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

PubMed

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

2016-01-01

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

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.

Evidence for environmental and ecological selection in a microbe with no geographic limits to gene flow.

PubMed

Whittaker, Kerry A; Rynearson, Tatiana A

2017-03-07

The ability for organisms to disperse throughout their environment is thought to strongly influence population structure and thus evolution of diversity within species. A decades-long debate surrounds processes that generate and support high microbial diversity, particularly in the ocean. The debate concerns whether diversification occurs primarily through geographic partitioning (where distance limits gene flow) or through environmental selection, and remains unresolved due to lack of empirical data. Here we show that gene flow in a diatom, an ecologically important eukaryotic microbe, is not limited by global-scale geographic distance. Instead, environmental and ecological selection likely play a more significant role than dispersal in generating and maintaining diversity. We detected significantly diverged populations ( F ST > 0.130) and discovered temporal genetic variability at a single site that was on par with spatial genetic variability observed over distances of 15,000 km. Relatedness among populations was decoupled from geographic distance across the global ocean and instead, correlated significantly with water temperature and whole-community chlorophyll a Correlations with temperature point to the importance of environmental selection in structuring populations. Correlations with whole-community chlorophyll a , a proxy for autotrophic biomass, suggest that ecological selection via interactions with other plankton may generate and maintain population genetic structure in marine microbes despite global-scale dispersal. Here, we provide empirical evidence for global gene flow in a marine eukaryotic microbe, suggesting that everything holds the potential to be everywhere, with environmental and ecological selection rather than geography or dispersal dictating the structure and evolution of diversity over space and time.

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

DOE PAGES

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

2016-02-24

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

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

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

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

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

Genome composition and phylogeny of microbes predict their co-occurrence in the environment

PubMed Central

2017-01-01

The genomic information of microbes is a major determinant of their phenotypic properties, yet it is largely unknown to what extent ecological associations between different species can be explained by their genome composition. To bridge this gap, this study introduces two new genome-wide pairwise measures of microbe-microbe interaction. The first (genome content similarity index) quantifies similarity in genome composition between two microbes, while the second (microbe-microbe functional association index) summarizes the topology of a protein functional association network built for a given pair of microbes and quantifies the fraction of network edges crossing organismal boundaries. These new indices are then used to predict co-occurrence between reference genomes from two 16S-based ecological datasets, accounting for phylogenetic relatedness of the taxa. Phylogenetic relatedness was found to be a strong predictor of ecological associations between microbes which explains about 10% of variance in co-occurrence data, but genome composition was found to be a strong predictor as well, it explains up to 4% the variance in co-occurrence when all genomic-based indices are used in combination, even after accounting for evolutionary relationships between the species. On their own, the metrics proposed here explain a larger proportion of variance than previously reported more complex methods that rely on metabolic network comparisons. In summary, results of this study indicate that microbial genomes do indeed contain detectable signal of organismal ecology, and the methods described in the paper can be used to improve mechanistic understanding of microbe-microbe interactions. PMID:28152007

Lipopolysaccharides in diazotrophic bacteria.

PubMed

Serrato, Rodrigo V

2014-01-01

Biological nitrogen fixation (BNF) is a process in which the atmospheric nitrogen (N2) is transformed into ammonia (NH3) by a select group of nitrogen-fixing organisms, or diazotrophic bacteria. In order to furnish the biologically useful nitrogen to plants, these bacteria must be in constant molecular communication with their host plants. Some of these molecular plant-microbe interactions are very specific, resulting in a symbiotic relationship between the diazotroph and the host. Others are found between associative diazotrophs and plants, resulting in plant infection and colonization of internal tissues. Independent of the type of ecological interaction, glycans, and glycoconjugates produced by these bacteria play an important role in the molecular communication prior and during colonization. Even though exopolysaccharides (EPS) and lipochitooligosaccharides (LCO) produced by diazotrophic bacteria and released onto the environment have their importance in the microbe-plant interaction, it is the lipopolysaccharides (LPS), anchored on the external membrane of these bacteria, that mediates the direct contact of the diazotroph with the host cells. These molecules are extremely variable among the several species of nitrogen fixing-bacteria, and there are evidences of the mechanisms of infection being closely related to their structure.

Interactive effects of global climate change and pollution on marine microbes: the way ahead.

PubMed

Coelho, Francisco J R C; Santos, Ana L; Coimbra, Joana; Almeida, Adelaide; Cunha, Angela; Cleary, Daniel F R; Calado, Ricardo; Gomes, Newton C M

2013-06-01

Global climate change has the potential to seriously and adversely affect marine ecosystem functioning. Numerous experimental and modeling studies have demonstrated how predicted ocean acidification and increased ultraviolet radiation (UVR) can affect marine microbes. However, researchers have largely ignored interactions between ocean acidification, increased UVR and anthropogenic pollutants in marine environments. Such interactions can alter chemical speciation and the bioavailability of several organic and inorganic pollutants with potentially deleterious effects, such as modifying microbial-mediated detoxification processes. Microbes mediate major biogeochemical cycles, providing fundamental ecosystems services such as environmental detoxification and recovery. It is, therefore, important that we understand how predicted changes to oceanic pH, UVR, and temperature will affect microbial pollutant detoxification processes in marine ecosystems. The intrinsic characteristics of microbes, such as their short generation time, small size, and functional role in biogeochemical cycles combined with recent advances in molecular techniques (e.g., metagenomics and metatranscriptomics) make microbes excellent models to evaluate the consequences of various climate change scenarios on detoxification processes in marine ecosystems. In this review, we highlight the importance of microbial microcosm experiments, coupled with high-resolution molecular biology techniques, to provide a critical experimental framework to start understanding how climate change, anthropogenic pollution, and microbiological interactions may affect marine ecosystems in the future.

Interactive effects of global climate change and pollution on marine microbes: the way ahead

PubMed Central

Coelho, Francisco J R C; Santos, Ana L; Coimbra, Joana; Almeida, Adelaide; Cunha, Ângela; Cleary, Daniel F R; Calado, Ricardo; Gomes, Newton C M

2013-01-01

Global climate change has the potential to seriously and adversely affect marine ecosystem functioning. Numerous experimental and modeling studies have demonstrated how predicted ocean acidification and increased ultraviolet radiation (UVR) can affect marine microbes. However, researchers have largely ignored interactions between ocean acidification, increased UVR and anthropogenic pollutants in marine environments. Such interactions can alter chemical speciation and the bioavailability of several organic and inorganic pollutants with potentially deleterious effects, such as modifying microbial-mediated detoxification processes. Microbes mediate major biogeochemical cycles, providing fundamental ecosystems services such as environmental detoxification and recovery. It is, therefore, important that we understand how predicted changes to oceanic pH, UVR, and temperature will affect microbial pollutant detoxification processes in marine ecosystems. The intrinsic characteristics of microbes, such as their short generation time, small size, and functional role in biogeochemical cycles combined with recent advances in molecular techniques (e.g., metagenomics and metatranscriptomics) make microbes excellent models to evaluate the consequences of various climate change scenarios on detoxification processes in marine ecosystems. In this review, we highlight the importance of microbial microcosm experiments, coupled with high-resolution molecular biology techniques, to provide a critical experimental framework to start understanding how climate change, anthropogenic pollution, and microbiological interactions may affect marine ecosystems in the future. PMID:23789087

Milk bioactives may manipulate microbes to mediate parent–offspring conflict

PubMed Central

Allen-Blevins, Cary R.; Sela, David A.; Hinde, Katie

2015-01-01

Among mammals, milk constituents directly influence the ecology of the infant’s commensal microbiota. The immunological and nutritional impacts of breast milk and microbiota are increasingly well understood; less clear are the consequences for infant behavior. Here, we propose that interactions among bioactives in mother’s milk and microbes in the infant gut contribute to infant behavioral phenotype and, in part, have the potential to mediate parent–offspring conflict. We hypothesize that infant behavior likely varies as a function of their mother’s milk composition interacting with the infant’s neurobiology directly and indirectly through the commensal gut bacteria. In this article, we will explore our hypothesis of a milk-microbiota-brain-behavior dynamic in the context of the coevolution between human milk oligosaccharides, bacteria, the gut–brain axis and behavior. Integrating established features of these systems allows us to generate novel hypotheses to motivate future research and consider potential implications of current and emerging clinical treatments. PMID:25835022

Beyond the standard plate count: genomic views into microbial food ecology

USDA-ARS?s Scientific Manuscript database

Food spoilage is a complex process that involves multiple species with specific niches and metabolic processes; bacterial culturing techniques are the traditional methods for identifying the microbes responsible. These culture-dependent methods may be considered selective, targeting the isolation of...

Compositional Stability of the Bacterial Community in a Climate-Sensitive Sub-Arctic Peatland.

PubMed

Weedon, James T; Kowalchuk, George A; Aerts, Rien; Freriks, Stef; Röling, Wilfred F M; van Bodegom, Peter M

2017-01-01

The climate sensitivity of microbe-mediated soil processes such as carbon and nitrogen cycling offers an interesting case for evaluating the corresponding sensitivity of microbial community composition to environmental change. Better understanding of the degree of linkage between functional and compositional stability would contribute to ongoing efforts to build mechanistic models aiming at predicting rates of microbe-mediated processes. We used an amplicon sequencing approach to test if previously observed large effects of experimental soil warming on C and N cycle fluxes (50-100% increases) in a sub-arctic Sphagnum peatland were reflected in changes in the composition of the soil bacterial community. We found that treatments that previously induced changes to fluxes did not associate with changes in the phylogenetic composition of the soil bacterial community. For both DNA- and RNA-based analyses, variation in bacterial communities could be explained by the hierarchy: spatial variation (12-15% of variance explained) > temporal variation (7-11%) > climate treatment (4-9%). We conclude that the bacterial community in this environment is stable under changing conditions, despite the previously observed sensitivity of process rates-evidence that microbe-mediated soil processes can alter without concomitant changes in bacterial communities. We propose that progress in linking soil microbial communities to ecosystem processes can be advanced by further investigating the relative importance of community composition effects versus physico-chemical factors in controlling biogeochemical process rates in different contexts.

Natural products in soil microbe interactions and evolution.

PubMed

Traxler, Matthew F; Kolter, Roberto

2015-07-01

In recent years, bacterial interspecies interactions mediated by small molecule natural products have been found to give rise to a surprising array of phenotypes in soil-dwelling bacteria, especially among Streptomyces and Bacillus species. This review examines these interspecies interactions, and the natural products involved, as they have been presented in literature stemming from four disciplines: soil science, interspecies microbiology, ecology, and evolutionary biology. We also consider how these interactions fit into accepted paradigms of signaling, cueing, and coercion.

Understanding and Designing the Strategies for the Microbe-Mediated Remediation of Environmental Contaminants Using Omics Approaches.

PubMed

Malla, Muneer A; Dubey, Anamika; Yadav, Shweta; Kumar, Ashwani; Hashem, Abeer; Abd Allah, Elsayed Fathi

2018-01-01

Rapid industrialization and population explosion has resulted in the generation and dumping of various contaminants into the environment. These harmful compounds deteriorate the human health as well as the surrounding environments. Current research aims to harness and enhance the natural ability of different microbes to metabolize these toxic compounds. Microbial-mediated bioremediation offers great potential to reinstate the contaminated environments in an ecologically acceptable approach. However, the lack of the knowledge regarding the factors controlling and regulating the growth, metabolism, and dynamics of diverse microbial communities in the contaminated environments often limits its execution. In recent years the importance of advanced tools such as genomics, proteomics, transcriptomics, metabolomics, and fluxomics has increased to design the strategies to treat these contaminants in ecofriendly manner. Previously researchers has largely focused on the environmental remediation using single omics-approach, however the present review specifically addresses the integrative role of the multi-omics approaches in microbial-mediated bioremediation. Additionally, we discussed how the multi-omics approaches help to comprehend and explore the structural and functional aspects of the microbial consortia in response to the different environmental pollutants and presented some success stories by using these approaches.

Understanding and Designing the Strategies for the Microbe-Mediated Remediation of Environmental Contaminants Using Omics Approaches

PubMed Central

Malla, Muneer A.; Dubey, Anamika; Yadav, Shweta; Kumar, Ashwani; Hashem, Abeer; Abd_Allah, Elsayed Fathi

2018-01-01

Rapid industrialization and population explosion has resulted in the generation and dumping of various contaminants into the environment. These harmful compounds deteriorate the human health as well as the surrounding environments. Current research aims to harness and enhance the natural ability of different microbes to metabolize these toxic compounds. Microbial-mediated bioremediation offers great potential to reinstate the contaminated environments in an ecologically acceptable approach. However, the lack of the knowledge regarding the factors controlling and regulating the growth, metabolism, and dynamics of diverse microbial communities in the contaminated environments often limits its execution. In recent years the importance of advanced tools such as genomics, proteomics, transcriptomics, metabolomics, and fluxomics has increased to design the strategies to treat these contaminants in ecofriendly manner. Previously researchers has largely focused on the environmental remediation using single omics-approach, however the present review specifically addresses the integrative role of the multi-omics approaches in microbial-mediated bioremediation. Additionally, we discussed how the multi-omics approaches help to comprehend and explore the structural and functional aspects of the microbial consortia in response to the different environmental pollutants and presented some success stories by using these approaches. PMID:29915565

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

PubMed

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

2017-01-01

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

Lipopolysaccharides in diazotrophic bacteria

PubMed Central

Serrato, Rodrigo V.

2014-01-01

Biological nitrogen fixation (BNF) is a process in which the atmospheric nitrogen (N2) is transformed into ammonia (NH3) by a select group of nitrogen-fixing organisms, or diazotrophic bacteria. In order to furnish the biologically useful nitrogen to plants, these bacteria must be in constant molecular communication with their host plants. Some of these molecular plant-microbe interactions are very specific, resulting in a symbiotic relationship between the diazotroph and the host. Others are found between associative diazotrophs and plants, resulting in plant infection and colonization of internal tissues. Independent of the type of ecological interaction, glycans, and glycoconjugates produced by these bacteria play an important role in the molecular communication prior and during colonization. Even though exopolysaccharides (EPS) and lipochitooligosaccharides (LCO) produced by diazotrophic bacteria and released onto the environment have their importance in the microbe-plant interaction, it is the lipopolysaccharides (LPS), anchored on the external membrane of these bacteria, that mediates the direct contact of the diazotroph with the host cells. These molecules are extremely variable among the several species of nitrogen fixing-bacteria, and there are evidences of the mechanisms of infection being closely related to their structure. PMID:25232535

Q&A: Friends (but sometimes foes) within: the complex evolutionary ecology of symbioses between host and microbes.

PubMed

Gerardo, Nicole; Hurst, Gregory

2017-12-27

Over the past decade, there has been a pronounced shift in the study of host-microbe associations, with recognition that many of these associations are beneficial, and often critical, for a diverse array of hosts. There may also be pronounced benefits for the microbes, though this is less well empirically understood. Significant progress has been made in understanding how ecology and evolution shape simple associations between hosts and one or a few microbial species, and this work can serve as a foundation to study the ecology and evolution of host associations with their often complex microbial communities (microbiomes).

Can nanotechnology deliver the promised benefits without negatively impacting soil microbial life?

PubMed

Dimkpa, Christian O

2014-09-01

Nanotechnology exploits the enhanced reactivity of materials at the atomic scale to improve various applications for humankind. In agriculture, potential nanotechnology applications include crop protection and fertilization. However, such benefits could come with risks for the environment: non-target plants, plant-beneficial soil microbes and other life forms could be impacted if nanoparticles (nanomaterials) contaminate the environment. This review evaluates the impact of the major metallic nanoparticles (Ag, ZnO, CuO, CeO2 , TiO2 , and FeO-based nanoparticles) on soil microbes involved in agricultural processes. The current literature indicate that in addition to population and organismal-scale effects on microbes, other subtle impacts of nanoparticles are seen in the nitrogen cycle, soil enzyme activities, and processes involved in iron metabolism, phytohormone, and antibiotic production. These effects are negative or positive, the outcome being dependent on specific nanoparticles. Collectively, published results suggest that nanotechnology portends considerable, many negative, implications for soil microbes and, thus, agricultural processes that are microbially driven. Nonetheless, the potential of plant and soil microbial processes to mitigate the bioreactivity of nanoparticles also are observed. Whereas the roots of most terrestrial plants are associated with microbes, studies of nanoparticle interactions with plants and microbes are generally conducted separately. The few studies in actual microbe-plant systems found effects of nanoparticles on the functioning of arbuscular mycorrhizal fungi, nitrogen fixation, as well as on the production of microbial siderophores in the plant rhizosphere. It is suggested that a better understanding of the agro-ecological ramifications of nanoparticles would require more in-depth interactive studies in combined plant-microbe-nanoparticle systems. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Compositional Stability of the Bacterial Community in a Climate-Sensitive Sub-Arctic Peatland

PubMed Central

Weedon, James T.; Kowalchuk, George A.; Aerts, Rien; Freriks, Stef; Röling, Wilfred F. M.; van Bodegom, Peter M.

2017-01-01

The climate sensitivity of microbe-mediated soil processes such as carbon and nitrogen cycling offers an interesting case for evaluating the corresponding sensitivity of microbial community composition to environmental change. Better understanding of the degree of linkage between functional and compositional stability would contribute to ongoing efforts to build mechanistic models aiming at predicting rates of microbe-mediated processes. We used an amplicon sequencing approach to test if previously observed large effects of experimental soil warming on C and N cycle fluxes (50–100% increases) in a sub-arctic Sphagnum peatland were reflected in changes in the composition of the soil bacterial community. We found that treatments that previously induced changes to fluxes did not associate with changes in the phylogenetic composition of the soil bacterial community. For both DNA- and RNA-based analyses, variation in bacterial communities could be explained by the hierarchy: spatial variation (12–15% of variance explained) > temporal variation (7–11%) > climate treatment (4–9%). We conclude that the bacterial community in this environment is stable under changing conditions, despite the previously observed sensitivity of process rates—evidence that microbe-mediated soil processes can alter without concomitant changes in bacterial communities. We propose that progress in linking soil microbial communities to ecosystem processes can be advanced by further investigating the relative importance of community composition effects versus physico-chemical factors in controlling biogeochemical process rates in different contexts. PMID:28326062

Turning the Table: Plants Consume Microbes as a Source of Nutrients

PubMed Central

Paungfoo-Lonhienne, Chanyarat; Rentsch, Doris; Robatzek, Silke; Webb, Richard I.; Sagulenko, Evgeny; Näsholm, Torgny

2010-01-01

Interactions between plants and microbes in soil, the final frontier of ecology, determine the availability of nutrients to plants and thereby primary production of terrestrial ecosystems. Nutrient cycling in soils is considered a battle between autotrophs and heterotrophs in which the latter usually outcompete the former, although recent studies have questioned the unconditional reign of microbes on nutrient cycles and the plants' dependence on microbes for breakdown of organic matter. Here we present evidence indicative of a more active role of plants in nutrient cycling than currently considered. Using fluorescent-labeled non-pathogenic and non-symbiotic strains of a bacterium and a fungus (Escherichia coli and Saccharomyces cerevisiae, respectively), we demonstrate that microbes enter root cells and are subsequently digested to release nitrogen that is used in shoots. Extensive modifications of root cell walls, as substantiated by cell wall outgrowth and induction of genes encoding cell wall synthesizing, loosening and degrading enzymes, may facilitate the uptake of microbes into root cells. Our study provides further evidence that the autotrophy of plants has a heterotrophic constituent which could explain the presence of root-inhabiting microbes of unknown ecological function. Our discovery has implications for soil ecology and applications including future sustainable agriculture with efficient nutrient cycles. PMID:20689833

Synergy among Microbiota and Their Hosts: Leveraging the Hawaiian Archipelago and Local Collaborative Networks To Address Pressing Questions in Microbiome Research

PubMed Central

Frank, Kiana L.; Alegado, Rosanna A.; Amend, Anthony S.; Arif, Mohammad; Bennett, Gordon M.; Jani, Andrea J.; Medeiros, Matthew C. I.; Mileyko, Yuriy; Nguyen, Nhu H.; Nigro, Olivia D.; Prisic, Sladjana; Shin, Sangwoo; Takagi, Daisuke; Wilson, Samuel T.; Yew, Joanne Y.

2018-01-01

ABSTRACT Despite increasing acknowledgment that microorganisms underpin the healthy functioning of basically all multicellular life, few cross-disciplinary teams address the diversity and function of microbiota across organisms and ecosystems. Our newly formed consortium of junior faculty spanning fields such as ecology and geoscience to mathematics and molecular biology from the University of Hawai‘i at Mānoa aims to fill this gap. We are united in our mutual interest in advancing a new paradigm for biology that incorporates our modern understanding of the importance of microorganisms. As our first concerted research effort, we will assess the diversity and function of microbes across an entire watershed on the island of Oahu, Hawai‘i. Due to its high ecological diversity across tractable areas of land and sea, Hawai‘i provides a model system for the study of complex microbial communities and the processes they mediate. Owing to our diverse expertise, we will leverage this study system to advance the field of biology. PMID:29556540

Non-pathogenic rhizobacteria interfere with the attraction of parasitoids to aphid-induced plant volatiles via jasmonic acid signalling.

PubMed

Pineda, Ana; Soler, Roxina; Weldegergis, Berhane T; Shimwela, Mpoki M; VAN Loon, Joop J A; Dicke, Marcel

2013-02-01

Beneficial soil-borne microbes, such as mycorrhizal fungi or rhizobacteria, can affect the interactions of plants with aboveground insects at several trophic levels. While the mechanisms of interactions with herbivorous insects, that is, the second trophic level, are starting to be understood, it remains unknown how plants mediate the interactions between soil microbes and carnivorous insects, that is, the third trophic level. Using Arabidopsis thaliana Col-0 and the aphid Myzus persicae, we evaluate here the underlying mechanisms involved in the plant-mediated interaction between the non-pathogenic rhizobacterium Pseudomonas fluorescens and the parasitoid Diaeretiella rapae, by combining ecological, chemical and molecular approaches. Rhizobacterial colonization modifies the composition of the blend of herbivore-induced plant volatiles. The volatile blend from rhizobacteria-treated aphid-infested plants is less attractive to an aphid parasitoid, in terms of both olfactory preference behaviour and oviposition, than the volatile blend from aphid-infested plants without rhizobacteria. Importantly, the effect of rhizobacteria on both the emission of herbivore-induced volatiles and parasitoid response to aphid-infested plants is lost in an Arabidopsis mutant (aos/dde2-2) that is impaired in jasmonic acid production. By modifying the blend of herbivore-induced plant volatiles that depend on the jasmonic acid-signalling pathway, root-colonizing microbes interfere with the attraction of parasitoids of leaf herbivores. © 2012 Blackwell Publishing Ltd.

New developments in microbial interspecies signaling.

PubMed

Shank, Elizabeth Anne; Kolter, Roberto

2009-04-01

There is a growing appreciation that in addition to well-documented intraspecies quorum sensing systems, small molecules act as signals between microbes of different species. This review will focus on how bacterial small molecules modulate these interspecies interactions. We will particularly emphasize complex relationships such as those between microbes and insects, interactions resulting in non-antagonistic outcomes (i.e. developmental and morphological processes), how co-culture can lead to the discovery of new small molecules, and the use of known compounds to evoke unexpected responses and mediate crosstalk between microbes.

The fascinating facets of plant selenium accumulation - biochemistry, physiology, evolution and ecology.

PubMed

Schiavon, Michela; Pilon-Smits, Elizabeth A H

2017-03-01

Contents 1582 I. 1582 II. 1583 III. 1588 IV. 1590 V. 1592 1592 References 1592 SUMMARY: The importance of selenium (Se) for medicine, industry and the environment is increasingly apparent. Se is essential for many species, including humans, but toxic at elevated concentrations. Plant Se accumulation and volatilization may be applied in crop biofortification and phytoremediation. Topics covered here include beneficial and toxic effects of Se on plants, mechanisms of Se accumulation and tolerance in plants and algae, Se hyperaccumulation, and ecological and evolutionary aspects of these processes. Plant species differ in the concentration and forms of Se accumulated, Se partitioning at the whole-plant and tissue levels, and the capacity to distinguish Se from sulfur. Mechanisms of Se hyperaccumulation and its adaptive significance appear to involve constitutive up-regulation of sulfate/selenate uptake and assimilation, associated with elevated concentrations of defense-related hormones. Hyperaccumulation has evolved independently in at least three plant families, probably as an elemental defense mechanism and perhaps mediating elemental allelopathy. Elevated plant Se protects plants from generalist herbivores and pathogens, but also gives rise to the evolution of Se-resistant specialists. Plant Se accumulation affects ecological interactions with herbivores, pollinators, neighboring plants, and microbes. Hyperaccumulation tends to negatively affect Se-sensitive ecological partners while facilitating Se-resistant partners, potentially affecting species composition and Se cycling in seleniferous ecosystems. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

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

PubMed Central

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

2017-01-01

Recent analyses revealed that most of the biodiversity observed in marine microbial communities is represented by organisms with low abundance but, nonetheless essential for ecosystem dynamics and processes across both temporal and spatial scales. Surprisingly, few studies have considered the effect of macroorganism–microbe interactions on the ecology and distribution dynamics of rare microbial taxa. In this review, we synthesize several lines of evidence that these relationships cannot be neglected any longer. First, we provide empirical support that the microbiota of macroorganisms represents a significant part of marine bacterial biodiversity and that host-microbe interactions benefit to certain microbial populations which are part of the rare biosphere (i.e., opportunistic copiotrophic organisms). Second, we reveal the major role that macroorganisms may have on the dispersal and the geographic distribution of microbes. Third, we introduce an innovative and integrated view of the interactions between microbes and macroorganisms, namely sustaining the rares, which suggests that macroorganisms favor the maintenance of marine microbial diversity and are involved in the regulation of its richness and dynamics. Finally, we show how this hypothesis complements existing theories in microbial ecology and offers new perspectives about the importance of macroorganisms for the microbial biosphere, particularly the rare members. PMID:28611749

Evolutionary Ecology of Multitrophic Interactions between Plants, Insect Herbivores and Entomopathogens.

PubMed

Shikano, Ikkei

2017-06-01

Plants play an important role in the interactions between insect herbivores and their pathogens. Since the seminal review by Cory and Hoover (2006) on plant-mediated effects on insect-pathogen interactions, considerable progress has been made in understanding the complexity of these tritrophic interactions. Increasing interest in the areas of nutritional and ecological immunology over the last decade have revealed that plant primary and secondary metabolites can influence the outcomes of insect-pathogen interactions by altering insect immune functioning and physical barriers to pathogen entry. Some insects use plant secondary chemicals and nutrients to prevent infections (prophylactic medication) and medicate to limit the severity of infections (therapeutic medication). Recent findings suggest that there may be selectable plant traits that enhance entomopathogen efficacy, suggesting that entomopathogens could potentially impose selection pressure on plant traits that improve both pathogen and plant fitness. Moreover, plants in nature are inhabited by diverse communities of microbes, in addition to entomopathogens, some of which can trigger immune responses in insect herbivores. Plants are also shared by numerous other herbivorous arthropods with different modes of feeding that can trigger different defensive responses in plants. Some insect symbionts and gut microbes can degrade ingested defensive phytochemicals and be orally secreted onto wounded plant tissue during herbivory to alter plant defenses. Since non-entomopathogenic microbes and other arthropods are likely to influence the outcomes of plant-insect-entomopathogen interactions, I discuss a need to consider these multitrophic interactions within the greater web of species interactions.

Interactions Among Plants, Insects, and Microbes: Elucidation of Inter-Organismal Chemical Communications in Agricultural Ecology.

PubMed

Beck, John J; Alborn, Hans; Block, Anna; Christensen, Shawn A; Hunter, Charles T; Rering, Caitlin C; Seidl-Adams, Irmgard; Stuhl, Charles; Torto, Baldwyn; Tumlinson, James H

2018-06-12

The last two decades have witnessed a sustained increase in the study of plant-emitted volatiles and their role in plant-insect, plant-microbe and plant-plant interactions. While each of these binary systems involves complex chemical and biochemical processes between two organisms, the progression of increasing complexity of a ternary system (i.e., plant-insect-microbe), and the study of a ternary system requires non-trivial planning. This planning can include: an experimental design that factors in potential overarching ecological interactions regarding the binary or ternary system; correctly identifying and understanding unexpected observations that may occur during the experiment; and, thorough interpretation of the resultant data. This challenge of planning, performing and interpreting a plant's defensive response to multiple biotic stressors will be even greater when abiotic stressors (i.e., temperature or water) are factored into the system. To fully understand the system, we need to not only continue to investigate and understand the volatile profiles, but also include and understand the biochemistry of the plant's response to these stressors. In this paper, we provide examples and discuss interaction considerations with respect to how readers and future authors of the Journal of Agricultural and Food Chemistry can contribute their expertise toward the extraction and interpretation of chemical information exchanged between agricultural commodities and their associated pests. This holistic, multidisciplinary and thoughtful approach to interactions of plants, insects, and microbes, and the resultant response of the plants, can lead to a better understanding of agricultural ecology, in turn leading to practical and viable solutions to agricultural problems.

Vertebrate Decomposition Is Accelerated by Soil Microbes

PubMed Central

Lauber, Christian L.; Metcalf, Jessica L.; Keepers, Kyle; Ackermann, Gail; Carter, David O.

2014-01-01

Carrion decomposition is an ecologically important natural phenomenon influenced by a complex set of factors, including temperature, moisture, and the activity of microorganisms, invertebrates, and scavengers. The role of soil microbes as decomposers in this process is essential but not well understood and represents a knowledge gap in carrion ecology. To better define the role and sources of microbes in carrion decomposition, lab-reared mice were decomposed on either (i) soil with an intact microbial community or (ii) soil that was sterilized. We characterized the microbial community (16S rRNA gene for bacteria and archaea, and the 18S rRNA gene for fungi and microbial eukaryotes) for three body sites along with the underlying soil (i.e., gravesoils) at time intervals coinciding with visible changes in carrion morphology. Our results indicate that mice placed on soil with intact microbial communities reach advanced stages of decomposition 2 to 3 times faster than those placed on sterile soil. Microbial communities associated with skin and gravesoils of carrion in stages of active and advanced decay were significantly different between soil types (sterile versus untreated), suggesting that substrates on which carrion decompose may partially determine the microbial decomposer community. However, the source of the decomposer community (soil- versus carcass-associated microbes) was not clear in our data set, suggesting that greater sequencing depth needs to be employed to identify the origin of the decomposer communities in carrion decomposition. Overall, our data show that soil microbial communities have a significant impact on the rate at which carrion decomposes and have important implications for understanding carrion ecology. PMID:24907317

The maturing of microbial ecology.

PubMed

Schmidt, Thomas M

2006-09-01

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

Uncovering the drivers of host-associated microbiota with joint species distribution modelling.

PubMed

Björk, Johannes R; Hui, Francis K C; O'Hara, Robert B; Montoya, Jose M

2018-06-01

In addition to the processes structuring free-living communities, host-associated microbiota are directly or indirectly shaped by the host. Therefore, microbiota data have a hierarchical structure where samples are nested under one or several variables representing host-specific factors, often spanning multiple levels of biological organization. Current statistical methods do not accommodate this hierarchical data structure and therefore cannot explicitly account for the effect of the host in structuring the microbiota. We introduce a novel extension of joint species distribution models (JSDMs) which can straightforwardly accommodate and discern between effects such as host phylogeny and traits, recorded covariates such as diet and collection site, among other ecological processes. Our proposed methodology includes powerful yet familiar outputs seen in community ecology overall, including (a) model-based ordination to visualize and quantify the main patterns in the data; (b) variance partitioning to assess how influential the included host-specific factors are in structuring the microbiota; and (c) co-occurrence networks to visualize microbe-to-microbe associations. © 2018 John Wiley & Sons Ltd.

Reviews and syntheses: to the bottom of carbon processing at the seafloor

NASA Astrophysics Data System (ADS)

Middelburg, Jack J.

2018-01-01

Organic carbon processing at the seafloor is studied by biogeochemists to quantify burial and respiration, by organic geochemists to elucidate compositional changes and by ecologists to follow carbon transfers within food webs. Here I review these disciplinary approaches and discuss where they agree and disagree. It will be shown that the biogeochemical approach (ignoring the identity of organisms) and the ecological approach (focussing on growth and biomass of organisms) are consistent on longer timescales. Secondary production by microbes and animals is identified to potentially impact the composition of sedimentary organic matter. Animals impact sediment organic carbon processing by microbes in multiple ways: by governing organic carbon supply to sediments, by aeration via bio-irrigation and by mixing labile organic matter to deeper layers. I will present an inverted microbial loop in which microbes profit from bioturbation rather than animals profiting from microbial processing of otherwise lost dissolved organic resources. Sediments devoid of fauna therefore function differently and are less efficient in processing organic matter with the consequence that more organic matter is buried and transferred from Vernadsky's biosphere to the geosphere.

Ecology, Microbial

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

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, theymore » 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.« less

MICROFRACTURE SURFACE GEOCHEMISTRY AND ADHERENT MICROBIAL POPULATION METABOLISM IN TCE-CONTAMINATED COMPETENT BEDROCK

EPA Science Inventory

A TCE-contaminated competent bedrock site in Portsmouth, NH was used to determine if a relation existed between microfracture (MF) surface geochemistry and the ecology and metabolic activity of attached microbes relative to terminal electron accepting processes (TEAPs) and TCE bi...

Microbe-surface interactions in biofouling and biocorrosion processes.

PubMed

Beech, Iwona B; Sunner, Jan A; Hiraoka, Kenzo

2005-09-01

The presence of microorganisms on material surfaces can have a profound effect on materials performance. Surface-associated microbial growth, i.e. a biofilm, is known to instigate biofouling. The presence of biofilms may promote interfacial physico-chemical reactions that are not favored under abiotic conditions. In the case of metallic materials, undesirable changes in material properties due to a biofilm (or a biofouling layer) are referred to as biocorrosion or microbially influenced corrosion (MIC). Biofouling and biocorrosion occur in aquatic and terrestrial habitats varying in nutrient content, temperature, pressure and pH. Interfacial chemistry in such systems reflects a wide variety of physiological activities carried out by diverse microbial populations thriving within biofilms. Biocorrosion can be viewed as a consequence of coupled biological and abiotic electron-transfer reactions, i.e. redox reactions of metals, enabled by microbial ecology. Microbially produced extracellular polymeric substances (EPS), which comprise different macromolecules, mediate initial cell adhesion to the material surface and constitute a biofilm matrix. Despite their unquestionable importance in biofilm development, the extent to which EPS contribute to biocorrosion is not well-understood. This review offers a current perspective on material/microbe interactions pertinent to biocorrosion and biofouling, with EPS as a focal point, while emphasizing the role atomic force spectroscopy and mass spectrometry techniques can play in elucidating such interactions.

Microbes in Beach Sands: Integrating Environment, Ecology and Public Health

PubMed Central

Whitman, Richard; Harwood, Valerie J.; Edge, Thomas A.; Nevers, Meredith; Byappanahalli, Muruleedhara; Vijayavel, Kannappan; Brandão, João; Sadowsky, Michael J.; Alm, Elizabeth Wheeler; Crowe, Allan; Ferguson, Donna; Ge, Zhongfu; Halliday, Elizabeth; Kinzelman, Julie; Kleinheinz, Greg; Przybyla-Kelly, Kasia; Staley, Christopher; Staley, Zachery; Solo-Gabriele, Helena M.

2014-01-01

SUMMARY Beach sand is a habitat that supports many microbes, including viruses, bacteria, fungi and protozoa (micropsammon). The apparently inhospitable conditions of beach sand environments belie the thriving communities found there. Physical factors, such as water availability and protection from insolation; biological factors, such as competition, predation, and biofilm formation; and nutrient availability all contribute to the characteristics of the micropsammon. Sand microbial communities include autochthonous species/phylotypes indigenous to the environment. Allochthonous microbes, including fecal indicator bacteria (FIB) and waterborne pathogens, are deposited via waves, runoff, air, or animals. The fate of these microbes ranges from death, to transient persistence and/or replication, to establishment of thriving populations (naturalization) and integration in the autochthonous community. Transport of the micropsammon within the habitat occurs both horizontally across the beach, and vertically from the sand surface and ground water table, as well as at various scales including interstitial flow within sand pores, sediment transport for particle-associated microbes, and the large-scale processes of wave action and terrestrial runoff. The concept of beach sand as a microbial habitat and reservoir of FIB and pathogens has begun to influence our thinking about human health effects associated with sand exposure and recreational water use. A variety of pathogens have been reported from beach sands, and recent epidemiology studies have found some evidence of health risks associated with sand exposure. Persistent or replicating populations of FIB and enteric pathogens have consequences for watershed/beach management strategies and regulatory standards for safe beaches. This review summarizes our understanding of the community structure, ecology, fate, transport, and public health implications of microbes in beach sand. It concludes with recommendations for future work in this vastly under-studied area. PMID:25383070

Uncoupling of microbial community structure and function in decomposing litter across beech forest ecosystems in Central Europe.

PubMed

Purahong, Witoon; Schloter, Michael; Pecyna, Marek J; Kapturska, Danuta; Däumlich, Veronika; Mital, Sanchit; Buscot, François; Hofrichter, Martin; Gutknecht, Jessica L M; Krüger, Dirk

2014-11-12

The widespread paradigm in ecology that community structure determines function has recently been challenged by the high complexity of microbial communities. Here, we investigate the patterns of and connections between microbial community structure and microbially-mediated ecological function across different forest management practices and temporal changes in leaf litter across beech forest ecosystems in Central Europe. Our results clearly indicate distinct pattern of microbial community structure in response to forest management and time. However, those patterns were not reflected when potential enzymatic activities of microbes were measured. We postulate that in our forest ecosystems, a disconnect between microbial community structure and function may be present due to differences between the drivers of microbial growth and those of microbial function.

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

Microbial Ecology of Soil Aggregation in Agroecosystems

NASA Astrophysics Data System (ADS)

Hofmockel, K. S.; Bell, S.; Tfailly, M.; Thompson, A.; Callister, S.

2017-12-01

Crop selection and soil texture influence the physicochemical attributes of the soil, which structures microbial communities and influences soil C cycling storage. At the molecular scale, microbial metabolites and necromass alter the soil environment, which creates feedbacks that influence ecosystem functions, including soil C accumulation. By integrating lab to field studies we aim to identify the molecules, organisms and metabolic pathways that control carbon cycling and stabilization in bioenergy soils. We investigated the relative influence of plants, microbes, and minerals on soil aggregate ecology at the Great Lakes Bioenergy Research experiment. Sites in WI and MI, USA have been in corn and switchgrass cropping systems for a decade. By comparing soil aggregate ecology across sites and cropping systems we are able to test the relative importance of plant, microbe, mineral influences on soil aggregate dynamics. Soil microbial communities (16S) differ in diversity and phylogeny among sites and cropping systems. FT-ICR MS revealed differences in the molecular composition of water-soluble fraction of soil organic matter for cropping systems and soil origin for both relative abundance of assigned formulas and biogeochemical classes of compounds. We found the degree of aggregation, measured by mean weighted diameter of aggregate fractions, is influenced by plant-soil interactions. Similarly, the proportion of soil aggregate fractions varied by both soil and plant factors. Differences in aggregation were reflected in differences in bacterial, but not fungal community composition across aggregate fractions, within each soil. Scanning electron microscopy revealed stark differences in mineral-organic interactions that influence the microbial niche and the accessibility of substrates within the soil. The clay soils show greater surface heterogeneity, enabling interactions with organic fraction of the soil. This is consistent with molecular data that reveal differences in the abundance of chemical classes in clay loams compared to sandy loams. Together our data demonstrate that the potential for aggregation and C storage is strongly influenced by soil mineralogy with important implications for plant-microbe interactions that mediate C biogeochemistry.

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

Konopka, Allan

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, theymore » 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.« less

Ticks and Tick-Borne Infections: Complex Ecology, Agents, and Host Interactions.

PubMed

Wikel, Stephen K

2018-06-20

Ticks transmit the most diverse array of infectious agents of any arthropod vector. Both ticks and the microbes they transmit are recognized as significant threats to human and veterinary public health. This article examines the potential impacts of climate change on the distribution of ticks and the infections they transmit; the emergence of novel tick-borne pathogens, increasing geographic range and incidence of tick-borne infections; and advances in the characterization of tick saliva mediated modulation of host defenses and the implications of those interactions for transmission, establishment, and control of tick infestation and tick-borne infectious agents.

Environmental microbiology as a mosaic of explored ecosystems and issues.

PubMed

Faure, Denis; Bonin, Patricia; Duran, Robert

2015-09-01

Microbes are phylogenetically (Archaea, Bacteria, Eukarya, and viruses) and functionally diverse. They colonize highly varied environments and rapidly respond to and evolve as a response to local and global environmental changes, including those induced by pollutants resulting from human activities. This review exemplifies the Microbial Ecology EC2CO consortium's efforts to explore the biology, ecology, diversity, and roles of microbes in aquatic and continental ecosystems.

Sponge-Associated Microorganisms: Evolution, Ecology, and Biotechnological Potential†

PubMed Central

Taylor, Michael W.; Radax, Regina; Steger, Doris; Wagner, Michael

2007-01-01

Summary: Marine sponges often contain diverse and abundant microbial communities, including bacteria, archaea, microalgae, and fungi. In some cases, these microbial associates comprise as much as 40% of the sponge volume and can contribute significantly to host metabolism (e.g., via photosynthesis or nitrogen fixation). We review in detail the diversity of microbes associated with sponges, including extensive 16S rRNA-based phylogenetic analyses which support the previously suggested existence of a sponge-specific microbiota. These analyses provide a suitable vantage point from which to consider the potential evolutionary and ecological ramifications of these widespread, sponge-specific microorganisms. Subsequently, we examine the ecology of sponge-microbe associations, including the establishment and maintenance of these sometimes intimate partnerships, the varied nature of the interactions (ranging from mutualism to host-pathogen relationships), and the broad-scale patterns of symbiont distribution. The ecological and evolutionary importance of sponge-microbe associations is mirrored by their enormous biotechnological potential: marine sponges are among the animal kingdom's most prolific producers of bioactive metabolites, and in at least some cases, the compounds are of microbial rather than sponge origin. We review the status of this important field, outlining the various approaches (e.g., cultivation, cell separation, and metagenomics) which have been employed to access the chemical wealth of sponge-microbe associations. PMID:17554047

The influence of e-waste recycling on the molecular ecological network of soil microbial communities in Pakistan and China.

PubMed

Jiang, Longfei; Cheng, Zhineng; Zhang, Dayi; Song, Mengke; Wang, Yujie; Luo, Chunling; Yin, Hua; Li, Jun; Zhang, Gan

2017-12-01

Primitive electronic waste (e-waste) recycling releases large amounts of organic pollutants and heavy metals into the environment. As crucial moderators of geochemical cycling processes and pollutant remediation, soil microbes may be affected by these contaminants. We collected soil samples heavily contaminated by e-waste recycling in China and Pakistan, and analyzed the indigenous microbial communities. The results of this work revealed that the microbial community composition and diversity, at both whole and core community levels, were affected significantly by polycyclic aromatic hydrocarbons (PAHs), polybrominated diphenyl ethers (PBDEs) and heavy metals (e.g., Cu, Zn, and Pb). The geographical distance showed limited impacts on microbial communities compared with geochemical factors. The constructed ecological network of soil microbial communities illustrated microbial co-occurrence, competition and antagonism across soils, revealing the response of microbes to soil properties and pollutants. Two of the three main modules constructed with core operational taxonomic units (OTUs) were sensitive to nutrition (total organic carbon and total nitrogen) and pollutants. Five key OTUs assigned to Acidobacteria, Proteobacteria, and Nitrospirae in ecological network were identified. This is the first study to report the effects of e-waste pollutants on soil microbial network, providing a deeper understanding of the ecological influence of crude e-waste recycling activities on soil ecological functions. Copyright © 2017 Elsevier Ltd. All rights reserved.

The ecology of anaerobic degraders of BTEX hydrocarbons in aquifers

PubMed Central

Lueders, Tillmann

2017-01-01

Abstract The degradation of benzene, toluene, ethylbenzene and xylene (BTEX) contaminants in groundwater relies largely on anaerobic processes. While the physiology and biochemistry of selected relevant microbes have been intensively studied, research has now started to take the generated knowledge back to the field, in order to trace the populations truly responsible for the anaerobic degradation of BTEX hydrocarbons in situ and to unravel their ecology in contaminated aquifers. Here, recent advances in our knowledge of the identity, diversity and ecology of microbes involved in these important ecosystem services are discussed. At several sites, distinct lineages within the Desulfobulbaceae, the Rhodocyclaceae and the Gram-positive Peptococcaceae have been shown to dominate the degradation of different BTEX hydrocarbons. Especially for the functional guild of anaerobic toluene degraders, specific molecular detection systems have been developed, allowing researchers to trace their diversity and distribution in contaminated aquifers. Their populations appear enriched in hot spots of biodegradation in situ. 13C-labelling experiments have revealed unexpected pathways of carbon sharing and obligate syntrophic interactions to be relevant in degradation. Together with feedback mechanisms between abiotic and biotic habitat components, this promotes an enhanced ecological perspective of the anaerobic degradation of BTEX hydrocarbons, as well as its incorporation into updated concepts for site monitoring and bioremediation. PMID:27810873

Ecological suicide in microbes.

PubMed

Ratzke, Christoph; Denk, Jonas; Gore, Jeff

2018-05-01

The growth and survival of organisms often depend on interactions between them. In many cases, these interactions are positive and caused by a cooperative modification of the environment. Examples are the cooperative breakdown of complex nutrients in microbes or the construction of elaborate architectures in social insects, in which the individual profits from the collective actions of her peers. However, organisms can similarly display negative interactions by changing the environment in ways that are detrimental for them, for example by resource depletion or the production of toxic byproducts. Here we find an extreme type of negative interactions, in which Paenibacillus sp. bacteria modify the environmental pH to such a degree that it leads to a rapid extinction of the whole population, a phenomenon that we call ecological suicide. Modification of the pH is more pronounced at higher population densities, and thus ecological suicide is more likely to occur with increasing bacterial density. Correspondingly, promoting bacterial growth can drive populations extinct whereas inhibiting bacterial growth by the addition of harmful substances-such as antibiotics-can rescue them. Moreover, ecological suicide can cause oscillatory dynamics, even in single-species populations. We found ecological suicide in a wide variety of microbes, suggesting that it could have an important role in microbial ecology and evolution.

Can microbes mediate nano-transformation?

NASA Astrophysics Data System (ADS)

Prasad, K.; Jha, Anal K.; Prasad, Kamlesh; Kulkarni, A. R.

2010-10-01

A green low-cost and reproducible microbe ( Lactobacillus) and baker's yeast ( Saccharomyces cerevisiae) mediated biosynthesis of metallic and oxide nanoparticles are reported. Silver and copper oxide nanoparticles are synthesized using Lactobacillus sp. and Saccharomyces cerevisiae. The synthesis is performed akin to room temperature in the laboratory ambience. X-ray and transmission electron microscopy analyses are performed to ascertain the formation of metallic and oxide nanoparticles. Individual nanoparticles having the dimensions of 2-6 nm (metallic) and 10-20 nm (oxide) are found. A possible mechanism involved for the synthesis of metallic and oxide nanoparticles has also been proposed in which pH as well as the partial pressure of gaseous hydrogen (r-H2) or redox potential of the culture solution seem to play an important role in the process.

Does plant-Microbe interaction confer stress tolerance in plants: A review?

PubMed

Kumar, Akhilesh; Verma, Jay Prakash

2018-03-01

The biotic and abiotic stresses are major constraints for crop yield, food quality and global food security. A number of parameters such as physiological, biochemical, molecular of plants are affected under stress condition. Since the use of inorganic fertilizers and pesticides in agriculture practices cause degradation of soil fertility and environmental pollutions. Hence it is necessary to develop safer and sustainable means for agriculture production. The application of plant growth promoting microbes (PGPM) and mycorrhizal fungi enhance plant growth, under such conditions. It offers an economically fascinating and ecologically sound ways for protecting plants against stress condition. PGPM may promote plant growth by regulating plant hormones, improve nutrition acquisition, siderophore production and enhance the antioxidant system. While acquired systemic resistance (ASR) and induced systemic resistance (ISR) effectively deal with biotic stress. Arbuscular mycorrhiza (AM) enhance the supply of nutrients and water during stress condition and increase tolerance to stress. This plant-microbe interaction is vital for sustainable agriculture and industrial purpose, because it depends on biological processes and replaces conventional agriculture practices. Therefore, microbes may play a key role as an ecological engineer to solve environmental stress problems. So, it is a feasible and potential technology in future to feed global population at available resources with reduced impact on environmental quality. In this review, we have attempted to explore about abiotic and biotic stress tolerant beneficial microorganisms and their modes of action to enhance the sustainable agricultural production. Copyright © 2017 Elsevier GmbH. All rights reserved.

Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast

PubMed Central

Libkind, Diego; Hittinger, Chris Todd; Valério, Elisabete; Gonçalves, Carla; Dover, Jim; Johnston, Mark; Gonçalves, Paula; Sampaio, José Paulo

2011-01-01

Domestication of plants and animals promoted humanity's transition from nomadic to sedentary lifestyles, demographic expansion, and the emergence of civilizations. In contrast to the well-documented successes of crop and livestock breeding, processes of microbe domestication remain obscure, despite the importance of microbes to the production of food, beverages, and biofuels. Lager-beer, first brewed in the 15th century, employs an allotetraploid hybrid yeast, Saccharomyces pastorianus (syn. Saccharomyces carlsbergensis), a domesticated species created by the fusion of a Saccharomyces cerevisiae ale-yeast with an unknown cryotolerant Saccharomyces species. We report the isolation of that species and designate it Saccharomyces eubayanus sp. nov. because of its resemblance to Saccharomyces bayanus (a complex hybrid of S. eubayanus, Saccharomyces uvarum, and S. cerevisiae found only in the brewing environment). Individuals from populations of S. eubayanus and its sister species, S. uvarum, exist in apparent sympatry in Nothofagus (Southern beech) forests in Patagonia, but are isolated genetically through intrinsic postzygotic barriers, and ecologically through host-preference. The draft genome sequence of S. eubayanus is 99.5% identical to the non-S. cerevisiae portion of the S. pastorianus genome sequence and suggests specific changes in sugar and sulfite metabolism that were crucial for domestication in the lager-brewing environment. This study shows that combining microbial ecology with comparative genomics facilitates the discovery and preservation of wild genetic stocks of domesticated microbes to trace their history, identify genetic changes, and suggest paths to further industrial improvement. PMID:21873232

Soil ecological interactions: comparisons between tropical and subalpine forests

Treesearch

Grizelle Gonzalez; Ruth E. Ley; Steven K. Schmidt; Xiaoming Zou; Timothy R. Seastedt

2001-01-01

Soil fauna can influence soil processes through interactions with the microbial community. Due to the complexity of the functional roles of fauna and their effects on microbes, little consensus has been reached on the extent to which soil fauna can regulate microbial activities. We quantified soil microbial biomass and maximum growth rates in control and fauna-excluded...

The Microbe-Free Plant: Fact or Artifact?

PubMed Central

Partida-Martínez, Laila P.; Heil, Martin

2011-01-01

Plant–microbe interactions are ubiquitous. Plants are threatened by pathogens, but they are even more commonly engaged in neutral or mutualistic interactions with microbes: belowground microbial plant associates are mycorrhizal fungi, Rhizobia, and plant-growth promoting rhizosphere bacteria, aboveground plant parts are colonized by internally living bacteria and fungi (endophytes) and by microbes in the phyllosphere (epiphytes). We emphasize here that a completely microbe-free plant is an exotic exception rather than the biologically relevant rule. The complex interplay of such microbial communities with the host–plant affects multiple vital parameters such as plant nutrition, growth rate, resistance to biotic and abiotic stressors, and plant survival and distribution. The mechanisms involved reach from direct ones such as nutrient acquisition, the production of plant hormones, or direct antibiosis, to indirect ones that are mediated by effects on host resistance genes or via interactions at higher trophic levels. Plant-associated microbes are heterotrophic and cause costs to their host plant, whereas the benefits depend on the current environment. Thus, the outcome of the interaction for the plant host is highly context dependent. We argue that considering the microbe-free plant as the “normal” or control stage significantly impairs research into important phenomena such as (1) phenotypic and epigenetic plasticity, (2) the “normal” ecological outcome of a given interaction, and (3) the evolution of plants. For the future, we suggest cultivation-independent screening methods using direct PCR from plant tissue of more than one fungal and bacterial gene to collect data on the true microbial diversity in wild plants. The patterns found could be correlated to host species and environmental conditions, in order to formulate testable hypotheses on the biological roles of plant endophytes in nature. Experimental approaches should compare different host–endophyte combinations under various relevant environmental conditions and study at the genetic, epigenetic, transcriptional, and physiological level the parameters that cause the interaction to shift along the mutualism–parasitism continuum. PMID:22639622

Friend, foe or food? Recognition and the role of antimicrobial peptides in gut immunity and Drosophila-microbe interactions.

PubMed

Broderick, Nichole A

2016-05-26

Drosophila melanogaster lives, breeds and feeds on fermenting fruit, an environment that supports a high density, and often a diversity, of microorganisms. This association with such dense microbe-rich environments has been proposed as a reason that D. melanogaster evolved a diverse and potent antimicrobial peptide (AMP) response to microorganisms, especially to combat potential pathogens that might occupy this niche. Yet, like most animals, D. melanogaster also lives in close association with the beneficial microbes that comprise its microbiota, or microbiome, and recent studies have shown that antimicrobial peptides (AMPs) of the epithelial immune response play an important role in dictating these interactions and controlling the host response to gut microbiota. Moreover, D. melanogaster also eats microbes for food, consuming fermentative microbes of decaying plant material and their by-products as both larvae and adults. The processes of nutrient acquisition and host defence are remarkably similar and use shared functions for microbe detection and response, an observation that has led to the proposal that the digestive and immune systems have a common evolutionary origin. In this manner, D. melanogaster provides a powerful model to understand how, and whether, hosts differentiate between the microbes they encounter across this spectrum of associations.This article is part of the themed issue 'Evolutionary ecology of arthropod antimicrobial peptides'. © 2016 The Author(s).

Friend, foe or food? Recognition and the role of antimicrobial peptides in gut immunity and Drosophila–microbe interactions

PubMed Central

2016-01-01

Drosophila melanogaster lives, breeds and feeds on fermenting fruit, an environment that supports a high density, and often a diversity, of microorganisms. This association with such dense microbe-rich environments has been proposed as a reason that D. melanogaster evolved a diverse and potent antimicrobial peptide (AMP) response to microorganisms, especially to combat potential pathogens that might occupy this niche. Yet, like most animals, D. melanogaster also lives in close association with the beneficial microbes that comprise its microbiota, or microbiome, and recent studies have shown that antimicrobial peptides (AMPs) of the epithelial immune response play an important role in dictating these interactions and controlling the host response to gut microbiota. Moreover, D. melanogaster also eats microbes for food, consuming fermentative microbes of decaying plant material and their by-products as both larvae and adults. The processes of nutrient acquisition and host defence are remarkably similar and use shared functions for microbe detection and response, an observation that has led to the proposal that the digestive and immune systems have a common evolutionary origin. In this manner, D. melanogaster provides a powerful model to understand how, and whether, hosts differentiate between the microbes they encounter across this spectrum of associations. This article is part of the themed issue ‘Evolutionary ecology of arthropod antimicrobial peptides’. PMID:27160597

Multiplex Identification of Microbes ▿ †

PubMed Central

Hyman, Richard W.; St.Onge, Robert P.; Allen, Edward A.; Miranda, Molly; Aparicio, Ana Maria; Fukushima, Marilyn; Davis, Ronald W.

2010-01-01

We have adapted molecular inversion probe technology to identify microbes in a highly multiplexed procedure. This procedure does not require growth of the microbes. Rather, the technology employs DNA homology twice: once for the molecular probe to hybridize to its homologous DNA and again for the 20-mer oligonucleotide barcode on the molecular probe to hybridize to a commercially available molecular barcode array. As proof of concept, we have designed, tested, and employed 192 molecular probes for 40 microbes. While these particular molecular probes are aimed at our interest in the microbes in the human vagina, this molecular probe method could be employed to identify the microbes in any ecological niche. PMID:20418427

The cystic fibrosis microbiome in an ecological perspective and its impact in antibiotic therapy.

PubMed

Magalhães, Andreia P; Azevedo, Nuno F; Pereira, Maria O; Lopes, Susana P

2016-02-01

The recent focus on the cystic fibrosis (CF) complex microbiome has led to the recognition that the microbes can interact between them and with the host immune system, affecting the disease progression and treatment routes. Although the main focus remains on the interactions between traditional pathogens, growing evidence supports the contribution and the role of emergent species. Understanding the mechanisms and the biological effects involved in polymicrobial interactions may be the key to improve effective therapies and also to define new strategies for disease control. This review focuses on the interactions between microbe-microbe and host-microbe, from an ecological point of view, discussing their impact on CF disease progression. There are increasing indications that these interactions impact the success of antimicrobial therapy. Consequently, a new approach where therapy is personalized to patients by taking into account their individual CF microbiome is suggested.

Using Plant Phylogenetic Relatedness as a Predictor for Plants' Control on Soil Microbial Communities and Nitrogen Cycling

NASA Astrophysics Data System (ADS)

Potter, T.; Bowman, W. D.

2016-12-01

Despite the known importance of soil microbes and their influence on soil processes, a mechanistic understanding is still needed to predict how plants and soil microbes interact at scales that are relevant to community and ecosystem-scale processes. Closely related plant species have similar traits aboveground, but we don't know whether this is also true for belowground traits that affect soil microbial community structure and function. Determining how tightly plant phylogeny and plant functional traits are linked to soil microbial communities is a useful approach for discovering plant-microbe associations that are generalizable across plant species (a limitation of studies that employ a single or few plant species). Using this approach, we conducted a greenhouse study with seven congeneric grasses (genus Poa) and their native soils to examine whether plants' influences on microbial community structure were consistent with plant phylogenetic relatedness and/or plant functional traits. Seeds of each Poa species were planted in native soil (from the seed source population) as well as a homogenized soil from all seven populations. Additionally, a nitrogen treatment was added to address how an environmental change (such as nitrogen deposition) alters plant-microbe associations. Rhizosphere community composition of bacteria and fungi was obtained via marker gene sequencing to compare community composition across plant species. Patterns in plant-microbe associations across plant species reveal plant control on nutrient cycling via plant species' influence on microbial community structure. These results determine if we are ready to generalize about plant-microbe interactions at the genus level, an important stepping-stone to applying knowledge of plant-microbe interactions to larger ecological scales.

A new theory of plant-microbe nutrient competition resolves inconsistencies between observations and model predictions.

PubMed

Zhu, Qing; Riley, William J; Tang, Jinyun

2017-04-01

Terrestrial plants assimilate anthropogenic CO 2 through photosynthesis and synthesizing new tissues. However, sustaining these processes requires plants to compete with microbes for soil nutrients, which therefore calls for an appropriate understanding and modeling of nutrient competition mechanisms in Earth System Models (ESMs). Here, we survey existing plant-microbe competition theories and their implementations in ESMs. We found no consensus regarding the representation of nutrient competition and that observational and theoretical support for current implementations are weak. To reconcile this situation, we applied the Equilibrium Chemistry Approximation (ECA) theory to plant-microbe nitrogen competition in a detailed grassland 15 N tracer study and found that competition theories in current ESMs fail to capture observed patterns and the ECA prediction simplifies the complex nature of nutrient competition and quantitatively matches the 15 N observations. Since plant carbon dynamics are strongly modulated by soil nutrient acquisition, we conclude that (1) predicted nutrient limitation effects on terrestrial carbon accumulation by existing ESMs may be biased and (2) our ECA-based approach may improve predictions by mechanistically representing plant-microbe nutrient competition. © 2016 by the Ecological Society of America.

Methane producing bacteria: Immunological characterization: Progress report, April 1, 1984--June 30, 1988

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

Conway de Macario, E.; Macario, A.J.L.; Wolin, M.J.

1988-01-01

A major contribution of this research has been a significant advance of the immunology of methanogens and other archaebacteria (e.g., extreme halophiles). The foundations have been laid to begin the immunologic study of microbes which are non-methanogens themselves but are important for the fermentation process. This work helped to make clear that bacterial immunology goes beyond the study of pathogens for man, animals, or plants. Immunology can be applied successfully to the study of isolates of importance to understand evolution, phylogeny, ecology, bio-conversion systems, and to advance methanogenic biotechnology. Immunology holds considerable potential to aid in genetic and genetic engineeringmore » manipulations as well as in in situ handling of microbes relevant to methanogenesis. Thus, antibodies can help in the discovery of useful microbes, the generation of improved stains, the selection of desirable microorganisms, and in the monitoring and controlling of bioreactors. Immunogolic work in this new field should generate knowledge and devices relevant to areas such as Biological Energy Research, Ecology of Microorganisms, and Environmental (Sanitary) Engineering. In this regard, this work has contributed a comprehensive antiserum bank, a large panel of calibrated polyclonal antibody probes, and techniques for producing and utilizing these probes in the study of methanogens and related bacteria. 67 refs.« less

Reactive Transport Modeling of Microbe-mediated Fe (II) Oxidation for Enhanced Oil Recovery

NASA Astrophysics Data System (ADS)

Surasani, V.; Li, L.

2011-12-01

Microbially Enhanced Oil Recovery (MEOR) aims to improve the recovery of entrapped heavy oil in depleted reservoirs using microbe-based technology. Reservoir ecosystems often contain diverse microbial communities those can interact with subsurface fluids and minerals through a network of nutrients and energy fluxes. Microbe-mediated reactions products include gases, biosurfactants, biopolymers those can alter the properties of oil and interfacial interactions between oil, brine, and rocks. In addition, the produced biomass and mineral precipitates can change the reservoir permeability profile and increase sweeping efficiency. Under subsurface conditions, the injection of nitrate and Fe (II) as the electron acceptor and donor allows bacteria to grow. The reaction products include minerals such as Fe(OH)3 and nitrogen containing gases. These reaction products can have large impact on oil and reservoir properties and can enhance the recovery of trapped oil. This work aims to understand the Fe(II) oxidation by nitrate under conditions relevant to MEOR. Reactive transport modeling is used to simulate the fluid flow, transport, and reactions involved in this process. Here we developed a complex reactive network for microbial mediated nitrate-dependent Fe (II) oxidation that involves both thermodynamic controlled aqueous reactions and kinetic controlled Fe (II) mineral reaction. Reactive transport modeling is used to understand and quantify the coupling between flow, transport, and reaction processes. Our results identify key parameter controls those are important for the alteration of permeability profile under field conditions.

Metagenomic applications in environmental monitoring and bioremediation.

