and phosphoinositide-3-kinases (PI3K)/PI3K-protein kinase B (Akt) signaling pathways in the jejunum and ileum. In the jejunum, glutamine supplementation decreased the abundance of Firmicutes, while increased mRNA levels for antibacterial substances in association with the activation of NF-κB and PI3K-Akt pathways. In the ileum, glutamine supplementation induced a shift in the Firmicutes:Bacteroidetes ratio in favor of Bacteroidetes, and enhanced mRNA levels for Tlr4, pro-inflammatory cytokines, and antibacterial substances participating in NF-κB and JNK signaling pathways. These results indicate that the effects of glutamine on the intestine vary with its segments and compartments. Collectively, dietary glutamine supplementation of mice beneficially alters intestinal bacterial community and activates the innate immunity in the small intestine through NF-κB, MAPK and PI3K-Akt signaling pathways.

  8. Microbial ecology of a novel sulphur cycling consortia from AMD: implications for acid generation

    NASA Astrophysics Data System (ADS)

    Loiselle, L. M.; Norlund, K. L.; Hitchcock, A. P.; Warren, L. A.

    2009-05-01

    Recent work1 identified a novel microbial consortia consisting of two bacterial strains common to acid mine drainage (AMD) environments (autotrophic sulphur oxidizer Acidithiobacillus ferrooxidans and heterotrophic Acidiphilium spp.) in an environmental enrichment from a mine tailings lake. The two strains showed a specific spatial arrangement within an EPS macrostructure or "pod" allowing linked metabolic redox cycling of sulphur. Sulphur species characterisation of the pods using scanning transmission X-ray microscopy (STXM) indicated that autotrophic tetrathionate disproportionation by A. ferrooxidans producing colloidal elemental sulphur (S0) is coupled to heterotrophic S0 reduction by Acidiphilium spp. Geochemical modelling of the microbial sulphur reactions indicated that if they are widespread in AMD environments, then global AMD-driven CO2 liberation from mineral weathering have been overestimated by 40-90%1. Given the common co-occurrence of these two bacteria in AMD settings, the purpose of this study was to evaluate if these pods could be induced in the laboratory by pure strains and if so, whether their combined sulphur geochemistry mimicked the previous findings. Laboratory batch experiments assessed the development of pods with pure strain type cultures (A. ferrooxidans ATCC 19859 with mixotroph Acidiphilium acidophilum ATCC 738 or strict heterotroph Acp. cryptum ATCC 2158) using fluorescent in situ hybridization (FISH) imaging. The microbial sulphur geochemistry was characterized under autotrophic conditions identical to those used with the environmental AMD enrichment in which the pods were discovered. Results showed that the combined pure strain A. ferrooxidans and Acp. acidophilum form pods identical in structure to the AMD enrichment. To test the hypothesis that these pods form for mutual metabolic benefit, experiments were performed amending pure strain and AMD enrichment bacterial treatments with organic carbon and/or additional sulphur to

  9. Improving rumen ecology and microbial population by dried rumen digesta in beef cattle.

    PubMed

    Cherdthong, Anusorn; Wanapat, Metha; Saenkamsorn, Anuthida; Supapong, Chanadol; Anantasook, Nirawan; Gunun, Pongsatorn

    2015-06-01

    Four Thai native beef cattle with initial body weight (BW) of 91.8 ± 4.75 kg were randomly assigned according to a 4 × 4 Latin square design to receive four concentrates replacement levels of soybean meal (SBM) by dried rumen digesta (DRD) at 0, 33, 67, and 100 % on dry matter (DM) basis. All cattle were fed rice straw ad libitum while additional concentrate was fed at 0.5 % BW daily. The experiment was conducted for four periods of 21 days. Rumen fluid was analyzed for predominant cellulolytic bacterial population by using real-time PCR technique. Increasing levels of DRD did not alter total feed intake, ruminal pH and temperature, and plasma urea nitrogen (P > 0.05). Protozoa and fungal population were not differed by DRD supplementation while population of bacteria at 4 h post feeding was increased when SBM was replaced with DRD at 66 and 100 % DM. Population of total bacteria and R. flavefaciens at 4 h post feeding were significantly highest with inclusion of 100 % of DRD in the ration. The experimental diets has no effect on excretion and absorption of purine derivatives (P > 0.05), while microbial crude protein and efficiency of microbial N synthesis were significantly increased with DRD inclusion in the diet and highest with 100 % DRD replacement (P > 0.05). Replacement of SBM by DRD at 100 % DM improved the rumen ecology and microbial population in beef cattle fed on rice straw.

  10. Controlling Salmonella infection in weanling pigs through water delivery of direct-fed microbials or organic acids: Part II. Effects on intestinal histology and active nutrient transport

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this study was to evaluate the effects of water-delivered direct-fed microbials (DFM) or organic acids on intestinal morphology and active nutrient absorption in weanling pigs following deliberate Salmonella infection. Pigs (n = 88) were weaned at 19 ± 2 d of age and assigned to one...

  11. Impact of chronic exposure to low doses of chlorpyrifos on the intestinal microbiota in the Simulator of the Human Intestinal Microbial Ecosystem (SHIME) and in the rat.

    PubMed

    Joly, Claire; Gay-Quéheillard, Jérôme; Léké, André; Chardon, Karen; Delanaud, Stéphane; Bach, Véronique; Khorsi-Cauet, Hafida

    2013-05-01

    The impact of the insecticide chlorpyrifos (CPF) on the mammalian digestive system has been poorly described. The present study aimed at evaluating the effect of chronic, low-dose exposure to CPF on the composition of the gut microbiota in a Simulator of the Human Intestinal Microbial Ecosystem: the SHIME and in rats. The SHIME comprises six reactor vessels (stomach to colon). The colonic segments were inoculated with feces from healthy humans. Then, the simulator was exposed to a daily dose of 1 mg of CPF for 30 days. The changes over time in the populations of bacteria were examined at different time points: prior to pesticide exposure (as a control) and after exposure. In parallel, pregnant rats were gavaged daily with 1 mg/kg of CPF (or vehicle) until the pups were weaned. Next, the rats were gavaged with same dose of CPF until 60 days of age (adulthood). Then, samples of different parts of the digestive tract were collected under sterile conditions for microbiological assessment. Chronic, low-dose exposure to CPF in the SHIME and in the rat was found to induce dysbiosis in the microbial community with, in particular, proliferation of subpopulations of some strains and a decrease in the numbers of others bacteria. In compliance with European guidelines, the use of the SHIME in vitro tool would help to (1) elucidate the final health effect of toxic agents and (2) minimize (though not fully replace) animal testing. Indeed, certain parameters would still have to be studied further in vivo. PMID:23135753

  12. Bacteria–phage coevolution as a driver of ecological and evolutionary processes in microbial communities

    PubMed Central

    Koskella, Britt; Brockhurst, Michael A

    2014-01-01

    Bacteria–phage coevolution, the reciprocal evolution between bacterial hosts and the phages that infect them, is an important driver of ecological and evolutionary processes in microbial communities. There is growing evidence from both laboratory and natural populations that coevolution can maintain phenotypic and genetic diversity, increase the rate of bacterial and phage evolution and divergence, affect community structure, and shape the evolution of ecologically relevant bacterial traits. Although the study of bacteria–phage coevolution is still in its infancy, with open questions regarding the specificity of the interaction, the gene networks of coevolving partners, and the relative importance of the coevolving interaction in complex communities and environments, there have recently been major advancements in the field. In this review, we sum up our current understanding of bacteria–phage coevolution both in the laboratory and in nature, discuss recent findings on both the coevolutionary process itself and the impact of coevolution on bacterial phenotype, diversity and interactions with other species (particularly their eukaryotic hosts), and outline future directions for the field. PMID:24617569

  13. Bacterial adaptation to sublethal antibiotic gradients can change the ecological properties of multitrophic microbial communities

    PubMed Central

    Friman, Ville-Petri; Guzman, Laura Melissa; Reuman, Daniel C.; Bell, Thomas

    2015-01-01

    Antibiotics leak constantly into environments due to widespread use in agriculture and human therapy. Although sublethal concentrations are well known to select for antibiotic-resistant bacteria, little is known about how bacterial evolution cascades through food webs, having indirect effect on species not directly affected by antibiotics (e.g. via population dynamics or pleiotropic effects). Here, we used an experimental evolution approach to test how temporal patterns of antibiotic stress, as well as migration within metapopulations, affect the evolution and ecology of microcosms containing one prey bacterium, one phage and two protist predators. We found that environmental variability, autocorrelation and migration had only subtle effects for population and evolutionary dynamics. However, unexpectedly, bacteria evolved greatest fitness increases to both antibiotics and enemies when the sublethal levels of antibiotics were highest, indicating positive pleiotropy. Crucially, bacterial adaptation cascaded through the food web leading to reduced predator-to-prey abundance ratio, lowered predator community diversity and increased instability of populations. Our results show that the presence of natural enemies can modify and even reverse the effects of antibiotics on bacteria, and that antibiotic selection can change the ecological properties of multitrophic microbial communities by having indirect effects on species not directly affected by antibiotics. PMID:25833854

  14. Bacterial adaptation to sublethal antibiotic gradients can change the ecological properties of multitrophic microbial communities.

    PubMed

    Friman, Ville-Petri; Guzman, Laura Melissa; Reuman, Daniel C; Bell, Thomas

    2015-05-01

    Antibiotics leak constantly into environments due to widespread use in agriculture and human therapy. Although sublethal concentrations are well known to select for antibiotic-resistant bacteria, little is known about how bacterial evolution cascades through food webs, having indirect effect on species not directly affected by antibiotics (e.g. via population dynamics or pleiotropic effects). Here, we used an experimental evolution approach to test how temporal patterns of antibiotic stress, as well as migration within metapopulations, affect the evolution and ecology of microcosms containing one prey bacterium, one phage and two protist predators. We found that environmental variability, autocorrelation and migration had only subtle effects for population and evolutionary dynamics. However, unexpectedly, bacteria evolved greatest fitness increases to both antibiotics and enemies when the sublethal levels of antibiotics were highest, indicating positive pleiotropy. Crucially, bacterial adaptation cascaded through the food web leading to reduced predator-to-prey abundance ratio, lowered predator community diversity and increased instability of populations. Our results show that the presence of natural enemies can modify and even reverse the effects of antibiotics on bacteria, and that antibiotic selection can change the ecological properties of multitrophic microbial communities by having indirect effects on species not directly affected by antibiotics.

  15. Quantifying the biases in metagenome mining for realistic assessment of microbial ecology of naturally fermented foods

    PubMed Central

    Keisam, Santosh; Romi, Wahengbam; Ahmed, Giasuddin; Jeyaram, Kumaraswamy

    2016-01-01

    Cultivation-independent investigation of microbial ecology is biased by the DNA extraction methods used. We aimed to quantify those biases by comparative analysis of the metagenome mined from four diverse naturally fermented foods (bamboo shoot, milk, fish, soybean) using eight different DNA extraction methods with different cell lysis principles. Our findings revealed that the enzymatic lysis yielded higher eubacterial and yeast metagenomic DNA from the food matrices compared to the widely used chemical and mechanical lysis principles. Further analysis of the bacterial community structure by Illumina MiSeq amplicon sequencing revealed a high recovery of lactic acid bacteria by the enzymatic lysis in all food types. However, Bacillaceae, Acetobacteraceae, Clostridiaceae and Proteobacteria were more abundantly recovered when mechanical and chemical lysis principles were applied. The biases generated due to the differential recovery of operational taxonomic units (OTUs) by different DNA extraction methods including DNA and PCR amplicons mix from different methods have been quantitatively demonstrated here. The different methods shared only 29.9–52.0% of the total OTUs recovered. Although similar comparative research has been performed on other ecological niches, this is the first in-depth investigation of quantifying the biases in metagenome mining from naturally fermented foods. PMID:27669673

  16. Urolithins, Intestinal Microbial Metabolites of Pomegranate Ellagitannins, Exhibit Potent Antioxidant Activity in Cell-Based Assay

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Many health benefits of pomegranate products have been attributed to the potent antioxidant action of their tannin components, mainly punicalagins and ellagic acid. While moving through the intestines, ellagitannins are metabolized by gut bacteria into urolithins that readily enter systemic circulat...

  17. Intestinal microbial affects of yeast products on weaned and transport stressed pigs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Study objectives were to determine effects of a commercially available yeast product (XPC, Diamond-V Mills) and stress of transportation on total Enterobacteriaceae, Escherichia coli, coliforms, and Lactobacilli populations in the intestine of weaning pigs. In a RCB design with a 2 x 2 factorial ar...

  18. Nutritional iron turned inside out: intestinal stress from a gut microbial perspective.

    PubMed

    Kortman, Guus A M; Raffatellu, Manuela; Swinkels, Dorine W; Tjalsma, Harold

    2014-11-01

    Iron is abundantly present on earth, essential for most microorganisms and crucial for human health. Human iron deficiency that is nevertheless highly prevalent in developing regions of the world can be effectively treated by oral iron administration. Accumulating evidence indicates that excess of unabsorbed iron that enters the colonic lumen causes unwanted side effects at the intestinal host-microbiota interface. The chemical properties of iron, the luminal environment and host iron withdrawal mechanisms, especially during inflammation, can turn the intestine in a rather stressful milieu. Certain pathogenic enteric bacteria can, however, deal with this stress at the expense of other members of the gut microbiota, while their virulence also seems to be stimulated in an iron-rich intestinal environment. This review covers the multifaceted aspects of nutritional iron stress with respect to growth, composition, metabolism and pathogenicity of the gut microbiota in relation to human health. We aim to present an unpreceded view on the dynamic effects and impact of oral iron administration on intestinal host-microbiota interactions to provide leads for future research and other applications. PMID:25205464

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

    NASA Technical Reports Server (NTRS)

    Beboutl, Brad M.; Bucaria, Robin

    2004-01-01

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

  20. Urolithins, intestinal microbial metabolites of Pomegranate ellagitannins, exhibit potent antioxidant activity in a cell-based assay.

    PubMed

    Bialonska, Dobroslawa; Kasimsetty, Sashi G; Khan, Shabana I; Ferreira, Daneel

    2009-11-11

    Many health benefits of pomegranate products have been attributed to the potent antioxidant action of their tannin components, mainly punicalagins and ellagic acid. While moving through the intestines, ellagitannins are metabolized by gut bacteria into urolithins that readily enter systemic circulation. In this study, the antioxidant properties of seven urolithin derivatives were evaluated in a cell-based assay. This method is biologically more relevant because it reflects bioavailability of the test compound to the cells, and the antioxidant action is determined in the cellular environment. Our results showed that the antioxidant activity of urolithins was correlated with the number of hydroxy groups as well as the lipophilicity of the molecule. The most potent antioxidants are urolithins C and D with IC(50) values of 0.16 and 0.33 microM, respectively, when compared to IC(50) values of 1.1 and 1.4 microM of the parent ellagic acid and punicalagins, respectively. The dihydroxylated urolithin A showed weaker antioxidant activity, with an IC(50) value 13.6 microM, however, the potency was within the range of urolithin A plasma concentrations. Therefore, products of the intestinal microbial transformation of pomegranate ellagitannins may account for systemic antioxidant effects.

  1. Intestinal function and gut microflora of broiler chickens as influenced by cereal grains and microbial enzyme supplementation.

    PubMed

    Shakouri, M D; Iji, P A; Mikkelsen, L L; Cowieson, A J

    2009-10-01

    A study was conducted to investigate the effect of the key cereal grains and a microbial enzyme supplement on broiler chicken performance, gut microflora and intestinal function. Ingestion of the barley-based diet was associated with low 28-day body weight, decreased feed intake and high FCR. The supplemental enzyme increased feed intake and weight gain of the chickens on a wheat-based diet. The pH of the gizzard and caecal contents varied with the grain type. Enzyme supplementation reduced ileal viscosity, particularly in birds that received the diet based on wheat. The birds on the barley-based diet had lower ileal digestibility of dry matter, protein and energy than those given maize and sorghum-based diets. The ileal digestibility of starch was increased by enzyme supplementation. Enzyme supplementation increased the number of total anaerobic bacteria in the gizzard of birds fed on sorghum and increased lactobacilli in the gizzard of those fed both sorghum and wheat. The birds fed the sorghum-based diet had the lowest counts of caecal total anaerobic bacteria and lactobacilli. Jejunal villus height and villus:crypt ratio of birds fed the barley-based diet were the lowest when compared with those fed the other diets. Enzyme application induced an increase in villus height and villus:crypt ratio of birds on wheat, crypt depth on barley and a reduction in crypt depth of chickens on the sorghum-based diets. The highest activity of maltase and the lowest activity of sucrase were observed in tissue from birds fed on maize and sorghum-based diets respectively. The differences in the performance of broilers on cereal grains could be explained by changes in intestinal morphology, enzyme activities and gut microflora as well as nutrient digestibility. The improved performance by supplemental enzyme in wheat-fed chickens was associated with beneficial changes in intestinal morphology and digesta viscosity.

  2. Intestinal microbial metabolism of phosphatidylcholine: a novel insight in the cardiovascular risk scenario

    PubMed Central

    Sorrentino, Claudia; Principi, Mariabeatrice; Giorgio, Floriana; Losurdo, Giuseppe; Di Leo, Alfredo

    2015-01-01

    Intestinal microbiota is a “dynamic organ” influencing host metabolism, nutrition, physiology and immune system. Among its several interactions, the role of a phosphatidylcholine metabolite derived by gut flora activity, i.e., trimethylamine-N-oxide (TMAO), allows perceiving a novel insight in the cardiovascular risk scenario, being a strong predictor of this condition. Based on current reports, including the paper of Tang et al., we describe here: the possible role of intestinal microbiota in cardiovascular risk as well as potential interventions to reduce gut flora TMAO production by diet, probiotics and antibiotics. Finally, we highlight the possibility of evaluating, monitoring and modulating TMAO in order to use its serum levels as a marker of cardiovascular risk in the next future, when the need of controlled studies on large series will be satisfied. PMID:26312245

  3. Absence of MHC class II on cDCs results in microbial-dependent intestinal inflammation

    PubMed Central

    Loschko, Jakob; Schreiber, Heidi A.; Rieke, Gereon J.; Esterházy, Daria; Meredith, Matthew M.; Pedicord, Virginia A.; Yao, Kai-Hui; Caballero, Silvia; Pamer, Eric G.; Mucida, Daniel

    2016-01-01

    Conventional dendritic cells (cDCs) play an essential role in host immunity by initiating adaptive T cell responses and by serving as innate immune sensors. Although both innate and adaptive functions of cDCs are well documented, their relative importance in maintaining immune homeostasis is poorly understood. To examine the significance of cDC-initiated adaptive immunity in maintaining homeostasis, independent of their innate activities, we generated a cDC-specific Cre mouse and crossed it to a floxed MHC class II (MHCII) mouse. Absence of MHCII on cDCs resulted in chronic intestinal inflammation that was alleviated by antibiotic treatment and entirely averted under germ-free conditions. Uncoupling innate and adaptive functions of cDCs revealed that innate immune functions of cDCs are insufficient to maintain homeostasis and antigen presentation by cDCs is essential for a mutualistic relationship between the host and intestinal bacteria. PMID:27001748

  4. The microbial metabolite butyrate regulates intestinal macrophage function via histone deacetylase inhibition.

    PubMed

    Chang, Pamela V; Hao, Liming; Offermanns, Stefan; Medzhitov, Ruslan

    2014-02-11

    Given the trillions of microbes that inhabit the mammalian intestines, the host immune system must constantly maintain a balance between tolerance to commensals and immunity against pathogens to avoid unnecessary immune responses against otherwise harmless bacteria. Misregulated responses can lead to inflammatory bowel diseases such as ulcerative colitis or Crohn's disease. The mechanisms by which the immune system maintains this critical balance remain largely undefined. Here, we demonstrate that the short-chain fatty acid n-butyrate, which is secreted in high amounts by commensal bacteria, can modulate the function of intestinal macrophages, the most abundant immune cell type in the lamina propria. Treatment of macrophages with n-butyrate led to the down-regulation of lipopolysaccharide-induced proinflammatory mediators, including nitric oxide, IL-6, and IL-12, but did not affect levels of TNF-α or MCP-1. These effects were independent of toll-like receptor signaling and activation of G-protein-coupled receptors, two pathways that could be affected by short-chain fatty acids. In this study, we provide several lines of evidence that suggest that these effects are due to the inhibition of histone deacetylases by n-butyrate. These findings elucidate a pathway in which the host may maintain tolerance to intestinal microbiota by rendering lamina propria macrophages hyporesponsive to commensal bacteria through the down-regulation of proinflammatory effectors.

  5. The microbial metabolite butyrate regulates intestinal macrophage function via histone deacetylase inhibition.

    PubMed

    Chang, Pamela V; Hao, Liming; Offermanns, Stefan; Medzhitov, Ruslan

    2014-02-11

    Given the trillions of microbes that inhabit the mammalian intestines, the host immune system must constantly maintain a balance between tolerance to commensals and immunity against pathogens to avoid unnecessary immune responses against otherwise harmless bacteria. Misregulated responses can lead to inflammatory bowel diseases such as ulcerative colitis or Crohn's disease. The mechanisms by which the immune system maintains this critical balance remain largely undefined. Here, we demonstrate that the short-chain fatty acid n-butyrate, which is secreted in high amounts by commensal bacteria, can modulate the function of intestinal macrophages, the most abundant immune cell type in the lamina propria. Treatment of macrophages with n-butyrate led to the down-regulation of lipopolysaccharide-induced proinflammatory mediators, including nitric oxide, IL-6, and IL-12, but did not affect levels of TNF-α or MCP-1. These effects were independent of toll-like receptor signaling and activation of G-protein-coupled receptors, two pathways that could be affected by short-chain fatty acids. In this study, we provide several lines of evidence that suggest that these effects are due to the inhibition of histone deacetylases by n-butyrate. These findings elucidate a pathway in which the host may maintain tolerance to intestinal microbiota by rendering lamina propria macrophages hyporesponsive to commensal bacteria through the down-regulation of proinflammatory effectors. PMID:24390544

  6. Comparative analysis of fecal microbiota and intestinal microbial metabolic activity in captive polar bears.

    PubMed

    Schwab, Clarissa; Gänzle, Michael

    2011-03-01

    The composition of the intestinal microbiota depends on gut physiology and diet. Ursidae possess a simple gastrointestinal system composed of a stomach, small intestine, and indistinct hindgut. This study determined the composition and stability of fecal microbiota of 3 captive polar bears by group-specific quantitative PCR and PCR-DGGE (denaturing gradient gel electrophoresis) using the 16S rRNA gene as target. Intestinal metabolic activity was determined by analysis of short-chain fatty acids in feces. For comparison, other Carnivora and mammals were included in this study. Total bacterial abundance was approximately log 8.5 DNA gene copies·(g feces)-1 in all 3 polar bears. Fecal polar bear microbiota was dominated by the facultative anaerobes Enterobacteriaceae and enterococci, and the Clostridium cluster I. The detection of the Clostridium perfringens α-toxin gene verified the presence of C. perfringens. Composition of the fecal bacterial population was stable on a genus level; according to results obtained by PCR-DGGE, dominant bacterial species fluctuated. The total short-chain fatty acid content of Carnivora and other mammals analysed was comparable; lactate was detected in feces of all carnivora but present only in trace amounts in other mammals. In comparison, the fecal microbiota and metabolic activity of captive polar bears mostly resembled the closely related grizzly and black bears.

  7. Comparative analysis of fecal microbiota and intestinal microbial metabolic activity in captive polar bears.

    PubMed

    Schwab, Clarissa; Gänzle, Michael

    2011-03-01

    The composition of the intestinal microbiota depends on gut physiology and diet. Ursidae possess a simple gastrointestinal system composed of a stomach, small intestine, and indistinct hindgut. This study determined the composition and stability of fecal microbiota of 3 captive polar bears by group-specific quantitative PCR and PCR-DGGE (denaturing gradient gel electrophoresis) using the 16S rRNA gene as target. Intestinal metabolic activity was determined by analysis of short-chain fatty acids in feces. For comparison, other Carnivora and mammals were included in this study. Total bacterial abundance was approximately log 8.5 DNA gene copies·(g feces)-1 in all 3 polar bears. Fecal polar bear microbiota was dominated by the facultative anaerobes Enterobacteriaceae and enterococci, and the Clostridium cluster I. The detection of the Clostridium perfringens α-toxin gene verified the presence of C. perfringens. Composition of the fecal bacterial population was stable on a genus level; according to results obtained by PCR-DGGE, dominant bacterial species fluctuated. The total short-chain fatty acid content of Carnivora and other mammals analysed was comparable; lactate was detected in feces of all carnivora but present only in trace amounts in other mammals. In comparison, the fecal microbiota and metabolic activity of captive polar bears mostly resembled the closely related grizzly and black bears. PMID:21358758

  8. Supplementation of piglets with nutrient-dense complex milk replacer improves intestinal development and microbial fermentation.

    PubMed

    de Greeff, A; Resink, J W; van Hees, H M J; Ruuls, L; Klaassen, G J; Rouwers, S M G; Stockhofe-Zurwieden, N

    2016-03-01

    Weaning of piglets causes stress due to environmental, behavioral, and nutritional stressors and can lead to postweaning diarrhea and impaired gut development. The diet changes experienced during weaning require extensive adaptation of the digestive system. A well-developed piglet that had creep-feed experience before weaning performs better after weaning. In the current study, the effect of providing sow-fed piglets with a supplemental nutrient-dense complex milk replacer (NDM) on gut development and growth performance was studied. Litters of sows with similar parities (3.6 ± 0.8) and similar numbers of live born piglets (13.5 ± 0.3) were assigned to 1 of 2 groups: 1 group of piglets had ad libitum access to NDM from Day 2 through 21 after birth, whereas the other group was used as controls. Nutrient-dense complex milk replacer-fed piglets were shown to be significantly heavier after 21 d of supplementation compared with the control piglets. At Day 21, 3 piglets from each litter were euthanized for morphological and functional analyses of the intestinal tract. The small intestines of NDM-fed piglets had significantly higher weights (g) as well as significantly higher relative weight:length ratios (g//cm) compared with the small intestines of control piglets ( < 0.05). Morphometric analysis demonstrated that villi length and numbers of goblet cells did not differ between groups. However, NDM-fed piglets had deeper crypts ( < 0.001) and an increased expression of the cell-proliferation marker proliferating cell nuclear antigen in crypts ( < 0.05), suggesting higher cell-proliferation rates. The gene encoding IGF-1 showed a tendency to higher gene expression in the jejunum from NDM-fed piglets ( = 0.07) compared with the jejunum from control piglets, suggesting that IGF-1 might be involved in the regulation of cell proliferation and intestinal growth. Finally, as a result of dietary fiber in NDM, piglets showed significantly increased concentrations of metabolic

  9. Microbial ecology of Vietnamese Tra fish (Pangasius hypophthalmus) fillets during processing.

    PubMed

    Tong Thi, Anh Ngoc; Noseda, Bert; Samapundo, Simbarashe; Nguyen, Binh Ly; Broekaert, Katrien; Rasschaert, Geertrui; Heyndrickx, Marc; Devlieghere, Frank

    2013-10-15

    There are numerous factors that can have an impact on the microbial ecology and quality of frozen Pangasius hypophthalmus fillets during processing in Vietnam. The presence of spoilage bacteria along the processing line can shorten the shelf-life of thawed frozen fish products. Therefore, the spoilage microbiota throughout the processing chain of two companies (BC: large scale factory, chlorine-based process, BW: large scale factory, water-based process and SC: small scale factory, chlorine-based process) was identified by culture-dependent techniques and 16S rRNA gene sequencing. The microbiological counts were observed to be insignificantly different (p>0.05) between BC and BW. Surprisingly, chlorine treated fillets from the SC line were revealed to have significantly higher microbial counts than potable water treated fillets at BW line. This was determined to be a result of temperature abuse during processing at SC, with temperatures even greater than 10 °C being recorded from skinning onwards. On the contrary, the microbiota related to spoilage for BC and BW lines was determined by 16S rRNA gene sequencing to be more diverse than that on the SC line. A total of 174 isolates, 20 genera and 38 species were identified along the processing chains. The genera Aeromonas, Acinetobacter, Lactococcus and Enterococcus were prevalent at various processing steps on all the processing lines evaluated. A diverse range of isolates belonging to the Enterobacteriaceae such as Providencia, Shigella, Klebsiella, Enterobacter and Wautersiella were isolated from fillets sampled on the SC line whereas Serratia was only observed on fillets sampled on the BC and BW lines. The results can be used to improve Good Manufacturing Practices for processed Pangasius fillets and to select effective measures to prolong the shelf-life of thawed Vietnamese Pangasius fillets products. PMID:24140808

  10. Microbial ecology of Vietnamese Tra fish (Pangasius hypophthalmus) fillets during processing.

    PubMed

    Tong Thi, Anh Ngoc; Noseda, Bert; Samapundo, Simbarashe; Nguyen, Binh Ly; Broekaert, Katrien; Rasschaert, Geertrui; Heyndrickx, Marc; Devlieghere, Frank

    2013-10-15

    There are numerous factors that can have an impact on the microbial ecology and quality of frozen Pangasius hypophthalmus fillets during processing in Vietnam. The presence of spoilage bacteria along the processing line can shorten the shelf-life of thawed frozen fish products. Therefore, the spoilage microbiota throughout the processing chain of two companies (BC: large scale factory, chlorine-based process, BW: large scale factory, water-based process and SC: small scale factory, chlorine-based process) was identified by culture-dependent techniques and 16S rRNA gene sequencing. The microbiological counts were observed to be insignificantly different (p>0.05) between BC and BW. Surprisingly, chlorine treated fillets from the SC line were revealed to have significantly higher microbial counts than potable water treated fillets at BW line. This was determined to be a result of temperature abuse during processing at SC, with temperatures even greater than 10 °C being recorded from skinning onwards. On the contrary, the microbiota related to spoilage for BC and BW lines was determined by 16S rRNA gene sequencing to be more diverse than that on the SC line. A total of 174 isolates, 20 genera and 38 species were identified along the processing chains. The genera Aeromonas, Acinetobacter, Lactococcus and Enterococcus were prevalent at various processing steps on all the processing lines evaluated. A diverse range of isolates belonging to the Enterobacteriaceae such as Providencia, Shigella, Klebsiella, Enterobacter and Wautersiella were isolated from fillets sampled on the SC line whereas Serratia was only observed on fillets sampled on the BC and BW lines. The results can be used to improve Good Manufacturing Practices for processed Pangasius fillets and to select effective measures to prolong the shelf-life of thawed Vietnamese Pangasius fillets products.

  11. Significance of Microbial Communities and Interactions in Safeguarding Reactive Mine Tailings by Ecological Engineering▿†

    PubMed Central

    N̆ancucheo, Ivan; Johnson, D. Barrie

    2011-01-01

    Pyritic mine tailings (mineral waste generated by metal mining) pose significant risk to the environment as point sources of acidic, metal-rich effluents (acid mine drainage [AMD]). While the accelerated oxidative dissolution of pyrite and other sulfide minerals in tailings by acidophilic chemolithotrophic prokaryotes has been widely reported, other acidophiles (heterotrophic bacteria that catalyze the dissimilatory reduction of iron and sulfur) can reverse the reactions involved in AMD genesis, and these have been implicated in the “natural attenuation” of mine waters. We have investigated whether by manipulating microbial communities in tailings (inoculating with iron- and sulfur-reducing acidophilic bacteria and phototrophic acidophilic microalgae) it is possible to mitigate the impact of the acid-generating and metal-mobilizing chemolithotrophic prokaryotes that are indigenous to tailing deposits. Sixty tailings mesocosms were set up, using five different microbial inoculation variants, and analyzed at regular intervals for changes in physicochemical and microbiological parameters for up to 1 year. Differences between treatment protocols were most apparent between tailings that had been inoculated with acidophilic algae in addition to aerobic and anaerobic heterotrophic bacteria and those that had been inoculated with only pyrite-oxidizing chemolithotrophs; these differences included higher pH values, lower redox potentials, and smaller concentrations of soluble copper and zinc. The results suggest that empirical ecological engineering of tailing lagoons to promote the growth and activities of iron- and sulfate-reducing bacteria could minimize their risk of AMD production and that the heterotrophic populations could be sustained by facilitating the growth of microalgae to provide continuous inputs of organic carbon. PMID:21965397

  12. Dynamic autoinoculation and the microbial ecology of a deep water hydrocarbon irruption.

    PubMed

    Valentine, David L; Mezić, Igor; Maćešić, Senka; Črnjarić-Žic, Nelida; Ivić, Stefan; Hogan, Patrick J; Fonoberov, Vladimir A; Loire, Sophie

    2012-12-11

    The irruption of gas and oil into the Gulf of Mexico during the Deepwater Horizon event fed a deep sea bacterial bloom that consumed hydrocarbons in the affected waters, formed a regional oxygen anomaly, and altered the microbiology of the region. In this work, we develop a coupled physical-metabolic model to assess the impact of mixing processes on these deep ocean bacterial communities and their capacity for hydrocarbon and oxygen use. We find that observed biodegradation patterns are well-described by exponential growth of bacteria from seed populations present at low abundance and that current oscillation and mixing processes played a critical role in distributing hydrocarbons and associated bacterial blooms within the northeast Gulf of Mexico. Mixing processes also accelerated hydrocarbon degradation through an autoinoculation effect, where water masses, in which the hydrocarbon irruption had caused blooms, later returned to the spill site with hydrocarbon-degrading bacteria persisting at elevated abundance. Interestingly, although the initial irruption of hydrocarbons fed successive blooms of different bacterial types, subsequent irruptions promoted consistency in the structure of the bacterial community. These results highlight an impact of mixing and circulation processes on biodegradation activity of bacteria during the Deepwater Horizon event and suggest an important role for mixing processes in the microbial ecology of deep ocean environments.

  13. Microbial ecology studies of spontaneous fermentation: starter culture selection for prickly pear wine production.

    PubMed

    Rodríguez-Lerma, G K; Gutiérrez-Moreno, K; Cárdenas-Manríquez, M; Botello-Álvarez, E; Jiménez-Islas, H; Rico-Martínez, R; Navarrete-Bolaños, J L

    2011-08-01

    A procedure for designing starter cultures for fermentation is illustrated for prickly pear wine production. The illustration includes kinetic studies on inoculated and spontaneous fermentation, microorganism identification studies based on molecular biology tools, and microbial ecology studies, which led to the selection of strains that are capable of synthesizing alcohol and desirable volatile compounds. Results show that a mixed starter inoculum containing Pichia fermentans and Saccharomyces cerevisiae leads to a fermented product that contains 8.37% alcohol (v/v). The gas chromatography and mass spectrometry (GC-MS) analysis shows the presence of 9 major volatile compounds (Isobutanol, Isopentanol, Ethyl acetate, Isoamyl acetate, Ethyl octanoate, Ethyl decanoate, Ethyl 9-decanoate, β-Phenylethyl acetate, and Phenylethyl alcohol) that have ethereal, fruity, aromatic notes that are considered to be essential for a fine wine flavor. These compounds harmonically synergize with the alcohol to produce a fermented product with a unique flavor and taste. Several assays using the mixed culture show that the process is stable, predictable, controllable, and reproducible. Moreover, the results show that a mixed culture leads to a broader range of aromatic products than that produced by a single, pure culture. Therefore, we conclude that combinations of Saccharomyces strains and non-Saccharomyces strains can be used to obtain high-quality fermented beverages from prickly pear juice. PMID:22417507

  14. Role of bacterial adhesion in the microbial ecology of biofilms in cooling tower systems

    PubMed Central

    Liu, Yang; Zhang, Wei; Sileika, Tadas; Warta, Richard; Cianciotto, Nicholas P.; Packman, Aaron

    2009-01-01

    The fate of the three heterotrophic biofilm forming bacteria, Pseudomonas aeruginosa, Klebsiella pneumoniae and Flavobacterium sp. in pilot scale cooling towers was evaluated both by observing the persistence of each species in the recirculating water and the formation of biofilms on steel coupons placed in each cooling tower water reservoir. Two different cooling tower experiments were performed: a short-term study (6 days) to observe the initial bacterial colonization of the cooling tower, and a long-term study (3 months) to observe the ecological dynamics with repeated introduction of the test strains. An additional set of batch experiments (6 days) was carried out to evaluate the adhesion of each strain to steel surfaces under similar conditions to those found in the cooling tower experiments. Substantial differences were observed in the microbial communities that developed in the batch systems and cooling towers. P. aeruginosa showed a low degree of adherence to steel surfaces both in batch and in the cooling towers, but grew much faster than K. pneumoniae and Flavobacterium in mixed-species biofilms and ultimately became the dominant organism in the closed batch systems. However, the low degree of adherence caused P. aeruginosa to be rapidly washed out of the open cooling tower systems, and Flavobacterium became the dominant microorganism in the cooling towers in both the short-term and long-term experiments. These results indicate that adhesion, retention and growth on solid surfaces play important roles in the bacterial community that develops in cooling tower systems. PMID:19177226

  15. Precision-guided antimicrobial peptide as a targeted modulator of human microbial ecology

    PubMed Central

    Guo, Lihong; McLean, Jeffrey S.; Yang, Youngik; Eckert, Randal; Kaplan, Christopher W.; Kyme, Pierre; Sheikh, Omid; Varnum, Brian; Lux, Renate; Shi, Wenyuan; He, Xuesong

    2015-01-01

    One major challenge to studying human microbiome and its associated diseases is the lack of effective tools to achieve targeted modulation of individual species and study its ecological function within multispecies communities. Here, we show that C16G2, a specifically targeted antimicrobial peptide, was able to selectively kill cariogenic pathogen Streptococcus mutans with high efficacy within a human saliva-derived in vitro oral multispecies community. Importantly, a significant shift in the overall microbial structure of the C16G2-treated community was revealed after a 24-h recovery period: several bacterial species with metabolic dependency or physical interactions with S. mutans suffered drastic reduction in their abundance, whereas S. mutans’ natural competitors, including health-associated Streptococci, became dominant. This study demonstrates the use of targeted antimicrobials to modulate the microbiome structure allowing insights into the key community role of specific bacterial species and also indicates the therapeutic potential of C16G2 to achieve a healthy oral microbiome. PMID:26034276

  16. The effect of malathion on the activity, performance, and microbial ecology of activated sludge.

    PubMed

    Rauglas, Erik; Martin, Seth; Bailey, Kandace; Magnuson, Matthew; Phillips, Rebecca; Harper, Willie F

    2016-12-01

    This study evaluated the effect of a VX (O-ethyl S-[2-(diisopropylamino)ethyl] methylphosphonothioate) surrogate (malathion) on the activity, performance, and ecology of activated sludge bioreactors. In the presence of malathion, the maximum observed respiration rates varied between 43 and 53 μg/O2 min, generally similar to the 49 μg O2/min rates observed in controls. Malathion did not alter the respiration ratio of O2 consumed-to-CO2 produced nor did it impact the shape of the oxygen consumption curves during respirometry. Shorter term (12 h) batch tests showed that both chemical oxygen demand (COD) and ammonia removal were not negatively impacted by the presence of 0.1-3 mg/L malathion. Longer term continuous addition (i.e. 40 days) of 0.1 mg/L of malathion also had no effect on COD and ammonia removal. In contrast to shorter term exposures, longer term continuous addition of 3 mg/L of malathion negatively impacted both COD and nitrogen removal and was associated with shifts in the abundance of species that are common to activated sludge. These results illustrate the impact that chemicals like malathion may have on COD removal, and nitrification, as well as the robustness of activated sludge microbial communities.