PubMed

Techtmann, Stephen M; Hazen, Terry C

2016-10-01

With the rapid advances in sequencing technology, the cost of sequencing has dramatically dropped and the scale of sequencing projects has increased accordingly. This has provided the opportunity for the routine use of sequencing techniques in the monitoring of environmental microbes. While metagenomic applications have been routinely applied to better understand the ecology and diversity of microbes, their use in environmental monitoring and bioremediation is increasingly common. In this review we seek to provide an overview of some of the metagenomic techniques used in environmental systems biology, addressing their application and limitation. We will also provide several recent examples of the application of metagenomics to bioremediation. We discuss examples where microbial communities have been used to predict the presence and extent of contamination, examples of how metagenomics can be used to characterize the process of natural attenuation by unculturable microbes, as well as examples detailing the use of metagenomics to understand the impact of biostimulation on microbial communities.

Construction and Screening of Marine Metagenomic Large Insert Libraries.

PubMed

Weiland-Bräuer, Nancy; Langfeldt, Daniela; Schmitz, Ruth A

2017-01-01

The marine environment covers more than 70 % of the world's surface. Marine microbial communities are highly diverse and have evolved during extended evolutionary processes of physiological adaptations under the influence of a variety of ecological conditions and selection pressures. They harbor an enormous diversity of microbes with still unknown and probably new physiological characteristics. In the past, marine microbes, mostly bacteria of microbial consortia attached to marine tissues of multicellular organisms, have proven to be a rich source of highly potent bioactive compounds, which represent a considerable number of drug candidates. However, to date, the biodiversity of marine microbes and the versatility of their bioactive compounds and metabolites have not been fully explored. This chapter describes sampling in the marine environment, construction of metagenomic large insert libraries from marine habitats, and exemplarily one function based screen of metagenomic clones for identification of quorum quenching activities.

Metabolic Flexibility as a Major Predictor of Spatial Distribution in Microbial Communities

PubMed Central

Carbonero, Franck; Oakley, Brian B.; Purdy, Kevin J.

2014-01-01

A better understand the ecology of microbes and their role in the global ecosystem could be achieved if traditional ecological theories can be applied to microbes. In ecology organisms are defined as specialists or generalists according to the breadth of their niche. Spatial distribution is often used as a proxy measure of niche breadth; generalists have broad niches and a wide spatial distribution and specialists a narrow niche and spatial distribution. Previous studies suggest that microbial distribution patterns are contrary to this idea; a microbial generalist genus (Desulfobulbus) has a limited spatial distribution while a specialist genus (Methanosaeta) has a cosmopolitan distribution. Therefore, we hypothesise that this counter-intuitive distribution within generalist and specialist microbial genera is a common microbial characteristic. Using molecular fingerprinting the distribution of four microbial genera, two generalists, Desulfobulbus and the methanogenic archaea Methanosarcina, and two specialists, Methanosaeta and the sulfate-reducing bacteria Desulfobacter were analysed in sediment samples from along a UK estuary. Detected genotypes of both generalist genera showed a distinct spatial distribution, significantly correlated with geographic distance between sites. Genotypes of both specialist genera showed no significant differential spatial distribution. These data support the hypothesis that the spatial distribution of specialist and generalist microbes does not match that seen with specialist and generalist large organisms. It may be that generalist microbes, while having a wider potential niche, are constrained, possibly by intrageneric competition, to exploit only a small part of that potential niche while specialists, with far fewer constraints to their niche, are more capable of filling their potential niche more effectively, perhaps by avoiding intrageneric competition. We suggest that these counter-intuitive distribution patterns may be a common feature of microbes in general and represent a distinct microbial principle in ecology, which is a real challenge if we are to develop a truly inclusive ecology. PMID:24465487

From birth to ‘immuno-health’, allergies and enterocolitis

PubMed Central

Houghteling, Pearl D.; Walker, W. Allan

2015-01-01

Microbial signals stimulate development and maintenance of the neonatal immune system. The process begins in utero, with limited exposure to microbes in the intrauterine environment, as well as maternal immune signals priming the developing immune system. After birth and initial colonization, the immune system must be able to activate against pathogens, but also achieve oral tolerance of food and resident gut microbes. Through microbial signals and appropriate nutrition, the immune system is able to achieve homeostasis. Major challenges to successful colonization and immune system regulation include abnormal microbial inoculi (cesarean section, hygiene) and antibiotics. When normal colonization is interrupted, dysbiosis occurs. This imbalance of microbes and subsequently of the immune system can result in allergic diseases, asthma or necrotizing enterocolitis. Probiotics and probiotic-derived therapies represent an exciting avenue to replete the population of commensal microbes and to prevent the immune-mediated sequelae of dysbiosis. PMID:26447970

Innovative MIOR Process Utilizing Indigenous Reservoir Constituents

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

Hitzman, D.O.; Stepp, A.K.; Dennis, D.M.

This research program was directed at improving the knowledge of reservoir ecology and developing practical microbial solutions for improving oil production. The goal was to identify indigenous microbial populations which can produce beneficial metabolic products and develop a methodology to stimulate those select microbes with inorganic nutrient amendments to increase oil recovery. This microbial technology has the capability of producing multiple oil-releasing agents.

Innovative MIOR Process Utilizing Indigenous Reservoir Constituents

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

Hitzman, D.O.; stepp, A.K.; Dennis, D.M.

This research program was directed at improving the knowledge of reservoir ecology and developing practical microbial solutions for improving oil production. The goal was to identify indigenous microbial populations which can produce beneficial metabolic products and develop a methodology to stimulate those select microbes with nutrient amendments to increase oil recovery. This microbial technology has the capability of producing multiple oil-releasing agents.

Decoding molecular interactions in microbial communities

PubMed Central

Abreu, Nicole A.; Taga, Michiko E.

2016-01-01

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

Microbes: Agents of Isotopic Change

NASA Astrophysics Data System (ADS)

Fogel, M. L.

2012-12-01

Microbes drive many of the important oxidation and reduction reactions on Earth; digest almost all forms of organic matter; and can serve as both primary and secondary producers. Because of their versatile biochemistry and physiology, they impart unique isotopic signatures to organic and inorganic materials, which have proven to be key measurements for understanding elemental cycling now and throughout Earth's history. Understanding microbial isotope fractionations in laboratory experiments has been important for interpreting isotopic patterns measured in natural settings. In fact, the pairing of simple experiment with natural observation has been the pathway for interpreting the fingerprint of microbial processes in ancient sediments and rocks. Examples of how key experiments have explained stable isotope fractionations by microbes and advanced the field of microbial ecology will be presented. Learning the isotopic signatures of Earth's microbes is a valuable exercise for predicting what isotopic signatures could be displayed by possible extant or extinct extraterrestrial life. Given the potential for discovery on Mars, Enceladus, and other solar system bodies, new methods and techniques for pinpointing what is unique about microbial isotope signatures is particularly relevant.

Managing Rosacea

MedlinePlus

... System Vascular Changes Demodex & Microbes Bibliography Genetics The Ecology of Your Face It Works for Me: Patient ... Tips Skin Care & Cosmetics Causes of Rosacea The Ecology of Your Face It Works for Me: Patient ...

The ecology of anaerobic degraders of BTEX hydrocarbons in aquifers.

PubMed

Lueders, Tillmann

2017-01-01

The degradation of benzene, toluene, ethylbenzene and xylene (BTEX) contaminants in groundwater relies largely on anaerobic processes. While the physiology and biochemistry of selected relevant microbes have been intensively studied, research has now started to take the generated knowledge back to the field, in order to trace the populations truly responsible for the anaerobic degradation of BTEX hydrocarbons in situ and to unravel their ecology in contaminated aquifers. Here, recent advances in our knowledge of the identity, diversity and ecology of microbes involved in these important ecosystem services are discussed. At several sites, distinct lineages within the Desulfobulbaceae, the Rhodocyclaceae and the Gram-positive Peptococcaceae have been shown to dominate the degradation of different BTEX hydrocarbons. Especially for the functional guild of anaerobic toluene degraders, specific molecular detection systems have been developed, allowing researchers to trace their diversity and distribution in contaminated aquifers. Their populations appear enriched in hot spots of biodegradation in situ 13 C-labelling experiments have revealed unexpected pathways of carbon sharing and obligate syntrophic interactions to be relevant in degradation. Together with feedback mechanisms between abiotic and biotic habitat components, this promotes an enhanced ecological perspective of the anaerobic degradation of BTEX hydrocarbons, as well as its incorporation into updated concepts for site monitoring and bioremediation. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

The role of adaptive immunity as an ecological filter on the gut microbiota in zebrafish.

PubMed

Stagaman, Keaton; Burns, Adam R; Guillemin, Karen; Bohannan, Brendan Jm

2017-07-01

All animals live in intimate association with communities of microbes, collectively referred to as their microbiota. Certain host traits can influence which microbial taxa comprise the microbiota. One potentially important trait in vertebrate animals is the adaptive immune system, which has been hypothesized to act as an ecological filter, promoting the presence of some microbial taxa over others. Here we surveyed the intestinal microbiota of 68 wild-type zebrafish, with functional adaptive immunity, and 61 rag1 - zebrafish, lacking functional B- and T-cell receptors, to test the role of adaptive immunity as an ecological filter on the intestinal microbiota. In addition, we tested the robustness of adaptive immunity's filtering effects to host-host interaction by comparing the microbiota of fish populations segregated by genotype to those containing both genotypes. The presence of adaptive immunity individualized the gut microbiota and decreased the contributions of neutral processes to gut microbiota assembly. Although mixing genotypes led to increased phylogenetic diversity in each, there was no significant effect of adaptive immunity on gut microbiota composition in either housing condition. Interestingly, the most robust effect on microbiota composition was co-housing within a tank. In all, these results suggest that adaptive immunity has a role as an ecological filter of the zebrafish gut microbiota, but it can be overwhelmed by other factors, including transmission of microbes among hosts.

National Rosacea Society

MedlinePlus

... System Vascular Changes Demodex & Microbes Bibliography Genetics The Ecology of Your Face It Works for Me: Patient ... Care & Cosmetics Makeup Tips Causes of Rosacea The Ecology of Your Face It Works for Me: Patient ...

Viral control of phytoplankton populations--a review.

PubMed

Brussaard, Corina P D

2004-01-01

Phytoplankton population dynamics are the result of imbalances between reproduction and losses. Losses include grazing, sinking, and natural mortality. As the importance of microbes in aquatic ecology has been recognized, so has the potential significance of viruses as mortality agents for phytoplankton. The field of algal virus ecology is steadily changing and advancing as new viruses are isolated and new methods are developed for quantifying the impact of viruses on phytoplankton dynamics and diversity. With this development, evidence is accumulating that viruses can control phytoplankton dynamics through reduction of host populations, or by preventing algal host populations from reaching high levels. The identification of highly specific host ranges of viruses is changing our understanding of population dynamics. Viral-mediated mortality may not only affect algal species succession, but may also affect intraspecies succession. Through cellular lysis, viruses indirectly affect the fluxes of energy, nutrients, and organic matter, especially during algal bloom events when biomass is high. Although the importance of viruses is presently recognized, it is apparent that many aspects of viral-mediated mortality of phytoplankton are still poorly understood. It is imperative that future research addresses the mechanisms that regulate virus infectivity, host resistance, genotype richness, abundance, and the fate of viruses over time and space.

Fifty important research questions in microbial ecology.

PubMed

Antwis, Rachael E; Griffiths, Sarah M; Harrison, Xavier A; Aranega-Bou, Paz; Arce, Andres; Bettridge, Aimee S; Brailsford, Francesca L; de Menezes, Alexandre; Devaynes, Andrew; Forbes, Kristian M; Fry, Ellen L; Goodhead, Ian; Haskell, Erin; Heys, Chloe; James, Chloe; Johnston, Sarah R; Lewis, Gillian R; Lewis, Zenobia; Macey, Michael C; McCarthy, Alan; McDonald, James E; Mejia-Florez, Nasmille L; O'Brien, David; Orland, Chloé; Pautasso, Marco; Reid, William D K; Robinson, Heather A; Wilson, Kenneth; Sutherland, William J

2017-05-01

Microbial ecology provides insights into the ecological and evolutionary dynamics of microbial communities underpinning every ecosystem on Earth. Microbial communities can now be investigated in unprecedented detail, although there is still a wealth of open questions to be tackled. Here we identify 50 research questions of fundamental importance to the science or application of microbial ecology, with the intention of summarising the field and bringing focus to new research avenues. Questions are categorised into seven themes: host-microbiome interactions; health and infectious diseases; human health and food security; microbial ecology in a changing world; environmental processes; functional diversity; and evolutionary processes. Many questions recognise that microbes provide an extraordinary array of functional diversity that can be harnessed to solve real-world problems. Our limited knowledge of spatial and temporal variation in microbial diversity and function is also reflected, as is the need to integrate micro- and macro-ecological concepts, and knowledge derived from studies with humans and other diverse organisms. Although not exhaustive, the questions presented are intended to stimulate discussion and provide focus for researchers, funders and policy makers, informing the future research agenda in microbial ecology. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Decomposition

USGS Publications Warehouse

Middleton, Beth A.

2014-01-01

A cornerstone of ecosystem ecology, decomposition was recognized as a fundamental process driving the exchange of energy in ecosystems by early ecologists such as Lindeman 1942 and Odum 1960). In the history of ecology, studies of decomposition were incorporated into the International Biological Program in the 1960s to compare the nature of organic matter breakdown in various ecosystem types. Such studies still have an important role in ecological studies of today. More recent refinements have brought debates on the relative role microbes, invertebrates and environment in the breakdown and release of carbon into the atmosphere, as well as how nutrient cycling, production and other ecosystem processes regulated by decomposition may shift with climate change. Therefore, this bibliography examines the primary literature related to organic matter breakdown, but it also explores topics in which decomposition plays a key supporting role including vegetation composition, latitudinal gradients, altered ecosystems, anthropogenic impacts, carbon storage, and climate change models. Knowledge of these topics is relevant to both the study of ecosystem ecology as well projections of future conditions for human societies.

The niche of an invasive marine microbe in a subtropical freshwater impoundment

PubMed Central

David Hambright, K; Beyer, Jessica E; Easton, James D; Zamor, Richard M; Easton, Anne C; Hallidayschult, Thayer C

2015-01-01

Growing attention in aquatic ecology is focusing on biogeographic patterns in microorganisms and whether these potential patterns can be explained within the framework of general ecology. The long-standing microbiologist's credo ‘Everything is everywhere, but, the environment selects' suggests that dispersal is not limiting for microbes, but that the environment is the primary determining factor in microbial community composition. Advances in molecular techniques have provided new evidence that biogeographic patterns exist in microbes and that dispersal limitation may actually have an important role, yet more recent study using extremely deep sequencing predicts that indeed everything is everywhere. Using a long-term field study of the ‘invasive' marine haptophyte Prymnesium parvum, we characterize the environmental niche of P. parvum in a subtropical impoundment in the southern United States. Our analysis contributes to a growing body of evidence that indicates a primary role for environmental conditions, but not dispersal, in the lake-wide abundances and seasonal bloom patterns in this globally important microbe. PMID:24950108

Adaptive radiation by waves of gene transfer leads to fine-scale resource partitioning in marine microbes

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

Hehemann, Jan -Hendrik; Arevalo, Philip; Datta, Manoshi S.

Adaptive radiations are important drivers of niche filling, since they rapidly adapt a single clade of organisms to ecological opportunities. Although thought to be common for animals and plants, adaptive radiations have remained difficult to document for microbes in the wild. Here we describe a recent adaptive radiation leading to fine-scale ecophysiological differentiation in the degradation of an algal glycan in a clade of closely related marine bacteria. Horizontal gene transfer is the primary driver in the diversification of the pathway leading to several ecophysiologically differentiated Vibrionaceae populations adapted to different physical forms of alginate. Furthermore, pathway architecture is predictivemore » of function and ecology, underscoring that horizontal gene transfer without extensive regulatory changes can rapidly assemble fully functional pathways in microbes.« less

Adaptive radiation by waves of gene transfer leads to fine-scale resource partitioning in marine microbes

DOE PAGES

Hehemann, Jan -Hendrik; Arevalo, Philip; Datta, Manoshi S.; ...

2016-09-22

Adaptive radiations are important drivers of niche filling, since they rapidly adapt a single clade of organisms to ecological opportunities. Although thought to be common for animals and plants, adaptive radiations have remained difficult to document for microbes in the wild. Here we describe a recent adaptive radiation leading to fine-scale ecophysiological differentiation in the degradation of an algal glycan in a clade of closely related marine bacteria. Horizontal gene transfer is the primary driver in the diversification of the pathway leading to several ecophysiologically differentiated Vibrionaceae populations adapted to different physical forms of alginate. Furthermore, pathway architecture is predictivemore » of function and ecology, underscoring that horizontal gene transfer without extensive regulatory changes can rapidly assemble fully functional pathways in microbes.« less

Adaptive radiation by waves of gene transfer leads to fine-scale resource partitioning in marine microbes

PubMed Central

Hehemann, Jan-Hendrik; Arevalo, Philip; Datta, Manoshi S.; Yu, Xiaoqian; Corzett, Christopher H.; Henschel, Andreas; Preheim, Sarah P.; Timberlake, Sonia; Alm, Eric J.; Polz, Martin F.

2016-01-01

Adaptive radiations are important drivers of niche filling, since they rapidly adapt a single clade of organisms to ecological opportunities. Although thought to be common for animals and plants, adaptive radiations have remained difficult to document for microbes in the wild. Here we describe a recent adaptive radiation leading to fine-scale ecophysiological differentiation in the degradation of an algal glycan in a clade of closely related marine bacteria. Horizontal gene transfer is the primary driver in the diversification of the pathway leading to several ecophysiologically differentiated Vibrionaceae populations adapted to different physical forms of alginate. Pathway architecture is predictive of function and ecology, underscoring that horizontal gene transfer without extensive regulatory changes can rapidly assemble fully functional pathways in microbes. PMID:27653556

Candida albicans Pathogenesis: Fitting within the Host-Microbe Damage Response Framework

PubMed Central

Kong, Eric F.; Tsui, Christina; Nguyen, M. Hong; Clancy, Cornelius J.; Fidel, Paul L.; Noverr, Mairi

2016-01-01

Historically, the nature and extent of host damage by a microbe were considered highly dependent on virulence attributes of the microbe. However, it has become clear that disease is a complex outcome which can arise because of pathogen-mediated damage, host-mediated damage, or both, with active participation from the host microbiota. This awareness led to the formulation of the damage response framework (DRF), a revolutionary concept that defined microbial virulence as a function of host immunity. The DRF outlines six classifications of host damage outcomes based on the microbe and the strength of the immune response. In this review, we revisit this concept from the perspective of Candida albicans, a microbial pathogen uniquely adapted to its human host. This fungus commonly colonizes various anatomical sites without causing notable damage. However, depending on environmental conditions, a diverse array of diseases may occur, ranging from mucosal to invasive systemic infections resulting in microbe-mediated and/or host-mediated damage. Remarkably, C. albicans infections can fit into all six DRF classifications, depending on the anatomical site and associated host immune response. Here, we highlight some of these diverse and site-specific diseases and how they fit the DRF classifications, and we describe the animal models available to uncover pathogenic mechanisms and related host immune responses. PMID:27430274

Detoxifying symbiosis: microbe-mediated detoxification of phytotoxins and pesticides in insects.

PubMed

Itoh, Hideomi; Tago, Kanako; Hayatsu, Masahito; Kikuchi, Yoshitomo

2018-04-12

Covering: up to 2018Insects live in a world full of toxic compounds such as plant toxins and manmade pesticides. To overcome the effects of these toxins, herbivorous insects have evolved diverse, elaborate mechanisms of resistance, such as toxin avoidance, target-site alteration, and detoxification. These resistance mechanisms are thought to be encoded by the insects' own genomes, and in many cases, this holds true. However, recent omics analyses, in conjunction with classic culture-dependent analyses, have revealed that a number of insects possess specific gut microorganisms, some of which significantly contribute to resistance against phytotoxins and pesticides by degrading such chemical compounds. Here, we review recent advances in our understanding on the symbiont-mediated degradation of natural and artificial toxins, with a special emphasis on their underlying genetic basis, focus on the importance of environmental microbiota as a resource of toxin-degrading microorganisms, and discuss the ecological and evolutionary significance of these symbiotic associations.

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

PubMed

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

2015-07-01

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

A great leap forward in microbial ecology.

PubMed

Okabe, Satoshi; Oshiki, Mamoru; Kamagata, Yoichi; Yamaguchi, Nobuyasu; Toyofuku, Masanori; Yawata, Yutaka; Tashiro, Yosuke; Nomura, Nobuhiko; Ohta, Hiroyuki; Ohkuma, Moriya; Hiraishi, Akira; Minamisawa, Kiwamu

2010-01-01

Ribosomal RNA (rRNA) sequence-based molecular techniques emerged in the late 1980s, which completely changed our general view of microbial life. Coincidentally, the Japanese Society of Microbial Ecology (JSME) was founded, and its official journal "Microbes and Environments (M&E)" was launched, in 1985. Thus, the past 25 years have been an exciting and fruitful period for M&E readers and microbiologists as demonstrated by the numerous excellent papers published in M&E. In this minireview, recent progress made in microbial ecology and related fields is summarized, with a special emphasis on 8 landmark areas; the cultivation of uncultured microbes, in situ methods for the assessment of microorganisms and their activities, biofilms, plant microbiology, chemolithotrophic bacteria in early volcanic environments, symbionts of animals and their ecology, wastewater treatment microbiology, and the biodegradation of hazardous organic compounds.

Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition

PubMed Central

Lim, Yan Wei; Cuevas, Daniel A.; Silva, Genivaldo Gueiros Z.; Aguinaldo, Kristen; Dinsdale, Elizabeth A.; Haas, Andreas F.; Hatay, Mark; Sanchez, Savannah E.; Wegley-Kelly, Linda; Dutilh, Bas E.; Harkins, Timothy T.; Lee, Clarence C.; Tom, Warren; Sandin, Stuart A.; Smith, Jennifer E.; Zgliczynski, Brian; Vermeij, Mark J.A.; Rohwer, Forest

2014-01-01

Genomics and metagenomics have revolutionized our understanding of marine microbial ecology and the importance of microbes in global geochemical cycles. However, the process of DNA sequencing has always been an abstract extension of the research expedition, completed once the samples were returned to the laboratory. During the 2013 Southern Line Islands Research Expedition, we started the first effort to bring next generation sequencing to some of the most remote locations on our planet. We successfully sequenced twenty six marine microbial genomes, and two marine microbial metagenomes using the Ion Torrent PGM platform on the Merchant Yacht Hanse Explorer. Onboard sequence assembly, annotation, and analysis enabled us to investigate the role of the microbes in the coral reef ecology of these islands and atolls. This analysis identified phosphonate as an important phosphorous source for microbes growing in the Line Islands and reinforced the importance of L-serine in marine microbial ecosystems. Sequencing in the field allowed us to propose hypotheses and conduct experiments and further sampling based on the sequences generated. By eliminating the delay between sampling and sequencing, we enhanced the productivity of the research expedition. By overcoming the hurdles associated with sequencing on a boat in the middle of the Pacific Ocean we proved the flexibility of the sequencing, annotation, and analysis pipelines. PMID:25177534

Sequencing at sea: challenges and experiences in Ion Torrent PGM sequencing during the 2013 Southern Line Islands Research Expedition.

PubMed

Lim, Yan Wei; Cuevas, Daniel A; Silva, Genivaldo Gueiros Z; Aguinaldo, Kristen; Dinsdale, Elizabeth A; Haas, Andreas F; Hatay, Mark; Sanchez, Savannah E; Wegley-Kelly, Linda; Dutilh, Bas E; Harkins, Timothy T; Lee, Clarence C; Tom, Warren; Sandin, Stuart A; Smith, Jennifer E; Zgliczynski, Brian; Vermeij, Mark J A; Rohwer, Forest; Edwards, Robert A

2014-01-01

Genomics and metagenomics have revolutionized our understanding of marine microbial ecology and the importance of microbes in global geochemical cycles. However, the process of DNA sequencing has always been an abstract extension of the research expedition, completed once the samples were returned to the laboratory. During the 2013 Southern Line Islands Research Expedition, we started the first effort to bring next generation sequencing to some of the most remote locations on our planet. We successfully sequenced twenty six marine microbial genomes, and two marine microbial metagenomes using the Ion Torrent PGM platform on the Merchant Yacht Hanse Explorer. Onboard sequence assembly, annotation, and analysis enabled us to investigate the role of the microbes in the coral reef ecology of these islands and atolls. This analysis identified phosphonate as an important phosphorous source for microbes growing in the Line Islands and reinforced the importance of L-serine in marine microbial ecosystems. Sequencing in the field allowed us to propose hypotheses and conduct experiments and further sampling based on the sequences generated. By eliminating the delay between sampling and sequencing, we enhanced the productivity of the research expedition. By overcoming the hurdles associated with sequencing on a boat in the middle of the Pacific Ocean we proved the flexibility of the sequencing, annotation, and analysis pipelines.

From where and how do plants and microbes get nitrogen? Revisiting paradigms of soil nitrogen availability

NASA Astrophysics Data System (ADS)

Grandy, S.

2017-12-01

Despite decades of research progress, soil biogeochemists are still debating in different ecosystems what pools and fluxes provide N to plants and microbes. Current concepts argue that N mineralization regulates the supply of N for plants and microorganisms, and is a `gatekeeper' for environmental N losses. The prevailing paradigm also argues that the chemistry of plant litter inputs (e.g. initial C:N ratio) primarily drives N mineralization rates, existing as a universal regulator of a switch between net N immobilization versus net N mineralization. However, decomposer community enzyme upregulation drives proteolysis, the exocellular first step in N mineralization; then, cellular carbon use efficiency and stoichiometry are internal microbial physiological processes driving ammonification rates. Further, N mineralization is only one of multiple, microbial-driven sequences in soils that regulate bioavailable N. Emerging evidence and new conceptual models from both the ecological and biogeoscience communities argue that while depolymerization is a critical first step, clay minerals may be an important and overlooked mediator of bioavailable N, and especially in the soil rhizosphere they are both a large source and sink for N. Mineral-associated organic matter (MAOM) can hold up to 20x more N than particulate fractions, is a rich reservoir of proteins, amino acids, and nucleic acids, and is mobilized by microbes and their interactions with plants. We use this and other emerging information to develop a new model of N availability in soils, highlighting: mineralization is strongly influenced by microbial physiological traits; the various steps in N mineralization have different drivers and can become decoupled; minerals are a strong sink and source for bioavailable N that is regulated by interactions between plants and microbial communities; and plants are a driving force in the soil N cycle for their ability to prime mineral N, and influence the structure and function of microbial communities. Plants and microbes are far from passive players in the cycling of N in soils, actively regulating N mineralization, interactions of bioavailable N with minerals, and ultimately plant N uptake.

Coping with Rosacea: Managing Psychosocial Aspects of Rosacea

MedlinePlus

... System Vascular Changes Demodex & Microbes Bibliography Genetics The Ecology of Your Face It Works for Me: Patient ... Tips Skin Care & Cosmetics Causes of Rosacea The Ecology of Your Face It Works for Me: Patient ...

Eavesdropping on plant-insect-microbe chemical communications in agricultural ecology: a virtual issue on semiochemicals

USDA-ARS?s Scientific Manuscript database

Studies of plant-insect interactions, and more recently the interactions among plants, insects, and microbes, have revealed that volatiles often facilitate insect movement, aggregation, and host location by herbivores, predators and parasitoids, all of which could be used to help protect agriculture...

Physiological and molecular implications of plant polyamine metabolism during biotic interactions

PubMed Central

Jiménez-Bremont, Juan F.; Marina, María; Guerrero-González, María de la Luz; Rossi, Franco R.; Sánchez-Rangel, Diana; Rodríguez-Kessler, Margarita; Ruiz, Oscar A.; Gárriz, Andrés

2014-01-01

During ontogeny, plants interact with a wide variety of microorganisms. The association with mutualistic microbes results in benefits for the plant. By contrast, pathogens may cause a remarkable impairment of plant growth and development. Both types of plant–microbe interactions provoke notable changes in the polyamine (PA) metabolism of the host and/or the microbe, being each interaction a complex and dynamic process. It has been well documented that the levels of free and conjugated PAs undergo profound changes in plant tissues during the interaction with microorganisms. In general, this is correlated with a precise and coordinated regulation of PA biosynthetic and catabolic enzymes. Interestingly, some evidence suggests that the relative importance of these metabolic pathways may depend on the nature of the microorganism, a concept that stems from the fact that these amines mediate the activation of plant defense mechanisms. This effect is mediated mostly through PA oxidation, even though part of the response is activated by non-oxidized PAs. In the last years, a great deal of effort has been devoted to profile plant gene expression following microorganism recognition. In addition, the phenotypes of transgenic and mutant plants in PA metabolism genes have been assessed. In this review, we integrate the current knowledge on this field and analyze the possible roles of these amines during the interaction of plants with microbes. PMID:24672533

Metagenomic applications in environmental monitoring and bioremediation

DOE PAGES

Techtmann, Stephen M.; Hazen, Terry C.

2016-01-01

With the rapid advances in sequencing technology, the cost of sequencing has dramatically dropped and the scale of sequencing projects has increased accordingly. This has provided the opportunity for the routine use of sequencing techniques in the monitoring of environmental microbes. While metagenomic applications have been routinely applied to better understand the ecology and diversity of microbes, their use in environmental monitoring and bioremediation is increasingly common. In this review we seek to provide an overview of some of the metagenomic techniques used in environmental systems biology, addressing their application and limitation. We will also provide several recent examples ofmore » the application of metagenomics to bioremediation. We discuss examples where microbial communities have been used to predict the presence and extent of contamination, examples of how metagenomics can be used to characterize the process of natural attenuation by unculturable microbes, as well as examples detailing the use of metagenomics to understand the impact of biostimulation on microbial communities.« less

Disentangling the influence of earthworms in sugarcane rhizosphere

PubMed Central

Braga, Lucas P. P.; Yoshiura, Caio A.; Borges, Clovis D.; Horn, Marcus A.; Brown, George G.; Drake, Harold L.; Tsai, Siu M.

2016-01-01

For the last 150 years many studies have shown the importance of earthworms for plant growth, but the exact mechanisms involved in the process are still poorly understood. Many important functions required for plant growth can be performed by soil microbes in the rhizosphere. To investigate earthworm influence on the rhizosphere microbial community, we performed a macrocosm experiment with and without Pontoscolex corethrurus (EW+ and EW−, respectively) and followed various soil and rhizosphere processes for 217 days with sugarcane. In EW+ treatments, N2O concentrations belowground (15 cm depth) and relative abundances of nitrous oxide genes (nosZ) were higher in bulk soil and rhizosphere, suggesting that soil microbes were able to consume earthworm-induced N2O. Shotgun sequencing (total DNA) revealed that around 70 microbial functions in bulk soil and rhizosphere differed between EW+ and EW− treatments. Overall, genes indicative of biosynthetic pathways and cell proliferation processes were enriched in EW+ treatments, suggesting a positive influence of worms. In EW+ rhizosphere, functions associated with plant-microbe symbiosis were enriched relative to EW− rhizosphere. Ecological networks inferred from the datasets revealed decreased niche diversification and increased keystone functions as an earthworm-derived effect. Plant biomass was improved in EW+ and worm population proliferated. PMID:27976685

Environmental bacteriophages: viruses of microbes in aquatic ecosystems

PubMed Central

Sime-Ngando, Télesphore

2014-01-01

Since the discovery 2–3 decades ago that viruses of microbes are abundant in marine ecosystems, viral ecology has grown increasingly to reach the status of a full scientific discipline in environmental sciences. A dedicated ISVM society, the International Society for Viruses of Microorganisms, (http://www.isvm.org/) was recently launched. Increasing studies in viral ecology are sources of novel knowledge related to the biodiversity of living things, the functioning of ecosystems, and the evolution of the cellular world. This is because viruses are perhaps the most diverse, abundant, and ubiquitous biological entities in the biosphere, although local environmental conditions enrich for certain viral types through selective pressure. They exhibit various lifestyles that intimately depend on the deep-cellular mechanisms, and are ultimately replicated by members of all three domains of cellular life (Bacteria, Eukarya, Archaea), as well as by giant viruses of some eukaryotic cells. This establishes viral parasites as microbial killers but also as cell partners or metabolic manipulators in microbial ecology. The present chapter sought to review the literature on the diversity and functional roles of viruses of microbes in environmental microbiology, focusing primarily on prokaryotic viruses (i.e., phages) in aquatic ecosystems, which form the bulk of our knowledge in modern environmental viral ecology. PMID:25104950

The microbiology of deep-sea hydrothermal vent plumes: ecological and biogeographic linkages to seafloor and water column habitats.

PubMed

Dick, Gregory J; Anantharaman, Karthik; Baker, Brett J; Li, Meng; Reed, Daniel C; Sheik, Cody S

2013-01-01

Hydrothermal plumes are an important yet understudied component of deep-sea vent microbial ecosystems. The significance of plume microbial processes can be appreciated from three perspectives: (1) mediation of plume biogeochemistry, (2) dispersal of seafloor hydrothermal vent microbes between vents sites, (3) as natural laboratories for understanding the ecology, physiology, and function of microbial groups that are distributed throughout the pelagic deep sea. Plume microbiology has been largely neglected in recent years, especially relative to the extensive research conducted on seafloor and subseafloor systems. Rapidly advancing technologies for investigating microbial communities provide new motivation and opportunities to characterize this important microbial habitat. Here we briefly highlight microbial contributions to plume and broader ocean (bio)geochemistry and review recent work to illustrate the ecological and biogeographic linkages between plumes, seafloor vent habitats, and other marine habitats such as oxygen minimum zones (OMZs), cold seeps, and oil spills. 16S rRNA gene surveys and metagenomic/-transcriptomic data from plumes point to dominant microbial populations, genes, and functions that are also operative in OMZs (SUP05, ammonia-oxidizing Archaea, and SAR324 Deltaproteobacteria) and hydrocarbon-rich environments (methanotrophs). Plume microbial communities are distinct from those on the seafloor or in the subsurface but contain some signatures of these habitats, consistent with the notion that plumes are potential vectors for dispersal of microorganisms between seafloor vent sites. Finally, we put forward three pressing questions for the future of deep-sea hydrothermal plume research and consider interactions between vents and oceans on global scales.

The microbiology of deep-sea hydrothermal vent plumes: ecological and biogeographic linkages to seafloor and water column habitats

PubMed Central

Dick, Gregory J.; Anantharaman, Karthik; Baker, Brett J.; Li, Meng; Reed, Daniel C.; Sheik, Cody S.

2013-01-01

Hydrothermal plumes are an important yet understudied component of deep-sea vent microbial ecosystems. The significance of plume microbial processes can be appreciated from three perspectives: (1) mediation of plume biogeochemistry, (2) dispersal of seafloor hydrothermal vent microbes between vents sites, (3) as natural laboratories for understanding the ecology, physiology, and function of microbial groups that are distributed throughout the pelagic deep sea. Plume microbiology has been largely neglected in recent years, especially relative to the extensive research conducted on seafloor and subseafloor systems. Rapidly advancing technologies for investigating microbial communities provide new motivation and opportunities to characterize this important microbial habitat. Here we briefly highlight microbial contributions to plume and broader ocean (bio)geochemistry and review recent work to illustrate the ecological and biogeographic linkages between plumes, seafloor vent habitats, and other marine habitats such as oxygen minimum zones (OMZs), cold seeps, and oil spills. 16S rRNA gene surveys and metagenomic/-transcriptomic data from plumes point to dominant microbial populations, genes, and functions that are also operative in OMZs (SUP05, ammonia-oxidizing Archaea, and SAR324 Deltaproteobacteria) and hydrocarbon-rich environments (methanotrophs). Plume microbial communities are distinct from those on the seafloor or in the subsurface but contain some signatures of these habitats, consistent with the notion that plumes are potential vectors for dispersal of microorganisms between seafloor vent sites. Finally, we put forward three pressing questions for the future of deep-sea hydrothermal plume research and consider interactions between vents and oceans on global scales. PMID:23720658

From bacteria to elephants: Effects of land-use legacies on biodiversity and ecosystem structure in the Serengeti-Mara ecosystem: Chapter 8

USGS Publications Warehouse

Verchot, Louis V.; Ward, Naomi L.; Belnap, Jayne; Bossio, Deborah; Coughenour, Michael; Gibson, John; Hanotte, Olivier; Muchiru, Andrew N.; Phillips, Susan L.; Steven, Blaire; Wall, Diana H.; Reid, Robin S.

2015-01-01

Generally, ecological research has considered the aboveground and belowground components of ecosystems separately. Consequently, frameworks for integrating the two components are not well developed. Integrating the microbial components into ecosystem ecology requires different approaches from those offered by plant ecology, partly because of the scales at which microbial processes operate and partly because of measurement constraints. Studies have begun to relate microbial community structure to ecosystem function. results suggest that excluding people and livestock from the MMNR, or preventing heavier livestock from grazing around settlements, may not change the general structure of the ecosystem (soils, plant structure), but can change the numbers and diversity of wildlife, nematodes and microbes in this ecosystem in subtle ways.

Experimentally reduced root–microbe interactions reveal limited plasticity in functional root traits in Acer and Quercus

USDA-ARS?s Scientific Manuscript database

Abstract. Background and Aims Interactions between roots and soil microbes are critical components of below-ground ecology. It is essential to quantify the magnitude of root trait variation both among and within species, including variation due to plasticity. In addition to contextualizing the mag...

Exploring the evolutionary ecology of fungal endophytes in agricultural systems: using functional traits to reveal mechanisms in community processes

PubMed Central

Saunders, Megan; Glenn, Anthony E; Kohn, Linda M

2010-01-01

All plants, including crop species, harbor a community of fungal endophyte species, yet we know little about the biotic factors that are important in endophyte community assembly. We suggest that the most direct route to understanding the mechanisms underlying community assembly is through the study of functional trait variation in the host and its fungal consortium. We review studies on crop endophytes that investigate plant and fungal traits likely to be important in endophyte community processes. We focus on approaches that could speed detection of general trends in endophyte community assembly: (i) use of the ‘assembly rules’ concept to identify specific mechanisms that influence endophyte community dynamics, (ii) measurement of functional trait variation in plants and fungi to better understand endophyte community processes and plant–fungal interactions, and (iii) investigation of microbe–microbe interactions, and fungal traits that mediate them. This approach is well suited for research in agricultural systems, where pair-wise host–fungus interactions and mechanisms of fungal–fungal competition have frequently been described. Areas for consideration include the possibility that human manipulation of crop phenotype and deployment of fungal biocontrol species can significantly influence endophyte community assembly. Evaluation of endophyte assembly rules may help to fine-tune crop management strategies. PMID:25567944

Networks within networks: floods, droughts, and the assembly of algal-based food webs in a Mediterranean river

NASA Astrophysics Data System (ADS)

Power, M. E.; Limm, M.; Finlay, J. C.; Welter, J.; Furey, P.; Lowe, R.; Hondzo, M.; Dietrich, W. E.; Bode, C. A.; National CenterEarth Surface Dynamics

2011-12-01

Riverine biota live within several networks. Organisms are embedded in food webs, whose structure and dynamics respond to environmental changes down river drainages. In sunlit rivers, food webs are fueled by attached algae. Primary producer biomass in the Eel River of Northwestern California, as in many sunlit, temperate rivers worldwide, is dominated by the macroalga Cladophora, which grows as a hierarchical, branched network. Cladophora proliferations vastly amplify the ecological surface area and the diversity microhabitats available to microbes. Environmental conditions (light, substrate age or stability, flow, redox gradients) change in partially predictable ways along both Cladophora fronds and river drainage networks, from the frond tips (or headwaters) to their base (or river mouth). We are interested in the ecological and biogeochemical consequences, at the catchment scale, of cross-scale interactions of microbial food webs on Cladophora with macro-organismal food webs, as these change down river drainages. We are beginning to explore how seasonal, hydrologic and macro-consumer control over the production and fate of Cladophora and its epiphytes could mediate ecosystem linkages of the river, its watershed, and nearshore marine ecosystems. Of the four interacting networks we consider, the web of microbial interactions is the most poorly known, and possibly the least hierarchical due to the prevalence of metabolic processing chains (waste products of some members become resources for others) and mutualisms.

Shared signals and the potential for phylogenetic espionage between plants and animals.

PubMed

Schultz, Jack C

2002-07-01

Until recently, the study and understanding of plant and animal signalling and response mechanisms have developed independently. Recent biochemical and molecular work is producing a growing list of elements involved in responses to biotic and abiotic stimuli that are very similar across kingdoms. Some of the more interesting examples of these include prostaglandin/octadecanoid-mediated responses to wounding, steroid-based signalling systems, and pathogen-recognition mechanisms. Some of these similarities probably represent evolutionary convergence; others may be ancestral to plants and animals. Ecological and evolutionary implications of such overlaps include the existence of pathogens that can cause disease in plants and animals, the ability of herbivores to manipulate plant responses, usurpation of microbial mechanisms and genes by herbivorous animals and plants, evolution of plant defenses exploiting shared signals in animals, and the medicinal use of plants by humans. Comparative study of the signalling and response mechanisms used by plants, animals, and microbes provides novel and useful insights to the ecology and evolution of interactions across kingdoms.

Microbial-mediated method for metal oxide nanoparticle formation

DOEpatents

Rondinone, Adam J.; Moon, Ji Won; Love, Lonnie J.; Yeary, Lucas W.; Phelps, Tommy J.

2015-09-08

The invention is directed to a method for producing metal oxide nanoparticles, the method comprising: (i) subjecting a combination of reaction components to conditions conducive to microbial-mediated formation of metal oxide nanoparticles, wherein said combination of reaction components comprise: metal-reducing microbes, a culture medium suitable for sustaining said metal-reducing microbes, an effective concentration of one or more surfactants, a reducible metal oxide component containing one or more reducible metal species, and one or more electron donors that provide donatable electrons to said metal-reducing microbes during consumption of the electron donor by said metal-reducing microbes; and (ii) isolating said metal oxide nanoparticles, which contain a reduced form of said reducible metal oxide component. The invention is also directed to metal oxide nanoparticle compositions produced by the inventive method.

Phosphatic precipitates associated with actinomycetes in speleothems from Grand Cayman, British West Indies

NASA Astrophysics Data System (ADS)

Jones, Brian

2009-07-01

Calcitic speleothems from a cave located on the north central coast of Grand Cayman commonly include corrosion surfaces that developed when calcite precipitation ceased and corrosion mediated by condensates became the operative process. Dissolution features associated with these surfaces, including etched crystal surfaces, microcavities, and solution-widened boundaries between crystals, are commonly occupied by microbes and microbial mats that have been replaced by calcium phosphate and/or coated with calcium phosphate. No mineralized microbes were found in the calcite crystals that form the speleothems. The morphology of the mineralized hyphae (eight morphotypes) and spores (nine morphotypes) are indicative of actinomycetes, a group of microbes that are ideally adapted to life in oligotrophic cave environs. Superb preservation of the delicate hyphae, aerial hyphae, and delicate ornamentation on the hyphae and spores indicate that the microbes underwent rapid mineralized while close to their original life positions. Although these actinomycetes were extremely susceptible to replacement by calcium phosphate, there is no evidence that they directly or indirectly controlled precipitation. Nevertheless, the association between the P-rich precipitates and microbes shows that the use of phosphorus as a proxy for seasonal climate changes in paleoclimate analyses must be treated with caution.

Functional genomics and microbiome profiling of the Asian longhorned beetle (Anoplophora glabripennis) reveal insights into the digestive physiology and nutritional ecology of wood feeding beetles.

PubMed

Scully, Erin D; Geib, Scott M; Carlson, John E; Tien, Ming; McKenna, Duane; Hoover, Kelli

2014-12-12

Wood-feeding beetles harbor an ecologically rich and taxonomically diverse assemblage of gut microbes that appear to promote survival in woody tissue, which is devoid of nitrogen and essential nutrients. Nevertheless, the contributions of these apparent symbionts to digestive physiology and nutritional ecology remain uncharacterized in most beetle lineages. Through parallel transcriptome profiling of beetle- and microbial- derived mRNAs, we demonstrate that the midgut microbiome of the Asian longhorned beetle (Anoplophora glabripennis), a member of the beetle family Cerambycidae, is enriched in biosynthetic pathways for the synthesis of essential amino acids, vitamins, and sterols. Consequently, the midgut microbiome of A. glabripennis can provide essential nutrients that the beetle cannot obtain from its woody diet or synthesize itself. The beetle gut microbiota also produce their own suite of transcripts that can enhance lignin degradation, degrade hemicellulose, and ferment xylose and wood sugars. An abundance of cellulases from several glycoside hydrolase families are expressed endogenously by A. glabripennis, as well as transcripts that allow the beetle to convert microbe-synthesized essential amino acids into non-essential amino acids. A. glabripennis and its gut microbes likely collaborate to digest carbohydrates and convert released sugars and amino acid intermediates into essential nutrients otherwise lacking from their woody host plants. The nutritional provisioning capabilities of the A. glabripennis gut microbiome may contribute to the beetles' unusually broad host range. The presence of some of the same microbes in the guts of other Cerambycidae and other wood-feeding beetles suggests that partnerships with microbes may be a facilitator of evolutionary radiations in beetles, as in certain other groups of insects, allowing access to novel food sources through enhanced nutritional provisioning.

Microbial imprint on soil-atmosphere H2, COS, and CO2 fluxes

NASA Astrophysics Data System (ADS)

Meredith, L. K.; Commane, R.; Munger, J. W.; Wofsy, S. C.; Prinn, R. G.

2013-12-01

Microorganisms drive large trace gas fluxes between soil and atmosphere, but the signal can be difficult to detect and quantify in the presence of stronger exchange processes in an ecosystem. Partitioning methods are often needed to estimate trace gas budgets and to develop process-based models to explore the sensitivity of microbe-mediated fluxes. In this study, we test the performance of trace gases with predominantly microbe-mediated soil fluxes as a metric of the soil microbial uptake activity of other trace gases. Using simultaneous, collocated measurements at Harvard Forest, we consider three trace gases with microbe-mediated soil fluxes of various importance relative to their other (mainly plant-mediated) ecosystem fluxes: molecular hydrogen (H2), carbonyl sulfide (COS), and carbon dioxide (CO2). These gases probe different aspects of the soil trace-gas microbiology. Soil H2 uptake is a redox reaction driving the energy metabolism of a portion of the microbial community, while soil CO2 respiration is a partial proxy for the overall soil microbial metabolism. In comparison, very little is understood about the microbiological and environmental drivers of soil COS uptake and emissions. In this study, we find that H2, COS, and CO2 soil uptake rates are often correlated, but the relative soil uptake between gases is not constant, and is influenced by seasonality and local environmental conditions. We also consider how differences in the microbial communities and pathways involved in the soil fluxes may explain differences in the observations. Our results are important for informing previous studies using tracer approaches. For example, H2 has been used to estimate COS soil uptake, which must be accounted for to use COS as a carbon cycle tracer. Furthermore, the global distribution of H2 deposition velocity has been inferred from net primary productivity (CO2). Given that insufficient measurement frequency and spatial distribution exists to partition global net ecosystem fluxes of many climate-relevant trace gases, insight into the use of certain trace gases to estimate rates of more general biogeochemical processes is useful.

Genomic reconstruction of novel sediment phyla enlightens roles in sedimentary biogeochemical cycling

NASA Astrophysics Data System (ADS)

Baker, B.; Lazar, C.; Seitz, K.; Teske, A.; Hinrichs, K. U.; Dick, G.

2015-12-01

Estuaries are among the most productive habitats on the planet. Microbes in estuary sediments control the turnover of organic carbon, and the anaerobic cycling of nitrogen and sulfur. These communities are complex and primarily made up of uncultured lineages, thus little is known about how ecological and metabolic processes are partitioned in sediments. We reconstructed 82 bacterial and 24 archaeal high-quality genomes from different redox regimes (sulfate-rich, sulfate-methane transition zone, and methane-rich zones) of estuary sediments. These bacteria belong to 23 distinct groups, including uncultured candidate phyla (eg. KSB1, TA06, and KD3-62), and three newly described phyla (WOR-1, and -2, and -3). The archaea encompass 8 widespread sediment lineages including MGB-D, RC-III and IV, Z7ME43, Parvarchaeota, Lokiarchoaeta (MBG-B), SAGMEG, Bathyarchaeota (groups MCG-1, -6, -7, and -15) and previously unrecognized deeply branched phylum "Thorarchaeota". The uncultured phyla mediate essential biogeochemical processes of the estuarine environment. Z7ME43 archaea have genes for S disproportionation (S0 reduction and thiosulfate reduction and oxidation). SAGMEG appear to be strict anaerobes capable of coupling CO/H2 oxidation to either S0 or nitrite reduction and have novel RubisCO genes for carbon fixation. Thorarchaeota contain pathways for acetate production from the degradation of detrital proteins and intermediate S cycling. Furthermore, the gene content of this group revealed links in the evolutionary histories of archaea and eukaryotes. This dataset extents our knowledge of the metabolic potential of several uncultured phyla. We were able to chart the flow of carbon and nutrients through the multiple layers of bacterial processing and reveal potential ecological interactions within the communities.

Application of a neutral community model to assess structuring of the human lung microbiome.

PubMed

Venkataraman, Arvind; Bassis, Christine M; Beck, James M; Young, Vincent B; Curtis, Jeffrey L; Huffnagle, Gary B; Schmidt, Thomas M

2015-01-20

DNA from phylogenetically diverse microbes is routinely recovered from healthy human lungs and used to define the lung microbiome. The proportion of this DNA originating from microbes adapted to the lungs, as opposed to microbes dispersing to the lungs from other body sites and the atmosphere, is not known. We use a neutral model of community ecology to distinguish members of the lung microbiome whose presence is consistent with dispersal from other body sites and those that deviate from the model, suggesting a competitive advantage to these microbes in the lungs. We find that the composition of the healthy lung microbiome is consistent with predictions of the neutral model, reflecting the overriding role of dispersal of microbes from the oral cavity in shaping the microbial community in healthy lungs. In contrast, the microbiome of diseased lungs was readily distinguished as being under active selection. We also assessed the viability of microbes from lung samples by cultivation with a variety of media and incubation conditions. Bacteria recovered by cultivation from healthy lungs represented species that comprised 61% of the 16S rRNA-encoding gene sequences derived from bronchoalveolar lavage samples. Neutral distribution of microbes is a distinguishing feature of the microbiome in healthy lungs, wherein constant dispersal of bacteria from the oral cavity overrides differential growth of bacteria. No bacterial species consistently deviated from the model predictions in healthy lungs, although representatives of many of the dispersed species were readily cultivated. In contrast, bacterial populations in diseased lungs were identified as being under active selection. Quantification of the relative importance of selection and neutral processes such as dispersal in shaping the healthy lung microbiome is a first step toward understanding its impacts on host health. Copyright © 2015 Venkataraman et al.

Abiotic Stress Responses and Microbe-Mediated Mitigation in Plants: The Omics Strategies

PubMed Central

Meena, Kamlesh K.; Sorty, Ajay M.; Bitla, Utkarsh M.; Choudhary, Khushboo; Gupta, Priyanka; Pareek, Ashwani; Singh, Dhananjaya P.; Prabha, Ratna; Sahu, Pramod K.; Gupta, Vijai K.; Singh, Harikesh B.; Krishanani, Kishor K.; Minhas, Paramjit S.

2017-01-01

Abiotic stresses are the foremost limiting factors for agricultural productivity. Crop plants need to cope up adverse external pressure created by environmental and edaphic conditions with their intrinsic biological mechanisms, failing which their growth, development, and productivity suffer. Microorganisms, the most natural inhabitants of diverse environments exhibit enormous metabolic capabilities to mitigate abiotic stresses. Since microbial interactions with plants are an integral part of the living ecosystem, they are believed to be the natural partners that modulate local and systemic mechanisms in plants to offer defense under adverse external conditions. Plant-microbe interactions comprise complex mechanisms within the plant cellular system. Biochemical, molecular and physiological studies are paving the way in understanding the complex but integrated cellular processes. Under the continuous pressure of increasing climatic alterations, it now becomes more imperative to define and interpret plant-microbe relationships in terms of protection against abiotic stresses. At the same time, it also becomes essential to generate deeper insights into the stress-mitigating mechanisms in crop plants for their translation in higher productivity. Multi-omics approaches comprising genomics, transcriptomics, proteomics, metabolomics and phenomics integrate studies on the interaction of plants with microbes and their external environment and generate multi-layered information that can answer what is happening in real-time within the cells. Integration, analysis and decipherization of the big-data can lead to a massive outcome that has significant chance for implementation in the fields. This review summarizes abiotic stresses responses in plants in-terms of biochemical and molecular mechanisms followed by the microbe-mediated stress mitigation phenomenon. We describe the role of multi-omics approaches in generating multi-pronged information to provide a better understanding of plant–microbe interactions that modulate cellular mechanisms in plants under extreme external conditions and help to optimize abiotic stresses. Vigilant amalgamation of these high-throughput approaches supports a higher level of knowledge generation about root-level mechanisms involved in the alleviation of abiotic stresses in organisms. PMID:28232845

Abiotic Stress Responses and Microbe-Mediated Mitigation in Plants: The Omics Strategies.

PubMed

Meena, Kamlesh K; Sorty, Ajay M; Bitla, Utkarsh M; Choudhary, Khushboo; Gupta, Priyanka; Pareek, Ashwani; Singh, Dhananjaya P; Prabha, Ratna; Sahu, Pramod K; Gupta, Vijai K; Singh, Harikesh B; Krishanani, Kishor K; Minhas, Paramjit S

2017-01-01

Abiotic stresses are the foremost limiting factors for agricultural productivity. Crop plants need to cope up adverse external pressure created by environmental and edaphic conditions with their intrinsic biological mechanisms, failing which their growth, development, and productivity suffer. Microorganisms, the most natural inhabitants of diverse environments exhibit enormous metabolic capabilities to mitigate abiotic stresses. Since microbial interactions with plants are an integral part of the living ecosystem, they are believed to be the natural partners that modulate local and systemic mechanisms in plants to offer defense under adverse external conditions. Plant-microbe interactions comprise complex mechanisms within the plant cellular system. Biochemical, molecular and physiological studies are paving the way in understanding the complex but integrated cellular processes. Under the continuous pressure of increasing climatic alterations, it now becomes more imperative to define and interpret plant-microbe relationships in terms of protection against abiotic stresses. At the same time, it also becomes essential to generate deeper insights into the stress-mitigating mechanisms in crop plants for their translation in higher productivity. Multi-omics approaches comprising genomics, transcriptomics, proteomics, metabolomics and phenomics integrate studies on the interaction of plants with microbes and their external environment and generate multi-layered information that can answer what is happening in real-time within the cells. Integration, analysis and decipherization of the big-data can lead to a massive outcome that has significant chance for implementation in the fields. This review summarizes abiotic stresses responses in plants in-terms of biochemical and molecular mechanisms followed by the microbe-mediated stress mitigation phenomenon. We describe the role of multi-omics approaches in generating multi-pronged information to provide a better understanding of plant-microbe interactions that modulate cellular mechanisms in plants under extreme external conditions and help to optimize abiotic stresses. Vigilant amalgamation of these high-throughput approaches supports a higher level of knowledge generation about root-level mechanisms involved in the alleviation of abiotic stresses in organisms.

Microbes in the coral holobiont: partners through evolution, development, and ecological interactions

PubMed Central

Thompson, Janelle R.; Rivera, Hanny E.; Closek, Collin J.; Medina, Mónica

2015-01-01

In the last two decades, genetic and genomic studies have revealed the astonishing diversity and ubiquity of microorganisms. Emergence and expansion of the human microbiome project has reshaped our thinking about how microbes control host health—not only as pathogens, but also as symbionts. In coral reef environments, scientists have begun to examine the role that microorganisms play in coral life history. Herein, we review the current literature on coral-microbe interactions within the context of their role in evolution, development, and ecology. We ask the following questions, first posed by McFall-Ngai et al. (2013) in their review of animal evolution, with specific attention to how coral-microbial interactions may be affected under future environmental conditions: (1) How do corals and their microbiome affect each other's genomes? (2) How does coral development depend on microbial partners? (3) How is homeostasis maintained between corals and their microbial symbionts? (4) How can ecological approaches deepen our understanding of the multiple levels of coral-microbial interactions? Elucidating the role that microorganisms play in the structure and function of the holobiont is essential for understanding how corals maintain homeostasis and acclimate to changing environmental conditions. PMID:25621279

Engineered microbes and methods for microbial oil production

DOEpatents

Stephanopoulos, Gregory; Tai, Mitchell; Chakraborty, Sagar

2015-02-10

Some aspects of this invention provide engineered microbes for oil production. Methods for microbe engineering and for use of engineered microbes are also provided herein. In some embodiments, microbes are provided that are engineered to modulate a combination of rate-controlling steps of lipid synthesis, for example, a combination of a step generating metabolites, acetyl-CoA, ATP or NADPH for lipid synthesis (a push step), and a step sequestering a product or an intermediate of a lipid synthesis pathway that mediates feedback inhibition of lipid synthesis (a pull step). Such push-and-pull engineered microbes exhibit greatly enhanced conversion yields and TAG synthesis and storage properties.

Biotic Interactions in Microbial Communities as Modulators of Biogeochemical Processes: Methanotrophy as a Model System

PubMed Central

Ho, Adrian; Angel, Roey; Veraart, Annelies J.; Daebeler, Anne; Jia, Zhongjun; Kim, Sang Yoon; Kerckhof, Frederiek-Maarten; Boon, Nico; Bodelier, Paul L. E.

2016-01-01

Microbial interaction is an integral component of microbial ecology studies, yet the role, extent, and relevance of microbial interaction in community functioning remains unclear, particularly in the context of global biogeochemical cycles. While many studies have shed light on the physico-chemical cues affecting specific processes, (micro)biotic controls and interactions potentially steering microbial communities leading to altered functioning are less known. Yet, recent accumulating evidence suggests that the concerted actions of a community can be significantly different from the combined effects of individual microorganisms, giving rise to emergent properties. Here, we exemplify the importance of microbial interaction for ecosystem processes by analysis of a reasonably well-understood microbial guild, namely, aerobic methane-oxidizing bacteria (MOB). We reviewed the literature which provided compelling evidence for the relevance of microbial interaction in modulating methane oxidation. Support for microbial associations within methane-fed communities is sought by a re-analysis of literature data derived from stable isotope probing studies of various complex environmental settings. Putative positive interactions between active MOB and other microbes were assessed by a correlation network-based analysis with datasets covering diverse environments where closely interacting members of a consortium can potentially alter the methane oxidation activity. Although, methanotrophy is used as a model system, the fundamentals of our postulations may be applicable to other microbial guilds mediating other biogeochemical processes. PMID:27602021

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

Furlow, Julie Maupin-

Archaea, one of three major evolutionary lineages of life, are a fascinating and diverse group of microbes with deep roots overlapping those of eukaryotes. The focus of the 'Archaea: Ecology Metabolism & Molecular Biology' GRC conference expands on a number of emerging topics highlighting new paradigms in archaeal metabolism, genome function and systems biology; information processing; evolution and the tree of life; the ecology and diversity of archaea and their viruses; and industrial applications. The strength of this conference lies in its ability to couple a field with a rich history in high quality research with new scientific findings inmore » an atmosphere of stimulating exchange. This conference remains an excellent opportunity for younger scientists to interact with world experts in this field.« less

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

Keneth Stedman

Archaea, one of three major evolutionary lineages of life, are a fascinating and diverse group of microbes with deep roots overlapping those of eukaryotes. The focus of the 'Archaea: Ecology Metabolism & Molecular Biology' GRC conference expands on a number of emerging topics highlighting new paradigms in archaeal metabolism, genome function and systems biology; information processing; evolution and the tree of life; the ecology and diversity of archaea and their viruses. The strength of this conference lies in its ability to couple a field with a rich history in high quality research with new scientific findings in an atmosphere ofmore » stimulating exchange. This conference remains an excellent opportunity for younger scientists to interact with world experts in this field.« less

Microbial seascapes revisited.

PubMed

DeLong, E F

2001-06-01

A remarkable array of new discoveries is emerging from studies of naturally occurring marine microbes. These discoveries originate from novel applications of evolving technologies, ranging from molecular phylogenetics to stable isotope analyses, to advanced microscopic techniques, to genomics. As a consequence, new perspectives on the natural history of marine microbes, the inseparable nature of the geological and biological worlds, and a plethora of unexpected new genotypes, phenotypes and physiologies are now being revealed. As our observations of naturally occurring microbes become increasingly more sophisticated, so will theory, technical applications and predictive capabilities in microbial ecology.

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.

Effects of Bacillus subtilis endospore surface reactivity on the rate of forsterite dissolution

NASA Astrophysics Data System (ADS)

Harrold, Z.; Gorman-Lewis, D.

2013-12-01

Primary mineral dissolution products, such as silica (Si), calcium (Ca) and magnesium (Mg), play an important role in numerous biologic and geochemical cycles including microbial metabolism, plant growth and secondary mineral precipitation. The flux of these and other dissolution products into the environment is largely controlled by the rate of primary silicate mineral dissolution. Bacteria, a ubiquitous component in water-rock systems, are known to facilitate mineral dissolution and may play a substantial role in determining the overall flux of dissolution products into the environment. Bacterial cell walls are complex and highly reactive organic surfaces that can affect mineral dissolution rates directly through microbe-mineral adsorption or indirectly by complexing dissolution products. The effect of bacterial surface adsorption on chemical weathering rates may even outweigh the influence of active processes in environments where a high proportion of cells are metabolically dormant or cell metabolism is slow. Complications associated with eliminating or accounting for ongoing metabolic processes in long-term dissolution studies have made it challenging to isolate the influence of cell wall interactions on mineral dissolution rates. We utilized Bacillus subtilis endospores, a robust and metabolically dormant cell type, to isolate and quantify the effects of bacterial surface reactivity on forsterite (Mg2SiO4) dissolution rates. We measured the influence of both direct and indirect microbe-mineral interactions on forsterite dissolution. Indirect pathways were isolated using dialysis tubing to prevent mineral-microbe contact while allowing free exchange of dissolved mineral products and endospore-ion adsorption. Homogenous experimental assays allowed both direct microbe-mineral and indirect microbe-ion interactions to affect forsterite dissolution rates. Dissolution rates were calculated based on silica concentrations and zero-order dissolution kinetics. Additional analyses including Mg concentrations, microprobe and BET analyses support mineral dissolution rate calculations and stoichiometry considerations. All experimental assays containing endospores show increased forsterite dissolution rates relative to abiotic controls. Forsterite dissolution rates increased by approximately one order of magnitude in dialysis bound, biotic experiments relative to abiotic assays. Homogenous biotic assays exhibited a more complex dissolution rate profile that changes over time. All microbially mediated forsterite dissolution rates returned to abiotic control rates after 10 to 15 days of incubation. This shift in dissolution rate likely corresponds to maximum endospore surface adsorption capacity. The Bacillus subtilis endospore surface serves as a first-order proxy for studying the effect of metabolizing microbe surfaces on silicate dissolution rates. Comparisons with published abiotic, microbial, and organic acid mediated forsterite dissolution rates will provide insight on the importance of bacterial surfaces in primary mineral dissolution processes.

75 years of dryland science: Trends and gaps in arid ecology literature.

PubMed

Greenville, Aaron C; Dickman, Chris R; Wardle, Glenda M

2017-01-01

Growth in the publication of scientific articles is occurring at an exponential rate, prompting a growing need to synthesise information in a timely manner to combat urgent environmental problems and guide future research. Here, we undertake a topic analysis of dryland literature over the last 75 years (8218 articles) to identify areas in arid ecology that are well studied and topics that are emerging. Four topics-wetlands, mammal ecology, litter decomposition and spatial modelling, were identified as 'hot topics' that showed higher than average growth in publications from 1940 to 2015. Five topics-remote sensing, climate, habitat and spatial, agriculture and soils-microbes, were identified as 'cold topics', with lower than average growth over the survey period, but higher than average numbers of publications. Topics in arid ecology clustered into seven broad groups on word-based similarity. These groups ranged from mammal ecology and population genetics, broad-scale management and ecosystem modelling, plant ecology, agriculture and ecophysiology, to populations and paleoclimate. These patterns may reflect trends in the field of ecology more broadly. We also identified two broad research gaps in arid ecology: population genetics, and habitat and spatial research. Collaborations between population genetics and ecologists and investigations of ecological processes across spatial scales would contribute profitably to the advancement of arid ecology and to ecology more broadly.

Harnessing Host-Vector Microbiome for Sustainable Plant Disease Management of Phloem-Limited Bacteria.

PubMed

Trivedi, Pankaj; Trivedi, Chanda; Grinyer, Jasmine; Anderson, Ian C; Singh, Brajesh K

2016-01-01

Plant health and productivity is strongly influenced by their intimate interaction with deleterious and beneficial organisms, including microbes, and insects. Of the various plant diseases, insect-vectored diseases are of particular interest, including those caused by obligate parasites affecting plant phloem such as Candidatus ( Ca .) Phytoplasma species and several species of Ca. Liberibacter. Recent studies on plant-microbe and plant-insect interactions of these pathogens have demonstrated that plant-microbe-insect interactions have far reaching consequences for the functioning and evolution of the organisms involved. These interactions take place within complex pathosystems and are shaped by a myriad of biotic and abiotic factors. However, our current understanding of these processes and their implications for the establishment and spread of insect-borne diseases remains limited. This article highlights the molecular, ecological, and evolutionary aspects of interactions among insects, plants, and their associated microbial communities with a focus on insect vectored and phloem-limited pathogens belonging to Ca. Phytoplasma and Ca. Liberibacter species. We propose that innovative and interdisciplinary research aimed at linking scales from the cellular to the community level will be vital for increasing our understanding of the mechanisms underpinning plant-insect-microbe interactions. Examination of such interactions could lead us to applied solutions for sustainable disease and pest management.

Gene-centric approach to integrating environmental genomics and biogeochemical models.

PubMed

Reed, Daniel C; Algar, Christopher K; Huber, Julie A; Dick, Gregory J

2014-02-04

Rapid advances in molecular microbial ecology have yielded an unprecedented amount of data about the evolutionary relationships and functional traits of microbial communities that regulate global geochemical cycles. Biogeochemical models, however, are trailing in the wake of the environmental genomics revolution, and such models rarely incorporate explicit representations of bacteria and archaea, nor are they compatible with nucleic acid or protein sequence data. Here, we present a functional gene-based framework for describing microbial communities in biogeochemical models by incorporating genomics data to provide predictions that are readily testable. To demonstrate the approach in practice, nitrogen cycling in the Arabian Sea oxygen minimum zone (OMZ) was modeled to examine key questions about cryptic sulfur cycling and dinitrogen production pathways in OMZs. Simulations support previous assertions that denitrification dominates over anammox in the central Arabian Sea, which has important implications for the loss of fixed nitrogen from the oceans. Furthermore, cryptic sulfur cycling was shown to attenuate the secondary nitrite maximum often observed in OMZs owing to changes in the composition of the chemolithoautotrophic community and dominant metabolic pathways. Results underscore the need to explicitly integrate microbes into biogeochemical models rather than just the metabolisms they mediate. By directly linking geochemical dynamics to the genetic composition of microbial communities, the method provides a framework for achieving mechanistic insights into patterns and biogeochemical consequences of marine microbes. Such an approach is critical for informing our understanding of the key role microbes play in modulating Earth's biogeochemistry.

Rarity in aquatic microbes: placing protists on the map.

PubMed

Logares, Ramiro; Mangot, Jean-François; Massana, Ramon

2015-12-01

Most microbial richness at any given time tends to be represented by low-abundance (rare) taxa, which are collectively referred to as the "rare biosphere". Here we review works on the rare biosphere using high-throughput sequencing (HTS), with a particular focus on unicellular eukaryotes or protists. Evidence thus far indicates that the rare biosphere encompasses dormant as well as metabolically active microbes that could potentially play key roles in ecosystem functioning. Rare microbes appear to have biogeography, and sometimes the observed patterns can be similar to what is observed among abundant taxa, suggesting similar community-structuring mechanisms. There is limited evidence indicating that the rare biosphere contains taxa that are phylogenetically distantly related to abundant counterparts; therefore, the rare biosphere may act as a reservoir of deep-branching phylogenetic diversity. The potential role of the rare biosphere as a bank of redundant functions that can help to maintain continuous ecosystem function following oscillations in taxonomic abundances is hypothesized as its main ecological role. Future studies focusing on rare microbes are crucial for advancing our knowledge of microbial ecology and evolution and unveiling their links with ecosystem function. Copyright © 2015 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Bio-rescue of marine environments: On the track of microbially-based metal/metalloid remediation.

PubMed

Marques, Catarina R

2016-09-15

The recent awareness of the huge relevance of marine resources and ecological services is driving regulatory demands for their protection from overwhelming contaminants, such as metals/metalloids. These contaminants enter and accumulate in different marine niches, hence deeply compromising their quality and integrity. Bioremediation has been flourishing to counteract metal/metalloid impacts, since it provides cost-effective and sustainable options by relying on ecology-based technologies. The potential of marine microbes for metal/metalloid bioremediation is the core of many studies, due to their high plasticity to overcome successive environmental hurdles. However, any thorough review on the advances of metal/metalloid bioremediation in marine environments was so far unveiled. This review is designed to (i) outline the characteristics and potential of marine microbes for metal/metalloid bioremediation, (ii) describe the underlying pathways of resistance and detoxification, as well as useful methodologies for their characterization, (iii) identify major bottlenecks on metal/metalloid bioremediation with marine microbes, (iv) present alternative strategies based on microbial consortia and engineered microbes for enhanced bioremediation, and (v) propose key research avenues to keep pace with a changing society, science and economy in a sustainable manner. Copyright © 2016 Elsevier B.V. All rights reserved.

Emergence of increased frequency and severity of multiple infections by viruses due to spatial clustering of hosts

NASA Astrophysics Data System (ADS)

Taylor, Bradford P.; Penington, Catherine J.; Weitz, Joshua S.

2016-12-01

Multiple virus particles can infect a target host cell. Such multiple infections (MIs) have significant and varied ecological and evolutionary consequences for both virus and host populations. Yet, the in situ rates and drivers of MIs in virus-microbe systems remain largely unknown. Here, we develop an individual-based model (IBM) of virus-microbe dynamics to probe how spatial interactions drive the frequency and nature of MIs. In our IBMs, we identify increasingly spatially correlated clusters of viruses given sufficient decreases in viral movement. We also identify increasingly spatially correlated clusters of viruses and clusters of hosts given sufficient increases in viral infectivity. The emergence of clusters is associated with an increase in multiply infected hosts as compared to expectations from an analogous mean field model. We also observe long-tails in the distribution of the multiplicity of infection in contrast to mean field expectations that such events are exponentially rare. We show that increases in both the frequency and severity of MIs occur when viruses invade a cluster of uninfected microbes. We contend that population-scale enhancement of MI arises from an aggregate of invasion dynamics over a distribution of microbe cluster sizes. Our work highlights the need to consider spatially explicit interactions as a potentially key driver underlying the ecology and evolution of virus-microbe communities.

A comprehensive insight into functional profiles of free-living microbial community responses to a toxic Akashiwo sanguinea bloom

NASA Astrophysics Data System (ADS)

Yang, Caiyun; Li, Yi; Zhou, Yanyan; Lei, Xueqian; Zheng, Wei; Tian, Yun; van Nostrand, Joy D.; He, Zhili; Wu, Liyou; Zhou, Jizhong; Zheng, Tianling

2016-10-01

Phytoplankton blooms are a worldwide problem and can greatly affect ecological processes in aquatic systems, but its impacts on the functional potential of microbial communities are limited. In this study, a high-throughput microarray-based technology (GeoChip) was used to profile the functional potential of free-living microbes from the Xiamen Sea Area in response to a 2011 Akashiwo sanguinea bloom. The bloom altered the overall community functional structure. Genes that were significantly (p < 0.05) increased during the bloom included carbon degradation genes and genes involved in nitrogen (N) and/or phosphorus (P) limitation stress. Such significantly changed genes were well explained by chosen environmental factors (COD, nitrite-N, nitrate-N, dissolved inorganic phosphorus, chlorophyll-a and algal density). Overall results suggested that this bloom might enhance the microbial converting of nitrate to N2 and ammonia nitrogen, decrease P removal from seawater, activate the glyoxylate cycle, and reduce infection activity of bacteriophage. This study presents new information on the relationship of algae to other microbes in aquatic systems, and provides new insights into our understanding of ecological impacts of phytoplankton blooms.

The Oral and Skin Microbiomes of Captive Komodo Dragons Are Significantly Shared with Their Habitat

PubMed Central

Hyde, Embriette R.; Navas-Molina, Jose A.; Kueneman, Jordan G.; Ackermann, Gail; Cardona, Cesar; Humphrey, Gregory; Boyer, Don; Weaver, Tom; Mendelson, Joseph R.; McKenzie, Valerie J.; Gilbert, Jack A.

2016-01-01

ABSTRACT Examining the way in which animals, including those in captivity, interact with their environment is extremely important for studying ecological processes and developing sophisticated animal husbandry. Here we use the Komodo dragon (Varanus komodoensis) to quantify the degree of sharing of salivary, skin, and fecal microbiota with their environment in captivity. Both species richness and microbial community composition of most surfaces in the Komodo dragon’s environment are similar to the Komodo dragon’s salivary and skin microbiota but less similar to the stool-associated microbiota. We additionally compared host-environment microbiome sharing between captive Komodo dragons and their enclosures, humans and pets and their homes, and wild amphibians and their environments. We observed similar host-environment microbiome sharing patterns among humans and their pets and Komodo dragons, with high levels of human/pet- and Komodo dragon-associated microbes on home and enclosure surfaces. In contrast, only small amounts of amphibian-associated microbes were detected in the animals’ environments. We suggest that the degree of sharing between the Komodo dragon microbiota and its enclosure surfaces has important implications for animal health. These animals evolved in the context of constant exposure to a complex environmental microbiota, which likely shaped their physiological development; in captivity, these animals will not receive significant exposure to microbes not already in their enclosure, with unknown consequences for their health. IMPORTANCE Animals, including humans, have evolved in the context of exposure to a variety of microbial organisms present in the environment. Only recently have humans, and some animals, begun to spend a significant amount of time in enclosed artificial environments, rather than in the more natural spaces in which most of evolution took place. The consequences of this radical change in lifestyle likely extend to the microbes residing in and on our bodies and may have important implications for health and disease. A full characterization of host-microbe sharing in both closed and open environments will provide crucial information that may enable the improvement of health in humans and in captive animals, both of which experience a greater incidence of disease (including chronic illness) than counterparts living under more ecologically natural conditions. PMID:27822543

The Oral and Skin Microbiomes of Captive Komodo Dragons Are Significantly Shared with Their Habitat.

PubMed

Hyde, Embriette R; Navas-Molina, Jose A; Song, Se Jin; Kueneman, Jordan G; Ackermann, Gail; Cardona, Cesar; Humphrey, Gregory; Boyer, Don; Weaver, Tom; Mendelson, Joseph R; McKenzie, Valerie J; Gilbert, Jack A; Knight, Rob

2016-01-01

Examining the way in which animals, including those in captivity, interact with their environment is extremely important for studying ecological processes and developing sophisticated animal husbandry. Here we use the Komodo dragon ( Varanus komodoensis ) to quantify the degree of sharing of salivary, skin, and fecal microbiota with their environment in captivity. Both species richness and microbial community composition of most surfaces in the Komodo dragon's environment are similar to the Komodo dragon's salivary and skin microbiota but less similar to the stool-associated microbiota. We additionally compared host-environment microbiome sharing between captive Komodo dragons and their enclosures, humans and pets and their homes, and wild amphibians and their environments. We observed similar host-environment microbiome sharing patterns among humans and their pets and Komodo dragons, with high levels of human/pet- and Komodo dragon-associated microbes on home and enclosure surfaces. In contrast, only small amounts of amphibian-associated microbes were detected in the animals' environments. We suggest that the degree of sharing between the Komodo dragon microbiota and its enclosure surfaces has important implications for animal health. These animals evolved in the context of constant exposure to a complex environmental microbiota, which likely shaped their physiological development; in captivity, these animals will not receive significant exposure to microbes not already in their enclosure, with unknown consequences for their health. IMPORTANCE Animals, including humans, have evolved in the context of exposure to a variety of microbial organisms present in the environment. Only recently have humans, and some animals, begun to spend a significant amount of time in enclosed artificial environments, rather than in the more natural spaces in which most of evolution took place. The consequences of this radical change in lifestyle likely extend to the microbes residing in and on our bodies and may have important implications for health and disease. A full characterization of host-microbe sharing in both closed and open environments will provide crucial information that may enable the improvement of health in humans and in captive animals, both of which experience a greater incidence of disease (including chronic illness) than counterparts living under more ecologically natural conditions.

Extrinsic and Intrinsic Responses to Environmental Change: Insights from Terrestrial Paleoecological Archives

NASA Astrophysics Data System (ADS)

Seddon, A. W. R.; Mackay, A. W.

2015-12-01

Current understanding of ecological behaviour indicates that systems can experience sudden and abrupt changes in state, driven either by a large external change in environmental conditions (extrinsically forced), or the result of a set local feedbacks and site-specific interactions (intrinsically mediated responses). Responses mediated by intrinsic processes are notoriously diffi- cult to predict, they can occur as slow environmental variables gradually erode the resilience of the system eventually resulting in threshold transitions between alternative stable states. Finding ways to identify, model and predict such complex ecosystem behavior has been identified as a priority research challenge for both ecology and paleoecology. The paleoecological record can play a role in understanding the processes behind abrupt ecological change because it enables the reconstruction of processes occurring over decadal-centennial timescales or longer. Therefore, paleoecological data can be used to identify the existence of ecological thresholds and to investigate the environmental processes that can lead to loss of resilience and abrupt transitions between alternate states. In addition, incidences of abrupt vegetation changes in the past can serve as palaeoecological model systems; analogues of abrupt dynamics which can be used to test theories surrounding ecological responses to climate change. Here, I present examples from a range of terrestrial ecosystems (Holocene environmental changes from a coastal lagoon in the Galapagos Islands; Northern European vegetation changes since the last deglaciation; the North American hemlock decline) demonstrating evidence of abrupt ecosystem change. For each system I present a set of statistical techniques tailored to distin- guish between extrinsic versus intrinsically mediated ecological responses. Examples are provided from both single sites (i.e. landscape scale) and multiple sites (regional-continental scale). These techniques provide a useful way to identify when and where intrinsically mediated responses to environmental change occurs; the next challenge is to understand and quantify the processes that underlie these intrinsic responses.

Engineered microbes and methods for microbial oil production

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

Stephanopoulos, Gregory; Tai, Mitchell; Chakraborty, Sagar

Some aspects of this invention provide engineered microbes for oil production. Methods for microbe engineering and for use of engineered microbes are also provided herein. In some embodiments, microbes are provided that are engineered to modulate a combination of rate-controlling steps of lipid synthesis, for example, a combination of a step generating metabolites, acetyl-CoA, ATP or NADPH for lipid synthesis (a push step), and a step sequestering a product or an intermediate of a lipid synthesis pathway that mediates feedback inhibition of lipid synthesis (a pull step). Such push-and-pull engineered microbes exhibit greatly enhanced conversion yields and TAG synthesis andmore » storage properties.« less

Microbially-mediated method for synthesis of non-oxide semiconductor nanoparticles

DOEpatents

Phelps, Tommy J.; Lauf, Robert J.; Moon, Ji Won; Rondinone, Adam J.; Love, Lonnie J.; Duty, Chad Edward; Madden, Andrew Stephen; Li, Yiliang; Ivanov, Ilia N.; Rawn, Claudia Jeanette

2014-06-24

The invention is directed to a method for producing non-oxide semiconductor nanoparticles, the method comprising: (a) subjecting a combination of reaction components to conditions conducive to microbially-mediated formation of non-oxide semiconductor nanoparticles, wherein said combination of reaction components comprises i) anaerobic microbes, ii) a culture medium suitable for sustaining said anaerobic microbes, iii) a metal component comprising at least one type of metal ion, iv) a non-metal component containing at least one non-metal selected from the group consisting of S, Se, Te, and As, and v) one or more electron donors that provide donatable electrons to said anaerobic microbes during consumption of the electron donor by said anaerobic microbes; and (b) isolating said non-oxide semiconductor nanoparticles, which contain at least one of said metal ions and at least one of said non-metals. The invention is also directed to non-oxide semiconductor nanoparticle compositions produced as above and having distinctive properties.

What is microbial community ecology?

PubMed

Konopka, Allan

2009-11-01

The activities of complex communities of microbes affect biogeochemical transformations in natural, managed and engineered ecosystems. Meaningfully defining what constitutes a community of interacting microbial populations is not trivial, but is important for rigorous progress in the field. Important elements of research in microbial community ecology include the analysis of functional pathways for nutrient resource and energy flows, mechanistic understanding of interactions between microbial populations and their environment, and the emergent properties of the complex community. Some emergent properties mirror those analyzed by community ecologists who study plants and animals: biological diversity, functional redundancy and system stability. However, because microbes possess mechanisms for the horizontal transfer of genetic information, the metagenome may also be considered as a community property.

Antimicrobial peptide expression in a wild tobacco plant reveals the limits of host-microbe-manipulations in the field

PubMed Central

Karimi Dorcheh, Elham; Li, Ran; Rameshkumar, Natarajan; Baldwin, Ian T

2018-01-01

Plant-microbe associations are thought to be beneficial for plant growth and resistance against biotic or abiotic stresses, but for natural ecosystems, the ecological analysis of microbiome function remains in its infancy. We used transformed wild tobacco plants (Nicotiana attenuata) which constitutively express an antimicrobial peptide (Mc-AMP1) of the common ice plant, to establish an ecological tool for plant-microbe studies in the field. Transgenic plants showed in planta activity against plant-beneficial bacteria and were phenotyped within the plants´ natural habitat regarding growth, fitness and the resistance against herbivores. Multiple field experiments, conducted over 3 years, indicated no differences compared to isogenic controls. Pyrosequencing analysis of the root-associated microbial communities showed no major alterations but marginal effects at the genus level. Experimental infiltrations revealed a high heterogeneity in peptide tolerance among native isolates and suggests that the diversity of natural microbial communities can be a major obstacle for microbiome manipulations in nature. PMID:29661271

Antimicrobial peptide expression in a wild tobacco plant reveals the limits of host-microbe-manipulations in the field.

PubMed

Weinhold, Arne; Karimi Dorcheh, Elham; Li, Ran; Rameshkumar, Natarajan; Baldwin, Ian T

2018-04-17

Plant-microbe associations are thought to be beneficial for plant growth and resistance against biotic or abiotic stresses, but for natural ecosystems, the ecological analysis of microbiome function remains in its infancy. We used transformed wild tobacco plants ( Nicotiana attenuata ) which constitutively express an antimicrobial peptide (Mc-AMP1) of the common ice plant, to establish an ecological tool for plant-microbe studies in the field. Transgenic plants showed in planta activity against plant-beneficial bacteria and were phenotyped within the plants´ natural habitat regarding growth, fitness and the resistance against herbivores. Multiple field experiments, conducted over 3 years, indicated no differences compared to isogenic controls. Pyrosequencing analysis of the root-associated microbial communities showed no major alterations but marginal effects at the genus level. Experimental infiltrations revealed a high heterogeneity in peptide tolerance among native isolates and suggests that the diversity of natural microbial communities can be a major obstacle for microbiome manipulations in nature. © 2018, Weinhold et al.

Genomic dissection of host-microbe and microbe-microbe interactions for advanced plant breeding.

PubMed

Kroll, Samuel; Agler, Matthew T; Kemen, Eric

2017-04-01

Agriculture faces many emerging challenges to sustainability, including limited nutrient resources, losses from diseases caused by current and emerging pathogens and environmental degradation. Microorganisms have great importance for plant growth and performance, including the potential to increase yields, nutrient uptake and pathogen resistance. An urgent need is therefore to understand and engineer plants and their associated microbial communities. Recent massive genomic sequencing of host plants and associated microbes offers resources to identify novel mechanisms of communal assembly mediated by the host. For example, host-microbe and microbe-microbe interactions are involved in niche formation, thereby contributing to colonization. By leveraging genomic resources, genetic traits underlying those mechanisms will become important resources to design plants selecting and hosting beneficial microbial communities. Copyright © 2017 Elsevier Ltd. All rights reserved.

Functional diversity and redundancy across fish gut, sediment and water bacterial communities.

PubMed

Escalas, Arthur; Troussellier, Marc; Yuan, Tong; Bouvier, Thierry; Bouvier, Corinne; Mouchet, Maud A; Flores Hernandez, Domingo; Ramos Miranda, Julia; Zhou, Jizhong; Mouillot, David

2017-08-01

This article explores the functional diversity and redundancy in a bacterial metacommunity constituted of three habitats (sediment, water column and fish gut) in a coastal lagoon under anthropogenic pressure. Comprehensive functional gene arrays covering a wide range of ecological processes and stress resistance genes to estimate the functional potential of bacterial communities were used. Then, diversity partitioning was used to characterize functional diversity and redundancy within (α), between (β) and across (γ) habitats. It was showed that all local communities exhibit a highly diversified potential for the realization of key ecological processes and resistance to various environmental conditions, supporting the growing evidence that macro-organisms microbiomes harbour a high functional potential and are integral components of functional gene dynamics in aquatic bacterial metacommunities. Several levels of functional redundancy at different scales of the bacterial metacommunity were observed (within local communities, within habitats and at the metacommunity level). The results suggested a high potential for the realization of spatial ecological insurance within this ecosystem, that is, the functional compensation among microorganisms for the realization and maintenance of key ecological processes, within and across habitats. Finally, the role of macro-organisms as dispersal vectors of microbes and their potential influence on marine metacommunity dynamics were discussed. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Nutrient and Rainfall Additions Shift Phylogenetically Estimated Traits of Soil Microbial Communities.

PubMed

Gravuer, Kelly; Eskelinen, Anu

2017-01-01

Microbial traits related to ecological responses and functions could provide a common currency facilitating synthesis and prediction; however, such traits are difficult to measure directly for all taxa in environmental samples. Past efforts to estimate trait values based on phylogenetic relationships have not always distinguished between traits with high and low phylogenetic conservatism, limiting reliability, especially in poorly known environments, such as soil. Using updated reference trees and phylogenetic relationships, we estimated two phylogenetically conserved traits hypothesized to be ecologically important from DNA sequences of the 16S rRNA gene from soil bacterial and archaeal communities. We sampled these communities from an environmental change experiment in California grassland applying factorial addition of late-season precipitation and soil nutrients to multiple soil types for 3 years prior to sampling. Estimated traits were rRNA gene copy number, which contributes to how rapidly a microbe can respond to an increase in resources and may be related to its maximum growth rate, and genome size, which suggests the breadth of environmental and substrate conditions in which a microbe can thrive. Nutrient addition increased community-weighted mean estimated rRNA gene copy number and marginally increased estimated genome size, whereas precipitation addition decreased these community means for both estimated traits. The effects of both treatments on both traits were associated with soil properties, such as ammonium, available phosphorus, and pH. Estimated trait responses within several phyla were opposite to the community mean response, indicating that microbial responses, although largely consistent among soil types, were not uniform across the tree of life. Our results show that phylogenetic estimation of microbial traits can provide insight into how microbial ecological strategies interact with environmental changes. The method could easily be applied to any of the thousands of existing 16S rRNA sequence data sets and offers potential to improve our understanding of how microbial communities mediate ecosystem function responses to global changes.

What ecologists can tell virologists.

PubMed

Dennehy, John J

2014-01-01

I pictured myself as a virus…and tried to sense what it would be like. --Jonas Salk. Ecology as a science evolved from natural history, the observational study of the interactions of plants and animals with each other and their environments. As natural history matured, it became increasingly quantitative, experimental, and taxonomically broad. Focus diversified beyond the Eukarya to include the hidden world of microbial life. Microbes, particularly viruses, were shown to exist in unfathomable numbers, affecting every living organism. Slowly viruses came to be viewed in an ecological context rather than as abstract, disease-causing agents. This shift is exemplified by an increasing tendency to refer to viruses as living organisms instead of inert particles. In recent years, researchers have recognized the critical contributions of viruses to fundamental ecological processes such as biogeochemical cycling, competition, community structuring, and horizontal gene transfer. This review describes virus ecology from a virus's perspective. If we are, like Jonas Salk, to imagine ourselves as a virus, what kind of world would we experience?

Interspecies Interactions Determine the Impact of the Gut Microbiota on Nutrient Allocation in Drosophila melanogaster

PubMed Central

Douglas, Angela E.

2014-01-01

The animal gut is perpetually exposed to microorganisms, and this microbiota affects development, nutrient allocation, and immune homeostasis. A major challenge is to understand the contribution of individual microbial species and interactions among species in shaping these microbe-dependent traits. Using the Drosophila melanogaster gut microbiota, we tested whether microbe-dependent performance and nutritional traits of Drosophila are functionally modular, i.e., whether the impact of each microbial taxon on host traits is independent of the presence of other microbial taxa. Gnotobiotic flies were constructed with one or a set of five of the Acetobacter and Lactobacillus species which dominate the gut microbiota of conventional flies (Drosophila with untreated microbiota). Axenic (microbiota-free) flies exhibited prolonged development time and elevated glucose and triglyceride contents. The low glucose content of conventional flies was recapitulated in gnotobiotic Drosophila flies colonized with any of the 5 bacterial taxa tested. In contrast, the development rates and triglyceride levels in monocolonized flies varied depending on the taxon present: Acetobacter species supported the largest reductions, while most Lactobacillus species had no effect. Only flies with both Acetobacter and Lactobacillus had triglyceride contents restored to the level in conventional flies. This could be attributed to two processes: Lactobacillus-mediated promotion of Acetobacter abundance in the fly and a significant negative correlation between fly triglyceride content and Acetobacter abundance. We conclude that the microbial basis of host traits varies in both specificity and modularity; microbe-mediated reduction in glucose is relatively nonspecific and modular, while triglyceride content is influenced by interactions among microbes. PMID:24242251

Preventing regime shifts on the Colorado Plateau: Application of ecological threshold concepts to land management decision making

USDA-ARS?s Scientific Manuscript database

Investigating the mechanisms responsible for ecological thresholds is essential to understanding processes leading to ecosystem regime shifts. Dryland ecosystems are especially prone to threshold behavior wherein stressor-mediated alteration of patterns and processes can shift systems to alternative...

Plant-microbe interaction in aquatic system and their role in the management of water quality: a review

NASA Astrophysics Data System (ADS)

Srivastava, Jatin K.; Chandra, Harish; Kalra, Swinder J. S.; Mishra, Pratibha; Khan, Hena; Yadav, Poonam

2017-06-01

Microbial assemblage as biofilm around the aquatic plant forms a firm association that largely depends upon the mutual supplies of nutrients, e.g., microbes interact with plants in an aquatic system most likely for organic carbon and oxygen, whereas plants receive defensive immunity and mineral exchange. Apart from the mutual benefits, plant-microbe interactions also influence the water quality especially at rhizosphere providing inherent ability to the aquatic system for the mitigation of pollution from the water column. The review presents and in-depth information along with certain research advancements made in the field of ecological and bio/chemical aspects of plant-microbe interactions and the underlying potential to improve water quality.

Dynamic intervention: pathogen disarmament of mitochondrial-based immune surveillance.

PubMed

Holland, Robin L; Blanke, Steven R

2014-11-12

In this issue of Cell Host & Microbe, Suzuki et al. (2014) describe a Vibrio cholerae Type-III-secreted effector that targets mitochondrial dynamics to dampen host innate immune signaling. This suggests that mammalian hosts possess surveillance mechanisms to monitor pathogen-mediated alterations in the integrity of normal cellular processes and organelles. Copyright © 2014 Elsevier Inc. All rights reserved.

Innovative MIOR Process Utilizing Indigenous Reservoir Constituents

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

Hitzman, D.O.; Stepp, A.K.

This research program was directed at improving the knowledge of reservoir ecology and developing practical microbial solutions for improving oil production. The goal was to identify indigenous microbial populations which can produce beneficial metabolic products and develop a methodology to stimulate those select microbes with inorganic nutrient amendments to increase oil recovery. This microbial technology has the capability of producing multiple oil-releasing agents. The potential of the system will be illustrated and demonstrated by the example of biopolymer production on oil recovery.

Innovative MIOR Process Utilizing Indigenous Reservoir Constituents

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

Hitzman, D.O.; Bailey, S.A.; Stepp, A.K.

This research program was directed at improving the knowledge of reservoir ecology and developing practical microbial solutions for improving oil production. The goal was to identify indigenous microbial populations which can produce beneficial metabolic products and develop a methodology to stimulate those select microbes with inorganic nutrient amendments to increase oil recovery. This microbial technology has the capability of producing multiple oil releasing agents. The potential of the system will be illustrated and demonstrated by the example of biopolymer production on oil recovery.

Observation to Theory in Deep Subsurface Microbiology Research: Can We Piece It Together?

NASA Astrophysics Data System (ADS)

Colwell, F. S.; Thurber, A. R.

2016-12-01

Three decades of observations of microbes in deep environments have led to startling discoveries of life in the subsurface. Now, a few theoretical frameworks exist that help to define Stygian life. Temperature, redox gradients, productivity (e.g., in the overlying ocean), and microbial power requirements are thought to determine the distribution of microbes in the subsurface. Still, we struggle to comprehend the spatial and temporal spectra of Earth processes that define how deep microbe communities survive. Stommel diagrams, originally used to guide oceanographic sampling, may be useful in depicting the subsurface where microbial communities are impacted by co-occurring spatial and temporal phenomena that range across exponential scales. Spatially, the geological settings that influence the activity and distribution of microbes range from individual molecules or minerals all the way up to the planetary-scale where geological formations, occupying up to 105 km3, dictate the bio- and functional geography of microbial communities. Temporally, life in the subsurface may respond in time units familiar to humans (e.g., seconds to days) or to events that unfold over hundred millennial time periods. While surface community dynamics are underpinned by solar and lunar cycles, these cycles only fractionally dictate survival underground where phenomena like tectonic activity, isostatic rebound, and radioactive decay are plausible drivers of microbial life. Geological or planetary processes that occur on thousand or million year cycles could be uniquely important to microbial viability in the subsurface. Such an approach aims at a holistic comprehension of the interaction of Earth system dynamics with microbial ecology.

Incorporating the gut microbiota into models of human and non-human primate ecology and evolution.

PubMed

Amato, Katherine R

2016-01-01

The mammalian gut is home to a diverse community of microbes. Advances in technology over the past two decades have allowed us to examine this community, the gut microbiota, in more detail, revealing a wide range of influences on host nutrition, health, and behavior. These host-gut microbe interactions appear to shape host plasticity and fitness in a variety of contexts, and therefore represent a key factor missing from existing models of human and non-human primate ecology and evolution. However, current studies of the gut microbiota tend to include limited contextual data or are clinical, making it difficult to directly test broad anthropological hypotheses. Here, I review what is known about the animal gut microbiota and provide examples of how gut microbiota research can be integrated into the study of human and non-human primate ecology and evolution with targeted data collection. Specifically, I examine how the gut microbiota may impact primate diet, energetics, disease resistance, and cognition. While gut microbiota research is proliferating rapidly, especially in the context of humans, there remain important gaps in our understanding of host-gut microbe interactions that will require an anthropological perspective to fill. Likewise, gut microbiota research will be an important tool for filling remaining gaps in anthropological research. © 2016 Wiley Periodicals, Inc.

Harnessing Insect-Microbe Chemical Communications To Control Insect Pests of Agricultural Systems.

PubMed

Beck, John J; Vannette, Rachel L

2017-01-11

Insect pests cause serious economic, yield, and food safety problems to managed crops worldwide. Compounding these problems, insect pests often vector pathogenic or toxigenic microbes to plants. Previous work has considered plant-insect and plant-microbe interactions separately. Although insects are well-understood to use plant volatiles to locate hosts, microorganisms can produce distinct and abundant volatile compounds that in some cases strongly attract insects. In this paper, we focus on the microbial contribution to plant volatile blends, highlighting the compounds emitted and the potential for variation in microbial emission. We suggest that these aspects of microbial volatile emission may make these compounds ideal for use in agricultural applications, as they may be more specific or enhance methods currently used in insect control or monitoring. Our survey of microbial volatiles in insect-plant interactions suggests that these emissions not only signal host suitability but may indicate a distinctive time frame for optimal conditions for both insect and microbe. Exploitation of these host-specific microbe semiochemicals may provide important microbe- and host-based attractants and a basis for future plant-insect-microbe chemical ecology investigations.

The evolution of ethylene signaling in plant chemical ecology.

PubMed

Groen, Simon C; Whiteman, Noah K

2014-07-01

Ethylene is a key hormone in plant development, mediating plant responses to abiotic environmental stress, and interactions with attackers and mutualists. Here, we provide a synthesis of the role of ethylene in the context of plant ecology and evolution, and a prospectus for future research in this area. We focus on the regulatory function of ethylene in multi-organismal interactions. In general, plant interactions with different types of organisms lead to reduced or enhanced levels of ethylene. This in turn affects not only the plant's response to the interacting organism at hand, but also to other organisms in the community. These community-level effects become observable as enhanced or diminished relationships with future commensals, and systemic resistance or susceptibility to secondary attackers. Ongoing comparative genomic and phenotypic analyses continue to shed light on these interactions. These studies have revealed that plants and interacting organisms from separate kingdoms of life have independently evolved the ability to produce, perceive, and respond to ethylene. This signature of convergent evolution of ethylene signaling at the phenotypic level highlights the central role ethylene metabolism and signaling plays in plant interactions with microbes and animals.

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

NASA Astrophysics Data System (ADS)

Kim, Minsu; Or, Dani

2017-12-01

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

75 years of dryland science: Trends and gaps in arid ecology literature

PubMed Central

Dickman, Chris R.; Wardle, Glenda M.

2017-01-01

Growth in the publication of scientific articles is occurring at an exponential rate, prompting a growing need to synthesise information in a timely manner to combat urgent environmental problems and guide future research. Here, we undertake a topic analysis of dryland literature over the last 75 years (8218 articles) to identify areas in arid ecology that are well studied and topics that are emerging. Four topics—wetlands, mammal ecology, litter decomposition and spatial modelling, were identified as ‘hot topics’ that showed higher than average growth in publications from 1940 to 2015. Five topics—remote sensing, climate, habitat and spatial, agriculture and soils-microbes, were identified as ‘cold topics’, with lower than average growth over the survey period, but higher than average numbers of publications. Topics in arid ecology clustered into seven broad groups on word-based similarity. These groups ranged from mammal ecology and population genetics, broad-scale management and ecosystem modelling, plant ecology, agriculture and ecophysiology, to populations and paleoclimate. These patterns may reflect trends in the field of ecology more broadly. We also identified two broad research gaps in arid ecology: population genetics, and habitat and spatial research. Collaborations between population genetics and ecologists and investigations of ecological processes across spatial scales would contribute profitably to the advancement of arid ecology and to ecology more broadly. PMID:28384186

Characteristics and Kinetic Analysis of AQS Transformation and Microbial Goethite Reduction:Insight into "Redox mediator-Microbe-Iron oxide" Interaction Process.

PubMed

Zhu, Weihuang; Shi, Mengran; Yu, Dan; Liu, Chongxuan; Huang, Tinglin; Wu, Fengchang

2016-03-29

The characteristics and kinetics of redox transformation of a redox mediator, anthraquinone-2-sulfonate (AQS), during microbial goethite reduction by Shewanella decolorationis S12, a dissimilatory iron reduction bacterium (DIRB), were investigated to provide insights into "redox mediator-iron oxide" interaction in the presence of DIRB. Two pre-incubation reaction systems of the "strain S12- goethite" and the "strain S12-AQS" were used to investigate the dynamics of goethite reduction and AQS redox transformation. Results show that the concentrations of goethite and redox mediator, and the inoculation cell density all affect the characteristics of microbial goethite reduction, kinetic transformation between oxidized and reduced species of the redox mediator. Both abiotic and biotic reactions and their coupling regulate the kinetic process for "Quinone-Iron" interaction in the presence of DIRB. Our results provide some new insights into the characteristics and mechanisms of interaction among "quinone-DIRB- goethite" under biotic/abiotic driven.

Modeling selective pressures on phytoplankton in the global ocean.

PubMed

Bragg, Jason G; Dutkiewicz, Stephanie; Jahn, Oliver; Follows, Michael J; Chisholm, Sallie W

2010-03-10

Our view of marine microbes is transforming, as culture-independent methods facilitate rapid characterization of microbial diversity. It is difficult to assimilate this information into our understanding of marine microbe ecology and evolution, because their distributions, traits, and genomes are shaped by forces that are complex and dynamic. Here we incorporate diverse forces--physical, biogeochemical, ecological, and mutational--into a global ocean model to study selective pressures on a simple trait in a widely distributed lineage of picophytoplankton: the nitrogen use abilities of Synechococcus and Prochlorococcus cyanobacteria. Some Prochlorococcus ecotypes have lost the ability to use nitrate, whereas their close relatives, marine Synechococcus, typically retain it. We impose mutations for the loss of nitrogen use abilities in modeled picophytoplankton, and ask: in which parts of the ocean are mutants most disadvantaged by losing the ability to use nitrate, and in which parts are they least disadvantaged? Our model predicts that this selective disadvantage is smallest for picophytoplankton that live in tropical regions where Prochlorococcus are abundant in the real ocean. Conversely, the selective disadvantage of losing the ability to use nitrate is larger for modeled picophytoplankton that live at higher latitudes, where Synechococcus are abundant. In regions where we expect Prochlorococcus and Synechococcus populations to cycle seasonally in the real ocean, we find that model ecotypes with seasonal population dynamics similar to Prochlorococcus are less disadvantaged by losing the ability to use nitrate than model ecotypes with seasonal population dynamics similar to Synechococcus. The model predictions for the selective advantage associated with nitrate use are broadly consistent with the distribution of this ability among marine picocyanobacteria, and at finer scales, can provide insights into interactions between temporally varying ocean processes and selective pressures that may be difficult or impossible to study by other means. More generally, and perhaps more importantly, this study introduces an approach for testing hypotheses about the processes that underlie genetic variation among marine microbes, embedded in the dynamic physical, chemical, and biological forces that generate and shape this diversity.

Do volatiles produced by nectar-dwelling microbes affect honey bee preferences?

USDA-ARS?s Scientific Manuscript database

The microbiome of plants mediates many interactions in natural and managed systems. Among these, plant-pollinator interactions are important for ensuring high crop yields, pollinator health and successful plant reproduction. Despite initial work demonstrating effects of floral microbes on pollinatio...

RevEcoR: an R package for the reverse ecology analysis of microbiomes.

PubMed

Cao, Yang; Wang, Yuanyuan; Zheng, Xiaofei; Li, Fei; Bo, Xiaochen

2016-07-29

All species live in complex ecosystems. The structure and complexity of a microbial community reflects not only diversity and function, but also the environment in which it occurs. However, traditional ecological methods can only be applied on a small scale and for relatively well-understood biological systems. Recently, a graph-theory-based algorithm called the reverse ecology approach has been developed that can analyze the metabolic networks of all the species in a microbial community, and predict the metabolic interface between species and their environment. Here, we present RevEcoR, an R package and a Shiny Web application that implements the reverse ecology algorithm for determining microbe-microbe interactions in microbial communities. This software allows users to obtain large-scale ecological insights into species' ecology directly from high-throughput metagenomic data. The software has great potential for facilitating the study of microbiomes. RevEcoR is open source software for the study of microbial community ecology. The RevEcoR R package is freely available under the GNU General Public License v. 2.0 at http://cran.r-project.org/web/packages/RevEcoR/ with the vignette and typical usage examples, and the interactive Shiny web application is available at http://yiluheihei.shinyapps.io/shiny-RevEcoR , or can be installed locally with the source code accessed from https://github.com/yiluheihei/shiny-RevEcoR .

Growth Rates of Microbes in the Oceans.

PubMed

Kirchman, David L

2016-01-01

A microbe's growth rate helps to set its ecological success and its contribution to food web dynamics and biogeochemical processes. Growth rates at the community level are constrained by biomass and trophic interactions among bacteria, phytoplankton, and their grazers. Phytoplankton growth rates are approximately 1 d(-1), whereas most heterotrophic bacteria grow slowly, close to 0.1 d(-1); only a few taxa can grow ten times as fast. Data from 16S rRNA and other approaches are used to speculate about the growth rate and the life history strategy of SAR11, the most abundant clade of heterotrophic bacteria in the oceans. These strategies are also explored using genomic data. Although the methods and data are imperfect, the available data can be used to set limits on growth rates and thus on the timescale for changes in the composition and structure of microbial communities.

Searching for an alternative form of life on Earth

NASA Astrophysics Data System (ADS)

Davies, P. C. W.

2007-09-01

Biologists tacitly assume that all life on Earth descended from a common origin. This assumption is based on biochemical similarities and gene sequencing, which enables organisms to be positioned on a common tree of life. However, most terrestrial organisms are microbes, and it is impossible to deduce their biochemical nature from morphology alone. The vast majority of microbes remain unclassified, leaving open the possibility that some of them might be an alternative form of life, arising either from an independent origin, or representing a hitherto overlooked very ancient branch of the known tree. Thus there may exist an extinct, or even extant, shadow biosphere. I discuss various research proposals for locating and identifying "alien" organisms on Earth, both ecologically separate and ecologically integrated.

Bioremediation of Southern Mediterranean oil polluted sites comes of age.

PubMed

Daffonchio, Daniele; Ferrer, Manuel; Mapelli, Francesca; Cherif, Ameur; Lafraya, Alvaro; Malkawi, Hanan I; Yakimov, Michail M; Abdel-Fattah, Yasser R; Blaghen, Mohamed; Golyshin, Peter N; Kalogerakis, Nicolas; Boon, Nico; Magagnini, Mirko; Fava, Fabio

2013-09-25

Mediterranean Sea is facing a very high risk of oil pollution due to the high number of oil extractive and refining sites along the basin coasts, and the intense maritime traffic of oil tankers. All the Mediterranean countries have adopted severe regulations for minimizing pollution events and bioremediation feasibility studies for the most urgent polluted sites are undergoing. However, the analysis of the scientific studies applying modern 'meta-omics' technologies that have been performed on marine oil pollution worldwide showed that the Southern Mediterranean side has been neglected by the international research. Most of the studies in the Mediterranean Sea have been done in polluted sites of the Northern side of the basin. Those of the Southern side are poorly studied, despite many of the Southern countries being major oil producers and exporters. The recently EU-funded research project ULIXES has as a major objective to increase the knowledge of the bioremediation potential of sites from the Southern Mediterranean countries. ULIXES is targeting four major polluted sites on the coastlines of Egypt, Jordan, Morocco and Tunisia, including seashore sands, lagoons, and oil refinery polluted sediments. The research is designed to unravel, categorize, catalogue, exploit and manage the diversity and ecology of microorganisms thriving in these polluted sites. Isolation of novel hydrocarbon degrading microbes and a series of state of the art 'meta-omics' technologies are the baseline tools for improving our knowledge on biodegradation capacities mediated by microbes under different environmental settings and for designing novel site-tailored bioremediation approaches. A network of twelve European and Southern Mediterranean partners is cooperating for plugging the existing gap of knowledge for the development of novel bioremediation processes targeting such poorly investigated polluted sites. Copyright © 2013 Elsevier B.V. All rights reserved.

Using pyrosequencing to shed light on deep mine microbial ecology

PubMed Central

Edwards, Robert A; Rodriguez-Brito, Beltran; Wegley, Linda; Haynes, Matthew; Breitbart, Mya; Peterson, Dean M; Saar, Martin O; Alexander, Scott; Alexander, E Calvin; Rohwer, Forest

2006-01-01

Background Contrasting biological, chemical and hydrogeological analyses highlights the fundamental processes that shape different environments. Generating and interpreting the biological sequence data was a costly and time-consuming process in defining an environment. Here we have used pyrosequencing, a rapid and relatively inexpensive sequencing technology, to generate environmental genome sequences from two sites in the Soudan Mine, Minnesota, USA. These sites were adjacent to each other, but differed significantly in chemistry and hydrogeology. Results Comparisons of the microbes and the subsystems identified in the two samples highlighted important differences in metabolic potential in each environment. The microbes were performing distinct biochemistry on the available substrates, and subsystems such as carbon utilization, iron acquisition mechanisms, nitrogen assimilation, and respiratory pathways separated the two communities. Although the correlation between much of the microbial metabolism occurring and the geochemical conditions from which the samples were isolated could be explained, the reason for the presence of many pathways in these environments remains to be determined. Despite being physically close, these two communities were markedly different from each other. In addition, the communities were also completely different from other microbial communities sequenced to date. Conclusion We anticipate that pyrosequencing will be widely used to sequence environmental samples because of the speed, cost, and technical advantages. Furthermore, subsystem comparisons rapidly identify the important metabolisms employed by the microbes in different environments. PMID:16549033

The Role of Heterotrophic Microbial Communities in Estuarine C Budgets and the Biogeochemical C Cycle with Implications for Global Warming: Research Opportunities and Challenges.

PubMed

Anderson, O Roger

2016-05-01

Estuaries are among the most productive and economically important marine ecosystems at the land-ocean interface and contribute significantly to exchange of CO2 with the atmosphere. Estuarine microbial communities are major links in the biogeochemical C cycle and flow of C in food webs from primary producers to higher consumers. Considerable attention has been given to bacteria and autotrophic eukaryotes in estuarine ecosystems, but less research has been devoted to the role of heterotrophic eukaryotic microbes. Current research is reviewed here on the role of heterotrophic eukaryotic microbes in C biogeochemistry and ecology of estuaries, with particular attention to C budgets, trophodynamics, and the metabolic fate of C in microbial communities. Some attention is given to the importance of these processes in climate change and global warming, especially in relation to sources and sinks of atmospheric CO2 , while also documenting the current paucity of research on the role of eukaryotic microbes that contribute to this larger question of C biogeochemistry and the environment. Some recommendations are made for future directions of research and opportunities of applying newer technologies and analytical approaches to a more refined analysis of the role of C in estuarine microbial community processes and the biogeochemical C cycle. © 2015 The Author Journal of Eukaryotic Microbiology © 2015 International Society of Protistologists.

Microbially-mediated method for synthesis of non-oxide semiconductor nanoparticles

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

Phelps, Tommy J.; Lauf, Robert J.; Moon, Ji-Won

The invention is directed to a method for producing non-oxide semiconductor nanoparticles, the method comprising: (a) subjecting a combination of reaction components to conditions conducive to microbially-mediated formation of non-oxide semiconductor nanoparticles, wherein said combination of reaction components comprises i) anaerobic microbes, ii) a culture medium suitable for sustaining said anaerobic microbes, iii) a metal component comprising at least one type of metal ion, iv) a non-metal component comprising at least one non-metal selected from the group consisting of S, Se, Te, and As, and v) one or more electron donors that provide donatable electrons to said anaerobic microbes duringmore » consumption of the electron donor by said anaerobic microbes; and (b) isolating said non-oxide semiconductor nanoparticles, which contain at least one of said metal ions and at least one of said non-metals. The invention is also directed to non-oxide semiconductor nanoparticle compositions produced as above and having distinctive properties.« less

Giardia Alters Commensal Microbial Diversity throughout the Murine Gut

PubMed Central

Barash, N. R.; Maloney, J. G.

2017-01-01

ABSTRACT Giardia lamblia is the most frequently identified protozoan cause of intestinal infection. Over 200 million people are estimated to have acute or chronic giardiasis, with infection rates approaching 90% in areas where Giardia is endemic. Despite its significance in global health, the mechanisms of pathogenesis associated with giardiasis remain unclear, as the parasite neither produces a known toxin nor induces a robust inflammatory response. Giardia colonization and proliferation in the small intestine of the host may, however, disrupt the ecological homeostasis of gastrointestinal commensal microbes and contribute to diarrheal disease associated with giardiasis. To evaluate the impact of Giardia infection on the host microbiota, we used culture-independent methods to quantify shifts in the diversity of commensal microbes throughout the gastrointestinal tract in mice infected with Giardia. We discovered that Giardia's colonization of the small intestine causes a systemic dysbiosis of aerobic and anaerobic commensal bacteria. Specifically, Giardia colonization is typified by both expansions in aerobic Proteobacteria and decreases in anaerobic Firmicutes and Melainabacteria in the murine foregut and hindgut. Based on these shifts, we created a quantitative index of murine Giardia-induced microbial dysbiosis. This index increased at all gut regions during the duration of infection, including both the proximal small intestine and the colon. Giardiasis could be an ecological disease, and the observed dysbiosis may be mediated directly via the parasite's unique anaerobic fermentative metabolism or indirectly via parasite induction of gut inflammation. This systemic alteration of murine gut commensal diversity may be the cause or the consequence of inflammatory and metabolic changes throughout the gut. Shifts in the commensal microbiota may explain observed variations in giardiasis between hosts with respect to host pathology, degree of parasite colonization, infection initiation, and eventual clearance. PMID:28396324

Microbial communities and bioactive compounds in marine sponges of the family irciniidae-a review.

PubMed

Hardoim, Cristiane C P; Costa, Rodrigo

2014-09-30

Marine sponges harbour complex microbial communities of ecological and biotechnological importance. Here, we propose the application of the widespread sponge family Irciniidae as an appropriate model in microbiology and biochemistry research. Half a gram of one Irciniidae specimen hosts hundreds of bacterial species-the vast majority of which are difficult to cultivate-and dozens of fungal and archaeal species. The structure of these symbiont assemblages is shaped by the sponge host and is highly stable over space and time. Two types of quorum-sensing molecules have been detected in these animals, hinting at microbe-microbe and host-microbe signalling being important processes governing the dynamics of the Irciniidae holobiont. Irciniids are vulnerable to disease outbreaks, and concerns have emerged about their conservation in a changing climate. They are nevertheless amenable to mariculture and laboratory maintenance, being attractive targets for metabolite harvesting and experimental biology endeavours. Several bioactive terpenoids and polyketides have been retrieved from Irciniidae sponges, but the actual producer (host or symbiont) of these compounds has rarely been clarified. To tackle this, and further pertinent questions concerning the functioning, resilience and physiology of these organisms, truly multi-layered approaches integrating cutting-edge microbiology, biochemistry, genetics and zoology research are needed.

Microbial control over carbon cycling in soil

PubMed Central

Schimel, Joshua P.; Schaeffer, Sean M.

2012-01-01

A major thrust of terrestrial microbial ecology is focused on understanding when and how the composition of the microbial community affects the functioning of biogeochemical processes at the ecosystem scale (meters-to-kilometers and days-to-years). While research has demonstrated these linkages for physiologically and phylogenetically “narrow” processes such as trace gas emissions and nitrification, there is less conclusive evidence that microbial community composition influences the “broad” processes of decomposition and organic matter (OM) turnover in soil. In this paper, we consider how soil microbial community structure influences C cycling. We consider the phylogenetic level at which microbes form meaningful guilds, based on overall life history strategies, and suggest that these are associated with deep evolutionary divergences, while much of the species-level diversity probably reflects functional redundancy. We then consider under what conditions it is possible for differences among microbes to affect process dynamics, and argue that while microbial community structure may be important in the rate of OM breakdown in the rhizosphere and in detritus, it is likely not important in the mineral soil. In mineral soil, physical access to occluded or sorbed substrates is the rate-limiting process. Microbial community influences on OM turnover in mineral soils are based on how organisms allocate the C they take up – not only do the fates of the molecules differ, but they can affect the soil system differently as well. For example, extracellular enzymes and extracellular polysaccharides can be key controls on soil structure and function. How microbes allocate C may also be particularly important for understanding the long-term fate of C in soil – is it sequestered or not? PMID:23055998

Microbially Mediated Glass Alteration in the Geological Record: Textural clues for Microbial Functions.

NASA Astrophysics Data System (ADS)

Staudigel, H.; Furnes, H.; McLoughlin, N.; Banerjee, N.

2007-12-01

Fe and Mn oxidizing microbes interact with their environment through the microbially mediated formation of Fe/Mn oxides and through the corrosion textures they may leave behind in the solids they colonize and from which they extract nutrients. Understanding the geo-biology of Fe and Mn oxidation may focus on the study of the microbes themselves, the mineral products, its biocorrosion features and the relationships between these types of observations. We have reviewed our own data on glass bio-corrosion and in particular the wider literature on microbial mineral tunneling to develop a two stage biocorrosion model for volcanic glass that offers feedback for our understanding of the mechanisms and the dynamics of microbial dissolution. Traces of microbially mediated dissolution of volcanic glass are commonly observed in volcanic glass found in submarine volcanoes on the seafloor, and in uplifted submarine volcanoes of almost any geological age back to the origin of life. Two main bioalteration textures care observed, granular and tubular. Based on a comparison of these features in particular with tunneling by ectomycorrhizal fungi, we propose two distinct types of biocorrosion that affects glass: (1) Granular alteration textures, made up of colonies of microbe-sized, near spherical mineral - filled cavities that form irregular clusters ranging to a tens of micron thick bands at the glas surfaces. These granular textures are interpreted as the result of microbial colonization. accompanied by dissolution of the glass in their contact surface, deposition of authigenic minerals and the formation of a biofilm, that eventually seals the glass from easy access by seawater for hydration, or from microbes accessing Fe (II) in the glass. (2) The most spectacular bioalteration feature, repesented by the formation of tubes cannot be easily formed by the former mechanism because near spherical, individual microbes are likely not to produce the directionality that is required to produce the near linear or sometimes coiled tubes. Instead, we envision the activity of hyphae-like organelles or filaments, that may radiate out from a host body located in direct contact with circulating water, possibly penetrating a biofilm and entering/drilling into the fresh glass. Such microdrilling is well described in soils, where hyphae can slowly drill into silicates, in a process that takes about 1000 years to become visible as tunnels.

Down by the riverside: urban riparian ecology

Treesearch

Peter M. Groffman; Daniel J. Bain; Lawrence E. Band; Kenneth T. Belt; Grace S. Brush; J. Morgan Grove; Richard V. Pouyat; Ian C. Yesilonis; Wayne C. Zipperer

2003-01-01

Riparian areas are hotspots of interactions between plants, soil, water, microbes, and people. While urban land use change has been shown to have dramatic effects on watershed hydrology, there has been surprisingly little analysis of its effects on riparian areas. Here we examine the ecology of urban riparian zones, focusing on work done in the Baltimore Ecosystem...

Urban microbiomes and urban ecology: how do microbes in the built environment affect human sustainability in cities?

PubMed

King, Gary M

2014-09-01

Humans increasingly occupy cities. Globally, about 50% of the total human population lives in urban environments, and in spite of some trends for deurbanization, the transition from rural to urban life is expected to accelerate in the future, especially in developing nations and regions. The Republic of Korea, for example, has witnessed a dramatic rise in its urban population, which now accounts for nearly 90% of all residents; the increase from about 29% in 1955 has been attributed to multiple factors, but has clearly been driven by extraordinary growth in the gross domestic product accompanying industrialization. While industrialization and urbanization have unarguably led to major improvements in quality of life indices in Korea and elsewhere, numerous serious problems have also been acknowledged, including concerns about resource availability, water quality, amplification of global warming and new threats to health. Questions about sustainability have therefore led Koreans and others to consider deurbanization as a management policy. Whether this offers any realistic prospects for a sustainable future remains to be seen. In the interim, it has become increasingly clear that built environments are no less complex than natural environments, and that they depend on a variety of internal and external connections involving microbes and the processes for which microbes are responsible. I provide here a definition of the urban microbiome, and through examples indicate its centrality to human function and wellbeing in urban systems. I also identify important knowledge gaps and unanswered questions about urban microbiomes that must be addressed to develop a robust, predictive and general understanding of urban biology and ecology that can be used to inform policy-making for sustainable systems.

Molecular Insights on Dissolved Organic Matter Transformation by Supraglacial Microbial Communities.

PubMed

Antony, Runa; Willoughby, Amanda S; Grannas, Amanda M; Catanzano, Victoria; Sleighter, Rachel L; Thamban, Meloth; Hatcher, Patrick G; Nair, Shanta

2017-04-18

Snow overlays the majority of Antarctica and is an important repository of dissolved organic matter (DOM). DOM transformations by supraglacial microbes are not well understood. We use ultrahigh resolution mass spectrometry to elucidate molecular changes in snowpack DOM by in situ microbial processes (up to 55 days) in a coastal Antarctic site. Both autochthonous and allochthonous DOM is highly bioavailable and is transformed by resident microbial communities through parallel processes of degradation and synthesis. DOM thought to be of a more refractory nature, such as dissolved black carbon and carboxylic-rich alicyclic molecules, was also rapidly and extensively reworked. Microbially reworked DOM exhibits an increase in the number and magnitude of N-, S-, and P-containing formulas, is less oxygenated, and more aromatic when compared to the initial DOM. Shifts in the heteroatom composition suggest that microbial processes may be important in the cycling of not only C, but other elements such as N, S, and P. Microbial reworking also produces photoreactive compounds, with potential implications for DOM photochemistry. Refined measurements of supraglacial DOM and their cycling by microbes is critical for improving our understanding of supraglacial DOM cycling and the biogeochemical and ecological impacts of DOM export to downstream environments.

Community structures and activity of denitrifying microbes in a forested catchment in central Japan: survey using nitrite reductase genes

NASA Astrophysics Data System (ADS)

Ohte, N.; Aoki, M.; Katsuyama, C.; Suwa, Y.; Tange, T.

2012-12-01

To elucidate the mechanisms of denitrification processes in the forested catchment, microbial ecological approaches have been applied in an experimental watershed that has previously investigated its hydrological processes. The study catchment is located in the Chiba prefecture in central Japan under the temperate Asian monsoon climate. Potential activities of denitrification of soil samples were measured by incubation experiments under anoxic condition associated with Na15NO3 addition. Existence and variety of microbes having nitrite reductase genes were investigated by PCR amplification, cloning and sequencings of nirK and nirS fragments after DNA extraction. Contrary to our early expectation that the potential denitrification activity was higher at deeper soil horizon with consistent groundwater residence than that in the surface soil, denitrification potential was higher in shallower soil horizons than deeper soils. This suggested that the deficiency of NO3- as a respiratory substrate for denitrifier occurred in deeper soils especially in the summer. However, high denitrification activity and presence of microbes having nirK and nirS in surface soils usually under aerobic condition was explainable by the fact that the majority of denitrifying bacteria have been recognized as a facultative anaerobic bacterium. This also suggests the possibility of that denitrification occurs even in the surface soils if the wet condition is provided by rainwater during and after a storm event. Community structures of microbes having nirK were different between near surface and deeper soil horizons, and ones having nirS was different between saturated zone (under groundwater table) and unsaturated soil horizons. These imply that microbial communities with nisK are sensitive to the concentration of soil organic matters and ones with nirS is sensitive to soil moisture contents.

Virophages to viromes: a report from the frontier of viral oceanography.

PubMed

Culley, Alexander I

2011-07-01

The investigation of marine viruses has advanced our understanding of ecology, evolution, microbiology, oceanography and virology. Significant findings discussed in this review include the discovery of giant viruses that have genome sizes and metabolic capabilities that distort the line between virus and cell, viruses that participate in photosynthesis and apoptosis, the detection of communities of viruses of all genomic compositions and the preeminence of viruses in the evolution of marine microbes. Although we have made great progress, we have yet to synthesize the rich archive of viral genomic data with oceanographic processes. The development of cutting edge methods such as single virus genomics now provide a toolset to better integrate viruses into the ecology of the ocean. Copyright © 2011 Elsevier B.V. All rights reserved.

Enzymes from solvent-tolerant microbes: useful biocatalysts for non-aqueous enzymology.

PubMed

Gupta, Anshu; Khare, S K

2009-01-01

Solvent-tolerant microbes are a newly emerging class that possesses the unique ability to thrive in the presence of organic solvents. Their enzymes adapted to mediate cellular and metabolic processes in a solvent-rich environment and are logically stable in the presence of organic solvents. Enzyme catalysis in non-aqueous/low-water media is finding increasing applications for the synthesis of industrially important products, namely peptides, esters, and other trans-esterification products. Solvent stability, however, remains a prerequisite for employing enzymes in non-aqueous systems. Enzymes, in general, get inactivated or give very low rates of reaction in non-aqueous media. Thus, early efforts, and even some recent ones, have aimed at stabilization of enzymes in organic media by immobilization, surface modifications, mutagenesis, and protein engineering. Enzymes from solvent-tolerant microbes appear to be the choicest source for studying solvent-stable enzymes because of their unique ability to survive in the presence of a range of organic solvents. These bacteria circumvent the solvent's toxic effects by virtue of various adaptations, e.g. at the level of the cytoplasmic membrane, by degradation and transformation of solvents, and by active excretion of solvents. The recent screening of these exotic microbes has generated some naturally solvent-stable proteases, lipases, cholesterol oxidase, cholesterol esterase, cyclodextrin glucanotransferase, and other important enzymes. The unique properties of these novel biocatalysts have great potential for applications in non-aqueous enzymology for a range of industrial processes.