  17. The effect of malathion on the activity, performance, and microbial ecology of activated sludge.

    PubMed

    Rauglas, Erik; Martin, Seth; Bailey, Kandace; Magnuson, Matthew; Phillips, Rebecca; Harper, Willie F

    2016-12-01

    This study evaluated the effect of a VX (O-ethyl S-[2-(diisopropylamino)ethyl] methylphosphonothioate) surrogate (malathion) on the activity, performance, and ecology of activated sludge bioreactors. In the presence of malathion, the maximum observed respiration rates varied between 43 and 53 μg/O2 min, generally similar to the 49 μg O2/min rates observed in controls. Malathion did not alter the respiration ratio of O2 consumed-to-CO2 produced nor did it impact the shape of the oxygen consumption curves during respirometry. Shorter term (12 h) batch tests showed that both chemical oxygen demand (COD) and ammonia removal were not negatively impacted by the presence of 0.1-3 mg/L malathion. Longer term continuous addition (i.e. 40 days) of 0.1 mg/L of malathion also had no effect on COD and ammonia removal. In contrast to shorter term exposures, longer term continuous addition of 3 mg/L of malathion negatively impacted both COD and nitrogen removal and was associated with shifts in the abundance of species that are common to activated sludge. These results illustrate the impact that chemicals like malathion may have on COD removal, and nitrification, as well as the robustness of activated sludge microbial communities. PMID:27594690

  18. Role of bacterial adhesion in the microbial ecology of biofilms in cooling tower systems.

    PubMed

    Liu, Yang; Zhang, Wei; Sileika, Tadas; Warta, Richard; Cianciotto, Nicholas P; Packman, Aaron

    2009-01-01

    The fate of the three heterotrophic biofilm forming bacteria, Pseudomonas aeruginosa, Klebsiella pneumoniae and Flavobacterium sp. in pilot scale cooling towers was evaluated both by observing the persistence of each species in the recirculating water and the formation of biofilms on steel coupons placed in each cooling tower water reservoir. Two different cooling tower experiments were performed: a short-term study (6 days) to observe the initial bacterial colonization of the cooling tower, and a long-term study (3 months) to observe the ecological dynamics with repeated introduction of the test strains. An additional set of batch experiments (6 days) was carried out to evaluate the adhesion of each strain to steel surfaces under similar conditions to those found in the cooling tower experiments. Substantial differences were observed in the microbial communities that developed in the batch systems and cooling towers. P. aeruginosa showed a low degree of adherence to steel surfaces both in batch and in the cooling towers, but grew much faster than K. pneumoniae and Flavobacterium in mixed-species biofilms and ultimately became the dominant organism in the closed batch systems. However, the low degree of adherence caused P. aeruginosa to be rapidly washed out of the open cooling tower systems, and Flavobacterium became the dominant microorganism in the cooling towers in both the short-term and long-term experiments. These results indicate that adhesion, retention and growth on solid surfaces play important roles in the bacterial community that develops in cooling tower systems. PMID:19177226

  19. Ecology and metabolism of the beneficial intestinal commensal bacterium Faecalibacterium prausnitzii

    PubMed Central

    Miquel, Sylvie; Martín, Rebeca; Bridonneau, Chantal; Robert, Véronique; Sokol, Harry; Bermúdez-Humarán, Luis G; Thomas, Muriel; Langella, Philippe

    2014-01-01

    Faecalibacterium prausnitzii is a major commensal bacterium, and its prevalence is often decreased in conditions of intestinal dysbiosis. The phylogenic identity of this bacterium was described only recently. It is still poorly characterized, and its specific growth requirements in the human gastrointestinal tract are not known. In this review, we consider F. prausnitzii metabolism, its ecophysiology in both humans and animals, and the effects of drugs and nutrition on its population. We list important questions about this beneficial and ubiquitous commensal bacterium that it would be valuable to answer. PMID:24637606

  20. Ecology and metabolism of the beneficial intestinal commensal bacterium Faecalibacterium prausnitzii.

    PubMed

    Miquel, Sylvie; Martín, Rebeca; Bridonneau, Chantal; Robert, Véronique; Sokol, Harry; Bermúdez-Humarán, Luis G; Thomas, Muriel; Langella, Philippe

    2014-01-01

    Faecalibacterium prausnitzii is a major commensal bacterium, and its prevalence is often decreased in conditions of intestinal dysbiosis. The phylogenic identity of this bacterium was described only recently. It is still poorly characterized, and its specific growth requirements in the human gastrointestinal tract are not known. In this review, we consider F. prausnitzii metabolism, its ecophysiology in both humans and animals, and the effects of drugs and nutrition on its population. We list important questions about this beneficial and ubiquitous commensal bacterium that it would be valuable to answer.

  1. [Intestinal microbial biocenosis in patients with systemic lupus erythematosus treated with prednisolone].

    PubMed

    Gul'neva, M Iu; Shilkina, N P

    2009-01-01

    This study of intestinal microflora included 60 patients with systemic lupus erythematosus (LE) and 30 ones with cardiologic problems (controls). LE was diagnosed using criteria of American Rheumatologic Association (1982). Activity of the disease was estimated based on the ECLAM index. Nineteen patients with grade II LE were given with prednisolone (15 mg/day) and 15 ones did not receive this treatment. The qualitative and quantitative composition of intestinal microflora was evaluated by bacteriological methods. Results of the study were analysed with the use of STATISTICA 6.0 software system (StatSoft). Prednisolone was shown to alter the qualitative composition of microflora and the structure of symbiotic interactions between different organisms. Specifically, colonic flora contained more enterococci and organisms possessed of hemolytic activity whereas quantitative composition remained practically unchanged. Enterococci and colibacilli with modified enzymatic activity became predominant forms. It is concluded that prednisolone therapy affects colonic microbiocenosis in patients with LE favouring the development of enterococci, atypical colibacilli, and organisms with hemolytic activity. PMID:19670716

  2. Earth's Earliest Ecosystems in the Classroom: The Use of Microbial Mats to Illustrate and Demonstrate General Principles of Scientific Inquiry and Microbial Ecology

    NASA Astrophysics Data System (ADS)

    Bebout, B. M.; Bucaria, R.

    2004-12-01

    Microbial mats are living examples of the most ancient biological communities on Earth. As Earth's earliest ecosystems, they are centrally important to understanding the history of life on our planet and are useful models for the search for life elsewhere. As relatively small (but complete) ecosystems, microbial mats are also extremely useful for educational activities. Mats may be used to demonstrate a wide variety of concepts in general and microbial ecology, including the biogeochemical cycling of elements, photosynthesis and respiration, and the and the origin of the Earth's present oxygen containing atmosphere. Microbial mats can be found in a number of common environments accessible to teachers, and laboratory microbial mats can even be constructed using materials purchased from biological supply houses. With funding from NASA's Exobiology program, provided as a supplement to our research funding, we are developing curriculum and web-based activities centered on the use of microbial mats as tools for demonstrating general principles in ecology, and the scientific process. A web site with useful background information and links is now on-line. The curriculum, now in the pilot phase, is an integrated module having Science, Math and Language Art threads. A "Web Lab", featuring living mats maintained in a mini-aquarium, and complete with remotely-operable instrumentation not commonly available in classrooms, will be available to classrooms over the Internet. Using that system, the responses of the mat community to changes in environmental parameters, (e.g., light, pH, flow, and temperature) can be monitored using microsensors. Students will be able to develop hypotheses and propose experiments in the Web Lab to test them. Data from these experiments will be posted in real time and students will be able to collect the data, analyze it, and post results and conclusions back to the web page in a true implementation of the scientific inquiry process. The web site

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

    Pharmaceuticals and other micropollutants have been detected in drinking water, groundwater, surface water, and soil around the world. Even in locations where wastewater treatment is required, they can be found in drinking water wells, municipal water supplies, and agricultural soils. It is clear conventional wastewater treatment technologies are not meeting the challenge of the mounting pressures on global freshwater supplies. Cost-effective ecological wastewater treatment technologies have been developed in response. To determine whether the removal of micropollutants in ecological wastewater treatment plants (WWTPs) is promoted by the plant-microbe interactions, as has been reported for other recalcitrant xenobiotics, biofilm microbial communities growing on the surfaces of plant roots were profiled by whole metagenome sequencing and compared to the microbial communities residing in the wastewater. In this study, the concentrations of pharmaceuticals and personal care products (PPCPs) were quantified in each treatment tank of the ecological WWTP treating human wastewater at a highway rest stop and visitor center in Vermont. The concentrations of detected PPCPs were substantially greater than values reported for conventional WWTPs likely due to onsite recirculation of wastewater. The greatest reductions in PPCPs concentrations were observed in the anoxic treatment tank where Bacilli dominated the biofilm community. Benzoate degradation was the most abundant xenobiotic metabolic category identified throughout the system. Collectively, the microbial communities residing in the wastewater were taxonomically and metabolically more diverse than the immersed plant root biofilm. However, greater heterogeneity and higher relative abundances of xenobiotic metabolism genes was observed for the root biofilm. PMID:27610223

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

    PubMed

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

    2015-07-01

    Impacts of warming with open-top chambers on microbial communities in wet conditions and in conditions resulting from moderate water-level drawdown (WLD) were studied across 0-50 cm depth in northern and southern boreal sedge fens. Warming alone decreased microbial biomass especially in the northern fen. Impact of warming on microbial PLFA and fungal ITS composition was more obvious in the northern fen and linked to moisture regime and sample depth. Fungal-specific PLFA increased in the surface peat in the drier regime and decreased in layers below 10 cm in the wet regime after warming. OTUs representing Tomentella and Lactarius were observed in drier regime and Mortierella in wet regime after warming in the northern fen. The ectomycorrhizal fungi responded only to WLD. Interestingly, warming together with WLD decreased archaeal 16S rRNA copy numbers in general, and fungal ITS copy numbers in the northern fen. Expectedly, many results indicated that microbial response on warming may be linked to the moisture regime. Results indicated that microbial community in the northern fen representing Arctic soils would be more sensitive to environmental changes. The response to future climate change clearly may vary even within a habitat type, exemplified here by boreal sedge fen. PMID:26066028

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

    PubMed

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

    2015-07-01

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

  7. Fumonisins affect the intestinal microbial homeostasis in broiler chickens, predisposing to necrotic enteritis.

    PubMed

    Antonissen, Gunther; Croubels, Siska; Pasmans, Frank; Ducatelle, Richard; Eeckhaut, Venessa; Devreese, Mathias; Verlinden, Marc; Haesebrouck, Freddy; Eeckhout, Mia; De Saeger, Sarah; Antlinger, Birgit; Novak, Barbara; Martel, An; Van Immerseel, Filip

    2015-09-23

    Fumonisins (FBs) are mycotoxins produced by Fusarium fungi. This study aimed to investigate the effect of these feed contaminants on the intestinal morphology and microbiota composition, and to evaluate whether FBs predispose broilers to necrotic enteritis. One-day-old broiler chicks were divided into a group fed a control diet, and a group fed a FBs contaminated diet (18.6 mg FB1+FB2/kg feed). A significant increase in the plasma sphinganine/sphingosine ratio in the FBs-treated group (0.21 ± 0.016) compared to the control (0.14 ± 0.014) indicated disturbance of the sphingolipid biosynthesis. Furthermore, villus height and crypt depth of the ileum was significantly reduced by FBs. Denaturing gradient gel electrophoresis showed a shift in the microbiota composition in the ileum in the FBs group compared to the control. A reduced presence of low-GC containing operational taxonomic units in ileal digesta of birds exposed to FBs was demonstrated, and identified as a reduced abundance of Candidatus Savagella and Lactobaccilus spp. Quantification of total Clostridium perfringens in these ileal samples, previous to experimental infection, using cpa gene (alpha toxin) quantification by qPCR showed an increase in C. perfringens in chickens fed a FBs contaminated diet compared to control (7.5 ± 0.30 versus 6.3 ± 0.24 log10 copies/g intestinal content). After C. perfringens challenge, a higher percentage of birds developed subclinical necrotic enteritis in the group fed a FBs contaminated diet as compared to the control (44.9 ± 2.22% versus 29.8 ± 5.46%).

  8. Fine-scale distribution patterns of Synechococcus ecological diversity in microbial mats of Mushroom Spring, Yellowstone National Park.

    PubMed

    Becraft, Eric D; Cohan, Frederick M; Kühl, Michael; Jensen, Sheila I; Ward, David M

    2011-11-01

    Past analyses of sequence diversity in high-resolution protein-encoding genes have identified putative ecological species of unicellular cyanobacteria in the genus Synechococcus, which are specialized to 60°C but not 65°C in Mushroom Spring microbial mats. Because these studies were limited to only two habitats, we studied the distribution of Synechococcus sequence variants at 1°C intervals along the effluent flow channel and at 80-μm vertical-depth intervals throughout the upper photic layer of the microbial mat. Diversity at the psaA locus, which encodes a photosynthetic reaction center protein (PsaA), was sampled by PCR amplification, cloning, and sequencing methods at 60, 63, and 65°C sites. The evolutionary simulation programs Ecotype Simulation and AdaptML were used to identify putative ecologically distinct populations (ecotypes). Ecotype Simulation predicted a higher number of putative ecotypes in cases where habitat variation was limited, while AdaptML predicted a higher number of ecologically distinct phylogenetic clades in cases where habitat variation was high. Denaturing gradient gel electrophoresis was used to track the distribution of dominant sequence variants of ecotype populations relative to temperature variation and to O₂, pH, and spectral irradiance variation, as measured using microsensors. Different distributions along effluent channel flow and vertical gradients, where temperature, light, and O₂ concentrations are known to vary, confirmed the ecological distinctness of putative ecotypes.

  9. Fine-Scale Distribution Patterns of Synechococcus Ecological Diversity in Microbial Mats of Mushroom Spring, Yellowstone National Park▿†

    PubMed Central

    Becraft, Eric D.; Cohan, Frederick M.; Kühl, Michael; Jensen, Sheila I.; Ward, David M.

    2011-01-01

    Past analyses of sequence diversity in high-resolution protein-encoding genes have identified putative ecological species of unicellular cyanobacteria in the genus Synechococcus, which are specialized to 60°C but not 65°C in Mushroom Spring microbial mats. Because these studies were limited to only two habitats, we studied the distribution of Synechococcus sequence variants at 1°C intervals along the effluent flow channel and at 80-μm vertical-depth intervals throughout the upper photic layer of the microbial mat. Diversity at the psaA locus, which encodes a photosynthetic reaction center protein (PsaA), was sampled by PCR amplification, cloning, and sequencing methods at 60, 63, and 65°C sites. The evolutionary simulation programs Ecotype Simulation and AdaptML were used to identify putative ecologically distinct populations (ecotypes). Ecotype Simulation predicted a higher number of putative ecotypes in cases where habitat variation was limited, while AdaptML predicted a higher number of ecologically distinct phylogenetic clades in cases where habitat variation was high. Denaturing gradient gel electrophoresis was used to track the distribution of dominant sequence variants of ecotype populations relative to temperature variation and to O2, pH, and spectral irradiance variation, as measured using microsensors. Different distributions along effluent channel flow and vertical gradients, where temperature, light, and O2 concentrations are known to vary, confirmed the ecological distinctness of putative ecotypes. PMID:21890675

  10. Ecological effects of combined pollution associated with e-waste recycling on the composition and diversity of soil microbial communities.

    PubMed

    Liu, Jun; He, Xiao-Xin; Lin, Xue-Rui; Chen, Wen-Ce; Zhou, Qi-Xing; Shu, Wen-Sheng; Huang, Li-Nan

    2015-06-01

    The crude processing of electronic waste (e-waste) has led to serious contamination in soils. While microorganisms may play a key role in remediation of the contaminated soils, the ecological effects of combined pollution (heavy metals, polychlorinated biphenyls, and polybrominated diphenyl ethers) on the composition and diversity of microbial communities remain unknown. In this study, a suite of e-waste contaminated soils were collected from Guiyu, China, and the indigenous microbial assemblages were profiled by 16S rRNA high-throughput sequencing and clone library analysis. Our data revealed significant differences in microbial taxonomic composition between the contaminated and the reference soils, with Proteobacteria, Acidobacteria, Bacteroidetes, and Firmicutes dominating the e-waste-affected communities. Genera previously identified as organic pollutants-degrading bacteria, such as Acinetobacter, Pseudomonas, and Alcanivorax, were frequently detected. Canonical correspondence analysis revealed that approximately 70% of the observed variation in microbial assemblages in the contaminated soils was explained by eight environmental variables (including soil physiochemical parameters and organic pollutants) together, among which moisture content, decabromodiphenyl ether (BDE-209), and copper were the major factors. These results provide the first detailed phylogenetic look at the microbial communities in e-waste contaminated soils, demonstrating that the complex combined pollution resulting from improper e-waste recycling may significantly alter soil microbiota.

  11. Biochemistry and Ecology of Novel Cytochromes Catalyzing Fe(II) Oxidation by an Acidophilic Microbial Community

    NASA Astrophysics Data System (ADS)

    Singer, S. W.; Jeans, C. J.; Thelen, M. P.; Verberkmoes, N. C.; Hettich, R. C.; Chan, C. S.; Banfield, J. F.

    2007-12-01

    An acidophilic microbial community found in the Richmond Mine at Iron Mountain, CA forms abundant biofilms in extremely acidic (pH<1) and toxic metal conditions. In this ecosystem, biological Fe(II) oxidation is critical to the metabolic functioning of the community, and in turn this process generates acid mine drainage, causing an environmental catastrophe. Two conspicuous novel proteins isolated from these biofilms were identified as gene products of Leptospirillum group II and were characterized as cytochromes with unique properties. Sulfuric acid extraction of biofilm samples liberated one of these proteins, a 16 kDa cytochrome with an unusual alpha-band absorption at 579 (Cyt579). Genomic sequencing of multiple biofilms indicated that several variants of Cyt579 were present in Leptospirillum strains. Intact protein MS analysis identified the dominant variants in each biofilm and documented multiple N-terminal cleavage sites for Cyt579. By combining biochemical, geochemical and microbiological data, we established that the sequence variation and N-terminal processing of Cyt579 are selected by ecological conditions. In addition to the soluble Cyt579, the second cytochrome appears as a much larger protein complex of ~210 kDa predominant in the biofilm membrane fraction, and has an alpha-band absorption at 572 nm. The 60 kDa cytochrome subunit, Cyt572, resides in the outer membrane of LeptoII, and readily oxidizes Fe(II) at low pH (0.95 - 3.0). Several genes encoding Cyt572 were localized within a recombination hotspot between two strains of LeptoII, causing a large range of variation in the sequences. Genomic sequencing and MS proteomic studies established that the variants were also selected by ecological conditions. A general mechanistic model for Fe(II) oxidation has been developed from these studies. Initial Fe(II) oxidation by Cyt572 occurs at the outer membrane. Cyt572 then transfers electrons to Cyt579, perhaps representing an initial step in energy flow

  12. Constraining Microbial Cycling of Carbon and Sulfur and Relationships to Macrofaunal Ecology in Cretaceous Cold Seeps

    NASA Astrophysics Data System (ADS)

    Lyons, T.; Shapiro, R.; Benjamin, G.; Bates, S.; Anderson, J.; Gilhooly, W.; Parsons-Hubbard, K.

    2007-12-01

    , location (surface vs. subsurface), mechanisms, and specific microbial factors behind carbonate authigenesis and their relationships to macrofaunal ecology.

  13. Molecular ecological tools to decipher the role of our microbial mass in obesity.

    PubMed

    Hermes, G D A; Zoetendal, E G; Smidt, H

    2015-03-01

    After birth, our gastrointestinal (GI) tract is colonised by a highly complex assemblage of microbes, collectively termed the GI microbiota, that develops intimate interactions with our body. Recent evidence indicates that the GI microbiota and its products may contribute to the development of obesity and related diseases. This, coupled with the current worldwide epidemic of obesity, has moved microbiome research into the spotlight of attention. Although the main cause of obesity and its associated metabolic complications is excess caloric intake compared with expenditure, differences in GI tract microbial ecology between individuals might be an important biomarker, mediator or new therapeutic target. This can be investigated using a diverse set of complementary so called -omics technologies, such as 16S ribosomal RNA gene-targeted composition profiling, metabolomics, metagenomics, metatranscriptomics and metaproteomics. This review aims to describe the different molecular approaches and their contributions to our understanding of the role of the GI microbiota in host energy homeostasis. Correspondingly, we highlight their respective strengths, but also try to create awareness for their specific limitations. However, it is currently still unclear which bacterial groups play a role in the development of obesity in humans. This might partly be explained by the heterogeneity in genotype, lifestyle, diet and the complex ethology of obesity and its associated metabolic disorders (OAMD). Nevertheless, recent research on this matter has shown a conceptual shift by focusing on more homogenous subpopulations, through the use of both anthropometric (weight, total body fat) as well as biochemical variables (insulin resistance, hyperlipidaemia) to define categories. Combined with technological advances, recent data suggests that an OAMD associated microbiota can be characterised by a potential pro-inflammatory composition, with less potential for the production of short chain

  14. The Starting Lineup: Key Microbial Players in Intestinal Immunity and Homeostasis

    PubMed Central

    Reading, Nicola C.; Kasper, Dennis L.

    2011-01-01

    The complexity of microbiota inhabiting the intestine is increasingly apparent. Delicate balance of numerous bacterial species can affect development of the immune system, how susceptible a host is to pathogenic organisms, and the auto-inflammatory state of the host. In the last decade, with the increased use of germ-free mice, gnotobiotic mice, and animal models in which a germ-free animal has been colonized with a foreign microbiota such as humanized mice, it has been possible to delineate relationships that specific bacteria have with the host immune system and to show what role they may play in overall host health. These models have not only allowed us to tease out the roles of individual species, but have also allowed the discovery and characterization of functionally unknown organisms. For example, segmented filamentous bacteria (SFB) have been shown to play a vital role in expansion of IL-17 producing cells. Prior to linking their key role in immune system development, little was known about these organisms. Bacteroides fragilis can rescue some of the immune defects of gnotobiotic mice after mono-colonization and have anti-inflammatory properties that can alleviate colitis and experimental allergic encephalitis in murine models. Additionally, Clostridium species have most recently been shown to expand regulatory T-cell populations leading to anti-inflammatory conditions. This review will highlight and summarize some of the major findings within the last decade concerning the role of select groups of bacteria including SFB, Clostridium, Bacteroides, Bifidobacterium, and Lactobacillus, and their impact on host mucosal immune systems. PMID:21779278

  15. Prebiotic effect of fructooligosaccharide in the simulator of the human intestinal microbial ecosystem (SHIME® model).

    PubMed

    Sivieri, Katia; Morales, Martha L Villarreal; Saad, Susana M I; Adorno, Maria A Tallarico; Sakamoto, Isabel Kimiko; Rossi, Elizeu A

    2014-08-01

    Maintaining "gut health" is a goal for scientists throughout the world. Therefore, microbiota management models for testing probiotics, prebiotics, and synbiotics have been developed. The SHIME(®) model was used to study the effect of fructooligosaccharide (FOS) on the fermentation pattern of the colon microbiota. Initially, an inoculum prepared from human feces was introduced into the reactor vessels and stabilized over 2 weeks using a culture medium. This stabilization period was followed by a 2-week control period during which the microbiota was monitored. The microbiota was then subjected to a 4-week treatment period by adding 5 g/day-1 FOS to vessel one (the "stomach" compartment). Plate counts, Denaturing Gradient Gel Electrophoresis (DGGE), short-chain fatty acid (SCFA), and ammonium analyses were used to observe the influence of FOS treatment in simulated colon compartments. A significant increase (P<.01) in the Lactobacillus spp. and Bifidobacterium spp. populations was observed during the treatment period. The DGGE obtained showed the overall microbial community was changed in the ascending colon compartment of the SHIME reactor. FOS induced increase of the SCFA concentration (P<.05) during the treatment period, mainly due to significant increased levels of acetic and butyric acids. However, ammonium concentrations increased during the same period (P<.01). This study indicates the usefulness of in vitro methods that simulate the colon region as part of research towards the improvement of human health.

  16. Prebiotic effect of fructooligosaccharide in the simulator of the human intestinal microbial ecosystem (SHIME® model).

    PubMed

    Sivieri, Katia; Morales, Martha L Villarreal; Saad, Susana M I; Adorno, Maria A Tallarico; Sakamoto, Isabel Kimiko; Rossi, Elizeu A

    2014-08-01

    Maintaining "gut health" is a goal for scientists throughout the world. Therefore, microbiota management models for testing probiotics, prebiotics, and synbiotics have been developed. The SHIME(®) model was used to study the effect of fructooligosaccharide (FOS) on the fermentation pattern of the colon microbiota. Initially, an inoculum prepared from human feces was introduced into the reactor vessels and stabilized over 2 weeks using a culture medium. This stabilization period was followed by a 2-week control period during which the microbiota was monitored. The microbiota was then subjected to a 4-week treatment period by adding 5 g/day-1 FOS to vessel one (the "stomach" compartment). Plate counts, Denaturing Gradient Gel Electrophoresis (DGGE), short-chain fatty acid (SCFA), and ammonium analyses were used to observe the influence of FOS treatment in simulated colon compartments. A significant increase (P<.01) in the Lactobacillus spp. and Bifidobacterium spp. populations was observed during the treatment period. The DGGE obtained showed the overall microbial community was changed in the ascending colon compartment of the SHIME reactor. FOS induced increase of the SCFA concentration (P<.05) during the treatment period, mainly due to significant increased levels of acetic and butyric acids. However, ammonium concentrations increased during the same period (P<.01). This study indicates the usefulness of in vitro methods that simulate the colon region as part of research towards the improvement of human health. PMID:24654949

  17. Ecological Effect of Ceftaroline-Avibactam on the Normal Human Intestinal Microbiota

    PubMed Central

    Rashid, Mamun-Ur; Rosenborg, Staffan; Panagiotidis, Georgios; Söderberg-Löfdal, Karin; Weintraub, Andrej

    2015-01-01

    Ceftaroline-avibactam is a new combination of the antibiotic ceftaroline with a novel non-β-lactam β-lactamase inhibitor, avibactam. The purpose of the present study was to investigate the effect of ceftaroline-avibactam on the human intestinal microbiota. Fourteen healthy volunteers received ceftaroline-avibactam (600 mg ceftaroline fosamil and 600 mg avibactam) intravenously over 2 h every 8 h on days 1 to 6 and as a single dose on day 7. Fecal samples were collected on day −1 (within 24 h of the first infusion on day 1) and on days 2, 5, 7, 9, 14, and 21. Escherichia coli numbers decreased during the study and normalized on day 21. An increased number of Klebsiella bacteria appeared on day 14 and normalized on day 21. The number of other enterobacteria decreased during the study, and the number of enterococci decreased from days 2 to 7 and normalized on day 9. Candida numbers increased from days 5 to 9 and normalized after day 14. The number of lactobacilli decreased during the study and recovered on day 14. The number of bifidobacteria decreased on day 2 and normalized on day 21. The number of Bacteroides bacteria was unchanged. Clostridium difficile numbers decreased on days 7 and 9 and increased on days 14 and 21. A toxigenic C. difficile strain was detected in one volunteer on day 21 with no reported adverse events. Plasma samples were collected on days −1, 2, 5, and 7. Ceftaroline and avibactam concentrations were 0 to 34.5 mg/liter and 0 to 61.6 mg/liter, respectively, in plasma and 0 to 35.4 mg/kg and 0 to 98.5 mg/kg, respectively, in feces. (This study is registered in the European Clinical Trials Database [https://eudract.ema.europa.eu/] under number EudraCT 2012 004921-25.) PMID:25987638

  18. The effect of some ecological factors on the intestinal parasite loads of the Asian elephant (Elephas maximus) in southern India.

    PubMed

    Vidya, T N C; Sukumar, R

    2002-09-01

    Some ecological factors that might potentially influence intestinal parasite loads in the Asian elephant (Elephas maximus Linn.) were investigated in the Nilgiris, southern India. Fresh dung samples from identified animals were analysed, and the number of eggs/g of dung used as an index of parasite load. Comparisons across seasons and habitats revealed that parasite loads were significantly higher during the dry season than the wet season, but were not different between the dry-deciduous and dry-thorn forests in either season. After accounting for the effect of age on body condition, there was no correlation between body condition, assessed visually using morphological criteria, and parasite load in either season. Individuals of different elephant herds were not characterized by distinct parasite communities in either season. When intra-individual variation was examined, samples collected from the same individual within a day differed significantly in egg densities, while the temporal variation over several weeks or months (within a season) was much less. Egg densities within dung piles were uniform, enabling a simpler collection method henceforth.

  19. Analysis of the intestinal microbial community structure of healthy and long-living elderly residents in Gaotian Village of Liuyang City.

    PubMed

    Yu, Xiaomin; Wu, Xiaoli; Qiu, Liang; Wang, Dengyuan; Gan, Min; Chen, Xingxing; Wei, Hua; Xu, Feng

    2015-11-01

    Gaotian, one typical conservative village in rural area of South China, is differentiated from other adjacent village for its longevity and health situation of residents. To ascertain the difference of intestinal microbial community between Gaotian and other region, high-throughput sequencing and systematical bioinformation analyses was adopted to compare 21 samples in long life group with 28 in control group. The α diversity showed that the diversity of species of intestinal flora of Gaotian villagers was higher than that of control group, while the β diversity showed that the similarity of intestinal flora for Gaotian residents was also much higher than that of control group. OTU cluster analysis and Venn diagram showed that the intestinal microbial community of Gaotian villagers is different from that of control group. To quantitatively compare the main flora constitution in all samples, real-time PCR was performed, and the results showed that the biomass of Enterococcus, Lactobacillus, Enterobacteriaceae, Clostridium perfringens, and Bacteroides of Gaotian villages is generally significantly higher than that of control group. Remarkably, some special species, i.e., Methanobacterium, Butyricimonas, Deinococcus, and Streptococcaceae, have been found in Gaotian villagers. Overall, this study lays a preparatory basis for exploration of the resources of special species from healthy and long-living elderly Gaotian villagers and for proposal of a hypothesis, namely, the diversity in intestinal flora of Gaotian might contribute to the longevity and health of local residents. Further study should be focused on screening and functional evaluation of the special species in the long-life residents. PMID:26298698

  20. Growth performance and gastrointestinal microbial ecology responses of piglets receiving Saccharomyces cerevisiae fermentation products after an oral challenge with Escherichia coli (K88).

    PubMed

    Kiarie, E; Bhandari, S; Scott, M; Krause, D O; Nyachoti, C M

    2011-04-01

    The effects of Saccharomyces cerevisiae fermentation products (YFP) on growth performance and gastrointestinal (GIT) microbial ecology in 90 weanling pigs orally challenged with Escherichia coli K88(+) (ETEC) were investigated. The YFP were an original YFP product (XPC) and a water-suspendable yeast fermentation prototype (WSYFP) from a commercial company. Treatments consisted of a negative control (NC, no in-feed or in-water additive), carbadox (AB, 55 mg of carbadox/kg of feed), XPC (in feed, 0.2%), and WSYFP (in water, 0.5, 1, or 2 g/pig per day), and each was allotted to 5 pens (3 pigs/pen). The diets met the 1998 NRC specifications. Pigs were acclimated to treatments for a 7-d period before an ETEC challenge. On d 8, blood was collected from pigs to determine the baseline packed cell volume (PCV) measurement, and pigs were orally challenged with ETEC. At various time points postchallenge, blood samples were taken, performance measures and fecal consistency scores were recorded, and gut digesta and tissue samples were taken to evaluate GIT morphology, microbial ecology, and metabolites. Preplanned contrasts were used for comparison. Pigs receiving YFP had greater ADFI than NC pigs on d 3 (424 vs. 378 g/d; P = 0.01) and d 7 (506 vs. 458 g/d; P = 0.03) postchallenge. This effect of YFP on ADFI was similar to that of AB on d 3, but pigs receiving AB ate more (576 vs. 506 g/d; P = 0.03) at d 7 than pigs receiving YFP. Pigs exhibited reduced (P < 0.001) PCV upon ETEC challenge; however, pigs receiving additives sustained a greater (P < 0.05) PCV at 72 h compared with the NC group. Compared with the NC pigs, pigs receiving YFP showed a smaller (P < 0.05) number of ileal mucosa adherent ETEC and prevalence of the order Enterobacteriales in the ileal digesta, which corresponded to less (5.09 vs. 6.97 mg/dL; P = 0.03) colonic ammonia on d 7 postchallenge. Most of the indices for ileal digesta bacterial richness and diversity were greater (P < 0.01) for YFP pigs compared

  1. Effect of sulfate and lactate loading rates on the respiration process and microbial population changes measured by ecological indices.

    PubMed

    García-Saucedo, C; Fernández, F J; Cuervo-López, F M; Gómez, J

    2015-01-01

    In a sulfate reducing process, increasing loading rates and sulfide accumulation may induce population changes resulting in decreasing effectiveness of the process. Thus, the relationship between microbial metabolism changes and population dynamics was studied. An upflow anaerobic sludge blanket reactor was operated at different sulfate loading rates (SLR), from 290 to 981 mg SO4-S/L d at a constant carbon/sulfur ratio of 0.75. When the SLR was increased, the total organic carbon and sulfate consumption efficiencies decreased to nearly 30% and 25%, respectively. The acetate and propionate yields increased with increasing SLR and 385±7 mg sulfide-S/L d was reached. The ecological indices, determined by random amplified polymorphic DNA and denaturing gradient gel electrophoresis techniques, diversity and evenness were found to be constant, and similarity coefficient values remained higher than 76%. The results suggest that the microbial population changes were negligible compared with metabolic changes when SLR was increased. The sulfide accumulation did not modify the microbial diversity. The sequencing of 16S rRNA genes showed strains related to sulfate reducing, fermentation, and methanogenesis processes. The results indicated that the decreasing of effectiveness, under the experimental conditions tested, was dependent more on operational parameters than microbial changes. PMID:25607675

  2. Kinetics and microbial ecology of batch sulfidogenic bioreactors for co-treatment of municipal wastewater and acid mine drainage.

    PubMed

    Deng, Dongyang; Weidhaas, Jennifer L; Lin, Lian-Shin

    2016-03-15

    The kinetics and microbial ecology in sulfidogenic bioreactors used in a novel two-stage process for co-treatment of acid mine drainage (AMD) and municipal wastewater (MWW) were investigated. Michaelis-Menten modeling of COD oxidation by sulfate reducing bacteria (SRB) (Vmax=0.33mgL(-1)min(-1), Km=4.3mgL(-1)) suggested that the Vmax can be reasonably achieved given the typical COD values in MWW and anticipated mixing with AMD. Non-competitive inhibition modeling (Ki=6.55mgL(-1)) indicated that excessive iron level should be avoided to limit its effects on SRB. The COD oxidation rate was positively correlated to COD/sulfate ratio and SRB population, as evidenced by dsrA gene copies. Phylogenetic analysis revealed diverse microbial communities dominated by sulfate reducing delta-proteobacteria. Microbial community and relative quantities of SRB showed significant differences under different COD/sulfate ratios (0.2, 1 and 2), and the highest dsrA gene concentration and most complex microbial diversity were observed under COD/sulfate ratio 2. Major species were associated with Desulfovirga, Desulfobulbus, Desulfovibrio, and Syntrophus sp. The reported COD kinetics, SRB abundances and the phylogenetic profile provide insights into the co-treatment process and help identify the parameters of concerns for such technology development. PMID:26686479

  3. Kinetics and microbial ecology of batch sulfidogenic bioreactors for co-treatment of municipal wastewater and acid mine drainage.

    PubMed

    Deng, Dongyang; Weidhaas, Jennifer L; Lin, Lian-Shin

    2016-03-15

    The kinetics and microbial ecology in sulfidogenic bioreactors used in a novel two-stage process for co-treatment of acid mine drainage (AMD) and municipal wastewater (MWW) were investigated. Michaelis-Menten modeling of COD oxidation by sulfate reducing bacteria (SRB) (Vmax=0.33mgL(-1)min(-1), Km=4.3mgL(-1)) suggested that the Vmax can be reasonably achieved given the typical COD values in MWW and anticipated mixing with AMD. Non-competitive inhibition modeling (Ki=6.55mgL(-1)) indicated that excessive iron level should be avoided to limit its effects on SRB. The COD oxidation rate was positively correlated to COD/sulfate ratio and SRB population, as evidenced by dsrA gene copies. Phylogenetic analysis revealed diverse microbial communities dominated by sulfate reducing delta-proteobacteria. Microbial community and relative quantities of SRB showed significant differences under different COD/sulfate ratios (0.2, 1 and 2), and the highest dsrA gene concentration and most complex microbial diversity were observed under COD/sulfate ratio 2. Major species were associated with Desulfovirga, Desulfobulbus, Desulfovibrio, and Syntrophus sp. The reported COD kinetics, SRB abundances and the phylogenetic profile provide insights into the co-treatment process and help identify the parameters of concerns for such technology development.

  4. Application of Sequence-based Methods in Human MicrobialEcology

    SciTech Connect

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

    2005-08-29

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

  5. Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato)

    PubMed Central

    2013-01-01

    Background Research to understand and control microbiological risks associated with the consumption of fresh fruits and vegetables has examined many environments in the farm to fork continuum. An important data gap however, that remains poorly studied is the baseline description of microflora that may be associated with plant anatomy either endemically or in response to environmental pressures. Specific anatomical niches of plants may contribute to persistence of human pathogens in agricultural environments in ways we have yet to describe. Tomatoes have been implicated in outbreaks of Salmonella at least 17 times during the years spanning 1990 to 2010. Our research seeks to provide a baseline description of the tomato microbiome and possibly identify whether or not there is something distinctive about tomatoes or their growing ecology that contributes to persistence of Salmonella in this important food crop. Results DNA was recovered from washes of epiphytic surfaces of tomato anatomical organs; leaves, stems, roots, flowers and fruits of Solanum lycopersicum (BHN602), grown at a site in close proximity to commercial farms previously implicated in tomato-Salmonella outbreaks. DNA was amplified for targeted 16S and 18S rRNA genes and sheared for shotgun metagenomic sequencing. Amplicons and metagenomes were used to describe “native” bacterial microflora for diverse anatomical parts of Virginia-grown tomatoes. Conclusions Distinct groupings of microbial communities were associated with different tomato plant organs and a gradient of compositional similarity could be correlated to the distance of a given plant part from the soil. Unique bacterial phylotypes (at 95% identity) were associated with fruits and flowers of tomato plants. These include Microvirga, Pseudomonas, Sphingomonas, Brachybacterium, Rhizobiales, Paracocccus, Chryseomonas and Microbacterium. The most frequently observed bacterial taxa across aerial plant regions were Pseudomonas and Xanthomonas

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

    PubMed

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

    2014-01-01

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

  7. Small intestinal bacterial overgrowth syndrome

    PubMed Central

    Bures, Jan; Cyrany, Jiri; Kohoutova, Darina; Förstl, Miroslav; Rejchrt, Stanislav; Kvetina, Jaroslav; Vorisek, Viktor; Kopacova, Marcela

    2010-01-01

    Human intestinal microbiota create a complex polymicrobial ecology. This is characterised by its high population density, wide diversity and complexity of interaction. Any dysbalance of this complex intestinal microbiome, both qualitative and quantitative, might have serious health consequence for a macro-organism, including small intestinal bacterial overgrowth syndrome (SIBO). SIBO is defined as an increase in the number and/or alteration in the type of bacteria in the upper gastrointestinal tract. There are several endogenous defence mechanisms for preventing bacterial overgrowth: gastric acid secretion, intestinal motility, intact ileo-caecal valve, immunoglobulins within intestinal secretion and bacteriostatic properties of pancreatic and biliary secretion. Aetiology of SIBO is usually complex, associated with disorders of protective antibacterial mechanisms (e.g. achlorhydria, pancreatic exocrine insufficiency, immunodeficiency syndromes), anatomical abnormalities (e.g. small intestinal obstruction, diverticula, fistulae, surgical blind loop, previous ileo-caecal resections) and/or motility disorders (e.g. scleroderma, autonomic neuropathy in diabetes mellitus, post-radiation enteropathy, small intestinal pseudo-obstruction). In some patients more than one factor may be involved. Symptoms related to SIBO are bloating, diarrhoea, malabsorption, weight loss and malnutrition. The gold standard for diagnosing SIBO is still microbial investigation of jejunal aspirates. Non-invasive hydrogen and methane breath tests are most commonly used for the diagnosis of SIBO using glucose or lactulose. Therapy for SIBO must be complex, addressing all causes, symptoms and complications, and fully individualised. It should include treatment of the underlying disease, nutritional support and cyclical gastro-intestinal selective antibiotics. Prognosis is usually serious, determined mostly by the underlying disease that led to SIBO. PMID:20572300

  8. The role of microbial diversity in the dynamics and stability of global methane consumption: microbial methane oxidation as a model-system for microbial ecology (ESF EuroDiversity METHECO)

    NASA Astrophysics Data System (ADS)

    Frenzel, P.; Metheco-Team

    2009-04-01

    Ecosystems collectively determine biogeochemical processes that regulate the Earth System. Loss of biodiversity is detrimental to ecosystems and therefore has been a central issue for environmental scientists. Although microorganisms form a major part of the Earth's biomass and biodiversity, and have a critical role in biogeochemistry and ecosystem functioning, they do not feature highly in ongoing debates about global biodiversity loss, global change and conservations issues. The neglect of microbial diversity in conservation issues is because microbial communities are regarded as being highly redundant, omnipresent, and therefore inextinguishable. This, however, is a misconception. Recently, the application of advanced molecular techniques has indicated that microbial communities display habitat preferences and are not universally distributed. Even the highly diverse microbial communities in soils can be affected by agricultural use, indicating that genetic erosion may potentially affect these communities as well. Moreover, many important environmental functions are catalyzed by specific groups of microbes with a very narrow ecological range. Recovery of these functional microbial communities after disturbance may take decades. Even if the species making up the community do not become extinct and eventually re-colonize an environment, the function and service to the biosphere is lost long enough to exert permanent, irreversible damage to the environment. Considering the global importance of microbes, combined with our ignorance of how the composition and functioning of these communities is affected, necessitates the assessment of the vulnerability and the resilience of microbial diversity. The latter is a pressing concern in biodiversity research and conservation policy, urgently needing attention in order to be able to anticipate environmental challenges we are facing. Our general hypothesis is: microbial diversity is linked to important ecosystem services and

  9. LIPID ANALYSIS TO DETERMINE THE EFFECT OF A SOURCE REMEDIAL TECHNOLOGY IN MICROBIAL ECOLOGY

    EPA Science Inventory

    Microbial community structures and related changes in the subsurface environment were investigated following in situ chemical oxidation (ISCO) treatment at Launch Complex 34, Cape Canaveral Air Station, Florida. The site has dense non-aqueous phase (DNAPL) concentrations of TCE ...

  10. Microbial ecology of four coral atolls in the Northern Line Islands.

    PubMed

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

    2008-01-01

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

  11. Microbial ecology of four coral atolls in the Northern Line Islands.

    PubMed

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

    2008-02-27

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

  12. Microbial Ecology of Four Coral Atolls in the Northern Line Islands

    PubMed Central

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

    2008-01-01

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

  13. Use of Metabolic Inhibitors to Characterize Ecological Interactions in an Estuarine Microbial Food Web.

    PubMed

    DeLorenzo, M.E.; Lewitus, A.J.; Scott, G.I.; Ross, P.E.

    2001-10-01

    Understanding microbial food web dynamics is complicated by the multitude of competitive or interdependent trophic interactions involved in material and energy flow. Metabolic inhibitors can be used to gain information on the relative importance of trophic pathways by uncoupling selected microbial components and examining the net effect on ecosystem structure and function. A eukaryotic growth inhibitor (cycloheximide), a prokaryotic growth inhibitor (antibiotic mixture), and an inhibitor of photosynthesis (DCMU) were used to examine the trophodynamics of microbial communities from the tidal creek in North Inlet, a salt marsh estuary near Georgetown, South Carolina. Natural microbial communities were collected in the spring, summer, and fall after colonization onto polyurethane foam substrates deployed in the tidal creek. Bacterial abundance and productivity, heterotrophic ciliate and flagellate abundance, and phototrophic productivity, biomass, and biovolume were measured at five time points after inhibitor additions. The trophic responses of the estuarine microbial food web to metabolic inhibitors varied with season. In the summer, a close interdependency among phototrophs, bacteria, and protozoa was indicated, and the important influence of microzooplanktonic nutrient recycling was evident (i.e., a positive feedback loop). In the fall, phototroph and bacteria interactions were competitive rather than interdependent, and grazer nutrient regeneration did not appear to be an important regulatory factor for bacterial or phototrophic activities. The results indicate a seasonal shift in microbial food web structure and function in North Inlet, from a summer community characterized by microbial loop dynamics to a more linear trophic system in the fall. This study stresses the important role of microbial loops in driving primary and secondary production in estuaries such as North Inlet that are tidally dominated by fluctuations in nutrient supply and a summer

  14. Effects of soil type and farm management on soil ecological functional genes and microbial activities

    SciTech Connect

    Reeve, Jennifer; Schadt, Christopher Warren; Carpenter-Boggs, Lynne; Kang, S.; Zhou, Jizhong; Reganold, John P.

    2010-01-01

    Relationships between soil microbial diversity and soil function are the subject of much debate. Process-level analyses have shown that microbial function varies with soil type and responds to soil management. However, such measurements cannot determine the role of community structure and diversity in soil function. The goal of this study was to investigate the role of gene frequency and diversity, measured by microarray analysis, on soil processes. The study was conducted in an agro-ecosystem characterized by contrasting management practices and soil types. Eight pairs of adjacent commercial organic and conventional strawberry fields were matched for soil type, strawberry variety, and all other environmental conditions. Soil physical, chemical and biological analyses were conducted including functional gene microarrays (FGA). Soil physical and chemical characteristics were primarily determined by soil textural type (coarse vs fine-textured), but biological and FGA measures were more influenced by management (organic vs conventional). Organically managed soils consistently showed greater functional activity as well as FGA signal intensity (SI) and diversity. Overall FGA SI and diversity were correlated to total soil microbial biomass. Functional gene group SI and/or diversity were correlated to related soil chemical and biological measures such as microbial biomass, cellulose, dehydrogenase, ammonium and sulfur. Management was the dominant determinant of soil biology as measured by microbial gene frequency and diversity, which paralleled measured microbial processes.

  15. Fractal Hypothesis of the Pelagic Microbial Ecosystem—Can Simple Ecological Principles Lead to Self-Similar Complexity in the Pelagic Microbial Food Web?

    PubMed Central

    Våge, Selina; Thingstad, T. Frede

    2015-01-01

    Trophic interactions are highly complex and modern sequencing techniques reveal enormous biodiversity across multiple scales in marine microbial communities. Within the chemically and physically relatively homogeneous pelagic environment, this calls for an explanation beyond spatial and temporal heterogeneity. Based on observations of simple parasite-host and predator-prey interactions occurring at different trophic levels and levels of phylogenetic resolution, we present a theoretical perspective on this enormous biodiversity, discussing in particular self-similar aspects of pelagic microbial food web organization. Fractal methods have been used to describe a variety of natural phenomena, with studies of habitat structures being an application in ecology. In contrast to mathematical fractals where pattern generating rules are readily known, however, identifying mechanisms that lead to natural fractals is not straight-forward. Here we put forward the hypothesis that trophic interactions between pelagic microbes may be organized in a fractal-like manner, with the emergent network resembling the structure of the Sierpinski triangle. We discuss a mechanism that could be underlying the formation of repeated patterns at different trophic levels and discuss how this may help understand characteristic biomass size-spectra that hint at scale-invariant properties of the pelagic environment. If the idea of simple underlying principles leading to a fractal-like organization of the pelagic food web could be formalized, this would extend an ecologists mindset on how biological complexity could be accounted for. It may furthermore benefit ecosystem modeling by facilitating adequate model resolution across multiple scales. PMID:26648929

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

    PubMed

    Imhoff, Johannes F

    2016-01-01

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

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

    PubMed

    Imhoff, Johannes F

    2016-01-01

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

  18. Effects of cow's and goat's milk as fermentation media on the microbial ecology of sugary kefir grains.

    PubMed

    Hsieh, Hsin-Hui; Wang, Sheng-Yao; Chen, Tzu-Li; Huang, Yen-Lin; Chen, Ming-Ju

    2012-06-15

    In the present study, we have investigated the importance of fermentation media on grain formation and the microbial characteristics of sugary kefir. The sugary kefir grains were fermented in brown sugar, cow's milk or goat's milk. Using culture-dependent and culture-independent methods, we identified the microorganisms present in both the grains and filtrate and then evaluated their distribution. The structure of the grains was also observed by scanning electronic microscopy (SEM). The identification results indicated that there were remarkable changes in microbial ecological profiles of the sugary kefir grains and their filtrates when brown sugar and milk were compared as fermentation media. Three lactic acid bacteria (LAB) species (Leuconostoc mesenteroides, Lactobacillus mali and Lactobacillus hordei) were found in the grains fermented using brown sugar. However, four species, named Leu. mesenteroides, Lactococcus lactis, Bifidobacterium psychraerophilum and Enterococcus faecalis, were identified in the grains fermented using either cow's or goat's milk. The size and structure of the kefir grains were also significantly influenced by the culture medium. We hypothesize that the grains originally may contain many different microorganisms and the identified changes are an adaption to each specific medium during grain formation and growth. The distribution of strains thus may vary depending on the carbon and energy sources available for grain fermentation and these microbial changes will further affect the granulation and growth of the grains. This study is important to our understanding of the mechanism of kefir grain formation and growth because it explores the relationship between fermentation media and kefir microorganisms.

  19. A Gut Microbial Metabolite of Linoleic Acid, 10-Hydroxy-cis-12-octadecenoic Acid, Ameliorates Intestinal Epithelial Barrier Impairment Partially via GPR40-MEK-ERK Pathway*

    PubMed Central

    Miyamoto, Junki; Mizukure, Taichi; Park, Si-Bum; Kishino, Shigenobu; Kimura, Ikuo; Hirano, Kanako; Bergamo, Paolo; Rossi, Mauro; Suzuki, Takuya; Arita, Makoto; Ogawa, Jun; Tanabe, Soichi

    2015-01-01

    Gut microbial metabolites of polyunsaturated fatty acids have attracted much attention because of their various physiological properties. Dysfunction of tight junction (TJ) in the intestine contributes to the pathogenesis of many disorders such as inflammatory bowel disease. We evaluated the effects of five novel gut microbial metabolites on tumor necrosis factor (TNF)-α-induced barrier impairment in Caco-2 cells and dextran sulfate sodium-induced colitis in mice. 10-Hydroxy-cis-12-octadecenoic acid (HYA), a gut microbial metabolite of linoleic acid, suppressed TNF-α and dextran sulfate sodium-induced changes in the expression of TJ-related molecules, occludin, zonula occludens-1, and myosin light chain kinase. HYA also suppressed the expression of TNF receptor 2 (TNFR2) mRNA and protein expression in Caco-2 cells and colonic tissue. In addition, HYA suppressed the protein expression of TNFR2 in murine intestinal epithelial cells. Furthermore, HYA significantly up-regulated G protein-coupled receptor (GPR) 40 expression in Caco-2 cells. It also induced [Ca2+]i responses in HEK293 cells expressing human GPR40 with higher sensitivity than linoleic acid, its metabolic precursor. The barrier-recovering effects of HYA were abrogated by a GPR40 antagonist and MEK inhibitor in Caco-2 cells. Conversely, 10-hydroxyoctadacanoic acid, which is a gut microbial metabolite of oleic acid and lacks a carbon-carbon double bond at Δ12 position, did not show these TJ-restoring activities and down-regulated GPR40 expression. Therefore, HYA modulates TNFR2 expression, at least partially, via the GPR40-MEK-ERK pathway and may be useful in the treatment of TJ-related disorders such as inflammatory bowel disease. PMID:25505251

  20. Microbial Ecology of the Dark Ocean above, at, and below the Seafloor†

    PubMed Central

    Orcutt, Beth N.; Sylvan, Jason B.; Knab, Nina J.; Edwards, Katrina J.

    2011-01-01

    Summary: The majority of life on Earth—notably, microbial life—occurs in places that do not receive sunlight, with the habitats of the oceans being the largest of these reservoirs. Sunlight penetrates only a few tens to hundreds of meters into the ocean, resulting in large-scale microbial ecosystems that function in the dark. Our knowledge of microbial processes in the dark ocean—the aphotic pelagic ocean, sediments, oceanic crust, hydrothermal vents, etc.—has increased substantially in recent decades. Studies that try to decipher the activity of microorganisms in the dark ocean, where we cannot easily observe them, are yielding paradigm-shifting discoveries that are fundamentally changing our understanding of the role of the dark ocean in the global Earth system and its biogeochemical cycles. New generations of researchers and experimental tools have emerged, in the last decade in particular, owing to dedicated research programs to explore the dark ocean biosphere. This review focuses on our current understanding of microbiology in the dark ocean, outlining salient features of various habitats and discussing known and still unexplored types of microbial metabolism and their consequences in global biogeochemical cycling. We also focus on patterns of microbial diversity in the dark ocean and on processes and communities that are characteristic of the different habitats. PMID:21646433

  1. Ecological Forecasting: Microbial Contamination and Atmospheric Loadings of Nutrients to Land and Water

    EPA Science Inventory

    The development of ecological forecasts, namely, methodologies to predict the chemical, biological, and physical changes in terrestrial and aquatic ecosystems is desirable so that effective strategies for reducing the adverse impacts of human activities and extreme natural events...

  2. Post-Genomics Approaches towards Monitoring Changes within the Microbial Ecology of the Gut

    NASA Astrophysics Data System (ADS)

    Tuohy, Kieran M.; Abecia, Leticia; Deaville, Eddie R.; Fava, Francesca; Klinder, Annett; Shen, Qing

    The human gut microbiota, comprising many hundreds of different microbial species, has closely co-evolved with its human host over the millennia. Diet has been a major driver of this co-evolution, in particular dietary non-digestible carbohydrates. This dietary fraction reaches the colon and becomes available for microbial fermentation, and it is in the colon that the great diversity of gut microorganisms resides. For the vast majority of our evolutionary history humans followed hunter-gatherer life-styles and consumed diets with many times more non-digestible carbohydrates, fiber and whole plant polyphenol rich foods than typical Western style diets today.

  3. Planetary biology and microbial ecology. Biochemistry of carbon and early life

    NASA Technical Reports Server (NTRS)

    Margulis, L. (Editor); Nealson, K. H. (Editor); Taylor, I. (Editor)

    1983-01-01

    Experiments made with cyanobacteria, phototrophic bacteria, and methanogenic bacteria are detailed. Significant carbon isotope fractionation data is included. Taken from well documented extant microbial communities, this data provides a basis of comparison for isotope fractionation values measured in Archean and Proterozoic (preCambrian) rocks. Media, methods, and techniques used to acquire data are also described.

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

    EPA Science Inventory

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

  5. Board-invited review: Rumen microbiology: Leading the way in microbial ecology

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  6. Marine coastal sediments microbial hydrocarbon degradation processes: contribution of experimental ecology in the omics’era

    PubMed Central

    Cravo-Laureau, Cristiana; Duran, Robert

    2014-01-01

    Coastal marine sediments, where important biological processes take place, supply essential ecosystem services. By their location, such ecosystems are particularly exposed to human activities as evidenced by the recent Deepwater Horizon disaster. This catastrophe revealed the importance to better understand the microbial processes involved on hydrocarbon degradation in marine sediments raising strong interests of the scientific community. During the last decade, several studies have shown the key role played by microorganisms in determining the fate of hydrocarbons in oil-polluted sediments but only few have taken into consideration the whole sediment’s complexity. Marine coastal sediment ecosystems are characterized by remarkable heterogeneity, owning high biodiversity and are subjected to fluctuations in environmental conditions, especially to important oxygen oscillations due to tides. Thus, for understanding the fate of hydrocarbons in such environments, it is crucial to study microbial activities, taking into account sediment characteristics, physical-chemical factors (electron acceptors, temperature), nutrients, co-metabolites availability as well as sediment’s reworking due to bioturbation activities. Key information could be collected from in situ studies, which provide an overview of microbial processes, but it is difficult to integrate all parameters involved. Microcosm experiments allow to dissect in-depth some mechanisms involved in hydrocarbon degradation but exclude environmental complexity. To overcome these lacks, strategies have been developed, by creating experiments as close as possible to environmental conditions, for studying natural microbial communities subjected to oil pollution. We present here a review of these approaches, their results and limitation, as well as the promising future of applying “omics” approaches to characterize in-depth microbial communities and metabolic networks involved in hydrocarbon degradation. In addition

  7. Diets high in resistant starch and arabinoxylan modulate digestion processes and SCFA pool size in the large intestine and faecal microbial composition in pigs.

    PubMed

    Nielsen, Tina S; Lærke, Helle N; Theil, Peter K; Sørensen, Jens F; Saarinen, Markku; Forssten, Sofia; Knudsen, Knud E Bach

    2014-12-14

    The effects of a high level of dietary fibre (DF) either as arabinoxylan (AX) or resistant starch (RS) on digestion processes, SCFA concentration and pool size in various intestinal segments and on the microbial composition in the faeces were studied in a model experiment with pigs. A total of thirty female pigs (body weight 63.1 (sem 4.4) kg) were fed a low-DF, high-fat Western-style control diet (WSD), an AX-rich diet (AXD) or a RS-rich diet (RSD) for 3 weeks. Diet significantly affected the digestibility of DM, protein, fat, NSP and NSP components, and the arabinose:xylose ratio, as well as the disappearance of NSP and AX in the large intestine. RS was mainly digested in the caecum. AX was digested at a slower rate than RS. The digesta from AXD-fed pigs passed from the ileum to the distal colon more than twice as fast as those from WSD-fed pigs, with those from RSD-fed pigs being intermediate (P< 0.001). AXD feeding resulted in a higher number of Faecalibacterium prausnitzii, Roseburia intestinalis, Blautia coccoides-Eubacterium rectale, Bifidobacterium spp. and Lactobacillus spp. in the faeces sampled at week 3 of the experimental period (P< 0.05). In the caecum, proximal and mid colon, AXD feeding resulted in a 3- to 5-fold higher pool size of butyrate compared with WSD feeding, with the RSD being intermediate (P <0.001). In conclusion, the RSD and AXD differently affected digestion processes compared with the WSD, and the AXD most efficiently shifted the microbial composition towards butyrogenic species in the faeces and increased the large-intestinal butyrate pool size.

  8. Comparison of Yacon (Smallanthus sonchifolius) Tuber with Commercialized Fructo-oligosaccharides (FOS) in Terms of Physiology, Fermentation Products and Intestinal Microbial Communities in Rats

    PubMed Central

    UTAMI, Ni Wayan Arya; SONE, Teruo; TANAKA, Michiko; NAKATSU, Cindy H; SAITO, Akihiko; ASANO, Kozo

    2013-01-01

    The yacon (Smallanthus sonchifolius) tuber was examined with regard to its prebiotic effects compared with commercialized fructo-oligosaccharides (FOS). A feed containing 10% yacon tuber, which is equivalent to 5% commercialized FOS in terms of the amount of fructo-oligosaccharides (GF2, GF3 and GF4), was administrated to rats for 28 days. The yacon diet changed the intestinal microbial communities beginning in the first week, resulting in a twofold greater concentration of cecal short-chain fatty acids (SCFAs). The SCFA composition differed, but the cecal pH in rats fed yacon tuber was equal to that in rats fed FOS. Serum triglycerides were lower in rats fed yacon compared with rats fed FOS and the control diet. Cecal size was greater with the yacon tuber diet compared with the control diet. The abundant fermentation in the intestines created a selective environment for the intestinal microbiota, which included Lactobacillus acidophilus, Bifidobacterium pseudolongum, Bifidobacterium animalis and Barnesiella spp. according to identification with culture-independent analysis, 16S rRNA gene PCR-DGGE combined with cloning and sequencing. Barnesiella spp. and B. pseudolongum were only found in the rats fed the yacon diet, while L. acidophilus and B. animalis were found in abundance in rats fed both the yacon and FOS diets. The genus Barnesiella has not previously been reported to be associated with yacon or FOS fermentation. We concluded that the physiological and microbiological effects of the yacon tuber were different from those of FOS. Differences in cecal size, blood triglycerides and microbial community profiles including their metabolites (SCFAs) between the yacon tuber and FOS were shown to be more greatly affected by the yacon tuber rather than FOS. PMID:24936376

  9. Microbial Ecology of Subseafloor Communities at Deep-sea Hydrothermal Seamounts of the Pacific Ocean

    NASA Astrophysics Data System (ADS)

    Huber, J. A.; Bolton, S.; Butterfield, D. A.; Baross, J. A.; Sogin, M. L.

    2006-12-01

    Circulation of hydrothermal fluids and seawater occurs within the upper 500 m of porous oceanic crust and provides a rich environment for microbial growth in the subseafloor. Enrichment cultures, geochemical indicators, and sequence analyses of PCR amplicons of ribosomal RNA genes demonstrate that these crustal fluids host a microbial community composed of organisms indigenous to the subseafloor and organisms from other deep-sea habitats, such as seawater. However, the subseafloor microbial communities remain undersampled and our knowledge of what microbes are present and how they are distributed in this dynamic environment over time and space is fragmentary. This work focuses on determining the microbial diversity and genomic content of the subseafloor microbial community at geographically and geochemically distinct deep- sea hydrothermal seamounts. The approach uses a combination of methods, including DNA-based, culturing, and geochemical methods applied to diffuse fluids from two locations: Axial Seamount on the Juan de Fuca Ridge in the northeast Pacific Ocean (45.92° N, 130° W) and seamounts along the Mariana Arc (14-22° N, 143-146° E) in the western Pacific. Both locations host recently eruptive seamounts located above 2000 m with diffusely venting fluids that contain high concentrations of carbon dioxide. However, their geological and chemical setting differs greatly; Axial is a mid-ocean ridge seamount with fluids dominated by high concentrations of hydrogen sulfide, and the Mariana seamounts are at a convergent plate boundary and host a variety of fluids, including those with very low pH and high concentrations of particulate sulfur. Initial studies reveal bacterial communities at both sites consist mainly of epsilon-proteobacteria, a physiologically and phylogenetically diverse group known to have a widespread distribution and dominance in many deep-sea vent habitats. However, while subseafloor archaeal communities at Axial are composed of autotrophic

  10. Immune and genetic gardening of the intestinal microbiome.

    PubMed

    Jacobs, Jonathan P; Braun, Jonathan

    2014-11-17

    The mucosal immune system - consisting of adaptive and innate immune cells as well as the epithelium - is profoundly influenced by its microbial environment. There is now growing evidence that the converse is also true, that the immune system shapes the composition of the intestinal microbiome. During conditions of health, this bidirectional interaction achieves a homeostasis in which inappropriate immune responses to non-pathogenic microbes are averted and immune activity suppresses blooms of potentially pathogenic microbes (pathobionts). Genetic alteration in immune/epithelial function can affect host gardening of the intestinal microbiome, contributing to the diversity of intestinal microbiota within a population and in some cases allowing for unfavorable microbial ecologies (dysbiosis) that confer disease susceptibility.

  11. Immune and genetic gardening of the intestinal microbiome

    PubMed Central

    Jacobs, Jonathan P.; Braun, Jonathan

    2014-01-01

    The mucosal immune system – consisting of adaptive and innate immune cells as well as the epithelium – is profoundly influenced by its microbial environment. There is now growing evidence that the converse is also true, that the immune system shapes the composition of the intestinal microbiome. During conditions of health, this bidirectional interaction achieves a homeostasis in which inappropriate immune responses to nonpathogenic microbes are averted and immune activity suppresses blooms of potentially pathogenic microbes (pathobionts). Genetic alteration in immune/epithelial function can affect host gardening of the intestinal microbiome, contributing to the diversity of intestinal microbiota within a population and in some cases allowing for unfavorable microbial ecologies (dysbiosis) that confer disease susceptibility. PMID:24613921

  12. Nitrification inhibition by hexavalent chromium Cr(VI)--Microbial ecology, gene expression and off-gas emissions.

    PubMed

    Kim, Young Mo; Park, Hongkeun; Chandran, Kartik

    2016-04-01

    The goal of this study was to investigate the responses in the physiology, microbial ecology and gene expression of nitrifying bacteria to imposition of and recovery from Cr(VI) loading in a lab-scale nitrification bioreactor. Exposure to Cr(VI) in the reactor strongly inhibited nitrification performance resulting in a parallel decrease in nitrate production and ammonia consumption. Cr(VI) exposure also led to an overall decrease in total bacterial concentrations in the reactor. However, the fraction of ammonia oxidizing bacteria (AOB) decreased to a greater extent than the fraction of nitrite oxidizing bacteria (NOB). In terms of functional gene expression, a rapid decrease in the transcript concentrations of amoA gene coding for ammonia oxidation in AOB was observed in response to the Cr(VI) shock. In contrast, transcript concentrations of the nxrA gene coding for nitrite oxidation in NOB were relatively unchanged compared to Cr(VI) pre-exposure levels. Therefore, Cr(VI) exposure selectively and directly inhibited activity of AOB, which indirectly resulted in substrate (nitrite) limitation to NOB. Significantly, trends in amoA expression preceded performance trends both during imposition of and recovery from inhibition. During recovery from the Cr(VI) shock, the high ammonia concentrations in the bioreactor resulted in an irreversible shift towards AOB populations, which are expected to be more competitive in high ammonia environments. An inadvertent impact during recovery was increased emission of nitrous oxide (N2O) and nitric oxide (NO), consistent with recent findings linking AOB activity and the production of these gases. Therefore, Cr(VI) exposure elicited multiple responses on the microbial ecology, gene expression and both aqueous and gaseous nitrogenous conversion in a nitrification process. A complementary interrogation of these multiple responses facilitated an understanding of both direct and indirect inhibitory impacts on nitrification. PMID:26874778

  13. Microbial ecology in anaerobic digestion at agitated and non-agitated conditions.

    PubMed

    Tian, Zhuoli; Cabrol, Léa; Ruiz-Filippi, Gonzalo; Pullammanappallil, Pratap

    2014-01-01

    To investigate the distribution and dynamics of microbial community in anaerobic digestion at agitated and non-agitated condition, 454 pyrosequencing of 16s rRNA was conducted. It revealed the distinct community compositions between the two digesters and their progressive shifting over time. Methanogens and syntrophic bacteria were found much less abundant in the agitated digester, which was mainly attributed to the presence of bacterial genera Acetanaerobacterium and Ruminococcus with relatively high abundance. The characterization of the microbial community corroborated the digestion performance affected at the agitated condition, where lower methane yield and delayed methane production rate were observed. This was further verified by the accumulation of propionic acid in the agitated digester.

  14. Microbial Ecology in Anaerobic Digestion at Agitated and Non-Agitated Conditions

    PubMed Central

    Tian, Zhuoli; Cabrol, Léa; Ruiz-Filippi, Gonzalo; Pullammanappallil, Pratap

    2014-01-01

    To investigate the distribution and dynamics of microbial community in anaerobic digestion at agitated and non-agitated condition, 454 pyrosequencing of 16s rRNA was conducted. It revealed the distinct community compositions between the two digesters and their progressive shifting over time. Methanogens and syntrophic bacteria were found much less abundant in the agitated digester, which was mainly attributed to the presence of bacterial genera Acetanaerobacterium and Ruminococcus with relatively high abundance. The characterization of the microbial community corroborated the digestion performance affected at the agitated condition, where lower methane yield and delayed methane production rate were observed. This was further verified by the accumulation of propionic acid in the agitated digester. PMID:25313520

  15. Emerging concepts on microbial processes in the bathypelagic ocean - ecology, biogeochemistry, and genomics

    NASA Astrophysics Data System (ADS)

    Nagata, Toshi; Tamburini, Christian; Arístegui, Javier; Baltar, Federico; Bochdansky, Alexander B.; Fonda-Umani, Serena; Fukuda, Hideki; Gogou, Alexandra; Hansell, Dennis A.; Hansman, Roberta L.; Herndl, Gerhard J.; Panagiotopoulos, Christos; Reinthaler, Thomas; Sohrin, Rumi; Verdugo, Pedro; Yamada, Namiha; Yamashita, Youhei; Yokokawa, Taichi; Bartlett, Douglas H.

    2010-08-01

    This paper synthesizes recent findings regarding microbial distributions and processes in the bathypelagic ocean (depth >1000 m). Abundance, production and respiration of prokaryotes reflect supplies of particulate and dissolved organic matter to the bathypelagic zone. Better resolution of carbon fluxes mediated by deep microbes requires further testing on the validity of conversion factors. Archaea, especially marine Crenarchaeota Group I, are abundant in deep waters where they can fix dissolved inorganic carbon. Viruses appear to be important in the microbial loop in deep waters, displaying remarkably high virus to prokaryote abundance ratios in some oceanic regions. Sequencing of 18S rRNA genes revealed a tremendous diversity of small-sized protists in bathypelagic waters. Abundances of heterotrophic nanoflagellates (HNF) and ciliates decrease with depth more steeply than prokaryotes; nonetheless, data indicated that HNF consumed half of prokaryote production in the bathypelagic zone. Aggregates are important habitats for deep-water microbes, which produce more extracellular enzymes (on a per-cell basis) than surface communities. The theory of marine gel formation provides a framework to unravel complex interactions between microbes and organic polymers. Recent data on the effects of hydrostatic pressure on microbial activities indicate that bathypelagic microbial activity is generally higher under in situ pressure conditions than at atmospheric pressures. High-throughput sequencing of 16S rRNA genes revealed a remarkable diversity of Bacteria in the bathypelagic ocean. Metagenomics and comparative genomics of piezophiles reveal not only the high diversity of deep sea microbes but also specific functional attributes of these piezophilic microbes, interpreted as an adaptation to the deep water environment. Taken together, the data compiled on bathypelagic microbes indicate that, despite high-pressure and low-temperature conditions, microbes in the bathypelagic

  16. Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities

    SciTech Connect

    Denef, Vincent; Kalnejals, Linda; Muller, R; Wilmes, P; Baker, Brett J.; Thomas, Brian; Verberkmoes, Nathan C; Hettich, Robert {Bob} L; Banfield, Jillian F.

    2010-01-01

    Bacterial species concepts are controversial. More widely accepted is the need to understand how differences in gene content and sequence lead to ecological divergence. To address this relationship in ecosystem context, we investigated links between genotype and ecology of two genotypic groups of Leptospirillumgroup II bacteria in comprehensively characterized, natural acidophilic biofilm communities. These groups share 99.7% 16S rRNA gene sequence identity and 95% average amino acid identity between their orthologs. One genotypic group predominates during early colonization, and the other group typically proliferates in later successional stages, forming distinct patches tens to hundreds of micrometers in diameter. Among early colonizing populations, we observed dominance of five genotypes that differed from each other by the extent of recombination with the late colonizing type. Our analyses suggest that the specific recombinant variant within the early colonizing group is selected for by environmental parameters such as temperature, consistent with recombination as a mechanism for ecological fine tuning. Evolutionary signatures, and strain-resolved expression patterns measured via mass spectrometry based proteomics, indicate increased cobalamin biosynthesis, (de)methylation, and glycine cleavage in the late colonizer. This may suggest environmental changes within the biofilm during development, accompanied by redirection of compatible solutes from osmoprotectants toward metabolism. Across 27 communities, comparative proteogenomic analyses show that differential regulation of shared genes and expression of a small subset of the 15% of genes unique to each genotype are involved in niche partitioning. In summary, the results show how subtle genetic variations can lead to distinct ecological strategies.

  17. Life in a drop of Ocean: microfluidic insights into microbial ecology

    NASA Astrophysics Data System (ADS)

    Stocker, Roman

    2008-03-01

    Bacteria are the most abundant and successful form of life on Earth. Their physico-chemical interactions with their fluid environment are surprisingly complex and have enormous implications, which we can only hope to grasp if we learn to study microorganisms within realistic microenvironments. Microfluidics for the first time enables us to create microhabitats, including chemical and fluid mechanical landscapes, while visualizing bacterial behavior at a single-cell resolution. Here I focus on the application of microfluidics to gain insight in the life of marine bacteria. In their quest for nturients, marine bacteria often experience the Ocean as a desert, where rare and ephemeral nutrient patches represent transient resource oases. In this patchy seascape, swimming and chemotaxis represent critical assets, but effective patch utilization is constrained by energetic requirements. And then there are predators and viruses... These interactions form the basis of the 'microbial loop', the ensemble of microbial processes known to directly impact the productivity of marine ecosystems and the rates of carbon turnover in the Ocean. I will show how fundamental new insight on selected aspects of microbial life in a drop of Ocean can be achieved by a combination of microfluidic experiments and theoretical modeling.

  18. Ecosystems on ice: the microbial ecology of Markham Ice Shelf in the high Arctic.

    PubMed

    Vincent, Warwick F; Mueller, Derek R; Bonilla, Sylvia

    2004-04-01

    Microbial communities occur throughout the cryosphere in a diverse range of ice-dominated habitats including snow, sea ice, glaciers, permafrost, and ice clouds. In each of these environments, organisms must be capable of surviving freeze-thaw cycles, persistent low temperatures for growth, extremes of solar radiation, and prolonged dormancy. These constraints may have been especially important during global cooling events in the past, including the Precambrian glaciations. One analogue of these early Earth conditions is the thick, landfast sea ice that occurs today at certain locations in the Arctic and Antarctic. These ice shelves contain liquid water for a brief period each summer, and support luxuriant microbial mat communities. Our recent studies of these mats on the Markham Ice Shelf (Canadian high Arctic) by high performance liquid chromatography (HPLC) showed that they contain high concentrations of chlorophylls a and b, and several carotenoids notably lutein, echinenone and beta-carotene. The largest peaks in the HPLC chromatograms were two UV-screening compounds known to be produced by cyanobacteria, scytonemin, and its decomposition product scytonemin-red. Microscopic analyses of the mats showed that they were dominated by the chlorophyte genera cf. Chlorosarcinopsis, Pleurastrum, Palmellopsis, and Bracteococcus, and cyanobacteria of the genera Nostoc, Phormidium, Leptolyngbya, and Gloeocapsa. From point transects and localized sampling we estimated a total standing stock on this ice shelf of up to 11,200 tonnes of organic matter. These observations underscore the ability of microbial communities to flourish despite the severe constraints imposed by the cryo-ecosystem environment.

  19. Physico-chemical gradients within the hydrothermal chimney Roane define sharp boundaries for microbial community ecology

    NASA Astrophysics Data System (ADS)

    Frank, K. L.; Kelley, D. S.; Girguis, P. R.

    2011-12-01

    The unique physico-chemical gradients characteristic of hydrothermal vents provide diverse niches for prokaryotic communities. To date, our knowledge of environmental constraints on microbial colonization and metabolic activity within active sulfide structures has been limited by the lack of co-registered in situ chemistry and appropriate, taxonomic and metabolic genetic markers. Here we characterize de novo endolithic microbial colonization using a sulfide microbial incubator within the hydrothermal vent Roane during a one-year deployment, with co-registered temperature, fluid chemistry and mineralogy. Taxanomic assessment of phylogenetic diversity via 16S rDNA extracted from the outer (40-70°C) and middle (150-240°C) chambers of the incubator revealed patterns of distribution comparable to previously published observations. However, quantitative and statistical analyses of 16S rDNA sequences from two chambers revealed very distinct communities, with less than 5% of the identified operational taxonomic units common to both chambers. Analyses of metagenomic data suggest an elevated potential for motility and select biosynthetic pathways in the outer chamber community. In contrast, the middle chamber community exhibits a greater potential for quorum sensing, biofilm formation and archaeal lipid biosynthesis. Striking differences in metabolic potential were also apparent. These data suggest that the distribution, abundance and physiological capacity of these communities is strongly governed by chemical and physical variability of the environment.

  20. IMNGS: A comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies

    PubMed Central

    Lagkouvardos, Ilias; Joseph, Divya; Kapfhammer, Martin; Giritli, Sabahattin; Horn, Matthias; Haller, Dirk; Clavel, Thomas

    2016-01-01

    The SRA (Sequence Read Archive) serves as primary depository for massive amounts of Next Generation Sequencing data, and currently host over 100,000 16S rRNA gene amplicon-based microbial profiles from various host habitats and environments. This number is increasing rapidly and there is a dire need for approaches to utilize this pool of knowledge. Here we created IMNGS (Integrated Microbial Next Generation Sequencing), an innovative platform that uniformly and systematically screens for and processes all prokaryotic 16S rRNA gene amplicon datasets available in SRA and uses them to build sample-specific sequence databases and OTU-based profiles. Via a web interface, this integrative sequence resource can easily be queried by users. We show examples of how the approach allows testing the ecological importance of specific microorganisms in different hosts or ecosystems, and performing targeted diversity studies for selected taxonomic groups. The platform also offers a complete workflow for de novo analysis of users’ own raw 16S rRNA gene amplicon datasets for the sake of comparison with existing data. IMNGS can be accessed at www.imngs.org. PMID:27659943

  1. Microbial Ecology Dynamics Reveal a Succession in the Core Microbiota Involved in the Ripening of Pasta Filata Caciocavallo Pugliese Cheese

    PubMed Central

    De Pasquale, Ilaria; Buchin, Solange; De Angelis, Maria; Gobbetti, Marco

    2014-01-01

    Pyrosequencing of the 16S rRNA targeting RNA, community-level physiological profiles made with Biolog EcoPlates, proteolysis, and volatile component (VOC) analyses were mainly used to characterize the manufacture and ripening of the pasta filata cheese Caciocavallo Pugliese. Plate counts revealed that cheese manufacture affected the microbial ecology. The results agreed with those from culture-independent approaches. As shown by urea-PAGE, reverse-phase high pressure liquid chromatography (RP-HPLC), and free-amino-acid (FAA) analyses, the extent of secondary proteolysis mainly increased after 30 to 45 days of ripening. VOCs and volatile free fatty acids (VFFA) were identified by a purge-and-trap method (PT) and solid-phase microextraction (SPME) coupled with gas chromatography-mass spectrometry (GC-MS), respectively. Except for aldehydes, the levels of most of VOCs and VFFA mainly increased from 30 to 45 days onwards. As shown through pyrosequencing analysis, raw cows' milk was contaminated by Firmicutes (53%), Proteobacteria (39%), Bacteroidetes (7.8%), Actinobacteria (0.06%), and Fusobacteria (0.03%), with heterogeneity at the genus level. The primary starter Streptococcus thermophilus dominated the curd population. Other genera occurred at low incidence or sporadically. The microbial dynamics reflected on the overall physiological diversity. At 30 days, a microbial succession was clearly highlighted. The relative abundance of Streptococcus sp. and especially St. thermophilus decreased, while that of Lactobacillus casei, Lactobacillus sp., and especially Lactobacillus paracasei increased consistently. Despite the lower relative abundance compared to St. thermophilus, mesophilic lactobacilli were the only organisms positively correlated with the concentration of FAAs, area of hydrophilic peptide peaks, and several VOCs (e.g., alcohols, ketones, esters and all furans). This study showed that a core microbiota was naturally selected during middle ripening, which

  2. Microbial ecology, bacterial pathogens, and antibiotic resistant genes in swine manure wastewater as influenced by three swine management systems.

    PubMed

    Brooks, John P; Adeli, Ardeshir; McLaughlin, Michael R

    2014-06-15

    The environmental influence of farm management in concentrated animal feeding operations (CAFO) can yield vast changes to the microbial biota and ecological structure of both the pig and waste manure lagoon wastewater. While some of these changes may not be negative, it is possible that CAFOs can enrich antibiotic resistant bacteria or pathogens based on farm type, thereby influencing the impact imparted by the land application of its respective wastewater. The purpose of this study was to measure the microbial constituents of swine-sow, -nursery, and -finisher farm manure lagoon wastewater and determine the changes induced by farm management. A total of 37 farms were visited in the Mid-South USA and analyzed for the genes 16S rRNA, spaQ (Salmonella spp.), Camp-16S (Campylobacter spp.), tetA, tetB, ermF, ermA, mecA, and intI using quantitative PCR. Additionally, 16S rRNA sequence libraries were created. Overall, it appeared that finisher farms were significantly different from nursery and sow farms in nearly all genes measured and in 16S rRNA clone libraries. Nearly all antibiotic resistance genes were detected in all farms. Interestingly, the mecA resistance gene (e.g. methicillin resistant Staphylococcus aureus) was below detection limits on most farms, and decreased as the pigs aged. Finisher farms generally had fewer antibiotic resistance genes, which corroborated previous phenotypic data; additionally, finisher farms produced a less diverse 16S rRNA sequence library. Comparisons of Camp-16S and spaQ GU (genomic unit) values to previous culture data demonstrated ratios from 10 to 10,000:1 depending on farm type, indicating viable but not cultivatable bacteria were dominant. The current study indicated that swine farm management schemes positively and negatively affect microbial and antibiotic resistant populations in CAFO wastewater which has future "downstream" implications from both an environmental and public health perspective.