Bioremediation: a genuine technology to remediate radionuclides from the environment

PubMed Central

Prakash, Dhan; Gabani, Prashant; Chandel, Anuj K; Ronen, Zeev; Singh, Om V

2013-01-01

Summary Radionuclides in the environment are a major human and environmental health concern. Like the Chernobyl disaster of 1986, the Fukushima Daiichi nuclear disaster in 2011 is once again causing damage to the environment: a large quantity of radioactive waste is being generated and dumped into the environment, and if the general population is exposed to it, may cause serious life-threatening disorders. Bioremediation has been viewed as the ecologically responsible alternative to environmentally destructive physical remediation. Microorganisms carry endogenous genetic, biochemical and physiological properties that make them ideal agents for pollutant remediation in soil and groundwater. Attempts have been made to develop native or genetically engineered (GE) microbes for the remediation of environmental contaminants including radionuclides. Microorganism-mediated bioremediation can affect the solubility, bioavailability and mobility of radionuclides. Therefore, we aim to unveil the microbial-mediated mechanisms for biotransformation of radionuclides under various environmental conditions as developing strategies for waste management of radionuclides. A discussion follows of ‘-omics’-integrated genomics and proteomics technologies, which can be used to trace the genes and proteins of interest in a given microorganism towards a cell-free bioremediation strategy. PMID:23617701

Eicosanoids up-regulate production of reactive oxygen species by NADPH-dependent oxidase in Spodoptera exigua phagocytic hemocytes

USDA-ARS?s Scientific Manuscript database

Eicosanoids mediate cellular immune responses in insects, including phagocytosis of invading microbes. Phagocytosis entails two major steps, the internalization of microbes and the subsequent killing of them via formation of reactive oxygen species (ROS). Here, we posed the hypothesis that eicosanoi...

Nitrogen Cycling in the Mycorrhizosphere: Multipartite Interactions and Plant Nitrogen Uptake Vary with Fertilization Legacy

NASA Astrophysics Data System (ADS)

Hestrin, R.; Lehmann, J.

2017-12-01

Soil microbes play an important role in rhizosphere nutrient cycling and plant productivity. In this study, the contributions of soil microbes to organic matter mineralization and plant nitrogen uptake were investigated using incubation and microcosm experiments. Microbial inocula included arbuscular mycorrhizal fungi and microbial communities sampled across a long-term gradient of nitrogen fertilization. Stable isotopes, nanoSIMS imaging, and phospholipid fatty acid analysis were used to track carbon and nitrogen movement from organic matter into microbes, mycorrhizal fungi, and plants. Results show that multipartite relationships between plants and microbes increased plant growth and access to nitrogen from organic matter, and that nitrogen fertilization history had a lasting effect on microbial contributions to fungal and plant nitrogen uptake. This research links rhizosphere ecology and land management with terrestrial biogeochemistry.

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.

Microbial mediation of biogeochemical cycles revealed by simulation of global changes with soil transplant and cropping

PubMed Central

Zhao, Mengxin; Xue, Kai; Wang, Feng; Liu, Shanshan; Bai, Shijie; Sun, Bo; Zhou, Jizhong; Yang, Yunfeng

2014-01-01

Despite microbes' key roles in driving biogeochemical cycles, the mechanism of microbe-mediated feedbacks to global changes remains elusive. Recently, soil transplant has been successfully established as a proxy to simulate climate changes, as the current trend of global warming coherently causes range shifts toward higher latitudes. Four years after southward soil transplant over large transects in China, we found that microbial functional diversity was increased, in addition to concurrent changes in microbial biomass, soil nutrient content and functional processes involved in the nitrogen cycle. However, soil transplant effects could be overridden by maize cropping, which was attributed to a negative interaction. Strikingly, abundances of nitrogen and carbon cycle genes were increased by these field experiments simulating global change, coinciding with higher soil nitrification potential and carbon dioxide (CO2) efflux. Further investigation revealed strong correlations between carbon cycle genes and CO2 efflux in bare soil but not cropped soil, and between nitrogen cycle genes and nitrification. These findings suggest that changes of soil carbon and nitrogen cycles by soil transplant and cropping were predictable by measuring microbial functional potentials, contributing to a better mechanistic understanding of these soil functional processes and suggesting a potential to incorporate microbial communities in greenhouse gas emission modeling. PMID:24694714

Bioherbicides: Current knowledge on weed control mechanism.

PubMed

Radhakrishnan, Ramalingam; Alqarawi, Abdulaziz A; Abd Allah, Elsayed Fathi

2018-04-17

Weed control is a challenging event during crop cultivation. Integrated management, including the application of bioherbicides, is an emerging method for weed control in sustainable agriculture. Plant extracts, allelochemicals and some microbes are utilized as bioherbicides to control weed populations. Bioherbicides based on plants and microbes inhibit the germination and growth of weeds; however,few studies conducted in weed physiology. This review ascribes the current knowledge of the physiological changes in weeds that occur during the exposure to bioherbicides. Plant extracts or metabolites are absorbed by weed seeds, which initiates damage to the cell membrane, DNA, mitosis, amylase activity and other biochemical processes and delays or inhibits seed germination. The growth of weeds is also retarded due to low rates of root-cell division, nutrient uptake, photosynthetic pigment synthesis, and plant growth hormone synthesis, while the productions of reactive oxygen species (ROS) and stress-mediated hormones increase, including irregular antioxidant activity. However, lytic enzymes and toxic substances secreted from microbes degrade the weed seed coat and utilize the endosperm for survival, which inhibits seed germination. The microbes grow through the intercellular spaces to reach the root core, and the deposition of toxins in the cells affects cell division and cellular functions. Some of the metabolites of deleterious microbes cause disease, necrosis and chlorosis,which inhibit the germination and growth of weed seeds by suppressing photosynthesis and gibberellin activities and enhancing ROS, abscisic acid and ethylene. This review explains the effects of bioherbicides (derived from plants and microbes) on weed-plant physiology to elucidate their modes of action. Copyright © 2018 Elsevier Inc. All rights reserved.

Microbial Lifestyle and Genome Signatures

PubMed Central

Dutta, Chitra; Paul, Sandip

2012-01-01

Microbes are known for their unique ability to adapt to varying lifestyle and environment, even to the extreme or adverse ones. The genomic architecture of a microbe may bear the signatures not only of its phylogenetic position, but also of the kind of lifestyle to which it is adapted. The present review aims to provide an account of the specific genome signatures observed in microbes acclimatized to distinct lifestyles or ecological niches. Niche-specific signatures identified at different levels of microbial genome organization like base composition, GC-skew, purine-pyrimidine ratio, dinucleotide abundance, codon bias, oligonucleotide composition etc. have been discussed. Among the specific cases highlighted in the review are the phenomena of genome shrinkage in obligatory host-restricted microbes, genome expansion in strictly intra-amoebal pathogens, strand-specific codon usage in intracellular species, acquisition of genome islands in pathogenic or symbiotic organisms, discriminatory genomic traits of marine microbes with distinct trophic strategies, and conspicuous sequence features of certain extremophiles like those adapted to high temperature or high salinity. PMID:23024607

Microbial contributions to climate change through carbon cycle feedbacks.

PubMed

Bardgett, Richard D; Freeman, Chris; Ostle, Nicholas J

2008-08-01

There is considerable interest in understanding the biological mechanisms that regulate carbon exchanges between the land and atmosphere, and how these exchanges respond to climate change. An understanding of soil microbial ecology is central to our ability to assess terrestrial carbon cycle-climate feedbacks, but the complexity of the soil microbial community and the many ways that it can be affected by climate and other global changes hampers our ability to draw firm conclusions on this topic. In this paper, we argue that to understand the potential negative and positive contributions of soil microbes to land-atmosphere carbon exchange and global warming requires explicit consideration of both direct and indirect impacts of climate change on microorganisms. Moreover, we argue that this requires consideration of complex interactions and feedbacks that occur between microbes, plants and their physical environment in the context of climate change, and the influence of other global changes which have the capacity to amplify climate-driven effects on soil microbes. Overall, we emphasize the urgent need for greater understanding of how soil microbial ecology contributes to land-atmosphere carbon exchange in the context of climate change, and identify some challenges for the future. In particular, we highlight the need for a multifactor experimental approach to understand how soil microbes and their activities respond to climate change and consequences for carbon cycle feedbacks.

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

Walters, Jill L.

The journal Microbial Ecology will be publishing a special issue dedicated to microbes in outer space. This tribute will be included in the issue, in memory of the shuttle crew who gave their lives earlier this year.

A Study of Pupils' Conceptions and Reasoning in Connection with "Microbes", as a Contribution To Research in Biotechnology Education.

ERIC Educational Resources Information Center

Simonneaux, Laurence

2000-01-01

Students' conceptions about "microbes" tend to condition their understanding of biotechnology. Explores connections between the status given to diseases, a hygiene-oriented culture, layman's versus school knowledge, personal experience, socio-cultural mediation, linguistic confusions, and students' conceptions. (Contains 21 references.)…

Potential applications of insect symbionts in biotechnology.

PubMed

Berasategui, Aileen; Shukla, Shantanu; Salem, Hassan; Kaltenpoth, Martin

2016-02-01

Symbiotic interactions between insects and microorganisms are widespread in nature and are often the source of ecological innovations. In addition to supplementing their host with essential nutrients, microbial symbionts can produce enzymes that help degrade their food source as well as small molecules that defend against pathogens, parasites, and predators. As such, the study of insect ecology and symbiosis represents an important source of chemical compounds and enzymes with potential biotechnological value. In addition, the knowledge on insect symbiosis can provide novel avenues for the control of agricultural pest insects and vectors of human diseases, through targeted manipulation of the symbionts or the host-symbiont associations. Here, we discuss different insect-microbe interactions that can be exploited for insect pest and human disease control, as well as in human medicine and industrial processes. Our aim is to raise awareness that insect symbionts can be interesting sources of biotechnological applications and that knowledge on insect ecology can guide targeted efforts to discover microorganisms of applied value.

Seeing the Light: The Roles of Red- and Blue-Light Sensing in Plant Microbes.

PubMed

Beattie, Gwyn A; Hatfield, Bridget M; Dong, Haili; McGrane, Regina S

2018-05-16

Plants collect, concentrate, and conduct light throughout their tissues, thus enhancing light availability to their resident microbes. This review explores the role of photosensing in the biology of plant-associated bacteria and fungi, including the molecular mechanisms of red-light sensing by phytochromes and blue-light sensing by LOV (light-oxygen-voltage)-domain proteins in these microbes. Bacteriophytochromes function as major drivers of the bacterial transcriptome and mediate light-regulated suppression of virulence, motility, and conjugation in some phytopathogens and light-regulated induction of the photosynthetic apparatus in a stem-nodulating symbiont. Bacterial LOV proteins also influence light-mediated changes in both symbiotic and pathogenic phenotypes. Although red-light sensing by fungal phytopathogens is poorly understood, fungal LOV proteins contribute to blue-light regulation of traits, including asexual development and virulence. Collectively, these studies highlight that plant microbes have evolved to exploit light cues and that light sensing is often coupled with sensing other environmental signals. Expected final online publication date for the Annual Review of Phytopathology Volume 56 is August 25, 2018. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Characteristics and kinetic analysis of AQS transformation and microbial goethite reduction: Insight into “redox mediator-microbe-iron oxide” interaction process

DOE PAGES

Zhu, Weihuang; Shi, Mengran; Yu, Dan; ...

2016-03-29

Here, the characteristics and kinetics of redox transformation of a redox mediator, anthraquinone-2-sulfonate (AQS), during microbial goethite reduction by Shewanella decolorationis S12, a dissimilatory iron reduction bacterium (DIRB), were investigated to provide insights into “redox mediator-iron oxide” interaction in the presence of DIRB. Two pre-incubation reaction systems of the “strain S12-goethite” and the “strain S12-AQS” were used to investigate the dynamics of goethite reduction and AQS redox transformation. Results show that the concentrations of goethite and redox mediator, and the inoculation cell density all affect the characteristics of microbial goethite reduction, kinetic transformation between oxidized and reduced species of themore » redox mediator. Both abiotic and biotic reactions and their coupling regulate the kinetic process for “Quinone-Iron” interaction in the presence of DIRB. Our results provide some new insights into the characteristics and mechanisms of interaction among “quinone-DIRB- goethite” under biotic/abiotic driven.« less

Where microorganisms meet rocks in the Earth's Critical Zone

NASA Astrophysics Data System (ADS)

Akob, D. M.; Küsel, K.

2011-12-01

The Critical Zone (CZ) is the Earth's outer shell where all the fundamental physical, chemical, and biological processes critical for sustaining life occur and interact. As microbes in the CZ drive many of these biogeochemical cycles, understanding their impact on life-sustaining processes starts with an understanding of their biodiversity. In this review, we summarize the factors controlling where terrestrial CZ microbes (prokaryotes and micro-eukaryotes) live and what is known about their diversity and function. Microbes are found throughout the CZ, down to 5 km below the surface, but their functional roles change with depth due to habitat complexity, e.g. variability in pore spaces, water, oxygen, and nutrients. Abundances of prokaryotes and micro-eukaryotes decrease from 1010 or 107 cells g soil-1 or rock-1, or ml water-1 by up to eight orders of magnitude with depth. Although symbiotic mycorrhizal fungi and free-living decomposers have been studied extensively in soil habitats, where they occur up to 103 cells g soil-1, little is known regarding their identity or impact on weathering in the deep subsurface. The relatively low abundance of micro-eukaryotes in the deep subsurface suggests that they are limited in space, nutrients, are unable to cope with oxygen limitations, or some combination thereof. Since deep regions of the CZ have limited access to recent photosynthesis-derived carbon, microbes there depend on deposited organic material or a chemolithoautotrophic metabolism that allows for a complete food chain, independent from the surface, although limited energy flux means cell growth may take tens to thousands of years. Microbes are found in all regions of the CZ and can mediate important biogeochemical processes, but more work is needed to understand how microbial populations influence the links between different regions of the CZ and weathering processes. With the recent development of "omics" technologies, microbial ecologists have new methods that can be used to link the composition and function of in situ microbial communities. In particular, these methods can be used to search for new metabolic pathways that are relevant to biogeochemical nutrient cycling and determine how the activity of microorganisms can affect transport of carbon, particulates, and reactive gases between and within CZ regions.

Termites promote resistance of decomposition to spatiotemporal variability in rainfall.

PubMed

Veldhuis, Michiel P; Laso, Francisco J; Olff, Han; Berg, Matty P

2017-02-01

The ecological impact of rapid environmental change will depend on the resistance of key ecosystems processes, which may be promoted by species that exert strong control over local environmental conditions. Recent theoretical work suggests that macrodetritivores increase the resistance of African savanna ecosystems to changing climatic conditions, but experimental evidence is lacking. We examined the effect of large fungus-growing termites and other non-fungus-growing macrodetritivores on decomposition rates empirically with strong spatiotemporal variability in rainfall and temperature. Non-fungus-growing larger macrodetritivores (earthworms, woodlice, millipedes) promoted decomposition rates relative to microbes and small soil fauna (+34%) but both groups reduced their activities with decreasing rainfall. However, fungus-growing termites increased decomposition rates strongest (+123%) under the most water-limited conditions, making overall decomposition rates mostly independent from rainfall. We conclude that fungus-growing termites are of special importance in decoupling decomposition rates from spatiotemporal variability in rainfall due to the buffered environment they create within their extended phenotype (mounds), that allows decomposition to continue when abiotic conditions outside are less favorable. This points at a wider class of possibly important ecological processes, where soil-plant-animal interactions decouple ecosystem processes from large-scale climatic gradients. This may strongly alter predictions from current climate change models. © 2016 by the Ecological Society of America.

Phytohormone mediation of interactions between herbivores and plant pathogens.

PubMed

Lazebnik, Jenny; Frago, Enric; Dicke, Marcel; van Loon, Joop J A

2014-07-01

Induced plant defenses against either pathogens or herbivore attackers are regulated by phytohormones. These phytohormones are increasingly recognized as important mediators of interactions between organisms associated with plants. In this review, we discuss the role of plant defense hormones in sequential tri-partite interactions among plants, pathogenic microbes, and herbivorous insects, based on the most recent literature. We discuss the importance of pathogen trophic strategy in the interaction with herbivores that exhibit different feeding modes. Plant resistance mechanisms also affect plant quality in future interactions with attackers. We discuss exemplary evidence for the hypotheses that (i) biotrophic pathogens can facilitate chewing herbivores, unless plants exhibit effector-triggered immunity, but (ii) facilitate or inhibit phloem feeders. (iii) Necrotrophic pathogens, on the other hand, can inhibit both phloem feeders and chewers. We also propose herbivore feeding mode as predictor of effects on pathogens of different trophic strategies, providing evidence for the hypotheses that (iv) phloem feeders inhibit pathogen attack by increasing SA induction, whereas (v) chewing herbivores tend not to affect necrotrophic pathogens, while they may either inhibit or facilitate biotrophic pathogens. Putting these hypotheses to the test will increase our understanding of phytohormonal regulation of plant defense to sequential attack by plant pathogens and insect herbivores. This will provide valuable insight into plant-mediated ecological interactions among members of the plant-associated community.

Bioremediation of oil spills by whale microbes. Final report, 1994-1995

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

Craig, A.M.; Wachenheim, D.

1995-06-01

Baleen whale forestomach anaerobic microbes were studied for their ability to detoxify recalcitrant environmental pollutants; these include components of crude oil and some chlorinated aromatic compounds which are constituents of oil spills not biodegraded by aerobic microbes. In this study, forestomach rumen samples were collected on two occasions on the North Slope. When incubated with anthracene and naphthalene (PAH), these pollutants were degraded in the majority of sample sets. All simple aromatic hydrocarbons (benzine, toluene, xylenes, ethylbenzene) were degraded. PCBs were biodegraded by microbes from only two of the whales. Variable results were found with picric acid, trinitrotoluene (TNT), andmore » atrazine, and were likely due to analytical difficulties. Whale forestomach bacteria have adapted to an ecological niche where flow rates, mixing, and catabolism occur at rapid rates. These rates and the ability to metabolize complex molecules far exceed those of aerobic sediment and soil bacteria in biodegradation of environmental pollutants.« less

Shifts in priming partly explain impacts of long-term nitrogen input in different chemical forms on soil organic carbon storage.

PubMed

Song, Minghua; Guo, Yu; Yu, Feihai; Zhang, Xianzhou; Cao, Guangmin; Cornelissen, Johannes H C

2018-05-10

Input of labile organic carbon can enhance decomposition of extant soil organic carbon (SOC) through priming. We hypothesized that long-term nitrogen (N) input in different chemical forms alters SOC pools by altering priming effects associated with N-mediated changes in plants and soil microbes. The hypothesis was tested by integrating field experimental data of plants, soil microbes and two incubation experiments with soils that had experienced 10 years of N enrichment with three chemical forms (ammonium, nitrate and both ammonium and nitrate) in an alpine meadow on the Tibetan Plateau. Incubations with glucose- 13 C addition at three rates were used to quantify effects of exogenous organic carbon input on the priming of SOC. Incubations with microbial inocula extracted from soils that had experienced different long-term N treatments were conducted to detect effects of N-mediated changes in soil microbes on priming effects. We found strong evidence and a mechanistic explanation for alteration of SOC pools following 10 years of N enrichment with different chemical forms. We detected significant negative priming effects both in soils collected from ammonium-addition plots and in sterilized soils inoculated with soil microbes extracted from ammonium-addition plots. In contrast, significant positive priming effects were found both in soils collected from nitrate-addition plots and in sterilized soils inoculated with soil microbes extracted from nitrate-addition plots. Meanwhile, the abundance and richness of graminoids were higher and the abundance of soil microbes was lower in ammonium-addition than in nitrate-addition plots. Our findings provide evidence that shifts toward higher graminoid abundance and changes in soil microbial abundance mediated by N chemical forms are key drivers for priming effects and SOC pool changes, thereby linking human interference with the N cycle to climate change. © 2018 John Wiley & Sons Ltd.

Utilization of microbial iron assimilation processes for the development of new antibiotics and inspiration for the design of new anticancer agents.

PubMed

Miller, Marvin J; Zhu, Helen; Xu, Yanping; Wu, Chunrui; Walz, Andrew J; Vergne, Anne; Roosenberg, John M; Moraski, Garrett; Minnick, Albert A; McKee-Dolence, Julia; Hu, Jingdan; Fennell, Kelley; Kurt Dolence, E; Dong, Li; Franzblau, Scott; Malouin, Francois; Möllmann, Ute

2009-02-01

Pathogenic microbes rapidly develop resistance to antibiotics. To keep ahead in the "microbial war", extensive interdisciplinary research is needed. A primary cause of drug resistance is the overuse of antibiotics that can result in alteration of microbial permeability, alteration of drug target binding sites, induction of enzymes that destroy antibiotics (ie., beta-lactamase) and even induction of efflux mechanisms. A combination of chemical syntheses, microbiological and biochemical studies demonstrate that the known critical dependence of iron assimilation by microbes for growth and virulence can be exploited for the development of new approaches to antibiotic therapy. Iron recognition and active transport relies on the biosyntheses and use of microbe-selective iron-chelating compounds called siderophores. Our studies, and those of others, demonstrate that siderophores and analogs can be used for iron transport-mediated drug delivery ("Trojan Horse" antibiotics) and induction of iron limitation/starvation (Development of new agents to block iron assimilation). Recent extensions of the use of siderophores for the development of novel potent and selective anticancer agents are also described.

Utilization of microbial iron assimilation processes for the development of new antibiotics and inspiration for the design of new anticancer agents

PubMed Central

Zhu, Helen; Xu, Yanping; Wu, Chunrui; Walz, Andrew J.; Vergne, Anne; Roosenberg, John M.; Moraski, Garrett; Minnick, Albert A.; McKee-Dolence, Julia; Hu, Jingdan; Fennell, Kelley; Dolence, E. Kurt; Dong, Li; Franzblau, Scott; Malouin, Francois; Möllmann, Ute

2014-01-01

Pathogenic microbes rapidly develop resistance to antibiotics. To keep ahead in the “microbial war”, extensive interdisciplinary research is needed. A primary cause of drug resistance is the overuse of antibiotics that can result in alteration of microbial permeability, alteration of drug target binding sites, induction of enzymes that destroy antibiotics (ie., beta-lactamase) and even induction of efflux mechanisms. A combination of chemical syntheses, microbiological and biochemical studies demonstrate that the known critical dependence of iron assimilation by microbes for growth and virulence can be exploited for the development of new approaches to antibiotic therapy. Iron recognition and active transport relies on the biosyntheses and use of microbe-selective iron-chelating compounds called siderophores. Our studies, and those of others, demonstrate that siderophores and analogs can be used for iron transport-mediated drug delivery (“Trojan Horse” antibiotics) and induction of iron limitation/starvation (Development of new agents to block iron assimilation). Recent extensions of the use of siderophores for the development of novel potent and selective anticancer agents are also described. PMID:19130268

Interhost dispersal alters microbiome assembly and can overwhelm host innate immunity in an experimental zebrafish model.

PubMed

Burns, Adam R; Miller, Elizabeth; Agarwal, Meghna; Rolig, Annah S; Milligan-Myhre, Kathryn; Seredick, Steve; Guillemin, Karen; Bohannan, Brendan J M

2017-10-17

The diverse collections of microorganisms associated with humans and other animals, collectively referred to as their "microbiome," are critical for host health, but the mechanisms that govern their assembly are poorly understood. This has made it difficult to identify consistent host factors that explain variation in microbiomes across hosts, despite large-scale sampling efforts. While ecological theory predicts that the movement, or dispersal, of individuals can have profound and predictable consequences on community assembly, its role in the assembly of animal-associated microbiomes remains underexplored. Here, we show that dispersal of microorganisms among hosts can contribute substantially to microbiome variation, and is able to overwhelm the effects of individual host factors, in an experimental test of ecological theory. We manipulated dispersal among wild-type and immune-deficient myd88 knockout zebrafish and observed that interhost dispersal had a large effect on the diversity and composition of intestinal microbiomes. Interhost dispersal was strong enough to overwhelm the effects of host factors, largely eliminating differences between wild-type and immune-deficient hosts, regardless of whether dispersal occurred within or between genotypes, suggesting dispersal can independently alter the ecology of microbiomes. Our observations are consistent with a predictive model that assumes metacommunity dynamics and are likely mediated by dispersal-related microbial traits. These results illustrate the importance of microbial dispersal to animal microbiomes and motivate its integration into the study of host-microbe systems.

Antimicrobial Pesticides

MedlinePlus

... requires special tests to ensure efficacy of public health pesticides when the pests are invisible disease-causing microbes, rather than insects or rodents that may be harboring disease organisms. Determining human and ecological risks from exposure to antimicrobial pesticides ...

A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome.

PubMed

Warinner, Christina; Speller, Camilla; Collins, Matthew J

2015-01-19

The field of palaeomicrobiology is dramatically expanding thanks to recent advances in high-throughput biomolecular sequencing, which allows unprecedented access to the evolutionary history and ecology of human-associated and environmental microbes. Recently, human dental calculus has been shown to be an abundant, nearly ubiquitous, and long-term reservoir of the ancient oral microbiome, preserving not only microbial and host biomolecules but also dietary and environmental debris. Modern investigations of native human microbiota have demonstrated that the human microbiome plays a central role in health and chronic disease, raising questions about changes in microbial ecology, diversity and function through time. This paper explores the current state of ancient oral microbiome research and discusses successful applications, methodological challenges and future possibilities in elucidating the intimate evolutionary relationship between humans and their microbes.

Revisiting the ants of Melanesia and the taxon cycle: historical and human-mediated invasions of a tropical archipelago.

PubMed

Economo, Evan P; Sarnat, Eli M

2012-07-01

Understanding the historical evolution of biotas and the dynamics of contemporary human-mediated species introductions are two central tasks of biology. One hypothesis may address both-the taxon cycle. Taxon cycles are phases of range expansion and contraction coupled to ecological and evolutionary niche shifts. These historical invasion processes resemble human-mediated invasions in pattern and possibly mechanism, but both the existence of historical cycles and the roles of recent introductions are in question. We return to the system that originally inspired the taxon cycle-Melanesian ants-and perform novel tests of the hypothesis. We analyze (i) the habitat distributions of Fiji's entire ant fauna (183 species), (ii) ecological shifts associated with the in situ radiation of Fijian Pheidole in a phylogenetic context, and (iii) the ecological structure of a massive exotic ant invasion of the archipelago. Our analyses indicate lineages shift toward primary habitats, higher elevation, rarity, and ecological specialization with increasing level of endemism, consistent with taxon cycle predictions. The marginal habitats that historically formed a dispersal conduit in the Pacific are now mostly replaced by human-modified habitats dominated by a colonization pulse of exotic species. We propose this may represent the first phase of an incipient global cycle of human-mediated colonization, ecological shifts, and diversification.

The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation.

PubMed

Langdon, Amy; Crook, Nathan; Dantas, Gautam

2016-04-13

The widespread use of antibiotics in the past 80 years has saved millions of human lives, facilitated technological progress and killed incalculable numbers of microbes, both pathogenic and commensal. Human-associated microbes perform an array of important functions, and we are now just beginning to understand the ways in which antibiotics have reshaped their ecology and the functional consequences of these changes. Mounting evidence shows that antibiotics influence the function of the immune system, our ability to resist infection, and our capacity for processing food. Therefore, it is now more important than ever to revisit how we use antibiotics. This review summarizes current research on the short-term and long-term consequences of antibiotic use on the human microbiome, from early life to adulthood, and its effect on diseases such as malnutrition, obesity, diabetes, and Clostridium difficile infection. Motivated by the consequences of inappropriate antibiotic use, we explore recent progress in the development of antivirulence approaches for resisting infection while minimizing resistance to therapy. We close the article by discussing probiotics and fecal microbiota transplants, which promise to restore the microbiota after damage of the microbiome. Together, the results of studies in this field emphasize the importance of developing a mechanistic understanding of gut ecology to enable the development of new therapeutic strategies and to rationally limit the use of antibiotic compounds.

Harnessing Host-Vector Microbiome for Sustainable Plant Disease Management of Phloem-Limited Bacteria

PubMed Central

Trivedi, Pankaj; Trivedi, Chanda; Grinyer, Jasmine; Anderson, Ian C.; Singh, Brajesh K.

2016-01-01

Plant health and productivity is strongly influenced by their intimate interaction with deleterious and beneficial organisms, including microbes, and insects. Of the various plant diseases, insect-vectored diseases are of particular interest, including those caused by obligate parasites affecting plant phloem such as Candidatus (Ca.) Phytoplasma species and several species of Ca. Liberibacter. Recent studies on plant–microbe and plant–insect interactions of these pathogens have demonstrated that plant–microbe–insect interactions have far reaching consequences for the functioning and evolution of the organisms involved. These interactions take place within complex pathosystems and are shaped by a myriad of biotic and abiotic factors. However, our current understanding of these processes and their implications for the establishment and spread of insect-borne diseases remains limited. This article highlights the molecular, ecological, and evolutionary aspects of interactions among insects, plants, and their associated microbial communities with a focus on insect vectored and phloem-limited pathogens belonging to Ca. Phytoplasma and Ca. Liberibacter species. We propose that innovative and interdisciplinary research aimed at linking scales from the cellular to the community level will be vital for increasing our understanding of the mechanisms underpinning plant–insect–microbe interactions. Examination of such interactions could lead us to applied solutions for sustainable disease and pest management. PMID:27746788

Microbial Communities and Bioactive Compounds in Marine Sponges of the Family Irciniidae—A Review

PubMed Central

Hardoim, Cristiane C. P.; Costa, Rodrigo

2014-01-01

Marine sponges harbour complex microbial communities of ecological and biotechnological importance. Here, we propose the application of the widespread sponge family Irciniidae as an appropriate model in microbiology and biochemistry research. Half a gram of one Irciniidae specimen hosts hundreds of bacterial species—the vast majority of which are difficult to cultivate—and dozens of fungal and archaeal species. The structure of these symbiont assemblages is shaped by the sponge host and is highly stable over space and time. Two types of quorum-sensing molecules have been detected in these animals, hinting at microbe-microbe and host-microbe signalling being important processes governing the dynamics of the Irciniidae holobiont. Irciniids are vulnerable to disease outbreaks, and concerns have emerged about their conservation in a changing climate. They are nevertheless amenable to mariculture and laboratory maintenance, being attractive targets for metabolite harvesting and experimental biology endeavours. Several bioactive terpenoids and polyketides have been retrieved from Irciniidae sponges, but the actual producer (host or symbiont) of these compounds has rarely been clarified. To tackle this, and further pertinent questions concerning the functioning, resilience and physiology of these organisms, truly multi-layered approaches integrating cutting-edge microbiology, biochemistry, genetics and zoology research are needed. PMID:25272328

Management of Indigenous Plant-Microbe Symbioses Aids Restoration of Desertified Ecosystems

PubMed Central

Requena, Natalia; Perez-Solis, Estefania; Azcón-Aguilar, Concepción; Jeffries, Peter; Barea, José-Miguel

2001-01-01

Disturbance of natural plant communities is the first visible indication of a desertification process, but damage to physical, chemical, and biological soil properties is known to occur simultaneously. Such soil degradation limits reestablishment of the natural plant cover. In particular, desertification causes disturbance of plant-microbe symbioses which are a critical ecological factor in helping further plant growth in degraded ecosystems. Here we demonstrate, in two long-term experiments in a desertified Mediterranean ecosystem, that inoculation with indigenous arbuscular mycorrhizal fungi and with rhizobial nitrogen-fixing bacteria not only enhanced the establishment of key plant species but also increased soil fertility and quality. The dual symbiosis increased the soil nitrogen (N) content, organic matter, and hydrostable soil aggregates and enhanced N transfer from N-fixing to nonfixing species associated within the natural succession. We conclude that the introduction of target indigenous species of plants associated with a managed community of microbial symbionts is a successful biotechnological tool to aid the recovery of desertified ecosystems. PMID:11157208

[Macro- and microevolution as related to the problem of origin and global expansion of the plague pathogen Yersinia pestis].

PubMed

Suntsov, V V; Suntsova, N I

2008-01-01

The ratio of macro- and microevolutionary processes is considered with reference to the ecological scenario of the origin of the plague pathogen and its subsequent natural and anthropogenic global expansion. The macroevolutionary transformation of the ancestral pseudotuberculosis microbe clone into the initial plague microbe Yersinia pestis tarbagani occurred in Central Asia at the end of the Late Pleistocene by a "vertical" Darwinian way in an inadaptive heterothermal continual intermediate environment--the Mongolian marmot Marmota sibirica-flea Oropsylla silantiewi system--via a sequence of unstable and currently extinct intermediate forms. Its natural geographic expansion on the "oil spot" principle in the postglacial time led to the microevolutionary formation of 20-30 hostal subspecies circulating in populations of the background species of burrowing rodents and pikas in arid areas of Eurasia. The intercontinental spread of the "marmot" and "rat" pathogen subspecies in the past few centuries has been exclusively anthropogenic, with the involvement of synanthropic (ship) rats.

Biogeographic patterns in ocean microbes emerge in a neutral agent-based model.

PubMed

Hellweger, Ferdi L; van Sebille, Erik; Fredrick, Neil D

2014-09-12

A key question in ecology and evolution is the relative role of natural selection and neutral evolution in producing biogeographic patterns. We quantify the role of neutral processes by simulating division, mutation, and death of 100,000 individual marine bacteria cells with full 1 million-base-pair genomes in a global surface ocean circulation model. The model is run for up to 100,000 years and output is analyzed using BLAST (Basic Local Alignment Search Tool) alignment and metagenomics fragment recruitment. Simulations show the production and maintenance of biogeographic patterns, characterized by distinct provinces subject to mixing and periodic takeovers by neighbors (coalescence), after which neutral evolution reestablishes the province and the patterns reorganize. The emergent patterns are substantial (e.g., down to 99.5% DNA identity between North and Central Pacific provinces) and suggest that microbes evolve faster than ocean currents can disperse them. This approach can also be used to explore environmental selection. Copyright © 2014, American Association for the Advancement of Science.

Prediction and prevention of the next pandemic zoonosis

PubMed Central

Morse, Stephen S; Mazet, Jonna A K; Woolhouse, Mark; Parrish, Colin R; Carroll, Dennis; Karesh, William B; Zambrana-Torrelio, Carlos; Lipkin, W Ian; Daszak, Peter

2013-01-01

Most pandemics—eg, HIV/AIDS, severe acute respiratory syndrome, pandemic influenza—originate in animals, are caused by viruses, and are driven to emerge by ecological, behavioural, or socioeconomic changes. Despite their substantial effects on global public health and growing understanding of the process by which they emerge, no pandemic has been predicted before infecting human beings. We review what is known about the pathogens that emerge, the hosts that they originate in, and the factors that drive their emergence. We discuss challenges to their control and new efforts to predict pandemics, target surveillance to the most crucial interfaces, and identify prevention strategies. New mathematical modelling, diagnostic, communications, and informatics technologies can identify and report hitherto unknown microbes in other species, and thus new risk assessment approaches are needed to identify microbes most likely to cause human disease. We lay out a series of research and surveillance opportunities and goals that could help to overcome these challenges and move the global pandemic strategy from response to pre-emption. PMID:23200504

Temperature mediates continental-scale diversity of microbes in forest soils

PubMed Central

Zhou, Jizhong; Deng, Ye; Shen, Lina; Wen, Chongqing; Yan, Qingyun; Ning, Daliang; Qin, Yujia; Xue, Kai; Wu, Liyou; He, Zhili; Voordeckers, James W.; Nostrand, Joy D. Van; Buzzard, Vanessa; Michaletz, Sean T.; Enquist, Brian J.; Weiser, Michael D.; Kaspari, Michael; Waide, Robert; Yang, Yunfeng; Brown, James H.

2016-01-01

Climate warming is increasingly leading to marked changes in plant and animal biodiversity, but it remains unclear how temperatures affect microbial biodiversity, particularly in terrestrial soils. Here we show that, in accordance with metabolic theory of ecology, taxonomic and phylogenetic diversity of soil bacteria, fungi and nitrogen fixers are all better predicted by variation in environmental temperature than pH. However, the rates of diversity turnover across the global temperature gradients are substantially lower than those recorded for trees and animals, suggesting that the diversity of plant, animal and soil microbial communities show differential responses to climate change. To the best of our knowledge, this is the first study demonstrating that the diversity of different microbial groups has significantly lower rates of turnover across temperature gradients than other major taxa, which has important implications for assessing the effects of human-caused changes in climate, land use and other factors. PMID:27377774

Chemical ecology of marine angiosperms: opportunities at the interface of marine and terrestrial systems.

PubMed

Sieg, R Drew; Kubanek, Julia

2013-06-01

This review examines the state of the field for chemically mediated interactions involving marine angiosperms (seagrasses, mangroves, and salt marsh angiosperms). Small-scale interactions among these plants and their herbivores, pathogens, fouling organisms, and competitors are explored, as are community-level effects of plant secondary metabolites. At larger spatial scales, secondary metabolites from marine angiosperms function as reliable cues for larval settlement, molting, or habitat selection by fish and invertebrates, and can influence community structure and ecosystem function. Several recent studies illustrate the importance of chemical defenses from these plants that deter feeding by herbivores and infection by pathogens, but the extent to which allelopathic compounds kill or inhibit the growth of competitors is less clear. While some phenolic compounds such as ferulic acid and caffeic acid act as critical defenses against herbivores and pathogens, we find that a high total concentration of phenolic compounds within bulk plant tissues is not a strong predictor of defense. Residual chemical defenses prevent shredding or degradation of plant detritus by detritivores and microbes, delaying the time before plant matter can enter the microbial loop. Mangroves, marsh plants, and seagrasses remain plentiful sources of new natural products, but ecological functions are known for only a small proportion of these compounds. As new analytical techniques are incorporated into ecological studies, opportunities are emerging for chemical ecologists to test how subtle environmental cues affect the production and release of marine angiosperm chemical defenses or signaling molecules. Throughout this review, we point to areas for future study, highlighting opportunities for new directions in chemical ecology that will advance our understanding of ecological interactions in these valuable ecosystems.

[Effects of Different Reclaimed Scenarios on Soil Microbe and Enzyme Activities in Mining Areas].

PubMed

Li, Jun-jian; Liu, Feng; Zhou, Xiao-mei

2015-05-01

Abstract: Ecological degradation in the mining areas is greatly aggravated in recent several decades, and ecological restoration has become the primary measure for the sustainable development. Soil microbe and enzyme activity are sensitive indices to evaluate soil quality. Ecological reconstruction was initiated in Antaibao mining area, and we tested soil physicochemical properties, microbial populations of azotobacteria, nitrifying-bacteria and denitrifying-bacteria, and enzyme activities (including sucrose, polyphenol oxidase, dehydrogenase and urease) under different regeneration scenarios. Regeneration scenarios had significant effects on soil physicochemical properties, microbial population and enzyme activities. Total nitrogen was strongly correlated with azotobacteria and nitrifying-bacteria, however, total nitrogen was not correlated with denitrifying-bacteria. Phenol oxidase activity was negatively correlated with soil organic carbon and total nitrogen, but other enzyme activities were positively correlated with soil organic carbon and total nitrogen. Principal Component Analysis ( PCA) was applied to analyze the integrated fertility index (IFI). The highest and lowest IFIs were in Robinia pseudoacacia-Pinus tabuliformis mixed forests and un-reclaimed area, respectively. R. pseudoacacia-P. tabuliformis mixed forests were feasible for reclaimed mining areas in semi-arid region Northwest Shanxi.

A perspective on inter-kingdom signaling in plant-beneficial microbe interactions.

PubMed

Rosier, Amanda; Bishnoi, Usha; Lakshmanan, Venkatachalam; Sherrier, D Janine; Bais, Harsh P

2016-04-01

Recent work has shown that the rhizospheric and phyllospheric microbiomes of plants are composed of highly diverse microbial species. Though the information pertaining to the diversity of the aboveground and belowground microbes associated with plants is known, an understanding of the mechanisms by which these diverse microbes function is still in its infancy. Plants are sessile organisms, that depend upon chemical signals to interact with the microbiota. Of late, the studies related to the impact of microbes on plants have gained much traction in the research literature, supporting diverse functional roles of microbes on plant health. However, how these microbes interact as a community to confer beneficial traits to plants is still poorly understood. Recent advances in the use of "biologicals" as bio-fertilizers and biocontrol agents for sustainable agricultural practices is promising, and a fundamental understanding of how microbes in community work on plants could help this approach be more successful. This review attempts to highlight the importance of different signaling events that mediate a beneficial plant microbe interaction. Fundamental research is needed to understand how plants react to different benign microbes and how these microbes are interacting with each other. This review highlights the importance of chemical signaling, and biochemical and genetic events which determine the efficacy of benign microbes to promote the development of beneficial traits in plants.

Bacterial Communities of Diverse Drosophila Species: Ecological Context of a Host–Microbe Model System

PubMed Central

Bhatnagar, Srijak; Eisen, Jonathan A.; Kopp, Artyom

2011-01-01

Drosophila melanogaster is emerging as an important model of non-pathogenic host–microbe interactions. The genetic and experimental tractability of Drosophila has led to significant gains in our understanding of animal–microbial symbiosis. However, the full implications of these results cannot be appreciated without the knowledge of the microbial communities associated with natural Drosophila populations. In particular, it is not clear whether laboratory cultures can serve as an accurate model of host–microbe interactions that occur in the wild, or those that have occurred over evolutionary time. To fill this gap, we characterized natural bacterial communities associated with 14 species of Drosophila and related genera collected from distant geographic locations. To represent the ecological diversity of Drosophilids, examined species included fruit-, flower-, mushroom-, and cactus-feeders. In parallel, wild host populations were compared to laboratory strains, and controlled experiments were performed to assess the importance of host species and diet in shaping bacterial microbiome composition. We find that Drosophilid flies have taxonomically restricted bacterial communities, with 85% of the natural bacterial microbiome composed of only four bacterial families. The dominant bacterial taxa are widespread and found in many different host species despite the taxonomic, ecological, and geographic diversity of their hosts. Both natural surveys and laboratory experiments indicate that host diet plays a major role in shaping the Drosophila bacterial microbiome. Despite this, the internal bacterial microbiome represents only a highly reduced subset of the external bacterial communities, suggesting that the host exercises some level of control over the bacteria that inhabit its digestive tract. Finally, we show that laboratory strains provide only a limited model of natural host–microbe interactions. Bacterial taxa used in experimental studies are rare or absent in wild Drosophila populations, while the most abundant associates of natural Drosophila populations are rare in the lab. PMID:21966276

Value added phytoremediation of metal stressed soils using phosphate solubilizing microbial consortium.

PubMed

Gupta, Pratishtha; Kumar, Vipin

2017-01-01

The presence of heavy metals in the soil is a matter of growing concern due to their toxic and non-biodegradable nature. Lack of effectiveness of various conventional methods due to economic and technical constraints resulted in the search for an eco-friendly and cost-effective biological techniques for heavy metal removal from the environment. Until now, phytoremediation has emerged as an innovative technique to address the problem. However, the efficiency of phytoremediation process is hindered under the high metal concentration conditions. Hence, phosphate solubilizing microbes (PSM) assisted phytoremediation technique is gaining more insight as it can reduce the contamination load even under elevated metal stressed conditions. These microbes convert heavy metals into soluble and bioavailable forms, which consequently facilitate phytoremediation. Several studies have reported that the use of microbial consortium for remediation is considered more effective as compared to single strain pure culture. Therefore, this review paper focuses on the current trends in research related to PSM mediated uptake of heavy metal by plants. The efficiency of PSM consortia in enhancing the phytoremediation process has also been reviewed. Moreover, the role of phosphatase enzymes in the mineralization of organic forms of phosphate in soil is further discussed. Biosurfactant mediated bioremediation of metal polluted soils is a matter of extensive research nowadays. Hence, the recent advancement of using biosurfactants in enhanced phytoremediation of metal stressed soils is also described.

Local domestication of lactic acid bacteria via cassava beer fermentation.

PubMed

Colehour, Alese M; Meadow, James F; Liebert, Melissa A; Cepon-Robins, Tara J; Gildner, Theresa E; Urlacher, Samuel S; Bohannan, Brendan J M; Snodgrass, J Josh; Sugiyama, Lawrence S

2014-01-01

Cassava beer, or chicha, is typically consumed daily by the indigenous Shuar people of the Ecuadorian Amazon. This traditional beverage made from cassava tuber (Manihot esculenta) is thought to improve nutritional quality and flavor while extending shelf life in a tropical climate. Bacteria responsible for chicha fermentation could be a source of microbes for the human microbiome, but little is known regarding the microbiology of chicha. We investigated bacterial community composition of chicha batches using Illumina high-throughput sequencing. Fermented chicha samples were collected from seven Shuar households in two neighboring villages in the Morona-Santiago region of Ecuador, and the composition of the bacterial communities within each chicha sample was determined by sequencing a region of the 16S ribosomal gene. Members of the genus Lactobacillus dominated all samples. Significantly greater phylogenetic similarity was observed among chicha samples taken within a village than those from different villages. Community composition varied among chicha samples, even those separated by short geographic distances, suggesting that ecological and/or evolutionary processes, including human-mediated factors, may be responsible for creating locally distinct ferments. Our results add to evidence from other fermentation systems suggesting that traditional fermentation may be a form of domestication, providing endemic beneficial inocula for consumers, but additional research is needed to identify the mechanisms and extent of microbial dispersal.

Local domestication of lactic acid bacteria via cassava beer fermentation

PubMed Central

Meadow, James F.; Liebert, Melissa A.; Cepon-Robins, Tara J.; Gildner, Theresa E.; Urlacher, Samuel S.; Bohannan, Brendan J.M.; Snodgrass, J. Josh; Sugiyama, Lawrence S.

2014-01-01

Cassava beer, or chicha, is typically consumed daily by the indigenous Shuar people of the Ecuadorian Amazon. This traditional beverage made from cassava tuber (Manihot esculenta) is thought to improve nutritional quality and flavor while extending shelf life in a tropical climate. Bacteria responsible for chicha fermentation could be a source of microbes for the human microbiome, but little is known regarding the microbiology of chicha. We investigated bacterial community composition of chicha batches using Illumina high-throughput sequencing. Fermented chicha samples were collected from seven Shuar households in two neighboring villages in the Morona-Santiago region of Ecuador, and the composition of the bacterial communities within each chicha sample was determined by sequencing a region of the 16S ribosomal gene. Members of the genus Lactobacillus dominated all samples. Significantly greater phylogenetic similarity was observed among chicha samples taken within a village than those from different villages. Community composition varied among chicha samples, even those separated by short geographic distances, suggesting that ecological and/or evolutionary processes, including human-mediated factors, may be responsible for creating locally distinct ferments. Our results add to evidence from other fermentation systems suggesting that traditional fermentation may be a form of domestication, providing endemic beneficial inocula for consumers, but additional research is needed to identify the mechanisms and extent of microbial dispersal. PMID:25071997

Environmental and social influences on emerging infectious diseases: past, present and future.

PubMed Central

McMichael, A J

2004-01-01

During the processes of human population dispersal around the world over the past 50 000-100 000 years, along with associated cultural evolution and inter-population contact and conflict, there have been several major transitions in the relationships of Homo sapiens with the natural world, animate and inanimate. Each of these transitions has resulted in the emergence of new or unfamiliar infectious diseases.The three great historical transitions since the initial advent of agriculture and livestock herding, from ca. 10 000 years ago, occurred when: (i) early agrarian-based settlements enabled sylvatic enzootic microbes to make contact with Homo sapiens; (ii) early Eurasian civilizations (such as the Greek and Roman empires, China and south Asia) came into military and commercial contact, ca. 3000-2000 years ago, swapping their dominant infections; and (iii) European expansionism, over the past five centuries, caused the transoceanic spread of often lethal infectious diseases. This latter transition is best known in relation to the conquest of the Americas by Spanish conquistadores, when the inadvertent spread of measles, smallpox and influenza devastated the Amerindian populations.Today, we are living through the fourth of these great transitional periods. The contemporary spread and increased lability of various infectious diseases, new and old, reflect the combined and increasingly widespread impacts of demographic, environmental, behavioural, technological and other rapid changes in human ecology. Modern clinical medicine has, via blood transfusion, organ transplantation, and the use of hypodermic syringes, created new opportunities for microbes. These have contributed to the rising iatrogenic problems of hepatitis C, HIV/AIDS and several other viral infections. Meanwhile, the injudicious use of antibiotics has been a rare instance of human action actually increasing 'biodiversity'.Another aspect of this fourth transition is that modern hyper-hygienic living restricts microbial exposure in early life. This, in the 1950s, may have contributed to an epidemic of more serious, disabling, poliomyelitis, affecting older children than those affected in earlier, more endemic decades. As with previous human-microbe transitions, a new equilibrial state may lie ahead. However, it certainly will not entail a world free of infectious diseases. Any mature, sustainable, human ecology must come to terms with both the need for, and the needs of, the microbial species that help to make up the interdependent system of life on Earth. Humans and microbes are not "at war"; rather, both parties are engaged in amoral, self-interested, coevolutionary struggle. We need to understand better, and therefore anticipate, the dynamics of that process. PMID:15306389

Microbes and associated soluble and volatile chemicals on periodically wet household surfaces.

PubMed

Adams, Rachel I; Lymperopoulou, Despoina S; Misztal, Pawel K; De Cassia Pessotti, Rita; Behie, Scott W; Tian, Yilin; Goldstein, Allen H; Lindow, Steven E; Nazaroff, William W; Taylor, John W; Traxler, Matt F; Bruns, Thomas D

2017-09-26

Microorganisms influence the chemical milieu of their environment, and chemical metabolites can affect ecological processes. In built environments, where people spend the majority of their time, very little is known about how surface-borne microorganisms influence the chemistry of the indoor spaces. Here, we applied multidisciplinary approaches to investigate aspects of chemical microbiology in a house. We characterized the microbial and chemical composition of two common and frequently wet surfaces in a residential setting: kitchen sink and bathroom shower. Microbial communities were studied using culture-dependent and independent techniques, including targeting RNA for amplicon sequencing. Volatile and soluble chemicals from paired samples were analyzed using state-of-the-art techniques to explore the links between the observed microbiota and chemical exudates. Microbial analysis revealed a rich biological presence on the surfaces exposed in kitchen sinks and bathroom shower stalls. Microbial composition, matched for DNA and RNA targets, varied by surface type and sampling period. Bacteria were found to have an average of 25× more gene copies than fungi. Biomass estimates based on qPCR were well correlated with measured total volatile organic compound (VOC) emissions. Abundant VOCs included products associated with fatty acid production. Molecular networking revealed a diversity of surface-borne compounds that likely originate from microbes and from household products. Microbes played a role in structuring the chemical profiles on and emitted from kitchen sinks and shower stalls. Microbial VOCs (mVOCs) were predominately associated with the processing of fatty acids. The mVOC composition may be more stable than that of microbial communities, which can show temporal and spatial variation in their responses to changing environmental conditions. The mVOC output from microbial metabolism on kitchen sinks and bathroom showers should be apparent through careful measurement, even against a broader background of VOCs in homes, some of which may originate from microbes in other locations within the home. A deeper understanding of the chemical interactions between microbes on household surfaces will require experimentation under relevant environmental conditions, with a finer temporal resolution, to build on the observational study results presented here.

TEM study of a silicate-carbonate-microbe interface prepared by focused ion beam milling

NASA Astrophysics Data System (ADS)

Benzerara, Karim; Menguy, Nicolas; Guyot, François; Vanni, Christian; Gillet, Philippe

2005-03-01

The biogeochemical alteration of an Mg-Fe orthopyroxene, reacted for 70 yr under arid conditions in a desert environment, was studied by transmission electron microscopy. For this purpose, an electron transparent cross-section of the interface between a single microorganism, an orthopyroxene and nanometer-sized calcite crystals, was prepared with a focused ion beam system. X-ray energy dispersive spectrometry and electron energy loss spectroscopy allowed one to clearly distinguish the microorganism en route to fossilization from the nanometer-sized calcite crystals, showing the usefulness of such a protocol for identifying unambiguously traces of life in rocks. A 100-nm-deep depression was observed in the orthopyroxene close to the microorganism, suggesting an enhanced dissolution mediated by the microbe. However, an Al- and Si-rich amorphous altered layer restricted to the area just below the microorganism could be associated with decreased silicate dissolution rates at this location, suggesting complex effects of the microorganism on the silicate dissolution process. The close association observed between silicate dissolution and carbonate formation at the micrometer scale suggests that Urey-type CO 2 sequestration reactions could be mediated by microorganisms under arid conditions.

Conflict in the Intracellular Lives of Endosymbionts and Viruses: A Mechanistic Look at Wolbachia-Mediated Pathogen-blocking

PubMed Central

Newton, Irene L. G.; Hardy, Richard W.

2018-01-01

At the forefront of vector control efforts are strategies that leverage host-microbe associations to reduce vectorial capacity. The most promising of these efforts employs Wolbachia, a maternally transmitted endosymbiotic bacterium naturally found in 40% of insects. Wolbachia can spread through a population of insects while simultaneously inhibiting the replication of viruses within its host. Despite successes in using Wolbachia-transfected mosquitoes to limit dengue, Zika, and chikungunya transmission, the mechanisms behind pathogen-blocking have not been fully characterized. Firstly, we discuss how Wolbachia and viruses both require specific host-derived structures, compounds, and processes to initiate and maintain infection. There is significant overlap in these requirements, and infection with either microbe often manifests as cellular stress, which may be a key component of Wolbachia’s anti-viral effect. Secondly, we discuss the current understanding of pathogen-blocking through this lens of cellular stress and develop a comprehensive view of how the lives of Wolbachia and viruses are fundamentally in conflict with each other. A thorough understanding of the genetic and cellular determinants of pathogen-blocking will significantly enhance the ability of vector control programs to deploy and maintain effective Wolbachia-mediated control measures. PMID:29561780

Molecular Ecology of Drinking Water

EPA Science Inventory

The presentation consists of examples of molecular research: –Detection and control (removal and/or inactivation) of microbes in drinking source waters –Changing microbial quality of water during distribution and storage –Detection and identification of microbial agents, incl...

A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome

PubMed Central

Warinner, Christina; Speller, Camilla; Collins, Matthew J.

2015-01-01

The field of palaeomicrobiology is dramatically expanding thanks to recent advances in high-throughput biomolecular sequencing, which allows unprecedented access to the evolutionary history and ecology of human-associated and environmental microbes. Recently, human dental calculus has been shown to be an abundant, nearly ubiquitous, and long-term reservoir of the ancient oral microbiome, preserving not only microbial and host biomolecules but also dietary and environmental debris. Modern investigations of native human microbiota have demonstrated that the human microbiome plays a central role in health and chronic disease, raising questions about changes in microbial ecology, diversity and function through time. This paper explores the current state of ancient oral microbiome research and discusses successful applications, methodological challenges and future possibilities in elucidating the intimate evolutionary relationship between humans and their microbes. PMID:25487328

Ecology and thermal inactivation of microbes in and on interplanetary space vehicle components

NASA Technical Reports Server (NTRS)

Reyes, A. L.

1974-01-01

Dry heat inactivation characteristics were compared for 4-6 (B. brevis) spores and microbes from the Cincinnati soil samples at 105, 112, and 125. Characterized were the survival curves of 4-6 (B. brevis) spores at 112, 115, 118, 120, and 125 C, and 1.2 microgram of water per ml of headspace air (closed tin-can system), and the morphological characteristics of 4-6 (B. brevis), 6-12 (B. lentus), 7-11 (B. coagulans), and B. subtilis var. niger spores by scanning electron microscopy.

Strategies Influencing Spatial Heterogeneity of Microbial Life in a Soil Lysimeter

NASA Astrophysics Data System (ADS)

Sengupta, A.; Neilson, J. W.; Meira, A.; Wang, Y.; Meza, M.; Chorover, J.; Maier, R. M.; Troch, P. A. A.

2016-12-01

Soil microorganisms are critical drivers of biogeochemical processes. These microbes, in conjunction with their physical and chemical environment, contribute to ecosystem functioning and services of the landscape, have a profound impact on soil formation, and are of particular importance in oligotrophic environments; ecosystems that are characterized by low biotic diversity due to extremely low nutrient levels. Here, we present a study of microbial heterogeneity in a soil lysimeter under incipient conditions. The key questions asked were: 1) what is the spatial heterogeneity of microbes over a new and evolving landscape with inherent oligotrophic conditions, and 2) can patterns in diversity translate to patterns in microbe-mediated weathering processes and soil formation? We hypothesized that stratification of environmental conditions, brought about by varying water potential, flow paths, and redox conditions, will drive the heterogeneity of microbial life in a sub-meter scale. A suite of traditional and current microbiological tools were employed to study community characteristics. These included isolation on R2A media, quantitative polymerase chain reactions targeted at 16S rRNA bacterial and archaeal genes, and 18S fungal genes, and iTAG phylogenetic gene amplification. Illumina Mi-Seq platform generated sequences were analyzed using various bioinformatics pipelines to identify community patterns, classify microbial metabolic functions, and identify variables affecting the community dynamics. Numerous phyla (Verrucomicrobia, Actinobacteria, Planctomycetes, Proteobacteria, and Euryarchaeota) were identified. The surface layer had distinctly different distribution of communities compared to the other layers. Metabolically heterogeneous groups were found with respect to depth, with metabolic functions further confirmed by predictive functional profiling of the microbial communities. Therefore, despite being highly oligotrophic, the system was rich in species and functional diversity. Alongside physical and chemical data, the patterns observed in spatial and functional heterogeneity of microbes under incipient conditions is unique, and allows us to predict strategies undertaken by these microbes to survive in, and influence their oligotrophic environments.

Live microbial cells adsorb Mg2+ more effectively than lifeless organic matter

NASA Astrophysics Data System (ADS)

Qiu, Xuan; Yao, Yanchen; Wang, Hongmei; Duan, Yong

2018-03-01

The Mg2+ content is essential in determining different Mg-CaCO3 minerals. It has been demonstrated that both microbes and the organic matter secreted by microbes are capable of allocating Mg2+ and Ca2+ during the formation of Mg-CaCO3, yet detailed scenarios remain unclear. To investigate the mechanism that microbes and microbial organic matter potentially use to mediate the allocation of Mg2+ and Ca2+ in inoculating systems, microbial mats and four marine bacterial strains ( Synechococcus elongatus, Staphylococcus sp., Bacillus sp., and Desulfovibrio vulgaris) were incubated in artificial seawater media with Mg/Ca ratios ranging from 0.5 to 10.0. At the end of the incubation, the morphology of the microbial mats and the elements adsorbed on them were analyzed using scanning electronic microscopy (SEM) and energy diffraction spectra (EDS), respectively. The content of Mg2+ and Ca2+ adsorbed by the extracellular polysaccharide substances (EPS) and cells of the bacterial strains were analyzed with atomic adsorption spectroscopy (AAS). The functional groups on the surface of the cells and EPS of S. elongatus were estimated using automatic potentiometric titration combined with a chemical equilibrium model. The results show that live microbial mats generally adsorb larger amounts of Mg2+ than Ca2+, while this rarely is the case for autoclaved microbial mats. A similar phenomenon was also observed for the bacterial strains. The living cells adsorb more Mg2+ than Ca2+, yet a reversed trend was observed for EPS. The functional group analysis indicates that the cell surface of S. elongatus contains more basic functional groups (87.24%), while the EPS has more acidic and neutral functional groups (83.08%). These features may be responsible for the different adsorption behavior of Mg2+ and Ca2+ by microbial cells and EPS. Our work confirms the differential Mg2+ and Ca2+ mediation by microbial cells and EPS, which may provide insight into the processes that microbes use to induce Mg-carbonate formation.

Bioremediation: a genuine technology to remediate radionuclides from the environment.

PubMed

Prakash, Dhan; Gabani, Prashant; Chandel, Anuj K; Ronen, Zeev; Singh, Om V

2013-07-01

Radionuclides in the environment are a major human and environmental health concern. Like the Chernobyl disaster of 1986, the Fukushima Daiichi nuclear disaster in 2011 is once again causing damage to the environment: a large quantity of radioactive waste is being generated and dumped into the environment, and if the general population is exposed to it, may cause serious life-threatening disorders. Bioremediation has been viewed as the ecologically responsible alternative to environmentally destructive physical remediation. Microorganisms carry endogenous genetic, biochemical and physiological properties that make them ideal agents for pollutant remediation in soil and groundwater. Attempts have been made to develop native or genetically engineered (GE) microbes for the remediation of environmental contaminants including radionuclides. Microorganism-mediated bioremediation can affect the solubility, bioavailability and mobility of radionuclides. Therefore, we aim to unveil the microbial-mediated mechanisms for biotransformation of radionuclides under various environmental conditions as developing strategies for waste management of radionuclides. A discussion follows of '-omics'-integrated genomics and proteomics technologies, which can be used to trace the genes and proteins of interest in a given microorganism towards a cell-free bioremediation strategy. © 2013 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Linking Carbonic Anhydrase Abundance and Diversity in Soils to Ecological Function

NASA Astrophysics Data System (ADS)

Pang, E.; Meredith, L. K.; Welander, P. V.

2015-12-01

Carbonic anhydrase (CA) is an ancient enzyme widespread among bacteria, archaea, and eukarya that catalyzes the following reaction: CO2 + H2O ⇌ HCO3- + H+. Its functions are critical for key cellular processes such as concentrating CO2 for autotrophic growth, pH regulation, and pathogen survival in hosts. Currently, there are six known CA classes (α, β, γ, δ, η, ζ) arising from several distinct evolutionary lineages. CA are widespread in sequenced genomes, with many organisms containing multiple classes of CA or multiple CA of the same class. Soils host rich microbial communities with diverse and important ecological functions, but the diversity and abundance of CA in soils has not been explored. CA appears to play an important, but poorly understood, role in some biogeochemical cycles such as those of CO2 and its oxygen isotope composition and also carbonyl sulfide (COS), which are potential tracers in predictive carbon cycle models. Recognizing the prevalence and functional significance of CA in soils, we used a combined bioinformatics and molecular biology approach to address fundamental questions regarding the abundance, diversity, and function of CA in soils. To characterize the abundance and diversity of the different CA classes in soils, we analyzed existing soil metagenomic and metatranscriptomic data from the DOE Joint Genome Institute databases. Out of the six classes of CA, we only found the α, β, and γ classes to be present in soils, with the β class being the most abundant. We also looked at genomes of sequenced soil microorganisms to learn what combination of CA classes they contain, from which we can begin to predict the physiological role of CA. To characterize the functional roles of the different CA classes in soils, we collected soil samples from a variety of biomes with diverse chemical and physical properties and quantified the rate of two CA-mediated processes: soil uptake of COS and acceleration of the oxygen isotope exchange between CO2 and H2O. We employed PCR-based methods to quantify the abundance and diversity of CA encoding genes and their expression in our samples to link CA classes to the gas flux data. These studies provide the first survey of CA in soils, a step towards understanding CA's potentially significant role in microbial survival and microbe-mediated biogeochemical cycles.

Soil microbiology and soil health assessment

USDA-ARS?s Scientific Manuscript database

Soil scientists have long recognized the importance of soil biology in ecological health. In particular, soil microbes are crucial for many soil functions including decomposition, nutrient cycling, synthesis of plant growth regulators, and degradation of synthetic chemicals. Currently, soil biologis...

Metagenomic insights into the ecology and physiology of microbes in bioelectrochemical systems.