  3. Microbial ecology, bacterial pathogens, and antibiotic resistant genes in swine manure wastewater as influenced by three swine management systems.

    PubMed

    Brooks, John P; Adeli, Ardeshir; McLaughlin, Michael R

    2014-06-15

    The environmental influence of farm management in concentrated animal feeding operations (CAFO) can yield vast changes to the microbial biota and ecological structure of both the pig and waste manure lagoon wastewater. While some of these changes may not be negative, it is possible that CAFOs can enrich antibiotic resistant bacteria or pathogens based on farm type, thereby influencing the impact imparted by the land application of its respective wastewater. The purpose of this study was to measure the microbial constituents of swine-sow, -nursery, and -finisher farm manure lagoon wastewater and determine the changes induced by farm management. A total of 37 farms were visited in the Mid-South USA and analyzed for the genes 16S rRNA, spaQ (Salmonella spp.), Camp-16S (Campylobacter spp.), tetA, tetB, ermF, ermA, mecA, and intI using quantitative PCR. Additionally, 16S rRNA sequence libraries were created. Overall, it appeared that finisher farms were significantly different from nursery and sow farms in nearly all genes measured and in 16S rRNA clone libraries. Nearly all antibiotic resistance genes were detected in all farms. Interestingly, the mecA resistance gene (e.g. methicillin resistant Staphylococcus aureus) was below detection limits on most farms, and decreased as the pigs aged. Finisher farms generally had fewer antibiotic resistance genes, which corroborated previous phenotypic data; additionally, finisher farms produced a less diverse 16S rRNA sequence library. Comparisons of Camp-16S and spaQ GU (genomic unit) values to previous culture data demonstrated ratios from 10 to 10,000:1 depending on farm type, indicating viable but not cultivatable bacteria were dominant. The current study indicated that swine farm management schemes positively and negatively affect microbial and antibiotic resistant populations in CAFO wastewater which has future "downstream" implications from both an environmental and public health perspective. PMID:24704907

  4. Microbial ecology of the closed artificial ecosystem MELiSSA (Micro-Ecological Life Support System Alternative): reinventing and compartmentalizing the Earth's food and oxygen regeneration system for long-haul space exploration missions.

    PubMed

    Hendrickx, Larissa; De Wever, Heleen; Hermans, Veronik; Mastroleo, Felice; Morin, Nicolas; Wilmotte, Annick; Janssen, Paul; Mergeay, Max

    2006-01-01

    MELiSSA is a bioregenerative life support system designed by the European Space Agency (ESA) for the complete recycling of gas, liquid and solid wastes during long distance space exploration. The system uses the combined activity of different living organisms: microbial cultures in bioreactors, a plant compartment and a human crew. In this minireview, the development of a short-cut ecological system for the biotransformation of organic waste is discussed from a microorganism's perspective. The artificial ecological model--still in full development--that is inspired by Earth's own geomicrobiological ecosystem serves as an ideal study object on microbial ecology and will become an indispensable travel companion in manned space exploration.

  5. Ecology.

    ERIC Educational Resources Information Center

    National Audubon Society, New York, NY.

    This set of teaching aids consists of nine Audubon Nature Bulletins, providing teachers and students with informational reading on various ecological topics. The bulletins have these titles: Schoolyard Laboratories, Owls and Predators, The Forest Community, Life in Freshwater Marshes, Camouflage in the Animal World, Life in the Desert, The…

  6. Shift in the microbial ecology of a hospital hot water system following the introduction of an on-site monochloramine disinfection system.

    PubMed

    Baron, Julianne L; Vikram, Amit; Duda, Scott; Stout, Janet E; Bibby, Kyle

    2014-01-01

    Drinking water distribution systems, including premise plumbing, contain a diverse microbiological community that may include opportunistic pathogens. On-site supplemental disinfection systems have been proposed as a control method for opportunistic pathogens in premise plumbing. The majority of on-site disinfection systems to date have been installed in hospitals due to the high concentration of opportunistic pathogen susceptible occupants. The installation of on-site supplemental disinfection systems in hospitals allows for evaluation of the impact of on-site disinfection systems on drinking water system microbial ecology prior to widespread application. This study evaluated the impact of supplemental monochloramine on the microbial ecology of a hospital's hot water system. Samples were taken three months and immediately prior to monochloramine treatment and monthly for the first six months of treatment, and all samples were subjected to high throughput Illumina 16S rRNA region sequencing. The microbial community composition of monochloramine treated samples was dramatically different than the baseline months. There was an immediate shift towards decreased relative abundance of Betaproteobacteria, and increased relative abundance of Firmicutes, Alphaproteobacteria, Gammaproteobacteria, Cyanobacteria and Actinobacteria. Following treatment, microbial populations grouped by sampling location rather than sampling time. Over the course of treatment the relative abundance of certain genera containing opportunistic pathogens and genera containing denitrifying bacteria increased. The results demonstrate the driving influence of supplemental disinfection on premise plumbing microbial ecology and suggest the value of further investigation into the overall effects of premise plumbing disinfection strategies on microbial ecology and not solely specific target microorganisms. PMID:25033448

  7. Ecological patterns, diversity and core taxa of microbial communities in groundwater-fed rapid gravity filters

    PubMed Central

    Gülay, Arda; Musovic, Sanin; Albrechtsen, Hans-Jørgen; Al-Soud, Waleed Abu; Sørensen, Søren J; Smets, Barth F

    2016-01-01

    Here, we document microbial communities in rapid gravity filtration units, specifically serial rapid sand filters (RSFs), termed prefilters (PFs) and after- filters (AFs), fed with anoxic groundwaters low in organic carbon to prepare potable waters. A comprehensive 16S rRNA-based amplicon sequencing survey revealed a core RSF microbiome comprising few bacterial taxa (29–30 genera) dominated by Nitrospirae, Proteobacteria and Acidobacteria, with a strikingly high abundance (75–87±18%) across five examined waterworks in Denmark. Lineages within the Nitrospira genus consistently comprised the second most and most abundant fraction in PFs (27±23%) and AFs (45.2±23%), respectively, and were far more abundant than typical proteobacterial ammonium-oxidizing bacteria, suggesting a physiology beyond nitrite oxidation for Nitrospira. Within the core taxa, sequences closely related to types with ability to oxidize ammonium, nitrite, iron, manganese and methane as primary growth substrate were identified and dominated in both PFs (73.6±6%) and AFs (61.4±21%), suggesting their functional importance. Surprisingly, operational taxonomic unit richness correlated strongly and positively with sampling location in the drinking water treatment plant (from PFs to AFs), and a weaker negative correlation held for evenness. Significant spatial heterogeneity in microbial community composition was detected in both PFs and AFs, and was higher in the AFs. This is the first comprehensive documentation of microbial community diversity in RSFs treating oligotrophic groundwaters. We have identified patterns of local spatial heterogeneity and dispersal, documented surprising energy–diversity relationships, observed a large and diverse Nitrospira fraction and established a core RSF microbiome. PMID:26953601

  8. Ecological patterns, diversity and core taxa of microbial communities in groundwater-fed rapid gravity filters.

    PubMed

    Gülay, Arda; Musovic, Sanin; Albrechtsen, Hans-Jørgen; Al-Soud, Waleed Abu; Sørensen, Søren J; Smets, Barth F

    2016-09-01

    Here, we document microbial communities in rapid gravity filtration units, specifically serial rapid sand filters (RSFs), termed prefilters (PFs) and after- filters (AFs), fed with anoxic groundwaters low in organic carbon to prepare potable waters. A comprehensive 16S rRNA-based amplicon sequencing survey revealed a core RSF microbiome comprising few bacterial taxa (29-30 genera) dominated by Nitrospirae, Proteobacteria and Acidobacteria, with a strikingly high abundance (75-87±18%) across five examined waterworks in Denmark. Lineages within the Nitrospira genus consistently comprised the second most and most abundant fraction in PFs (27±23%) and AFs (45.2±23%), respectively, and were far more abundant than typical proteobacterial ammonium-oxidizing bacteria, suggesting a physiology beyond nitrite oxidation for Nitrospira. Within the core taxa, sequences closely related to types with ability to oxidize ammonium, nitrite, iron, manganese and methane as primary growth substrate were identified and dominated in both PFs (73.6±6%) and AFs (61.4±21%), suggesting their functional importance. Surprisingly, operational taxonomic unit richness correlated strongly and positively with sampling location in the drinking water treatment plant (from PFs to AFs), and a weaker negative correlation held for evenness. Significant spatial heterogeneity in microbial community composition was detected in both PFs and AFs, and was higher in the AFs. This is the first comprehensive documentation of microbial community diversity in RSFs treating oligotrophic groundwaters. We have identified patterns of local spatial heterogeneity and dispersal, documented surprising energy-diversity relationships, observed a large and diverse Nitrospira fraction and established a core RSF microbiome. PMID:26953601

  9. The Influence of Staphylococcus aureus on Gut Microbial Ecology in an In Vitro Continuous Culture Human Colonic Model System

    PubMed Central

    Sannasiddappa, Thippeswamy H.; Costabile, Adele; Gibson, Glenn R.; Clarke, Simon R.

    2011-01-01

    An anaerobic three-stage continuous culture model of the human colon (gut model), which represent different anatomical areas of the large intestine, was used to study the effect of S. aureus infection of the gut on the resident faecal microbiota. Studies on the development of the microbiota in the three vessels were performed and bacteria identified by culture independent fluorescence in situ hybridization (FISH). Furtheremore, short chain fatty acids (SCFA), as principal end products of gut bacterial metabolism, were measured along with a quantitative assessment of the predominant microbiota. During steady state conditions, numbers of S. aureus cells stabilised until they were washed out, but populations of indigenous bacteria were transiently altered; thus S. aureus was able to compromise colonisation resistance by the colonic microbiota. Furthermore, the concentration of butyric acid in the vessel representing the proximal colon was significantly decreased by infection. Thus infection by S. aureus appears to be able to alter the overall structure of the human colonic microbiota and the microbial metabolic profiles. This work provides an initial in vitro model to analyse interactions with pathogens. PMID:21858036

  10. Microbial Ecology and Resultant Biomarkers Preserved in a Terrestrial Analog of a Martian Spring System

    NASA Astrophysics Data System (ADS)

    Giska, J. R.; Moreau, J.; Rowland, J.; Cervini-Silva, J.; Manga, M.; Banfield, J.

    2005-12-01

    On Mars, groundwater discharge, heated by geological processes at depth, represents a likely late-stage reservoir of liquid water available for biological activity. Photo-geological observations of the Martian surface support geologically, relatively young groundwater discharge via sapping and/or fault-controlled springs. Our approach to the investigation of the possible biological potential of such reservoirs has been to characterize analogous, terrestrial spring systems. Our study site is a fault-driven, mesophilic, sulfur spring system between the Hayward and Calaveras faults in California. We have examined hydro-geological variables, nutrient availability for microbial metabolism, differences in extant community structure, and the seasonal changes associated with these variables. The springs under study also precipitate calcite and form large mounds, offering the potential to evaluate the preservation of biosignatures. The geochemistry and isotopic composition (2H/18O) of spring waters indicate that the various springs discharge waters represent differing amounts of mixing between deeper, connate water with shallow meteoric inputs. Clone libraries of 16S rDNA and fluorescence in situ hybridization experiments suggest that oxidation of sulfur compounds by Epsilon- and Gammaproteobacteria is a significant process occurring in the springs, and lipid analyses support these observations. While the studied springs undergo seasonal shifts in their respective geochemistries, only the microbial community at one of the springs elicits a commensurate seasonal variation. During the dry season, the community at this spring shifts to a red, plaque-like biofilm and iron-cycling organisms from the Alphaproteobacteria class increase significantly in their relative abundance within the community. Preliminary chemical analysis of the calcite accretions indicates abundant organic carbon, and thus, suggests a possible record of prior microbial ecosystems. On-going investigations of

  11. Effects of Subsurface Microbial Ecology on Geochemical Evolution of a Crude-Oil Contaminated Aquifer

    NASA Astrophysics Data System (ADS)

    Bekins, B. A.; Cozzarelli, I. M.; Godsy, E. M.; Warren, E.; Hostettler, F. D.

    2001-12-01

    We have identified several subsurface habitats for microorganisms in a crude oil contaminated located near Bemidji, Minnesota. These aquifer habitats include: 1) the unsaturated zone contaminated by hydrocarbon vapors, 2) the zones containing separate-phase crude oil, and 3) the aqueous-phase contaminant plume. The surficial glacial outwash aquifer was contaminated when a crude oil pipeline burst in 1979. We analyzed sediment samples from the contaminated aquifer for the most probable numbers of aerobes, iron reducers, fermenters, and three types of methanogens. The microbial data were then related to gas, water, and oil chemistry, sediment extractable iron, and permeability. The microbial populations in the various contaminated subsurface habitats each have special characteristics and these affect the aquifer and contaminant chemistry. In the eight-meter-thick, vapor-contaminated vadose zone, a substantial aerobic population has developed that is supported by hydrocarbon vapors and methane. Microbial numbers peak in locations where access to both hydrocarbons and nutrients infiltrating from the surface is maximized. The activity of this population prevents hydrocarbon vapors from reaching the land surface. In the zone where separate-phase crude oil is present, a consortium of methanogens and fermenters dominates the populations both above and below the water table. Moreover, gas concentration data indicate that methane production has been active in the oily zone since at least 1986. Analyses of the extracted separate-phase oil show that substantial degradation of C15 -C35 n-alkanes has occurred since 1983, raising the possibility that significant degradation of C15 and higher n-alkanes has occurred under methanogenic conditions. However, lab and field data suggest that toxic inhibition by crude oil results in fewer acetate-utilizing methanogens within and adjacent to the separate-phase oil. Data from this and other sites indicate that toxic inhibition of

  12. The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes

    PubMed Central

    van Overbeek, Leonard S.; Berg, Gabriele; Pirttilä, Anna Maria; Compant, Stéphane; Campisano, Andrea; Döring, Matthias; Sessitsch, Angela

    2015-01-01

    SUMMARY All plants are inhabited internally by diverse microbial communities comprising bacterial, archaeal, fungal, and protistic taxa. These microorganisms showing endophytic lifestyles play crucial roles in plant development, growth, fitness, and diversification. The increasing awareness of and information on endophytes provide insight into the complexity of the plant microbiome. The nature of plant-endophyte interactions ranges from mutualism to pathogenicity. This depends on a set of abiotic and biotic factors, including the genotypes of plants and microbes, environmental conditions, and the dynamic network of interactions within the plant biome. In this review, we address the concept of endophytism, considering the latest insights into evolution, plant ecosystem functioning, and multipartite interactions. PMID:26136581

  13. Molecular Ecological and Stable Isotopic Studies of Nitrogen Fixation in Modern Microbial Mats

    NASA Technical Reports Server (NTRS)

    Bebout, B. M.; Crumbliss, L. L.; DesMarais, D. J.; Hogan, M. E.; Omoregie, E.; Turk, K. A.; Zehr, J. P.

    2003-01-01

    Nitrogen is usually the element limiting biological productivity in the marine environment. Microbial mats, laminated microbial communities analogous to some of the oldest forms of life on Earth, are often the sites of high rates of N fixation (the energetically expensive conversion of atmospheric dinitrogen into a biologically useful form). The N fixing enzyme nitrogenase is generally considered to be of ancient origin, and is widely distributed throughout the Bacterial and Archaeal domains of life, indicating an important role for this process over evolutionary time. The stable isotopic signature of N fixation is purportedly recognizable in organic matter (ancient kerogens as well as present-day microbial mats) as a delta (15)N(sub organic) near zero. We studied two microbial mats exhibiting different rates of N fixation in order to better understand the impact of N fixation on the delta (15)N (sub organic) of the mats, as well as what organisms are important in this process. Mats dominated by the cyanobacterium Microcoleus chthonoplastes grow in permanently submerged hypersaline salterns, and exhibit low rates of N fixation, whereas mats dominated by the cyanobacterium Lyngbya spp grow in an intertidal area, and exhibit rates of N fixation an order of magnitude higher. To examine successional stages in mat growth, both developing and established mats at each location were sampled. PCR and RT-PCR based approaches were used to identify, respectively, the organisms containing nifH (one of the genes that encode nitrogenase) as well as those expressing nifH in these mats. Both mats exhibited a distinct diel cycle of N fixation, with highest rates occurring at night. The delta (15)N(sub organic) of the subtidal Microcoleus mats is near zero whereas the delta (15)N(sub organic) is slightly more positive (+ 2-3%), in the intertidal Lyngbya mats, an interesting difference in view of the fact that overall rates of activity in the intertidal mats are much higher that those

  14. Dispersing misconceptions and identifying opportunities for the use of 'omics' in soil microbial ecology.

    PubMed

    Prosser, James I

    2015-07-01

    Technological advances are enabling the sequencing of environmental DNA and RNA at increasing depth and with decreasing costs. Metagenomic and transcriptomic analysis of soil microbial communities and the assembly of 'population genomes' from soil DNA are therefore now feasible. Although the value of such 'omic' approaches is limited by the associated technical and bioinformatic difficulties, even if these obstacles were eliminated and 'perfect' metagenomes and metatranscriptomes were available, important conceptual challenges remain. This Opinion article considers these conceptual challenges in the context of the current use of omics in soil microbiology, but the main arguments presented are also relevant to the application of omics to marine, freshwater, gut or other environments.

  15. The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes.

    PubMed

    Hardoim, Pablo R; van Overbeek, Leonard S; Berg, Gabriele; Pirttilä, Anna Maria; Compant, Stéphane; Campisano, Andrea; Döring, Matthias; Sessitsch, Angela

    2015-09-01

    All plants are inhabited internally by diverse microbial communities comprising bacterial, archaeal, fungal, and protistic taxa. These microorganisms showing endophytic lifestyles play crucial roles in plant development, growth, fitness, and diversification. The increasing awareness of and information on endophytes provide insight into the complexity of the plant microbiome. The nature of plant-endophyte interactions ranges from mutualism to pathogenicity. This depends on a set of abiotic and biotic factors, including the genotypes of plants and microbes, environmental conditions, and the dynamic network of interactions within the plant biome. In this review, we address the concept of endophytism, considering the latest insights into evolution, plant ecosystem functioning, and multipartite interactions.

  16. Microbial ecology of corals, sponges, and algae in mesophotic coral environments

    USGS Publications Warehouse

    Olson, Julie B.; Kellogg, Christina A.

    2010-01-01

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

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

    NASA Technical Reports Server (NTRS)

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

    2002-01-01

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

  18. Mesophilic versus thermophilic anaerobic digestion of cattle manure: methane productivity and microbial ecology.

    PubMed

    Moset, Veronica; Poulsen, Morten; Wahid, Radziah; Højberg, Ole; Møller, Henrik Bjarne

    2015-09-01

    In this study, productivity and physicochemical and microbiological (454 sequencing) parameters, as well as environmental criteria, were investigated in anaerobic reactors to contribute to the ongoing debate about the optimal temperature range for treating animal manure, and expand the general knowledge on the relation between microbiological and physicochemical process indicators. For this purpose, two reactor sizes were used (10 m(3) and 16 l), in which two temperature conditions (35°C and 50°C) were tested. In addition, the effect of the hydraulic retention time was evaluated (16 versus 20 days). Thermophilic anaerobic digestion showed higher organic matter degradation (especially fiber), higher pH and higher methane (CH₄) yield, as well as better percentage of ultimate CH₄ yield retrieved and lower residual CH₄ emission, when compared with mesophilic conditions. In addition, lower microbial diversity was found in the thermophilic reactors, especially for Bacteria, where a clear intensification towards Clostridia class members was evident. Independent of temperature, some similarities were found in digestates when comparing with animal manure, including low volatile fatty acids concentrations and a high fraction of Euryarchaeota in the total microbial community, in which members of Methanosarcinales dominated for both temperature conditions; these indicators could be considered a sign of process stability.

  19. An underground tale: contribution of microbial activity to plant iron acquisition via ecological processes

    PubMed Central

    Jin, Chong Wei; Ye, Yi Quan; Zheng, Shao Jian

    2014-01-01

    Background Iron (Fe) deficiency in crops is a worldwide agricultural problem. Plants have evolved several strategies to enhance Fe acquisition, but increasing evidence has shown that the intrinsic plant-based strategies alone are insufficient to avoid Fe deficiency in Fe-limited soils. Soil micro-organisms also play a critical role in plant Fe acquisition; however, the mechanisms behind their promotion of Fe acquisition remain largely unknown. Scope This review focuses on the possible mechanisms underlying the promotion of plant Fe acquisition by soil micro-organisms. Conclusions Fe-deficiency-induced root exudates alter the microbial community in the rhizosphere by modifying the physicochemical properties of soil, and/or by their antimicrobial and/or growth-promoting effects. The altered microbial community may in turn benefit plant Fe acquisition via production of siderophores and protons, both of which improve Fe bioavailability in soil, and via hormone generation that triggers the enhancement of Fe uptake capacity in plants. In addition, symbiotic interactions between micro-organisms and host plants could also enhance plant Fe acquisition, possibly including: rhizobium nodulation enhancing plant Fe uptake capacity and mycorrhizal fungal infection enhancing root length and the nutrient acquisition area of the root system, as well as increasing the production of Fe3+ chelators and protons. PMID:24265348

  20. Mesophilic versus thermophilic anaerobic digestion of cattle manure: methane productivity and microbial ecology

    PubMed Central

    Moset, Veronica; Poulsen, Morten; Wahid, Radziah; Højberg, Ole; Møller, Henrik Bjarne

    2015-01-01

    In this study, productivity and physicochemical and microbiological (454 sequencing) parameters, as well as environmental criteria, were investigated in anaerobic reactors to contribute to the ongoing debate about the optimal temperature range for treating animal manure, and expand the general knowledge on the relation between microbiological and physicochemical process indicators. For this purpose, two reactor sizes were used (10 m3 and 16 l), in which two temperature conditions (35°C and 50°C) were tested. In addition, the effect of the hydraulic retention time was evaluated (16 versus 20 days). Thermophilic anaerobic digestion showed higher organic matter degradation (especially fiber), higher pH and higher methane (CH4) yield, as well as better percentage of ultimate CH4 yield retrieved and lower residual CH4 emission, when compared with mesophilic conditions. In addition, lower microbial diversity was found in the thermophilic reactors, especially for Bacteria, where a clear intensification towards Clostridia class members was evident. Independent of temperature, some similarities were found in digestates when comparing with animal manure, including low volatile fatty acids concentrations and a high fraction of Euryarchaeota in the total microbial community, in which members of Methanosarcinales dominated for both temperature conditions; these indicators could be considered a sign of process stability. PMID:25737010

  1. Microbial ecological perspectives of space-exposed microbes: A genetic approach

    NASA Astrophysics Data System (ADS)

    Venkateswaran, Kasthuri; Osman, Shariff; Spry, James A.; Mancinelli, Rocco; Rabbow, Elke; Rettberg, Petra; Horneck, Gerda

    2008-09-01

    A radiation resistant strain of Bacillus pumilus isolated from a spacecraft assembly environment is being exposed to several conditions associated with the space environment (Feb, 2008). The radiation exposures are being carried out aboard ISS using the European Technology Exposure Platform and Experiment Facility (EXPOSE) and include: (i) space vacuum, (ii) solar extraterrestrial UV radiation including vacuum-UV, (iii) simulated Martian UV radiation regime, and (iv) galactic cosmic radiation. The viability of exposed and unexposed microorganisms as well as the integrity of the cell wall or spore envelop (membrane, wall and coat layers) and damage to the DNA will be assessed when the exposed spores return to Earth. In addition to these standard methods for assessing cellular damage, the global response elicited in spores by space exposure will be probed in germinated spore survivors using transcription microarrays. During ground simulation experiments the desiccated spores survived full Martian UV (200 - 400 nm) for 5 min (30 W m-2) and were only slightly affected by Martian atmospheric conditions in the absence of UV. Although prolonged UV irradiation (>5 min to 12 hours; 30 W m-2) killed substantial portions of the spore microcosms (~5 to 6 logs reduction under Martian UV), dramatic spore survival was apparent when spores were shield by dust (~2 logs reduction). It is presumed that the mitigation of UV damage (200-400 nm) to dust covered, desiccated spores and their survival on spacecraft-grade aluminum is strain specific. The more pronounced UV resistances observed in wild-type strains, as compared to laboratory strains suggested that discussions and conclusions regarding the survival of microbes in extraterrestrial environments should not be generalized based solely on laboratory strain responses to simulated conditions. The data generated is important for the assessment of the probability and mechanisms of microbial survival, microbial contaminants of risk to

  2. An organotypic slice model for ex vivo study of neural, immune, and microbial interactions of mouse intestine.

    PubMed

    Schwerdtfeger, Luke A; Ryan, Elizabeth P; Tobet, Stuart A

    2016-02-15

    Organotypic tissue slices provide seminatural, three-dimensional microenvironments for use in ex vivo study of specific organs and have advanced investigative capabilities compared with isolated cell cultures. Several characteristics of the gastrointestinal tract have made in vitro models for studying the intestine challenging, such as maintaining the intricate structure of microvilli, the intrinsic enteric nervous system, Peyer's patches, the microbiome, and the active contraction of gut muscles. In the present study, an organotypic intestinal slice model was developed that allows for functional investigation across regions of the intestine. Intestinal tissue slices were maintained ex vivo for several days in a physiologically relevant environment that preserved normal enterocyte structure, intact and proliferating crypt cells, submucosal organization, and muscle wall composure. Cell death was measured by a membrane-impermeable DNA binding indicator, ethidium homodimer, and less than 5% of cells were labeled in all regions of the villi and crypt epithelia at 24 h ex vivo. This tissue slice model demonstrated intact myenteric and submucosal neuronal plexuses and functional interstitial cells of Cajal to the extent that nonstimulated, segmental contractions occurred for up to 48 h ex vivo. To detect changes in physiological responses, slices were also assessed for segmental contractions in the presence and absence of antibiotic treatment, which resulted in slices with lesser or greater amounts of commensal bacteria, respectively. Segmental contractions were significantly greater in slices without antibiotics and increased native microbiota. This model renders mechanisms of neuroimmune-microbiome interactions in a complex gut environment available to direct observation and controlled perturbation.

  3. Microbial Ecology of the Skin in the Era of Metagenomics and Molecular Microbiology

    PubMed Central

    Hannigan, Geoffrey D.; Grice, Elizabeth A.

    2013-01-01

    The skin is the primary physical barrier between the body and the external environment and is also a substrate for the colonization of numerous microbes. Previously, dermatological microbiology research was dominated by culture-based techniques, but significant advances in genomic technologies have enabled the development of less-biased, culture-independent approaches to characterize skin microbial communities. These molecular microbiology approaches illustrate the great diversity of microbiota colonizing the skin and highlight unique features such as site specificity, temporal dynamics, and interpersonal variation. Disruptions in skin commensal microbiota are associated with the progression of many dermatological diseases. A greater understanding of how skin microbes interact with each other and with their host, and how we can therapeutically manipulate those interactions, will provide powerful tools for treating and preventing dermatological disease. PMID:24296350

  4. Microbial ecology of the skin in the era of metagenomics and molecular microbiology.

    PubMed

    Hannigan, Geoffrey D; Grice, Elizabeth A

    2013-12-01

    The skin is the primary physical barrier between the body and the external environment and is also a substrate for the colonization of numerous microbes. Previously, dermatological microbiology research was dominated by culture-based techniques, but significant advances in genomic technologies have enabled the development of less-biased, culture-independent approaches to characterize skin microbial communities. These molecular microbiology approaches illustrate the great diversity of microbiota colonizing the skin and highlight unique features such as site specificity, temporal dynamics, and interpersonal variation. Disruptions in skin commensal microbiota are associated with the progression of many dermatological diseases. A greater understanding of how skin microbes interact with each other and with their host, and how we can therapeutically manipulate those interactions, will provide powerful tools for treating and preventing dermatological disease.

  5. Anaerobic digestion and co-digestion processes of vegetable and fruit residues: process and microbial ecology.

    PubMed

    Garcia-Peña, E I; Parameswaran, P; Kang, D W; Canul-Chan, M; Krajmalnik-Brown, R

    2011-10-01

    This study evaluated the feasibility of methane production from fruit and vegetable waste (FVW) obtained from the central food distribution market in Mexico City using an anaerobic digestion (AD) process. Batch systems showed that pH control and nitrogen addition had significant effects on biogas production, methane yield, and volatile solids (VS) removal from the FVW (0.42 m(biogas)(3)/kg VS, 50%, and 80%, respectively). Co-digestion of the FVW with meat residues (MR) enhanced the process performance and was also evaluated in a 30 L AD system. When the system reached stable operation, its methane yield was 0.25 (m(3)/kg TS), and the removal of the organic matter measured as the total chemical demand (tCOD) was 65%. The microbial population (general Bacteria and Archaea) in the 30 L system was also determined and characterized and was closely correlated with its potential function in the AD system.

  6. Apple replant disease: role of microbial ecology in cause and control.

    PubMed

    Mazzola, Mark; Manici, Luisa M

    2012-01-01

    Replant disease of apple is common to all major apple growing regions of the world. Difficulties in defining disease etiology, which can be exacerbated by abiotic factors, have limited progress toward developing alternatives to soil fumigation for disease control. However, the preponderance of data derived from studies of orchard soil biology employing multidisciplinary approaches has defined a complex of pathogens/parasites as causal agents of the disease. Approaches to manipulate microbial resources endemic to the orchard soil system have been proposed to induce a state of general soil suppressiveness to replant disease. Such a long-term strategy may benefit the existing orchard through extending the period of economic viability and reduce overall disease pressure to which young trees are exposed during establishment of successive plantings on the site. Alternatively, more near-term methods have been devised to achieve specific quantitative and qualitative changes in soil biology during the period of orchard renovation that may lead to effective disease suppression.

  7. Adaptive long-term monitoring of soil health in metal phytostabilization: ecological attributes and ecosystem services based on soil microbial parameters.

    PubMed

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

    2014-01-01

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

  8. Spreading Topsoil Encourages Ecological Restoration on Embankments: Soil Fertility, Microbial Activity and Vegetation Cover

    PubMed Central

    Rivera, Desirée; Mejías, Violeta; Jáuregui, Berta M.; López-Archilla, Ana Isabel; Peco, Begoña

    2014-01-01

    The construction of linear transport infrastructure has severe effects on ecosystem functions and properties, and the restoration of the associated roadslopes contributes to reduce its impact. This restoration is usually approached from the perspective of plant cover regeneration, ignoring plant-soil interactions and the consequences for plant growth. The addition of a 30 cm layer of topsoil is a common practice in roadslope restoration projects to increase vegetation recovery. However topsoil is a scarce resource. This study assesses the effects of topsoil spreading and its depth (10 to 30 cm) on two surrogates of microbial activity (β-glucosidase and phosphatase enzymes activity and soil respiration), and on plant cover, plant species richness and floristic composition of embankment vegetation. The study also evaluates the differences in selected physic-chemical properties related to soil fertility between topsoil and the original embankment substrate. Topsoil was found to have higher values of organic matter (11%), nitrogen (44%), assimilable phosphorous (50%) and silt content (54%) than the original embankment substrate. The topsoil spreading treatment increased microbial activity, and its application increased β-glucosidase activity (45%), phosphatase activity (57%) and soil respiration (60%). Depth seemed to affect soil respiration, β-glucosidase and phosphatase activity. Topsoil application also enhanced the species richness of restored embankments in relation to controls. Nevertheless, the depth of the spread topsoil did not significantly affect the resulting plant cover, species richness or floristic composition, suggesting that both depths could have similar effects on short-term recovery of the vegetation cover. A significant implication of these results is that it permits the application of thinner topsoil layers, with major savings in this scarce resource during the subsequent slope restoration work, but the quality of topsoil relative to the

  9. Endogenous isolation of replicon probes for assessing plasmid ecology of marine sediment microbial communities.

    PubMed

    Cook, M A; Osborn, A M; Bettandorff, J; Sobecky, P A

    2001-08-01

    Six functional replication origins (repGA14, repGA33, repGA70, repSD41, repSD164 and repSD172), obtained from endogenously isolated, broad-host-range (BHR) marine plasmids ranging in size from 5 to 60 kb, were used to determine plasmid occurrence in three coastal marine sediment sites (in California, Georgia and South Carolina, USA). The plasmid-specific replicons were isolated from plasmid-bearing marine sediment bacteria belonging to the alpha and gamma subclasses of the Proteobacteria. The plasmid sources of the endogenous replicons were considered to be cryptic due to a lack of identifiable phenotypic traits. The putative Rep proteins from a number of these replicons showed similarity to replicons of two recognized families: RCR group III (repSD164) and the FIA family of theta group A (repSD41, repSD121, repGA33 and repGA14). Plasmids isolated from marine bacteria belonging to the genera Pseudoalteromonas, Shewanella and Vibrio cultivated from geographically different coastal sites exhibited homology to two of the marine plasmid replicons, repSD41 and repGA70, obtained from a Vibrio sp. The repGA33 plasmid origin, obtained from a Shewanella sp. isolated from coastal Georgia, was detected in 7% of the Georgia marine sediment Shewanella sp. isolates. Microbial community DNA extracted from marine sediments was also screened for the presence of the plasmid replication sequences. Community DNA samples amplified by PCR yielded a positive signal for the repSD172 and repGA14 replication sequences. The replication origin of BHR plasmid RK2 (IncP) was also detected in marine Vibrio sp. and microbial community DNA extracted from the three coastal sites. These findings provide molecular evidence that marine sediment bacteria harbour an untapped population of BHR plasmids.

  10. Spreading topsoil encourages ecological restoration on embankments: soil fertility, microbial activity and vegetation cover.

    PubMed

    Rivera, Desirée; Mejías, Violeta; Jáuregui, Berta M; Costa-Tenorio, Marga; López-Archilla, Ana Isabel; Peco, Begoña

    2014-01-01

    The construction of linear transport infrastructure has severe effects on ecosystem functions and properties, and the restoration of the associated roadslopes contributes to reduce its impact. This restoration is usually approached from the perspective of plant cover regeneration, ignoring plant-soil interactions and the consequences for plant growth. The addition of a 30 cm layer of topsoil is a common practice in roadslope restoration projects to increase vegetation recovery. However topsoil is a scarce resource. This study assesses the effects of topsoil spreading and its depth (10 to 30 cm) on two surrogates of microbial activity (β-glucosidase and phosphatase enzymes activity and soil respiration), and on plant cover, plant species richness and floristic composition of embankment vegetation. The study also evaluates the differences in selected physic-chemical properties related to soil fertility between topsoil and the original embankment substrate. Topsoil was found to have higher values of organic matter (11%), nitrogen (44%), assimilable phosphorous (50%) and silt content (54%) than the original embankment substrate. The topsoil spreading treatment increased microbial activity, and its application increased β-glucosidase activity (45%), phosphatase activity (57%) and soil respiration (60%). Depth seemed to affect soil respiration, β-glucosidase and phosphatase activity. Topsoil application also enhanced the species richness of restored embankments in relation to controls. Nevertheless, the depth of the spread topsoil did not significantly affect the resulting plant cover, species richness or floristic composition, suggesting that both depths could have similar effects on short-term recovery of the vegetation cover. A significant implication of these results is that it permits the application of thinner topsoil layers, with major savings in this scarce resource during the subsequent slope restoration work, but the quality of topsoil relative to the

  11. Exogenous lactobacilli mitigate microbial changes associated with grain fermentation in vitro

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cereal grains are often included in equine diets. Sugars and starch in grains can be digested and absorbed in the small intestine, but a high proportion of grain in the diet can allow starch to reach the hindgut, disturbing the microbial ecology. Streptococci and lactobacilli both catabolize starch ...

  12. Responding to the threat of bioterrorism: a microbial ecology perspective--the case of anthrax.

    PubMed

    Atlas, R M

    2002-12-01

    Anthrax is a disease of herbivores caused by the gram-positive bacterium Bacillus anthracis. It can affect cattle, sheep, swine, horses and various species of wildlife. The routes for the spread among wildlife are reviewed. There are three kinds of human anthrax--inhalation, cutaneous, and intestinal anthrax--which differ in their routes of infection and outcomes. In the United States, confirmation of cases is made by the isolation of B. anthracis and by biochemical tests. Vaccination is not recommended for the general public; civilians who should be vaccinated include those who, in their work places, come in contact with products potentially contaminated with B. anthracis spores, and people engaged in research or diagnostic activities. After September 11, 2001, there were bioterrorism anthrax attacks in the United States: anthrax-laced letters sent to multiple locations were the source of infectious B. anthracis. The US Postal Service issued recommendations to prevent the danger of hazardous exposure to the bacterium. B. anthracis spores can spread easily and persist for very long times, which makes decontamination of buildings very difficult. Early detection, rapid diagnosis, and well-coordinated public health response are the key to minimizing casualties. The US Government is seeking new ways to deter bioterrorism, including a tighter control of research on infectious agents, even though pathogens such as B. anthracis are widely spread in nature and easy to grow. It is necessary to define the boundary between defensive and offensive biological weapons research. Deterring bioterrorism should not restrict critical scientific research. PMID:12497181

  13. Microbial ecology involved in the ripening of naturally fermented llama meat sausages. A focus on lactobacilli diversity.

    PubMed

    Fontana, Cecilia; Bassi, Daniela; López, Constanza; Pisacane, Vincenza; Otero, Maria Claudia; Puglisi, Edoardo; Rebecchi, Annalisa; Cocconcelli, Pier Sandro; Vignolo, Graciela

    2016-11-01

    Llama represents for the Andean regions a valid alternative to bovine and pork meat and thanks to the high proteins and low fat content; it can constitute a good product for the novel food market. In this study, culture-dependent and independent methods were applied to investigate the microbial ecology of naturally fermented llama sausages produced in Northwest Argentina. Two different production technologies of llama sausage were investigated: a pilot-plant scale (P) and an artisanal one (A). Results obtained by High-Throughput Sequencing (HTS) of 16S rRNA amplicons showed that the production technologies influenced the development of microbial communities with a different composition throughout the entire fermentation process. Both sequencing and microbiological counts demonstrated that Lactic Acid Bacteria (LAB) contributed largely to the dominant microbiota. When a total of 230 isolates were approached by RAPD-PCR, presumptive LAB strains from P production exhibited an initial variability in RAPD fingerprints switching to a single profile at the final of ripening, while A production revealed a more heterogeneous RAPD pattern during the whole fermentation process. The constant presence of Lactobacillus sakei along the fermentation in both productions was revealed by HTS and confirmed by species-specific PCR from isolated strains. The technological characterization of Lb. sakei isolates evidenced their ability to grow at 15°C, pH4.5 and 5% NaCl (95%). Most strains hydrolyzed myofibrillar and sarcoplasmic proteins. Bacteriocins encoding genes and antimicrobial resistance were found in 35% and 42.5% of the strains, respectively. An appropriate choice of a combination of autochthonous strains in a starter formulation is fundamental to improve and standardize llama sausages safety and quality. PMID:27434177

  14. Microbial ecology involved in the ripening of naturally fermented llama meat sausages. A focus on lactobacilli diversity.

    PubMed

    Fontana, Cecilia; Bassi, Daniela; López, Constanza; Pisacane, Vincenza; Otero, Maria Claudia; Puglisi, Edoardo; Rebecchi, Annalisa; Cocconcelli, Pier Sandro; Vignolo, Graciela

    2016-11-01

    Llama represents for the Andean regions a valid alternative to bovine and pork meat and thanks to the high proteins and low fat content; it can constitute a good product for the novel food market. In this study, culture-dependent and independent methods were applied to investigate the microbial ecology of naturally fermented llama sausages produced in Northwest Argentina. Two different production technologies of llama sausage were investigated: a pilot-plant scale (P) and an artisanal one (A). Results obtained by High-Throughput Sequencing (HTS) of 16S rRNA amplicons showed that the production technologies influenced the development of microbial communities with a different composition throughout the entire fermentation process. Both sequencing and microbiological counts demonstrated that Lactic Acid Bacteria (LAB) contributed largely to the dominant microbiota. When a total of 230 isolates were approached by RAPD-PCR, presumptive LAB strains from P production exhibited an initial variability in RAPD fingerprints switching to a single profile at the final of ripening, while A production revealed a more heterogeneous RAPD pattern during the whole fermentation process. The constant presence of Lactobacillus sakei along the fermentation in both productions was revealed by HTS and confirmed by species-specific PCR from isolated strains. The technological characterization of Lb. sakei isolates evidenced their ability to grow at 15°C, pH4.5 and 5% NaCl (95%). Most strains hydrolyzed myofibrillar and sarcoplasmic proteins. Bacteriocins encoding genes and antimicrobial resistance were found in 35% and 42.5% of the strains, respectively. An appropriate choice of a combination of autochthonous strains in a starter formulation is fundamental to improve and standardize llama sausages safety and quality.

  15. Microbial ecology of extreme environments: Antarctic dry valley yeasts and growth in substrate-limited habitats

    NASA Technical Reports Server (NTRS)

    Vishniac, H. S.

    1982-01-01

    The success of the Antarctic Dry Valley yeasts presumeably results from adaptations to multiple stresses, to low temperatures and substrate-limitation as well as prolonged resting periods enforced by low water availability. Previous investigations have suggested that the crucial stress is substrate limitation. Specific adaptations may be pinpointed by comparing the physiology of the Cryptococcus vishniacii complex, the yeasts of the Tyrol Valley, with their congeners from other habitats. Progress was made in methods of isolation and definition of ecological niches, in the design of experiments in competition for limited substrate, and in establishing the relationships of the Cryptococcus vishniacii complex with other yeasts. In the course of investigating relationships, a new method for 25SrRNA homology was developed. For the first time it appears that 25SrRNA homology may reflect parallel or convergent evolution.

  16. Microbial ecology of Actinobacillus actinomycetemcomitans, Eikenella corrodens and Capnocytophaga spp. in adult periodontitis.

    PubMed

    Müller, H P; Heinecke, A; Borneff, M; Knopf, A; Kiencke, C; Pohl, S

    1997-08-01

    Information on intraoral distribution of putative periodontal pathogens might be essential for controlling different forms of periodontal disease. Colonization may be either promoted or impeded by other bacteria competing in the subgingival ecosystem. In recent investigations microbial associations between dental organisms have been determined in a multitude of subgingival plaque samples within multiple patients and described by odds ratios, in most circumstances without taking into account the correlated structure of the observations within a single individual. The present investigation had 3 major objectives: (i) to describe the intraoral distribution of some facultatively anaerobic, Gram-negative rods, i.e. Actinobacillus actinomycetemcomitans, Eikenella corrodens-like organisms and Capnocytophaga spp., in a multitude of subgingival and extracrevicular samples of 10 adult subjects with A. actinomycetemcomitans-associated periodontitis; (ii) to analyse possible inconsistencies of microbial associations between these periodontal organisms; and (iii) to determine factors increasing the likelihood of isolating these bacteria in a given subgingival site by employing Generalized Estimation Equation (GEE) methods. Clinical examinations were carried out at 6 sites of every tooth present. In each subject, 13 extracrevicular (2 cheek mucosa, 3 tongue, 4 gingival, 2 tonsillar samples, 1 palatinal, 1 saliva sample) and between 22 and 44 subgingival samples from deepest sites of every tooth present (n = 296) were selectively cultivated for A. actinomycetemcomitans, E. corrodens and Capnocytophaga spp. In extracrevicular material, A. actinomycetemcomitans, Capnocytophaga spp. and E. corrodens were isolated in 9, 10 and 6 patients, and from 65, 82 and 15% samples, respectively. The organisms were recovered from 51, 62 and 27% subgingival plaque samples, respectively. Heterogeneity tests did not reveal significant inconsistencies of microbial associations between bacteria in

  17. Sterol-inhibiting fungicide impacts on soil microbial ecology in Atlantic Coastal Plain soils

    NASA Astrophysics Data System (ADS)

    White, P. M.; Potter, T. L.; Strickland, T. C.

    2008-12-01

    Seventy-five percent of the peanuts (Arachus hypogaia) produced in the United States are grown in the Atlantic Coastal Plain region. Portions of this area, including Alabama and Georgia, exhibit a subtropical climate that promotes soil-borne plant fungal diseases. Most fields receive repeated fungicide applications during the growing season to suppress the disease causing organisms, such as Sclerotium rolfsii, Rhizoctonia solani, and Cylindrocladium parasiticum. Information regarding fungicide effects on the soil microbial community, with components principally responsible for transformation and fate of fungicides and other soil-applied pesticides, is limited. The objectives of the study were to assess soil microbial community response to (1) varying rates of the sterol-inhibiting fungicide tebuconazole (0, single application, season max, 2x season max), and (2) field rates of the sterol-inhibitors cyproconazole, prothioconazole, tebuconazole, and flutriafol, and thiol-competitor chlorothalonil. The sterol-inhibitors exhibited different half lives, as listed in the FOOTPRINT database, ranging from <1 day to >1300 d. Chlorothalonil was chosen because it is the most frequently applied fungicide to peanut. Shifts in the fungi, gram positive and gram negative bacteria, were monitored during the experiments using phospholipid fatty acid (PLFA) profiles. Ergosterol levels and pesticide decay rates were also monitored to evaluate the effectiveness of the fungicide and soil residence time, respectively. In the rate study, the highest rate of tebuconazole reduced the fungal biomarker 18:2ω6,9c to 2.6 nmol g-1 dry soil at 17 d, as compared to the control (4.1 nmol g-1 dry soil). However, levels of the fungal PLFA biomarker were similar regardless of rate at 0 and 32 d. The gram negative bacterial PLFA mole percent was greater at 17 d for the two highest rates of tebuconazole, but was similar at 0 and 32 d. Gram positive and fungal mole percents were not affected at any time

  18. Performance and microbial ecology of a nitritation sequencing batch reactor treating high-strength ammonia wastewater

    PubMed Central

    Chen, Wenjing; Dai, Xiaohu; Cao, Dawen; Wang, Sha; Hu, Xiaona; Liu, Wenru; Yang, Dianhai

    2016-01-01

    The partial nitrification (PN) performance and the microbial community variations were evaluated in a sequencing batch reactor (SBR) for 172 days, with the stepwise elevation of ammonium concentration. Free ammonia (FA) and low dissolved oxygen inhibition of nitrite-oxidized bacteria (NOB) were used to achieve nitritation in the SBR. During the 172 days operation, the nitrogen loading rate of the SBR was finally raised to 3.6 kg N/m3/d corresponding the influent ammonium of 1500 mg/L, with the ammonium removal efficiency and nitrite accumulation rate were 94.12% and 83.54%, respectively, indicating that the syntrophic inhibition of FA and low dissolved oxygen contributed substantially to the stable nitrite accumulation. The results of the 16S rRNA high-throughput sequencing revealed that Nitrospira, the only nitrite-oxidizing bacteria in the system, were successively inhibited and eliminated, and the SBR reactor was dominated finally by Nitrosomonas, the ammonium-oxidizing bacteria, which had a relative abundance of 83%, indicating that the Nitrosomonas played the primary roles on the establishment and maintaining of nitritation. Followed by Nitrosomonas, Anaerolineae (7.02%) and Saprospira (1.86%) were the other mainly genera in the biomass. PMID:27762325

  19. Hypolithic cyanobacteria, dry limit of photosynthesis, and microbial ecology in the hyperarid Atacama Desert.

    PubMed

    Warren-Rhodes, Kimberley A; Rhodes, Kevin L; Pointing, Stephen B; Ewing, Stephanie A; Lacap, Donnabella C; Gómez-Silva, Benito; Amundson, Ronald; Friedmann, E Imre; McKay, Christopher P

    2006-10-01

    The occurrence of hypolithic cyanobacteria colonizing translucent stones was quantified along the aridity gradient in the Atacama Desert in Chile, from less arid areas to the hyperarid core where photosynthetic life and thus primary production reach their limits. As mean rainfall declines from 21 to microbially depauperate bare soil. These findings suggest that photosynthetic life is extremely unlikely on the present-day surface of Mars, but may have existed in the past. If so, such microhabitats would probably be widely dispersed, difficult to detect, and millimeters away from virtually lifeless surroundings.

  20. On the use of antibiotics to reduce rhizoplane microbial populations in root physiology and ecology investigations

    NASA Technical Reports Server (NTRS)

    Smart, D. R.; Ferro, A.; Ritchie, K.; Bugbee, B. G.

    1995-01-01

    No straightforward method exists for separating the proportion of ion exchange and respiration due to rhizoplane microbial organisms from that of root ion exchange and respiration. We examined several antibiotics that might be used for the temporary elimination of rhizoplane bacteria from hydroponically grown wheat roots (Triticum aestivum cv. Veery 10). Each antibiotic was tested for herbicidal activity and plate counts were used to enumerate bacteria and evaluate antibiotic kinetics. Only lactam antibiotics (penicillins and cephalosporins) did not reduce wheat growth rates. Aminoglycosides, the pyrimidine trimethoprim, colistin and rifampicin reduced growth rates substantially. Antibiotics acted slowly, with maximum reductions in rhizoplane bacteria occurring after more than 48 h of exposure. Combinations of nonphytotoxic antibiotics reduced platable rhizoplane bacteria by as much as 98%; however, this was generally a reduction from about 10(9) to 10(6) colony forming units per gram of dry root mass, so that many viable bacteria remained on root surfaces. We present evidence which suggests that insufficient bacterial biomass exists on root surfaces of nonstressed plants grown under well-aerated conditions to quantitatively interfere with root nitrogen absorption measurements.

  1. Microbial ecology of arsenic-mobilizing Cambodian sediments: lithological controls uncovered by stable-isotope probing.

    PubMed

    Héry, Marina; Rizoulis, Athanasios; Sanguin, Hervé; Cooke, David A; Pancost, Richard D; Polya, David A; Lloyd, Jonathan R

    2015-06-01

    Microbially mediated arsenic release from Holocene and Pleistocene Cambodian aquifer sediments was investigated using microcosm experiments and substrate amendments. In the Holocene sediment, the metabolically active bacteria, including arsenate-respiring bacteria, were determined by DNA stable-isotope probing. After incubation with (13) C-acetate and (13) C-lactate, active bacterial community in the Holocene sediment was dominated by different Geobacter spp.-related 16S rRNA sequences. Substrate addition also resulted in the enrichment of sequences related to the arsenate-respiring Sulfurospirillum spp. (13) C-acetate selected for ArrA related to Geobacter spp. whereas (13) C-lactate selected for ArrA which were not closely related to any cultivated organism. Incubation of the Pleistocene sediment with lactate favoured a 16S rRNA-phylotype related to the sulphate-reducing Desulfovibrio oxamicus DSM1925, whereas the ArrA sequences clustered with environmental sequences distinct from those identified in the Holocene sediment. Whereas limited As(III) release was observed in Pleistocene sediment after lactate addition, no arsenic mobilization occurred from Holocene sediments, probably because of the initial reduced state of As, as determined by X-ray Absorption Near Edge Structure. Our findings demonstrate that in the presence of reactive organic carbon, As(III) mobilization can occur in Pleistocene sediments, having implications for future strategies that aim to reduce arsenic contamination in drinking waters by using aquifers containing Pleistocene sediments.

  2. Occurrence and Ecological Significance of GTP in the Ocean and in Microbial Cells

    PubMed Central

    Karl, D. M.

    1978-01-01

    A comparison between the ATP concentrations based on peak height light emission values (0 to 3 s) and integrated light flux determinations (15 to 75 s) for a variety of seawater samples revealed that the integrated method of light detection consistently yielded higher ATP concentrations, ranging from 1.38 to 2.35 times larger than the corresponding peak ATP values. A significant correlation (r = 0.923) was observed for a plot of ΔADP (i.e., integrated ATP - peak ATP) versus GTP + UTP, suggesting that the analytical interference on the ATP assay was the result of the presence of non-adenine nucleotide triphosphates. Size-fractionation studies revealed an enrichment of the non-adenine nucleotide triphosphates, relative to ATP, in the smallest size fraction analyzed (<10 μm). Investigations were conducted with 20 species of unicellular marine algae to determine their intracellular nucleotide concentrations, and these determinations were compared to the levels measured in lab cultures of the marine bacterium Serratia marinorubra. These results indicated that the intracellular GTP/ATP ratios in S. marinorubra increase in direct proportion to the rate of cell growth, and that the GTP/ATP ratios in bacteria are much greater than in growing algae, presumably due to the differences in rates of cellular biosynthesis. It is concluded that quantitative determinations of GTP/ATP ratios in environmental sample extracts may be useful for measuring microbial growth. PMID:16345313

  3. Microbial Community Composition and Ecology of an Acidic Aquatic Environment: The Tinto River, Spain.

    PubMed

    López-Archilla, A.I.; Marin, I.; Amils, R.

    2001-01-01

    We studied the correlation between physicochemical and biological characteristics of an acidic river, the Tinto River, in Southwestern Spain. The Tinto River is an extreme environment characterized by its low pH (mean of 2.2) and high concentrations of heavy metals (Fe 2.3 g/L, Zn 0.22 g/L, Cu 0.11 g/L). These extreme conditions are the product of the metabolic activity of chemolithotrophic microorganisms, including iron- and sulfur-oxidizing bacteria, that can be found in high concentrations in its waters. The food chain in the river is very constrained and exclusively microbial. Primary productivity in the Tinto River is the sum of photosynthetic and chemolithotrophic activity. Heterotrophic bacteria and fungi are the major decomposers and protists are the major predators. A correlation analysis including the physicochemical and biological variables suggested a close relationship between the acidic pH values and abundance of both chemolithotrophic bacteria and filamentous fungi. Chemolithotrophic bacteria correlated with the heavy metals found in the river. A principal component analysis of the biotic and abiotic variables suggested that the Tinto River ecosystem can be described as a function of three main groups of variables: pH values, metal concentrations, and biological productivity.

  4. Deep Sequencing and Ecological Characterization of Gut Microbial Communities of Diverse Bumble Bee Species

    PubMed Central

    Lim, Haw Chuan; Chu, Chia-Ching; Seufferheld, Manfredo J.; Cameron, Sydney A.

    2015-01-01

    Gut bacterial communities of bumble bees are correlated with defense against pathogens. Further understanding this host-microbe association is vitally important as bumble bees are currently experiencing global population declines, potentially due in part to emergent diseases. In this study, we used pyrosequencing and community fingerprinting (ARISA) to characterize the gut microbial communities of nine bumble species from across the Bombus phylogeny. Overall, we delimited 74 bacterial taxa (operational taxonomic units or OTUs) belonging to Betaproteobacteria, Gammaproteobacteria, Bacilli, Actinobacteria, Flavobacteria and Alphaproteobacteria. Each bacterial community was taxonomically simple, containing an average of 1.9 common (relative abundance per sample > 5%) bacterial OTUs. The most abundant and prevalent (occurring in 92% of the samples) bacterial OTU, based on 16S rRNA sequences, closely matched that of the previously described Betaproteobacteria species Snodgrassella alvi. Bacteria that were first described in bee-related external environments dominated a number of gut bacterial communities, suggesting that they are not strictly dependent on the internal gut environment. The ARISA data showed a correlation between bacterial community structures and the geographic locations where the bees were sampled, suggesting that at least a subset of the bacterial species may be transmitted environmentally. Using light and fluorescent microscopy, we demonstrated that the gut bacteria form a biofilm on the internal epithelial surface of the ileum, corroborating results obtained from Apis mellifera. PMID:25768110

  5. Comparison of microbial community assays for the assessment of stream biofilm ecology.

    PubMed

    Vinten, A J A; Artz, R R E; Thomas, N; Potts, J M; Avery, L; Langan, S J; Watson, H; Cook, Y; Taylor, C; Abel, C; Reid, E; Singh, B K

    2011-06-01

    We investigated a range of microbiological community assays performed on scrapes of biofilms formed on artificial diffusing substrates deployed in 8 streams in eastern Scotland, with a view to using them to characterize ecological response to stream water quality. The assays considered were: Multiplex Terminal Restriction Fragment Length Polymorphism or M-TRFLP (a molecular method), Phospholipid Fatty Acid or PLFA analysis (a biochemical method) and MICRORESP™ (a physiological method) alongside TDI, diatom species, and chlorophyll a content. Four of the streams were classified as of excellent status (3-6μg/L Soluble Reactive Phosphorus (SRP)) with respect to soluble P content under the EU Water Framework Directive and four were of borderline good/moderate or moderate status (43-577μg/L SRP). At each site, 3 replicates of 3 solute diffusion treatments were deployed in a Latin square design. Solute diffusion treatments were: KCl (as a control solute), N and P (to investigate the effect of nutrient enrichment), or the herbicide isoproturon (as a "high impact" control, which aimed to affect biofilm growth in a way detectable by all assays). Biofilms were sampled after 4weeks deployment in a low flow period of early summer 2006. The chlorophyll a content of biofilms after 4weeks was 2.0±0.29mg/m(2) (mean±se). Dry matter content was 16.0±13.1g/m(2). The M-TRFLP was successfully used for generating community profiles of cyanobacteria, algae and bacteria and was much faster than diatom identification. The PFLA and TDI were successful after an increase in the sample size, due to low counts. The MICRORESP(™) assays were often below or near detection limit. We estimated the per-sample times for the successful assays as follows: M-TRFLP: 20min, PLFA 40min, TDI 90min. Using MANOVA on the first 5 principal co-ordinates, all the assays except MICRORESP(™) showed significant differences between sites, but none of the assays showed a significant effect of either initial

  6. Natural environments, ancestral diets, and microbial ecology: is there a modern "paleo-deficit disorder"? Part II.

    PubMed

    Logan, Alan C; Katzman, Martin A; Balanzá-Martínez, Vicent

    2015-01-01

    Famed microbiologist René J. Dubos (1901-1982) was an early pioneer in the developmental origins of health and disease (DOHaD) construct. In the 1960s, he conducted groundbreaking research concerning the ways in which early-life experience with nutrition, microbiota, stress, and other environmental variables could influence later-life health outcomes. He recognized the co-evolutionary relationship between microbiota and the human host. Almost 2 decades before the hygiene hypothesis, he suggested that children in developed nations were becoming too sanitized (vs. our ancestral past) and that scientists should determine whether the childhood environment should be "dirtied up in a controlled manner." He also argued that oft-celebrated growth chart increases via changes in the global food supply and dietary patterns should not be equated to quality of life and mental health. Here in the second part of our review, we reflect the words of Dubos off contemporary research findings in the areas of diet, the gut-brain-axis (microbiota and anxiety and depression) and microbial ecology. Finally, we argue, as Dubos did 40 years ago, that researchers should more closely examine the relevancy of silo-sequestered, reductionist findings in the larger picture of human quality of life. In the context of global climate change and the epidemiological transition, an allergy epidemic and psychosocial stress, our review suggests that discussions of natural environments, urbanization, biodiversity, microbiota, nutrition, and mental health, are often one in the same. PMID:25889196

  7. Natural environments, ancestral diets, and microbial ecology: is there a modern "paleo-deficit disorder"? Part II.

    PubMed

    Logan, Alan C; Katzman, Martin A; Balanzá-Martínez, Vicent

    2015-03-10

    Famed microbiologist René J. Dubos (1901-1982) was an early pioneer in the developmental origins of health and disease (DOHaD) construct. In the 1960s, he conducted groundbreaking research concerning the ways in which early-life experience with nutrition, microbiota, stress, and other environmental variables could influence later-life health outcomes. He recognized the co-evolutionary relationship between microbiota and the human host. Almost 2 decades before the hygiene hypothesis, he suggested that children in developed nations were becoming too sanitized (vs. our ancestral past) and that scientists should determine whether the childhood environment should be "dirtied up in a controlled manner." He also argued that oft-celebrated growth chart increases via changes in the global food supply and dietary patterns should not be equated to quality of life and mental health. Here in the second part of our review, we reflect the words of Dubos off contemporary research findings in the areas of diet, the gut-brain-axis (microbiota and anxiety and depression) and microbial ecology. Finally, we argue, as Dubos did 40 years ago, that researchers should more closely examine the relevancy of silo-sequestered, reductionist findings in the larger picture of human quality of life. In the context of global climate change and the epidemiological transition, an allergy epidemic and psychosocial stress, our review suggests that discussions of natural environments, urbanization, biodiversity, microbiota, nutrition, and mental health, are often one in the same.

  8. Biodegradation of dichlorodiphenyltrichloroethanes (DDTs) and hexachlorocyclohexanes (HCHs) with plant and nutrients and their effects on the microbial ecological kinetics.

    PubMed

    Sun, Guangdong; Zhang, Xu; Hu, Qing; Zhang, Heqing; Zhang, Dayi; Li, Guanghe

    2015-02-01

    Four pilot-scale test mesocosms were conducted for the remediation of organochlorine pesticides (OCPs)-contaminated aged soil. The results indicate that the effects on degradation of hexachlorocyclohexanes (HCHs) and dichlorodiphenyltrichloroethanes (DDTs) were in the following order: nutrients/plant bioaugmentation (81.18 % for HCHs; 85.4 % for DDTs) > nutrients bioaugmentation > plant bioaugmentation > only adding water > control, and nutrients/plant bioaugmentation greatly enhanced the degradation of HCHs (81.18 %) and DDTs (85.4 %). The bacterial community structure, diversity and composition were assessed by 454-pyrosequencing of 16S recombinant RNA (rRNA), whereas the abundance of linA gene was determined by quantitative polymerase chain reaction. Distinct differences in bacterial community composition, structure, and diversity were a function of remediation procedure. Predictability of HCH/DDT degradation in soils was also investigated. A positive correlation between linA gene abundance and the removal ratio of HCHs was indicated by correlation analyses. A similar relationship was also confirmed between the degradation of HCHs/DDTs and the abundance of some assemblages (Gammaproteobacteria and Flavobacteria). Our results offer microbial ecological insight into the degradation of HCHs and DDTs in aged contaminated soil, which is helpful for the intensification of bioremediation through modifying plant-microbe patterns, and cessation of costly and time-consuming assays.

  9. Improving the quality of rice straw by urea and calcium hydroxide on rumen ecology, microbial protein synthesis in beef cattle.

    PubMed

    Polyorach, S; Wanapat, M

    2015-06-01

    Four rumen-fistulated beef cattle were randomly assigned to four treatments according to a 4 × 4 Latin square design to study the influence of urea and calcium hydroxide [Ca(OH)2 ] treatment of rice straw to improve the nutritive value of rice straw. Four dietary treatments were as follows: untreated rice straw, 50 g/kg urea-treated rice straw, 20 g/kg urea + 20 g/kg calcium hydroxide-treated rice straw and 30 g/kg urea + 20 g/kg calcium hydroxide-treated rice straw. All animals were kept in individual pens and fed with concentrate at 0.5 g/kg of BW (DM), rice straw was fed ad libitum. The experiment was conducted for four periods, and each period lasted for 21 days. During the first 14 days, DM feed intake measurements were made while during the last 7 days, all cattle were moved to metabolism crates for total faeces and urine collections. The results revealed that 20 g/kg urea + 20 g/kg calcium hydroxide-treated rice straw improved the nutritive value of rice straw, in terms of dry matter intake, digestibility, ruminal volatile fatty acids, population of bacteria and fungi, nitrogen retention and microbial protein synthesis. Based on this study, it could be concluded that using urea plus calcium hydroxide was one alternative method to improve the nutritive value of rice straw, rumen ecology and fermentation and thus a reduction of treatment cost.

  10. Biodegradation of dichlorodiphenyltrichloroethanes (DDTs) and hexachlorocyclohexanes (HCHs) with plant and nutrients and their effects on the microbial ecological kinetics.

    PubMed

    Sun, Guangdong; Zhang, Xu; Hu, Qing; Zhang, Heqing; Zhang, Dayi; Li, Guanghe

    2015-02-01

    Four pilot-scale test mesocosms were conducted for the remediation of organochlorine pesticides (OCPs)-contaminated aged soil. The results indicate that the effects on degradation of hexachlorocyclohexanes (HCHs) and dichlorodiphenyltrichloroethanes (DDTs) were in the following order: nutrients/plant bioaugmentation (81.18 % for HCHs; 85.4 % for DDTs) > nutrients bioaugmentation > plant bioaugmentation > only adding water > control, and nutrients/plant bioaugmentation greatly enhanced the degradation of HCHs (81.18 %) and DDTs (85.4 %). The bacterial community structure, diversity and composition were assessed by 454-pyrosequencing of 16S recombinant RNA (rRNA), whereas the abundance of linA gene was determined by quantitative polymerase chain reaction. Distinct differences in bacterial community composition, structure, and diversity were a function of remediation procedure. Predictability of HCH/DDT degradation in soils was also investigated. A positive correlation between linA gene abundance and the removal ratio of HCHs was indicated by correlation analyses. A similar relationship was also confirmed between the degradation of HCHs/DDTs and the abundance of some assemblages (Gammaproteobacteria and Flavobacteria). Our results offer microbial ecological insight into the degradation of HCHs and DDTs in aged contaminated soil, which is helpful for the intensification of bioremediation through modifying plant-microbe patterns, and cessation of costly and time-consuming assays. PMID:25213654

  11. Going from microbial ecology to genome data and back: studies on a haloalkaliphilic bacterium isolated from Soap Lake, Washington State

    PubMed Central

    Mormile, Melanie R.

    2014-01-01

    Soap Lake is a meromictic, alkaline (∼pH 9.8) and saline (∼14–140 g liter-1) lake located in the semiarid area of eastern Washington State. Of note is the length of time it has been meromictic (at least 2000 years) and the extremely high sulfide level (∼140 mM) in its monimolimnion. As expected, the microbial ecology of this lake is greatly influenced by these conditions. A bacterium, Halanaerobium hydrogeniformans, was isolated from the mixolimnion region of this lake. Halanaerobium hydrogeniformans is a haloalkaliphilic bacterium capable of forming hydrogen from 5- and 6-carbon sugars derived from hemicellulose and cellulose. Due to its ability to produce hydrogen under saline and alkaline conditions, in amounts that rival genetically modified organisms, its genome was sequenced. This sequence data provides an opportunity to explore the unique metabolic capabilities of this organism, including the mechanisms for tolerating the extreme conditions of both high salinity and alkalinity of its environment. PMID:25477871

  12. Microbial and genetic ecology of tropical Vertisols under intensive chemical farming.

    PubMed

    Malhotra, Jaya; Aparna, K; Dua, Ankita; Sangwan, Naseer; Trimurtulu, N; Rao, D L N; Lal, Rup

    2015-01-01

    There are continued concerns on unscientific usage of chemical fertilizers and pesticides, particularly in many developing countries leading to adverse consequences for soil biological quality and agricultural sustainability. In farmers' fields in tropical Vertisols of peninsular India, "high" fertilizer and pesticide usage at about 2.3 times the recommended rates in black gram (Vigna mungo) did not have a deleterious effect on the abundance of culturable microorganisms, associative nitrogen fixers, nitrifiers, and 16S rRNA gene diversity compared to normal rates. However, "very high" application at about five times the fertilizers and 1.5 times pesticides in chilies (Capsicum annuum) adversely affected the populations of fungi, actinomycetes, and ammonifiers, along with a drastic change in the eubacterial community profile and diversity over normal rates. Actinobacteria were dominant in black gram normal (BG1) (47%), black gram high (BG2) (36%), and chili normal (CH1) (30%) and were least in chili very high (CH2) (14%). Geodermatophilus formed 20% of Actinobacteria in BG1 but disappeared in BG2, CH1, and CH2. Asticcacaulis dominated at "very high" input site (CH2). Diversity of nitrogen fixers was completely altered; Dechloromonas and Anaeromyxobacter were absent in BG1 but proliferated well in BG2. There was reduction in rhizobial nifH sequences in BG2 by 46%. Phylogenetic differences characterized by UniFrac and principal coordinate analysis showed that BG2 and CH2 clustered together depicting a common pattern of genetic shift, while BG1 and CH1 fell at different axis. Overall, there were adverse consequences of "very high" fertilizer and pesticide usage on soil microbial diversity and function in tropical Vertisols. PMID:25384370

  13. Managed bioremediation of soil contaminated with crude oil soil chemistry and microbial ecology three years later.

    PubMed

    Duncan, K; Levetin, E; Wells, H; Jennings, E; Hettenbach, S; Bailey, S; Lawlor, K; Sublette, K; Berton Fisher, J

    1997-01-01

    Analysis of samples taken from three experimental soil lysimeters demonstrated marked long-term effects of managed bioremediation on soil chemistry and on bacterial and fungal communities 3 yr after the application of crude oil or crude oil and fertilizer. The lysimeters were originally used to evaluate the short-term effectiveness of managed (application of fertilizer and water, one lysimeter) vs unmanaged bioremediation (one lysimeter) of Michigan Silurian crude oil compared to one uncontaminated control lysimeter. Three years following the original experiment, five 2-ft-long soil cores were extracted from each lysimeter, each divided into three sections, and the like sections mixed together to form composited soil samples. All subsequent chemical and microbiological analyses were performed on these nine composited samples. Substantial variation was found among the lysimeters for certain soil chemical characteristics (% moisture, pH, total Kjeldahl nitrogen [TKN], ammonia nitrogen [NH4-N], phosphate phosphorous [PO4-P], and sulfate [SO4 (-2)]). The managed lysimeter had 10% the level of total petroleum hydrocarbons (TPH-IR) found in the unmanaged lysimeter. Assessment of the microbial community was performed for heterotropic bacteria, fungi, and aromatic hydrocarbon-degrading bacteria (toluene, naphthalene, and phenanthrene) by dilution onto solid media. There was little difference in the number of heterotrophic bacteria, in contrast to counts of fungi, which were markedly higher in the contaminated lysimeters. Hydrocarbon-degrading bacteria were elevated in both oil-contaminated lysimeters. In terms of particular hydrocarbons as substrates, phenanthrene degraders were greater in number than naphthalene degraders, which outnumbered toluene degraders. Levels of sulfate-reducing bacteria seem to have been stimulated by hydrocarbon degradation. PMID:18576141

  14. The human gut microbial ecology associated with overweight and obesity determines ellagic acid metabolism.

    PubMed

    Selma, María V; Romo-Vaquero, María; García-Villalba, Rocío; González-Sarrías, Antonio; Tomás-Barberán, Francisco A; Espín, Juan C

    2016-04-01

    We recently identified three metabotypes (0, A and B) that depend on the metabolic profile of urolithins produced from polyphenol ellagic acid (EA). The gut microbiota and Gordonibacter spp. recently were identified as species able to produce urolithins. A higher percentage of metabotype B was found in patients with metabolic syndrome or colorectal cancer in comparison with healthy individuals. The aim of the present study was to analyse differences in EA metabolism between healthy overweight-obese and normoweight individuals and evaluate the role of gut microbial composition including Gordonibacter. Although the three metabotypes were confirmed in both groups, metabotype B prevailed in overweight-obese (31%) versus normoweight (20%) individuals while metabotype A was higher in normoweight (70%) than the overweight-obese group (57%). This suggests that weight gain favours the growth of bacteria capable of producing urolithin B and/or isourolithin A with respect to urolithin A-producing bacteria. Gordonibacter spp. levels were not significantly different between normoweight and overweight-obese groups but higher Gordonibacter levels were found in metabotype A individuals than in those with metabotype B. Other bacterial species have been reported to show a much closer relationship to obesity and dysbiosis than Gordonibacter. However, Gordonibacter levels are negatively correlated with metabotype B, which prevails in metabolic syndrome and colorectal cancer. This is the first report that links overweight and obesity with an alteration in the catabolism of EA, and where the correlation of Gordonibacter to this alteration is shown. Future investigation of Gordonibacter and urolithin metabotypes as potential biomarkers or therapeutic targets of obesity-related diseases is warranted.

  15. A novel ecological role of the Firmicutes identified in thermophilic microbial fuel cells.

    PubMed

    Wrighton, Kelly C; Agbo, Peter; Warnecke, Falk; Weber, Karrie A; Brodie, Eoin L; DeSantis, Todd Z; Hugenholtz, Philip; Andersen, Gary L; Coates, John D

    2008-11-01

    Significant effort is currently focused on microbial fuel cells (MFCs) as a source of renewable energy. Most studies concentrate on operation at mesophilic temperatures. However, anaerobic digestion studies have reported on the superiority of thermophilic operation and demonstrated a net energy gain in terms of methane yield. As such, our studies focused on MFC operation and microbiology at 55 degrees C. Over a 100-day operation, these MFCs were stable and achieved a power density of 37 mW m(-2) with a coulombic efficiency of 89%. To infer activity and taxonomic identity of dominant members of the electricity-producing community, we performed phylogenetic microarray and clone library analysis with small subunit ribosomal RNA (16S rRNA) and ribosomal RNA gene (16S rDNA). The results illustrated the dominance (80% of clone library sequences) of the Firmicutes in electricity production. Similarly, rRNA sequences from Firmicutes accounted for 50% of those taxa that increased in relative abundance from current-producing MFCs, implying their functional role in current production. We complemented these analyses by isolating the first organisms from a thermophilic MFC. One of the isolates, a Firmicutes Thermincola sp. strain JR, not only produced more current than known organisms (0.42 mA) in an H-cell system but also represented the first demonstration of direct anode reduction by a member of this phylum. Our research illustrates the importance of using a variety of molecular and culture-based methods to reliably characterize bacterial communities. Consequently, we revealed a previously unidentified functional role for Gram-positive bacteria in MFC current generation. PMID:18769460

  16. Geochemistry and microbial ecology in alkaline hot springs of Ambitle Island, Papua New Guinea.

    PubMed

    Meyer-Dombard, D'Arcy R; Amend, Jan P

    2014-07-01

    The availability of microbiological and geochemical data from island-based and high-arsenic hydrothermal systems is limited. Here, the microbial diversity in island-based hot springs on Ambitle Island (Papua New Guinea) was investigated using culture-dependent and -independent methods. Waramung and Kapkai are alkaline springs high in sulfide and arsenic, related hydrologically to previously described hydrothermal vents in nearby Tutum Bay. Enrichments were carried out at 24 conditions with varying temperature (45, 80 °C), pH (6.5, 8.5), terminal electron acceptors (O2, SO4 (2-), S(0), NO3 (-)), and electron donors (organic carbon, H2, As(III)). Growth was observed in 20 of 72 tubes, with media targeting heterotrophic metabolisms the most successful. 16S ribosomal RNA gene surveys of environmental samples revealed representatives in 15 bacterial phyla and 8 archaeal orders. While the Kapkai 4 bacterial clone library is primarily made up of Thermodesulfobacteria (74%), no bacterial taxon represents a majority in the Kapkai 3 and Waramung samples (40% Proteobacteria and 39% Aquificae, respectively). Deinococcus/Thermus and Thermotogae are observed in all samples. The Thermococcales dominate the archaeal clone libraries (65-85%). Thermoproteales, Desulfurococcales, and uncultured Eury- and Crenarchaeota make up the remaining archaeal taxonomic diversity. The culturing and phylogenetic results are consistent with the geochemistry of the alkaline, saline, and sulfide-rich fluids. When compared to other alkaline, island-based, high-arsenic, or shallow-sea hydrothermal communities, the Ambitle Island archaeal communities are unique in geochemical conditions, and in taxonomic diversity, richness, and evenness.

  17. Microbial and genetic ecology of tropical Vertisols under intensive chemical farming.

    PubMed

    Malhotra, Jaya; Aparna, K; Dua, Ankita; Sangwan, Naseer; Trimurtulu, N; Rao, D L N; Lal, Rup

    2015-01-01

    There are continued concerns on unscientific usage of chemical fertilizers and pesticides, particularly in many developing countries leading to adverse consequences for soil biological quality and agricultural sustainability. In farmers' fields in tropical Vertisols of peninsular India, "high" fertilizer and pesticide usage at about 2.3 times the recommended rates in black gram (Vigna mungo) did not have a deleterious effect on the abundance of culturable microorganisms, associative nitrogen fixers, nitrifiers, and 16S rRNA gene diversity compared to normal rates. However, "very high" application at about five times the fertilizers and 1.5 times pesticides in chilies (Capsicum annuum) adversely affected the populations of fungi, actinomycetes, and ammonifiers, along with a drastic change in the eubacterial community profile and diversity over normal rates. Actinobacteria were dominant in black gram normal (BG1) (47%), black gram high (BG2) (36%), and chili normal (CH1) (30%) and were least in chili very high (CH2) (14%). Geodermatophilus formed 20% of Actinobacteria in BG1 but disappeared in BG2, CH1, and CH2. Asticcacaulis dominated at "very high" input site (CH2). Diversity of nitrogen fixers was completely altered; Dechloromonas and Anaeromyxobacter were absent in BG1 but proliferated well in BG2. There was reduction in rhizobial nifH sequences in BG2 by 46%. Phylogenetic differences characterized by UniFrac and principal coordinate analysis showed that BG2 and CH2 clustered together depicting a common pattern of genetic shift, while BG1 and CH1 fell at different axis. Overall, there were adverse consequences of "very high" fertilizer and pesticide usage on soil microbial diversity and function in tropical Vertisols.

  18. The effects of inulin, dried Jerusalem artichoke tuber and a multispecies probiotic preparation on microbiota ecology and immune status of the large intestine in young pigs.

    PubMed

    Barszcz, Marcin; Taciak, Marcin; Skomiał, Jacek

    2016-08-01

    The study aimed at determining the effect of two types of prebiotics and a multispecies probiotic on microbiota activity and composition, as well as mucosal immunity in the large intestine of young pigs. In total 48 piglets were divided into 6 groups (n = 8), which received from day 10 of life probiotic-unsupplemented (PU) or probiotic-supplemented (PS) diets. Probiotics were added at 0.5 g/kg diet and contained: Lactococcus lactis, Carnobacterium divergens, Lactobacillus casei, Lactobacillus plantarum and Saccharomyces cerevisiae. The PU and PS diets were formulated without prebiotic addition (control) or with addition of 2% of inulin from chicory root (IN) or 4% of dried Jerusalem artichoke tubers (DJA). After 40 days of feeding, digesta and tissue samples were taken from the caecum and three sections of the colon for analyses of microbiota activity and composition, secretory immunoglobulin A (sIgA) and intraepithelial lymphocytes (IEL). IN diets decreased the caecal digesta pH and β-glucosidase activity but increased propionic, valeric and total short chain fatty acid (SCFA) concentrations compared to control diets. Feeding DJA diets increased caecal valeric acid level, decreased the concentration of isoacids in the colon, reduced β-glucosidase and β-glucuronidase activity in the middle colon and increased Bifidobacterium spp. populations in the proximal and distal colon. PS diets increased the caecal acetic acid and total SCFA level, and Clostridium spp. populations in the distal colon. Neither probiotic nor prebiotics affected sIgA level or IEL number in the large intestine. In conclusion, DJA modified the microbiota ecology in the large intestine of young pigs to a greater extent than IN and the applied probiotic did not enhance effects of prebiotics.

  19. The effects of inulin, dried Jerusalem artichoke tuber and a multispecies probiotic preparation on microbiota ecology and immune status of the large intestine in young pigs.