PubMed

Kouzuma, Atsushi; Ishii, Shun'ichi; Watanabe, Kazuya

2018-05-01

In bioelectrochemical systems (BESs), electrons are transferred between electrochemically active microbes (EAMs) and conductive materials, such as electrodes, via extracellular electron transfer (EET) pathways, and electrons thus transferred stimulate intracellular catabolic reactions. Catabolic and EET pathways have extensively been studied for several model EAMs, such as Shewanella oneidensis MR-1 and Geobacter sulfurreducens PCA, whereas it is also important to understand the ecophysiology of EAMs in naturally occurring microbiomes, such as those in anode biofilms in microbial fuel cells treating wastewater. Recent studies have exploited metagenomics and metatranscriptomics (meta-omics) approaches to characterize EAMs in BES-associated microbiomes. Here we review recent BES studies that used meta-omics approaches and show that these studies have discovered unexpected features of EAMs and deepened our understanding of functions and behaviors of microbes in BESs. It is desired that more studies will employ meta-omics approaches for advancing our knowledge on microbes in BESs. Copyright © 2018 Elsevier Ltd. All rights reserved.

Retention and Migration of Fine Organic Particles within an Agricultural Stream: Toenepi, Waikato, New Zealand

NASA Astrophysics Data System (ADS)

Drummond, J. D.; Davies-Colley, R.; Stott, R.; Sukias, J.; Nagels, J.; Sharp, A.; Packman, A. I.

2013-12-01

Fine organic particle dynamics are important to stream biogeochemistry, ecology, and transport of contaminant microbes. These particles migrate downstream through a series of deposition and resuspension events, which results in a wide range of residence times. This retention influences biogeochemical processing and in-stream stores of contaminant microbes that may mobilize during flood events and present a hazard to downstream uses such as water supplies and recreation. We are conducting studies to gain insights into organic particle dynamics in streams, with a campaign of experiments and modeling. The results should improve understanding of nutrient (C, N, P) spiraling and fine sediment movement in streams, and have particular application to microbial hazards. We directly measure microbial transport by including the indicator organism, E. coli, as a tracer, which is compared to a fluorescent inert particle tracer and conservative solute to gain insight on both microbial ecology and waterborne disease transmission. We developed a stochastic model to describe the transport and retention of fine suspended particles in rivers, including advective delivery of particles to the streambed, transport through porewaters, and reversible filtration within the streambed. Because fine particles are only episodically transported in streams, with intervening periods at rest in the bed, this transport process violates conventional advection-dispersion assumptions. Instead we adopt a stochastic mobile-immobile model formulation to describe fine particle transport. We apply this model to measurements of particle transport from multiple tracer experiments in an agricultural stream in the Waikato dairy region of New Zealand, and use the model to improve interpretation of baseflow particle dynamics. Our results show the importance of the benthic and hyporheic regions and in-stream vegetation as a reservoir for fine organic particles in streams.

Coercion in the Evolution of Plant-Microbe Communication: A Perspective.

PubMed

Rowe, S L; Norman, J S; Friesen, M L

2018-06-06

Plants and microbes are dependent on chemical signals as a means of interkingdom communication. There are two predicted paths for the evolution of these signals. Ritualization is the oft-assumed pathway for the evolution of plant-microbe communication systems. In this process, chemical signals, which benefit both receiver and sender, evolve from chemical cues, which benefit only the receiver. However, plant-microbe signaling may evolve from coercive interactions as well, a process known as sensory manipulation. Here, we aim to highlight the prevalence of coercive interactions and discuss sensory manipulation in the context of plant-microbe interactions. We present two examples of stabilized coercion: microbial coercion of plants via the release of phytohormones and plant coercion of microbes via manipulation of quorum-sensing compounds. Furthermore, we provide an evolutionary framework for the emergence of signaling from coercive plant-microbe interactions through the process of sensory manipulation. We hope that researchers will recognize the relevance of coercive interactions in plant-microbe systems and consider sensory manipulation as a plausible evolutionary trajectory for the emergence of plant-microbe signaling.

Active migration is associated with specific and consistent changes to gut microbiota in Calidris shorebirds.

PubMed

Risely, Alice; Waite, David W; Ujvari, Beata; Hoye, Bethany J; Klaassen, Marcel

2018-03-01

Gut microbes are increasingly recognised for their role in regulating an animal's metabolism and immunity. However, identifying repeatable associations between host physiological processes and their gut microbiota has proved challenging, in part because microbial communities often respond stochastically to host physiological stress (e.g. fasting, forced exercise or infection). Migratory birds provide a valuable system in which to test host-microbe interactions under physiological extremes because these hosts are adapted to predictable metabolic and immunological challenges as they undergo seasonal migrations, including temporary gut atrophy during long-distance flights. These physiological challenges may either temporarily disrupt gut microbial ecosystems, or, alternatively, promote predictable host-microbe associations during migration. To determine the relationship between migration and gut microbiota, we compared gut microbiota composition between migrating and non-migrating ("resident") conspecific shorebirds sharing a flock. We performed this across two sandpiper species, Calidris ferruginea and Calidris ruficollis, in north-western Australia, and an additional C. ruficollis population 3,000 km away in southern Australia. We found that migrants consistently had higher abundances of the bacterial genus Corynebacterium (average 28% abundance) compared to conspecific residents (average <1% abundance), with this effect holding across both species and sites. However, other than this specific association, community structure and diversity was almost identical between migrants and residents, with migration status accounting for only 1% of gut community variation when excluding Corynebacterium. Our findings suggest a consistent relationship between Corynebacterium and Calidris shorebirds during migration, with further research required to identify causal mechanisms behind the association, and to elucidate functionality to the host. However, outside this specific association, migrating shorebirds broadly maintained gut community structure, which may allow them to quickly recover gut function after a migratory flight. This study provides a rare example of a repeatable and specific response of the gut microbiota to a major physiological challenge across two species and two distant populations. © 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.

Partitioning Nitrification Between Specific Archaeal and Bacterial Clades in a Large, Nitrogen-Rich Estuary (San Francisco Bay, CA)

NASA Astrophysics Data System (ADS)

Damashek, J.; Casciotti, K. L.; Francis, C. A.

2014-12-01

Nitrification is the sole link between nitrogen inputs and losses in marine ecosystems, and understanding the microbial ecology and biogeochemistry of nitrification is therefore crucial for understanding how aquatic ecosystems process nitrogen. Recently-discovered ammonia-oxidizing archaea (AOA), rather than ammonia-oxidizing bacteria (AOB), appear to drive ammonia oxidation in many ecosystems, including much of the ocean. However, few studies have investigated these microbes in estuary waters, despite the fact nitrogen concentrations in estuaries are often far higher than the ocean, and can cause drastic ecological harm. We sought to determine the roles of AOA and AOB in driving pelagic nitrification throughout San Francisco Bay, by combining biogeochemical rate measurements with a suite of measurements of the abundance and diversity of AOA and AOB. It addition to traditional functional gene analyses and high-throughput 16S amplicon sequencing, we developed novel qPCR assays to selectively target the ammonia-oxidizing clades found in this estuary, which gave insights into clade-specific distributional patterns. Our biogeochemical data suggest a sizable fraction of ammonium in the bay is oxidized in the water column, likely by AOA, with nitrification in bottom waters also oxidizing a substantial portion of the ammonium exuded by sediments. Generally, Sacramento River waters and Suisun Bay bottom waters had the highest nitrification rates. AOA outnumbered AOB at most stations, and were present in high abundance at both the marine and freshwater ends of the estuary, while AOB abundance was highest in the low-salinity, brackish regions. Different archaeal clades were found at either end of the estuary, suggesting strong niche partitioning along the salinity gradient, with a third clade present largely in brackish waters. This work helps to assess the ability of ammonia-oxidizing microbes in estuaries to transform nitrogen prior to water discharge into the sea, and furthers our understanding of the roles of specific clades of these microbes in complex estuarine ecosystems.

Current ecological understanding of fungal-like pathogens of fish: what lies beneath?

PubMed Central

Gozlan, Rodolphe E.; Marshall, Wyth L.; Lilje, Osu; Jessop, Casey N.; Gleason, Frank H.; Andreou, Demetra

2014-01-01

Despite increasingly sophisticated microbiological techniques, and long after the first discovery of microbes, basic knowledge is still lacking to fully appreciate the ecological importance of microbial parasites in fish. This is likely due to the nature of their habitats as many species of fish suffer from living beneath turbid water away from easy recording. However, fishes represent key ecosystem services for millions of people around the world and the absence of a functional ecological understanding of viruses, prokaryotes, and small eukaryotes in the maintenance of fish populations and of their diversity represents an inherent barrier to aquatic conservation and food security. Among recent emerging infectious diseases responsible for severe population declines in plant and animal taxa, fungal and fungal-like microbes have emerged as significant contributors. Here, we review the current knowledge gaps of fungal and fungal-like parasites and pathogens in fish and put them into an ecological perspective with direct implications for the monitoring of fungal fish pathogens in the wild, their phylogeography as well as their associated ecological impact on fish populations. With increasing fish movement around the world for farming, releases into the wild for sport fishing and human-driven habitat changes, it is expected, along with improved environmental monitoring of fungal and fungal-like infections, that the full extent of the impact of these pathogens on wild fish populations will soon emerge as a major threat to freshwater biodiversity. PMID:24600442

The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions

PubMed Central

Kwong, Waldan K.; McFrederick, Quinn; Anderson, Kirk E.; Barribeau, Seth Michael; Chandler, James Angus; Cornman, R. Scott; Dainat, Jacques; Doublet, Vincent; Emery, Olivier; Evans, Jay D.; Farinelli, Laurent; Flenniken, Michelle L.; Granberg, Fredrik; Grasis, Juris A.; Gauthier, Laurent; Hayer, Juliette; Koch, Hauke; Kocher, Sarah; Martinson, Vincent G.; Moran, Nancy; Munoz-Torres, Monica; Newton, Irene; Paxton, Robert J.; Powell, Eli; Sadd, Ben M.; Schmid-Hempel, Paul; Schmid-Hempel, Regula; Schwarz, Ryan S.; vanEngelsdorp, Dennis

2016-01-01

ABSTRACT As pollinators, bees are cornerstones for terrestrial ecosystem stability and key components in agricultural productivity. All animals, including bees, are associated with a diverse community of microbes, commonly referred to as the microbiome. The bee microbiome is likely to be a crucial factor affecting host health. However, with the exception of a few pathogens, the impacts of most members of the bee microbiome on host health are poorly understood. Further, the evolutionary and ecological forces that shape and change the microbiome are unclear. Here, we discuss recent progress in our understanding of the bee microbiome, and we present challenges associated with its investigation. We conclude that global coordination of research efforts is needed to fully understand the complex and highly dynamic nature of the interplay between the bee microbiome, its host, and the environment. High-throughput sequencing technologies are ideal for exploring complex biological systems, including host-microbe interactions. To maximize their value and to improve assessment of the factors affecting bee health, sequence data should be archived, curated, and analyzed in ways that promote the synthesis of different studies. To this end, the BeeBiome consortium aims to develop an online database which would provide reference sequences, archive metadata, and host analytical resources. The goal would be to support applied and fundamental research on bees and their associated microbes and to provide a collaborative framework for sharing primary data from different research programs, thus furthering our understanding of the bee microbiome and its impact on pollinator health. PMID:27118586

The bee microbiome: Impact on bee health and model for evolution and ecology of host-microbe interactions

USGS Publications Warehouse

Engel, Philipp; Kwong, Waldan K.; McFrederick, Quinn; Anderson, Kirk E.; Barribeau, Seth Michael; Chandler, James Angus; Cornman, Robert S.; Dainat, Jacques; de Miranda, Joachim R.; Doublet, Vincent; Emery, Olivier; Evans, Jay D.; Farinelli, Laurent; Flenniken, Michelle L.; Granberg, Fredrik; Grasis, Juris A.; Gauthier, Laurent; Hayer, Juliette; Koch, Hauke; Kocher, Sarah; Martinson, Vincent G.; Moran, Nancy; Munoz-Torres, Monica; Newton, Irene; Paxton, Robert J.; Powell, Eli; Sadd, Ben M.; Schmid-Hempel, Paul; Schmid-Hempel, Regula; Song, Se Jin; Schwarz, Ryan S.; vanEngelsdorp, Dennis; Dainat, Benjamin

2016-01-01

As pollinators, bees are cornerstones for terrestrial ecosystem stability and key components in agricultural productivity. All animals, including bees, are associated with a diverse community of microbes, commonly referred to as the microbiome. The bee microbiome is likely to be a crucial factor affecting host health. However, with the exception of a few pathogens, the impacts of most members of the bee microbiome on host health are poorly understood. Further, the evolutionary and ecological forces that shape and change the microbiome are unclear. Here, we discuss recent progress in our understanding of the bee microbiome, and we present challenges associated with its investigation. We conclude that global coordination of research efforts is needed to fully understand the complex and highly dynamic nature of the interplay between the bee microbiome, its host, and the environment. High-throughput sequencing technologies are ideal for exploring complex biological systems, including host-microbe interactions. To maximize their value and to improve assessment of the factors affecting bee health, sequence data should be archived, curated, and analyzed in ways that promote the synthesis of different studies. To this end, the BeeBiome consortium aims to develop an online database which would provide reference sequences, archive metadata, and host analytical resources. The goal would be to support applied and fundamental research on bees and their associated microbes and to provide a collaborative framework for sharing primary data from different research programs, thus furthering our understanding of the bee microbiome and its impact on pollinator health.

The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions.

PubMed

Engel, Philipp; Kwong, Waldan K; McFrederick, Quinn; Anderson, Kirk E; Barribeau, Seth Michael; Chandler, James Angus; Cornman, R Scott; Dainat, Jacques; de Miranda, Joachim R; Doublet, Vincent; Emery, Olivier; Evans, Jay D; Farinelli, Laurent; Flenniken, Michelle L; Granberg, Fredrik; Grasis, Juris A; Gauthier, Laurent; Hayer, Juliette; Koch, Hauke; Kocher, Sarah; Martinson, Vincent G; Moran, Nancy; Munoz-Torres, Monica; Newton, Irene; Paxton, Robert J; Powell, Eli; Sadd, Ben M; Schmid-Hempel, Paul; Schmid-Hempel, Regula; Song, Se Jin; Schwarz, Ryan S; vanEngelsdorp, Dennis; Dainat, Benjamin

2016-04-26

As pollinators, bees are cornerstones for terrestrial ecosystem stability and key components in agricultural productivity. All animals, including bees, are associated with a diverse community of microbes, commonly referred to as the microbiome. The bee microbiome is likely to be a crucial factor affecting host health. However, with the exception of a few pathogens, the impacts of most members of the bee microbiome on host health are poorly understood. Further, the evolutionary and ecological forces that shape and change the microbiome are unclear. Here, we discuss recent progress in our understanding of the bee microbiome, and we present challenges associated with its investigation. We conclude that global coordination of research efforts is needed to fully understand the complex and highly dynamic nature of the interplay between the bee microbiome, its host, and the environment. High-throughput sequencing technologies are ideal for exploring complex biological systems, including host-microbe interactions. To maximize their value and to improve assessment of the factors affecting bee health, sequence data should be archived, curated, and analyzed in ways that promote the synthesis of different studies. To this end, the BeeBiome consortium aims to develop an online database which would provide reference sequences, archive metadata, and host analytical resources. The goal would be to support applied and fundamental research on bees and their associated microbes and to provide a collaborative framework for sharing primary data from different research programs, thus furthering our understanding of the bee microbiome and its impact on pollinator health. Copyright © 2016 Engel et al.

An internal thioester in a pathogen surface protein mediates covalent host binding

PubMed Central

Walden, Miriam; Edwards, John M; Dziewulska, Aleksandra M; Bergmann, Rene; Saalbach, Gerhard; Kan, Su-Yin; Miller, Ona K; Weckener, Miriam; Jackson, Rosemary J; Shirran, Sally L; Botting, Catherine H; Florence, Gordon J; Rohde, Manfred; Banfield, Mark J; Schwarz-Linek, Ulrich

2015-01-01

To cause disease and persist in a host, pathogenic and commensal microbes must adhere to tissues. Colonization and infection depend on specific molecular interactions at the host-microbe interface that involve microbial surface proteins, or adhesins. To date, adhesins are only known to bind to host receptors non-covalently. Here we show that the streptococcal surface protein SfbI mediates covalent interaction with the host protein fibrinogen using an unusual internal thioester bond as a ‘chemical harpoon’. This cross-linking reaction allows bacterial attachment to fibrin and SfbI binding to human cells in a model of inflammation. Thioester-containing domains are unexpectedly prevalent in Gram-positive bacteria, including many clinically relevant pathogens. Our findings support bacterial-encoded covalent binding as a new molecular principle in host-microbe interactions. This represents an as yet unexploited target to treat bacterial infection and may also offer novel opportunities for engineering beneficial interactions. DOI: http://dx.doi.org/10.7554/eLife.06638.001 PMID:26032562

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. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

The effect of titanium dioxide (TiO2) nano-objects, and their aggregates and agglomerates greater than 100nm (NOAA) on microbes under UV irradiation.

PubMed

Yamada, Ikuho; Nomura, Kazuki; Iwahashi, Hitoshi; Horie, Masanori

2016-01-01

Today, nanoparticles are used in many products. One of the most common nanoparticles is titanium dioxide (TiO2). These particles generate reactive oxygen species (ROS) upon UV irradiation. Although nanoparticles are very useful in many products, there are concerns about their biological and ecological effects when released into the environment. Thus, it was assessed that the effect of TiO2 nano-objects, and their aggregates and agglomerates greater than 100nm (NOAA) on microbes under UV irradiation by using Escherichia coli and Saccharomyces cerevisiae. ROS generation was evaluated by adding TiO2 nanoparticles and methylene blue to distilled water. We also assessed growth inhibition by adding TiO2 nanoparticles and microbes in minimal agar medium. Moreover, microbial inactivation was assessed by adding TiO2 nanoparticles and microbes to PBS. Upon UV irradiation, TiO2-NOAAs decomposed methylene blue and generated ROS. TiO2-NOAAs also decomposed methylene blue in minimal agar medium under UV irradiation; however, they did not inhibit microbial growth. Surprisingly, TiO2-NOAAs in the medium protect microbes from UV irradiation as colony formation was observed only near TiO2-NOAAs. In PBS, TiO2-NOAAs did not inactivate microbes but instead protected microbes from lethal UV irradiation. These results suggest that the amount of ROS generated by TiO2-NOAAs is not enough to inactivate microbes. In fact, our results suggest that TiO2-NOAAs may protect microbes from UV irradiations. Copyright © 2015 Elsevier Ltd. All rights reserved.

Investigating the context-dependency of plant-soil-AMF-microbe interactions along a pollution gradient

NASA Astrophysics Data System (ADS)

Glassman, S. I.; Casper, B. B.

2010-12-01

Background/Question/Methods Investigating how arbuscular mycorrhizal fungi (AMF)-plant interactions vary with edaphic conditions provides an opportunity to test the context-dependency of interspecific interactions, which is currently recognized as a major avenue of future research. We study plant-mycorrhiza symbiotic relationships along a gradient of heavy metal contamination at a recently revegetated “Superfund” site on Blue Mountain, in Palmerton, Pennsylvania. We investigated the interactions involving the native mycorrhizal fungi, non-mycorrhizal soil microbes, soil, and two plant species (a C3 and C4 grass) along the contamination gradient. The native C3 study species Deschampsia flexuosa, is dominant along the gradient and established naturally; the C4 Sorghastrum nutans, is native to Pennsylvania but not to the site and was introduced during restoration. Because C4 grasses are obligate mycotrophs, we expected S. nutans to have a different effect on and response to the soil symbiont community than the C3 grass. We carried out a full factorial greenhouse experiment using field-collected seeds of D. flexuosa and S. nutans, soil, AMF spores, and non-mycorrhizal microbes from both high and low contaminated ends of the gradient. After 11 weeks of growth in the greenhouses, we harvested above and belowground plant biomass, and quantified AMF root colonization and AMF sporulation. Results/Conclusions Our results indicate that context-dependent function is an important factor driving specific ecological interactions between plants and soil microbes. We found that soil origin significantly affected plant growth. Plants from both species grew much larger in soil from low contaminated (LC) origin than high contaminated (HC) origin. Furthermore, we found that the efficacy of AMF in promoting plant growth depended on AMF origin. Specifically, AMF from LC improved growth of D. flexuosa best in either soil background and improved survivorship of S. nutans in HC soil compared to AMF from HC. We also found that the origin of non-mycorrhizal soil microbes affects the benefit provided to plants and likely interacts with AMF in affecting AMF function. Non-mycorrhizal soil microbes from HC origin decreased mean plant size in D. flexuosa while microbes from LC origin increased mean plant size compared to plants with no non-mycorrhizal soil microbes added. Our results may be useful for improving our basic ecological understanding of plant-soil interactions and ecotypic variation/context-dependent function. There are also potential applications for restoration of heavy metal polluted sites.

Eco-evolutionary feedbacks drive species interactions

PubMed Central

Andrade-Domínguez, Andrés; Salazar, Emmanuel; del Carmen Vargas-Lagunas, María; Kolter, Roberto; Encarnación, Sergio

2014-01-01

In the biosphere, many species live in close proximity and can thus interact in many different ways. Such interactions are dynamic and fall along a continuum between antagonism and cooperation. Because interspecies interactions are the key to understanding biological communities, it is important to know how species interactions arise and evolve. Here, we show that the feedback between ecological and evolutionary processes has a fundamental role in the emergence and dynamics of species interaction. Using a two-species artificial community, we demonstrate that ecological processes and rapid evolution interact to influence the dynamics of the symbiosis between a eukaryote (Saccharomyces cerevisiae) and a bacterium (Rhizobium etli). The simplicity of our experimental design enables an explicit statement of causality. The niche-constructing activities of the fungus were the key ecological process: it allowed the establishment of a commensal relationship that switched to ammensalism and provided the selective conditions necessary for the adaptive evolution of the bacteria. In this latter state, the bacterial population radiates into more than five genotypes that vary with respect to nutrient transport, metabolic strategies and global regulation. Evolutionary diversification of the bacterial populations has strong effects on the community; the nature of interaction subsequently switches from ammensalism to antagonism where bacteria promote yeast extinction. Our results demonstrate the importance of the evolution-to-ecology pathway in the persistence of interactions and the stability of communities. Thus, eco-evolutionary dynamics have the potential to transform the structure and functioning of ecosystems. Our results suggest that these dynamics should be considered to improve our understanding of beneficial and detrimental host–microbe interactions. PMID:24304674

Bacterial attraction and quorum sensing inhibition in Caenorhabditis elegans exudates

USDA-ARS?s Scientific Manuscript database

Caenorhabditis elegans, a bacterivorous soil nematode, lives in a complex environment that requires chemical communication for mating, monitoring population density, recognition of food, avoidance of pathogenic microbes, and other essential ecological functions. Despite being one of the best-studied...

Ecology and thermal inactivation of microbes in and on interplanetary space vehicle components. [bibliography

NASA Technical Reports Server (NTRS)

Reyes, A. L.; Campbell, J. E.

1976-01-01

Almost 600 articles and books published since 1960 about microbial and viral inactivation are listed. This bibliography is presented to facilitate literature reviews on chemical, heat, and radiation inactivation of microorganisms and viral particles.

Prominent Human Health Impacts from Several Marine Microbes: History, Ecology, and Public Health Implications

PubMed Central

Bienfang, P. K.; DeFelice, S. V.; Laws, E. A.; Brand, L. E.; Bidigare, R. R.; Christensen, S.; Trapido-Rosenthal, H.; Hemscheidt, T. K.; McGillicuddy, D. J.; Anderson, D. M.; Solo-Gabriele, H. M.; Boehm, A. B.; Backer, L. C.

2011-01-01

This paper overviews several examples of important public health impacts by marine microbes and directs readers to the extensive literature germane to these maladies. These examples include three types of dinoflagellates (Gambierdiscus spp., Karenia brevis, and Alexandrium fundyense), BMAA-producing cyanobacteria, and infectious microbes. The dinoflagellates are responsible for ciguatera fish poisoning, neurotoxic shellfish poisoning, and paralytic shellfish poisoning, respectively, that have plagued coastal populations over time. Research interest on the potential for marine cyanobacteria to contribute BMAA into human food supplies has been derived by BMAA's discovery in cycad seeds and subsequent implication as the putative cause of amyotrophic lateral sclerosis/parkinsonism dementia complex among the Chamorro people of Guam. Recent UPLC/MS analyses indicate that recent reports that BMAA is prolifically distributed among marine cyanobacteria at high concentrations may be due to analyte misidentification in the analytical protocols being applied for BMAA. Common infectious microbes (including enterovirus, norovirus, Salmonella, Campylobacter, Shigella, Staphylococcus aureus, Cryptosporidium, and Giardia) cause gastrointestinal and skin-related illness. These microbes can be introduced from external human and animal sources, or they can be indigenous to the marine environment. PMID:20976073

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

PubMed

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

2018-04-06

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

Spatial pattern formation of microbes at the soil microscale affect soil C and N turnover in an individual-based microbial community model

NASA Astrophysics Data System (ADS)

Kaiser, Christina; Evans, Sarah; Dieckmann, Ulf; Widder, Stefanie

2016-04-01

At the μm-scale, soil is a highly structured and complex environment, both in physical as well as in biological terms, characterized by non-linear interactions between microbes, substrates and minerals. As known from mathematics and theoretical ecology, spatial structure significantly affects the system's behaviour by enabling synergistic dynamics, facilitating diversity, and leading to emergent phenomena such as self-organisation and self-regulation. Such phenomena, however, are rarely considered when investigating mechanisms of microbial soil organic matter turnover. Soil organic matter is the largest terrestrial reservoir for organic carbon (C) and nitrogen (N) and plays a pivotal role in global biogeochemical cycles. Still, the underlying mechanisms of microbial soil organic matter buildup and turnover remain elusive. We explored mechanisms of microbial soil organic matter turnover using an individual-based, stoichiometrically and spatially explicit computer model, which simulates the microbial de-composer system at the soil microscale (i.e. on a grid of 100 x 100 soil microsites). Soil organic matter dynamics in our model emerge as the result of interactions among individual microbes with certain functional traits (f.e. enzyme production rates, growth rates, cell stoichiometry) at the microscale. By degrading complex substrates, and releasing labile substances microbes in our model continusly shape their environment, which in turn feeds back to spatiotemporal dynamics of the microbial community. In order to test the effect of microbial functional traits and organic matter input rate on soil organic matter turnover and C and N storage, we ran the model into steady state using continuous inputs of fresh organic material. Surprisingly, certain parameter settings that induce resource limitation of microbes lead to regular spatial pattern formation (f.e. moving spiral waves) of microbes and substrate at the μm-scale at steady-state. The occurrence of these pattern can be explained by the Turing mechanism. These pattern formation had strong consequences for process rates, as well as for C and N storage in the soil at the steady state: Scenarios that exhibited pattern formation were generally associated with higher C storage at steady state compared to those without pattern formation (i.e. at non-limiting conditions for microbes). Moreover, pattern formation lead to a spatial decoupling of C and N turnover processes, and to a spatial decoupling of microbial N mineralization and N immobilization. Taken together, our theoretical analysis shows that self-organisation may be a feature of the soil decomposer system, with consequences for process rates of microbial C and N turnover. Pattern formation through spatial self-organization, which has been observed on larger spatial scales in other resource-limited communities (e.g., vegetation patterns in arid or wetland eco-systems), may also occur at the soil microscale, leaving its mark on the soil's storage capacity for C and N.

Temperature alters the relative abundance and population growth rates of species within the Dendroctonus frontalis (Coleoptera: Curculionidae) community.

Treesearch

L. Evans; Richard Hoffstetter; Matthew Ayres; Kier Klepzig

2011-01-01

Temperature has strong effects on metabolic processes ofindividuals and demographics of populations, but effects on ecological communities are not well known. Many economically and ecologically important pest species have obligate associations with other organisms; therefore, effects of temperature on these species might be mediated by strong interactions. The southern...

Embracing Community Ecology in Plant Microbiome Research.

PubMed

Dini-Andreote, Francisco; Raaijmakers, Jos M

2018-06-01

Community assembly is mediated by selection, dispersal, drift, and speciation. Environmental selection is mostly used to date to explain patterns in plant microbiome assembly, whereas the influence of the other processes remains largely elusive. Recent studies highlight that adopting community ecology concepts provides a mechanistic framework for plant microbiome research. Copyright © 2018 Elsevier Ltd. All rights reserved.

Factors Influencing Bacterial Diversity and Community Composition in Municipal Drinking Waters in the Ohio River Basin, USA

PubMed Central

Stanish, Lee F.; Hull, Natalie M.; Robertson, Charles E.; Harris, J. Kirk; Stevens, Mark J.; Spear, John R.; Pace, Norman R.

2016-01-01

The composition and metabolic activities of microbes in drinking water distribution systems can affect water quality and distribution system integrity. In order to understand regional variations in drinking water microbiology in the upper Ohio River watershed, the chemical and microbiological constituents of 17 municipal distribution systems were assessed. While sporadic variations were observed, the microbial diversity was generally dominated by fewer than 10 taxa, and was driven by the amount of disinfectant residual in the water. Overall, Mycobacterium spp. (Actinobacteria), MLE1-12 (phylum Cyanobacteria), Methylobacterium spp., and sphingomonads were the dominant taxa. Shifts in community composition from Alphaproteobacteria and Betaproteobacteria to Firmicutes and Gammaproteobacteria were associated with higher residual chlorine. Alpha- and beta-diversity were higher in systems with higher chlorine loads, which may reflect changes in the ecological processes structuring the communities under different levels of oxidative stress. These results expand the assessment of microbial diversity in municipal distribution systems and demonstrate the value of considering ecological theory to understand the processes controlling microbial makeup. Such understanding may inform the management of municipal drinking water resources. PMID:27362708

Factors Influencing Bacterial Diversity and Community Composition in Municipal Drinking Waters in the Ohio River Basin, USA.

PubMed

Stanish, Lee F; Hull, Natalie M; Robertson, Charles E; Harris, J Kirk; Stevens, Mark J; Spear, John R; Pace, Norman R

2016-01-01

The composition and metabolic activities of microbes in drinking water distribution systems can affect water quality and distribution system integrity. In order to understand regional variations in drinking water microbiology in the upper Ohio River watershed, the chemical and microbiological constituents of 17 municipal distribution systems were assessed. While sporadic variations were observed, the microbial diversity was generally dominated by fewer than 10 taxa, and was driven by the amount of disinfectant residual in the water. Overall, Mycobacterium spp. (Actinobacteria), MLE1-12 (phylum Cyanobacteria), Methylobacterium spp., and sphingomonads were the dominant taxa. Shifts in community composition from Alphaproteobacteria and Betaproteobacteria to Firmicutes and Gammaproteobacteria were associated with higher residual chlorine. Alpha- and beta-diversity were higher in systems with higher chlorine loads, which may reflect changes in the ecological processes structuring the communities under different levels of oxidative stress. These results expand the assessment of microbial diversity in municipal distribution systems and demonstrate the value of considering ecological theory to understand the processes controlling microbial makeup. Such understanding may inform the management of municipal drinking water resources.

Microbe-driven turnover offsets mineral-mediated storage of soil carbon under elevated CO2

Treesearch

Benjamin N. Sulman; Richard P. Phillips; A. Christopher Oishi; Elena Shevliakova; Stephen W. Pacala

2014-01-01

The sensitivity of soil organic carbon (SOC) to changing environmental conditions represents a critical uncertainty in coupled carbon cycle–climate models1.Much of this uncertainty arises from our limited understanding of the extent to which root–microbe interactions induce SOC losses (through accelerated decomposition or ‘priming’2) or indirectly promote SOC gains (...

Microfluidic Experiments Studying Pore Scale Interactions of Microbes and Geochemistry

NASA Astrophysics Data System (ADS)

Chen, M.; Kocar, B. D.

2016-12-01

Understanding how physical phenomena, chemical reactions, and microbial behavior interact at the pore-scale is crucial to understanding larger scale trends in groundwater chemistry. Recent studies illustrate the utility of microfluidic devices for illuminating pore-scale physical-biogeochemical processes and their control(s) on the cycling of iron, uranium, and other important elements 1-3. These experimental systems are ideal for examining geochemical reactions mediated by microbes, which include processes governed by complex biological phenomenon (e.g. biofilm formation, etc.)4. We present results of microfluidic experiments using a model metal reducing bacteria and varying pore geometries, exploring the limitations of the microorganisms' ability to access tight pore spaces, and examining coupled biogeochemical-physical controls on the cycling of redox sensitive metals. Experimental results will provide an enhanced understanding of coupled physical-biogeochemical processes transpiring at the pore-scale, and will constrain and compliment continuum models used to predict and describe the subsurface cycling of redox-sensitive elements5. 1. Vrionis, H. A. et al. Microbiological and geochemical heterogeneity in an in situ uranium bioremediation field site. Appl. Environ. Microbiol. 71, 6308-6318 (2005). 2. Pearce, C. I. et al. Pore-scale characterization of biogeochemical controls on iron and uranium speciation under flow conditions. Environ. Sci. Technol. 46, 7992-8000 (2012). 3. Zhang, C., Liu, C. & Shi, Z. Micromodel investigation of transport effect on the kinetics of reductive dissolution of hematite. Environ. Sci. Technol. 47, 4131-4139 (2013). 4. Ginn, T. R. et al. Processes in microbial transport in the natural subsurface. Adv. Water Resour. 25, 1017-1042 (2002). 5. Scheibe, T. D. et al. Coupling a genome-scale metabolic model with a reactive transport model to describe in situ uranium bioremediation. Microb. Biotechnol. 2, 274-286 (2009).

Volatile affairs in microbial interactions

PubMed Central

Schmidt, Ruth; Cordovez, Viviane; de Boer, Wietse; Raaijmakers, Jos; Garbeva, Paolina

2015-01-01

Microorganisms are important factors in shaping our environment. One key characteristic that has been neglected for a long time is the ability of microorganisms to release chemically diverse volatile compounds. At present, it is clear that the blend of volatiles released by microorganisms can be very complex and often includes many unknown compounds for which the chemical structures remain to be elucidated. The biggest challenge now is to unravel the biological and ecological functions of these microbial volatiles. There is increasing evidence that microbial volatiles can act as infochemicals in interactions among microbes and between microbes and their eukaryotic hosts. Here, we review and discuss recent advances in understanding the natural roles of volatiles in microbe–microbe interactions. Specific emphasis will be given to the antimicrobial activities of microbial volatiles and their effects on bacterial quorum sensing, motility, gene expression and antibiotic resistance. PMID:26023873

Analysis of Individual Social-ecological Mediators and Moderators and Their Ability to Explain Effect of a Randomized Neighborhood Walking Intervention.

PubMed

Michael, Yvonne L; Carlson, Nichole E

2009-07-30

Using data from the SHAPE trial, a randomized 6-month neighborhood-based intervention designed to increase walking activity among older adults, this study identified and analyzed social-ecological factors mediating and moderating changes in walking activity. Three potential mediators (social cohesion, walking efficacy, and perception of neighborhood problems) and minutes of brisk walking were assessed at baseline, 3-months, and 6-months. One moderator, neighborhood walkability, was assessed using an administrative GIS database. The mediating effect of change in process variables on change in brisk walking was tested using a product-of-coefficients test, and we evaluated the moderating effect of neighborhood walkability on change in brisk walking by testing the significance of the interaction between walkability and intervention status. Only one of the hypothesized mediators, walking efficacy, explained the intervention effect (product of the coefficients (95% CI) = 8.72 (2.53, 15.56). Contrary to hypotheses, perceived neighborhood problems appeared to suppress the intervention effects (product of the coefficients (95% CI = -2.48, -5.6, -0.22). Neighborhood walkability did not moderate the intervention effect. Walking efficacy may be an important mediator of lay-lead walking interventions for sedentary older adults. Social-ecologic theory-based analyses can support clinical interventions to elucidate the mediators and moderators responsible for producing intervention effects.

Inhibiting Microbial Toxins Using Plant-Derived Compounds and Plant Extracts

PubMed Central

Upadhyay, Abhinav; Mooyottu, Shankumar; Yin, Hsinbai; Surendran Nair, Meera; Bhattaram, Varunkumar; Venkitanarayanan, Kumar

2015-01-01

Many pathogenic bacteria and fungi produce potentially lethal toxins that cause cytotoxicity or impaired cellular function either at the site of colonization or other locations in the body through receptor-mediated interactions. Various factors, including biotic and abiotic environments, competing microbes, and chemical cues affect toxin expression in these pathogens. Recent work suggests that several natural compounds can modulate toxin production in pathogenic microbes. However, studies explaining the mechanistic basis for their effect are scanty. This review discusses the potential of various plant-derived compounds for reducing toxin production in foodborne and other microbes. In addition, studies highlighting their anti-toxigenic mechanism(s) are discussed. PMID:28930207

GROUP REPORT: PHYSIOLOGICAL AND ECOLOGICAL EFFECTS OF ACIDIFICATION ON AQUATIC BIOTA

EPA Science Inventory

Acidification affects all components of biological communities in lakes and streams: microbes, algae, macrophytes, invertebrates, fish, amphibians, and other vertebrates that rely on aquatic ecosystems for habitat or food. echanisms of effect are both direct (toxic responses to c...

Feedback between Population and Evolutionary Dynamics Determines the Fate of Social Microbial Populations

PubMed Central

Sanchez, Alvaro; Gore, Jeff

2013-01-01

The evolutionary spread of cheater strategies can destabilize populations engaging in social cooperative behaviors, thus demonstrating that evolutionary changes can have profound implications for population dynamics. At the same time, the relative fitness of cooperative traits often depends upon population density, thus leading to the potential for bi-directional coupling between population density and the evolution of a cooperative trait. Despite the potential importance of these eco-evolutionary feedback loops in social species, they have not yet been demonstrated experimentally and their ecological implications are poorly understood. Here, we demonstrate the presence of a strong feedback loop between population dynamics and the evolutionary dynamics of a social microbial gene, SUC2, in laboratory yeast populations whose cooperative growth is mediated by the SUC2 gene. We directly visualize eco-evolutionary trajectories of hundreds of populations over 50–100 generations, allowing us to characterize the phase space describing the interplay of evolution and ecology in this system. Small populations collapse despite continual evolution towards increased cooperative allele frequencies; large populations with a sufficient number of cooperators “spiral” to a stable state of coexistence between cooperator and cheater strategies. The presence of cheaters does not significantly affect the equilibrium population density, but it does reduce the resilience of the population as well as its ability to adapt to a rapidly deteriorating environment. Our results demonstrate the potential ecological importance of coupling between evolutionary dynamics and the population dynamics of cooperatively growing organisms, particularly in microbes. Our study suggests that this interaction may need to be considered in order to explain intraspecific variability in cooperative behaviors, and also that this feedback between evolution and ecology can critically affect the demographic fate of those species that rely on cooperation for their survival. PMID:23637571

Soil Microbial Communities and Gas Dynamics Contribute to Arbuscular Mycorrhizal Nitrogen Uptake and Transfer to Plants

NASA Astrophysics Data System (ADS)

Hestrin, R.; Harrison, M. J.; Lehmann, J.

2016-12-01

Arbuscular mycorrhizal fungi (AMF) associate with most terrestrial plants and influence ecosystem ecology and biogeochemistry. There is evidence that AMF play a role in soil nitrogen cycling, in part by taking up nitrogen and transferring it to plants. However, many aspects of this process are poorly understood, including the factors that control fungal access to nitrogen stored in soil organic matter. In this study, we used stable isotopes and root exclusion to track nitrogen movement from organic matter into AMF and host plants. AMF significantly increased total plant biomass and nitrogen content, but both AMF and other soil microbes seemed to compete with plants for nitrogen. Surprisingly, gaseous nitrogen species also contributed significantly to plant nitrogen content under alkaline soil conditions. Our current experiments investigate whether free-living microbial communities that have evolved under a soil nitrogen gradient influence AMF access to soil organic nitrogen and subsequent nitrogen transfer to plants. This research links interactions between plants, mycorrhizal symbionts, and free-living microbes with terrestrial carbon and nitrogen dynamics.

Patients as Patches: Ecology and Epidemiology in Healthcare Environments.

PubMed

Lofgren, Eric T; Egizi, Andrea M; Fefferman, Nina H

2016-12-01

The modern healthcare system involves complex interactions among microbes, patients, providers, and the built environment. It represents a unique and challenging setting for control of the emergence and spread of infectious diseases. We examine an extension of the perspectives and methods from ecology (and especially urban ecology) to address these unique issues, and we outline 3 examples: (1) viewing patients as individual microbial ecosystems; (2) the altered ecology of infectious diseases specifically within hospitals; and (3) ecosystem management perspectives for infection surveillance and control. In each of these cases, we explore the accuracy and relevance of analogies to existing urban ecological perspectives, and we demonstrate a few of the potential direct uses of this perspective for altering research into the control of healthcare-associated infections. Infect Control Hosp Epidemiol. 2016;1507-1512.

Rhodolith holobionts in a changing ocean: Ocean Acidification effects on the free-living coralline algae and their associated microbiota

NASA Astrophysics Data System (ADS)

Cavalcanti, G.

2016-02-01

Rhodoliths, free-living coralline algae (Rhodophyta, Corallinales), form extensive beds worldwide distributed, ecologically important for the functioning of marine environments. Rhodolith beds are large carbon sinks, but the growth of the Rhodolith holobiont might be affected by changes in ocean carbonate chemistry, predicted to occur in the near future. The term holobiont refers to any organism and all of its associated symbiotic microbes (parasites, mutualists, synergists and amensals), including endobionts and epibionts that perform diverse ecological roles. A holobiont occupies and adapts to an ecological niche, and is able to employ strategies unavailable in any one species alone when challenged by environmental perturbations. The impact of increasing acidification of oceans on Rhodolith holobiont growth might be due to dissolution of their calcium carbonated skeleton, effects over photosynthetic rates, as well as changes in their associated microbial community, herein investigated through physiological assays (photosynthesis) and metagenomics (WGS Illumina sequencing). We used a mesocosm experimental system to assess potential effects of OA on dead and live rhodoliths following a 5 week exposure to increased pCO2. Integrating both taxonomical and functional diversity from multiple players (Eukarya, Bacteria and Archaea) in the acidification context, we have demonstrated that the Rhodolith holobiont harbor an impressive stable microbiome, whereas high pCO2 affect the seawater microbes. Our study has extended the comprehension of physiological relationships within Rhodolith holobiont by including the microbial component in the response of this coralline algae to higher pCO2 levels, and endorsed previous works that indicated a parabolic photosynthetic response to pH and pCO2. The outcomes of this research are an increased understanding of microbes associated with Rhodoliths and additional hints on how the holobiont might thrive in face to global climate changes.

A novel nanoparticle approach for imaging nutrient uptake by soil bacteria

NASA Astrophysics Data System (ADS)

O'Brien, S. L.; Whiteside, M. D.; Sholto-Douglas, D.; Antonopoulos, D. A.; Boyanov, M.; Durall, D. M.; Jones, M. D.; Lai, B.; O'Loughlin, E. J.; Kemner, K. M.

2014-12-01

The metabolic activities of soil microbes are the primary drivers of biogeochemical processes controlling the terrestrial carbon cycle, nutrient availability to plants, contaminant remediation, water quality, and other ecosystem services. However, we have a limited understanding of microbial metabolic processes such as nutrient uptake rates, substrate preferences, or how microbes and microbial metabolism are distributed throughout their habitat. Here we use a novel imaging technique with quantum dots (QDs, engineered semiconductor nanoparticles that produce size or composition-dependent fluorescence) to measure bacterial uptake of substrates of varying complexity. Cultures of two organisms differing in cell wall structure — Bacillus subtilis and Pseudomonas fluorescens — were grown in one of four ecologically relevant experimental conditions: nitrogen (N) limitation, phosphorus (P) limitation, N and P limitation, or no nutrient limitation. The cultures were then exposed to QDs with and without organic nutrients attached. X-ray fluorescence imaging was performed at 2ID-D at the Advanced Photon Source (APS) to determine the elemental distributions within both planktonic and surface-adhered (i.e, biofilms) cells. Uptake of unconjugated QDs was neglibible, and QDs conjugated to organic substrates varied depending on growth conditions and substrate, suggesting that they are a useful indicator of bacterial ecology. Cellular uptake was similar for the two bacterial species (2212 ± 273 nanoparticles per cm3 of cell volume for B. subtilis and 1682 ± 264 for P. fluorescens). On average, QD assimilation was six times greater when N or P was limiting, and cells took up about twice as much phosphoserine compared to other substrates, likely because it was the only compound providing both N and P. These results showed that regardless of their cell wall structure, bacteria can selectively take up quantifiable levels of QDs based on substrate and environmental conditions. APS images are consistent with those produced with confocal and optical microscopes, indicating that the XRF approach can detect bacterial uptake of CdSe-core QDs. These findings offer a new way to experimentally investigate basic bacterial ecology such as metabolic activity and biofilm development and function.

Statistical Physics Approaches to Microbial Ecology

NASA Astrophysics Data System (ADS)

Mehta, Pankaj

The unprecedented ability to quantitatively measure and probe complex microbial communities has renewed interest in identifying the fundamental ecological principles governing community ecology in microbial ecosystems. Here, we present work from our group and others showing how ideas from statistical physics can help us uncover these ecological principles. Two major lessons emerge from this work. First, large, ecosystems with many species often display new, emergent ecological behaviors that are absent in small ecosystems with just a few species. To paraphrase Nobel laureate Phil Anderson, ''More is Different'', especially in community ecology. Second, the lack of trophic layer separation in microbial ecology fundamentally distinguishes microbial ecology from classical paradigms of community ecology and leads to qualitative different rules for community assembly in microbes. I illustrate these ideas using both theoretical modeling and novel new experiments on large microbial ecosystems performed by our collaborators (Joshua Goldford and Alvaro Sanchez). Work supported by Simons Investigator in MMLS and NIH R35 R35 GM119461.

Plants + soil/wetland microbes: Food crop systems that also clean air and water

NASA Astrophysics Data System (ADS)

Nelson, Mark; Wolverton, B. C.

2011-02-01

The limitations that will govern bioregenerative life support applications in space, especially volume and weight, make multi-purpose systems advantageous. This paper outlines two systems which utilize plants and associated microbial communities of root or growth medium to both produce food crops and clean air and water. Underlying these approaches are the large numbers and metabolic diversity of microbes associated with roots and found in either soil or other suitable growth media. Biogeochemical cycles have microbial links and the ability of microbes to metabolize virtually all trace gases, whether of technogenic or biogenic origin, has long been established. Wetland plants and the rootzone microbes of wetland soils/media also been extensively researched for their ability to purify wastewaters of a great number of potential water pollutants, from nutrients like N and P, to heavy metals and a range of complex industrial pollutants. There is a growing body of research on the ability of higher plants to purify air and water. Associated benefits of these approaches is that by utilizing natural ecological processes, the cleansing of air and water can be done with little or no energy inputs. Soil and rootzone microorganisms respond to changing pollutant types by an increase of the types of organisms with the capacity to use these compounds. Thus living systems have an adaptive capacity as long as the starting populations are sufficiently diverse. Tightly sealed environments, from office buildings to spacecraft, can have hundreds or even thousands of potential air pollutants, depending on the materials and equipment enclosed. Human waste products carry a plethora of microbes which are readily used in the process of converting its organic load to forms that can be utilized by green plants. Having endogenous means of responding to changing air and water quality conditions represents safety factors as these systems operate without the need for human intervention. We review this research and the ability of systems using these mechanisms to also produce food or other useful crops. Concerns about possible pathogens in soils and wastewater are discussed along with some methods to prevent contact, disease transmission and to pre-screen and decrease risks. The psychological benefits of having systems utilizing green plants are becoming more widely recognized. Some recent applications extending the benefits of plants and microbes to solve new environmental problems are presented. For space applications, we discuss the use of in situ space resources and ways of making these systems compact and light-weight.

Sediments and flow have mainly independent effects on multitrophic stream communities and ecosystem functions.

PubMed

Mustonen, Kaisa-Riikka; Mykrä, Heikki; Louhi, Pauliina; Markkola, Annamari; Tolkkinen, Mikko; Huusko, Ari; Alioravainen, Nico; Lehtinen, Sirkku; Muotka, Timo

2016-10-01

Stream ecosystems are affected by multiple abiotic stressors, and species responses to simultaneous stressors may differ from those predicted based on single-stressor responses. Using 12 semi-natural stream channels, we examined the individual and interactive effects of flow level (low or high flow) and addition of fine sediments (grain size <2 mm) on key ecosystem processes (leaf breakdown, algal biomass accrual) and benthic macroinvertebrate and fungal communities. Both stressors had mostly independent effects on biological responses, with sand addition being the more influential of the two. Sand addition decreased algal biomass and microbe-mediated leaf breakdown significantly, whereas invertebrate shredder-mediated breakdown only responded to flow level. Macroinvertebrate community composition responded significantly to both stressors. Fungal biomass decreased and shredder abundance increased when sand was added; thus, organisms at different trophic levels can exhibit highly variable responses to the same stressor. Terrestrial endophytic fungi were abundant in low-flow flumes where leaf mass loss was also highest, indicating that terrestrial endophytes may contribute importantly to leaf decomposition in the aquatic environment. Leaf breakdown rates depended on the identity and abundance of the dominant decomposer species, suggesting that the effects of anthropogenic activities on ecosystem processes may be driven by changes in the abundance of a few key species. The few observed interactive effects were all antagonistic (i.e., less than the sum of the individual effects); for example, increased flow stimulated algal biomass accumulation but this effect was largely cancelled by sand. While our finding that sand and stream flow did not have strong synergistic effects can be considered reassuring for management, future experiments should manipulate these and other human stressors in experiments that run for much longer periods, thus focusing on the long-term impacts of multiple simultaneously operating stressors. © 2016 by the Ecological Society of America.

2010 MICROBIAL STRESS RESPONSE GORDON RESEARCH CONFERENCE, JULY 18-23, 2010

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

Sarah Ades

2011-07-23

The 2010 Gordon Research Conference on Microbial Stress Responses provides an open and exciting forum for the exchange of scientific discoveries on the remarkable mechanisms used by microbes to survive in nearly every niche on the planet. Understanding these stress responses is critical for our ability to control microbial survival, whether in the context of biotechnology, ecology, or pathogenesis. From its inception in 1994, this conference has traditionally employed a very broad definition of stress in microbial systems. Sessions will cover the major steps of stress responses from signal sensing to transcriptional regulation to the effectors that mediate responses. Amore » wide range of stresses will be represented. Some examples include (but are not limited to) oxidative stress, protein quality control, antibiotic-induced stress and survival, envelope stress, DNA damage, and nutritional stress. The 2010 meeting will also focus on the role of stress responses in microbial communities, applied and environmental microbiology, and microbial development. This conference brings together researchers from both the biological and physical sciences investigating stress responses in medically- and environmentally relevant microbes, as well as model organisms, using cutting-edge techniques. Computational, systems-level, and biophysical approaches to exploring stress responsive circuits will be integrated throughout the sessions alongside the more traditional molecular, physiological, and genetic approaches. The broad range of excellent speakers and topics, together with the intimate and pleasant setting at Mount Holyoke College, provide a fertile ground for the exchange of new ideas and approaches.« less

The Active Bacterial Community in a Pristine Confined Aquifer

EPA Science Inventory

This study of the active bacteria residing in a pristine confined aquifer provides unexpected insights into the ecology of iron-reducing and sulfate-reducing bacteria in the subsurface. At 18 wells in east-central Illinois, we trapped the microbes that attached to aquifer sedimen...

Ecology and thermal inactivation of microbes in and on interplanetary space vehicle components

NASA Technical Reports Server (NTRS)

Reyes, A. L.; Campbell, J. E.; Wehby, A. J.; Crawford, R. G.; Wimsatt, J. C.; Peeler, J. T.

1976-01-01

The thermal resistance of vegetative cells in the percent RH range of 0.19 to 100 at 60 C was investigated. Staphylococcus aureus was used in the experiment because of the extension of the moisture range that can be examined.

Effects of heavy metals on soil microbial community

NASA Astrophysics Data System (ADS)

Chu, Dian

2018-02-01

Soil is one of the most important environmental natural resources for human beings living, which is of great significance to the quality of ecological environment and human health. The study of the function of arable soil microbes exposed to heavy metal pollution for a long time has a very important significance for the usage of farmland soil. In this paper, the effects of heavy metals on soil microbial community were reviewed. The main contents were as follows: the effects of soil microbes on soil ecosystems; the effects of heavy metals on soil microbial activity, soil enzyme activities and the composition of soil microbial community. In addition, a brief description of main methods of heavy metal detection for soil pollution is given, and the means of researching soil microbial community composition are introduced as well. Finally, it is concluded that the study of soil microbial community can well reflect the degree of soil heavy metal pollution and the impact of heavy metal pollution on soil ecology.

Invariant natural killer T cells trigger adaptive lymphocytes to churn up bile.

PubMed

Joyce, Sebastian; Van Kaer, Luc

2008-05-15

How innate immune response causes autoimmunity has remained an enigma. In this issue of Cell Host & Microbe, Mattner et al. demonstrate that invariant natural killer T cells activated by the mucosal commensal Novosphingobium aromaticivorans precipitate chronic T cell-mediated autoimmunity against small bile ducts that mirrors human primary biliary cirrhosis. These findings provide a mechanistic understanding of the role of innate immunity toward a microbe in the development of autoimmunity.

MiDAS: the field guide to the microbes of activated sludge.

PubMed

McIlroy, Simon Jon; Saunders, Aaron Marc; Albertsen, Mads; Nierychlo, Marta; McIlroy, Bianca; Hansen, Aviaja Anna; Karst, Søren Michael; Nielsen, Jeppe Lund; Nielsen, Per Halkjær

2015-01-01

The Microbial Database for Activated Sludge (MiDAS) field guide is a freely available online resource linking the identity of abundant and process critical microorganisms in activated sludge wastewater treatment systems to available data related to their functional importance. Phenotypic properties of some of these genera are described, but most are known only from sequence data. The MiDAS taxonomy is a manual curation of the SILVA taxonomy that proposes a name for all genus-level taxa observed to be abundant by large-scale 16 S rRNA gene amplicon sequencing of full-scale activated sludge communities. The taxonomy can be used to classify unknown sequences, and the online MiDAS field guide links the identity to the available information about their morphology, diversity, physiology and distribution. The use of a common taxonomy across the field will provide a solid foundation for the study of microbial ecology of the activated sludge process and related treatment processes. The online MiDAS field guide is a collaborative workspace intended to facilitate a better understanding of the ecology of activated sludge and related treatment processes--knowledge that will be an invaluable resource for the optimal design and operation of these systems. © The Author(s) 2015. Published by Oxford University Press.

Effects of Different Regeneration Scenarios and Fertilizer Treatments on Soil Microbial Ecology in Reclaimed Opencast Mining Areas on the Loess Plateau, China

PubMed Central

Li, Junjian; Zheng, Yuanming; Yan, Junxia; Li, Hongjian; Wang, Xiang; He, Jizheng; Ding, Guangwei

2013-01-01

The soil microbial community in reclaimed mining areas is fundamental to vegetative establishment. However, how this community responds to different regeneration scenarios and fertilizer treatments is poorly understood. This research evaluated plant and soil microbial communities from different regeneration scenarios and different fertilizer treatments. Regeneration scenarios significantly influenced soil bacterial, archaeal, and fungal rDNA abundance. The ratios of fungi to bacteria or archaea were increased with fertilizer application. The diversity of both plants and microbes was lowest in Lotus corniculatus grasslands. Regeneration scenario, fertilizer treatment, and their interaction influenced soil microbial richness, diversity and evenness indices. Labile carbon pool 2 was a significant factor affected plant and microbe communities in July, suggesting that plants and microbes may be competing for nutrients. The higher ratios of positive to negative association were found in soil bacteria and total microbe than in archaea and fungi. Stronger clustering of microbial communities from the same regeneration scenario indicated that the vegetative composition of regeneration site may have a greater influence on soil microbial communities than fertilizer treatment. PMID:23658819

Correlation of soil microbes and soil micro-environment under long-term safflower (Carthamus tinctorius L.) plantation in China.

PubMed

Lu, Shuang; Quan, Wang; Wang, Shao-Ming; Liu, Hong-Ling; Tan, Yong; Zeng, Guang-Ping; Zhang, Xia

2013-04-01

Microbial community structure and ecological functions are influenced by interactions between above and belowground biota. There is an urgent need for intensive monitoring of microbes feedback of soil micro-ecosystem for setting up a good agricultural practice. Recent researches have revealed that many soils characteristic can effect microbial community structure. In the present study factors affecting microbial community structure and soil in Carthamus tinctorius plantations in arid agricultural ecosystem of northern Xinjiang, China were identified. The result of the study revealed that soil type was the key factor in safflower yield; Unscientific field management resulted high fertility level (bacteria dominant) of soil to turn to low fertility level (fungi dominant), and Detruded Canonical Correspondence Analysis (DCCA) showed that soil water content, organic matter, available N, P and K were the dominant factors affecting distribution of microbial community. Soil water content showed a significant positive correlation with soil microbes quantity (P < 0.01), while others showed a significant quantity correlation with soil microbe quantity (P < 0.05).

Microstructured block copolymer surfaces for control of microbe capture and aggregation

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

Hansen, Ryan R; Shubert, Katherine R; Morrell, Jennifer L.

2014-01-01

The capture and arrangement of surface-associated microbes is influenced by biochemical and physical properties of the substrate. In this report, we develop lectin-functionalized substrates containing patterned, three-dimensional polymeric structures of varied shapes and densities and use these to investigate the effects of topology and spatial confinement on lectin-mediated microbe capture. Films of poly(glycidyl methacrylate)-block-4,4-dimethyl-2-vinylazlactone (PGMA-b-PVDMA) were patterned on silicon surfaces into line or square grid patterns with 5 m wide features and varied edge spacing. The patterned films had three-dimensional geometries with 900 nm film thickness. After surface functionalization with wheat germ agglutinin, the size of Pseudomonas fluorescens aggregates capturedmore » was dependent on the pattern dimensions. Line patterns with edge spacing of 5 m or less led to the capture of individual microbes with minimal formation of aggregates, while grid patterns with the same spacing also captured individual microbes with further reduction in aggregation. Both geometries allowed for increases in aggregate size distribution with increased in edge spacing. These engineered surfaces combine spatial confinement with affinity-based microbe capture based on exopolysaccharide content to control the degree of microbe aggregation, and can also be used as a platform to investigate intercellular interactions and biofilm formation in microbial populations of controlled sizes.« less

Cross-regulatory circuit between AHR and microbiota.

PubMed

Ji, Jian; Qu, Hao

2018-01-29

The gut microbes have a close symbiotic relationship with their host. Interactions between host and the microbiota affect the nutritional, immunological, and physiological status of the host. The aryl hydrocarbon receptor (AHR) is a ligand activated transcription factor that mediates the toxicity of xenobiotics. Recently, the relationship between the gut microbiota and AHR has attracted the attention of many researchers. The AHR influences the intestinal microbiota population and mediates host-microbe homeostasis. Interestingly, the gut microbiota also produces ligands of AHR from bacterial metabolism and thereby activates the AHR signaling pathway. This review presents current knowledge of the cross-regulatory circuit between the AHR and intestinal microbiota. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Molecular responses in root-associative rhizospheric bacteria to variations in plant exudates

NASA Astrophysics Data System (ADS)

Abdoun, Hamid; McMillan, Mary; Pereg, Lily

2015-04-01

Plant exudates are a major factor in the interface of plant-soil-microbe interactions and it is well documented that the microbial community structure in the rhizosphere is largely influenced by the particular exudates excreted by various plants. Azospirillum brasilense is a plant growth promoting rhizobacterium that is known to interact with a large number of plants, including important food crops. The regulatory gene flcA has an important role in this interaction as it controls morphological differentiation of the bacterium that is essential for attachment to root surfaces. Being a response regulatory gene, flcA mediates the response of the bacterial cell to signals from the surrounding rhizosphere. This makes this regulatory gene a good candidate for analysis of the response of bacteria to rhizospheric alterations, in this case, variations in root exudates. We will report on our studies on the response of Azospirillum, an ecologically, scientifically and agriculturally important bacterial genus, to variations in the rhizosphere.

Chemotrophic Microbial Mats and Their Potential for Preservation in the Rock Record

NASA Astrophysics Data System (ADS)

Bailey, Jake V.; Orphan, Victoria J.; Joye, Samantha B.; Corsetti, Frank A.

2009-11-01

Putative microbialites are commonly regarded to have formed in association with photosynthetic microorganisms, such as cyanobacteria. However, many modern microbial mat ecosystems are dominated by chemotrophic bacteria and archaea. Like phototrophs, filamentous sulfur-oxidizing bacteria form large mats at the sediment/water interface that can act to stabilize sediments, and their metabolic activities may mediate the formation of marine phosphorites. Similarly, bacteria and archaea associated with the anaerobic oxidation of methane (AOM) catalyze the precipitation of seafloor authigenic carbonates. When preserved, lipid biomarkers, isotopic signatures, body fossils, and lithological indicators of the local depositional environment may be used to identify chemotrophic mats in the rock record. The recognition of chemotrophic communities in the rock record has the potential to transform our understanding of ancient microbial ecologies, evolution, and geochemical conditions. Chemotrophic microbes on Earth occupy naturally occurring interfaces between oxidized and reduced chemical species and thus may provide a new set of search criteria to target life-detection efforts on other planets.

Phytoplasma infection of a tropical root crop triggers bottom-up cascades by favoring generalist over specialist herbivores

PubMed Central

Graziosi, Ignazio; Burra, Dharani Dhar; Walter, Abigail Jan

2017-01-01

Global interest on plant-microbe-insect interactions is rapidly growing, revealing the multiple ways in which microorganisms mediate plant-herbivore interactions. Phytopathogens regularly alter whole repertoires of plant phenotypic traits, and bring about shifts in key chemical or morphological characteristics of plant hosts. Pathogens can also cause cascading effects on higher trophic levels, and eventually shape entire plant-associated arthropod communities. We tested the hypothesis that a Candidatus Phytoplasma causing cassava witches’ broom (CWB) on cassava (Manihot esculenta Grantz) is altering species composition of invasive herbivores and their associated parasitic hymenopterans. We conducted observational studies in cassava fields in eastern Cambodia to assess the effect of CWB infection on abundance of specialist and generalist mealybugs (Homoptera: Pseudococcidae), and associated primary and hyper-parasitoid species. CWB infection positively affects overall mealybug abundance and species richness at a plant- and field-level, and disproportionately favors a generalist mealybug over a specialist feeder. CWB phytoplasma infection led to increased parasitoid richness and diversity, with richness of ‘comparative’ specialist taxa being the most significantly affected. Parasitism rate did not differ among infected and uninfected plants, and mealybug host suppression was not impacted. CWB phytoplasma modifies host plant quality for sap-feeding homopterans, differentially affects success rates of two invasive species, and generates niche opportunities for higher trophic orders. By doing so, a Candidatus phytoplasma affects broader food web structure and functioning, and assumes the role of an ecosystem engineer. Our work unveils key facets of phytoplasma ecology, and sheds light upon complex multi-trophic interactions mediated by an emerging phytopathogen. These findings have further implications for invasion ecology and management. PMID:28813469

Plants + microbes: Innovative food crop systems that also clean air and water

NASA Astrophysics Data System (ADS)

Nelson, Mark; Wolverton, B. C.