    PubMed

    Barszcz, Marcin; Taciak, Marcin; Skomiał, Jacek

    2016-08-01

    The study aimed at determining the effect of two types of prebiotics and a multispecies probiotic on microbiota activity and composition, as well as mucosal immunity in the large intestine of young pigs. In total 48 piglets were divided into 6 groups (n = 8), which received from day 10 of life probiotic-unsupplemented (PU) or probiotic-supplemented (PS) diets. Probiotics were added at 0.5 g/kg diet and contained: Lactococcus lactis, Carnobacterium divergens, Lactobacillus casei, Lactobacillus plantarum and Saccharomyces cerevisiae. The PU and PS diets were formulated without prebiotic addition (control) or with addition of 2% of inulin from chicory root (IN) or 4% of dried Jerusalem artichoke tubers (DJA). After 40 days of feeding, digesta and tissue samples were taken from the caecum and three sections of the colon for analyses of microbiota activity and composition, secretory immunoglobulin A (sIgA) and intraepithelial lymphocytes (IEL). IN diets decreased the caecal digesta pH and β-glucosidase activity but increased propionic, valeric and total short chain fatty acid (SCFA) concentrations compared to control diets. Feeding DJA diets increased caecal valeric acid level, decreased the concentration of isoacids in the colon, reduced β-glucosidase and β-glucuronidase activity in the middle colon and increased Bifidobacterium spp. populations in the proximal and distal colon. PS diets increased the caecal acetic acid and total SCFA level, and Clostridium spp. populations in the distal colon. Neither probiotic nor prebiotics affected sIgA level or IEL number in the large intestine. In conclusion, DJA modified the microbiota ecology in the large intestine of young pigs to a greater extent than IN and the applied probiotic did not enhance effects of prebiotics. PMID:27216555

  20. The effect of the macrolide antibiotic tylosin on microbial diversity in the canine small intestine as demonstrated by massive parallel 16S rRNA gene sequencing

    PubMed Central

    2009-01-01

    Background Recent studies have shown that the fecal microbiota is generally resilient to short-term antibiotic administration, but some bacterial taxa may remain depressed for several months. Limited information is available about the effect of antimicrobials on small intestinal microbiota, an important contributor to gastrointestinal health. The antibiotic tylosin is often successfully used for the treatment of chronic diarrhea in dogs, but its exact mode of action and its effect on the intestinal microbiota remain unknown. The aim of this study was to evaluate the effect of tylosin on canine jejunal microbiota. Tylosin was administered at 20 to 22 mg/kg q 24 hr for 14 days to five healthy dogs, each with a pre-existing jejunal fistula. Jejunal brush samples were collected through the fistula on days 0, 14, and 28 (14 days after withdrawal of tylosin). Bacterial diversity was characterized using massive parallel 16S rRNA gene pyrosequencing. Results Pyrosequencing revealed a previously unrecognized species richness in the canine small intestine. Ten bacterial phyla were identified. Microbial populations were phylogenetically more similar during tylosin treatment. However, a remarkable inter-individual response was observed for specific taxa. Fusobacteria, Bacteroidales, and Moraxella tended to decrease. The proportions of Enterococcus-like organisms, Pasteurella spp., and Dietzia spp. increased significantly during tylosin administration (p < 0.05). The proportion of Escherichia coli-like organisms increased by day 28 (p = 0.04). These changes were not accompanied by any obvious clinical effects. On day 28, the phylogenetic composition of the microbiota was similar to day 0 in only 2 of 5 dogs. Bacterial diversity resembled the pre-treatment state in 3 of 5 dogs. Several bacterial taxa such as Spirochaetes, Streptomycetaceae, and Prevotellaceae failed to recover at day 28 (p < 0.05). Several bacterial groups considered to be sensitive to tylosin increased in their

  1. Microbial ecology and performance of ammonia oxidizing bacteria (AOB) in biological processes treating petrochemical wastewater with high strength of ammonia: effect of Na(2)CO(3) addition.

    PubMed

    Whang, L M; Yang, K H; Yang, Y F; Han, Y L; Chen, Y J; Cheng, S S

    2009-01-01

    This study evaluated nitrification performance and microbial ecology of AOB in a full-scale biological process, powder activated carbon treatment (PACT), and a pilot-scale biological process, moving bed biofilm reactor (MBBR), treating wastewater collected from a petrochemical industry park. The petrochemical influent wastewater characteristics showed a relative low carbon to nitrogen ratio around 1 with average COD and ammonia concentrations of 310 mg/L and 325 mg-N/L, respectively. The average nitrification efficiency of the full-scale PACT process was around 11% during this study. For the pilot-scale MBBR, the average nitrification efficiency was 24% during the Run I operation mode, which provided a slightly better performance in nitrification than that of the PACT process. During the Run II operation, the pH control mode was switched from addition of NaOH to Na(2)CO(3), leading to a significant improvement in nitrification efficiency of 51%. In addition to a dramatic change in nitrification performance, the microbial ecology of AOB, monitored with the terminal restriction fragment length polymorphism (T-RFLP) molecular methodology, was found to be different between Runs I and II. The amoA-based TRFLP results indicated that Nitrosomonas europaea lineage was the dominant AOB population during Run I operation, while Nitrosospira-like AOB was dominant during Run II operation. To confirm the effects of Na(2)CO(3) addition on the nitrification performance and AOB microbial ecology observed in the MBBR process, batch experiments were conducted. The results suggest that addition of Na(2)CO(3) as a pH control strategy can improve nitrification performance and also influence AOB microbial ecology as well. Although the exact mechanisms are not clear at this time, the results showing the effects of adding different buffering chemicals such as NaOH or Na(2)CO(3) on AOB populations have never been demonstrated until this study. PMID:19182331

  2. Assessment of the microbial ecology of ruminal methanogens in cattle with different feed efficiencies.

    PubMed

    Zhou, Mi; Hernandez-Sanabria, Emma; Guan, Le Luo

    2009-10-01

    Cattle with high feed efficiencies (designated "efficient") produce less methane gas than those with low feed efficiencies (designated "inefficient"); however, the role of the methane producers in such difference is unknown. This study investigated whether the structures and populations of methanogens in the rumen were associated with differences in cattle feed efficiencies by using culture-independent methods. Two 16S rRNA libraries were constructed using approximately 800-bp amplicons generated from pooled total DNA isolated from efficient (n = 29) and inefficient (n = 29) animals. Sequence analysis of up to 490 randomly selected clones from each library showed that the methanogenic composition was variable: less species variation (22 operational taxonomic units [OTUs]) was detected in the rumens of efficient animals, compared to 27 OTUs in inefficient animals. The methanogenic communities in inefficient animals were more diverse than those in efficient ones, as revealed by the diversity indices of 0.84 and 0.42, respectively. Differences at the strain and genotype levels were also observed and found to be associated with feed efficiency in the host. No difference was detected in the total population of methanogens, but the prevalences of Methanosphaera stadtmanae and Methanobrevibacter sp. strain AbM4 were 1.92 (P < 0.05) and 2.26 (P < 0.05) times higher in inefficient animals, while Methanobrevibacter sp. strain AbM4 was reported for the first time to occur in the bovine rumen. Our data indicate that the methanogenic ecology at the species, strain, and/or genotype level in the rumen may play important roles in contributing to the difference in methane gas production between cattle with different feed efficiencies.

  3. Intestinal microbiota and immune related genes in sea cucumber (Apostichopus japonicus) response to dietary β-glucan supplementation.

    PubMed

    Yang, Gang; Xu, Zhenjiang; Tian, Xiangli; Dong, Shuanglin; Peng, Mo

    2015-02-27

    β-glucan is a prebiotic well known for its beneficial outcomes on sea cucumber health through modifying the host intestinal microbiota. High-throughput sequencing techniques provide an opportunity for the identification and characterization of microbes. In this study, we investigated the intestinal microbial community composition, interaction among species, and intestinal immune genes in sea cucumber fed with diet supplemented with or without β-glucan supplementation. The results show that the intestinal dominant classes in the control group are Flavobacteriia, Gammaproteobacteria, and Alphaproteobacteria, whereas Alphaproteobacteria, Flavobacteriia, and Verrucomicrobiae are enriched in the β-glucan group. Dietary β-glucan supplementation promoted the proliferation of the family Rhodobacteraceae of the Alphaproteobacteria class and the family Verrucomicrobiaceae of the Verrucomicrobiae class and reduced the relative abundance of the family Flavobacteriaceae of Flavobacteria class. The ecological network analysis suggests that dietary β-glucan supplementation can alter the network interactions among different microbial functional groups by changing the microbial community composition and topological roles of the OTUs in the ecological network. Dietary β-glucan supplementation has a positive impact on immune responses of the intestine of sea cucumber by activating NF-κB signaling pathway, probably through modulating the balance of intestinal microbiota.

  4. Establishment of Intestinal Bacteriology

    PubMed Central

    MITSUOKA, Tomotari

    2014-01-01

    Research on intestinal bacteria began around the end of the 19th century. During the last 5 decades of the 20th century, research on the intestinal microbiota made rapid progress. At first, in my work, I first developed a method of comprehensive analysis of the intestinal microbiota, and then I established classification and identification methods for intestinal anaerobes. Using these methods I discovered a number of ecological rules governing the intestinal microbiota and the role of the intestinl microbiota in health and disease. Moreover, using germfree animals, it was proven that the intestinal microbiota has a role in carcinogenesis and aging in the host. Thus, a new interdisciplinary field, “intestinal bacteriology” was established. PMID:25032084

  5. Nitrate and Inhibition of Ruminal Methanogenesis: Microbial Ecology, Obstacles, and Opportunities for Lowering Methane Emissions from Ruminant Livestock.

    PubMed

    Yang, Chengjian; Rooke, John A; Cabeza, Irene; Wallace, Robert J

    2016-01-01

    Ruminal methane production is among the main targets for greenhouse gas (GHG) mitigation for the animal agriculture industry. Many compounds have been evaluated for their efficacy to suppress enteric methane production by ruminal microorganisms. Of these, nitrate as an alternative hydrogen sink has been among the most promising, but it suffers from variability in efficacy for reasons that are not understood. The accumulation of nitrite, which is poisonous when absorbed into the animal's circulation, is also variable and poorly understood. This review identifies large gaps in our knowledge of rumen microbial ecology that handicap the further development and safety of nitrate as a dietary additive. Three main bacterial species have been associated historically with ruminal nitrate reduction, namely Wolinella succinogenes, Veillonella parvula, and Selenomonas ruminantium, but others almost certainly exist in the largely uncultivated ruminal microbiota. Indications are strong that ciliate protozoa can reduce nitrate, but the significance of their role relative to bacteria is not known. The metabolic fate of the reduced nitrate has not been studied in detail. It is important to be sure that nitrate metabolism and efforts to enhance rates of nitrite reduction do not lead to the evolution of the much more potent GHG, nitrous oxide. The relative importance of direct inhibition of archaeal methanogenic enzymes by nitrite or the efficiency of capture of hydrogen by nitrate reduction in lowering methane production is also not known, nor are nitrite effects on other members of the microbiota. How effective would combining mitigation methods be, based on our understanding of the effects of nitrate and nitrite on the microbiome? Answering these fundamental microbiological questions is essential in assessing the potential of dietary nitrate to limit methane emissions from ruminant livestock. PMID:26904008

  6. Nitrate and Inhibition of Ruminal Methanogenesis: Microbial Ecology, Obstacles, and Opportunities for Lowering Methane Emissions from Ruminant Livestock

    PubMed Central

    Yang, Chengjian; Rooke, John A.; Cabeza, Irene; Wallace, Robert J.

    2016-01-01

    Ruminal methane production is among the main targets for greenhouse gas (GHG) mitigation for the animal agriculture industry. Many compounds have been evaluated for their efficacy to suppress enteric methane production by ruminal microorganisms. Of these, nitrate as an alternative hydrogen sink has been among the most promising, but it suffers from variability in efficacy for reasons that are not understood. The accumulation of nitrite, which is poisonous when absorbed into the animal’s circulation, is also variable and poorly understood. This review identifies large gaps in our knowledge of rumen microbial ecology that handicap the further development and safety of nitrate as a dietary additive. Three main bacterial species have been associated historically with ruminal nitrate reduction, namely Wolinella succinogenes, Veillonella parvula, and Selenomonas ruminantium, but others almost certainly exist in the largely uncultivated ruminal microbiota. Indications are strong that ciliate protozoa can reduce nitrate, but the significance of their role relative to bacteria is not known. The metabolic fate of the reduced nitrate has not been studied in detail. It is important to be sure that nitrate metabolism and efforts to enhance rates of nitrite reduction do not lead to the evolution of the much more potent GHG, nitrous oxide. The relative importance of direct inhibition of archaeal methanogenic enzymes by nitrite or the efficiency of capture of hydrogen by nitrate reduction in lowering methane production is also not known, nor are nitrite effects on other members of the microbiota. How effective would combining mitigation methods be, based on our understanding of the effects of nitrate and nitrite on the microbiome? Answering these fundamental microbiological questions is essential in assessing the potential of dietary nitrate to limit methane emissions from ruminant livestock. PMID:26904008

  7. Empirical links between trace metal cycling and marine microbial ecology during a large perturbation to Earth's carbon cycle

    NASA Astrophysics Data System (ADS)

    Owens, Jeremy D.; Reinhard, Christopher T.; Rohrssen, Megan; Love, Gordon D.; Lyons, Timothy W.

    2016-09-01

    Understanding the global redox state of the oceans and its cause-and-effect relationship with periods of widespread organic-carbon deposition is vital to interpretations of Earth's climatic and biotic feedbacks during periods of expanded oceanic oxygen deficiency. Here, we present a compilation of new and published data from an organic-rich locality within the proto-North Atlantic Ocean during the Cenomanian-Turonian boundary event that shows a dramatic drawdown of redox-sensitive trace elements. Iron geochemistry independently suggests euxinic deposition (i.e., anoxic and sulfidic bottom waters) for the entire section, thus confirming its potential as an archive of global marine metal inventories. In particular, depleted molybdenum (Mo) and vanadium (V) concentrations effectively record the global expansion of euxinic and oxygen-deficient but non-sulfidic waters, respectively. The V drawdown precedes the OAE, fingerprinting an expansion of oxygen deficiency prior to an expansion of euxinia. Molybdenum drawdown, in contrast, is delayed with respect to V and coincides with the onset of OAE2. Parallel lipid biomarker analyses provide evidence for significant and progressive reorganization of marine microbial ecology during the OAE in this region of the proto-North Atlantic, with the smallest relative eukaryotic contributions to total primary production occurring during metal-depleted intervals. This relationship may be related to decreasing supplies of enzymatically important trace elements. Similarly, box modeling suggests that oceanic drawdown of Mo may have approached levels capable of affecting marine nitrogen fixation. Predictions of possible nitrogen stress on eukaryotic production, locally and globally, are consistent with the low observed levels of Mo and a rise in 2-methylhopane index values during the peak of the OAE. At the same time, the environmental challenge presented by low dissolved oxygen and euxinia coincides with increased turnover rates of

  8. Different land use intensities in grassland ecosystems drive ecology of microbial communities involved in nitrogen turnover in soil.

    PubMed

    Meyer, Annabel; Focks, Andreas; Radl, Viviane; Keil, Daniel; Welzl, Gerhard; Schöning, Ingo; Boch, Steffen; Marhan, Sven; Kandeler, Ellen; Schloter, Michael

    2013-01-01

    Understanding factors driving the ecology of N cycling microbial communities is of central importance for sustainable land use. In this study we report changes of abundance of denitrifiers, nitrifiers and nitrogen-fixing microorganisms (based on qPCR data for selected functional genes) in response to different land use intensity levels and the consequences for potential turnover rates. We investigated selected grassland sites being comparable with respect to soil type and climatic conditions, which have been continuously treated for many years as intensely used meadows (IM), intensely used mown pastures (IP) and extensively used pastures (EP), respectively. The obtained data were linked to above ground biodiversity pattern as well as water extractable fractions of nitrogen and carbon in soil. Shifts in land use intensity changed plant community composition from systems dominated by s-strategists in extensive managed grasslands to c-strategist dominated communities in intensive managed grasslands. Along the different types of land use intensity, the availability of inorganic nitrogen regulated the abundance of bacterial and archaeal ammonia oxidizers. In contrast, the amount of dissolved organic nitrogen determined the abundance of denitrifiers (nirS and nirK). The high abundance of nifH carrying bacteria at intensive managed sites gave evidence that the amounts of substrates as energy source outcompete the high availability of inorganic nitrogen in these sites. Overall, we revealed that abundance and function of microorganisms involved in key processes of inorganic N cycling (nitrification, denitrification and N fixation) might be independently regulated by different abiotic and biotic factors in response to land use intensity.

  9. Changes in soil microbial biomass and residual indices as ecological indicators of land use change in temperate permanent grassland.

    PubMed

    Murugan, Rajasekaran; Loges, Ralf; Taube, Friedhelm; Sradnick, André; Joergensen, Rainer Georg

    2014-05-01

    The relationship between microbial biomass, residues and their contribution to microbial turnover is important to understand ecosystem C storage. The effects of permanent grassland (100 % ryegrass--PG), conversion to modified grassland (mixture of grass and clover--MG) or maize monoculture (MM) on the dynamics of soil organic C (SOC), microbial biomass, fungal ergosterol and microbial residues (bacterial muramic acid and fungal glucosamine) were investigated. Cattle slurry was applied to quantify the effects of fertilisation on microbial residues and functional diversity of microbial community across land use types. Slurry application significantly increased the stocks of microbial biomass C and S and especially led to a shift in microbial residues towards bacterial tissue. The MM treatment decreased the stocks of SOC, microbial biomass C, N and S and microbial residues compared with the PG and MG treatments at 0-40 cm depth. The MM treatment led to a greater accumulation of saprotrophic fungi, as indicated by the higher ergosterol-to-microbial biomass C ratio and lower microbial biomass C/S ratio compared with the grassland treatments. The absence of a white clover population in the PG treatment caused a greater accumulation of fungal residues (presumably arbuscular mycorrhizal fungi (AMF), which do not contain ergosterol but glucosamine), as indicated by the significantly higher fungal C-to-bacterial C ratio and lower ergosterol-to-microbial biomass C ratio compared with the MG treatment. In addition to these microbial biomass and residual indices, the community level physiological profiles (CLPP) demonstrated distinct differences between the PG and MG treatments, suggesting the potential of these measurements to act as an integrative indicator of soil functioning.

  10. Using PLFA Biomarkers and Natural Abundance Stable and Radiocarbon Isotopes to Characterize the Microbial Ecology and Metabolism of Methane Cycling

    NASA Astrophysics Data System (ADS)

    Mills, C. T.; Mandernack, K. W.; Slater, G. F.; Dias, R. F.

    2008-12-01

    Methane generated in the subsurface is a major source of atmospheric CH4, but its release is mitigated by CH4-oxidizing bacteria (methanotrophs). Therefore, it is important to understand the ecology of methanotroph communities in various environments. Phospholipid fatty acid (PLFA) analyses are a particularly useful method for characterizing these communities for two reasons: (1) Many type I and II methanotrophs produce specific PLFA biomarkers that can be used to estimate their populations, and (2) because CH4 is often very depleted in 13C and sometimes 14C, natural abundance δ13CPLFA and Δ14CPLFA values can be used to trace the flow of CH4- derived carbon through microbial ecosystems. We used these tools to evaluate the role of methanotrophs in carbon flow in three different environments: (1) a soil column overlying a coal bed methane (CBM) seep in southwest CO, and pristine, oligotrophic groundwaters within (2) sedimentary and (3) granitic host rocks in Japan. In the soil column impacted by CBM seepage, concentrations of the biomarker PLFAs for type I (16:1ω8cis) and type II (18:1ω8cis) methanotrophs were as high as 13 and 18 nmoles (g dry soil)-1, respectively. Depth profiles of methanotroph PLFA concentrations varied over different sampling dates indicating dynamic populations. δ13CPLFA values of the CBM soils (-25.1 to - 66.9‰) were substantially more negative than those for the control soil (-14.5 to -32.5‰) indicating that CBM is an important carbon source for the CBM-impacted soil microbial community. Δ14CPLFA values (-351 to -936‰) indicate the importance of 14C-dead CBM as a carbon source to the microbial communities, contributing 32 to 66% of total carbon in PLFA structures isolated from shallow soils and 67 to 97% for those isolated from deeper soils. The biomarker for type II methanotrophs, comprised 3 and 18% of total PLFAs in sedimentary and granitic groundwaters, respectively. The Δ14C values determined for type II methanotroph PLFAs

  11. Intestinal microbiota and immune related genes in sea cucumber (Apostichopus japonicus) response to dietary β-glucan supplementation

    SciTech Connect

    Yang, Gang; Xu, Zhenjiang; Tian, Xiangli; Dong, Shuanglin; Peng, Mo

    2015-02-27

    β-glucan is a prebiotic well known for its beneficial outcomes on sea cucumber health through modifying the host intestinal microbiota. High-throughput sequencing techniques provide an opportunity for the identification and characterization of microbes. In this study, we investigated the intestinal microbial community composition, interaction among species, and intestinal immune genes in sea cucumber fed with diet supplemented with or without β-glucan supplementation. The results show that the intestinal dominant classes in the control group are Flavobacteriia, Gammaproteobacteria, and Alphaproteobacteria, whereas Alphaproteobacteria, Flavobacteriia, and Verrucomicrobiae are enriched in the β-glucan group. Dietary β-glucan supplementation promoted the proliferation of the family Rhodobacteraceae of the Alphaproteobacteria class and the family Verrucomicrobiaceae of the Verrucomicrobiae class and reduced the relative abundance of the family Flavobacteriaceae of Flavobacteria class. The ecological network analysis suggests that dietary β-glucan supplementation can alter the network interactions among different microbial functional groups by changing the microbial community composition and topological roles of the OTUs in the ecological network. Dietary β-glucan supplementation has a positive impact on immune responses of the intestine of sea cucumber by activating NF-κB signaling pathway, probably through modulating the balance of intestinal microbiota. - Highlights: • Dietary β-glucan supplementation increases the abundance of Rhodobacteraceae and Verrucomicrobiaceae in the intestine. • Dietary β-glucan supplementation changes the topological roles of OTUs in the ecological network. • Dietary β-glucan supplementation has a positive impact on the immune response of intestine of sea cucumber.

  12. Medium-chain triglyceride as an alternative of in-feed colistin sulfate to improve growth performance and intestinal microbial environment in newly weaned pigs.

    PubMed

    Yen, Hung-Che; Lai, Wei-Kang; Lin, Chuan-Shun; Chiang, Shu-Hsing

    2015-01-01

    Five hundred and twenty-eight newly weaned pigs were given four treatments, with eight replicates per treatment. Sixteen to 18 pigs were assigned per replicate and were fed diets supplemented with 0 or 3% medium-chain triglyceride (MCT) and 0 or 40 ppm colistin sulfate (CS) in a 2 × 2 factorial arrangement for 2 weeks. The results showed that dietary supplementation with MCT improved the gain-to-feed ratio during days 3-7 and in the overall period (P < 0.05). Dietary supplementation with MCT decreased coliforms counts (C) in colon and rectum content (P < 0.05). Dietary supplementation with CS decreased C and lactic acid bacteria plus C counts (L + C) in cecum (P < 0.05), and C, L + C (P < 0.01) and ratio of L and C (P < 0.05) in colon and rectum contents. The lack of interactions between MCT and CS indicates different modes of action and additive effects between the two supplementations. In conclusion, supplementation with MCT in diet with or without CS could improve the intestinal microbial environment and the feed utilization efficiency of newly weaned pigs.

  13. Adding mucins to an in vitro batch fermentation model of the large intestine induces changes in microbial population isolated from porcine feces depending on the substrate.

    PubMed

    Tran, T H T; Boudry, C; Everaert, N; Théwis, A; Portetelle, D; Daube, G; Nezer, C; Taminiau, B; Bindelle, J

    2016-02-01

    Adding mucus to in vitro fermentation models of the large intestine shows that some genera, namely lactobacilli, are dependent on host-microbiota interactions and that they rely on mucosal layers to increase their activity. This study investigated whether this dependence on mucus is substrate dependent and to what extent other genera are impacted by the presence of mucus. Inulin and cellulose were fermented in vitro by a fecal inoculum from pig in the presence or not of mucin beads in order to compare fermentation patterns and bacterial communities. Mucins increased final gas production with inulin and shifted short-chain fatty acid molar ratios (P < 0.001). Quantitative real-time PCR analyses revealed that Lactobacillus spp. and Bifidobacterium spp. decreased with mucins, but Bacteroides spp. increased when inulin was fermented. A more in-depth community analysis indicated that the mucins increased Proteobacteria (0.55 vs 0.25%, P = 0.013), Verrucomicrobia (5.25 vs 0.03%, P = 0.032), Ruminococcaceae, Bacteroidaceae and Akkermansia spp. Proteobacteria (5.67 vs 0.55%, P < 0.001) and Lachnospiraceae (33 vs 10.4%) were promoted in the mucus compared with the broth, while Ruminococcaceae decreased. The introduction of mucins affected many microbial genera and fermentation patterns, but from PCA results, the impact of mucus was independent of the fermentation substrate.

  14. The molecular dimension of microbial species: 1. Ecological distinctions among, and homogeneity within, putative ecotypes of Synechococcus inhabiting the cyanobacterial mat of Mushroom Spring, Yellowstone National Park.

    PubMed

    Becraft, Eric D; Wood, Jason M; Rusch, Douglas B; Kühl, Michael; Jensen, Sheila I; Bryant, Donald A; Roberts, David W; Cohan, Frederick M; Ward, David M

    2015-01-01

    Based on the Stable Ecotype Model, evolution leads to the divergence of ecologically distinct populations (e.g., with different niches and/or behaviors) of ecologically interchangeable membership. In this study, pyrosequencing was used to provide deep sequence coverage of Synechococcus psaA genes and transcripts over a large number of habitat types in the Mushroom Spring microbial mat. Putative ecological species [putative ecotypes (PEs)], which were predicted by an evolutionary simulation based on the Stable Ecotype Model (Ecotype Simulation), exhibited distinct distributions relative to temperature-defined positions in the effluent channel and vertical position in the upper 1 mm-thick mat layer. Importantly, in most cases variants predicted to belong to the same PE formed unique clusters relative to temperature and depth in the mat in canonical correspondence analysis, supporting the hypothesis that while the PEs are ecologically distinct, the members of each ecotype are ecologically homogeneous. PEs responded differently to experimental perturbations of temperature and light, but the genetic variation within each PE was maintained as the relative abundances of PEs changed, further indicating that each population responded as a set of ecologically interchangeable individuals. Compared to PEs that predominate deeper within the mat photic zone, the timing of transcript abundances for selected genes differed for PEs that predominate in microenvironments closer to upper surface of the mat with spatiotemporal differences in light and O2 concentration. All of these findings are consistent with the hypotheses that Synechococcus species in hot spring mats are sets of ecologically interchangeable individuals that are differently adapted, that these adaptations control their distributions, and that the resulting distributions constrain the activities of the species in space and time.

  15. The molecular dimension of microbial species: 1. Ecological distinctions among, and homogeneity within, putative ecotypes of Synechococcus inhabiting the cyanobacterial mat of Mushroom Spring, Yellowstone National Park

    PubMed Central

    Becraft, Eric D.; Wood, Jason M.; Rusch, Douglas B.; Kühl, Michael; Jensen, Sheila I.; Bryant, Donald A.; Roberts, David W.; Cohan, Frederick M.; Ward, David M.

    2015-01-01

    Based on the Stable Ecotype Model, evolution leads to the divergence of ecologically distinct populations (e.g., with different niches and/or behaviors) of ecologically interchangeable membership. In this study, pyrosequencing was used to provide deep sequence coverage of Synechococcus psaA genes and transcripts over a large number of habitat types in the Mushroom Spring microbial mat. Putative ecological species [putative ecotypes (PEs)], which were predicted by an evolutionary simulation based on the Stable Ecotype Model (Ecotype Simulation), exhibited distinct distributions relative to temperature-defined positions in the effluent channel and vertical position in the upper 1 mm-thick mat layer. Importantly, in most cases variants predicted to belong to the same PE formed unique clusters relative to temperature and depth in the mat in canonical correspondence analysis, supporting the hypothesis that while the PEs are ecologically distinct, the members of each ecotype are ecologically homogeneous. PEs responded differently to experimental perturbations of temperature and light, but the genetic variation within each PE was maintained as the relative abundances of PEs changed, further indicating that each population responded as a set of ecologically interchangeable individuals. Compared to PEs that predominate deeper within the mat photic zone, the timing of transcript abundances for selected genes differed for PEs that predominate in microenvironments closer to upper surface of the mat with spatiotemporal differences in light and O2 concentration. All of these findings are consistent with the hypotheses that Synechococcus species in hot spring mats are sets of ecologically interchangeable individuals that are differently adapted, that these adaptations control their distributions, and that the resulting distributions constrain the activities of the species in space and time. PMID:26157420

  16. Microbial ecology measurement system

    NASA Technical Reports Server (NTRS)

    1972-01-01

    The sensitivity and potential rapidity of the PIA test that was demonstrated during the feasibility study warranted continuing the effort to examine the possibility of adapting this test to an automated procedure that could be used during manned missions. The effort during this program has optimized the test conditions for two important respiratory pathogens, influenza virus and Mycoplasma pneumoniae, developed a laboratory model automated detection system, and investigated a group antigen concept for virus detection. Preliminary tests on the handling of oropharygeal clinical samples for PIA testing were performed using the adenovirus system. The results obtained indicated that the PIA signal is reduced in positive samples and is increased in negative samples. Treatment with cysteine appeared to reduce nonspecific agglutination in negative samples but did not maintain the signal in positive samples.

  17. Sequence-based Methods in Human Microbial Ecology: A The 2nd HumanGenome Comes of Age

    SciTech Connect

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

    2005-06-01

    Ecologists studying microbial life in the environment have recognized the enormous complexity of microbial diversity for more than a decade (Whitman et al. 1998). The development of a variety of culture-independent methods, many of them coupled with high-throughput DNA sequencing, has allowed this diversity to be explored in ever greater detail (Handelsman 2004; Harris et al. 2004; Hugenholtz et al. 1998; Moreira and Lopez-Garcia 2002; Rappe and Giovannoni 2003). Despite the widespread application of these new techniques to the characterization of uncultivated microbes and microbial communities in the environment, their application to human health and disease has lagged behind. Because these techniques now allow not only cataloging of microbial diversity, but also insight into microbial functions, it is time for clinical microbiologists to apply these tools to the microbial communities that abound on and within us, in what has been aptly called ''the second Human Genome Project'' (Relman and Falkow 2001). In this review we will discuss the sequence-based methods for microbial analysis that are currently available and their application to identify novel human pathogens, improve diagnosis and treatment of known infectious diseases, and finally to advance understanding of our relationship with microbial communities that normally reside in and on the human body.

  18. CMEIAS color segmentation: an improved computing technology to process color images for quantitative microbial ecology studies at single-cell resolution.

    PubMed

    Gross, Colin A; Reddy, Chandan K; Dazzo, Frank B

    2010-02-01

    Quantitative microscopy and digital image analysis are underutilized in microbial ecology largely because of the laborious task to segment foreground object pixels from background, especially in complex color micrographs of environmental samples. In this paper, we describe an improved computing technology developed to alleviate this limitation. The system's uniqueness is its ability to edit digital images accurately when presented with the difficult yet commonplace challenge of removing background pixels whose three-dimensional color space overlaps the range that defines foreground objects. Image segmentation is accomplished by utilizing algorithms that address color and spatial relationships of user-selected foreground object pixels. Performance of the color segmentation algorithm evaluated on 26 complex micrographs at single pixel resolution had an overall pixel classification accuracy of 99+%. Several applications illustrate how this improved computing technology can successfully resolve numerous challenges of complex color segmentation in order to produce images from which quantitative information can be accurately extracted, thereby gain new perspectives on the in situ ecology of microorganisms. Examples include improvements in the quantitative analysis of (1) microbial abundance and phylotype diversity of single cells classified by their discriminating color within heterogeneous communities, (2) cell viability, (3) spatial relationships and intensity of bacterial gene expression involved in cellular communication between individual cells within rhizoplane biofilms, and (4) biofilm ecophysiology based on ribotype-differentiated radioactive substrate utilization. The stand-alone executable file plus user manual and tutorial images for this color segmentation computing application are freely available at http://cme.msu.edu/cmeias/ . This improved computing technology opens new opportunities of imaging applications where discriminating colors really matter most

  19. Mixed culture models for predicting intestinal microbial interactions between Escherichia coli and Lactobacillus in the presence of probiotic Bacillus subtilis.

    PubMed

    Yang, J J; Niu, C C; Guo, X H

    2015-01-01

    Bacillus has been proposed as a probiotic due to its in vivo effectiveness in the gastrointestinal tract through antimicrobial activities. The present study investigates the effects of Lactobacillus alone or in the presence of Bacillus subtilis MA139 on the inhibition of pathogenic Escherichia coli K88. Mixed cultures were used to predict the possible interactions among these bacteria within the intestinal tract of animals. B. subtilis MA139 was first assayed for its inhibition against E. coli K88 both under shaking and static culture conditions. A co-culture assay was employed under static conditions to test the inhibitory effects of Lactobacillus reuteri on E. coli K88, with or without addition of B. subtilis MA139. The results showed that B. subtilis MA139 had marked inhibition against E. coli K88 under shaking conditions and weak inhibition under static conditions. Lactobacillus alone as well as in combination with B. subtilis MA139 spores exerted strong inhibition against E. coli K88 under static conditions. However, the inhibition by Lactobacillus in combination with B. subilis spores was much higher than that by Lactobacillus alone (P<0.01). B. subtilis MA139 significantly decreased the pH and oxidation-reduction potential values of the co-culture broth compared to that of Lactobacillus alone (P<0.05). The viability of Lactobacillus increased when co-cultured with B. subtilis MA139 because of significantly higher Lactobacillus counts and lower pH values in the broth (P<0.05). The role of Bacillus in the mixed culture models suggests that Bacillus may produce beneficial effects by increasing the viability of lactobacilli and subsequently inhibiting the growth of pathogenic E. coli. Therefore, the combination of Bacillus and Lactobacillus species as a probiotic is recommended. PMID:26259891

  20. Metagenomic insights into tetracycline effects on microbial community and antibiotic resistance of mouse gut.

    PubMed

    Yin, Jinbao; Zhang, Xu-Xiang; Wu, Bing; Xian, Qiming

    2015-12-01

    Antibiotics have been widely used for disease prevention and treatment of the human and animals, and for growth promotion in animal husbandry. Antibiotics can disturb the intestinal microbial community, which play a fundamental role in animals' health. Misuse or overuse of antibiotics can result in increase and spread of microbial antibiotic resistance, threatening human health and ecological safety. In this study, we used Illumina Hiseq sequencing, (1)H nuclear magnetic resonance spectroscopy and metagenomics approaches to investigate intestinal microbial community shift and antibiotic resistance alteration of the mice drinking the water containing tetracycline hydrochloride (TET). Two-week TET administration caused reduction of gut microbial diversity (from 194 to 89 genera), increase in Firmicutes abundance (from 24.9 to 39.8%) and decrease in Bacteroidetes abundance (from 69.8 to 51.2%). Metagenomic analysis showed that TET treatment affected the intestinal microbial functions of carbohydrate, ribosomal, cell wall/membrane/envelope and signal transduction, which is evidenced by the alteration in the metabolites of mouse serum. Meanwhile, in the mouse intestinal microbiota, TET treatment enhanced the abundance of antibiotic resistance genes (ARGs) (from 307.3 to 1492.7 ppm), plasmids (from 425.4 to 3235.1 ppm) and integrons (from 0.8 to 179.6 ppm) in mouse gut. Our results indicated that TET administration can disturb gut microbial community and physiological metabolism of mice, and increase the opportunity of ARGs and mobile genetic elements entering into the environment with feces discharge. PMID:26423395

  1. Metagenomic insights into tetracycline effects on microbial community and antibiotic resistance of mouse gut.

    PubMed

    Yin, Jinbao; Zhang, Xu-Xiang; Wu, Bing; Xian, Qiming

    2015-12-01

    Antibiotics have been widely used for disease prevention and treatment of the human and animals, and for growth promotion in animal husbandry. Antibiotics can disturb the intestinal microbial community, which play a fundamental role in animals' health. Misuse or overuse of antibiotics can result in increase and spread of microbial antibiotic resistance, threatening human health and ecological safety. In this study, we used Illumina Hiseq sequencing, (1)H nuclear magnetic resonance spectroscopy and metagenomics approaches to investigate intestinal microbial community shift and antibiotic resistance alteration of the mice drinking the water containing tetracycline hydrochloride (TET). Two-week TET administration caused reduction of gut microbial diversity (from 194 to 89 genera), increase in Firmicutes abundance (from 24.9 to 39.8%) and decrease in Bacteroidetes abundance (from 69.8 to 51.2%). Metagenomic analysis showed that TET treatment affected the intestinal microbial functions of carbohydrate, ribosomal, cell wall/membrane/envelope and signal transduction, which is evidenced by the alteration in the metabolites of mouse serum. Meanwhile, in the mouse intestinal microbiota, TET treatment enhanced the abundance of antibiotic resistance genes (ARGs) (from 307.3 to 1492.7 ppm), plasmids (from 425.4 to 3235.1 ppm) and integrons (from 0.8 to 179.6 ppm) in mouse gut. Our results indicated that TET administration can disturb gut microbial community and physiological metabolism of mice, and increase the opportunity of ARGs and mobile genetic elements entering into the environment with feces discharge.

  2. Effect of Scrophularia striata and Ferulago angulata, as alternatives to virginiamycin, on growth performance, intestinal microbial population, immune response, and blood constituents of broiler chickens.

    PubMed

    Rostami, Farhad; Ghasemi, Hossein A; Taherpour, Kamran

    2015-09-01

    An experiment was conducted to investigate the comparative effect of Scrophularia striata, Ferulago angulata, and virginiamycin (VM) on performance, intestinal microbial population, immune response, and blood constituents of broilers. A total of 300 Ross 308 male broiler chickens were randomly assigned to 5 treatments, with 5 replicates/treatment (10 chickens/pen). Birds were fed either a corn-soybean meal basal diet (control) or the basal diet supplemented with 200 mg/kg VM; 4 g/kg S. striata (SS1); 8 g/kg S. striata (SS2); 4 g/kg F. angulata (FA1); or 8 g/kg F. angulata (FA2). After 6 wk, the BW, ADG, and feed-to-gain ratio (F:G) of the VM, SS1, and FA1 groups were better (P<0.01) compared with the control group. At 42 d, cecal lactobacillus counts were higher (P=0.032) in SS2 and FA2 groups compared with the control and VM groups. In addition, broilers fed any of the diets exhibited lower coliform counts (P<0.05) in the ileum and ceca than those fed the control diet. Total and IgG antibody titers against SRBC for secondary responses, relative spleen weight, and lymphocyte counts were higher (P<0.05) in birds fed the SS2 or FA2 diet compared with the control group. Moreover, feeding the SS2 or FA2 diet decreased (P<0.05) the blood heterophil/lymphocyte ratio and plasma triglyceride level, whereas only the SS2 diet increased (P=0.037) the white blood cell counts compared with the control diet. All diets, except for the VM diet, decreased (P=0.009) the plasma cholesterol level compared to the control treatment. The plasma high-density lipoprotein cholesterol level was also increased (P=0.042) in the SS2 and FA2 groups. In conclusion, dietary S. striata or F. angulata at a level of 4 g/kg diet enhanced growth performance, which was comparable to that of VM used as an antibiotic growth promoter. Furthermore, a high dose of both herbs (8 g/kg diet) could beneficially affect the intestinal health and immune status of broilers. PMID:26217029

  3. Effect of Scrophularia striata and Ferulago angulata, as alternatives to virginiamycin, on growth performance, intestinal microbial population, immune response, and blood constituents of broiler chickens.