The limitations that will govern bioregenerative life support applications in space, especially volume and weight, make multi-purpose systems advantageous. This paper outlines two systems which utilize plants and associated microbial communities of root or growth medium to both produce food crops and clean air and water. Underlying these approaches are the large numbers and metabolic diversity of microbes associated with roots and found in either soil or other suitable growth media. It is known that most biogeochemical cycles have a microbial link, and the ability of microbes to metabolize virtually all trace gases, whether of technogenic or biogenic origin, have long been established. Wetland plants and soil/media also been extensively researched for their ability to purify wastewaters of all kinds of potential water pollutants, from nutrients like N and P, to heavy metals and a range of complex industrial pollutants. There is a growing body of research on the ability of higher plants to purify air and water. Associated benefits of these approaches is that by utilizing natural ecological processes, the cleansing of air and water can be done with little or no energy inputs. Soil and root microorganisms respond to changing pollutant types by an increase of the types of organisms with the capacity to use these compounds. Thus living systems have an extraordinary adaptive capacity as long as the starting populations are sufficiently diverse. It is known that tightly sealed environments, from office buildings to spacecraft, can have hundreds or even thousands of potential air pollutants, depending on the materials and machines enclosed. Human waste products carry a plethora of microbes can are readily used in the process of converting its organic load to forms that can be utilized by green plants. Having endogenous means of responding to changing air and water quality conditions represents safety factors which operate without the need for human direction. We will review this research and underline the ability of systems using these mechanisms to also produce food or other useful crops. The psychological benefits of having systems utilizing green plants are also becoming more widely recognized. Some recent applications extending the benefits of plants+microbes to solve new environmental problems are presented. For space applications, we discuss methods of making these systems compact and light-weight.

Temporal and Spatial Patterns of Plankton and Microbial Dynamics in the Offshore Gulf of Mexico After the Deepwater Horizon Oil Spill

NASA Astrophysics Data System (ADS)

Sutor, M.; Longnecker, K.

2016-02-01

The oligotrophic regions of the world oceans represent large and important marine ecosystems. The vast majority of animals in these zones are plankton and marine microbes and they play a key role in the export of carbon and organic matter to seafloor benthic communities and higher trophic levels. There is little published data on the ecology of plankton and microbes in the offshore waters of the Northern Gulf of Mexico. In the wake of the Deepwater Horizon oil spill, which was a primarily oceanic event, it is clear that understanding the microbial and planktonic community and how it responded to this event is critical to interpret any observed changes at higher trophic levels (i.e. fish). We conducted three cruises in the spring of 2011, 2012, and 2013 and measured the primary production, respiration, bacterial production, and community composition of plankton and marine microbes. The data show that there are important differences in these parameters between the surface waters and the deep chlorophyll maximum and proximity to the spill site in 2011. Spatial patterns in relation to the spill site are not pronounced in 2012 and 2013. These data represent an important estimate of the microbial and planktonic community ecology of this region and demonstrate the important role the deep chlorophyll maximum plays in this system.

Cnidarian-microbe interactions and the origin of innate immunity in metazoans.

PubMed

Bosch, Thomas C G

2013-01-01

Most epithelia in animals are colonized by microbial communities. These resident microbes influence fitness and thus ecologically important traits of their hosts, ultimately forming a metaorganism consisting of a multicellular host and a community of associated microorganisms. Recent discoveries in the cnidarian Hydra show that components of the innate immune system as well as transcriptional regulators of stem cells are involved in maintaining homeostasis between animals and their resident microbiota. Here I argue that components of the innate immune system with its host-specific antimicrobial peptides and a rich repertoire of pattern recognition receptors evolved in early-branching metazoans because of the need to control the resident beneficial microbes, not because of invasive pathogens. I also propose a mutual intertwinement between the stem cell regulatory machinery of the host and the resident microbiota composition, such that disturbances in one trigger a restructuring and resetting of the other.

Topological distortion and reorganized modular structure of gut microbial co-occurrence networks in inflammatory bowel disease

NASA Astrophysics Data System (ADS)

Baldassano, Steven N.; Bassett, Danielle S.

2016-05-01

The gut microbiome plays a key role in human health, and alterations of the normal gut flora are associated with a variety of distinct disease states. Yet, the natural dependencies between microbes in healthy and diseased individuals remain far from understood. Here we use a network-based approach to characterize microbial co-occurrence in individuals with inflammatory bowel disease (IBD) and healthy (non-IBD control) individuals. We find that microbial networks in patients with IBD differ in both global structure and local connectivity patterns. While a “core” microbiome is preserved, network topology of other densely interconnected microbe modules is distorted, with potent inflammation-mediating organisms assuming roles as integrative and highly connected inter-modular hubs. We show that while both networks display a rich-club organization, in which a small set of microbes commonly co-occur, the healthy network is more easily disrupted by elimination of a small number of key species. Further investigation of network alterations in disease might offer mechanistic insights into the specific pathogens responsible for microbiome-mediated inflammation in IBD.

Ecology and Fisheries: Dark Carbon on Your Dinner Plate.

PubMed

Petersen, Jillian M

2016-12-19

Chemosynthetic primary production by symbiotic microbes powers entire ecosystems in the remote deep sea. New research shows that in shallow waters chemosynthetic symbioses can contribute substantially to a vital economic resource - lobster fisheries in the Caribbean Sea. Copyright © 2016 Elsevier Ltd. All rights reserved.

Microbial gut diversity of Africanized and European honey bee larval instars

USDA-ARS?s Scientific Manuscript database

The first step in understanding gut microbial ecology is determining the presence and potential niche breadth of associated microbes. While the core gut bacteria of adult honey bees is becoming increasingly apparent, there is very little and inconsistent information concerning symbiotic bacterial co...

Stationary moments, diffusion limits, and extinction times for logistic growth with random catastrophes.

PubMed

Schlomann, Brandon H

2018-06-06

A central problem in population ecology is understanding the consequences of stochastic fluctuations. Analytically tractable models with Gaussian driving noise have led to important, general insights, but they fail to capture rare, catastrophic events, which are increasingly observed at scales ranging from global fisheries to intestinal microbiota. Due to mathematical challenges, growth processes with random catastrophes are less well characterized and it remains unclear how their consequences differ from those of Gaussian processes. In the face of a changing climate and predicted increases in ecological catastrophes, as well as increased interest in harnessing microbes for therapeutics, these processes have never been more relevant. To better understand them, I revisit here a differential equation model of logistic growth coupled to density-independent catastrophes that arrive as a Poisson process, and derive new analytic results that reveal its statistical structure. First, I derive exact expressions for the model's stationary moments, revealing a single effective catastrophe parameter that largely controls low order statistics. Then, I use weak convergence theorems to construct its Gaussian analog in a limit of frequent, small catastrophes, keeping the stationary population mean constant for normalization. Numerically computing statistics along this limit shows how they transform as the dynamics shifts from catastrophes to diffusions, enabling quantitative comparisons. For example, the mean time to extinction increases monotonically by orders of magnitude, demonstrating significantly higher extinction risk under catastrophes than under diffusions. Together, these results provide insight into a wide range of stochastic dynamical systems important for ecology and conservation. Copyright © 2018 Elsevier Ltd. All rights reserved.

The Importance of Microbes in Nutrition and Health of Honey Bee Colonies

USDA-ARS?s Scientific Manuscript database

Microbes play an essential role in the health of nearly every organism. Humans have innumerable microbes in their digestive system to help with the processing of food. Honey bee colonies also have an array of bacteria and fungi that are essential for the storing and processing of food (especially ...

“Every Gene Is Everywhere but the Environment Selects”: Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis

PubMed Central

Fondi, Marco; Karkman, Antti; Tamminen, Manu V.; Bosi, Emanuele; Virta, Marko; Fani, Renato; Alm, Eric; McInerney, James O.

2016-01-01

The spatial distribution of microbes on our planet is famously formulated in the Baas Becking hypothesis as “everything is everywhere but the environment selects.” While this hypothesis does not strictly rule out patterns caused by geographical effects on ecology and historical founder effects, it does propose that the remarkable dispersal potential of microbes leads to distributions generally shaped by environmental factors rather than geographical distance. By constructing sequence similarity networks from uncultured environmental samples, we show that microbial gene pool distributions are not influenced nearly as much by geography as ecology, thus extending the Bass Becking hypothesis from whole organisms to microbial genes. We find that gene pools are shaped by their broad ecological niche (such as sea water, fresh water, host, and airborne). We find that freshwater habitats act as a gene exchange bridge between otherwise disconnected habitats. Finally, certain antibiotic resistance genes deviate from the general trend of habitat specificity by exhibiting a high degree of cross-habitat mobility. The strong cross-habitat mobility of antibiotic resistance genes is a cause for concern and provides a paradigmatic example of the rate by which genes colonize new habitats when new selective forces emerge. PMID:27190206

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

USGS Publications Warehouse

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

2015-01-01

Stress factors quantified by this research include shallow soil (depth to bedrock ranging from 2.4 to 22.6 cm), volumetric soil water content levels seasonally ranging from xeric (below 5%) to saturated (above 50%), and seasonally extreme ground-surface temperatures (above 48°C). Findings from this research indicate that spatial and temporal heterogeneity exists in limestone cedar glades in terms of abiotic stress factors and soil physical and chemical properties. Several such soil properties (e.g. soil depth, organic matter levels, pH, and particle size distribution) are spatially correlated. These soil properties were statistically related to ecological structures and functions such as vegetation patterns, soil respiration, the density of culturable heterotrophic microbes in soil and metabolic diversity of soil microbial community profiles. In general, zones within limestone cedar glades that had relatively shallow soil, alkaline pH, low levels of organic matter and high levels of silt also tended to have depressed rates of soil respiration and reduced densities and metabolic diversity of culturable heterotrophic soil microbes. Additionally, seasonally-relevant stress factors including soil water content and temperatures at or near the soil surface were related to the same set of ecological structures and functions.

The Gut Microbiota: Ecology and Function

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

Willing, B.P.; Jansson, J.K.

The gastrointestinal (GI) tract is teeming with an extremely abundant and diverse microbial community. The members of this community have coevolved along with their hosts over millennia. Until recently, the gut ecosystem was viewed as black box with little knowledge of who or what was there or their specific functions. Over the past decade, however, this ecosystem has become one of fastest growing research areas of focus in microbial ecology and human and animal physiology. This increased interest is largely in response to studies tying microbes in the gut to important diseases afflicting modern society, including obesity, allergies, inflammatory bowelmore » diseases, and diabetes. Although the importance of a resident community of microorganisms in health was first hypothesized by Pasteur over a century ago (Sears, 2005), the multiplicity of physiological changes induced by commensal bacteria has only recently been recognized (Hooper et al., 2001). The term 'ecological development' was recently coined to support the idea that development of the GI tract is a product of the genetics of the host and the host's interactions with resident microbes (Hooper, 2004). The search for new therapeutic targets and disease biomarkers has escalated the need to understand the identities and functions of the microorganisms inhabiting the gut. Recent studies have revealed new insights into the membership of the gut microbial community, interactions within that community, as well as mechanisms of interaction with the host. This chapter focuses on the microbial ecology of the gut, with an emphasis on information gleaned from recent molecular studies.« less

Biological and geophysical feedbacks with fire in the Earth system

NASA Astrophysics Data System (ADS)

Archibald, S.; Lehmann, C. E. R.; Belcher, C. M.; Bond, W. J.; Bradstock, R. A.; Daniau, A.-L.; Dexter, K. G.; Forrestel, E. J.; Greve, M.; He, T.; Higgins, S. I.; Hoffmann, W. A.; Lamont, B. B.; McGlinn, D. J.; Moncrieff, G. R.; Osborne, C. P.; Pausas, J. G.; Price, O.; Ripley, B. S.; Rogers, B. M.; Schwilk, D. W.; Simon, M. F.; Turetsky, M. R.; Van der Werf, G. R.; Zanne, A. E.

2018-03-01

Roughly 3% of the Earth’s land surface burns annually, representing a critical exchange of energy and matter between the land and atmosphere via combustion. Fires range from slow smouldering peat fires, to low-intensity surface fires, to intense crown fires, depending on vegetation structure, fuel moisture, prevailing climate, and weather conditions. While the links between biogeochemistry, climate and fire are widely studied within Earth system science, these relationships are also mediated by fuels—namely plants and their litter—that are the product of evolutionary and ecological processes. Fire is a powerful selective force and, over their evolutionary history, plants have evolved traits that both tolerate and promote fire numerous times and across diverse clades. Here we outline a conceptual framework of how plant traits determine the flammability of ecosystems and interact with climate and weather to influence fire regimes. We explore how these evolutionary and ecological processes scale to impact biogeochemical and Earth system processes. Finally, we outline several research challenges that, when resolved, will improve our understanding of the role of plant evolution in mediating the fire feedbacks driving Earth system processes. Understanding current patterns of fire and vegetation, as well as patterns of fire over geological time, requires research that incorporates evolutionary biology, ecology, biogeography, and the biogeosciences.

Microbiology of sugar-rich environments: diversity, ecology and system constraints.

PubMed

Lievens, Bart; Hallsworth, John E; Pozo, Maria I; Belgacem, Zouhaier Ben; Stevenson, Andrew; Willems, Kris A; Jacquemyn, Hans

2015-02-01

Microbial habitats that contain an excess of carbohydrate in the form of sugar are widespread in the microbial biosphere. Depending on the type of sugar, prevailing water activity and other substances present, sugar-rich environments can be highly dynamic or relatively stable, osmotically stressful, and/or destabilizing for macromolecular systems, and can thereby strongly impact the microbial ecology. Here, we review the microbiology of different high-sugar habitats, including their microbial diversity and physicochemical parameters, which act to impact microbial community assembly and constrain the ecosystem. Saturated sugar beet juice and floral nectar are used as case studies to explore the differences between the microbial ecologies of low and higher water-activity habitats respectively. Nectar is a paradigm of an open, dynamic and biodiverse habitat populated by many microbial taxa, often yeasts and bacteria such as, amongst many others, Metschnikowia spp. and Acinetobacter spp., respectively. By contrast, thick juice is a relatively stable, species-poor habitat and is typically dominated by a single, xerotolerant bacterium (Tetragenococcus halophilus). A number of high-sugar habitats contain chaotropic solutes (e.g. ethyl acetate, phenols, ethanol, fructose and glycerol) and hydrophobic stressors (e.g. ethyl octanoate, hexane, octanol and isoamyl acetate), all of which can induce chaotropicity-mediated stresses that inhibit or prevent multiplication of microbes. Additionally, temperature, pH, nutrition, microbial dispersion and habitat history can determine or constrain the microbiology of high-sugar milieux. Findings are discussed in relation to a number of unanswered scientific questions. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Halophilic Archaea determined from geothermal steam vent aerosols.

PubMed

Ellis, Dean G; Bizzoco, Richard W; Kelley, Scott T

2008-06-01

Hydrothermal vents, known as 'fumaroles', are ubiquitous features of geothermal areas. Although their geology has been extensively characterized, little is known about the subsurface microbial ecology of fumaroles largely because of the difficulty in collecting sufficient numbers of cells from boiling steam water for DNA extraction and culture isolation. Here we describe the first collection, molecular analysis and isolation of microbes from fumarole steam waters in Russia (Kamchatka) and the USA (Hawaii, New Mexico, California and Wyoming). Surprisingly, the steam vent waters from all the fumaroles contained halophilic Archaea closely related to the Haloarcula spp. found in non-geothermal salt mats, saline soils, brine pools and salt lakes around the world. Microscopic cell counting estimated the cell dispersal rate at approximately 1.6 x 10(9) cells year(-1) from a single fumarole. We also managed to enrich microbes in high-salt media from every vent sample, and to isolate Haloarcula from a Yellowstone vent in a 20% salt medium after a month-long incubation, demonstrating both salt tolerance and viability of cells collected from high-temperature steam. Laboratory tests determined that microbes enriched in salt media survived temperatures greater than 75 degrees C for between 5 and 30 min during the collection process. Hawaiian fumaroles proved to contain the greatest diversity of halophilic Archaea with four new lineages that may belong to uncultured haloarchaeal genera. This high diversity may have resulted from the leaching of salts and minerals through the highly porous volcanic rock, creating a chemically complex saline subsurface.

Multiple soil nutrient competition between plants, microbes, and mineral surfaces: model development, parameterization, and example applications in several tropical forests

NASA Astrophysics Data System (ADS)

Zhu, Q.; Riley, W. J.; Tang, J.; Koven, C. D.

2015-03-01

Soil is a complex system where biotic (e.g., plant roots, micro-organisms) and abiotic (e.g., mineral surfaces) consumers compete for resources necessary for life (e.g., nitrogen, phosphorus). This competition is ecologically significant, since it regulates the dynamics of soil nutrients and controls aboveground plant productivity. Here we develop, calibrate, and test a nutrient competition model that accounts for multiple soil nutrients interacting with multiple biotic and abiotic consumers. As applied here for tropical forests, the Nutrient COMpetition model (N-COM) includes three primary soil nutrients (NH4+, NO3-, and POx (representing the sum of PO43-, HPO42-, and H2PO4-)) and five potential competitors (plant roots, decomposing microbes, nitrifiers, denitrifiers, and mineral surfaces). The competition is formulated with a quasi-steady-state chemical equilibrium approximation to account for substrate (multiple substrates share one consumer) and consumer (multiple consumers compete for one substrate) effects. N-COM successfully reproduced observed soil heterotrophic respiration, N2O emissions, free phosphorus, sorbed phosphorus, and free NH4+ at a tropical forest site (Tapajos). The overall model posterior uncertainty was moderately well constrained. Our sensitivity analysis revealed that soil nutrient competition was primarily regulated by consumer-substrate affinity rather than environmental factors such as soil temperature or soil moisture. Our results imply that the competitiveness (from most to least competitive) followed this order: (1) for NH4+, nitrifiers ~ decomposing microbes > plant roots, (2) for NO3-, denitrifiers ~ decomposing microbes > plant roots, (3) for POx, mineral surfaces > decomposing microbes ~ plant roots. Although smaller, plant relative competitiveness is of the same order of magnitude as microbes. We then applied the N-COM model to analyze field nitrogen and phosphorus perturbation experiments in two tropical forest sites (in Hawaii and Puerto Rico) not used in model development or calibration. Under soil inorganic nitrogen and phosphorus elevated conditions, the model accurately replicated the experimentally observed competition among different nutrient consumers. Although we used as many observations as we could obtain, more nutrient addition experiments in tropical systems would greatly benefit model testing and calibration. In summary, the N-COM model provides an ecologically consistent representation of nutrient competition appropriate for land BGC models integrated in Earth System Models.

Toxicological benchmarks for potential contaminants of concern for effects on soil and litter invertebrates and heterotrophic process

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

Will, M.E.; Suter, G.W. II

1995-09-01

An important step in ecological risk assessments is screening the chemicals occur-ring on a site for contaminants of potential concern. Screening may be accomplished by comparing reported ambient concentrations to a set of toxicological benchmarks. Multiple endpoints for assessing risks posed by soil-borne contaminants to organisms directly impacted by them have been established. This report presents benchmarks for soil invertebrates and microbial processes and addresses only chemicals found at United States Department of Energy (DOE) sites. No benchmarks for pesticides are presented. After discussing methods, this report presents the results of the literature review and benchmark derivation for toxicity tomore » earthworms (Sect. 3), heterotrophic microbes and their processes (Sect. 4), and other invertebrates (Sect. 5). The final sections compare the benchmarks to other criteria and background and draw conclusions concerning the utility of the benchmarks.« less

Innovative biological approaches for monitoring and improving water quality

PubMed Central

Aracic, Sanja; Manna, Sam; Petrovski, Steve; Wiltshire, Jennifer L.; Mann, Gülay; Franks, Ashley E.

2015-01-01

Water quality is largely influenced by the abundance and diversity of indigenous microbes present within an aquatic environment. Physical, chemical and biological contaminants from anthropogenic activities can accumulate in aquatic systems causing detrimental ecological consequences. Approaches exploiting microbial processes are now being utilized for the detection, and removal or reduction of contaminants. Contaminants can be identified and quantified in situ using microbial whole-cell biosensors, negating the need for water samples to be tested off-site. Similarly, the innate biodegradative processes can be enhanced through manipulation of the composition and/or function of the indigenous microbial communities present within the contaminated environments. Biological contaminants, such as detrimental/pathogenic bacteria, can be specifically targeted and reduced in number using bacteriophages. This mini-review discusses the potential application of whole-cell microbial biosensors for the detection of contaminants, the exploitation of microbial biodegradative processes for environmental restoration and the manipulation of microbial communities using phages. PMID:26322034

Disturbance Regimes Predictably Alter Diversity in an Ecologically Complex Bacterial System

PubMed Central

Scholz, Monika; Hutchison, Alan L.; Dinner, Aaron R.; Gilbert, Jack A.; Coleman, Maureen L.

2016-01-01

ABSTRACT Diversity is often associated with the functional stability of ecological communities from microbes to macroorganisms. Understanding how diversity responds to environmental perturbations and the consequences of this relationship for ecosystem function are thus central challenges in microbial ecology. Unimodal diversity-disturbance relationships, in which maximum diversity occurs at intermediate levels of disturbance, have been predicted for ecosystems where life history tradeoffs separate organisms along a disturbance gradient. However, empirical support for such peaked relationships in macrosystems is mixed, and few studies have explored these relationships in microbial systems. Here we use complex microbial microcosm communities to systematically determine diversity-disturbance relationships over a range of disturbance regimes. We observed a reproducible switch between community states, which gave rise to transient diversity maxima when community states were forced to mix. Communities showed reduced compositional stability when diversity was highest. To further explore these dynamics, we formulated a simple model that reveals specific regimes under which diversity maxima are stable. Together, our results show how both unimodal and non-unimodal diversity-disturbance relationships can be observed as a system switches between two distinct microbial community states; this process likely occurs across a wide range of spatially and temporally heterogeneous microbial ecosystems. PMID:27999158

Ecology and thermal inactivation of microbes in and on interplanetary space vehicle components

NASA Technical Reports Server (NTRS)

Reyes, A. L.; Campbell, J. E.; Wehby, A. J.; Crawford, R. G.; Wimsatt, J. C.; Peeler, J. T.

1976-01-01

Experiments performed on the heat resistant organism CK 4-6 are described. Its response to dry heat at two temperatures (125 C and 135 C) at eight humidity levels (0.001 percent to 100 percent RH) in a closed can system is studied.

Innovative MIOR Process Utilizing Indigenous Reservoir Constituents

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

D. O. Hitzman; A. K. Stepp; D. M. Dennis

This research program is directed at improving the knowledge of reservoir ecology and developing practical microbial solutions for improving oil production. The goal is to identify indigenous microbial populations which can produce beneficial metabolic products and develop a methodology to stimulate those select microbes with nutrient amendments to increase oil recovery. This microbial technology has the capability of producing multiple oil-releasing agents. Experimental laboratory work is underway. Microbial cultures have been isolated from produced water samples. Comparative laboratory studies demonstrating in situ production of microbial products as oil recovery agents were conducted in sand packs with natural field waters withmore » cultures and conditions representative of oil reservoirs. Field pilot studies are underway.« less

Nutritional modulation of gut microbiota - the impact on metabolic disease pathophysiology.

PubMed

Ojeda, Patricia; Bobe, Alexandria; Dolan, Kyle; Leone, Vanessa; Martinez, Kristina

2016-02-01

The obesity epidemic afflicts over one third of the United States population. With few therapies available to combat obesity, a greater understanding of the systemic causes of this and other metabolic disorders is needed to develop new, effective treatments. The mammalian intestinal microbiota contributes to metabolic processes in the host. This review summarizes the research demonstrating the interplay of diet, intestinal microbiota and host metabolism. We detail the effects of diet-induced modifications in microbial activity and resultant impact on (1) sensory perception of macronutrients and total energy intake; (2) nutrient absorption, transport and storage; (3) liver and biliary function; (4) immune-mediated signaling related to adipose inflammation; and (5) circadian rhythm. We also discuss therapeutic strategies aimed to modify host-microbe interactions, including prebiotics, probiotics and postbiotics, as well as fecal microbiota transplantation. Elucidating the role of gut microbes in shaping metabolic homeostasis or dysregulation provides greater insight into disease development and a promising avenue for improved treatment of metabolic dysfunction. Copyright © 2015 Elsevier Inc. All rights reserved.

Species associations overwhelm abiotic conditions to dictate the structure and function of wood-decay fungal communities.

PubMed

Maynard, Daniel S; Covey, Kristofer R; Crowther, Thomas W; Sokol, Noah W; Morrison, Eric W; Frey, Serita D; van Diepen, Linda T A; Bradford, Mark A

2018-04-01

Environmental conditions exert strong controls on the activity of saprotrophic microbes, yet abiotic factors often fail to adequately predict wood decomposition rates across broad spatial scales. Given that species interactions can have significant positive and negative effects on wood-decay fungal activity, one possibility is that biotic processes serve as the primary controls on community function, with abiotic controls emerging only after species associations are accounted for. Here we explore this hypothesis in a factorial field warming- and nitrogen-addition experiment by examining relationships among wood decomposition rates, fungal activity, and fungal community structure. We show that functional outcomes and community structure are largely unrelated to abiotic conditions, with microsite and plot-level abiotic variables explaining at most 19% of the total variability in decomposition and fungal activity, and 2% of the variability in richness and evenness. In contrast, taxonomic richness, evenness, and species associations (i.e., co-occurrence patterns) exhibited strong relationships with community function, accounting for 52% of the variation in decomposition rates and 73% in fungal activity. A greater proportion of positive vs. negative species associations in a community was linked to strong declines in decomposition rates and richness. Evenness emerged as a key mediator between richness and function, with highly even communities exhibiting a positive richness-function relationship and uneven communities exhibiting a negative or null response. These results suggest that community-assembly processes and species interactions are important controls on the function of wood-decay fungal communities, ultimately overwhelming substantial differences in abiotic conditions. © 2018 by the Ecological Society of America.

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

PubMed Central

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

2018-01-01

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

Microbes, Mineral Evolution, and the Rise of Microcontinents-Origin and Coevolution of Life with Early Earth.

PubMed

Grosch, Eugene G; Hazen, Robert M

2015-10-01

Earth is the most mineralogically diverse planet in our solar system, the direct consequence of a coevolving geosphere and biosphere. We consider the possibility that a microbial biosphere originated and thrived in the early Hadean-Archean Earth subseafloor environment, with fundamental consequences for the complex evolution and habitability of our planet. In this hypothesis paper, we explore possible venues for the origin of life and the direct consequences of microbially mediated, low-temperature hydrothermal alteration of the early oceanic lithosphere. We hypothesize that subsurface fluid-rock-microbe interactions resulted in more efficient hydration of the early oceanic crust, which in turn promoted bulk melting to produce the first evolved fragments of felsic crust. These evolved magmas most likely included sialic or tonalitic sheets, felsic volcaniclastics, and minor rhyolitic intrusions emplaced in an Iceland-type extensional setting as the earliest microcontinents. With the further development of proto-tectonic processes, these buoyant felsic crustal fragments formed the nucleus of intra-oceanic tonalite-trondhjemite-granitoid (TTG) island arcs. Thus microbes, by facilitating extensive hydrothermal alteration of the earliest oceanic crust through bioalteration, promoted mineral diversification and may have been early architects of surface environments and microcontinents on young Earth. We explore how the possible onset of subseafloor fluid-rock-microbe interactions on early Earth accelerated metavolcanic clay mineral formation, crustal melting, and subsequent metamorphic mineral evolution. We also consider environmental factors supporting this earliest step in geosphere-biosphere coevolution and the implications for habitability and mineral evolution on other rocky planets, such as Mars.

Patterns and Processes of Microbial Community Assembly

PubMed Central

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

2013-01-01

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

MiDAS: the field guide to the microbes of activated sludge

PubMed Central

McIlroy, Simon Jon; Saunders, Aaron Marc; Albertsen, Mads; Nierychlo, Marta; McIlroy, Bianca; Hansen, Aviaja Anna; Karst, Søren Michael; Nielsen, Jeppe Lund; Nielsen, Per Halkjær

2015-01-01

The Microbial Database for Activated Sludge (MiDAS) field guide is a freely available online resource linking the identity of abundant and process critical microorganisms in activated sludge wastewater treatment systems to available data related to their functional importance. Phenotypic properties of some of these genera are described, but most are known only from sequence data. The MiDAS taxonomy is a manual curation of the SILVA taxonomy that proposes a name for all genus-level taxa observed to be abundant by large-scale 16 S rRNA gene amplicon sequencing of full-scale activated sludge communities. The taxonomy can be used to classify unknown sequences, and the online MiDAS field guide links the identity to the available information about their morphology, diversity, physiology and distribution. The use of a common taxonomy across the field will provide a solid foundation for the study of microbial ecology of the activated sludge process and related treatment processes. The online MiDAS field guide is a collaborative workspace intended to facilitate a better understanding of the ecology of activated sludge and related treatment processes—knowledge that will be an invaluable resource for the optimal design and operation of these systems. Database URL: http://www.midasfieldguide.org PMID:26120139

Halogenated solvent remediation

DOEpatents

Sorenson, Jr., Kent S.

2008-11-11

Methods for enhancing bioremediation of ground water contaminated with nonaqueous halogenated solvents are disclosed. An illustrative method includes adding an electron donor for microbe-mediated anaerobic reductive dehalogenation of the halogenated solvents, which electron donor enhances mass transfer of the halogenated solvents from residual source areas into the aqueous phase of the ground water. Illustrative electron donors include C.sub.2-C.sub.4 carboxylic acids and hydroxy acids, salts thereof, esters of C.sub.2-C.sub.4 carboxylic acids and hydroxy acids, and mixtures thereof, of which lactic acid, salts of lactic acid--such as sodium lactate, lactate esters, and mixtures thereof are particularly illustrative. The microbes are either indigenous to the ground water, or such microbes can be added to the ground water in addition to the electron donor.

Ecology of micro-organisms in a small closed system - Potential benefits and problems for Space Station

NASA Technical Reports Server (NTRS)

Rodgers, E. B.; Seale, D. B.; Boraas, M. E.; Sommer, C. V.

1989-01-01

The probable sources and implications of microbial contamination on the proposed Space Station are discussed. Because of the limited availability of material, facilities and time on the Space Station, we are exploring the feasibility of replacing traditional incubation methods for assessing microbial contamination with rapid, automated methods. Some possibilities include: ATP measurement, microscopy and telecommunications, and molecular techniques such as DNA probes or monoclonal antibodies. Some of the important ecological factors that could alter microbes in space include microgravity, exposure to radiation, and antibiotic resistance.

The humpbacked species richness-curve: A contingent rule for community ecology

USGS Publications Warehouse

Graham, John H.; Duda, Jeffrey J.

2011-01-01

Functional relationships involving species richness may be unimodal, monotonically increasing, monotonically decreasing, bimodal, multimodal, U-shaped, or with no discernable pattern. The unimodal relationships are the most interesting because they suggest dynamic, nonequilibrium community processes. For that reason, they are also contentious. In this paper, we provide a wide-ranging review of the literature on unimodal (humpbacked) species richness-relationships. Though not as widespread as previously thought, unimodal patterns of species richness are often associated with disturbance, predation and herbivory, productivity, spatial heterogeneity, environmental gradients, time, and latitude. These unimodal patterns are contingent on organism and environment; we examine unimodal species richness-curves involving plants, invertebrates, vertebrates, plankton, and microbes in marine, lacustrine, and terrestrial habitats. A goal of future research is to understand the contingent patterns and the complex, interacting processes that generate them.

Chemical signaling involved in plant-microbe interactions.

PubMed

Chagas, Fernanda Oliveira; Pessotti, Rita de Cassia; Caraballo-Rodríguez, Andrés Mauricio; Pupo, Mônica Tallarico

2018-03-05

Microorganisms are found everywhere, and they are closely associated with plants. Because the establishment of any plant-microbe association involves chemical communication, understanding crosstalk processes is fundamental to defining the type of relationship. Although several metabolites from plants and microbes have been fully characterized, their roles in the chemical interplay between these partners are not well understood in most cases, and they require further investigation. In this review, we describe different plant-microbe associations from colonization to microbial establishment processes in plants along with future prospects, including agricultural benefits.

Mass Spectrometry Imaging of Complex Microbial Communities

PubMed Central

2016-01-01

Conspectus In the two decades since mass spectrometry imaging (MSI) was first applied to visualize the distribution of peptides across biological tissues and cells, the technique has become increasingly effective and reliable. MSI excels at providing complementary information to existing methods for molecular analysis—such as genomics, transcriptomics, and metabolomics—and stands apart from other chemical imaging modalities through its capability to generate information that is simultaneously multiplexed and chemically specific. Today a diverse family of MSI approaches are applied throughout the scientific community to study the distribution of proteins, peptides, and small-molecule metabolites across many biological models. The inherent strengths of MSI make the technique valuable for studying microbial systems. Many microbes reside in surface-attached multicellular and multispecies communities, such as biofilms and motile colonies, where they work together to harness surrounding nutrients, fend off hostile organisms, and shield one another from adverse environmental conditions. These processes, as well as many others essential for microbial survival, are mediated through the production and utilization of a diverse assortment of chemicals. Although bacterial cells are generally only a few microns in diameter, the ecologies they influence can encompass entire ecosystems, and the chemical changes that they bring about can occur over time scales ranging from milliseconds to decades. Because of their incredible complexity, our understanding of and influence over microbial systems requires detailed scientific evaluations that yield both chemical and spatial information. MSI is well-positioned to fulfill these requirements. With small adaptations to existing methods, the technique can be applied to study a wide variety of chemical interactions, including those that occur inside single-species microbial communities, between cohabitating microbes, and between microbes and their hosts. In recognition of this potential for scientific advancement, researchers have adapted MSI methodologies for the specific needs of the microbiology research community. As a result, workflows exist for imaging microbial systems with many of the common MSI ionization methods. Despite this progress, there is substantial room for improvements in instrumentation, sample preparation, and data interpretation. This Account provides a brief overview of the state of technology in microbial MSI, illuminates selected applications that demonstrate the potential of the technique, and highlights a series of development challenges that are needed to move the field forward. In the coming years, as microbial MSI becomes easier to use and more universally applicable, the technique will evolve into a fundamental tool widely applied throughout many divisions of science, medicine, and industry. PMID:28001363

Mass Spectrometry Imaging of Complex Microbial Communities.

PubMed

Dunham, Sage J B; Ellis, Joseph F; Li, Bin; Sweedler, Jonathan V

2017-01-17

In the two decades since mass spectrometry imaging (MSI) was first applied to visualize the distribution of peptides across biological tissues and cells, the technique has become increasingly effective and reliable. MSI excels at providing complementary information to existing methods for molecular analysis-such as genomics, transcriptomics, and metabolomics-and stands apart from other chemical imaging modalities through its capability to generate information that is simultaneously multiplexed and chemically specific. Today a diverse family of MSI approaches are applied throughout the scientific community to study the distribution of proteins, peptides, and small-molecule metabolites across many biological models. The inherent strengths of MSI make the technique valuable for studying microbial systems. Many microbes reside in surface-attached multicellular and multispecies communities, such as biofilms and motile colonies, where they work together to harness surrounding nutrients, fend off hostile organisms, and shield one another from adverse environmental conditions. These processes, as well as many others essential for microbial survival, are mediated through the production and utilization of a diverse assortment of chemicals. Although bacterial cells are generally only a few microns in diameter, the ecologies they influence can encompass entire ecosystems, and the chemical changes that they bring about can occur over time scales ranging from milliseconds to decades. Because of their incredible complexity, our understanding of and influence over microbial systems requires detailed scientific evaluations that yield both chemical and spatial information. MSI is well-positioned to fulfill these requirements. With small adaptations to existing methods, the technique can be applied to study a wide variety of chemical interactions, including those that occur inside single-species microbial communities, between cohabitating microbes, and between microbes and their hosts. In recognition of this potential for scientific advancement, researchers have adapted MSI methodologies for the specific needs of the microbiology research community. As a result, workflows exist for imaging microbial systems with many of the common MSI ionization methods. Despite this progress, there is substantial room for improvements in instrumentation, sample preparation, and data interpretation. This Account provides a brief overview of the state of technology in microbial MSI, illuminates selected applications that demonstrate the potential of the technique, and highlights a series of development challenges that are needed to move the field forward. In the coming years, as microbial MSI becomes easier to use and more universally applicable, the technique will evolve into a fundamental tool widely applied throughout many divisions of science, medicine, and industry.

Minerals and Microorganisms in Evaporite Environments

NASA Astrophysics Data System (ADS)

Morris, P. A.; Brigmon, R. L.

2010-12-01

Traditional analysis of evaporite environments have either focused on the geology or the halophilic organisms. It is relatively rare that the two have been combined and even rarer that both disciplines have been incorporated in comparing evaporite sites. The variation in evaporite environments does influence microbial ecology and fossilization processes as each site varies in pH, temperature, presence or absence springs, and spring chemistry. Understanding the evaporite environments is important for planetary scientists as they serve as analogs for evaluating extraterrestrial materials, including the potential for water and ultimately life. For example Mars lander, rover and orbital missions have identified the evaporite signatures of gypsum, carbonates and chlorides, all indicating that water existed at sometime in the planets geological history. Terrestrial evaporite sites all possess halophilic tolerant life. In some instances such as the Dead Sea, Israel, it is restricted to microbial life, but in other sites there are higher life forms. The microbes associated with these evaporite sites can produce biofilms as a method to develop their own microenvironments. Microorganisms can be observed colonizing specific ecological niches or gradients can be created by these environments. These gradients occur due the localized drying and weathering patterns that create different soil chemistry. The microorganisms in turn colonize specific areas more suitable to their specific metabolic needs. For example, under anaerobic conditions with sulfur and methane prevalent methanogenic and/or sulfur reducing microbial species may be observed. However, under similar chemistry environments with the exception of aerobic conditions sulfur oxidizer and/or methanotrophic microorganism may occur. Because of their conspicuous colored pigments purple sulfur bacteria are frequently observed in anoxic zones of lakes, sulfur springs, and stratified evaporite crusts. Some of these bacteria are of particular interest including Ectothiorhodospira spp. that deposit extracellular sulfur and are halophilic growing at high pH with NaCl concentrations approaching saturation. Fossilization and biofilm production appears to be relevant to the geochemistry of the systems. For example Dead Sea, Israel, microbes produce minimal biofilms, reside in the sediments, and the incidence of fossilization is low while hypersaline Storrs Lake, San Salvador, Bahamas microbes produce prodigious amounts of biofilms with many examples of fossilization. Some of the microbes appear to prefer solid substrates and may exhibit a preference, such as detrital or mineral, etc. In our studies we have found that some of the organisms, in relation to their substrate, can be tentatively characterized with laser confocal scanning microscopy. Terrestrial evaporite sites and understanding potential biomarkers and/or mineral signatures are important for identifying potential exoplanetary sites such as Mars that may harbor life.

Functional and Structural Succession of Soil Microbial Communities below Decomposing Human Cadavers

PubMed Central

Cobaugh, Kelly L.; Schaeffer, Sean M.; DeBruyn, Jennifer M.

2015-01-01

The ecological succession of microbes during cadaver decomposition has garnered interest in both basic and applied research contexts (e.g. community assembly and dynamics; forensic indicator of time since death). Yet current understanding of microbial ecology during decomposition is almost entirely based on plant litter. We know very little about microbes recycling carcass-derived organic matter despite the unique decomposition processes. Our objective was to quantify the taxonomic and functional succession of microbial populations in soils below decomposing cadavers, testing the hypotheses that a) periods of increased activity during decomposition are associated with particular taxa; and b) human-associated taxa are introduced to soils, but do not persist outside their host. We collected soils from beneath four cadavers throughout decomposition, and analyzed soil chemistry, microbial activity and bacterial community structure. As expected, decomposition resulted in pulses of soil C and nutrients (particularly ammonia) and stimulated microbial activity. There was no change in total bacterial abundances, however we observed distinct changes in both function and community composition. During active decay (7 - 12 days postmortem), respiration and biomass production rates were high: the community was dominated by Proteobacteria (increased from 15.0 to 26.1% relative abundance) and Firmicutes (increased from 1.0 to 29.0%), with reduced Acidobacteria abundances (decreased from 30.4 to 9.8%). Once decay rates slowed (10 - 23 d postmortem), respiration was elevated, but biomass production rates dropped dramatically; this community with low growth efficiency was dominated by Firmicutes (increased to 50.9%) and other anaerobic taxa. Human-associated bacteria, including the obligately anaerobic Bacteroides, were detected at high concentrations in soil throughout decomposition, up to 198 d postmortem. Our results revealed the pattern of functional and compositional succession in soil microbial communities during decomposition of human-derived organic matter, provided insight into decomposition processes, and identified putative predictor populations for time since death estimation. PMID:26067226

Tracing Personalized Health Curves during Infections

PubMed Central

Schneider, David S.

2011-01-01

It is difficult to describe host–microbe interactions in a manner that deals well with both pathogens and mutualists. Perhaps a way can be found using an ecological definition of tolerance, where tolerance is defined as the dose response curve of health versus parasite load. To plot tolerance, individual infections are summarized by reporting the maximum parasite load and the minimum health for a population of infected individuals and the slope of the resulting curve defines the tolerance of the population. We can borrow this method of plotting health versus microbe load in a population and make it apply to individuals; instead of plotting just one point that summarizes an infection in an individual, we can plot the values at many time points over the course of an infection for one individual. This produces curves that trace the course of an infection through phase space rather than over a more typical timeline. These curves highlight relationships like recovery and point out bifurcations that are difficult to visualize with standard plotting techniques. Only nine archetypical curves are needed to describe most pathogenic and mutualistic host–microbe interactions. The technique holds promise as both a qualitative and quantitative approach to dissect host–microbe interactions of all kinds. PMID:21957398

Skin microbes on frogs prevent morbidity and mortality caused by a lethal skin fungus.

PubMed

Harris, Reid N; Brucker, Robert M; Walke, Jenifer B; Becker, Matthew H; Schwantes, Christian R; Flaherty, Devon C; Lam, Brianna A; Woodhams, Douglas C; Briggs, Cheryl J; Vredenburg, Vance T; Minbiole, Kevin P C

2009-07-01

Emerging infectious diseases threaten human and wildlife populations. Altered ecological interactions between mutualistic microbes and hosts can result in disease, but an understanding of interactions between host, microbes and disease-causing organisms may lead to management strategies to affect disease outcomes. Many amphibian species in relatively pristine habitats are experiencing dramatic population declines and extinctions due to the skin disease chytridiomycosis, which is caused by the chytrid fungus Batrachochytrium dendrobatidis. Using a randomized, replicated experiment, we show that adding an antifungal bacterial species, Janthinobacterium lividum, found on several species of amphibians to the skins of the frog Rana muscosa prevented morbidity and mortality caused by the pathogen. The bacterial species produces the anti-chytrid metabolite violacein, which was found in much higher concentrations on frog skins in the treatments where J. lividum was added. Our results show that cutaneous microbes are a part of amphibians' innate immune system, the microbial community structure on frog skins is a determinant of disease outcome and altering microbial interactions on frog skins can prevent a lethal disease outcome. A bioaugmentation strategy may be an effective management tool to control chytridiomycosis in amphibian survival assurance colonies and in nature.

Plant-microbe Cross-talk in the Rhizosphere: Insight and Biotechnological Potential

PubMed Central

Haldar, Shyamalina; Sengupta, Sanghamitra

2015-01-01

Rhizosphere, the interface between soil and plant roots, is a chemically complex environment which supports the development and growth of diverse microbial communities. The composition of the rhizosphere microbiome is dynamic and controlled by multiple biotic and abiotic factors that include environmental parameters, physiochemical properties of the soil, biological activities of the plants and chemical signals from the plants and bacteria which inhabit the soil adherent to root-system. Recent advancement in molecular and microbiological techniques has unravelled the interactions among rhizosphere residents at different levels. In this review, we elaborate on various factors that determine plant-microbe and microbe-microbe interactions in the rhizosphere, with an emphasis on the impact of host genotype and developmental stages which together play pivotal role in shaping the nature and diversity of root exudations. We also discuss about the coherent functional groups of microorganisms that colonize rhizosphere and enhance plant growth and development by several direct and indirect mechanisms. Insights into the underlying structural principles of indigenous microbial population and the key determinants governing rhizosphere ecology will provide directions for developing techniques for profitable applicability of beneficial microorganisms in sustainable agriculture and nature restoration. PMID:25926899

Testing the Neutral Theory of Biodiversity with Human Microbiome Datasets.

PubMed

Li, Lianwei; Ma, Zhanshan Sam

2016-08-16

The human microbiome project (HMP) has made it possible to test important ecological theories for arguably the most important ecosystem to human health-the human microbiome. Existing limited number of studies have reported conflicting evidence in the case of the neutral theory; the present study aims to comprehensively test the neutral theory with extensive HMP datasets covering all five major body sites inhabited by the human microbiome. Utilizing 7437 datasets of bacterial community samples, we discovered that only 49 communities (less than 1%) satisfied the neutral theory, and concluded that human microbial communities are not neutral in general. The 49 positive cases, although only a tiny minority, do demonstrate the existence of neutral processes. We realize that the traditional doctrine of microbial biogeography "Everything is everywhere, but the environment selects" first proposed by Baas-Becking resolves the apparent contradiction. The first part of Baas-Becking doctrine states that microbes are not dispersal-limited and therefore are neutral prone, and the second part reiterates that the freely dispersed microbes must endure selection by the environment. Therefore, in most cases, it is the host environment that ultimately shapes the community assembly and tip the human microbiome to niche regime.

Testing the Neutral Theory of Biodiversity with Human Microbiome Datasets

PubMed Central

Li, Lianwei; Ma, Zhanshan (Sam)

2016-01-01

The human microbiome project (HMP) has made it possible to test important ecological theories for arguably the most important ecosystem to human health—the human microbiome. Existing limited number of studies have reported conflicting evidence in the case of the neutral theory; the present study aims to comprehensively test the neutral theory with extensive HMP datasets covering all five major body sites inhabited by the human microbiome. Utilizing 7437 datasets of bacterial community samples, we discovered that only 49 communities (less than 1%) satisfied the neutral theory, and concluded that human microbial communities are not neutral in general. The 49 positive cases, although only a tiny minority, do demonstrate the existence of neutral processes. We realize that the traditional doctrine of microbial biogeography “Everything is everywhere, but the environment selects” first proposed by Baas-Becking resolves the apparent contradiction. The first part of Baas-Becking doctrine states that microbes are not dispersal-limited and therefore are neutral prone, and the second part reiterates that the freely dispersed microbes must endure selection by the environment. Therefore, in most cases, it is the host environment that ultimately shapes the community assembly and tip the human microbiome to niche regime. PMID:27527985

Separation of Bacteria, Protozoa and Carbon Nanotubes by Density Gradient Centrifugation

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

Mortimer, Monika; Petersen, Elijah; Buchholz, Bruce

Sustainable production and use of carbon nanotube (CNT)-enabled materials require efficient assessment of CNT environmental hazards, including the potential for CNT bioaccumulation and biomagnification in environmental receptors. Microbes, as abundant organisms responsible for nutrient cycling in soil and water, are important ecological receptors for studying the effects of CNTs. Quantification of CNT association with microbial cells requires efficient separation of CNT-associated cells from individually dispersed CNTs and CNT agglomerates. Here in this paper, we designed, optimized, and demonstrated procedures for separating bacteria (Pseudomonas aeruginosa) from unbound multiwall carbon nanotubes (MWCNTs) and MWCNT agglomerates using sucrose density gradient centrifugation. We demonstratemore » separation of protozoa (Tetrahymena thermophila) from MWCNTs, bacterial agglomerates, and protozoan fecal pellets by centrifugation in an iodixanol solution. The presence of MWCNTs in the density gradients after centrifugation was determined by quantification of 14C-labeled MWCNTs; the recovery of microbes from the density gradient media was confirmed by optical microscopy. Protozoan intracellular contents of MWCNTs and of bacteria were also unaffected by the designed separation process. Lastly, the optimized methods contribute to improved efficiency and accuracy in quantifying MWCNT association with bacteria and MWCNT accumulation in protozoan cells, thus supporting improved assessment of CNT bioaccumulation.« less

Separation of Bacteria, Protozoa and Carbon Nanotubes by Density Gradient Centrifugation

DOE PAGES

Mortimer, Monika; Petersen, Elijah; Buchholz, Bruce; ...

2016-10-12

Sustainable production and use of carbon nanotube (CNT)-enabled materials require efficient assessment of CNT environmental hazards, including the potential for CNT bioaccumulation and biomagnification in environmental receptors. Microbes, as abundant organisms responsible for nutrient cycling in soil and water, are important ecological receptors for studying the effects of CNTs. Quantification of CNT association with microbial cells requires efficient separation of CNT-associated cells from individually dispersed CNTs and CNT agglomerates. Here in this paper, we designed, optimized, and demonstrated procedures for separating bacteria (Pseudomonas aeruginosa) from unbound multiwall carbon nanotubes (MWCNTs) and MWCNT agglomerates using sucrose density gradient centrifugation. We demonstratemore » separation of protozoa (Tetrahymena thermophila) from MWCNTs, bacterial agglomerates, and protozoan fecal pellets by centrifugation in an iodixanol solution. The presence of MWCNTs in the density gradients after centrifugation was determined by quantification of 14C-labeled MWCNTs; the recovery of microbes from the density gradient media was confirmed by optical microscopy. Protozoan intracellular contents of MWCNTs and of bacteria were also unaffected by the designed separation process. Lastly, the optimized methods contribute to improved efficiency and accuracy in quantifying MWCNT association with bacteria and MWCNT accumulation in protozoan cells, thus supporting improved assessment of CNT bioaccumulation.« less

Separation of Bacteria, Protozoa and Carbon Nanotubes by Density Gradient Centrifugation

PubMed Central

Mortimer, Monika; Petersen, Elijah J.; Buchholz, Bruce A.; Holden, Patricia A.

2016-01-01

Sustainable production and use of carbon nanotube (CNT)-enabled materials require efficient assessment of CNT environmental hazards, including the potential for CNT bioaccumulation and biomagnification in environmental receptors. Microbes, as abundant organisms responsible for nutrient cycling in soil and water, are important ecological receptors for studying the effects of CNTs. Quantification of CNT association with microbial cells requires efficient separation of CNT-associated cells from individually dispersed CNTs and CNT agglomerates. Here, we designed, optimized, and demonstrated procedures for separating bacteria (Pseudomonas aeruginosa) from unbound multiwall carbon nanotubes (MWCNTs) and MWCNT agglomerates using sucrose density gradient centrifugation. We demonstrate separation of protozoa (Tetrahymena thermophila) from MWCNTs, bacterial agglomerates, and protozoan fecal pellets by centrifugation in an iodixanol solution. The presence of MWCNTs in the density gradients after centrifugation was determined by quantification of 14C-labeled MWCNTs; the recovery of microbes from the density gradient media was confirmed by optical microscopy. Protozoan intracellular contents of MWCNTs and of bacteria were also unaffected by the designed separation process. The optimized methods contribute to improved efficiency and accuracy in quantifying MWCNT association with bacteria and MWCNT accumulation in protozoan cells, thus supporting improved assessment of CNT bioaccumulation. PMID:27917301

Microbially mediated carbon mineralization: Geoengineering a carbon-neutral mine

NASA Astrophysics Data System (ADS)

Power, I. M.; McCutcheon, J.; Harrison, A. L.; Wilson, S. A.; Dipple, G. M.; Southam, G.

2013-12-01

Ultramafic and mafic mine tailings are a potentially valuable feedstock for carbon mineralization, affording the mining industry an opportunity to completely offset their carbon emissions. Passive carbon mineralization has previously been documented at the abandoned Clinton Creek asbestos mine, and the active Diavik diamond mine and Mount Keith nickel mine, yet the majority of tailings remain unreacted. Examples of microbe-carbonate interactions at each mine suggest that biological pathways could be harnessed to promote carbon mineralization. In suitable environmental conditions, microbes can mediate geochemical processes to accelerate mineral dissolution, increase the supply of carbon dioxide (CO2), and induce carbonate precipitation, all of which may accelerate carbon mineralization. Tailings mineralogy and the availability of a CO2 point source are key considerations in designing tailings storage facilities (TSF) for optimizing carbon mineralization. We evaluate the efficacy of acceleration strategies including bioleaching, biologically induced carbonate precipitation, and heterotrophic oxidation of waste organics, as well as abiotic strategies including enhancing passive carbonation through modifying tailings management practices and use of CO2 point sources (Fig. 1). With the aim of developing carbon-neutral mines, implementation of carbon mineralization strategies into TSF design will be driven by economic incentives and public pressure for environmental sustainability in the mining industry. Figure 1. Schematic illustrating geoengineered scenarios for carbon mineralization of ultramafic mine tailings. Scenarios A and B are based on non-point and point sources of CO2, respectively.

Highly diverse endophytes in roots of Cycas bifida (Cycadaceae), an ancient but endangered gymnosperm.

PubMed

Zheng, Ying; Chiang, Tzen-Yuh; Huang, Chao-Li; Gong, Xun

2018-05-01

As an ancient seed plant, cycads are one of the few gymnosperms that develop a root symbiosis with cyanobacteria, which has allowed cycads to cope with harsh geologic and climatic conditions during the evolutionary process. However, the endophytic microbes in cycad roots remain poorly identified. In this study, using next-generation sequencing techniques, we investigated the microbial diversity and composition of both the coralloid and regular roots of Cycas bifida (Dyer) K.D. Hill. Highly diverse endophytic communities were observed in both the coralloid and regular roots. Of the associated bacteria, the top five families were the Nostocaceae, Sinobacteraceae, Bradyrhizobiaceae, Bacillaceae, and Hyphomicrobiaceae. The Nectriaceae, Trichocomaceae, and Incertae sedis were the predominant fungal families in all root samples. A significant difference in the endophytic bacterial community was detected between coralloid roots and regular roots, but no difference was observed between the fungal communities in the two root types. Cyanobacteria were more dominant in coralloid roots than in regular roots. The divergence of cycad root structures and the modified physiological processes may have contributed to the abundance of cyanobionts in coralloid roots. Consequently, the colonization of cyanobacteria inhibits the assemblage of other endophytes. Our results contribute to an understanding of the species diversity and composition of the cycad-endophyte microbiome and provide an abbreviated list of potential ecological roles of the core microbes present.

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

PubMed

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

2015-05-01

Achatinella mustelina is a critically endangered tree snail that subsists entirely by grazing microbes from leaf surfaces of native trees. Little is known about the fundamental aspects of these microbe assemblages: not taxonomic composition, how this varies with host plant or location, nor whether snails selectively consume microbes. To address these questions, we collected 102 snail faecal samples as a proxy for diet, and 102 matched-leaf samples from four locations. We used Illumina amplicon sequencing to determine bacterial and fungal community composition. Microbial community structure was significantly distinct between snail faeces and leaf samples, but the same microbes occurred in both. We conclude that snails are not 'picky' eaters at the microbial level, but graze the surface of whatever plant they are on. In a second experiment, the gut was dissected from non-endangered native tree snails in the same family as Achatinella to confirm that faecal samples reflect gut contents. Over 60% of fungal reads were shared between faeces, gut and leaf samples. Overall, location, sample type (faeces or leaf) and host plant identity all significantly explained the community composition and variation among samples. Understanding the microbial ecology of microbes grazed by tree snails enables effective management when conservation requires captive breeding or field relocation. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

A Mesoscale Total Dissolved Solids Quantity and Quality Study Integrating Responses of Multiple Biological Components in Small Stream Communities

EPA Science Inventory

A 42-day dosing test with ions comprising an excess TDS was run using mesocosms colonized with natural stream water fed continuously. In gridded gravel beds biota from microbes through macroinvertebrates are measured and interact in a manner realistic of stream riffle/run ecology...

Host-rumen microbe interactions may be leveraged to improve the productivity of dairy cows

USDA-ARS?s Scientific Manuscript database

The cattle rumen serves as a digestive bioreactor for the dairy cow, yet our knowledge of the microbial contents, ecology, and host selection within the rumen is only precursory. This is despite the knowledge that the volatile fatty acids (VFA) and microbial crude protein (MCP) produced by rumen mic...

Pyrosequencing reveals the predominance of Pseudomonadaceae in gut microbiome of a Gall Midge

USDA-ARS?s Scientific Manuscript database

Gut microbes are known to play various roles in insects such as digestion of inaccessible nutrients, synthesis of deficient amino acids, and interaction with ecological environments, including host plants. Here, we analyzed the gut microbiome in Hessian fly, a serious pest of wheat. A total of 3,654...

Microbiome diversity of the soybean aphid (Aphis glycines) with extensive superinfection of Arsenophonus and Wolbachia in native and invasive populations

USDA-ARS?s Scientific Manuscript database

The interaction among insects and microbes can lead to either symbiotic cooperation which could promote ecological and evolutionary adaptation, or a parasitic relationship through reproductive manipulation. We characterized the microbiome of the soybean aphid (Aphis glycines), with the long-term goa...

Micro-managing arthropod invasions: eradication and control of invasive arthropods with microbes

Treesearch

Ann E. Hajek; Patrick C. Tobin

2010-01-01

Non-indigenous arthropods are increasingly being introduced into new areas worldwide and occasionally they cause considerable ecological and economic harm. Many invasive arthropods particularly pose problems to areas of human habitation and native ecosystems. In these cases, the use of environmentally benign materials, such as host-specific entomopathogens, can be more...

Toxicity of carbon nanomaterials to plants, animals and microbes: Recent progress from 2015-present.

PubMed

Chen, Ming; Zhou, Shuang; Zhu, Yi; Sun, Yingzhu; Zeng, Guangming; Yang, Chunping; Xu, Piao; Yan, Ming; Liu, Zhifeng; Zhang, Wei

2018-05-04

Nanotechnology has gained significant development over the past decades, which led to the revolution in the fields of information, medicine, industry, food security and aerospace aviation. Nanotechnology has become a new research hot spot in the world. However, we cannot only pay attention to its benefit to the society and economy, because its wide use has been bringing potential environmental and health effects that should be noticed. This paper reviews the recent progress from 2015-present in the toxicity of various carbon nanomaterials to plants, animals and microbes, and lays the foundation for further study on the environmental and ecological risks of carbon nanomaterials. Copyright © 2018 Elsevier Ltd. All rights reserved.

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

Discontinuities, cross-scale patterns, and the organizationof ecosystems

EPA Science Inventory

Ecological structures and processes occur at specific spatiotemporal scales, and interactions that occur across multiple scales mediate scale-specific (e.g., individual,community, local, or regional) responses to disturbance. Despite the importance of scale,explicitly incorporat...

Microbially Mediated Plant Salt Tolerance and Microbiome-based Solutions for Saline Agriculture.

PubMed

Qin, Yuan; Druzhinina, Irina S; Pan, Xueyu; Yuan, Zhilin

2016-11-15

Soil salinization adversely affects plant growth and has become one of the major limiting factors for crop productivity worldwide. The conventional approach, breeding salt-tolerant plant cultivars, has often failed to efficiently alleviate the situation. In contrast, the use of a diverse array of microorganisms harbored by plants has attracted increasing attention because of the remarkable beneficial effects of microorganisms on plants. Multiple advanced '-omics' technologies have enabled us to gain insights into the structure and function of plant-associated microbes. In this review, we first focus on microbe-mediated plant salt tolerance, in particular on the physiological and molecular mechanisms underlying root-microbe symbiosis. Unfortunately, when introducing such microbes as single strains to soils, they are often ineffective in improving plant growth and stress tolerance, largely due to competition with native soil microbial communities and limited colonization efficiency. Rapid progress in rhizosphere microbiome research has revived the belief that plants may benefit more from association with interacting, diverse microbial communities (microbiome) than from individual members in a community. Understanding how a microbiome assembles in the continuous compartments (endosphere, rhizoplane, and rhizosphere) will assist in predicting a subset of core or minimal microbiome and thus facilitate synthetic re-construction of microbial communities and their functional complementarity and synergistic effects. These developments will open a new avenue for capitalizing on the cultivable microbiome to strengthen plant salt tolerance and thus to refine agricultural practices and production under saline conditions. Copyright © 2016 Elsevier Inc. All rights reserved.

Soil microbial communities buffer physiological responses to drought stress in three hardwood species.

PubMed

Kannenberg, Steven A; Phillips, Richard P

2017-03-01

Trees possess myriad adaptations for coping with drought stress, but the extent to which their drought responses are influenced by interactions with soil microbes is poorly understood. To explore the role of microbes in mediating tree responses to drought stress, we exposed saplings of three species (Acer saccharum, Liriodendron tulipifera, and Quercus alba) to a four week experimental drought in mesocosms. Half of the pots were inoculated with a live soil slurry (i.e., a microbial inoculum derived from soils beneath the canopies of mature A. saccharum, L. tulipifera or Q. alba stands), while the other half of the pots received a sterile soil slurry. Soil microbes ameliorated drought stress in L. tulipifera by minimizing reductions in leaf water potential and by reducing photosynthetic declines. In A. saccharum, soil microbes reduced drought stress by lessening declines in leaf water potential, though these changes did not buffer the trees from declining photosynthetic rates. In Q. alba, soil microbes had no effects on leaf physiological parameters during drought stress. In all species, microbes had no significant effects on dynamic C allocation during drought stress, suggesting that microbial effects on plant physiology were unrelated to source-sink dynamics. Collectively, our results suggest that soil microbes have the potential to alter key parameters that are used to diagnose drought sensitivity (i.e., isohydry or anisohydry). To the extent that our results reflect dynamics occurring in forests, a revised perspective on plant hydraulic strategies that considers root-microbe interactions may lead to improved predictions of forest vulnerability to drought.

Using process algebra to develop predator-prey models of within-host parasite dynamics.

PubMed

McCaig, Chris; Fenton, Andy; Graham, Andrea; Shankland, Carron; Norman, Rachel

2013-07-21

As a first approximation of immune-mediated within-host parasite dynamics we can consider the immune response as a predator, with the parasite as its prey. In the ecological literature of predator-prey interactions there are a number of different functional responses used to describe how a predator reproduces in response to consuming prey. Until recently most of the models of the immune system that have taken a predator-prey approach have used simple mass action dynamics to capture the interaction between the immune response and the parasite. More recently Fenton and Perkins (2010) employed three of the most commonly used prey-dependent functional response terms from the ecological literature. In this paper we make use of a technique from computing science, process algebra, to develop mathematical models. The novelty of the process algebra approach is to allow stochastic models of the population (parasite and immune cells) to be developed from rules of individual cell behaviour. By using this approach in which individual cellular behaviour is captured we have derived a ratio-dependent response similar to that seen in the previous models of immune-mediated parasite dynamics, confirming that, whilst this type of term is controversial in ecological predator-prey models, it is appropriate for models of the immune system. Copyright © 2013 Elsevier Ltd. All rights reserved.