    PubMed

    Rostami, Farhad; Ghasemi, Hossein A; Taherpour, Kamran

    2015-09-01

    An experiment was conducted to investigate the comparative effect of Scrophularia striata, Ferulago angulata, and virginiamycin (VM) on performance, intestinal microbial population, immune response, and blood constituents of broilers. A total of 300 Ross 308 male broiler chickens were randomly assigned to 5 treatments, with 5 replicates/treatment (10 chickens/pen). Birds were fed either a corn-soybean meal basal diet (control) or the basal diet supplemented with 200 mg/kg VM; 4 g/kg S. striata (SS1); 8 g/kg S. striata (SS2); 4 g/kg F. angulata (FA1); or 8 g/kg F. angulata (FA2). After 6 wk, the BW, ADG, and feed-to-gain ratio (F:G) of the VM, SS1, and FA1 groups were better (P<0.01) compared with the control group. At 42 d, cecal lactobacillus counts were higher (P=0.032) in SS2 and FA2 groups compared with the control and VM groups. In addition, broilers fed any of the diets exhibited lower coliform counts (P<0.05) in the ileum and ceca than those fed the control diet. Total and IgG antibody titers against SRBC for secondary responses, relative spleen weight, and lymphocyte counts were higher (P<0.05) in birds fed the SS2 or FA2 diet compared with the control group. Moreover, feeding the SS2 or FA2 diet decreased (P<0.05) the blood heterophil/lymphocyte ratio and plasma triglyceride level, whereas only the SS2 diet increased (P=0.037) the white blood cell counts compared with the control diet. All diets, except for the VM diet, decreased (P=0.009) the plasma cholesterol level compared to the control treatment. The plasma high-density lipoprotein cholesterol level was also increased (P=0.042) in the SS2 and FA2 groups. In conclusion, dietary S. striata or F. angulata at a level of 4 g/kg diet enhanced growth performance, which was comparable to that of VM used as an antibiotic growth promoter. Furthermore, a high dose of both herbs (8 g/kg diet) could beneficially affect the intestinal health and immune status of broilers.

  4. Controlling Salmonella infection in weanling pigs through water delivery of direct-fed microbials or organic acids: Part II. Effects on intestinal histology and active nutrient transport.

    PubMed

    Walsh, M C; Rostagno, M H; Gardiner, G E; Sutton, A L; Richert, B T; Radcliffe, J S

    2012-08-01

    The objective of this study was to evaluate the effects of water-delivered, direct-fed microbials (DFM) or organic acids on intestinal morphology and active nutrient absorption in weanling pigs after deliberate Salmonella infection. Pigs (n = 88) were weaned at 19 ± 2 d of age and assigned to 1 of the following treatments, which were administered for 14 d: 1) control diet; 2) control diet + DFM (Enterococcus faecium, Bacillus subtilis, and Bacillus licheniformis) in drinking water at 10(9) cfu/L for each strain of bacteria; 3) control diet + organic acid-based blend (predominantly propionic, acetic, and benzoic acids) in drinking water at 2.58 mL/L; and 4) control diet + 55 mg/kg carbadox. Pigs were challenged with 10(10) cfu Salmonella enterica var Typhimurium 6 d after commencement of treatments. Pigs (n = 22/d) were harvested before Salmonella challenge and on d 2, 4, and 8 after challenge. Duodenal, jejunal, and ileal mucosal tissues were sampled for measurement of villus height and crypt depth. Jejunal tissue was sampled for determination of active nutrient absorption in modified Ussing chambers. Duodenal villus height was greater in pigs fed in-feed antibiotic before infection (P < 0.05). Jejunal crypts were deeper in DFM- and acid-treated pigs on d 4 after infection compared with all other treatments (P < 0.05). Salmonella infection resulted in a linear decrease in phosphorus (P < 0.001) and glucose (P < 0.05) active transport, and an increase (P < 0.001) in glutamine uptake immediately after challenge. Salmonella infection reduced basal short-circuit current (I(sc)); however, water-delivered DFM or organic acid treatments caused greater basal I(sc) on d 2 after challenge than did carbadox. Carbachol-induced chloride ion secretion was greatest in negative control pigs before infection (P < 0.01) and DFM-treated pigs (P < 0.05) after infection. In conclusion, both the DFM and acidification treatments induced increases in basal active ion movement and jejunal

  5. Targeting Unknowns Just Underfoot: Microbial Ecology and Community Genomics of C Cycling in Soil Informed and Enabled with DNA-SIP

    NASA Astrophysics Data System (ADS)

    Pepe-Ranney, C. P.; Campbell, A.; Buckley, D. H.

    2015-12-01

    Microorganisms drive biogeochemical cycles and because soil is a large global carbon (C) reservoir (soil contains more C than plants and the atmosphere combined), soil microorganisms are important players in the global C-cycle. Frustratingly, however, many soil microorganisms resist cultivation and soil communities are astoundingly complex. This makes soil microbiology difficult to study and without a solid understanding of soil microbial ecology, models of soil C feedbacks to climate change are under-informed. Stable isotope probing (SIP) is a useful approach for establishing identity-function connections in microbial communities but has been challenging to employ in soil due to the inadequate resolution of microbial community fingerprinting techniques. High throughput DNA sequencing improves SIP resolving power transforming it into a powerful tool for studying the soil C cycle. We conducted a DNA-SIP experiment to track flow of xylose-C, a labile component of plant biomass, and cellulose-C, the most abundant global biopolymer, through a soil microbial community. We could track 13C into microbial DNA even when added 13C amounted to less than 5% of native C and found Spartobacteria, Chloroflexi, and Planctomycetes taxa were among those that assimilated 13C cellulose. These lineages are cosmopolitan in soil but little is known of their ecophysiology. By profiling SSU rRNA genes across entire DNA-SIP density gradients, we assessed relative DNA atom % 13C per taxon in 13C treatments and found cellulose degraders exhibited signal consistent with a specialist lifestyle with respect to C preference. Further, DNA-SIP enriches DNA of targeted microorganisms (Verrucomicrobia cellulose degraders were enriched by nearly two orders of magnitude) and this enriched DNA can serve as template for community genomics. We produced draft genomes from soil cellulose degraders including microorganisms belonging to Verrucomicrobia, Chloroflexi, and Planctomycetes from SIP enriched DNA

  6. Study of the succession of microbial communities for sulfur cycle response to ecological factors change in sediment of sewage system.

    PubMed

    Liu, Yanchen; Dong, Qian; Wu, Chen; Zhou, Xiaohong; Shi, Hanchang

    2015-06-01

    The biological reaction process of sulfur in biofilms and sediments causes serious problems of corrosion and odor in sewage systems. This study aims to reveal the distribution and shift of microbial diversity that survives inside the sediment in response to surrounding changes in sewage systems. The successions of microbial community were compared via denaturing gradient gel electrophoresis and by constructing phylogenetic trees via maximum likelihood method. The results indicated that the shift of microbial diversity is not significant along the vertical layer inside the sediment. The influences of sediment accumulation time on the shift in microbial diversity are evident, particularly with the switch of the accumulation stage. Implementing a control strategy for oxygen injection and nitrate addition evidently inhibits and stimulates some dominant sulfate-reducing bacterial strains in the sediment. The diversity in the total bacteria is positively related with ORP, dissolved oxygen, and sulfide concentration. PMID:25592909

  7. A step-wise expansion of intestinal intraepithelial T lymphocytes in association with microbial colonization is defined by sensitivity to cyclosporin A.

    PubMed Central

    Kawaguchi-Miyashita, M; Nanno, M; Shimada, S; Nagaoka, N; Okada, Y; Matsumoto, S; Umesaki, Y; Matsuoka, Y; Ohwaki, M

    1997-01-01

    Murine intestinal intraepithelial lymphocytes (IELs) consist of T cells bearing alpha beta-antigen receptor (alpha beta-IELs) and those bearing gamma delta-IELs). Although gamma delta-IELs outnumber alpha beta-IELs in germ-free (GF) mice, oral inoculation of fecal suspension from conventional (CV) mice into GF mice induced the increase in number of alpha beta-IELs, leaving the number of gamma delta-IELs unchanged, and the number of alpha beta-IELs reached the level of CV mice by 3 weeks after conventionalization. Expansion of alpha beta-IELs and increase in their CD44+ subset in conventionalized mice were not affected until 2 weeks after beginning of daily injection of cyclosporin A (CsA). However, further expansion of alpha beta-IELs during 2-3 weeks after conventionalization was blocked by injection of CsA. Although the relative constitution of CD4- 8-, CD4+ 8-, CD4- 8 alpha alpha+, CD4- 8 alpha beta+ and CD4+ 8+ subsets among alpha beta-IELs was comparable between control and CsA-treated groups, CsA injection resulted in the decrease in ratio of high-density fraction cells to low density fraction cells in IELs. CsA completely abrogated the expansion of T cells in peripheral lymph nodes stimulated by alloantigens in vivo, and proliferation of IELs from GF mice induced by immobilized anti-alpha beta-T-cell receptor (TCR) monoclonal antibodies (mAb) in vitro was also eliminated by CsA. These results indicate that microbial colonization-induced expansion of alpha beta-IELs is subdivided into two steps: the early phase of expansion takes place via TCR-non-mediated pathway and the late phase of expansion requires TCR-mediated signal transduction. Images Figure 4 PMID:9378505

  8. Intestinal Microbiota and Microbial Metabolites Are Changed in a Pig Model Fed a High-Fat/Low-Fiber or a Low-Fat/High-Fiber Diet.

    PubMed

    Heinritz, Sonja N; Weiss, Eva; Eklund, Meike; Aumiller, Tobias; Louis, Sandrine; Rings, Andreas; Messner, Sabine; Camarinha-Silva, Amélia; Seifert, Jana; Bischoff, Stephan C; Mosenthin, Rainer

    2016-01-01

    The intestinal microbiota and its metabolites appear to be an important factor for gastrointestinal function and health. However, research is still needed to further elaborate potential relationships between nutrition, gut microbiota and host's health by means of a suitable animal model. The present study examined the effect of two different diets on microbial composition and activity by using the pig as a model for humans. Eight pigs were equally allotted to two treatments, either fed a low-fat/high-fiber (LF), or a high-fat/low-fiber (HF) diet for 7 weeks. Feces were sampled at day 7 of every experimental week. Diet effects on fecal microbiota were assessed using quantitative real-time PCR, DNA fingerprinting and metaproteomics. Furthermore, fecal short-chain fatty acid (SCFA) profiles and ammonia concentrations were determined. Gene copy numbers of lactobacilli, bifidobacteria (P<0.001) and Faecalibacterium prausnitzii (P<0.05) were higher in the LF pigs, while Enterobacteriaceae were more abundant in the HF pigs (P<0.001). Higher numbers of proteins affiliated to Enterobacteriaceae were also present in the HF samples. Proteins for polysaccharide breakdown did almost exclusively originate from Prevotellaceae. Total and individual fecal SCFA concentrations were higher for pigs of the LF treatment (P<0.05), whereas fecal ammonia concentrations did not differ between treatments (P>0.05). Results provide evidence that beginning from the start of the experiment, the LF diet stimulated beneficial bacteria and SCFA production, especially butyrate (P<0.05), while the HF diet fostered those bacterial groups which have been associated with a negative impact on health conditions. These findings correspond to results in humans and might strengthen the hypothesis that the response of the porcine gut microbiota to a specific dietary modulation is in support of using the pig as suitable animal model for humans to assess diet-gut-microbiota interactions. Data are available via

  9. Intestinal Microbiota and Microbial Metabolites Are Changed in a Pig Model Fed a High-Fat/Low-Fiber or a Low-Fat/High-Fiber Diet

    PubMed Central

    Heinritz, Sonja N.; Weiss, Eva; Eklund, Meike; Aumiller, Tobias; Louis, Sandrine; Rings, Andreas; Messner, Sabine; Camarinha-Silva, Amélia; Seifert, Jana; Bischoff, Stephan C.; Mosenthin, Rainer

    2016-01-01

    The intestinal microbiota and its metabolites appear to be an important factor for gastrointestinal function and health. However, research is still needed to further elaborate potential relationships between nutrition, gut microbiota and host’s health by means of a suitable animal model. The present study examined the effect of two different diets on microbial composition and activity by using the pig as a model for humans. Eight pigs were equally allotted to two treatments, either fed a low-fat/high-fiber (LF), or a high-fat/low-fiber (HF) diet for 7 weeks. Feces were sampled at day 7 of every experimental week. Diet effects on fecal microbiota were assessed using quantitative real-time PCR, DNA fingerprinting and metaproteomics. Furthermore, fecal short-chain fatty acid (SCFA) profiles and ammonia concentrations were determined. Gene copy numbers of lactobacilli, bifidobacteria (P<0.001) and Faecalibacterium prausnitzii (P<0.05) were higher in the LF pigs, while Enterobacteriaceae were more abundant in the HF pigs (P<0.001). Higher numbers of proteins affiliated to Enterobacteriaceae were also present in the HF samples. Proteins for polysaccharide breakdown did almost exclusively originate from Prevotellaceae. Total and individual fecal SCFA concentrations were higher for pigs of the LF treatment (P<0.05), whereas fecal ammonia concentrations did not differ between treatments (P>0.05). Results provide evidence that beginning from the start of the experiment, the LF diet stimulated beneficial bacteria and SCFA production, especially butyrate (P<0.05), while the HF diet fostered those bacterial groups which have been associated with a negative impact on health conditions. These findings correspond to results in humans and might strengthen the hypothesis that the response of the porcine gut microbiota to a specific dietary modulation is in support of using the pig as suitable animal model for humans to assess diet-gut-microbiota interactions. Data are available

  10. Microbial and geochemical investigations of dissolved organic carbon and microbial ecology of native waters from the Biscayne and Upper Floridan Aquifers

    USGS Publications Warehouse

    Lisle, John T.; Harvey, Ron W.; Aiken, George R.; Metge, David W.

    2010-01-01

    Groundwater resources in the United States are under ever-increasing demands for potable, irrigation, and recreational uses. Additionally, aquifer systems are being used or targeted for use as storage areas for treated surface waters and (or) groundwaters via injection (for example, aquifer storage and recovery). To date, the influence that the nutrients, including carbon, in the injected water have on native microbial communities and the biogeochemistry in the subsurface zones used for storage of the injectate has not been determined. In this report, we describe a series of experiments that establishes a baseline dataset for the quantity and quality of organic and inorganic carbon and nutrients in the Biscayne Aquifer (BA) and Upper Floridan Aquifer (UFA) in south Florida. The most significant differences between the BA (26 meters below surface) and UFA (366 meters below surface) are the average specific conductance (0.552 and 6.12 microsiemens per centimeter, respectively), dissolved oxygen (1.6 and 0 milligrams per liter, respectively), and oxidation-reduction potential (40.3 and -358 millivolts, respectively). The dissolved organic carbon from the BA is characterized by carbon originating from terrestrial sources and microbial activities, while the UFA has a distinctive microbial signature. Acetate and lactate are the dominant carbon constituents in both aquifers. Additionally, components of the dissolved organic carbon from the UFA have a total trihalomethane-formation potential that is approximately threefold greater than the maximum contaminat level of 80 micrograms per liter established by the U.S. Environmental Protection Agency. The average native bacterial abundances in the aquifers are similar with 4.69x10^4 cells per milliliter in the BA and 1.33x10^4 cells per milliliter in the UFA. The average bacteriophage abundances are also similar with 1.15x10^5 virus-like particles in the BA and 1.92x10^5 virus-like particles in the UFA. Interestingly, ciliated

  11. Responses of soil microbial biomass and bacterial community structure to closed-off management (an ecological natural restoration measures): A case study of Dongting Lake wetland, middle China.

    PubMed

    Dai, Juan; Wu, Haipeng; Zhang, Chang; Zeng, Guangming; Liang, Jie; Guo, Shenglian; Li, Xiaodong; Huang, Lu; Lu, Lunhui; Yuan, Yujie

    2016-09-01

    Soil microbial biomass (SMB) and bacterial community structure, which are critical to global ecosystem and fundamental ecological processes, are sensitive to anthropogenic activities and environmental conditions. In this study, we examined the possible effects of closed-off management (an ecological natural restoration measures, ban on anthropogenic activity, widely employed for many important wetlands) on SMB, soil bacterial community structure and functional marker genes of nitrogen cycling in Dongting Lake wetland. Soil samples were collected from management area (MA) and contrast area (CA: human activities, such as hunting, fishing and draining, are permitted) in November 2013 and April 2014. Soil properties, microbial biomass carbon (MBC), and bacterial community structure were investigated. Comparison of the values of MA and CA showed that SMB and bacterial community diversity of the MA had a significant increase after 7 years closed-off management. The mean value of Shannon-Weiner diversity index of MA and CA respectively were 2.85 and 2.07. The gene copy numbers of 16S rRNA and nosZ of MA were significant higher than those of CA. the gene copy numbers of ammonia-oxidizing archaea (AOA) and nirK of MA were significant lower than those of CA. However, there was no significant change in the gene copy numbers of ammonia-oxidizing bacteria (AOB) and nirS.

  12. Responses of soil microbial biomass and bacterial community structure to closed-off management (an ecological natural restoration measures): A case study of Dongting Lake wetland, middle China.

    PubMed

    Dai, Juan; Wu, Haipeng; Zhang, Chang; Zeng, Guangming; Liang, Jie; Guo, Shenglian; Li, Xiaodong; Huang, Lu; Lu, Lunhui; Yuan, Yujie

    2016-09-01

    Soil microbial biomass (SMB) and bacterial community structure, which are critical to global ecosystem and fundamental ecological processes, are sensitive to anthropogenic activities and environmental conditions. In this study, we examined the possible effects of closed-off management (an ecological natural restoration measures, ban on anthropogenic activity, widely employed for many important wetlands) on SMB, soil bacterial community structure and functional marker genes of nitrogen cycling in Dongting Lake wetland. Soil samples were collected from management area (MA) and contrast area (CA: human activities, such as hunting, fishing and draining, are permitted) in November 2013 and April 2014. Soil properties, microbial biomass carbon (MBC), and bacterial community structure were investigated. Comparison of the values of MA and CA showed that SMB and bacterial community diversity of the MA had a significant increase after 7 years closed-off management. The mean value of Shannon-Weiner diversity index of MA and CA respectively were 2.85 and 2.07. The gene copy numbers of 16S rRNA and nosZ of MA were significant higher than those of CA. the gene copy numbers of ammonia-oxidizing archaea (AOA) and nirK of MA were significant lower than those of CA. However, there was no significant change in the gene copy numbers of ammonia-oxidizing bacteria (AOB) and nirS. PMID:27036597

  13. Microbial ecology, bacterial pathogens, and antibiotic resistant genes in swine manure as influenced by three swine management systems

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The environmental influence of farm management in concentrated animal feeding operations (CAFO) can yield vastly different microbial constituents in both the pig and the manure lagoons used to treat the fecal waste of the operation. While some of these changes may not be negative, it is possible th...

  14. The Human Intestinal Microbiome: A New Frontier of Human Biology

    PubMed Central

    Hattori, Masahira; Taylor, Todd D.

    2009-01-01

    To analyze the vast number and variety of microorganisms inhabiting the human intestine, emerging metagenomic technologies are extremely powerful. The intestinal microbes are taxonomically complex and constitute an ecologically dynamic community (microbiota) that has long been believed to possess a strong impact on human physiology. Furthermore, they are heavily involved in the maturation and proliferation of human intestinal cells, helping to maintain their homeostasis and can be causative of various diseases, such as inflammatory bowel disease and obesity. A simplified animal model system has provided the mechanistic basis for the molecular interactions that occur at the interface between such microbes and host intestinal epithelia. Through metagenomic analysis, it is now possible to comprehensively explore the genetic nature of the intestinal microbiome, the mutually interacting system comprising the host cells and the residing microbial community. The human microbiome project was recently launched as an international collaborative research effort to further promote this newly developing field and to pave the way to a new frontier of human biology, which will provide new strategies for the maintenance of human health. PMID:19147530

  15. Microbial Ecology of a Crewed Rover Traverse in the Arctic: Low Microbial Dispersal and Implications for Planetary Protection on Human Mars Missions.

    PubMed

    Schuerger, Andrew C; Lee, Pascal

    2015-06-01

    Between April 2009 and July 2011, the NASA Haughton-Mars Project (HMP) led the Northwest Passage Drive Expedition (NWPDX), a multi-staged long-distance crewed rover traverse along the Northwest Passage in the Arctic. In April 2009, the HMP Okarian rover was driven 496 km over sea ice along the Northwest Passage, from Kugluktuk to Cambridge Bay, Nunavut, Canada. During the traverse, crew members collected samples from within the rover and from undisturbed snow-covered surfaces around the rover at three locations. The rover samples and snow samples were stored at subzero conditions (-20°C to -1°C) until processed for microbial diversity in labs at the NASA Kennedy Space Center, Florida. The objective was to determine the extent of microbial dispersal away from the rover and onto undisturbed snow. Interior surfaces of the rover were found to be associated with a wide range of bacteria (69 unique taxa) and fungi (16 unique taxa). In contrast, snow samples from the upwind, downwind, uptrack, and downtrack sample sites exterior to the rover were negative for both bacteria and fungi except for two colony-forming units (cfus) recovered from one downwind (1 cfu; site A4) and one uptrack (1 cfu; site B6) sample location. The fungus, Aspergillus fumigatus (GenBank JX517279), and closely related bacteria in the genus Brevibacillus were recovered from both snow (B. agri, GenBank JX517278) and interior rover surfaces. However, it is unknown whether the microorganisms were deposited onto snow surfaces at the time of sample collection (i.e., from the clothing or skin of the human operator) or via airborne dispersal from the rover during the 12-18 h layovers at the sites prior to collection. Results support the conclusion that a crewed rover traveling over previously undisturbed terrain may not significantly contaminate the local terrain via airborne dispersal of propagules from the vehicle. PMID:26060984

  16. Microbial Ecology of a Crewed Rover Traverse in the Arctic: Low Microbial Dispersal and Implications for Planetary Protection on Human Mars Missions.

    PubMed

    Schuerger, Andrew C; Lee, Pascal

    2015-06-01

    Between April 2009 and July 2011, the NASA Haughton-Mars Project (HMP) led the Northwest Passage Drive Expedition (NWPDX), a multi-staged long-distance crewed rover traverse along the Northwest Passage in the Arctic. In April 2009, the HMP Okarian rover was driven 496 km over sea ice along the Northwest Passage, from Kugluktuk to Cambridge Bay, Nunavut, Canada. During the traverse, crew members collected samples from within the rover and from undisturbed snow-covered surfaces around the rover at three locations. The rover samples and snow samples were stored at subzero conditions (-20°C to -1°C) until processed for microbial diversity in labs at the NASA Kennedy Space Center, Florida. The objective was to determine the extent of microbial dispersal away from the rover and onto undisturbed snow. Interior surfaces of the rover were found to be associated with a wide range of bacteria (69 unique taxa) and fungi (16 unique taxa). In contrast, snow samples from the upwind, downwind, uptrack, and downtrack sample sites exterior to the rover were negative for both bacteria and fungi except for two colony-forming units (cfus) recovered from one downwind (1 cfu; site A4) and one uptrack (1 cfu; site B6) sample location. The fungus, Aspergillus fumigatus (GenBank JX517279), and closely related bacteria in the genus Brevibacillus were recovered from both snow (B. agri, GenBank JX517278) and interior rover surfaces. However, it is unknown whether the microorganisms were deposited onto snow surfaces at the time of sample collection (i.e., from the clothing or skin of the human operator) or via airborne dispersal from the rover during the 12-18 h layovers at the sites prior to collection. Results support the conclusion that a crewed rover traveling over previously undisturbed terrain may not significantly contaminate the local terrain via airborne dispersal of propagules from the vehicle.

  17. Intestinal leiomyoma

    MedlinePlus

    Leiomyoma - intestine ... McLaughlin P, Maher MM. The duodenum and small intestine. In: Adam A, Dixon AK, Gillard JH, Schaefer- ... Roline CE, Reardon RF. Disorders of the small intestine. In: Marx JA, Hockberger RS, Walls RM, et ...

  18. Intestinal Cancer

    MedlinePlus

    ... connects your stomach to your large intestine. Intestinal cancer is rare, but eating a high-fat diet ... increase your risk. Possible signs of small intestine cancer include Abdominal pain Weight loss for no reason ...

  19. The cladistic basis for the phylogenetic diversity (PD) measure links evolutionary features to environmental gradients and supports broad applications of microbial ecology's "phylogenetic beta diversity" framework.

    PubMed

    Faith, Daniel P; Lozupone, Catherine A; Nipperess, David; Knight, Rob

    2009-11-03

    The PD measure of phylogenetic diversity interprets branch lengths cladistically to make inferences about feature diversity. PD calculations extend conventional species-level ecological indices to the features level. The "phylogenetic beta diversity" framework developed by microbial ecologists calculates PD-dissimilarities between community localities. Interpretation of these PD-dissimilarities at the feature level explains the framework's success in producing ordinations revealing environmental gradients. An example gradients space using PD-dissimilarities illustrates how evolutionary features form unimodal response patterns to gradients. This features model supports new application of existing species-level methods that are robust to unimodal responses, plus novel applications relating to climate change, commercial products discovery, and community assembly.

  20. Microbial Ecology of a Crewed Rover Traverse in the Arctic: Low Microbial Dispersal and Implications for Planetary Protection on Human Mars Missions

    PubMed Central

    Lee, Pascal

    2015-01-01

    Abstract Between April 2009 and July 2011, the NASA Haughton-Mars Project (HMP) led the Northwest Passage Drive Expedition (NWPDX), a multi-staged long-distance crewed rover traverse along the Northwest Passage in the Arctic. In April 2009, the HMP Okarian rover was driven 496 km over sea ice along the Northwest Passage, from Kugluktuk to Cambridge Bay, Nunavut, Canada. During the traverse, crew members collected samples from within the rover and from undisturbed snow-covered surfaces around the rover at three locations. The rover samples and snow samples were stored at subzero conditions (−20°C to −1°C) until processed for microbial diversity in labs at the NASA Kennedy Space Center, Florida. The objective was to determine the extent of microbial dispersal away from the rover and onto undisturbed snow. Interior surfaces of the rover were found to be associated with a wide range of bacteria (69 unique taxa) and fungi (16 unique taxa). In contrast, snow samples from the upwind, downwind, uptrack, and downtrack sample sites exterior to the rover were negative for both bacteria and fungi except for two colony-forming units (cfus) recovered from one downwind (1 cfu; site A4) and one uptrack (1 cfu; site B6) sample location. The fungus, Aspergillus fumigatus (GenBank JX517279), and closely related bacteria in the genus Brevibacillus were recovered from both snow (B. agri, GenBank JX517278) and interior rover surfaces. However, it is unknown whether the microorganisms were deposited onto snow surfaces at the time of sample collection (i.e., from the clothing or skin of the human operator) or via airborne dispersal from the rover during the 12–18 h layovers at the sites prior to collection. Results support the conclusion that a crewed rover traveling over previously undisturbed terrain may not significantly contaminate the local terrain via airborne dispersal of propagules from the vehicle. Key Words: Planetary protection

  1. Microbial Ecology of a Crewed Rover Traverse in the Arctic: Low Microbial Dispersal and Implications for Planetary Protection on Human Mars Missions

    NASA Technical Reports Server (NTRS)

    Schuerger, Andrew C.; Lee, Pascal

    2015-01-01

    Between April 2009 and July 2011, the NASA Haughton-Mars Project (HMP) led the Northwest Passage Drive Expedition (NWPDX), a multi-staged long-distance crewed rover traverse along the Northwest Passage in the Arctic. In April 2009, the HMP Okarian rover was driven 496 km over sea ice along the Northwest Passage, from Kugluktuk to Cambridge Bay, Nunavut, Canada. During the traverse, crew members collected samples from within the rover and from undisturbed snow-covered surfaces around the rover at three locations. The rover samples and snow samples were stored at subzero conditions (-20C to -1C) until processed for microbial diversity in labs at the NASA Kennedy Space Center, Florida. The objective was to determine the extent of microbial dispersal away from the rover and onto undisturbed snow. Interior surfaces of the rover were found to be associated with a wide range of bacteria (69 unique taxa) and fungi (16 unique taxa). In contrast, snow samples from the upwind, downwind, uptrack, and downtrack sample sites exterior to the rover were negative for both bacteria and fungi except for two colony-forming units (cfus) recovered from one downwind (1 cfu; site A4) and one uptrack (1 cfu; site B6) sample location. The fungus, Aspergillus fumigatus (GenBank JX517279), and closely related bacteria in the genus Brevibacillus were recovered from both snow (B. agri, GenBank JX517278) and interior rover surfaces. However, it is unknown whether the microorganisms were deposited onto snow surfaces at the time of sample collection (i.e., from the clothing or skin of the human operator) or via airborne dispersal from the rover during the 12-18 h layovers at the sites prior to collection. Results support the conclusion that a crewed rover traveling over previously undisturbed terrain may not significantly contaminate the local terrain via airborne dispersal of propagules from the vehicle. Key Words: Planetary protection-Contamination-Habitability-Haughton Crater-Mars. Astrobiology

  2. Ecology and life history of an amoebomastigote, Paratetramitus jugosus, from a microbial mat: new evidence for multiple fission

    NASA Technical Reports Server (NTRS)

    Enzien, M.; McKhann, H. I.; Margulis, L.

    1989-01-01

    Five microbial habitats (gypsum crust, gypsum photosynthetic community, Microcoleus mat, Thiocapsa scum, and black mud) were sampled for the presence of the euryhaline, rapidly growing amoebomastigote, Paratetramitus jugosus. Field investigations of microbial mats from Baja California Norte, Mexico, and Salina Bido near Matanzas, Cuba, reveal that P. jugosus is most frequently found in the Thiocapsa layer of microbial mats. Various stages of the life history were studied using phase-contrast, differential-interference, and transmission electron microscopy. Mastigote stages were induced and studied by electron microscopy; mastigotes that actively feed on bacteria bear two or more undulipodia. A three-dimensional drawing of the kinetid ("basal apparatus") based on electron micrographs is presented. Although promitoses were occasionally observed, it is unlikely that they can account for the rapid growth of P. jugosus populations on culture media. Dense, refractile, spherical, and irregular-shaped bodies were seen at all times in all cultures along with small mononucleate (approximately 2-7 micrometers diameter) amoebae. Cytochemical studies employing two different fluorescent stains for DNA (DAPI, mithramycin) verified the presence of DNA in these small bodies. Chromatin-like material seen in electron micrographs within the cytoplasm and blebbing off nuclei were interpreted to the chromatin bodies. Our interpretation, consistent with the data but not proven, is that propagation by multiple fission of released chromatin bodies that become small amoebae may occur in Paratetramitus jugosus. These observations are consistent with descriptions of amoeba propagules in the early literature (Hogue, 1914).

  3. A morphogenetic survey on ciliate plankton from a mountain lake pinpoints the necessity of lineage-specific barcode markers in microbial ecology

    PubMed Central

    Stoeck, Thorsten; Breiner, Hans-Werner; Filker, Sabine; Ostermaier, Veronika; Kammerlander, Barbara; Sonntag, Bettina

    2014-01-01

    Analyses of high-throughput environmental sequencing data have become the ‘gold-standard’ to address fundamental questions of microbial diversity, ecology and biogeography. Findings that emerged from sequencing are, e.g. the discovery of the extensive ‘rare microbial biosphere’ and its potential function as a seed-bank. Even though applied since several years, results from high-throughput environmental sequencing have hardly been validated. We assessed how well pyrosequenced amplicons [the hypervariable eukaryotic V4 region of the small subunit ribosomal RNA (SSU rRNA) gene] reflected morphotype ciliate plankton. Moreover, we assessed if amplicon sequencing had the potential to detect the annual ciliate plankton stock. In both cases, we identified significant quantitative and qualitative differences. Our study makes evident that taxon abundance distributions inferred from amplicon data are highly biased and do not mirror actual morphotype abundances at all. Potential reasons included cell losses after fixation, cryptic morphotypes, resting stages, insufficient sequence data availability of morphologically described species and the unsatisfying resolution of the V4 SSU rRNA fragment for accurate taxonomic assignments. The latter two underline the necessity of barcoding initiatives for eukaryotic microbes to better and fully exploit environmental amplicon data sets, which then will also allow studying the potential of seed-bank taxa as a buffer for environmental changes. PMID:23848238

  4. TREATMENT OF LONG-EVANS RATS WITH A DEFINED MIXTURE OF DRINKING WATER DISINFECTION BY-PRODUCTS IMPACTS INTESTINAL MICROBIAL METABOLISM.

    EPA Science Inventory

    Water treatment results in the production of numerous halogenated disinfection by-products (DBPs), and has been associated with human colorectal cancer. Because the intestinal microbiota can bioactivate promutagens and procarcinogens, several studies have been done to examine the...

  5. Temporal changes in microbial ecology and geochemistry in produced water from hydraulically fractured Marcellus shale gas wells.

    PubMed

    Cluff, Maryam A; Hartsock, Angela; MacRae, Jean D; Carter, Kimberly; Mouser, Paula J

    2014-06-01

    Microorganisms play several important roles in unconventional gas recovery, from biodegradation of hydrocarbons to souring of wells and corrosion of equipment. During and after the hydraulic fracturing process, microorganisms are subjected to harsh physicochemical conditions within the kilometer-deep hydrocarbon-bearing shale, including high pressures, elevated temperatures, exposure to chemical additives and biocides, and brine-level salinities. A portion of the injected fluid returns to the surface and may be reused in other fracturing operations, a process that can enrich for certain taxa. This study tracked microbial community dynamics using pyrotag sequencing of 16S rRNA genes in water samples from three hydraulically fractured Marcellus shale wells in Pennsylvania, USA over a 328-day period. There was a reduction in microbial richness and diversity after fracturing, with the lowest diversity at 49 days. Thirty-one taxa dominated injected, flowback, and produced water communities, which took on distinct signatures as injected carbon and electron acceptors were attenuated within the shale. The majority (>90%) of the community in flowback and produced fluids was related to halotolerant bacteria associated with fermentation, hydrocarbon oxidation, and sulfur-cycling metabolisms, including heterotrophic genera Halolactibacillus, Vibrio, Marinobacter, Halanaerobium, and Halomonas, and autotrophs belonging to Arcobacter. Sequences related to halotolerant methanogenic genera Methanohalophilus and Methanolobus were detected at low abundance (<2%) in produced waters several months after hydraulic fracturing. Five taxa were strong indicators of later produced fluids. These results provide insight into the temporal trajectory of subsurface microbial communities after "fracking" and have important implications for the enrichment of microbes potentially detrimental to well infrastructure and natural gas fouling during this process.

  6. Fourier transform-infrared spectroscopic methods for microbial ecology: analysis of bacteria, bacteria-polymer mixtures and biofilms

    NASA Technical Reports Server (NTRS)

    Nichols, P. D.; Henson, J. M.; Guckert, J. B.; Nivens, D. E.; White, D. C.

    1985-01-01

    Fourier transform-infrared (FT-IR) spectroscopy has been used to rapidly and nondestructively analyze bacteria, bacteria-polymer mixtures, digester samples and microbial biofilms. Diffuse reflectance FT-IR (DRIFT) analysis of freeze-dried, powdered samples offered a means of obtaining structural information. The bacteria examined were divided into two groups. The first group was characterized by a dominant amide I band and the second group of organisms displayed an additional strong carbonyl stretch at approximately 1740 cm-1. The differences illustrated by the subtraction spectra obtained for microbes of the two groups suggest that FT-IR spectroscopy can be utilized to recognize differences in microbial community structure. Calculation of specific band ratios has enabled the composition of bacteria and extracellular or intracellular storage product polymer mixtures to be determined for bacteria-gum arabic (amide I/carbohydrate C-O approximately 1150 cm-1) and bacteria-poly-beta-hydroxybutyrate (amide I/carbonyl approximately 1740 cm-1). The key band ratios correlate with the compositions of the material and provide useful information for the application of FT-IR spectroscopy to environmental biofilm samples and for distinguishing bacteria grown under differing nutrient conditions. DRIFT spectra have been obtained for biofilms produced by Vibrio natriegens on stainless steel disks. Between 48 and 144 h, an increase in bands at approximately 1440 and 1090 cm-1 was seen in FT-IR spectra of the V. natriegens biofilm. DRIFT spectra of mixed culture effluents of anaerobic digesters show differences induced by shifts in input feedstocks. The use of flow-through attenuated total reflectance has permitted in situ real-time changes in biofilm formation to be monitored and provides a powerful tool for understanding the interactions within adherent microbial consortia.

  7. Temporal changes in microbial ecology and geochemistry in produced water from hydraulically fractured Marcellus shale gas wells.

    PubMed

    Cluff, Maryam A; Hartsock, Angela; MacRae, Jean D; Carter, Kimberly; Mouser, Paula J

    2014-06-01

    Microorganisms play several important roles in unconventional gas recovery, from biodegradation of hydrocarbons to souring of wells and corrosion of equipment. During and after the hydraulic fracturing process, microorganisms are subjected to harsh physicochemical conditions within the kilometer-deep hydrocarbon-bearing shale, including high pressures, elevated temperatures, exposure to chemical additives and biocides, and brine-level salinities. A portion of the injected fluid returns to the surface and may be reused in other fracturing operations, a process that can enrich for certain taxa. This study tracked microbial community dynamics using pyrotag sequencing of 16S rRNA genes in water samples from three hydraulically fractured Marcellus shale wells in Pennsylvania, USA over a 328-day period. There was a reduction in microbial richness and diversity after fracturing, with the lowest diversity at 49 days. Thirty-one taxa dominated injected, flowback, and produced water communities, which took on distinct signatures as injected carbon and electron acceptors were attenuated within the shale. The majority (>90%) of the community in flowback and produced fluids was related to halotolerant bacteria associated with fermentation, hydrocarbon oxidation, and sulfur-cycling metabolisms, including heterotrophic genera Halolactibacillus, Vibrio, Marinobacter, Halanaerobium, and Halomonas, and autotrophs belonging to Arcobacter. Sequences related to halotolerant methanogenic genera Methanohalophilus and Methanolobus were detected at low abundance (<2%) in produced waters several months after hydraulic fracturing. Five taxa were strong indicators of later produced fluids. These results provide insight into the temporal trajectory of subsurface microbial communities after "fracking" and have important implications for the enrichment of microbes potentially detrimental to well infrastructure and natural gas fouling during this process. PMID:24803059

  8. Sampling strategy in molecular microbial ecology: influence of soil sample size on DNA fingerprinting analysis of fungal and bacterial communities.

    PubMed

    Ranjard, Lionel; Lejon, David P H; Mougel, Christophe; Schehrer, Lucie; Merdinoglu, Didier; Chaussod, Rémi

    2003-11-01

    Assessing soil microbial community structure by the use of molecular techniques requires a satisfactory sampling strategy that takes into account the high microbial diversity and the heterogeneous distribution of microorganisms in the soil matrix. The influence of the sample size of three different soil types (sand, silt and clay soils) on the DNA yield and analysis of bacterial and fungal community structure were investigated. Six sample sizes from 0.125 g to 4 g were evaluated. The genetic community structure was assessed by automated ribosomal intergenic spacer analysis (A-RISA fingerprint). Variations between bacterial (B-ARISA) and fungal (F-ARISA) community structure were quantified by using principal component analysis (PCA). DNA yields were positively correlated with the sample size for the sandy and silty soils, suggesting an influence of the sample size on DNA recovery, whereas no correlation was observed in the clay soil. B-ARISA was shown to be consistent between the different sample sizes for each soil type indicating that the sampling procedure has no influence on the assessment of bacterial community structure. On the contrary for F-ARISA profiles, strong variations were observed between replicates of the smaller samples (<1 g). Principal component analysis analysis revealed that sampling aliquots of soil > or =1 g are required to obtain robust and reproducible fingerprinting analysis of the genetic structure of fungal communities. However, the smallest samples could be adequate for the detection of minor populations masked by dominant ones in larger samples. The sampling strategy should therefore be different according to the objectives: rather large soil samples (> or =1 g) for a global description of the genetic community structure, or a large number of small soil samples for a more complete inventory of microbial diversity.

  9. Final Technical Report: DOE-Biological Ocean Margins Program. Microbial Ecology of Denitrifying Bacteria in the Coastal Ocean.