Potential for Mercury Reduction by Microbes in the High Arctic▿

PubMed Central

Poulain, Alexandre J.; Ní Chadhain, Sinéad M.; Ariya, Parisa A.; Amyot, Marc; Garcia, Edenise; Campbell, Peter G. C.; Zylstra, Gerben J.; Barkay, Tamar

2007-01-01

The contamination of polar regions due to the global distribution of anthropogenic pollutants is of great concern because it leads to the bioaccumulation of toxic substances, methylmercury among them, in Arctic food chains. Here we present the first evidence that microbes in the high Arctic possess and express diverse merA genes, which specify the reduction of ionic mercury [Hg(II)] to the volatile elemental form [Hg(0)]. The sampled microbial biomass, collected from microbial mats in a coastal lagoon and from the surface of marine macroalgae, was comprised of bacteria that were most closely related to psychrophiles that had previously been described in polar environments. We used a kinetic redox model, taking into consideration photoredox reactions as well as mer-mediated reduction, to assess if the potential for Hg(II) reduction by Arctic microbes can affect the toxicity and environmental mobility of mercury in the high Arctic. Results suggested that mer-mediated Hg(II) reduction could account for most of the Hg(0) that is produced in high Arctic waters. At the surface, with only 5% metabolically active cells, up to 68% of the mercury pool was resolved by the model as biogenic Hg(0). At a greater depth, because of incident light attenuation, the significance of photoredox transformations declined and merA-mediated activity could account for up to 90% of Hg(0) production. These findings highlight the importance of microbial redox transformations in the biogeochemical cycling, and thus the toxicity and mobility, of mercury in polar regions. PMID:17293515

Planetary Evolution and Microbe-Environment Interactions

NASA Technical Reports Server (NTRS)

Mancinelli, Rocco L.

2002-01-01

During the three-year period of this Cooperative Agreement my laboratory conducted physiological and ecological studies regarding the abiotic/biotic relationship in microbial ecosystems. The overall objective of the research performed in the three years of this cooperative agreement is to determine how living systems respond to environmental stress. To accomplish this objective microbes were subjected to a variety of different environmental stresses including decreases in water activity, changes in radiation flux, and nutrient limitation. This research addressees two subsets of the astrobiology questions including: If life arose on early Mars what would have become of it once Mars lost most of its atmosphere and water? and if Earth organisms traveled to Mars what would become of them. To help answer this question we used microbes as model systems not only because they were the first living systems to arise, but also because they are the most likely to be able to withstand a broad range of environmental factors. To meet this objective we conducted laboratory and field work.

Co-occurrence Networks Among Bacteria and Microbial Eukaryotes of Lake Baikal During a Spring Phytoplankton Bloom.

PubMed

Mikhailov, Ivan S; Zakharova, Yulia R; Bukin, Yuri S; Galachyants, Yuri P; Petrova, Darya P; Sakirko, Maria V; Likhoshway, Yelena V

2018-06-07

The pelagic zone of Lake Baikal is an ecological niche where phytoplankton bloom causes increasing microbial abundance in spring which plays a key role in carbon turnover in the freshwater lake. Co-occurrence patterns revealed among different microbes can be applied to predict interactions between the microbes and environmental conditions in the ecosystem. We used 454 pyrosequencing of 16S rRNA and 18S rRNA genes to study bacterial and microbial eukaryotic communities and their co-occurrence patterns at the pelagic zone of Lake Baikal during a spring phytoplankton bloom. We found that microbes within one domain mostly correlated positively with each other and are highly interconnected. The highly connected taxa in co-occurrence networks were operational taxonomic units (OTUs) of Actinobacteria, Bacteroidetes, Alphaproteobacteria, and autotrophic and unclassified Eukaryota which might be analogous to microbial keystone taxa. Constrained correspondence analysis revealed the relationships of bacterial and microbial eukaryotic communities with geographical location.

"Every Gene Is Everywhere but the Environment Selects": Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis.

PubMed

Fondi, Marco; Karkman, Antti; Tamminen, Manu V; Bosi, Emanuele; Virta, Marko; Fani, Renato; Alm, Eric; McInerney, James O

2016-05-13

The spatial distribution of microbes on our planet is famously formulated in the Baas Becking hypothesis as "everything is everywhere but the environment selects." While this hypothesis does not strictly rule out patterns caused by geographical effects on ecology and historical founder effects, it does propose that the remarkable dispersal potential of microbes leads to distributions generally shaped by environmental factors rather than geographical distance. By constructing sequence similarity networks from uncultured environmental samples, we show that microbial gene pool distributions are not influenced nearly as much by geography as ecology, thus extending the Bass Becking hypothesis from whole organisms to microbial genes. We find that gene pools are shaped by their broad ecological niche (such as sea water, fresh water, host, and airborne). We find that freshwater habitats act as a gene exchange bridge between otherwise disconnected habitats. Finally, certain antibiotic resistance genes deviate from the general trend of habitat specificity by exhibiting a high degree of cross-habitat mobility. The strong cross-habitat mobility of antibiotic resistance genes is a cause for concern and provides a paradigmatic example of the rate by which genes colonize new habitats when new selective forces emerge. © The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Nanospecific Inhibition of Pyoverdine Siderophore Production in Pseudomonas Chlororaphis O6 by CuO Nanoparticles

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

Dimkpa, Christian O.; McLean, Joan E.; Britt, David W.

2012-03-01

As traditional antibiotics become less effective against a growing number of pathogens, engineered nanoparticles (NPs) are becoming more widely applied as biocides. NPs of Ag, ZnO, and CuO exhibit dose-dependent antimicrobial activity; however, information is scant on the impact of sublethal levels of NPs on bacteria. In this paper, we evaluated the effect of a sublethal concentration (200 mg/L) of commercial CuO NPs on the expression of genes involved in the production of the fluorescent siderophore, pyoverdine (PVD) in the plant-beneficial bacterium Pseudomonas chlororaphis O6. PVDs are important in microbe-microbe and microbe-plant interactions, and are a virulence factor in pathogenicmore » pseudomonads. Cells challenged with the NPs had reduced amounts of PVD in their periplasm and the external medium. The NPs impaired the expression of genes involved in transport of the PVD precursor through the plasmamembrane, PVD maturation in the periplasm, and export through the outer membrane. Also, expression from one of three predicted Fe-PVD receptors was reduced by the NPs. As these effects were not observed for cells challenged with copper ions, this is a nanoparticlespecific phenomenon mediating cellular reprogramming in bacteria, affecting secondary metabolism and thus associated critical microbial processes. The regulation of bacterial genes and secondary metabolites by sublethal doses of a common metal oxide NP has strong environmental and medical implications.« less

Empirical, Metagenomic, and Computational Techniques Illuminate the Mechanisms by which Fungicides Compromise Bee Health.

PubMed

Steffan, Shawn A; Dharampal, Prarthana S; Diaz-Garcia, Luis; Currie, Cameron R; Zalapa, Juan; Hittinger, Chris Todd

2017-10-09

Growers often use fungicide sprays during bloom to protect crops against disease, which exposes bees to fungicide residues. Although considered "bee-safe," there is mounting evidence that fungicide residues in pollen are associated with bee declines (for both honey and bumble bee species). While the mechanisms remain relatively unknown, researchers have speculated that bee-microbe symbioses are involved. Microbes play a pivotal role in the preservation and/or processing of pollen, which serves as nutrition for larval bees. By altering the microbial community, it is likely that fungicides disrupt these microbe-mediated services, and thereby compromise bee health. This manuscript describes the protocols used to investigate the indirect mechanism(s) by which fungicides may be causing colony decline. Cage experiments exposing bees to fungicide-treated flowers have already provided the first evidence that fungicides cause profound colony losses in a native bumble bee (Bombus impatiens). Using field-relevant doses of fungicides, a series of experiments have been developed to provide a finer description of microbial community dynamics of fungicide-exposed pollen. Shifts in the structural composition of fungal and bacterial assemblages within the pollen microbiome are investigated by next-generation sequencing and metagenomic analysis. Experiments developed herein have been designed to provide a mechanistic understanding of how fungicides affect the microbiome of pollen-provisions. Ultimately, these findings should shed light on the indirect pathway through which fungicides may be causing colony declines.

Skin microbiota and allergic symptoms associate with exposure to environmental microbes

PubMed Central

Sinkko, Hanna; Hielm-Björkman, Anna; Tiira, Katriina; Laatikainen, Tiina; Mäkeläinen, Sanna; Kaukonen, Maria; Uusitalo, Liisa; Hanski, Ilkka; Lohi, Hannes; Ruokolainen, Lasse

2018-01-01

A rural environment and farming lifestyle are known to provide protection against allergic diseases. This protective effect is expected to be mediated via exposure to environmental microbes that are needed to support a normal immune tolerance. However, the triangle of interactions between environmental microbes, host microbiota, and immune system remains poorly understood. Here, we have studied these interactions using a canine model (two breeds, n = 169), providing an intermediate approach between complex human studies and artificial mouse model studies. We show that the skin microbiota reflects both the living environment and the lifestyle of a dog. Remarkably, the prevalence of spontaneous allergies is also associated with residential environment and lifestyle, such that allergies are most common among urban dogs living in single-person families without other animal contacts, and least common among rural dogs having opposite lifestyle features. Thus, we show that living environment and lifestyle concurrently associate with skin microbiota and allergies, suggesting that these factors might be causally related. Moreover, microbes commonly found on human skin tend to dominate the urban canine skin microbiota, while environmental microbes are rich in the rural canine skin microbiota. This in turn suggests that skin microbiota is a feasible indicator of exposure to environmental microbes. As short-term exposure to environmental microbes via exercise is not associated with allergies, we conclude that prominent and sustained exposure to environmental microbiotas should be promoted by urban planning and lifestyle changes to support health of urban populations. PMID:29686089

Skin microbiota and allergic symptoms associate with exposure to environmental microbes.

PubMed

Lehtimäki, Jenni; Sinkko, Hanna; Hielm-Björkman, Anna; Salmela, Elina; Tiira, Katriina; Laatikainen, Tiina; Mäkeläinen, Sanna; Kaukonen, Maria; Uusitalo, Liisa; Hanski, Ilkka; Lohi, Hannes; Ruokolainen, Lasse

2018-05-08

A rural environment and farming lifestyle are known to provide protection against allergic diseases. This protective effect is expected to be mediated via exposure to environmental microbes that are needed to support a normal immune tolerance. However, the triangle of interactions between environmental microbes, host microbiota, and immune system remains poorly understood. Here, we have studied these interactions using a canine model (two breeds, n = 169), providing an intermediate approach between complex human studies and artificial mouse model studies. We show that the skin microbiota reflects both the living environment and the lifestyle of a dog. Remarkably, the prevalence of spontaneous allergies is also associated with residential environment and lifestyle, such that allergies are most common among urban dogs living in single-person families without other animal contacts, and least common among rural dogs having opposite lifestyle features. Thus, we show that living environment and lifestyle concurrently associate with skin microbiota and allergies, suggesting that these factors might be causally related. Moreover, microbes commonly found on human skin tend to dominate the urban canine skin microbiota, while environmental microbes are rich in the rural canine skin microbiota. This in turn suggests that skin microbiota is a feasible indicator of exposure to environmental microbes. As short-term exposure to environmental microbes via exercise is not associated with allergies, we conclude that prominent and sustained exposure to environmental microbiotas should be promoted by urban planning and lifestyle changes to support health of urban populations. Copyright © 2018 the Author(s). Published by PNAS.

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

Construction and screening of marine metagenomic libraries.

PubMed

Weiland, Nancy; Löscher, Carolin; Metzger, Rebekka; Schmitz, Ruth

2010-01-01

Marine microbial communities are highly diverse and have evolved during extended evolutionary processes of physiological adaptations under the influence of a variety of ecological conditions and selection pressures. They harbor an enormous diversity of microbes with still unknown and probably new physiological characteristics. Besides, the surfaces of marine multicellular organisms are typically covered by a consortium of epibiotic bacteria and act as barriers, where diverse interactions between microorganisms and hosts take place. Thus, microbial diversity in the water column of the oceans and the microbial consortia on marine tissues of multicellular organisms are rich sources for isolating novel bioactive compounds and genes. Here we describe the sampling, construction of large-insert metagenomic libraries from marine habitats and exemplarily one function based screen of metagenomic clones.

The human gut microbiome: current knowledge, challenges, and future directions.

PubMed

Dave, Maneesh; Higgins, Peter D; Middha, Sumit; Rioux, Kevin P

2012-10-01

The Human Genome Project was completed a decade ago, leaving a legacy of process, tools, and infrastructure now being turned to the study of the microbes that reside in and on the human body as determinants of health and disease, and has been branded "The Human Microbiome Project." Of the various niches under investigation, the human gut houses the most complex and abundant microbial community and is an arena for important host-microbial interactions that have both local and systemic impact. Initial studies of the human microbiome have been largely descriptive, a testing ground for innovative molecular techniques and new hypotheses. Methods for studying the microbiome have quickly evolved from low-resolution surveys of microbial community structure to high-definition description of composition, function, and ecology. Next-generation sequencing technologies combined with advanced bioinformatics place us at the doorstep of revolutionary insight into the composition, capability, and activity of the human intestinal microbiome. Renewed efforts to cultivate previously "uncultivable" microbes will be important to the overall understanding of gut ecology. There remain numerous methodological challenges to the effective study and understanding of the gut microbiome, largely relating to study design, sample collection, and the number of predictor variables. Strategic collaboration of clinicians, microbiologists, molecular biologists, computational scientists, and bioinformaticians is the ideal paradigm for success in this field. Meaningful interpretation of the gut microbiome requires that host genetic and environmental influences be controlled or accounted for. Understanding the gut microbiome in healthy humans is a foundation for discovering its influence in various important gastrointestinal and nutritional diseases (eg, inflammatory bowel disease, diabetes, and obesity), and for rational translation to human health gains. Copyright © 2012 Mosby, Inc. All rights reserved.

Leaf-Litter Breakdown

EPA Science Inventory

Terrestrial leaves are a major energy source for forested stream ecosystems around the world. Leaves entering streams as litterfall undergo a series of physical and chemical transformations mediated by internal chemistry and the interaction of microbes and invertebrates resulting...

The bee microbiome: impact on bee health and model for evolution and ecology of host-microbe interactions

USDA-ARS?s Scientific Manuscript database

Fanconi anemia (FA) is a rare genetic disorder caused by defects in DNA damage repair. FA patients often develop squamous cell carcinoma (SCC) at sites where high-risk human papillomaviruses (HPVs) are known to cause cancer, including the cervix. However, SCCs found in human FA patients are often HP...

From Attack to Emergence: Interactions between Southern Pine Beetle, Mites, Microbes, and Trees

Treesearch

Kier D. Klepzig; Richard W. Hofstetter

2011-01-01

Bark beetles are among the most ecologically and economically influential organisms in forest ecosystems worldwide. These important organisms are consistently associated in complex symbioses with fungi. Despite this, little is known of the net impacts of the fungi on their vectors, and mites are often completely overlooked. In this chapter, we will describe...

Geometry and mechanics of growing bacterial colonies

NASA Astrophysics Data System (ADS)

You, Zhihong; Pearce, Daniel; Sengupta, Anupam; Giomi, Luca

Bacterial colonies are abundant on living and non-living surfaces, and are known to mediate a broad range of processes in ecology, medicine and industry. Although extensively researched - from single cells up to the population levels - a comprehensive biophysical picture, highlighting the cell-to-colony dynamics, is still lacking. Here, using numerical and analytical models, we study the mechanics of self-organization leading to the colony morphology of cells growing on a substrate with free boundary. We consider hard rods to mimic the growth of rod-shaped non-motile cells, and show that the colony, as a whole, does not form an ordered nematic phase, nor does it result in a purely disordered (isotropic) phase. Instead, different sizes of domains, in which cells are highly aligned at specific orientations, are found. The distribution of the domain sizes follows an exponential relation - indicating the existence of a characteristic length scale that determines the domain size relative to that of the colony. A continuum theory, based on the hydrodynamics of liquid crystals, is built to account for these phenomena, and is applied to describe the buckling transition from a planar to three-dimensional (3D) colony. The theory supports preliminary experiments conducted with different strains of rod shaped bacterial cells, and reveals that the buckling transition can be regulated by varying the cell stiffness and aspect ratio. This work proposes that, in addition to biochemical pathways, the spatio-temporal organization in microbial colonies is significantly tuned by the biomechanical and geometric properties of the microbes in consideration.

Evolutionary engineering for industrial microbiology.

PubMed

Vanee, Niti; Fisher, Adam B; Fong, Stephen S

2012-01-01

Superficially, evolutionary engineering is a paradoxical field that balances competing interests. In natural settings, evolution iteratively selects and enriches subpopulations that are best adapted to a particular ecological niche using random processes such as genetic mutation. In engineering desired approaches utilize rational prospective design to address targeted problems. When considering details of evolutionary and engineering processes, more commonality can be found. Engineering relies on detailed knowledge of the problem parameters and design properties in order to predict design outcomes that would be an optimized solution. When detailed knowledge of a system is lacking, engineers often employ algorithmic search strategies to identify empirical solutions. Evolution epitomizes this iterative optimization by continuously diversifying design options from a parental design, and then selecting the progeny designs that represent satisfactory solutions. In this chapter, the technique of applying the natural principles of evolution to engineer microbes for industrial applications is discussed to highlight the challenges and principles of evolutionary engineering.

Getting the Hologenome Concept Right: an Eco-Evolutionary Framework for Hosts and Their Microbiomes.

PubMed

Theis, Kevin R; Dheilly, Nolwenn M; Klassen, Jonathan L; Brucker, Robert M; Baines, John F; Bosch, Thomas C G; Cryan, John F; Gilbert, Scott F; Goodnight, Charles J; Lloyd, Elisabeth A; Sapp, Jan; Vandenkoornhuyse, Philippe; Zilber-Rosenberg, Ilana; Rosenberg, Eugene; Bordenstein, Seth R

2016-01-01

Given the complexity of host-microbiota symbioses, scientists and philosophers are asking questions at new biological levels of hierarchical organization-what is a holobiont and hologenome? When should this vocabulary be applied? Are these concepts a null hypothesis for host-microbe systems or limited to a certain spectrum of symbiotic interactions such as host-microbial coevolution? Critical discourse is necessary in this nascent area, but productive discourse requires that skeptics and proponents use the same lexicon. For instance, critiquing the hologenome concept is not synonymous with critiquing coevolution, and arguing that an entity is not a primary unit of selection dismisses the fact that the hologenome concept has always embraced multilevel selection. Holobionts and hologenomes are incontrovertible, multipartite entities that result from ecological, evolutionary, and genetic processes at various levels. They are not restricted to one special process but constitute a wider vocabulary and framework for host biology in light of the microbiome.

Aboveground-belowground biodiversity linkages differ in early and late successional temperate forests

PubMed Central

Li, Hui; Wang, Xugao; Liang, Chao; Hao, Zhanqing; Zhou, Lisha; Ma, Sam; Li, Xiaobin; Yang, Shan; Yao, Fei; Jiang, Yong

2015-01-01

Understanding ecological linkages between above- and below-ground biota is critical for deepening our knowledge on the maintenance and stability of ecosystem processes. Nevertheless, direct comparisons of plant-microbe diversity at the community level remain scarce due to the knowledge gap between microbial ecology and plant ecology. We compared the α- and β- diversities of plant and soil bacterial communities in two temperate forests that represented early and late successional stages. We documented different patterns of aboveground-belowground diversity relationships in these forests. We observed no linkage between plant and bacterial α-diversity in the early successional forest, and even a negative correlation in the late successional forest, indicating that high bacterial α-diversity is not always linked to high plant α-diversity. Beta-diversity coupling was only found at the late successional stage, while in the early successional forest, the bacterial β-diversity was closely correlated with soil property distances. Additionally, we showed that the dominant competitive tree species in the late successional forest may play key roles in driving forest succession by shaping the soil bacterial community in the early successional stage. This study sheds new light on the potential aboveground-belowground linkage in natural ecosystems, which may help us understand the mechanisms that drive ecosystem succession. PMID:26184121

Microbial ecology of extreme environments: Antarctic yeasts and growth in substrate-limited habitats

NASA Technical Reports Server (NTRS)

Vishniac, H. S.

1984-01-01

An extreme environment is by definition one with a depauperate biota. While the Ross Desert is by no means homogeneous, the most exposed and arid habitats, soils in the unglaciated high valleys, do indeed contain a very sparse biota of low diversity. So sparse that the natives could easily be outnumbered by airborne exogenous microbes. Native biota must be capable of overwintering as well as growing in the high valley summer. Tourists may undergo a few divisions before contributing their enzymes and, ultimately, elements to the soil - or may die before landing. The simplest way to demonstrate the indigenicity of a particular microbe is therefore to establish unique distribution; occurrence only in the habitat in question precludes foreign origin.

Resource conflict and cooperation between human host and gut microbiota: implications for nutrition and health.

PubMed

Wasielewski, Helen; Alcock, Joe; Aktipis, Athena

2016-05-01

Diet has been known to play an important role in human health since at least the time period of the ancient Greek physician Hippocrates. In the last decade, research has revealed that microorganisms inhabiting the digestive tract, known as the gut microbiota, are critical factors in human health. This paper draws on concepts of cooperation and conflict from ecology and evolutionary biology to make predictions about host-microbiota interactions involving nutrients. To optimally extract energy from some resources (e.g., fiber), hosts require cooperation from microbes. Other nutrients can be utilized by both hosts and microbes (e.g., simple sugars, iron) in their ingested form, which may lead to greater conflict over these resources. This framework predicts that some negative health effects of foods are driven by the direct effects of these foods on human physiology and by indirect effects resulting from microbiome-host competition and conflict (e.g., increased invasiveness and inflammation). Similarly, beneficial effects of some foods on host health may be enhanced by resource sharing and other cooperative behaviors between host and microbes that may downregulate inflammation and virulence. Given that some foods cultivate cooperation between hosts and microbes while others agitate conflict, host-microbe interactions may be novel targets for interventions aimed at improving nutrition and human health. © 2016 The Authors. Annals of the New York Academy of Sciences published by Wiley Periodicals, Inc. on behalf of New York Academy of Sciences.

Schrödinger's microbes: Tools for distinguishing the living from the dead in microbial ecosystems.

PubMed

Emerson, Joanne B; Adams, Rachel I; Román, Clarisse M Betancourt; Brooks, Brandon; Coil, David A; Dahlhausen, Katherine; Ganz, Holly H; Hartmann, Erica M; Hsu, Tiffany; Justice, Nicholas B; Paulino-Lima, Ivan G; Luongo, Julia C; Lymperopoulou, Despoina S; Gomez-Silvan, Cinta; Rothschild-Mancinelli, Brooke; Balk, Melike; Huttenhower, Curtis; Nocker, Andreas; Vaishampayan, Parag; Rothschild, Lynn J

2017-08-16

While often obvious for macroscopic organisms, determining whether a microbe is dead or alive is fraught with complications. Fields such as microbial ecology, environmental health, and medical microbiology each determine how best to assess which members of the microbial community are alive, according to their respective scientific and/or regulatory needs. Many of these fields have gone from studying communities on a bulk level to the fine-scale resolution of microbial populations within consortia. For example, advances in nucleic acid sequencing technologies and downstream bioinformatic analyses have allowed for high-resolution insight into microbial community composition and metabolic potential, yet we know very little about whether such community DNA sequences represent viable microorganisms. In this review, we describe a number of techniques, from microscopy- to molecular-based, that have been used to test for viability (live/dead determination) and/or activity in various contexts, including newer techniques that are compatible with or complementary to downstream nucleic acid sequencing. We describe the compatibility of these viability assessments with high-throughput quantification techniques, including flow cytometry and quantitative PCR (qPCR). Although bacterial viability-linked community characterizations are now feasible in many environments and thus are the focus of this critical review, further methods development is needed for complex environmental samples and to more fully capture the diversity of microbes (e.g., eukaryotic microbes and viruses) and metabolic states (e.g., spores) of microbes in natural environments.

Some Ecological Mechanisms to Generate Habitability in Planetary Subsurface Areas by Chemolithotrophic Communities: The Ro Tinto Subsurface Ecosystem as a Model System

NASA Astrophysics Data System (ADS)

Fernández-Remolar, David C.; Gómez, Felipe; Prieto-Ballesteros, Olga; Schelble, Rachel T.; Rodríguez, Nuria; Amiols, Ricardo

2008-02-01

Chemolithotrophic communities that colonize subsurface habitats have great relevance for the astrobiological exploration of our Solar System. We hypothesize that the chemical and thermal stabilization of an environment through microbial activity could make a given planetary region habitable. The MARTE project ground-truth drilling campaigns that sampled cryptic subsurface microbial communities in the basement of the Ro Tinto headwaters have shown that acidic surficial habitats are the result of the microbial oxidation of pyritic ores. The oxidation process is exothermic and releases heat under both aerobic and anaerobic conditions. These microbial communities can maintain the subsurface habitat temperature through storage heat if the subsurface temperature does not exceed their maximum growth temperature. In the acidic solutions of the Ro Tinto, ferric iron acts as an effective buffer for controlling water pH. Under anaerobic conditions, ferric iron is the oxidant used by microbes to decompose pyrite through the production of sulfate, ferrous iron, and protons. The integration between the physical and chemical processes mediated by microorganisms with those driven by the local geology and hydrology have led us to hypothesize that thermal and chemical regulation mechanisms exist in this environment and that these homeostatic mechanisms could play an essential role in creating habitable areas for other types of microorganisms. Therefore, searching for the physicochemical expression of extinct and extant homeostatic mechanisms through physical and chemical anomalies in the Mars crust (i.e., local thermal gradient or high concentration of unusual products such as ferric sulfates precipitated out from acidic solutions produced by hypothetical microbial communities) could be a first step in the search for biological traces of a putative extant or extinct Mars biosphere.

Some ecological mechanisms to generate habitability in planetary subsurface areas by chemolithotrophic communities: the Río Tinto subsurface ecosystem as a model system.

PubMed

Fernández-Remolar, David C; Gómez, Felipe; Prieto-Ballesteros, Olga; Schelble, Rachel T; Rodríguez, Nuria; Amils, Ricardo

2008-02-01

Chemolithotrophic communities that colonize subsurface habitats have great relevance for the astrobiological exploration of our Solar System. We hypothesize that the chemical and thermal stabilization of an environment through microbial activity could make a given planetary region habitable. The MARTE project ground-truth drilling campaigns that sampled cryptic subsurface microbial communities in the basement of the Río Tinto headwaters have shown that acidic surficial habitats are the result of the microbial oxidation of pyritic ores. The oxidation process is exothermic and releases heat under both aerobic and anaerobic conditions. These microbial communities can maintain the subsurface habitat temperature through storage heat if the subsurface temperature does not exceed their maximum growth temperature. In the acidic solutions of the Río Tinto, ferric iron acts as an effective buffer for controlling water pH. Under anaerobic conditions, ferric iron is the oxidant used by microbes to decompose pyrite through the production of sulfate, ferrous iron, and protons. The integration between the physical and chemical processes mediated by microorganisms with those driven by the local geology and hydrology have led us to hypothesize that thermal and chemical regulation mechanisms exist in this environment and that these homeostatic mechanisms could play an essential role in creating habitable areas for other types of microorganisms. Therefore, searching for the physicochemical expression of extinct and extant homeostatic mechanisms through physical and chemical anomalies in the Mars crust (i.e., local thermal gradient or high concentration of unusual products such as ferric sulfates precipitated out from acidic solutions produced by hypothetical microbial communities) could be a first step in the search for biological traces of a putative extant or extinct Mars biosphere.

Carbonic anhydrase distribution across organisms and environments: genomic predictors for soil enzymatic fluxes of carbon cycle tracers δ18O and COS

NASA Astrophysics Data System (ADS)

Meredith, L. K.; Singer, E.

2016-12-01

Carbonyl sulfide (COS) and the oxygen isotope composition (δ18O) of CO2 are potential tools for differentiating the contributions of photosynthesis and respiration to the balance of global carbon cycling. These processes are coupled at the leaf level via the enzyme carbonic anhydrase (CA), which hydrolyzes CO2 in the first biochemical step of the photosynthetic pathway (CO2 + H2O ⇌ HCO3- + H+) and correspondingly structural analogue COS (COS + H2O → CO2 + H2S). CA also accelerates the exchange of oxygen isotopes between CO2 and H2O leading to a distinct isotopic imprint. The biogeochemical cycles of these tracers include significant, yet poorly characterized soil processes that challenge their utility for probing the carbon cycle. In soils, microbial CA also hydrolyze COS and accelerate O isotope exchange between CO2 and soil water. Genomic predictors of microbial CA activity may help account and predict for these soil fluxes. Using a bioinformatics approach, we assess the distribution of the six known CA classes (α, β, γ, δ, η, ζ) in organisms ranging from fungi and plants to archaea and bacteria, and ask whether CA diversity is linked to soil microbial diversity. We survey the diversity and relative abundance of CA in a wide variety of environments and estimate the sensitivity of CA to biome and land use. Finally, we compare the CA distribution in soils to measurements (oxygen isotope and COS fluxes) and models of CA activity to develop genomic predictors for CA activity. This work provides the first survey of CA in soils, a step towards understanding the significant role of CA in microbial ecology and microbe-mediated biogeochemical cycles.

Identifying microbial habitats in soil using quantum dots and x-ray fluorescence microtomography

NASA Astrophysics Data System (ADS)

O'Brien, S. L.; Whiteside, M. D.; Sholto-Douglas, D.; Dohnalkova, A.; Durall, D. M.; Gursoy, D.; Jones, M. D.; Kovarik, L.; Lai, B.; Roehrig, C.; Sullivan, S.; Vogt, S.; Kemner, K. M.

2015-12-01

The metabolic activities of soil microbes are the primary drivers of biogeochemical processes controlling the terrestrial carbon cycle, nutrient availability to plants, contaminant remediation, water quality, and other ecosystem services. However, we have a limited understanding of microbial metabolic processes such as nutrient uptake rates, substrate preferences, or how microbes and microbial metabolism are distributed throughout the three-dimensional pore network of the soil. Here we use a novel combination of imaging techniques with quantum dots (QDs, engineered semiconductor nanoparticles that produce size or composition-dependent fluorescence) to locate bacteria in the three-dimensional pore network of a soil aggregate. First, we show using confocal and aberration-corrected transmission electron microscopies that bacteria (Bacillus subtilis, Pseudomonas fluorescens, and Pseudomonas protogens) actively take up and internalize CdSe/ZnS core/shell QDs conjugated to biologically relevant substrates. Next, we show that cells bearing QDs can be identified using fluorescence imaging with hard x-rays at 2ID-D at the Advanced Photon Source (APS). Finally, we demonstrate that the Se constituent to the QDs can be used to label bacteria in three-dimensional tomographic reconstructions of natural soil at 0.5 nm spatial resolution using hard x-rays at 2ID-E at the APS. This is the first time soil bacteria have been imaged in the intact soil matrix at such high resolution. These results offer a new way to experimentally investigate basic bacterial ecology in situ, revealing constraints on microbial function in soil that will help improve connections between pore-scale and ecosystem-scale processes in models.

Evidence of Unique and Generalist Microbes in Distantly Related Sympatric Intertidal Marine Sponges (Porifera: Demospongiae)

PubMed Central

Alex, Anoop; Silva, Vitor; Vasconcelos, Vitor; Antunes, Agostinho

2013-01-01

The diversity and specificity of microbial communities in marine environments is a key aspect of the ecology and evolution of both the eukaryotic hosts and their associated prokaryotes. Marine sponges harbor phylogenetically diverse and complex microbial lineages. Here, we investigated the sponge bacterial community and distribution patterns of microbes in three sympatric intertidal marine demosponges, Hymeniacidon perlevis, Ophlitaspongia papilla and Polymastia penicillus, from the Atlantic coast of Portugal using classical isolation techniques and 16S rRNA gene clone libraries. Microbial composition assessment, with nearly full-length 16S rRNA gene sequences (ca. 1400 bp) from the isolates (n = 31) and partial sequences (ca. 280 bp) from clone libraries (n = 349), revealed diverse bacterial communities and other sponge-associated microbes. The majority of the bacterial isolates were members of the order Vibrionales and other symbiotic bacteria like Pseudovibrio ascidiaceiocola, Roseobacter sp., Hahellaceae sp. and Cobetia sp. Extended analyses using ecological metrics comprising 142 OTUs supported the clear differentiation of bacterial community profiles among the sponge hosts and their ambient seawater. Phylogenetic analyses were insightful in defining clades representing shared bacterial communities, particularly between H. perlevis and the geographically distantly-related H. heliophila, but also among other sponges. Furthermore, we also observed three distinct and unique bacterial groups, Betaproteobactria (∼81%), Spirochaetes (∼7%) and Chloroflexi (∼3%), which are strictly maintained in low-microbial-abundance host species O. papilla and P. penicillus. Our study revealed the largely generalist nature of microbial associations among these co-occurring intertidal marine sponges. PMID:24265835

Teleosts as Model Organisms To Understand Host-Microbe Interactions.

PubMed

Lescak, Emily A; Milligan-Myhre, Kathryn C

2017-08-01

Host-microbe interactions are influenced by complex host genetics and environment. Studies across animal taxa have aided our understanding of how intestinal microbiota influence vertebrate development, disease, and physiology. However, traditional mammalian studies can be limited by the use of isogenic strains, husbandry constraints that result in small sample sizes and limited statistical power, reliance on indirect characterization of gut microbial communities from fecal samples, and concerns of whether observations in artificial conditions are actually reflective of what occurs in the wild. Fish models are able to overcome many of these limitations. The extensive variation in the physiology, ecology, and natural history of fish enriches studies of the evolution and ecology of host-microbe interactions. They share physiological and immunological features common among vertebrates, including humans, and harbor complex gut microbiota, which allows identification of the mechanisms driving microbial community assembly. Their accelerated life cycles and large clutch sizes and the ease of sampling both internal and external microbial communities make them particularly well suited for robust statistical studies of microbial diversity. Gnotobiotic techniques, genetic manipulation of the microbiota and host, and transparent juveniles enable novel insights into mechanisms underlying development of the digestive tract and disease states. Many diseases involve a complex combination of genes which are difficult to manipulate in homogeneous model organisms. By taking advantage of the natural genetic variation found in wild fish populations, as well as of the availability of powerful genetic tools, future studies should be able to identify conserved genes and pathways that contribute to human genetic diseases characterized by dysbiosis. Copyright © 2017 Lescak and Milligan-Myhre.

Teleosts as Model Organisms To Understand Host-Microbe Interactions

PubMed Central

2017-01-01

ABSTRACT Host-microbe interactions are influenced by complex host genetics and environment. Studies across animal taxa have aided our understanding of how intestinal microbiota influence vertebrate development, disease, and physiology. However, traditional mammalian studies can be limited by the use of isogenic strains, husbandry constraints that result in small sample sizes and limited statistical power, reliance on indirect characterization of gut microbial communities from fecal samples, and concerns of whether observations in artificial conditions are actually reflective of what occurs in the wild. Fish models are able to overcome many of these limitations. The extensive variation in the physiology, ecology, and natural history of fish enriches studies of the evolution and ecology of host-microbe interactions. They share physiological and immunological features common among vertebrates, including humans, and harbor complex gut microbiota, which allows identification of the mechanisms driving microbial community assembly. Their accelerated life cycles and large clutch sizes and the ease of sampling both internal and external microbial communities make them particularly well suited for robust statistical studies of microbial diversity. Gnotobiotic techniques, genetic manipulation of the microbiota and host, and transparent juveniles enable novel insights into mechanisms underlying development of the digestive tract and disease states. Many diseases involve a complex combination of genes which are difficult to manipulate in homogeneous model organisms. By taking advantage of the natural genetic variation found in wild fish populations, as well as of the availability of powerful genetic tools, future studies should be able to identify conserved genes and pathways that contribute to human genetic diseases characterized by dysbiosis. PMID:28439034

Metabolic reconfigurations aimed at the detoxification of a multi-metal stress in Pseudomonas fluorescens: implications for the bioremediation of metal pollutants.

PubMed

Alhasawi, Azhar; Costanzi, Jacob; Auger, Christopher; Appanna, Nishma D; Appanna, Vasu D

2015-04-20

Although the ability of microbial systems to adapt to the toxic challenge posed by numerous metal pollutants individually has been well documented, there is little detailed information on how bacteria survive in a multiple-metal environment. Here we describe the metabolic reconfiguration invoked by the soil microbe Pseudomonas fluorescens in a medium with millimolar amounts of aluminum (Al), iron (Fe), gallium (Ga), calcium (Ca), and zinc (Zn). While enzymes involved in the production of NADH were decreased, there was a marked increase in enzymatic activities dedicated to NADPH formation. A modified tricarboxylic acid (TCA) cycle coupled to an alternate glyoxylate shunt mediated the synthesis of adenosine triphosphate (ATP) with the concomitant generation of oxalate. This dicarboxylic acid was a key ingredient in the sequestration of the metals that were detoxified as a lipid complex. It appears that the microbe favors this strategy as opposed to a detoxification process aimed at each metal separately. These findings have interesting implications for bioremediation technologies. Copyright © 2015 Elsevier B.V. All rights reserved.

Leaf-Cutter Ant Fungus Gardens Are Biphasic Mixed Microbial Bioreactors That Convert Plant Biomass to Polyols with Biotechnological Applications

PubMed Central

Somera, Alexandre F.; Lima, Adriel M.; dos Santos-Neto, Álvaro J.; Lanças, Fernando M.

2015-01-01

Leaf-cutter ants use plant matter to culture the obligate mutualistic basidiomycete Leucoagaricus gongylophorus. This fungus mediates ant nutrition on plant resources. Furthermore, other microbes living in the fungus garden might also contribute to plant digestion. The fungus garden comprises a young sector with recently incorporated leaf fragments and an old sector with partially digested plant matter. Here, we show that the young and old sectors of the grass-cutter Atta bisphaerica fungus garden operate as a biphasic solid-state mixed fermenting system. An initial plant digestion phase occurred in the young sector in the fungus garden periphery, with prevailing hemicellulose and starch degradation into arabinose, mannose, xylose, and glucose. These products support fast microbial growth but were mostly converted into four polyols. Three polyols, mannitol, arabitol, and inositol, were secreted by L. gongylophorus, and a fourth polyol, sorbitol, was likely secreted by another, unidentified, microbe. A second plant digestion phase occurred in the old sector, located in the fungus garden core, comprising stocks of microbial biomass growing slowly on monosaccharides and polyols. This biphasic operation was efficient in mediating symbiotic nutrition on plant matter: the microbes, accounting for 4% of the fungus garden biomass, converted plant matter biomass into monosaccharides and polyols, which were completely consumed by the resident ants and microbes. However, when consumption was inhibited through laboratory manipulation, most of the plant polysaccharides were degraded, products rapidly accumulated, and yields could be preferentially switched between polyols and monosaccharides. This feature might be useful in biotechnology. PMID:25911490

Leaf-cutter ant fungus gardens are biphasic mixed microbial bioreactors that convert plant biomass to polyols with biotechnological applications.

PubMed

Somera, Alexandre F; Lima, Adriel M; Dos Santos-Neto, Álvaro J; Lanças, Fernando M; Bacci, Maurício

2015-07-01

Leaf-cutter ants use plant matter to culture the obligate mutualistic basidiomycete Leucoagaricus gongylophorus. This fungus mediates ant nutrition on plant resources. Furthermore, other microbes living in the fungus garden might also contribute to plant digestion. The fungus garden comprises a young sector with recently incorporated leaf fragments and an old sector with partially digested plant matter. Here, we show that the young and old sectors of the grass-cutter Atta bisphaerica fungus garden operate as a biphasic solid-state mixed fermenting system. An initial plant digestion phase occurred in the young sector in the fungus garden periphery, with prevailing hemicellulose and starch degradation into arabinose, mannose, xylose, and glucose. These products support fast microbial growth but were mostly converted into four polyols. Three polyols, mannitol, arabitol, and inositol, were secreted by L. gongylophorus, and a fourth polyol, sorbitol, was likely secreted by another, unidentified, microbe. A second plant digestion phase occurred in the old sector, located in the fungus garden core, comprising stocks of microbial biomass growing slowly on monosaccharides and polyols. This biphasic operation was efficient in mediating symbiotic nutrition on plant matter: the microbes, accounting for 4% of the fungus garden biomass, converted plant matter biomass into monosaccharides and polyols, which were completely consumed by the resident ants and microbes. However, when consumption was inhibited through laboratory manipulation, most of the plant polysaccharides were degraded, products rapidly accumulated, and yields could be preferentially switched between polyols and monosaccharides. This feature might be useful in biotechnology. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Composition and functional diversity of microbial community across a mangrove-inhabited mudflat as revealed by 16S rDNA gene sequences.

PubMed

Zhang, Xiaoying; Hu, Bill X; Ren, Hejun; Zhang, Jin

2018-08-15

The gradient distribution of microbial communities has been detected in profiles along many natural environments. In a mangrove seedlings inhabited mudflat, the microbes drive a variety of biogeochemical processes and are associated with a dramatically changed environment across the tidal zones of mudflat. A better understanding of microbial composition, diversity and associated functional profiles in relation to physicochemical influences could provide more insights into the ecological functions of microbes in a coastal mangrove ecosystem. In this study, the variation of microbial community along successive tidal flats inhabited by mangrove seedlings were characterized based on the 16S rDNA gene sequences, and then the factors that shape the bacterial and archaeal communities were determined. Results showed that the tidal cycles strongly influence the distribution of bacterial and archaeal communities. Dissimilarity and gradient distribution of microbial communities were found among high tidal flat, mid-low tidal flat and seawater. Discrepancies were also as well observed from the surface to subsurface layers specifically in the high tidal flat. For example, Alphaproteobacteria displayed an increasing trend from low tidal to high tidal flat and vice versa for Deltaproteobacteria; Cyanobacteria and Thaumarchaeota were more dominant in the surface layer than the subsurface. In addition, by classifying the microorganisms into metabolic functional groups, we were able to identify the biogeochemical pathway that was dominant in each zone. The (oxygenic) photoautotrophy and nitrate reduction were enhanced in the mangrove inhabited mid tidal flat. It revealed the ability of xenobiotic metabolism microbes to degrade, transform, or accumulate environmental hydrocarbon pollutants in seawater, increasing sulfur-related respiration from high tidal to low tidal flat. An opposite distribution was found for major nitrogen cycling processes. The shift of both composition and function of microbial communities were significantly related to light, oxygen availability and total dissolved nitrogen instead of sediment types or salinity. Copyright © 2018 Elsevier B.V. All rights reserved.

Built-up resilience to climate change in peatlands

NASA Astrophysics Data System (ADS)

Wang, H.; Tian, J.; Ho, M.; Flanagan, N. E.; Vilgalys, R.; Richardson, C. J.

2017-12-01

Peatlands have stored about 30% of global soil carbon over millennia. Most studies suggest that climate change effects, like drought and warming, may decrease C sequestration and increase C loss in peatlands, thus resulting in a positive feedback on climate change. However, the long-term feedback between plant-microbe mediated carbon processes and climate change still remains highly uncertain. Here, we conducted a series of field and lab experiments in southern shrub and northern Sphagnum peatlands to document how previously unrecognized mechanisms regulate the buildup of anti-microbial phenolics, which protects stored carbon directly by reducing phenol oxidase activity during short-term drought, and indirectly through a shift from low-phenolics Sphagnum/herbs to high-phenolics shrubs after long-term moderate drought. We further showed a symbiosis of slow-growing decomposers concomitant with a shift of high-phenolic plants, which increased peat resistance to disturbance. Our results indicate that shrub expansion induced by climate change in boreal peatlands may be a long-term self-adaptive mechanism not only increasing carbon sequestration, but also potentially protecting soil carbon. Therefore, peatlands are highly resilient ecosystems in which the symbiotic adaption of both plants and microbes, triggered by persistent climate change, likely can acclimate to the stressors and maintain their carbon sequestration function and processes.

Anaerobic oxidation of methane: an “active” microbial process

PubMed Central

Cui, Mengmeng; Ma, Anzhou; Qi, Hongyan; Zhuang, Xuliang; Zhuang, Guoqiang

2015-01-01

The anaerobic oxidation of methane (AOM) is an important sink of methane that plays a significant role in global warming. AOM was first found to be coupled with sulfate reduction and mediated by anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB). ANME, often forming consortia with SRB, are phylogenetically related to methanogenic archaea. ANME-1 is even able to produce methane. Subsequently, it has been found that AOM can also be coupled with denitrification. The known microbes responsible for this process are Candidatus Methylomirabilis oxyfera (M. oxyfera) and Candidatus Methanoperedens nitroreducens (M. nitroreducens). Candidatus Methylomirabilis oxyfera belongs to the NC10 bacteria, can catalyze nitrite reduction through an “intra-aerobic” pathway, and may catalyze AOM through an aerobic methane oxidation pathway. However, M. nitroreducens, which is affiliated with ANME-2d archaea, may be able to catalyze AOM through the reverse methanogenesis pathway. Moreover, manganese (Mn4+) and iron (Fe3+) can also be used as electron acceptors of AOM. This review summarizes the mechanisms and associated microbes of AOM. It also discusses recent progress in some unclear key issues about AOM, including ANME-1 in hypersaline environments, the effect of oxygen on M. oxyfera, and the relationship of M. nitroreducens with ANME. PMID:25530008

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 worldwide. PMID:18301735

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 ecosystems worldwide.

Stress-free microbes lack vitality.

PubMed

Hallsworth, John E

2018-06-01

Stress is an inextricable aspect of life, and stress biology has been a field of intensive study over the last 200-300 years. In human psychology, we consider a stress-free condition to be one of relaxation or happiness, yet with respect to microbial cells we do not have a concept that describes being non-stressed. Stresses within, and stress tolerance of, microbial systems lie at the crux of critical global challenges, such as optimising soil- and plant-health and crop yields; reducing food spoilage; bioremediation of polluted environments; effective biological control and biofuel production; gaining insight into aging processes in humans; and understanding astrobiology. There is no consensus on how to measure cellular stress, or even how we define it. 'Stress' implies that physical forces act on the microbial system in such a way that impairs its ability to function. Ironically, however, a cell that exhibits optimal growth also has reduced energy generation, is less resilient to change, and can have poor competitive ability. Furthermore, rapid growth is associated with a high level of oxidative damage and compromised vitality of the system. Stresses induced by temperature, pH, water activity, chaotropicity, reactive oxygen species, dehydration-rehydration cycles, ionizing radiation, and changes in turgor or other mechanical forces are well-known. Our knowledge of cellular stress responses, such as signal-transduction pathways, compatible-solute metabolism, protein-stabilization proteins, and plasma-membrane adaptations, is also considerable. However, we have limited understanding of the complex and dynamic stresses that typically occur in microbial habitats or industrial systems, and how these impact the biophysics, cellular biology and evolutionary trajectories of microbes. There is also a paucity of information on why the cellular system ultimately fails under extremes of stress, and it is even debatable whether any microbe can ever be completely stress-free. However, cells that exhibit optimal rates of biotic activity are likely to exhibit low ecological fitness compared with those that are moderately stressed; in other words, stress can enhance microbial vitality, vigour and resilience. 'Stress' is sometimes applied mistakenly to describe the effects of toxic substances that have target site-specific modes-of-action (e.g. antibiotics) rather than and do not inhibit the cell via any type of stress-mediated mechanism. Whereas terms such as 'rapid-growth stress', 'nutrient stress' and 'biotic stress' span a range of logical categories, their modes-of-action do usually involve a biophysical component. Stress can impact all levels of biology (from biomacromolecules to ecosystems), is a potent driver for evolutionary processes and - it could be argued - is an inherent property of life itself. The published articles that follow include a number of unprecedented findings and were compiled for this special issue Biology of Fungal Systems under Stress. Collectively, they are testament to the breadth and importance of the stress-biology field. Copyright © 2018. Published by Elsevier Ltd.

Combinations of biocontrol agents for management of plant-parasitic nematodes and soilborne plant-pathogenic fungi.

PubMed

Meyer, Susan L F; Roberts, Daniel P

2002-03-01

Numerous microbes are antagonistic to plant-parasitic nematodes and soilborne plant-pathogenic fungi, but few of these organisms are commercially available for management of these pathogens. Inconsistent performance of applied biocontrol agents has proven to be a primary obstacle to the development of successful commercial products. One of the strategies for overcoming inconsistent performance is to combine the disease-suppressive activity of two (or more) beneficial microbes in a biocontrol preparation. Such combinations have potential for more extensive colonization of the rhizosphere, more consistent expression of beneficial traits under a broad range of soil conditions, and antagonism to a larger number of plant pests or pathogens than strains applied individually. Conversely, microbes applied in combination also may have antagonistic interactions with each other. Increased, decreased, and unaltered suppression of the target pathogen or pest has been observed when biocontrol microbes have been applied in combination. Unfortunately, the ecological basis for increased or decreased suppression has not been determined in many cases and needs further consideration. The complexity of interactions involved in the application of multiple organisms for biological control has slowed progress toward development of successful formulations. However, this approach has potential for overcoming some of the efficacy problems that occur with application of individual biocontrol agents.

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.

Convergence of External Crohn’s Disease Risk Factors on Intestinal Bacteria

PubMed Central

Oberc, Alexander; Coombes, Brian K.

2015-01-01

Crohn’s disease (CD) is an immune-mediated intestinal illness that significantly compromises health in many developed countries. Although definitive causes remain elusive, the required contribution of microbes in the progression of disease has become an accepted concept. Known CD risk factors, such as antibiotic use and acute infectious gastroenteritis, may impact the gut. This concept is now being explored with a view toward understanding the beneficial and unfavorable microbes that may be altered in numbers during such external insults. A comprehensive understanding of the microbial component to CD could be useful clinically as future therapies may focus on preventing risk exposures on susceptible individuals, eliminating harmful microbes, or restoring a protective gut microbiome. Here, we examine how acute infectious gastroenteritis and antibiotic exposure may impact the gut microbiota in the context of inflammation in CD. PMID:26579131

Halogenated solvent remediation

DOEpatents

Sorenson, Kent S.

2004-08-31

Methods for enhancing bioremediation of ground water contaminated with nonaqueous halogenated solvents are disclosed. A preferred method includes adding a composition to the ground water wherein the composition is an electron donor for microbe-mediated reductive dehalogenation of the halogenated solvents and enhances mass transfer of the halogenated solvents from residual source areas into the aqueous phase of the ground water. Illustrative compositions effective in these methods include surfactants such as C.sub.2 -C.sub.4 carboxylic acids and hydroxy acids, salts thereof, esters of C.sub.2 -C.sub.4 carboxylic acids and hydroxy acids, and mixtures thereof. Especially preferred compositions for use in these methods include lactic acid, salts of lactic acid, such as sodium lactate, lactate esters, and mixtures thereof. The microbes are either indigenous to the ground water, or such microbes can be added to the ground water in addition to the composition.

Developing and using artificial soils to analyze soil microbial processes

NASA Astrophysics Data System (ADS)

Gao, X.; Cheng, H. Y.; Boynton, L.; Masiello, C. A.; Silberg, J. J.

2017-12-01

Microbial diversity and function in soils are governed by soil characteristics such as mineral composition, particles size and aggregations, soil organic matter (SOM), and availability of nutrients and H2O. The spatial and temporal heterogeneity of soils creates a range of niches (hotspots) differing in the availability of O2, H2O, and nutrients, which shapes microbial activities at scales ranging from nanometer to landscape. Synthetic biologists often examine microbial response trigged by their environment conditions in nutrient-rich aqueous media using single strain microbes. While these studies provided useful insight in the role of soil microbes in important soil biogeochemical processes (e.g., C cycling, N cycling, etc.), the results obtained from the over-simplified model systems are often not applicable natural soil systems. On the contrary, soil microbiologists examine microbial processes in natural soils using longer incubation time. However, due to its physical, chemical and biological complexity of natural soils, it is often difficult to examine soil characteristics independently and understand how each characteristic influences soil microbial activities and their corresponding soil functioning. Therefore, it is necessary to bridge the gap and develop a model matrix to exclude unpredictable influences from the environment while still reliably mimicking real environmental conditions. The objective of this study is to design a range of ecologically-relevant artificial soils with varying texture (particle size distribution), structure, mineralogy, SOM content, and nutrient heterogeneity. We thoroughly characterize the artificial soils for pH, active surface area and surface morphology, cation exchange capacity (CEC), and water retention curve. We demonstrate the effectiveness of the artificial soils as useful matrix for microbial processes, such as microbial growth and horizontal gene transfer (HGT), using the gas-reporting biosensors recently developed in our lab.

Saccharomyces cerevisiae: a nomadic yeast with no niche?

PubMed

Goddard, Matthew R; Greig, Duncan

2015-05-01

Different species are usually thought to have specific adaptations, which allow them to occupy different ecological niches. But recent neutral ecology theory suggests that species diversity can simply be the result of random sampling, due to finite population sizes and limited dispersal. Neutral models predict that species are not necessarily adapted to specific niches, but are functionally equivalent across a range of habitats. Here, we evaluate the ecology of Saccharomyces cerevisiae, one of the most important microbial species in human history. The artificial collection, concentration and fermentation of large volumes of fruit for alcohol production produce an environment in which S. cerevisiae thrives, and therefore it is assumed that fruit is the ecological niche that S. cerevisiae inhabits and has adapted to. We find very little direct evidence that S. cerevisiae is adapted to fruit, or indeed to any other specific niche. We propose instead a neutral nomad model for S. cerevisiae, which we believe should be used as the starting hypothesis in attempting to unravel the ecology of this important microbe. © FEMS 2015.

Marine sediments microbes capable of electrode oxidation as a surrogate for lithotrophic insoluble substrate metabolism.

PubMed

Rowe, Annette R; Chellamuthu, Prithiviraj; Lam, Bonita; Okamoto, Akihiro; Nealson, Kenneth H

2014-01-01

Little is known about the importance and/or mechanisms of biological mineral oxidation in sediments, partially due to the difficulties associated with culturing mineral-oxidizing microbes. We demonstrate that electrochemical enrichment is a feasible approach for isolation of microbes capable of gaining electrons from insoluble minerals. To this end we constructed sediment microcosms and incubated electrodes at various controlled redox potentials. Negative current production was observed in incubations and increased as redox potential decreased (tested -50 to -400 mV vs. Ag/AgCl). Electrode-associated biomass responded to the addition of nitrate and ferric iron as terminal electron acceptors in secondary sediment-free enrichments. Elemental sulfur, elemental iron and amorphous iron sulfide enrichments derived from electrode biomass demonstrated products indicative of sulfur or iron oxidation. The microbes isolated from these enrichments belong to the genera Halomonas, Idiomarina, Marinobacter, and Pseudomonas of the Gammaproteobacteria, and Thalassospira and Thioclava from the Alphaproteobacteria. Chronoamperometry data demonstrates sustained electrode oxidation from these isolates in the absence of alternate electron sources. Cyclic voltammetry demonstrated the variability in dominant electron transfer modes or interactions with electrodes (i.e., biofilm, planktonic or mediator facilitated) and the wide range of midpoint potentials observed for each microbe (from 8 to -295 mV vs. Ag/AgCl). The diversity of extracellular electron transfer mechanisms observed in one sediment and one redox condition, illustrates the potential importance and abundance of these interactions. This approach has promise for increasing our understanding the extent and diversity of microbe mineral interactions, as well as increasing the repository of microbes available for electrochemical applications.

Tolerance to biodegraded crude oil in marine invertebrate embryos and larvae is associated with expression of a multixenobiotic resistance transporter.

PubMed

Hamdoun, Amro M; Griffin, Fred J; Cherr, Gary N

2002-11-13

The toxicity of water-soluble fractions of biodegraded crude oil (BWSF) to embryos and larvae of two marine invertebrates, the white sea urchin (Lytechinus anamesus) and the fat innkeeper (Urechis caupo), was studied. Santa Barbara Channel crude oil was artificially weathered and subjected to biodegradation using a mixed microbe culture obtained from natural oil seep sites. The degradation culture inoculated with seep sediment microbes accumulated 43.7 microg/l water-soluble hydrocarbons. In contrast water-soluble fractions from the non-degraded cultures (NWSF) only accumulated 3.05 microg/l. BWSF proved deleterious to Lytechinus embryo development at low concentrations (EC50 = 0.33 mg/l) but was essentially non-toxic to Urechis embryos/larvae up to 3.0 mg/l. An established mechanism for handling of a wide array of xenobiotics in Urechis embryos is the multixenobiotoic resistance transporter multixenobiotic response (MXR, also known as multidrug resistance, MDR). This mechanism is primarily mediated by ATP-dependent, efflux pumps that extrude a wide array of xenobiotic compounds. In this study, we show that Lytechinus larvae do not appear to express MXR efflux protein nor MXR mediated dye efflux capacity. In contrast, BWSF acts as a competitive inhibitor of MXR transport-mediated dye efflux in Urechis larvae. These results suggest that MXR may be an important mechanism for extrusion of the by-products of crude oil degradation by microbes, and that the level of its expression may determine the susceptibility of organisms to degraded oil hydrocarbons. Copyright 2002 Elsevier Science B.V.

Emerging infectious diseases in southeast Asia: regional challenges to control.

PubMed

Coker, Richard J; Hunter, Benjamin M; Rudge, James W; Liverani, Marco; Hanvoravongchai, Piya

2011-02-12

Southeast Asia is a hotspot for emerging infectious diseases, including those with pandemic potential. Emerging infectious diseases have exacted heavy public health and economic tolls. Severe acute respiratory syndrome rapidly decimated the region's tourist industry. Influenza A H5N1 has had a profound effect on the poultry industry. The reasons why southeast Asia is at risk from emerging infectious diseases are complex. The region is home to dynamic systems in which biological, social, ecological, and technological processes interconnect in ways that enable microbes to exploit new ecological niches. These processes include population growth and movement, urbanisation, changes in food production, agriculture and land use, water and sanitation, and the effect of health systems through generation of drug resistance. Southeast Asia is home to about 600 million people residing in countries as diverse as Singapore, a city state with a gross domestic product (GDP) of US$37,500 per head, and Laos, until recently an overwhelmingly rural economy, with a GDP of US$890 per head. The regional challenges in control of emerging infectious diseases are formidable and range from influencing the factors that drive disease emergence, to making surveillance systems fit for purpose, and ensuring that regional governance mechanisms work effectively to improve control interventions. Copyright © 2011 Elsevier Ltd. All rights reserved.

A Cognitive Ecological Model of Women’s Response to Male Sexual Coercion in Dating

PubMed Central

Nurius, Paula S.; Norris, Jeanette

2015-01-01

SUMMARY We offer a theoretical model that consolidates background, environmental, and intrapersonal variables related to women’s experience of sexual coercion in dating into a coherent ecological framework and present for the first time a cognitive analysis of the processes women use to formulate responses to sexual coercion. An underlying premise for this model is that a woman’s coping response to sexual coercion by an acquaintance is mediated through cognitive processing of background and situational influences. Because women encounter this form of sexual coercion in the context of relationships and situations that they presume will follow normative expectations (e.g., about making friends, socializing and dating), it is essential to consider normative processes of learning, cognitive mediation, and coping guiding their efforts to interpret and respond to this form of personal threat. Although acts of coercion unquestionably remain the responsibility of the perpetrator, a more complete understanding of the multilevel factors shaping women’s perception of and response to threats can strengthen future inquiry and prevention efforts. PMID:25729157

Functional genomics and microbiome profiling of the Asian longhorned beetle (Anoplophora glabripennis) reveal insights into the digestive physiology and nutritional ecology of wood feeding beetles

USDA-ARS?s Scientific Manuscript database

The gut microbial communities associated with xylophagous beetles are taxonomically rich and predominately comprised of taxa that are poised to promote survival in woody tissue, which is devoid of nitrogen and essential nutrients. However, the contributions of gut microbes to digestive physiology a...

Ecology and thermal inactivation of microbes in and on interplanetary space vehicle components

NASA Technical Reports Server (NTRS)

Campbell, J. E.; Reyes, A. L.; Wehby, A. J.; Crawford, R. G.; Wimsatt, J. C.; Peeler, J. T.

1974-01-01

Dry heat sterilization of spacecraft was investigated by studying the production of spore crops, and thermal inactivation of the spores, and bacillus subtillus. Spore assays were made by conventional plate count methods, and survival curves for the spores are presented. The results indicate that the inherent resistance of spores from a parent cell can be maintained.

Phenazines in the environment: microbes, habitats, and ecological relevance. In: Chincholkar, S., Thomashow, L., editors. Microbial phenazines: biosynthesis, agriculture and health. New York, NY; Springer

USDA-ARS?s Scientific Manuscript database

Phenazines, the pigmented, redox-active metabolites produced by certain fluorescent pseudomonads, streptomycetes, and members of a few other bacterial genera, have long been recognized for their broad-spectrum antibiotic activity. Much has been learned in recent years about the synthesis of these co...

Characterization and mediation of microbial deterioration of concrete bridge structures.

DOT National Transportation Integrated Search

2013-04-01

Samples obtained from deteriorated bridge structures in Texas were cultured in growth medium containing thiosulfate as an energy source and investigated for acid production, type of acid produced by microbes and the bio-deterioration of concrete cyli...

Host-to-host variation of ecological interactions in polymicrobial infections

NASA Astrophysics Data System (ADS)

Mukherjee, Sayak; Weimer, Kristin E.; Seok, Sang-Cheol; Ray, Will C.; Jayaprakash, C.; Vieland, Veronica J.; Swords, W. Edward; Das, Jayajit

2015-02-01

Host-to-host variability with respect to interactions between microorganisms and multicellular hosts are commonly observed in infection and in homeostasis. However, the majority of mechanistic models used to analyze host-microorganism relationships, as well as most of the ecological theories proposed to explain coevolution of hosts and microbes, are based on averages across a host population. By assuming that observed variations are random and independent, these models overlook the role of differences between hosts. Here, we analyze mechanisms underlying host-to-host variations of bacterial infection kinetics, using the well characterized experimental infection model of polymicrobial otitis media (OM) in chinchillas, in combination with population dynamic models and a maximum entropy (MaxEnt) based inference scheme. We find that the nature of the interactions between bacterial species critically regulates host-to-host variations in these interactions. Surprisingly, seemingly unrelated phenomena, such as the efficiency of individual bacterial species in utilizing nutrients for growth, and the microbe-specific host immune response, can become interdependent in a host population. The latter finding suggests a potential mechanism that could lead to selection of specific strains of bacterial species during the coevolution of the host immune response and the bacterial species.

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

PubMed Central

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

2013-01-01

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

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. Copyright © 2015 Elsevier Inc. All rights reserved.