    SciTech Connect

    Lee Kerkhof

    2013-01-01

    The focus of our research was to provide a comprehensive study of the bacterioplankton populations off the coast of New Jersey near the Rutgers University marine field station using terminal restriction fragment polymorphism analysis (TRFLP) coupled to 16S rRNA genes for large data set studies. Our three revised objectives to this study became: (1) to describe bacterioplankton population dynamics in the Mid Atlantic Bight using TRFLP analysis of 16S rRNA genes. (2) to determine whether spatial and temporal factors are driving bacterioplankton community dynamics in the MAB using monthly samping along our transect line over a 2-year period. (3) to identify dominant members of a coastal bacterioplankton population by clonal library analysis of 16S rDNA genes and sequencing of PCR product corresponding to specific TRFLP peaks in the data set. Although open ocean time-series sites have been areas of microbial research for years, relatively little was known about the population dynamics of bacterioplankton communities in the coastal ocean on kilometer spatial and seasonal temporal scales. To gain a better understanding of microbial community variability, monthly samples of bacterial biomass were collected in 1995-1996 along a 34-km transect near the Long-Term Ecosystem Observatory (LEO-15) off the New Jersey coast. Surface and bottom sampling was performed at seven stations along a transect line with depths ranging from 1 to 35m (n=178). The data revealed distinct temporal patterns among the bacterioplankton communities in the Mid-Atlantic Bight rather than grouping by sample location or depth (figure 2-next page). Principal components analysis models supported the temporal patterns. In addition, partial least squares regression modeling could not discern a significant correlation from traditional oceanographic physical and phytoplankton nutrient parameters on overall bacterial community variability patterns at LEO-15. These results suggest factors not traditionally

  10. DegePrime, a Program for Degenerate Primer Design for Broad-Taxonomic-Range PCR in Microbial Ecology Studies

    PubMed Central

    Hugerth, Luisa W.; Wefer, Hugo A.; Lundin, Sverker; Jakobsson, Hedvig E.; Lindberg, Mathilda; Rodin, Sandra; Engstrand, Lars

    2014-01-01

    The taxonomic composition of a microbial community can be deduced by analyzing its rRNA gene content by, e.g., high-throughput DNA sequencing or DNA chips. Such methods typically are based on PCR amplification of rRNA gene sequences using broad-taxonomic-range PCR primers. In these analyses, the use of optimal primers is crucial for achieving an unbiased representation of community composition. Here, we present the computer program DegePrime that, for each position of a multiple sequence alignment, finds a degenerate oligomer of as high coverage as possible and outputs its coverage among taxonomic divisions. We show that our novel heuristic, which we call weighted randomized combination, performs better than previously described algorithms for solving the maximum coverage degenerate primer design problem. We previously used DegePrime to design a broad-taxonomic-range primer pair that targets the bacterial V3-V4 region (341F-805R) (D. P. Herlemann, M. Labrenz, K. Jurgens, S. Bertilsson, J. J. Waniek, and A. F. Andersson, ISME J. 5:1571–1579, 2011, http://dx.doi.org/10.1038/ismej.2011.41), and here we use the program to significantly increase the coverage of a primer pair (515F-806R) widely used for Illumina-based surveys of bacterial and archaeal diversity. By comparison with shotgun metagenomics, we show that the primers give an accurate representation of microbial diversity in natural samples. PMID:24928874

  11. Effect of storage conditions on the microbial ecology and biochemical stability of cell wall components in brewers' spent grain.

    PubMed

    Robertson, James A; I'Anson, Kerry J A; Brocklehurst, Tim F; Faulds, Craig B; Waldron, Keith W

    2010-06-23

    The composition of brewers' spent grain (BSG) makes it susceptible to microbial attack and chemical deterioration. This can constrain its appeal as an industrial feedstock. The current study has monitored the effects of BSG storage as fresh material (20 degrees C), refrigerated and autoclaved, measured against frozen material in relation to microbial proliferation and modification to plant cell wall polysaccharides and component phenolic acids. At 20 degrees C there was a rapid colonization by microbes and an associated loss of components from BSG. Refrigeration gave a similar but lower level response. When stored frozen, BSG showed no changes in composition but autoclaving resulted in a solubilization of polysaccharides and associated phenolics. Changes were associated with the temperature profile determined during autoclaving and were also partially due to the breakdown of residual starch. Losses of highly branched arabinoxylan (AX) and the related decrease in ferulic acid cross-linking were also found. The results confirm the need for storage stabilization of BSG and demonstrate that the methods selected for stabilization can themselves lead to a substantial modification to BSG.

  12. High-Throughput Sequencing and Metagenomics: Moving Forward in the Culture-Independent Analysis of Food Microbial Ecology

    PubMed Central

    2013-01-01

    Following recent trends in environmental microbiology, food microbiology has benefited from the advances in molecular biology and adopted novel strategies to detect, identify, and monitor microbes in food. An in-depth study of the microbial diversity in food can now be achieved by using high-throughput sequencing (HTS) approaches after direct nucleic acid extraction from the sample to be studied. In this review, the workflow of applying culture-independent HTS to food matrices is described. The current scenario and future perspectives of HTS uses to study food microbiota are presented, and the decision-making process leading to the best choice of working conditions to fulfill the specific needs of food research is described. PMID:23475615

  13. High-throughput sequencing and metagenomics: moving forward in the culture-independent analysis of food microbial ecology.

    PubMed

    Ercolini, Danilo

    2013-05-01

    Following recent trends in environmental microbiology, food microbiology has benefited from the advances in molecular biology and adopted novel strategies to detect, identify, and monitor microbes in food. An in-depth study of the microbial diversity in food can now be achieved by using high-throughput sequencing (HTS) approaches after direct nucleic acid extraction from the sample to be studied. In this review, the workflow of applying culture-independent HTS to food matrices is described. The current scenario and future perspectives of HTS uses to study food microbiota are presented, and the decision-making process leading to the best choice of working conditions to fulfill the specific needs of food research is described.

  14. A synthetic ecology perspective: How well does behavior of model organisms in the laboratory predict microbial activities in natural habitats?

    DOE PAGESBeta

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

    2016-06-15

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

  15. Phototrophs in high-iron-concentration microbial mats: physiological ecology of phototrophs in an iron-depositing hot spring

    NASA Technical Reports Server (NTRS)

    Pierson, B. K.; Parenteau, M. N.; Griffin, B. M.

    1999-01-01

    At Chocolate Pots Hot Springs in Yellowstone National Park the source waters have a pH near neutral, contain high concentrations of reduced iron, and lack sulfide. An iron formation that is associated with cyanobacterial mats is actively deposited. The uptake of [(14)C]bicarbonate was used to assess the impact of ferrous iron on photosynthesis in this environment. Photoautotrophy in some of the mats was stimulated by ferrous iron (1.0 mM). Microelectrodes were used to determine the impact of photosynthetic activity on the oxygen content and the pH in the mat and sediment microenvironments. Photosynthesis increased the oxygen concentration to 200% of air saturation levels in the top millimeter of the mats. The oxygen concentration decreased with depth and in the dark. Light-dependent increases in pH were observed. The penetration of light in the mats and in the sediments was determined. Visible radiation was rapidly attenuated in the top 2 mm of the iron-rich mats. Near-infrared radiation penetrated deeper. Iron was totally oxidized in the top few millimeters, but reduced iron was detected at greater depths. By increasing the pH and the oxygen concentration in the surface sediments, the cyanobacteria could potentially increase the rate of iron oxidation in situ. This high-iron-content hot spring provides a suitable model for studying the interactions of microbial photosynthesis and iron deposition and the role of photosynthesis in microbial iron cycling. This model may help clarify the potential role of photosynthesis in the deposition of Precambrian banded iron formations.

  16. Phototrophs in High-Iron-Concentration Microbial Mats: Physiological Ecology of Phototrophs in an Iron-Depositing Hot Spring

    PubMed Central

    Pierson, B. K.; Parenteau, M. N.; Griffin, B. M.

    1999-01-01

    At Chocolate Pots Hot Springs in Yellowstone National Park the source waters have a pH near neutral, contain high concentrations of reduced iron, and lack sulfide. An iron formation that is associated with cyanobacterial mats is actively deposited. The uptake of [14C]bicarbonate was used to assess the impact of ferrous iron on photosynthesis in this environment. Photoautotrophy in some of the mats was stimulated by ferrous iron (1.0 mM). Microelectrodes were used to determine the impact of photosynthetic activity on the oxygen content and the pH in the mat and sediment microenvironments. Photosynthesis increased the oxygen concentration to 200% of air saturation levels in the top millimeter of the mats. The oxygen concentration decreased with depth and in the dark. Light-dependent increases in pH were observed. The penetration of light in the mats and in the sediments was determined. Visible radiation was rapidly attenuated in the top 2 mm of the iron-rich mats. Near-infrared radiation penetrated deeper. Iron was totally oxidized in the top few millimeters, but reduced iron was detected at greater depths. By increasing the pH and the oxygen concentration in the surface sediments, the cyanobacteria could potentially increase the rate of iron oxidation in situ. This high-iron-content hot spring provides a suitable model for studying the interactions of microbial photosynthesis and iron deposition and the role of photosynthesis in microbial iron cycling. This model may help clarify the potential role of photosynthesis in the deposition of Precambrian banded iron formations. PMID:10584006

  17. Phototrophs in high-iron-concentration microbial mats: physiological ecology of phototrophs in an iron-depositing hot spring.

    PubMed

    Pierson, B K; Parenteau, M N; Griffin, B M

    1999-12-01

    At Chocolate Pots Hot Springs in Yellowstone National Park the source waters have a pH near neutral, contain high concentrations of reduced iron, and lack sulfide. An iron formation that is associated with cyanobacterial mats is actively deposited. The uptake of [(14)C]bicarbonate was used to assess the impact of ferrous iron on photosynthesis in this environment. Photoautotrophy in some of the mats was stimulated by ferrous iron (1.0 mM). Microelectrodes were used to determine the impact of photosynthetic activity on the oxygen content and the pH in the mat and sediment microenvironments. Photosynthesis increased the oxygen concentration to 200% of air saturation levels in the top millimeter of the mats. The oxygen concentration decreased with depth and in the dark. Light-dependent increases in pH were observed. The penetration of light in the mats and in the sediments was determined. Visible radiation was rapidly attenuated in the top 2 mm of the iron-rich mats. Near-infrared radiation penetrated deeper. Iron was totally oxidized in the top few millimeters, but reduced iron was detected at greater depths. By increasing the pH and the oxygen concentration in the surface sediments, the cyanobacteria could potentially increase the rate of iron oxidation in situ. This high-iron-content hot spring provides a suitable model for studying the interactions of microbial photosynthesis and iron deposition and the role of photosynthesis in microbial iron cycling. This model may help clarify the potential role of photosynthesis in the deposition of Precambrian banded iron formations.

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

    PubMed Central

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

    2016-01-01

    In this perspective article, we question how well model organisms, the ones that are easy to cultivate in the laboratory and that show robust growth and biomass accumulation, reflect the dynamics and interactions of microbial communities observed in nature. Today’s -omics toolbox allows assessing the genomic potential of microbes in natural environments in a high-throughput fashion and at a strain-level resolution. However, understanding of the details of microbial activities and of the mechanistic bases of community function still requires experimental validation in simplified and fully controlled systems such as synthetic communities. We have studied methane utilization in Lake Washington sediment for a few decades and have identified a number of species genetically equipped for this activity. We have also identified co-occurring satellite species that appear to form functional communities together with the methanotrophs. Here, we compare experimental findings from manipulation of natural communities involved in metabolism of methane in this niche with findings from manipulation of synthetic communities assembled in the laboratory of species originating from the same study site, from very simple (two-species) to rather complex (50-species) synthetic communities. We observe some common trends in community dynamics between the two types of communities, toward representation of specific functional guilds. However, we also identify strong discrepancies between the dominant methane oxidizers in synthetic communities compared to natural communities, under similar incubation conditions. These findings highlight the challenges that exist in using the synthetic community approach to modeling dynamics and species interactions in natural communities. PMID:27379075

  19. Soil Ecology

    NASA Astrophysics Data System (ADS)

    Killham, Ken

    1994-04-01

    Soil Ecology is designed to meet the increasing challenge faced by today's environmental scientists, ecologists, agriculturalists, and biotechnologists for an integrated approach to soil ecology. It emphasizes the interrelations among plants, animals, and microbes, by first establishing the fundamental physical and chemical properties of the soil habitat and then functionally characterizing the major components of the soil biota and some of their most important interactions. The fundamental principles underpinning soil ecology are established and this then enables an integrated approach to explore and understand the processes of soil nutrient (carbon, nitrogen, and phosphorus) cycling and the ecology of extreme soil conditions such as soil-water stress. Two of the most topical aspects of applied soil ecology are then selected. First, the ecology of soil pollution is examined, focusing on acid deposition and radionuclide pollution. Second, manipulation of soil ecology through biotechnology is discussed, illustrating the use of pesticides and microbial inocula in soils and pointing toward the future by considering the impact of genetically modified inocula on soil ecology.

  20. Perinatal and neonatal manipulation of the intestinal microbiome: a note of caution.

    PubMed

    Neu, Josef

    2007-06-01

    As we learn more about interactions between microbes and the developing gastrointestinal (GI) tract, it is becoming clear that the establishment of the intestinal "microbiome" shortly after birth plays a critical role in the early origins of health and disease. Nutrition, mode of delivery, the use of maternal or postnatal antibiotics, and pre- and probiotics are factors that may alter the microbial ecology and affect lifelong gene expression. Because the neonatal period is a critical period of development when microbes become established in the GI tract, the long-term effects of manipulations of the GI microbial ecology during this time are more amplified than the effects of later manipulations. In this paper, recent research findings are reviewed with the intent of providing information about the benefits of early manipulation of the GI microbiome, but also to give a warning about its indiscriminant manipulation during the perinatal and neonatal time periods. PMID:17605304

  1. Marine microbial ecology in the sub-Antarctic Zone: Rates of bacterial and phytoplankton growth and grazing by heterotrophic protists

    NASA Astrophysics Data System (ADS)

    Pearce, Imojen; Davidson, Andrew T.; Thomson, Paul G.; Wright, Simon; van den Enden, Rick

    2011-11-01

    The sub-Antarctic zone (SAZ) of the Southern Ocean is considered one of the largest sinks for atmospheric CO 2 and as such is an important region for climate change research. To determine the importance of micro- and nano-heterotrophs in controlling microbial abundance within this region, we determined microbial standing stocks and rates of herbivory and bacterivory in relation to changes in the water masses south of Tasmania. The SAZ-Sense ('Sensitivity of the sub-Antarctic zone to environmental change') cruise traversed the SAZ during mid-late austral summer and focussed on process stations to the southeast (45°S, 153°E) and southwest (46°S, 140°E) of Tasmania and at the Polar Front (54°S, 147°E). Growth and grazing mortality of phytoplankton and bacteria were estimated by the grazing dilution technique using seawater from 10 m depth at 15 sites along the survey, along with concentrations of heterotrophic nanoflagellates (HNF), microzooplankton, bacteria, cyanobacteria and size fractionated (pico-, nano- and micro-sized) chlorophyll a (Chl a). Rates of herbivory ranged from 0.12 to 1.39 d -1 and were highest in the north-eastern SAZ (NE-SAZ) where concentrations of prey (as indicated by Chl a) and microzooplankton were also highest. Rates of herbivory were correlated with total rates of phytoplankton growth, bacterial growth and concentrations of microzooplankton. On average 82%, 67% and 42% primary production d -1 was consumed by microzooplankton and HNF at process stations in the north-western SAZ (NW-SAZ), NE-SAZ and polar frontal zone (PFZ), respectively. In the NW-SAZ, grazing pressure was highest on the pico-sized Chl a fraction, whereas in the NE-SAZ, grazing pressure was more evenly distributed across all three size fractions of Chl a. Bacterivory removed 77%, 93% and 39% of bacterial production d -1 in the NW-SAZ, NE-SAZ and PFZ, respectively, and rates of bacterivory ranged from 0.12 to 1.03 d -1. Rates of bacterivory were highest in the NE

  2. Oral exposure to environmental pollutant benzo[a]pyrene impacts the intestinal epithelium and induces gut microbial shifts in murine model

    PubMed Central

    Ribière, Céline; Peyret, Pierre; Parisot, Nicolas; Darcha, Claude; Déchelotte, Pierre J.; Barnich, Nicolas; Peyretaillade, Eric; Boucher, Delphine

    2016-01-01

    Gut microbiota dysbiosis are associated with a wide range of human diseases, including inflammatory bowel diseases. The physiopathology of these diseases has multifactorial aetiology in which environmental factors, particularly pollution could play a crucial role. Among the different pollutants listed, Polycyclic Aromatic Hydrocarbons (PAHs) are subject to increased monitoring due to their wide distribution and high toxicity on Humans. Here, we used 16S rRNA gene sequencing to investigate the impact of benzo[a]pyrene (BaP, most toxic PAH) oral exposure on the faecal and intestinal mucosa-associated bacteria in C57BL/6 mice. Intestinal inflammation was also evaluated by histological observations. BaP oral exposure significantly altered the composition and the abundance of the gut microbiota and led to moderate inflammation in ileal and colonic mucosa. More severe lesions were observed in ileal segment. Shifts in gut microbiota associated with moderate inflammatory signs in intestinal mucosa would suggest the establishment of a pro-inflammatory intestinal environment following BaP oral exposure. Therefore, under conditions of genetic susceptibility and in association with other environmental factors, exposure to this pollutant could trigger and/or accelerate the development of inflammatory pathologies. PMID:27503127

  3. Oral exposure to environmental pollutant benzo[a]pyrene impacts the intestinal epithelium and induces gut microbial shifts in murine model.

    PubMed

    Ribière, Céline; Peyret, Pierre; Parisot, Nicolas; Darcha, Claude; Déchelotte, Pierre J; Barnich, Nicolas; Peyretaillade, Eric; Boucher, Delphine

    2016-01-01

    Gut microbiota dysbiosis are associated with a wide range of human diseases, including inflammatory bowel diseases. The physiopathology of these diseases has multifactorial aetiology in which environmental factors, particularly pollution could play a crucial role. Among the different pollutants listed, Polycyclic Aromatic Hydrocarbons (PAHs) are subject to increased monitoring due to their wide distribution and high toxicity on Humans. Here, we used 16S rRNA gene sequencing to investigate the impact of benzo[a]pyrene (BaP, most toxic PAH) oral exposure on the faecal and intestinal mucosa-associated bacteria in C57BL/6 mice. Intestinal inflammation was also evaluated by histological observations. BaP oral exposure significantly altered the composition and the abundance of the gut microbiota and led to moderate inflammation in ileal and colonic mucosa. More severe lesions were observed in ileal segment. Shifts in gut microbiota associated with moderate inflammatory signs in intestinal mucosa would suggest the establishment of a pro-inflammatory intestinal environment following BaP oral exposure. Therefore, under conditions of genetic susceptibility and in association with other environmental factors, exposure to this pollutant could trigger and/or accelerate the development of inflammatory pathologies. PMID:27503127

  4. Discovery of new protein families and functions: new challenges in functional metagenomics for biotechnologies and microbial ecology

    PubMed Central

    Ufarté, Lisa; Potocki-Veronese, Gabrielle; Laville, Élisabeth

    2015-01-01

    The rapid expansion of new sequencing technologies has enabled large-scale functional exploration of numerous microbial ecosystems, by establishing catalogs of functional genes and by comparing their prevalence in various microbiota. However, sequence similarity does not necessarily reflect functional conservation, since just a few modifications in a gene sequence can have a strong impact on the activity and the specificity of the corresponding enzyme or the recognition for a sensor. Similarly, some microorganisms harbor certain identified functions yet do not have the expected related genes in their genome. Finally, there are simply too many protein families whose function is not yet known, even though they are highly abundant in certain ecosystems. In this context, the discovery of new protein functions, using either sequence-based or activity-based approaches, is of crucial importance for the discovery of new enzymes and for improving the quality of annotation in public databases. This paper lists and explores the latest advances in this field, along with the challenges to be addressed, particularly where microfluidic technologies are concerned. PMID:26097471

  5. Discovery of new protein families and functions: new challenges in functional metagenomics for biotechnologies and microbial ecology.

    PubMed

    Ufarté, Lisa; Potocki-Veronese, Gabrielle; Laville, Élisabeth

    2015-01-01

    The rapid expansion of new sequencing technologies has enabled large-scale functional exploration of numerous microbial ecosystems, by establishing catalogs of functional genes and by comparing their prevalence in various microbiota. However, sequence similarity does not necessarily reflect functional conservation, since just a few modifications in a gene sequence can have a strong impact on the activity and the specificity of the corresponding enzyme or the recognition for a sensor. Similarly, some microorganisms harbor certain identified functions yet do not have the expected related genes in their genome. Finally, there are simply too many protein families whose function is not yet known, even though they are highly abundant in certain ecosystems. In this context, the discovery of new protein functions, using either sequence-based or activity-based approaches, is of crucial importance for the discovery of new enzymes and for improving the quality of annotation in public databases. This paper lists and explores the latest advances in this field, along with the challenges to be addressed, particularly where microfluidic technologies are concerned.

  6. Effects of pH and ORP on microbial ecology and kinetics for hydrogen production in continuously dark fermentation.

    PubMed

    Song, Jiaxiu; An, Dong; Ren, Nanqi; Zhang, Yongming; Chen, Ying

    2011-12-01

    The microbial structure and kinetic characteristics of the hydrogen producing strains in two fermentative continuous stirred-tank reactors (CSTRs) were studied by controlling pH and oxidation and reduction potential (ORP). The fluorescence in situ hybridization (FISH) tests were conducted to investigate the fermentative performance of Clostridium histolyticum (C. histolyticum), Clostridium lituseburense (C. lituseburense) and Enterobacteriaceae. The experimental results showed that in ethanol-type reactor 1#, the relative abundance of the strains was 48%, 30% and 22%. Comparatively, the relative abundance in butyric acid-type reactor 2# was 24%, 55% and 19% with butyric acids and hydrogen as the main products. The kinetic results indicated that the hydrogen yield coefficients YP/X in both reactors were 8.357 and 5.951 l-H2/g, while the coefficients of the cellular yield were 0.0268 and 0.0350 g-Cell/g, respectively. At the same biomass, the hydrogen yield in ethanol-type reactors was more than that in butyric acid reactors. However, the cellular synthesis rate in ethanol-type reactors was low when the same carbon source was used.

  7. Microbial-induced meprin β cleavage in MUC2 mucin and a functional CFTR channel are required to release anchored small intestinal mucus

    PubMed Central

    Schütte, André; Ermund, Anna; Becker-Pauly, Christoph; Johansson, Malin E. V.; Rodriguez-Pineiro, Ana M.; Bäckhed, Fredrik; Müller, Stefan; Lottaz, Daniel; Bond, Judith S.; Hansson, Gunnar C.

    2014-01-01

    The mucus that covers and protects the epithelium of the intestine is built around its major structural component, the gel-forming MUC2 mucin. The gel-forming mucins have traditionally been assumed to be secreted as nonattached. The colon has a two-layered mucus system where the inner mucus is attached to the epithelium, whereas the small intestine normally has a nonattached mucus. However, the mucus of the small intestine of meprin β-deficient mice was now found to be attached. Meprin β is an endogenous zinc-dependent metalloprotease now shown to cleave the N-terminal region of the MUC2 mucin at two specific sites. When recombinant meprin β was added to the attached mucus of meprin β-deficient mice, the mucus was detached from the epithelium. Similar to meprin β-deficient mice, germ-free mice have attached mucus as they did not shed the membrane-anchored meprin β into the luminal mucus. The ileal mucus of cystic fibrosis (CF) mice with a nonfunctional cystic fibrosis transmembrane conductance regulator (CFTR) channel was recently shown to be attached to the epithelium. Addition of recombinant meprin β to CF mucus did not release the mucus, but further addition of bicarbonate rendered the CF mucus normal, suggesting that MUC2 unfolding exposed the meprin β cleavage sites. Mucus is thus secreted attached to the goblet cells and requires an enzyme, meprin β in the small intestine, to be detached and released into the intestinal lumen. This process regulates mucus properties, can be triggered by bacterial contact, and is nonfunctional in CF due to poor mucin unfolding. PMID:25114233

  8. Intestinal Malrotation

    MedlinePlus

    ... the intestines don't position themselves normally during fetal development and aren't attached inside properly as a result. The exact reason this occurs is unknown. When a fetus develops in the womb, the intestines start out ...

  9. Intestine Transplant

    MedlinePlus

    ... intestine segment, most intestine transplants involve a whole organ from a deceased donor. In addition, most intestine transplants are performed in ... blood before surgery. I am looking for ... allocation About UNOS Being a living donor Calculator - CPRA Calculator - KDPI Calculator - LAS Calculator - MELD ...

  10. Microbial-algal community changes during the latest Permian ecological crisis: Evidence from lipid biomarkers at Cili, South China

    NASA Astrophysics Data System (ADS)

    Luo, Genming; Wang, Yongbiao; Grice, Kliti; Kershaw, Steve; Algeo, Thomas J.; Ruan, Xiaoyan; Yang, Hao; Jia, Chengling; Xie, Shucheng

    2013-06-01

    Microbialites flourished globally immediately following the latest Permian mass extinction. In this study, lipid biomarker records were analyzed in the Cili section (Hunan Province, South China) in order to determine the types of microbes involved in microbialite formation and their response to contemporaneous environmental changes. Various biomarkers were identified in the aliphatic and aromatic fractions using gas chromatography (GC) and GC-mass spectrometry (GC-MS). Low abundance of steranes in the microbialite layer suggests that it did not contain large amounts of algae, in striking contrast to the abundant algal fossils and algal-derived steranes present in the underlying (pre-crisis) skeletal limestone. Although pristine/phytane (Pr/Ph) ratios increased in the microbialite layer, covariation of Pr/Ph with the ratio of low- to high-molecular-weight n-alkanes (C20 -/C20 +) suggests that the former proxy was controlled by microbial (particularly cyanobacterial) inputs rather than by redox conditions. The microbialite also yielded low ratios of hopanes to short-chain n-alkanes (HP/Lalk) and high abundances of C21n-alkylcyclohexane, indicating that, in addition to cyanobacteria, anaerobic bacteria, archaea, and possibly acritarchs flourished in the aftermath of the marine extinction event. The upper part of the thinly bedded micritic limestone overlying the microbialite exhibits a bimodal distribution of n-alkanes as well as increased abundances of extended tricyclic terpanes and steranes, suggesting a return of habitable shallow-marine conditions for eukaryotic algae several hundred thousand years after the latest Permian mass extinction. Increases in the dibenzofuran ratio (i.e., DBF/(DBF + DBT + F)) and in the coronene to phenanthrene ratio (Cor/P) in the skeletal limestone immediately below the microbialite are evidence of enhanced soil erosion rates and wildfire intensity, marking the collapse of terrestrial ecosystems. The terrestrial crisis thus slightly

  11. Microbial Amyloids Induce Interleukin 17A (IL-17A) and IL-22 Responses via Toll-Like Receptor 2 Activation in the Intestinal Mucosa

    PubMed Central

    Nishimori, Jessalyn H.; Newman, Tiffanny N.; Oppong, Gertrude O.; Rapsinski, Glenn J.; Yen, Jui-Hung; Biesecker, Steven G.; Wilson, R. Paul; Butler, Brian P.; Winter, Maria G.; Tsolis, Renee M.; Ganea, Doina

    2012-01-01

    The Toll-like receptor 2 (TLR2)/TLR1 receptor complex responds to amyloid fibrils, a common component of biofilm material produced by members of the phyla Firmicutes, Bacteroidetes, and Proteobacteria. To determine whether this TLR2/TLR1 ligand stimulates inflammatory responses when bacteria enter intestinal tissue, we investigated whether expression of curli amyloid fibrils by the invasive enteric pathogen Salmonella enterica serotype Typhimurium contributes to T helper 1 and T helper 17 responses by measuring cytokine production in the mouse colitis model. A csgBA mutant, deficient in curli production, elicited decreased expression of interleukin 17A (IL-17A) and IL-22 in the cecal mucosa compared to the S. Typhimurium wild type. In TLR2-deficient mice, IL-17A and IL-22 expression was blunted during S. Typhimurium infection, suggesting that activation of the TLR2 signaling pathway contributes to the expression of these cytokines. T cells incubated with supernatants from bone marrow-derived dendritic cells (BMDCs) treated with curli fibrils released IL-17A in a TLR2-dependent manner in vitro. Lower levels of IL-6 and IL-23 production were detected in the supernatants of the TLR2-deficient BMDCs treated with curli fibrils. Consistent with this, three distinct T-cell populations—CD4+ T helper cells, cytotoxic CD8+ T cells, and γδ T cells—produced IL-17A in response to curli fibrils in the intestinal mucosa during S. Typhimurium infection. Notably, decreased IL-6 expression by the dendritic cells and decreased IL-23 expression by the dendritic cells and macrophages were observed in the cecal mucosa of mice infected with the curli mutant. We conclude that TLR2 recognition of bacterial amyloid fibrils in the intestinal mucosa represents a novel mechanism of immunoregulation, which contributes to the generation of inflammatory responses, including production of IL-17A and IL-22, in response to bacterial entry into the intestinal mucosa. PMID:23027540

  12. Functional Molecular Ecological Networks

    PubMed Central

    Zhou, Jizhong; Deng, Ye; Luo, Feng; He, Zhili; Tu, Qichao; Zhi, Xiaoyang

    2010-01-01

    Biodiversity and its responses to environmental changes are central issues in ecology and for society. Almost all microbial biodiversity research focuses on “species” richness and abundance but not on their interactions. Although a network approach is powerful in describing ecological interactions among species, defining the network structure in a microbial community is a great challenge. Also, although the stimulating effects of elevated CO2 (eCO2) on plant growth and primary productivity are well established, its influences on belowground microbial communities, especially microbial interactions, are poorly understood. Here, a random matrix theory (RMT)-based conceptual framework for identifying functional molecular ecological networks was developed with the high-throughput functional gene array hybridization data of soil microbial communities in a long-term grassland FACE (free air, CO2 enrichment) experiment. Our results indicate that RMT is powerful in identifying functional molecular ecological networks in microbial communities. Both functional molecular ecological networks under eCO2 and ambient CO2 (aCO2) possessed the general characteristics of complex systems such as scale free, small world, modular, and hierarchical. However, the topological structures of the functional molecular ecological networks are distinctly different between eCO2 and aCO2, at the levels of the entire communities, individual functional gene categories/groups, and functional genes/sequences, suggesting that eCO2 dramatically altered the network interactions among different microbial functional genes/populations. Such a shift in network structure is also significantly correlated with soil geochemical variables. In short, elucidating network interactions in microbial communities and their responses to environmental changes is fundamentally important for research in microbial ecology, systems microbiology, and global change. PMID:20941329

  13. A new arhythmacanthid species (Acanthocephala) in the intestine of Symphurus plagiusa and Ciclopsetta chittendeni from the coast of Campeche, Mexico, with ecological and histopathological observations.

    PubMed

    Santana-Piñeros, Ana María; Cruz-Quintana, Yanis; Centeno-Chalé, Oscar Arturo; Vidal-Martínez, Victor M

    2013-10-01

    A new species of Acanthocephaloides was recovered in the intestine of Symphurus plagiusa, the blackcheek tonguefish, and Cyclopsetta chittendeni, the Mexican flounder, from the Campeche coast, Mexico. The new species is characterized by having proboscis hooks arranged in 14 to 16 longitudinal rows, with 6-7 rooted hooks per row, a trunk covered with small cuticular spines (except in the zone of gonopore or bursa), a bursa without sensory structures, and the relative position of male post-equatorial reproductive system. The prevalence of Acanthocephaloides plagiusae n. sp. from S. plagiusa was low (0-7.3%) from July to October and high (29.4-40%) in November, January, and March. Similarly, the prevalence of A. plagiusae n. sp. from Cyclopsetta chittendeni was low (1.7%) in July and high (5.8%) March. Both hosts exhibited low (0.1-3.4) mean abundance. The variation in prevalence could be explained by the seasonal freshwater discharge from rivers, which affects the dispersal of parasites and the distribution of the host. Pathology changes, such as inflammation, loss of intestinal folds, increased mucous and rodlet cells, and detachment of intestinal epithelium, were associated with the proboscis hooks and spiny surface of A. plagiusae. This is the first record of an Acanthocephaloides species from a Mexican coastal zone.

  14. Terpenes tell different tales at different scales: glimpses into the Chemical Ecology of conifer - bark beetle - microbial interactions.

    PubMed

    Raffa, Kenneth F

    2014-01-01

    , biochemical time), relationships among inducible and constitutive defenses, population dynamics, and plastic host-selection behavior (stand level, ecological time), and climate-driven range expansion of a native eruptive species into semi-naïve and potentially naïve habitats (geographical level, evolutionary time). I approach this problem by focusing primarily on one chemical group, terpenes, by emphasizing the curvilinear and threshold-structured basis of most underlying relationships, and by focusing on the system's feedback structure, which can either buffer or amplify relationships across scales.

  15. Antibiotic Resistance in Animal-waste-impacted Farm Soil: From Molecular Mechanisms to Microbial Evolution and Ecology

    NASA Astrophysics Data System (ADS)

    You, Y.; Ward, M. J.; Hilpert, M.

    2012-12-01

    Antibiotic resistance is a growing public health problem worldwide and the routine use of antibiotics in industrial animal production has sparked debate on whether this practice might constitute an environmental and public health concern. At a broiler farm, electromagnetic induction (EMI) surveying assisted soil sampling from a chicken-waste-impacted site and a marginally affected site. Consistent with the EMI survey, disparity existed between the two sites with regard to soil pH, tetracycline resistance (TcR) levels among heterotrophic culturable soil bacteria, and the incidence/prevalence of a number of tet and erm genes in the soils. No significant difference was observed in these aspects between the marginally affected site and several sites in a regional state forest that has not been in agricultural use for decades. Shortly after our sampling, the farm closed down and all the waste was removed. This unique change in situation offered us an unusual opportunity to examine the reversibility of any impact of the chicken waste on the soil microbial community. Two years after the event, several antibiotic resistance genes (ARGs) were still detected in the waste-impacted soil, and quantitative real-time PCR (qPCR) data showed that their relative abundance remained at substantial levels. A mobilizable tet(L)-carrying plasmid, pSU1, was identified in several chicken-waste-exposed soil bacteria of three different genera. Quantification of the plasmid's mobilization gene suggested that pSU1 had contributed to the prevalence and persistence of tet(L) in the waste-impacted soil. A second mobilizable tet(L)-carrying plasmid, pBSDMV9, isolated from the same soil, contained a region with 98.8% nucleotide identity to pSU1. The mosaic structure of the plasmids and the highly conserved nature of the tet(L) genes suggested that plasmid rearrangement favoring the acquisition of tet(L) may have occurred in the soil relatively recently. Additionally, in one chicken

  16. 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.

  17. Altitudinal Contrasts in Drought-Driven Aeolian Microbial Inputs to Montane Soil Ecology: Impacts of a 500-Year Drought in the Sierra Nevada, California

    NASA Astrophysics Data System (ADS)

    Aronson, E. L.; Carey, C.; Riebe, C. S.; Aciego, S.; Hart, S. C.

    2014-12-01

    Mounting evidence shows that California is currently experiencing the most severe drought since 1580, and it is likely that extreme droughts will become more common as the climate changes. Any drought - particularly one of this magnitude - can elevate dust transport, from fallow croplands and bare natural ecosystems, to sometimes distant locations. The transported dust may bring nutrients and microorganisms, with unknown, but potentially transformational, impacts on the ecosystems where dust is deposited. In this project, we are measuring the mass, provenance (using isotopic chemistry), chemical makeup, and microbial composition of dust transported to the Sierra Nevada mountain range. Dust is being collected at three sites along an elevational gradient in the Southern Sierra Critical Zone Observatory (SSCZO), ranging from 400 m to 2000 m elevation. At each site, dust has been collected monthly in Summer 2014 from passive dust collectors and from filters (1 um pore size) on the eddy covariance tower active CO2 samplers. To complement dust collection, soil samples (10 cm depth) have been collected within the footprint of the towers. Dust fluxes were found to be highest at the 2000 meter-high site, with a maximum of 231 mg dust collected in July 2014. The lowest dust fluxes were found at the medium elevation site, at 1100 m, with 21 mg dust in July. The provenance of dust samples will be determined using radiogenic strontium (Sr) and neodymium (Nd) isotopic tracers. Nutrients and microbial composition of dust and soil samples will also be analyzed. This approach will allow us to identify the effects of mega-droughts on i) dust-related contributions to the geobiology and biogeochemistry of soils and ecosystems, ii) the role of local versus distant dust sources of microorganisms, including bacteria, archaea and fungi, and of nutrients to the Sierra Nevada, and iii) the role of elevation in determining the ecological effects of mega-drought-induced dust transport. In the

  18. Synthetic Small Intestinal Scaffolds for Improved Studies of Intestinal Differentiation

    PubMed Central

    Costello, Cait M.; Hongpeng, Jia; Shaffiey, Shahab; Yu, Jiajie; Jain, Nina K.; Hackam, David

    2014-01-01

    In vitro intestinal models can provide new insights into small intestinal function, including cellular growth and proliferation mechanisms, drug absorption capabilities, and host-microbial interactions. These models are typically formed with cells cultured on 2D scaffolds or transwell inserts, but it is widely understood that epithelial cells cultured in 3D environments exhibit different phenotypes that are more reflective of native tissue. Our focus was to develop a porous, synthetic 3D tissue scaffold with villous features that could support the culture of epithelial cell types to mimic the natural microenvironment of the small intestine. We demonstrated that our scaffold could support the co-culture of Caco-2 cells with a mucus-producing cell line, HT29-MTX, as well as small intestinal crypts from mice for extended periods. By recreating the surface topography with accurately sized intestinal villi, we enable cellular differentiation along the villous axis in a similar manner to native intestines. In addition, we show that the biochemical microenvironments of the intestine can be further simulated via a combination of apical and basolateral feeding of intestinal cell types cultured on the 3D models. PMID:24390638

  19. Comparative microbial ecology of the water column of an extreme acidic pit lake, Nuestra Señora del Carmen, and the Río Tinto basin (Iberian Pyrite Belt).

    PubMed

    González-Toril, Elena; Santofimia, Esther; López-Pamo, Enrique; García-Moyano, Antonio; Aguilera, Ángeles; Amils, Ricardo

    2014-12-01

    The Iberian Pyrite Belt, located in Southwestern Spain, represents one of the world's largest accumulations of mine wastes and acid mine drainages. This study reports the comparative microbial ecology of the water column of Nuestra Señora del Carmen acid pit lake with the extreme acidic Río Tinto basin. The canonical correspondence analysis identified members of the Leptospirillum, Acidiphilium, Metallibacterium, Acidithiobacillus, Ferrimicrobium and Acidisphaera genera as the most representative microorganisms of both ecosystems. The presence of archaeal members is scarce in both systems. Only sequences clustering with the Thermoplasmata have been retrieved in the bottom layer of Nuestra Señora del Carmen and one station of Río Tinto. Although the photosynthetically active radiation values measured in this lake upper layer were low, they were sufficient to activate photosynthesis in acidophilic microorganisms. All identified photosynthetic microorganisms in Nuestra Señora del Carmen (members of the Chlamydomonas, Zygnemopsis and Klebsormidium genera) are major members of the photosynthetic eukaryotic community characterized in Río Tinto basin. This study demonstrates a close relationship between the microbial diversity of Nuestra Señora del Carmen pit lake and the diversity detected in the Río Tinto basin, which underlain the influence of the shared mineral substrates in the microbial ecology of these ecosystems. PMID:26421738

  20. Integrating ecology into biotechnology.

    PubMed

    McMahon, Katherine D; Martin, Hector Garcia; Hugenholtz, Philip

    2007-06-01

    New high-throughput culture-independent molecular tools are allowing the scientific community to characterize and understand the microbial communities underpinning environmental biotechnology processes in unprecedented ways. By creatively leveraging these new data sources, microbial ecology has the potential to transition from a purely descriptive to a predictive framework, in which ecological principles are integrated and exploited to engineer systems that are