Modifying and reacting to the environmental pH can drive bacterial interactions

PubMed Central

Ratzke, Christoph

2018-01-01

Microbes usually exist in communities consisting of myriad different but interacting species. These interactions are typically mediated through environmental modifications; microbes change the environment by taking up resources and excreting metabolites, which affects the growth of both themselves and also other microbes. We show here that the way microbes modify their environment and react to it sets the interactions within single-species populations and also between different species. A very common environmental modification is a change of the environmental pH. We find experimentally that these pH changes create feedback loops that can determine the fate of bacterial populations; they can either facilitate or inhibit growth, and in extreme cases will cause extinction of the bacterial population. Understanding how single species change the pH and react to these changes allowed us to estimate their pairwise interaction outcomes. Those interactions lead to a set of generic interaction motifs—bistability, successive growth, extended suicide, and stabilization—that may be independent of which environmental parameter is modified and thus may reoccur in different microbial systems. PMID:29538378

Parasite-Microbiota Interactions With the Vertebrate Gut: Synthesis Through an Ecological Lens

PubMed Central

Leung, Jacqueline M.; Graham, Andrea L.; Knowles, Sarah C. L.

2018-01-01

The vertebrate gut teems with a large, diverse, and dynamic bacterial community that has pervasive effects on gut physiology, metabolism, and immunity. Under natural conditions, these microbes share their habitat with a similarly dynamic community of eukaryotes (helminths, protozoa, and fungi), many of which are well-known parasites. Both parasites and the prokaryotic microbiota can dramatically alter the physical and immune landscape of the gut, creating ample opportunities for them to interact. Such interactions may critically alter infection outcomes and affect overall host health and disease. For instance, parasite infection can change how a host interacts with its bacterial flora, either driving or protecting against dysbiosis and inflammatory disease. Conversely, the microbiota can alter a parasite's colonization success, replication, and virulence, shifting it along the parasitism-mutualism spectrum. The mechanisms and consequences of these interactions are just starting to be elucidated in an emergent transdisciplinary area at the boundary of microbiology and parasitology. However, heterogeneity in experimental designs, host and parasite species, and a largely phenomenological and taxonomic approach to synthesizing the literature have meant that common themes across studies remain elusive. Here, we use an ecological perspective to review the literature on interactions between the prokaryotic microbiota and eukaryotic parasites in the vertebrate gut. Using knowledge about parasite biology and ecology, we discuss mechanisms by which they may interact with gut microbes, the consequences of such interactions for host health, and how understanding parasite-microbiota interactions may lead to novel approaches in disease control. PMID:29867790

Parasite-Microbiota Interactions With the Vertebrate Gut: Synthesis Through an Ecological Lens.

PubMed

Leung, Jacqueline M; Graham, Andrea L; Knowles, Sarah C L

2018-01-01

The vertebrate gut teems with a large, diverse, and dynamic bacterial community that has pervasive effects on gut physiology, metabolism, and immunity. Under natural conditions, these microbes share their habitat with a similarly dynamic community of eukaryotes (helminths, protozoa, and fungi), many of which are well-known parasites. Both parasites and the prokaryotic microbiota can dramatically alter the physical and immune landscape of the gut, creating ample opportunities for them to interact. Such interactions may critically alter infection outcomes and affect overall host health and disease. For instance, parasite infection can change how a host interacts with its bacterial flora, either driving or protecting against dysbiosis and inflammatory disease. Conversely, the microbiota can alter a parasite's colonization success, replication, and virulence, shifting it along the parasitism-mutualism spectrum. The mechanisms and consequences of these interactions are just starting to be elucidated in an emergent transdisciplinary area at the boundary of microbiology and parasitology. However, heterogeneity in experimental designs, host and parasite species, and a largely phenomenological and taxonomic approach to synthesizing the literature have meant that common themes across studies remain elusive. Here, we use an ecological perspective to review the literature on interactions between the prokaryotic microbiota and eukaryotic parasites in the vertebrate gut. Using knowledge about parasite biology and ecology, we discuss mechanisms by which they may interact with gut microbes, the consequences of such interactions for host health, and how understanding parasite-microbiota interactions may lead to novel approaches in disease control.

Parental Involvement and Children's School Achievement: Evidence for Mediating Processes

ERIC Educational Resources Information Center

Rogers, Maria A.; Theule, Jennifer; Ryan, Bruce A.; Adams, Gerald R.; Keating, Leo

2009-01-01

This study used path analytic techniques and an ecological framework to examine the association between children's perceptions of their parents' educational involvement, children's personal characteristics, and their school achievement. Fathers' academic pressure was predictive of lower achievement, whereas mothers' encouragement and support…

Understanding immune function as a pace of life trait requires environmental context.

PubMed

Tieleman, B Irene

2018-01-01

This article provides a brief historical perspective on the integration of physiology into the concept of the pace of life of birds, evaluates the fit of immune function into this framework, and asks what it will take to fruitfully understand immune functioning of birds in pace of life studies in the future. In the late 1970s, physiology started to seriously enter avian life history ecology, with energy as the main currency of interest, inspired by David Lack's work in the preceding decades emphasizing how food availability explained life history variation. In an effort to understand the trade-off between survival and reproduction, and specifically the mortality costs associated with hard work, in the 1980s and 1990s, other physiological phenomena entered the realm of animal ecologists, including endocrinology, oxidative stress, and immunology. Reviewing studies thus far to evaluate the role of immune function in a life history context and particularly to address the questions whether immune function (1) consistently varies with life history variation among free-living bird species and (2) mediates life history trade-offs in experiments with free-living bird species; I conclude that, unlike energy metabolism, the immune system does not closely covary with life history among species nor mediates the classical trade-offs within individuals. Instead, I propose that understanding the tremendous immunological variation uncovered among free-living birds over the past 25 years requires a paradigm shift. The paradigm should shift from viewing immune function as a costly trait involved in life history trade-offs to explicitly including the benefits of the immune system and placing it firmly in an environmental and ecological context. A first step forward will be to quantify the immunobiotic pressures presented by diverse environmental circumstances that both shape and challenge the immune system of free-living animals. Current developments in the fields of infectious wildlife diseases and host-microbe interactions provide promising steps in this direction.

Microscopic physical biomarkers in carbonate hot springs: implications in the search for life on Mars

NASA Technical Reports Server (NTRS)

Allen, C. C.; Albert, F. G.; Chafetz, H. S.; Combie, J.; Graham, C. R.; Kieft, T. L.; Kivett, S. J.; McKay, D. S.; Steele, A.; Taunton, A. E.;

Insights to plant-microbe interactions provide opportunities to improve resistance breeding against root diseases in grain legumes.

PubMed

Wille, Lukas; Messmer, Monika M; Studer, Bruno; Hohmann, Pierre

2018-04-12

Root and foot diseases severely impede grain legume cultivation worldwide. Breeding lines with resistance against individual pathogens exist, but these resistances are often overcome by the interaction of multiple pathogens in field situations. Novel tools allow to decipher plant-microbiome interactions in unprecedented detail and provide insights into resistance mechanisms that consider both simultaneous attacks of various pathogens and the interplay with beneficial microbes. Although it has become clear that plant-associated microbes play a key role in plant health, a systematic picture of how and to what extend plants can shape their own detrimental or beneficial microbiome remains to be drawn. There is increasing evidence for the existence of genetic variation in the regulation of plant-microbe interactions that can be exploited by plant breeders. We propose to consider the entire plant holobiont in resistance breeding strategies in order to unravel hidden parts of complex defence mechanisms. This review summarises (i) the current knowledge of resistance against soil-borne pathogens in grain legumes, (ii) evidence for genetic variation for rhizosphere-related traits, (iii) the role of root exudation in microbe-mediated disease resistance and elaborates (iv) how these traits can be incorporated in resistance breeding programmes. This article is protected by copyright. All rights reserved.

Pathogenomics: an updated European Research Agenda.

PubMed

Demuth, Andreas; Aharonowitz, Yair; Bachmann, Till T; Blum-Oehler, Gabriele; Buchrieser, Carmen; Covacci, Antonello; Dobrindt, Ulrich; Emödy, Levente; van der Ende, Arie; Ewbank, Jonathan; Fernández, Luis Angel; Frosch, Matthias; García-Del Portillo, Francisco; Gilmore, Michael S; Glaser, Philippe; Goebel, Werner; Hasnain, Seyed E; Heesemann, Jürgen; Islam, Khalid; Korhonen, Timo; Maiden, Martin; Meyer, Thomas F; Montecucco, Cesare; Oswald, Eric; Parkhill, Julian; Pucciarelli, M Graciela; Ron, Eliora; Svanborg, Catharina; Uhlin, Bernt Eric; Wai, Sun Nyunt; Wehland, Jürgen; Hacker, Jörg

2008-05-01

The emerging genomic technologies and bioinformatics provide novel opportunities for studying life-threatening human pathogens and to develop new applications for the improvement of human and animal health and the prevention, treatment, and diagnosis of infections. Based on the ecology and population biology of pathogens and related organisms and their connection to epidemiology, more accurate typing technologies and approaches will lead to better means of disease control. The analysis of the genome plasticity and gene pools of pathogenic bacteria including antigenic diversity and antigenic variation results in more effective vaccines and vaccine implementation programs. The study of newly identified and uncultivated microorganisms enables the identification of new threats. The scrutiny of the metabolism of the pathogen in the host allows the identification of new targets for anti-infectives and therapeutic approaches. The development of modulators of host responses and mediators of host damage will be facilitated by the research on interactions of microbes and hosts, including mechanisms of host damage, acute and chronic relationships as well as commensalisms. The study of multiple pathogenic and non-pathogenic microbes interacting in the host will improve the management of multiple infections and will allow probiotic and prebiotic interventions. Needless to iterate, the application of the results of improved prevention and treatment of infections into clinical tests will have a positive impact on the management of human and animal disease. The Pathogenomics Research Agenda draws on discussions with experts of the Network of Excellence "EuroPathoGenomics" at the management board meeting of the project held during 18-21 April 2007, in the Villa Vigoni, Menaggio, Italy. Based on a proposed European Research Agenda in the field of pathogenomics by the ERA-NET PathoGenoMics the meeting's participants updated the established list of topics as the research agenda for the future.

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

NASA Astrophysics Data System (ADS)

Wang, F.; Liang, Q.

2016-12-01

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

Urban stress is associated with variation in microbial species composition—but not richness—in Manhattan

PubMed Central

Reese, Aspen T; Savage, Amy; Youngsteadt, Elsa; McGuire, Krista L; Koling, Adam; Watkins, Olivia; Frank, Steven D; Dunn, Robert R

2016-01-01

The biological diversity and composition of microorganisms influences both human health outcomes and ecological processes; therefore, understanding the factors that influence microbial biodiversity is key to creating healthy, functional landscapes in which to live. In general, biological diversity is predicted to be limited by habitat size, which for green areas is often reduced in cities, and by chronic disturbance (stress). These hypotheses have not previously been tested in microbial systems in direct comparison to macroorganisms. Here we analyzed bacterial, fungal and ant communities in small road medians (average area 0.0008 km2) and larger parks (average area 0.64 km2) across Manhattan (NYC). Bacterial species richness was not significantly different between medians and parks, but community composition was significantly distinct. In contrast, ant communities differed both in composition and richness with fewer ant species in medians than parks. Fungi showed no significant variation in composition or richness but had few shared taxa between habitats or sites. The diversity and composition of microbes appears less sensitive to habitat patchiness or urban stress than those of macroorganisms. Microbes and their associated ecosystem services and functions may be more resilient to the negative effects of urbanization than has been previously appreciated. PMID:26394011

The biology of habitat dominance; can microbes behave as weeds?

PubMed Central

Cray, Jonathan A; Bell, Andrew N W; Bhaganna, Prashanth; Mswaka, Allen Y; Timson, David J; Hallsworth, John E

2013-01-01

Summary Competition between microbial species is a product of, yet can lead to a reduction in, the microbial diversity of specific habitats. Microbial habitats can resemble ecological battlefields where microbial cells struggle to dominate and/or annihilate each other and we explore the hypothesis that (like plant weeds) some microbes are genetically hard-wired to behave in a vigorous and ecologically aggressive manner. These ‘microbial weeds’ are able to dominate the communities that develop in fertile but uncolonized – or at least partially vacant – habitats via traits enabling them to out-grow competitors; robust tolerances to habitat-relevant stress parameters and highly efficient energy-generation systems; avoidance of or resistance to viral infection, predation and grazers; potent antimicrobial systems; and exceptional abilities to sequester and store resources. In addition, those associated with nutritionally complex habitats are extraordinarily versatile in their utilization of diverse substrates. Weed species typically deploy multiple types of antimicrobial including toxins; volatile organic compounds that act as either hydrophobic or highly chaotropic stressors; biosurfactants; organic acids; and moderately chaotropic solutes that are produced in bulk quantities (e.g. acetone, ethanol). Whereas ability to dominate communities is habitat-specific we suggest that some microbial species are archetypal weeds including generalists such as: Pichia anomala, Acinetobacter spp. and Pseudomonas putida; specialists such as Dunaliella salina, Saccharomyces cerevisiae, Lactobacillus spp. and other lactic acid bacteria; freshwater autotrophs Gonyostomum semen and Microcystis aeruginosa; obligate anaerobes such as Clostridium acetobutylicum; facultative pathogens such as Rhodotorula mucilaginosa, Pantoea ananatis and Pseudomonas aeruginosa; and other extremotolerant and extremophilic microbes such as Aspergillus spp., Salinibacter ruber and Haloquadratum walsbyi. Some microbes, such as Escherichia coli, Mycobacterium smegmatis and Pseudoxylaria spp., exhibit characteristics of both weed and non-weed species. We propose that the concept of nonweeds represents a ‘dustbin’ group that includes species such as Synodropsis spp., Polypaecilum pisce, Metschnikowia orientalis, Salmonella spp., and Caulobacter crescentus. We show that microbial weeds are conceptually distinct from plant weeds, microbial copiotrophs, r-strategists, and other ecophysiological groups of microorganism. Microbial weed species are unlikely to emerge from stationary-phase or other types of closed communities; it is open habitats that select for weed phenotypes. Specific characteristics that are common to diverse types of open habitat are identified, and implications of weed biology and open-habitat ecology are discussed in the context of further studies needed in the fields of environmental and applied microbiology. PMID:23336673

Polymers in the gut compress the colonic mucus hydrogel

PubMed Central

Datta, Sujit S.; Preska Steinberg, Asher

2016-01-01

Colonic mucus is a key biological hydrogel that protects the gut from infection and physical damage and mediates host–microbe interactions and drug delivery. However, little is known about how its structure is influenced by materials it comes into contact with regularly. For example, the gut abounds in polymers such as dietary fibers or administered therapeutics, yet whether such polymers interact with the mucus hydrogel, and if so, how, remains unclear. Although several biological processes have been identified as potential regulators of mucus structure, the polymeric composition of the gut environment has been ignored. Here, we demonstrate that gut polymers do in fact regulate mucus hydrogel structure, and that polymer–mucus interactions can be described using a thermodynamic model based on Flory–Huggins solution theory. We found that both dietary and therapeutic polymers dramatically compressed murine colonic mucus ex vivo and in vivo. This behavior depended strongly on both polymer concentration and molecular weight, in agreement with the predictions of our thermodynamic model. Moreover, exposure to polymer-rich luminal fluid from germ-free mice strongly compressed the mucus hydrogel, whereas exposure to luminal fluid from specific-pathogen-free mice—whose microbiota degrade gut polymers—did not; this suggests that gut microbes modulate mucus structure by degrading polymers. These findings highlight the role of mucus as a responsive biomaterial, and reveal a mechanism of mucus restructuring that must be integrated into the design and interpretation of studies involving therapeutic polymers, dietary fibers, and fiber-degrading gut microbes. PMID:27303035

Polymers in the gut compress the colonic mucus hydrogel.

PubMed

Datta, Sujit S; Preska Steinberg, Asher; Ismagilov, Rustem F

2016-06-28

Colonic mucus is a key biological hydrogel that protects the gut from infection and physical damage and mediates host-microbe interactions and drug delivery. However, little is known about how its structure is influenced by materials it comes into contact with regularly. For example, the gut abounds in polymers such as dietary fibers or administered therapeutics, yet whether such polymers interact with the mucus hydrogel, and if so, how, remains unclear. Although several biological processes have been identified as potential regulators of mucus structure, the polymeric composition of the gut environment has been ignored. Here, we demonstrate that gut polymers do in fact regulate mucus hydrogel structure, and that polymer-mucus interactions can be described using a thermodynamic model based on Flory-Huggins solution theory. We found that both dietary and therapeutic polymers dramatically compressed murine colonic mucus ex vivo and in vivo. This behavior depended strongly on both polymer concentration and molecular weight, in agreement with the predictions of our thermodynamic model. Moreover, exposure to polymer-rich luminal fluid from germ-free mice strongly compressed the mucus hydrogel, whereas exposure to luminal fluid from specific-pathogen-free mice-whose microbiota degrade gut polymers-did not; this suggests that gut microbes modulate mucus structure by degrading polymers. These findings highlight the role of mucus as a responsive biomaterial, and reveal a mechanism of mucus restructuring that must be integrated into the design and interpretation of studies involving therapeutic polymers, dietary fibers, and fiber-degrading gut microbes.

Microbe Phobia and Kitchen Microbiology.

ERIC Educational Resources Information Center

Williams, Robert P.; Gillen, Alan L.

1991-01-01

The authors present an exercise designed to help students overcome the misconception that most microbes make people sick. The activity helps students of all ages understand the important benefits of microbes such as in making bread, soy sauce, cheese, and wine. The role of microorganisms in processing cocoa and coffee and growing plants is also…

A review of metabolic potential of human gut microbiome in human nutrition.

PubMed

Yadav, Monika; Verma, Manoj Kumar; Chauhan, Nar Singh

2018-03-01

The human gut contains a plethora of microbes, providing a platform for metabolic interaction between the host and microbiota. Metabolites produced by the gut microbiota act as a link between gut microbiota and its host. These metabolites act as messengers having the capacity to alter the gut microbiota. Recent advances in the characterization of the gut microbiota and its symbiotic relationship with the host have provided a platform to decode metabolic interactions. The human gut microbiota, a crucial component for dietary metabolism, is shaped by the genetic, epigenetic and dietary factors. The metabolic potential of gut microbiota explains its significance in host health and diseases. The knowledge of interactions between microbiota and host metabolism, as well as modification of microbial ecology, is really beneficial to have effective therapeutic treatments for many diet-related diseases in near future. This review cumulates the information to map the role of human gut microbiota in dietary component metabolism, the role of gut microbes derived metabolites in human health and host-microbe metabolic interactions in health and diseases.

Eukaryotic microbes, principally fungi and labyrinthulomycetes, dominate biomass on bathypelagic marine snow

PubMed Central

Bochdansky, Alexander B; Clouse, Melissa A; Herndl, Gerhard J

2017-01-01

In the bathypelagic realm of the ocean, the role of marine snow as a carbon and energy source for the deep-sea biota and as a potential hotspot of microbial diversity and activity has not received adequate attention. Here, we collected bathypelagic marine snow by gentle gravity filtration of sea water onto 30 μm filters from ~1000 to 3900 m to investigate the relative distribution of eukaryotic microbes. Compared with sediment traps that select for fast-sinking particles, this method collects particles unbiased by settling velocity. While prokaryotes numerically exceeded eukaryotes on marine snow, eukaryotic microbes belonging to two very distant branches of the eukaryote tree, the fungi and the labyrinthulomycetes, dominated overall biomass. Being tolerant to cold temperature and high hydrostatic pressure, these saprotrophic organisms have the potential to significantly contribute to the degradation of organic matter in the deep sea. Our results demonstrate that the community composition on bathypelagic marine snow differs greatly from that in the ambient water leading to wide ecological niche separation between the two environments. PMID:27648811

Applying fluorescence microscopy to the investigation of the behavior of foodborne pathogens on produce

NASA Astrophysics Data System (ADS)

Brandl, Maria T.

2009-05-01

In the past decade, the development of new tools to better visualize microbes at the cellular scale has spurred a renaissance in the application of microscopy to the study of bacteria in their natural environment. This renewed interest in microscopy may be largely attributable to the advent of the confocal laser scanning microscope (CLSM) and to the discovery of the green fluorescent protein. This article provides information about the use of fluorescence microscopy combined with fluorescent labels such as GFP, DsRed, and DNA stains, with immunofluorescence, and with digital image analysis, to examine the behavior of bacteria and other microbes on plant surfaces. Some of the advantages and pitfalls of these methods will be described using practical examples derived from studies of the ecology of foodborne pathogens, namely Salmonella enterica and E. coli O157:H7, on fresh fruit and vegetables. Confocal microscopy has been a powerful approach to uncover some of the factors involved in the association of produce with epidemics caused by these human pathogens and their interaction with other microbes in their nonhost environment.

Discerning direct and mediated effects of ecological structures and processes on adolescents' educational outcomes.

PubMed

Benner, Aprile D; Graham, Sandra; Mistry, Rashmita S

2008-05-01

This short-term longitudinal study examined the relations among family and school characteristics, family-level processes (youth perceptions of parent-adolescent interactions), school-level processes (youth perceptions of school belonging, school climate), adolescents' school engagement, and later academic performance. Participants were an ethnically diverse, urban sample of 1,120 9th-grade students (M age = 14.6 years). The structural characteristics of families and schools influenced the proximal processes that occurred therein, and these proximal processes, in turn, influenced students' proximal (i.e., engagement) and distal educational outcomes (i.e., grades in school). Moreover, the structural characteristics of families and schools influenced proximal and distal outcomes indirectly through their influence on the proximal processes. The multimediated ecological model suggested that intervening at the process level may be a successful means of improving both adolescents' engagement in school and their subsequent school performance. (PsycINFO Database Record (c) 2008 APA, all rights reserved).

Relationships between and formation dynamics of the microbiota of consumers, producers, and the environment in an abalone aquatic system

PubMed Central

Zhao, Wang; Liu, Guang-Feng; Wang, Jiang-Yong

2017-01-01

An ecosystem is a community comprising living and nonliving components of the environment. Microbes are ubiquitous elements in each of these components. The dynamics of microbiota formation in an ecosystem is important to elucidate, because how the different components of a system exchange microbes, and how the microbes control ecological processes remain unresolved. In this study, an abalone, Haliotis diversicolor, seed-nursing pond was used as a model system. We first examined changes in bacterial communities during the seedling cultivation of this herbivorous juvenile aquatic invertebrate animal. Denaturing gradient gel electrophoresis (DGGE) and pyrosequencing were used to analyze bacterial community dynamics and spatio-temporal interactions of different system components: consumers (abalone), producers (algae or a substrate), and the environment (water). DGGE fingerprints revealed that the developmental stages of abalone influences bacterial communities of both the abalone and substrate. Although the communities in water fluctuated daily, they could be divided into two clusters that coincided with abalone stages, reflecting the transition from larva to juvenile at around day 21. Pyrosequencing showed that the microbiota in the abalone and substrate had more operational taxonomic units in common than that of either with water. The Bray-Curtis similarity index was used to quantify the formation dynamics of microbiota among the various components of the system. The bacterial communities in producers and consumers showed similar changes. These communities were unstable at the beginning and then slowly stabilized over time. The environmental bacterial community was more stable than the bacterial communities in consumers and producers, and may have been the basis for stability in the system. Our research provides insights into the dynamics of microbiota formation in various biotic elements of a system that will contribute to predictive systems modeling. PMID:28787009

Relationships between and formation dynamics of the microbiota of consumers, producers, and the environment in an abalone aquatic system.

PubMed

Jiang, Jing-Zhe; Zhao, Wang; Liu, Guang-Feng; Wang, Jiang-Yong

2017-01-01

An ecosystem is a community comprising living and nonliving components of the environment. Microbes are ubiquitous elements in each of these components. The dynamics of microbiota formation in an ecosystem is important to elucidate, because how the different components of a system exchange microbes, and how the microbes control ecological processes remain unresolved. In this study, an abalone, Haliotis diversicolor, seed-nursing pond was used as a model system. We first examined changes in bacterial communities during the seedling cultivation of this herbivorous juvenile aquatic invertebrate animal. Denaturing gradient gel electrophoresis (DGGE) and pyrosequencing were used to analyze bacterial community dynamics and spatio-temporal interactions of different system components: consumers (abalone), producers (algae or a substrate), and the environment (water). DGGE fingerprints revealed that the developmental stages of abalone influences bacterial communities of both the abalone and substrate. Although the communities in water fluctuated daily, they could be divided into two clusters that coincided with abalone stages, reflecting the transition from larva to juvenile at around day 21. Pyrosequencing showed that the microbiota in the abalone and substrate had more operational taxonomic units in common than that of either with water. The Bray-Curtis similarity index was used to quantify the formation dynamics of microbiota among the various components of the system. The bacterial communities in producers and consumers showed similar changes. These communities were unstable at the beginning and then slowly stabilized over time. The environmental bacterial community was more stable than the bacterial communities in consumers and producers, and may have been the basis for stability in the system. Our research provides insights into the dynamics of microbiota formation in various biotic elements of a system that will contribute to predictive systems modeling.

Significance of Plant Root Microorganisms in Reclaiming Water in CELSS

NASA Technical Reports Server (NTRS)

Bubenheim, David L.; Greene, Catherine; Wignarajah, Kanapathipillai; Kliss, Mark H. (Technical Monitor)

1996-01-01

Since many microorganisms demonstrate the ability to quickly break down complex mixtures of waste and environmental contaminants, examining their potential use for water recycling in a closed environment is appealing. Water contributes approximately 90 percent of the life sustaining provisions in a human space habitat. Nearly half of the daily water requirements will be used for personal hygiene and dish washing. The primary contaminants of the used "gray" water will be the cleansing agents or soaps used to carry out these functions. Reclaiming water from the gray water waste streams is one goal of the NASA program, Controlled Ecological Life Support Systems (CELSS). The microorganisms of plane roots are well documented to be of a beneficial effect to promote plant growth. Most plants exhibit a range of bacteria and fungi which can be highly plant-specific. In our investigations with lettuce grown in hydroponic culture, we identified a microflora of normal rhizosphere. When the roots were exposed to an anionic surfactant, the species diversity changed, based on morphological characteristics, with the numbers of species being reduced from 7 to 2 after 48 hours of exposure. In addition, the species that became dominant in the presence of the anionic surfactant also demonstrated a dramatic increase in population density which corresponded to the degradation of the surfactant in the root zone. The potential for using these or other rhizosphere bacteria as a primary or secondary waste processor is promising, but a number of issues still warrant investigation; these include but are not limited to: (1) the full identification of the microbes, (2) the classes of surfactants the microbes will degrade, (3) the environmental conditions required for optimal processing efficiency and (4) the ability of transferring the microbes to a non-living solid matrix such as a bioreactor.

Evolution of microbiology as seen in the textbooks of Edwin O. Jordan and William H. Park.

PubMed Central

Strick, J.

1999-01-01

Historians of science account the appearance of textbooks as an important step in the formation and consolidation of a new discipline. The texts of Park and Jordan were both very important in this light; however; they also can be used as a gauge of changing concepts within microbiology in the first four decades after its consolidation as a discipline, 1900-1940. This paper tracks these important texts and through them changing attitudes toward several important concepts: bacterial variation, human/bovine tuberculosis, and the existence of a non-symptomatic carrier state in infectious disease. The two texts are also compared regarding their view of microbes as pathogens vs. microbes as important and ubiquitous ecological agents. Images Figure 1 Figure 2 PMID:11049163

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.

Master manipulators: an update on Legionella pneumophila Icm/Dot translocated substrates and their host targets

PubMed Central

Isaac, Dervla T; Isberg, Ralph

2014-01-01

Macrophages are the front line of immune defense against invading microbes. Microbes, however, have evolved numerous and diverse mechanisms to thwart these host immune defenses and thrive intracellularly. Legionella pneumophila, a Gram-negative pathogen of amoebal and mammalian phagocytes, is one such microbe. In humans, it causes a potentially fatal pneumonia referred to as Legionnaires' disease. Armed with the Icm/Dot type IV secretion system, which is required for virulence, and approximately 300 translocated proteins, Legionella is able to enter host cells, direct the biogenesis of its own vacuolar compartment, and establish a replicative niche, where it grows to high levels before lysing the host cell. Efforts to understand the pathogenesis of this bacterium have focused on characterizing the molecular activities of its many effectors. In this article, we highlight recent strides that have been made in understanding how Legionella effectors mediate host-pathogen interactions. PMID:24762308

Response of humic acid formation to elevated nitrate during chicken manure composting.

PubMed

Shi, Mingzi; Wei, Zimin; Wang, Liqin; Wu, Junqiu; Zhang, Duoying; Wei, Dan; Tang, Yu; Zhao, Yue

2018-06-01

Nitrate can stimulate microbes to degrade aromatic compounds, whereas humic acid (HA) as a high molecular weight aromatic compound, its formation may be affected by elevated nitrate during composting. Therefore, this study is conducted to determine the effect of elevated nitrate on HA formation. Five tests were executed by adding different nitrate concentrations to chicken manure composting. Results demonstrate that the concentration of HA in treatment group is significantly decreased compared with control group (p < 0.05), especially in the highest nitrate concentration group. RDA indicates that the microbes associated with HA and environmental parameters are influenced by elevated nitrate. Furthermore, structural equation model reveals that elevated nitrate reduces HA formation by mediating microbes directly, or by affecting ammonia and pH as the indirect drivers to regulate microbial community structure. Copyright © 2018 Elsevier Ltd. All rights reserved.

The devil lies in the details: how variations in polysaccharide fine-structure impact the physiology and evolution of gut microbes

PubMed Central

Martens, Eric C.; Kelly, Amelia G.; Tauzin, Alexandra S.; Brumer, Harry

2014-01-01

The critical importance of gastrointestinal microbes to digestion of dietary fiber in humans and other mammals has been appreciated for decades. Symbiotic microorganisms expand mammalian digestive physiology by providing an armament of diverse polysaccharide degrading enzymes, which are largely absent in mammalian genomes. By out-sourcing this aspect of digestive physiology to our gut microbes, we maximize our ability to adapt to different carbohydrate nutrients on time scales as short as several hours, due to the ability of the gut microbial community to rapidly alter its physiology from meal-to-meal. Because of their ability to pick up new traits by lateral gene transfer, our gut microbes also enable adaption over time periods as long as centuries and millennia by adjusting their gene content to reflect cultural dietary trends. Despite a vast amount of sequence-based insight into the metabolic potential of gut microbes, the specific mechanisms by which symbiotic gut microorganisms recognize and attack complex carbohydrates remain largely undefined. Here, we review the recent literature on this topic and posit that numerous, subtle variations in polysaccharides diversify the spectrum of available nutrient niches, each of which may be best filled by a subset of microorganisms that possess the corresponding proteins to recognize and degrade different carbohydrates. Understanding these relationships at precise mechanistic levels will be essential to obtain a complete understanding of the forces shaping gut microbial ecology and genomic evolution, as well as devising strategies to intentionally manipulate the composition and physiology of the gut microbial community to improve health. PMID:25026064

The devil lies in the details: how variations in polysaccharide fine-structure impact the physiology and evolution of gut microbes.

PubMed

Martens, Eric C; Kelly, Amelia G; Tauzin, Alexandra S; Brumer, Harry

2014-11-25

The critical importance of gastrointestinal microbes to digestion of dietary fiber in humans and other mammals has been appreciated for decades. Symbiotic microorganisms expand mammalian digestive physiology by providing an armament of diverse polysaccharide-degrading enzymes, which are largely absent in mammalian genomes. By out-sourcing this aspect of digestive physiology to our gut microbes, we maximize our ability to adapt to different carbohydrate nutrients on timescales as short as several hours due to the ability of the gut microbial community to rapidly alter its physiology from meal to meal. Because of their ability to pick up new traits by lateral gene transfer, our gut microbes also enable adaption over time periods as long as centuries and millennia by adjusting their gene content to reflect cultural dietary trends. Despite a vast amount of sequence-based insight into the metabolic potential of gut microbes, the specific mechanisms by which symbiotic gut microorganisms recognize and attack complex carbohydrates remain largely undefined. Here, we review the recent literature on this topic and posit that numerous, subtle variations in polysaccharides diversify the spectrum of available nutrient niches, each of which may be best filled by a subset of microorganisms that possess the corresponding proteins to recognize and degrade different carbohydrates. Understanding these relationships at precise mechanistic levels will be essential to obtain a complete understanding of the forces shaping gut microbial ecology and genomic evolution, as well as devising strategies to intentionally manipulate the composition and physiology of the gut microbial community to improve health. Copyright © 2014 Elsevier Ltd. All rights reserved.

Effects of resveratrol on gut microbiota and fat storage in a mouse model with high-fat-induced obesity.

PubMed

Qiao, Yi; Sun, Jin; Xia, Shufang; Tang, Xue; Shi, Yonghui; Le, Guowei

2014-06-01

Recent studies have investigated the anti-obesity effect of resveratrol, but the pathways through which resveratrol resists obesity are not clear. In the present study, we hypothesize that resveratrol exerts anti-obesity effects that are likely mediated by mechanisms of regulating gut microbes, and in turn, improving fat storage and metabolism. Gut microbes, glucose and lipid metabolism in high-fat diet (HF) mice in vivo are investigated after resveratrol treatment. Several biochemical markers are measured. Fluorescence in situ hybridization and flow cytometry are used to monitor and quantify the changes in gut microbiota. The key genes related to fat storage and metabolism in the liver and visceral adipose tissues are measured by real-time PCR. The results show that resveratrol (200 mg per kg per day) significantly lowers both body and visceral adipose weights, and reduces blood glucose and lipid levels in HF mice. Resveratrol improves the gut microbiota dysbiosis induced by the HF diet, including increasing the Bacteroidetes-to-Firmicutes ratios, significantly inhibiting the growth of Enterococcus faecalis, and increasing the growth of Lactobacillus and Bifidobacterium. Furthermore, resveratrol significantly increases the fasting-induced adipose factor (Fiaf, a key gene negatively regulated by intestinal microbes) expression in the intestine. Resveratrol significantly decreases mRNA expression of Lpl, Scd1, Ppar-γ, Acc1, and Fas related to fatty acids synthesis, adipogenesis and lipogenesis, which may be driven by increased Fiaf expression. The Pearson's correlation coefficient shows that there is a negative correlation between the body weight and the ratios of Bacteroidetes-to-Firmicutes. Therefore, resveratrol mediates the composition of gut microbes, and in turn, through the Fiaf signaling pathway, accelerates the development of obesity.

Communicative interactions involving plants: information, evolution, and ecology.

PubMed

Mescher, Mark C; Pearse, Ian S

2016-08-01

The role of information obtained via sensory cues and signals in mediating the interactions of organisms with their biotic and abiotic environments has been a major focus of work on sensory and behavioral ecology. Information-mediated interactions also have important implications for broader ecological patterns emerging at the community and ecosystem levels that are only now beginning to be explored. Given the extent to which plants dominate the sensory landscapes of terrestrial ecosystems, information-mediated interactions involving plants should be a major focus of efforts to elucidate these broader patterns. Here we explore how such efforts might be enhanced by a clear understanding of information itself-a central and potentially unifying concept in biology that has nevertheless been the subject of considerable confusion-and of its relationship to adaptive evolution and ecology. We suggest that information-mediated interactions should be a key focus of efforts to more fully integrate evolutionary biology and ecology. Copyright © 2016 Elsevier Ltd. All rights reserved.

Marine sediments microbes capable of electrode oxidation as a surrogate for lithotrophic insoluble substrate metabolism

PubMed Central

Rowe, Annette R.; Chellamuthu, Prithiviraj; Lam, Bonita; Okamoto, Akihiro; Nealson, Kenneth H.

2015-01-01

Little is known about the importance and/or mechanisms of biological mineral oxidation in sediments, partially due to the difficulties associated with culturing mineral-oxidizing microbes. We demonstrate that electrochemical enrichment is a feasible approach for isolation of microbes capable of gaining electrons from insoluble minerals. To this end we constructed sediment microcosms and incubated electrodes at various controlled redox potentials. Negative current production was observed in incubations and increased as redox potential decreased (tested −50 to −400 mV vs. Ag/AgCl). Electrode-associated biomass responded to the addition of nitrate and ferric iron as terminal electron acceptors in secondary sediment-free enrichments. Elemental sulfur, elemental iron and amorphous iron sulfide enrichments derived from electrode biomass demonstrated products indicative of sulfur or iron oxidation. The microbes isolated from these enrichments belong to the genera Halomonas, Idiomarina, Marinobacter, and Pseudomonas of the Gammaproteobacteria, and Thalassospira and Thioclava from the Alphaproteobacteria. Chronoamperometry data demonstrates sustained electrode oxidation from these isolates in the absence of alternate electron sources. Cyclic voltammetry demonstrated the variability in dominant electron transfer modes or interactions with electrodes (i.e., biofilm, planktonic or mediator facilitated) and the wide range of midpoint potentials observed for each microbe (from 8 to −295 mV vs. Ag/AgCl). The diversity of extracellular electron transfer mechanisms observed in one sediment and one redox condition, illustrates the potential importance and abundance of these interactions. This approach has promise for increasing our understanding the extent and diversity of microbe mineral interactions, as well as increasing the repository of microbes available for electrochemical applications. PMID:25642220

Filthy lucre: A metagenomic pilot study of microbes found on circulating currency in New York City

PubMed Central

Maritz, Julia M.; Sullivan, Steven A.; Prill, Robert J.; Aksoy, Emre; Scheid, Paul; Carlton, Jane M.

2017-01-01

Background Paper currency by its very nature is frequently transferred from one person to another and represents an important medium for human contact with—and potential exchange of—microbes. In this pilot study, we swabbed circulating $1 bills obtained from a New York City bank in February (Winter) and June (Summer) 2013 and used shotgun metagenomic sequencing to profile the communities found on their surface. Using basic culture conditions, we also tested whether viable microbes could be recovered from bills. Results Shotgun metagenomics identified eukaryotes as the most abundant sequences on money, followed by bacteria, viruses and archaea. Eukaryotic assemblages were dominated by human, other metazoan and fungal taxa. The currency investigated harbored a diverse microbial population that was dominated by human skin and oral commensals, including Propionibacterium acnes, Staphylococcus epidermidis and Micrococcus luteus. Other taxa detected not associated with humans included Lactococcus lactis and Streptococcus thermophilus, microbes typically associated with dairy production and fermentation. Culturing results indicated that viable microbes can be isolated from paper currency. Conclusions We conducted the first metagenomic characterization of the surface of paper money in the United States, establishing a baseline for microbes found on $1 bills circulating in New York City. Our results suggest that money amalgamates DNA from sources inhabiting the human microbiome, food, and other environmental inputs, some of which can be recovered as viable organisms. These monetary communities may be maintained through contact with human skin, and DNA obtained from money may provide a record of human behavior and health. Understanding these microbial profiles is especially relevant to public health as money could potentially mediate interpersonal transfer of microbes. PMID:28384336

Isolation and Characterization of Microbes Mediating Thermodynamically Favorable Coupling of Anaerobic Oxidation of Methane and Metal Reduction

NASA Astrophysics Data System (ADS)

Glass, J. B.; Reed, B. C.; Sarode, N. D.; Kretz, C. B.; Bray, M. S.; DiChristina, T. J.; Stewart, F. J.; Fowle, D. A.; Crowe, S.

2014-12-01

Methane is the third most reduced environmentally relevant electron donor for microbial metabolisms after organic carbon and hydrogen. In anoxic ecosystems, the major sink for methane is anaerobic oxidation of methane (AOM) mediated by syntrophic microbial consortia that couple AOM to reduction of an oxidized electron acceptor to yield free energy. In marine sediments, AOM is generally coupled to reduction of sulfate despite an extremely small amount of free energy yield because sulfate is the most abundant electron acceptor in seawater. While AOM coupled to Fe(III) and Mn(IV) reduction (Fe- and Mn-AOM) is 10-30x more thermodynamically favorable than sulfate-AOM, and geochemical data suggests that it occurs in diverse environments, the microorganisms mediating Fe- and Mn-AOM remain unknown. Lake Matano, Indonesia is an ideal ecosystem to enrich for Fe- and Mn-AOM microbes because its anoxic ferruginous deep waters and sediments contain abundant Fe(III), Mn(IV) and methane, and extremely low sulfate and nitrate. Our research aims to isolate and characterize the microbes mediating Fe- and Mn-AOM from three layers of Lake Matano sediments through serial enrichment cultures in minimal media lacking nitrate and sulfate. 16S rRNA amplicon sequencing of sediment inoculum revealed the presence of the Fe(III)-reducing bacterium Geobacter (5-10% total microbial community in shallow sediment and 35-60% in deeper sediment) as well as 1-2% Euryarchaeota implicated in methane cycling, including ANME-1 and 2d and Methanosarcinales. After 90 days of primary enrichment, all three sediment layers showed high levels of Fe(III) reduction (60-90 μM Fe(II) d-1) in the presence of methane compared to no methane and heat-killed controls. Treatments with added Fe(III) as goethite contained higher abundances of Geobacter than the inoculum (60-80% in all layers), suggesting that Geobacter may be mediating Fe(III) reduction in these enrichments. Quantification of AOM rates is underway, and will be used to estimate the plausibility of metal-AOM as a thermodynamically favorable methane sink in anoxic ecosystems of both the modern and ancient Earth.

Ecology and thermal inactivation of microbes in and on interplanetary space vehicle components

NASA Technical Reports Server (NTRS)

Campbell, J. E.

1972-01-01

A set of conditions in which 90 C was a more lethal temperature than 125 C for the destruction of Bacillus subtilis var. niger was identified as a function of relative humidity, with maximum effectiveness at 100% R.H. A systematic study of the influence of head-space moisture and temperature on the destruction of B. subtilis var. niger is reported.

Review of termite forest ecology and opportunities to investigate the relationship of termites to fire

Treesearch

Christopher Peterson

2010-01-01

In forests, termites serve as “soil engineers,” translocating mineral soil to the surface, constructing macropores to improve water infiltration, increase soil minerals and organic carbon, facilitate the growth of microbes and affect the growth of vegetation. The future productivity of a forest site therefore depends to some degree on termite activity. Termites could...

Molecular musings in microbial ecology and evolution

PubMed Central

2011-01-01

A few major discoveries have influenced how ecologists and evolutionists study microbes. Here, in the format of an interview, we answer questions that directly relate to how these discoveries are perceived in these two branches of microbiology, and how they have impacted on both scientific thinking and methodology. The first question is "What has been the influence of the 'Universal Tree of Life' based on molecular markers?" For evolutionists, the tree was a tool to understand the past of known (cultured) organisms, mapping the invention of various physiologies on the evolutionary history of microbes. For ecologists the tree was a guide to discover the current diversity of unknown (uncultured) organisms, without much knowledge of their physiology. The second question we ask is "What was the impact of discovering frequent lateral gene transfer among microbes?" In evolutionary microbiology, frequent lateral gene transfer (LGT) made a simple description of relationships between organisms impossible, and for microbial ecologists, functions could not be easily linked to specific genotypes. Both fields initially resisted LGT, but methods or topics of inquiry were eventually changed in one to incorporate LGT in its theoretical models (evolution) and in the other to achieve its goals despite that phenomenon (ecology). The third and last question we ask is "What are the implications of the unexpected extent of diversity?" The variation in the extent of diversity between organisms invalidated the universality of species definitions based on molecular criteria, a major obstacle to the adaptation of models developed for the study of macroscopic eukaryotes to evolutionary microbiology. This issue has not overtly affected microbial ecology, as it had already abandoned species in favor of the more flexible operational taxonomic units. This field is nonetheless moving away from traditional methods to measure diversity, as they do not provide enough resolution to uncover what lies below the species level. The answers of the evolutionary microbiologist and microbial ecologist to these three questions illustrate differences in their theoretical frameworks. These differences mean that both fields can react quite distinctly to the same discovery, incorporating it with more or less difficulty in their scientific practice. Reviewers This article was reviewed by W. Ford Doolittle, Eugene V. Koonin and Maureen A. O'Malley. PMID:22074255

Genome evolution and nitrogen fixation in bacterial ectosymbionts of a protist inhabiting wood-feeding cockroaches

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

Tai, Vera; Carpenter, Kevin J.; Weber, Peter K.

By combining genomics and isotope imaging analysis using high-resolution secondary ion mass spectrometry (NanoSIMS), we examined the function and evolution of Bacteroidales ectosymbionts of the protistBarbulanymphafrom the hindguts of the wood-eating cockroachCryptocercus punctulatus. In particular, we investigated the structure of ectosymbiont genomes, which, in contrast to those of endosymbionts, has been little studied to date, and tested the hypothesis that these ectosymbionts fix nitrogen. Unlike with most obligate endosymbionts, genome reduction has not played a major role in the evolution of the Barbulanympha ectosymbionts. Instead, interaction with the external environment has remained important for this symbiont as genes for synthesismore » of transporters, outer membrane proteins, lipopolysaccharides, and lipoproteins have been retained. The ectosymbiont genome carried two complete operons for nitrogen fixation, a urea transporter, and a urease, indicating the availability of nitrogen as a driving force behind the symbiosis. NanoSIMS analysis ofC. punctulatushindgut symbionts exposedin vivoto 15N 2 supports the hypothesis thatBarbulanymphaectosymbionts are capable of nitrogen fixation. This genomic andin vivofunctional investigation of protist ectosymbionts highlights the diversity of evolutionary forces and trajectories that shape symbiotic interactions. The ecological and evolutionary importance of symbioses is increasingly clear, but the overall diversity of symbiotic interactions remains poorly explored. Here in this study, we investigated the evolution and nitrogen fixation capabilities of ectosymbionts attached to the protist Barbulanympha from the hindgut of the wood-eating cockroach Cryptocercus punctulatus. In addressing genome evolution of protist ectosymbionts, our data suggest that the ecological pressures influencing the evolution of extracellular symbionts clearly differ from intracellular symbionts and organelles. Using NanoSIMS analysis, we also obtained direct imaging evidence of a specific hindgut microbe playing a role in nitrogen fixation. These results demonstrate the power of combining NanoSIMS and genomics tools for investigating the biology of uncultivable microbes. This investigation paves the way for a more precise understanding of microbial interactions in the hindguts of wood-eating insects and further exploration of the diversity and ecological significance of symbiosis between microbes.« less

Genome evolution and nitrogen fixation in bacterial ectosymbionts of a protist inhabiting wood-feeding cockroaches

DOE PAGES

Tai, Vera; Carpenter, Kevin J.; Weber, Peter K.; ...

2016-05-27

By combining genomics and isotope imaging analysis using high-resolution secondary ion mass spectrometry (NanoSIMS), we examined the function and evolution of Bacteroidales ectosymbionts of the protistBarbulanymphafrom the hindguts of the wood-eating cockroachCryptocercus punctulatus. In particular, we investigated the structure of ectosymbiont genomes, which, in contrast to those of endosymbionts, has been little studied to date, and tested the hypothesis that these ectosymbionts fix nitrogen. Unlike with most obligate endosymbionts, genome reduction has not played a major role in the evolution of the Barbulanympha ectosymbionts. Instead, interaction with the external environment has remained important for this symbiont as genes for synthesismore » of transporters, outer membrane proteins, lipopolysaccharides, and lipoproteins have been retained. The ectosymbiont genome carried two complete operons for nitrogen fixation, a urea transporter, and a urease, indicating the availability of nitrogen as a driving force behind the symbiosis. NanoSIMS analysis ofC. punctulatushindgut symbionts exposedin vivoto 15N 2 supports the hypothesis thatBarbulanymphaectosymbionts are capable of nitrogen fixation. This genomic andin vivofunctional investigation of protist ectosymbionts highlights the diversity of evolutionary forces and trajectories that shape symbiotic interactions. The ecological and evolutionary importance of symbioses is increasingly clear, but the overall diversity of symbiotic interactions remains poorly explored. Here in this study, we investigated the evolution and nitrogen fixation capabilities of ectosymbionts attached to the protist Barbulanympha from the hindgut of the wood-eating cockroach Cryptocercus punctulatus. In addressing genome evolution of protist ectosymbionts, our data suggest that the ecological pressures influencing the evolution of extracellular symbionts clearly differ from intracellular symbionts and organelles. Using NanoSIMS analysis, we also obtained direct imaging evidence of a specific hindgut microbe playing a role in nitrogen fixation. These results demonstrate the power of combining NanoSIMS and genomics tools for investigating the biology of uncultivable microbes. This investigation paves the way for a more precise understanding of microbial interactions in the hindguts of wood-eating insects and further exploration of the diversity and ecological significance of symbiosis between microbes.« less

Molecular musings in microbial ecology and evolution.

PubMed

Case, Rebecca J; Boucher, Yan

2011-11-10

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

Identification of novel eubacteria from spent mushroom compost (SMC) waste by DNA sequence typing: ecological considerations of disposal on agricultural land.

PubMed

Watabe, M; Rao, J R; Xu, J; Millar, B C; Ward, R F; Moore, J E

2004-01-01

A small study was undertaken to examine the microbiological characteristics of spent mushroom compost (SMC), which is the major waste by-product of the mushroom industry and which is regularly disposed off by application to agricultural land. The primary aim of this study was to examine SMC for the presence of faecal bacterial pathogens, including Campylobacter spp., Salmonella spp. and Listeria monocytogenes. Secondly it was desirable to quantify bacterial and fungal populations within SMC, and also qualitatively identify the diversity of bacterial populations within SMC, through employment of rDNA PCR and direct sequencing techniques on the culturable microflora. Conventional microbiological analyses of SMC material (n=30) from six commercial operations in both Northern Ireland and the Republic of Ireland, failed to detect Salmonella spp, Listeria spp. or Campylobacter spp. in any of the SMC material examined. Total aerobic plate counts gave a mean count of log10 7.01 colony forming units (cfu) per gram SMC material (range: log10 6.53-7.52 cfu/g). Fungal counts gave a mean count of log(10) 4.57 cfu per gram SMC material (range: log10 3.93-4.98 cfu/g). From a total of greater than 50 colony picks, a total of 12 bacterial morphotypes were identified and were further examined by employment of partial 16S rRNA gene amplification and sequencing techniques, yielding several genera and species, including Bacillus licheniformis, Bacillus subtilis, Klebsiella/Enterobacter sp. Microbacterium sp. Paenibacillus lentimorbus, Pseudomonas mevalonii, Sphingobacterium multivorum and Stenotrophomonas sp. This is the first preliminary report on the microbial diversity of SMC waste and demonstrates the presence of several species that have not been previously described in SMC, in addition to two potentially novel species within the genera Microbacterium and Stenotrophomonas. It is thereby important to examine the ecological microbe-microbe and plant-microbe interactions that are occurring between the native bacterial soil flora and those added annually (theoretically estimated at approximately 10(18) cells) through the application of SMC. Such studies would be beneficial in helping to ascertain the ecological consequences involved in the disposal of SMC waste on agricultural land.

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

NASA Astrophysics Data System (ADS)

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

2016-12-01

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

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Heavy metal mining using microbes.

PubMed

Rawlings, Douglas E

2002-01-01

The use of acidiphilic, chemolithotrophic iron- and sulfur-oxidizing microbes in processes to recover metals from certain types of copper, uranium, and gold-bearing minerals or mineral concentrates is now well established. During these processes insoluble metal sulfides are oxidized to soluble metal sulfates. Mineral decomposition is believed to be mostly due to chemical attack by ferric iron, with the main role of the microorganisms being to reoxidize the resultant ferrous iron back to ferric iron. Currently operating industrial biomining processes have used bacteria that grow optimally from ambient to 50 degrees C, but thermophilic microbes have been isolated that have the potential to enable mineral biooxidation to be carried out at temperatures of 80 degrees C or higher. The development of higher-temperature processes will extend the variety of minerals that can be commercially processed.

Cooperative microbial tolerance behaviors in host-microbiota mutualism

PubMed Central

Ayres, Janelle S.

2016-01-01

Animal defense strategies against microbes are most often thought of as a function of the immune system, the primary function of which is to sense and kill microbes through the execution of resistance mechanisms. However, this antagonistic view creates complications for our understanding of beneficial host-microbe interactions. Pathogenic microbes are described as employing a few common behaviors that promote their fitness at the expense of host health and fitness. Here, a complementary framework is proposed to suggest that in addition to pathogens, beneficial microbes have evolved behaviors to manipulate host processes in order to promote their own fitness and do so through the promotion of host health and fitness. In this Perspective, I explore the idea that patterns or behaviors traditionally ascribed to pathogenic microbes are also employed by beneficial microbes to promote host tolerance defense strategies. Such strategies would promote host health without having a negative impact on microbial fitness and would thereby yield cooperative evolutionary dynamics that are likely required to drive mutualistic co-evolution of hosts and microbes. PMID:27259146

Cytokinin production by Pseudomonas fluorescens G20-18 determines biocontrol activity against Pseudomonas syringae in Arabidopsis

PubMed Central

Großkinsky, Dominik K.; Tafner, Richard; Moreno, María V.; Stenglein, Sebastian A.; García de Salamone, Inés E.; Nelson, Louise M.; Novák, Ondřej; Strnad, Miroslav; van der Graaff, Eric; Roitsch, Thomas

2016-01-01

Plant beneficial microbes mediate biocontrol of diseases by interfering with pathogens or via strengthening the host. Although phytohormones, including cytokinins, are known to regulate plant development and physiology as well as plant immunity, their production by microorganisms has not been considered as a biocontrol mechanism. Here we identify the ability of Pseudomonas fluorescens G20-18 to efficiently control P. syringae infection in Arabidopsis, allowing maintenance of tissue integrity and ultimately biomass yield. Microbial cytokinin production was identified as a key determinant for this biocontrol effect on the hemibiotrophic bacterial pathogen. While cytokinin-deficient loss-of-function mutants of G20-18 exhibit impaired biocontrol, functional complementation with cytokinin biosynthetic genes restores cytokinin-mediated biocontrol, which is correlated with differential cytokinin levels in planta. Arabidopsis mutant analyses revealed the necessity of functional plant cytokinin perception and salicylic acid-dependent defence signalling for this biocontrol mechanism. These results demonstrate microbial cytokinin production as a novel microbe-based, hormone-mediated concept of biocontrol. This mechanism provides a basis to potentially develop novel, integrated plant protection strategies combining promotion of growth, a favourable physiological status and activation of fine-tuned direct defence and abiotic stress resilience. PMID:26984671

Cytokinin production by Pseudomonas fluorescens G20-18 determines biocontrol activity against Pseudomonas syringae in Arabidopsis.

PubMed

Großkinsky, Dominik K; Tafner, Richard; Moreno, María V; Stenglein, Sebastian A; García de Salamone, Inés E; Nelson, Louise M; Novák, Ondřej; Strnad, Miroslav; van der Graaff, Eric; Roitsch, Thomas

2016-03-17

Plant beneficial microbes mediate biocontrol of diseases by interfering with pathogens or via strengthening the host. Although phytohormones, including cytokinins, are known to regulate plant development and physiology as well as plant immunity, their production by microorganisms has not been considered as a biocontrol mechanism. Here we identify the ability of Pseudomonas fluorescens G20-18 to efficiently control P. syringae infection in Arabidopsis, allowing maintenance of tissue integrity and ultimately biomass yield. Microbial cytokinin production was identified as a key determinant for this biocontrol effect on the hemibiotrophic bacterial pathogen. While cytokinin-deficient loss-of-function mutants of G20-18 exhibit impaired biocontrol, functional complementation with cytokinin biosynthetic genes restores cytokinin-mediated biocontrol, which is correlated with differential cytokinin levels in planta. Arabidopsis mutant analyses revealed the necessity of functional plant cytokinin perception and salicylic acid-dependent defence signalling for this biocontrol mechanism. These results demonstrate microbial cytokinin production as a novel microbe-based, hormone-mediated concept of biocontrol. This mechanism provides a basis to potentially develop novel, integrated plant protection strategies combining promotion of growth, a favourable physiological status and activation of fine-tuned direct defence and abiotic stress resilience.

Plant Microbe Interactions in Post Genomic Era: Perspectives and Applications

PubMed Central

Imam, Jahangir; Singh, Puneet K.; Shukla, Pratyoosh

2016-01-01

Deciphering plant–microbe interactions is a promising aspect to understand the benefits and the pathogenic effect of microbes and crop improvement. The advancement in sequencing technologies and various ‘omics’ tool has impressively accelerated the research in biological sciences in this area. The recent and ongoing developments provide a unique approach to describing these intricate interactions and test hypotheses. In the present review, we discuss the role of plant-pathogen interaction in crop improvement. The plant innate immunity has always been an important aspect of research and leads to some interesting information like the adaptation of unique immune mechanisms of plants against pathogens. The development of new techniques in the post - genomic era has greatly enhanced our understanding of the regulation of plant defense mechanisms against pathogens. The present review also provides an overview of beneficial plant–microbe interactions with special reference to Agrobacterium tumefaciens-plant interactions where plant derived signal molecules and plant immune responses are important in pathogenicity and transformation efficiency. The construction of various Genome-scale metabolic models of microorganisms and plants presented a better understanding of all metabolic interactions activated during the interactions. This review also lists the emerging repertoire of phytopathogens and its impact on plant disease resistance. Outline of different aspects of plant-pathogen interactions is presented in this review to bridge the gap between plant microbial ecology and their immune responses. PMID:27725809

Climate change impairs processes of soil and plant N cycling in European beech forests on marginal soil

NASA Astrophysics Data System (ADS)

Tejedor, Javier; Gasche, Rainer; Gschwendtner, Silvia; Leberecht, Martin; Bimüller, Carolin; Kögel-Knabner, Ingrid; Pole, Andrea; Schloter, Michael; Rennenberg, Heinz; Simon, Judy; Hanewinkel, Marc; Baltensweiler, Andri; Bilela, Silvija; Dannenmann, Michael

2014-05-01

Beech forests of Central Europe are covering large areas with marginal calcareous soils, but provide important ecological services and represent a significant economical value. The vulnerability of these ecosystems to projected climate conditions (higher temperatures, increase of extreme drought and precipitation events) is currently unclear. Here we present comprehensive data on the influence of climate change conditions on ecosystem performance, considering soil nitrogen biogeochemistry, soil microbiology, mycorrhiza ecology and plant physiology. We simultaneously quantified major plant and soil gross N turnover processes by homogenous triple 15N isotope labeling of intact beech natural regeneration-soil-microbe systems. This isotope approach was combined with a space for time climate change experiment, i.e. we transferred intact beech seedling-soil-microbe mesocosms from a slope with N-exposure (representing present day climate conditions) to a slope with S exposure (serving as a warmer and drier model climate for future conditions). Transfers within N slope served as controls. After an equilibration period of 1 year, three isotope labeling/harvest cycles were performed. Reduced soil water content resulted in a persistent decline of ammonia oxidizing bacteria in soil (AOB). Consequently, we found a massive five-fold reduction of gross nitrification in the climate change treatment and a subsequent strong decline in soil nitrate concentrations as well as nitrate uptake by microorganisms and beech. Because nitrate was the major nutrient for beech in this forest type with little importance of ammonium and amino acids, this resulted in a strongly reduced performance of beech natural regeneration with reduced N content, N metabolite concentrations and plant biomass. These findings provided an explanation for a large-scale decline of distribution of beech forests on calcareous soils in Europe by almost 80% until 2080 predicted by statistical modeling. Hence, we question the sustainability of such forests under projected climate change conditions, but also discuss potential mitigation and adaptation options. Important comment: The topic of this abstract is subject to a press embargo, because it is in review at a Nature Journal

Linking Nitrogen-Cycling Microbial Communities to Environmental Fluctuations and Biogeochemical Activity in a Large, Urban Estuary: the San Francisco Bay-Delta

NASA Astrophysics Data System (ADS)

Francis, C.

2015-12-01

Nitrogen (N) availability is an important factor controlling productivity and thus carbon cycling in estuaries. The fate of N in estuaries depends on the activities of the microbes that carry out the N-cycle, which in turn depend on factors such as organic matter availability, dissolved inorganic N, salinity, oxygen, and temperature. Key microbial N transformations include nitrification (the aerobic oxidation of ammonia to nitrite and nitrate) and denitrification (the anaerobic reduction of nitrate to dinitrogen gas). While denitrification leads to N loss, nitrification is the only link between reduced N (produced by decomposition) and oxidized N (substrates for N loss processes), and both processes are known to produce nitrous oxide (N2O), a potent greenhouse gas. Understanding controls of N-cycling in the San Francisco Bay-Delta (SFBD)—the largest estuary on the west coast of North America—is particularly important, as this urban estuary is massively polluted with N, even compared to classic "eutrophic" systems. Interestingly, the SFBD has been spared the detrimental consequences of nutrient enrichment, largely due to high suspended sediment concentrations (and thus low light penetration) throughout the water column, combined with high grazing pressure. However, the recent "clearing" of SFBD waters due to a sharp decrease in suspended sediments may significantly alter the ecology of the estuary, by increasing phytoplankton growth. Thus, the SFBD may be losing its historical resilience to eutrophication, and may soon be "high-nutrient, low-chlorophyll" no more. Elucidating the environmental factors affecting the community structure, activity, and functioning of N-cycling microbes in SFBD is crucial for determining how changes in turbidity and productivity will be propagated throughout the ecosystem. While substantial ecological research in the SFBD has focused on phytoplankton and food webs, bacterial and archaeal communities have received far less attention. Using a combination of molecular, biogeochemical, and 'omics' approaches, we have been examining how N-cycling microbial communities throughout the SFBD change in relation to environmental fluctuations—a critical step in understanding how microbial populations drive biogeochemical cycling in this estuary.

A moving view: subcellular trafficking processes in pattern recognition receptor-triggered plant immunity.

PubMed

Ben Khaled, Sara; Postma, Jelle; Robatzek, Silke

2015-01-01

A significant challenge for plants is to induce localized defense responses at sites of pathogen attack. Therefore, host subcellular trafficking processes enable accumulation and exchange of defense compounds, which contributes to the plant on-site defenses in response to pathogen perception. This review summarizes our current understanding of the transport processes that facilitate immunity, the significance of which is highlighted by pathogens reprogramming membrane trafficking through host cell translocated effectors. Prominent immune-related cargos of plant trafficking pathways are the pattern recognition receptors (PRRs), which must be present at the plasma membrane to sense microbes in the apoplast. We focus on the dynamic localization of the FLS2 receptor and discuss the pathways that regulate receptor transport within the cell and their link to FLS2-mediated immunity. One emerging theme is that ligand-induced late endocytic trafficking is conserved across different PRR protein families as well as across different plant species.

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

Ecological Assets and Academic Procrastination among Adolescents: The Mediating Role of Commitment to Learning.

PubMed

Chen, Bin-Bin; Han, Wen

2017-01-01

Academic procrastination is defined as a purposive delay of academic tasks that must be completed. Within the framework of the ecological model of resiliency, this study examined how ecological assets were related to academic procrastination among adolescents. Participants in the study were 577 adolescents (53.5% boys) from Shanghai, China. They completed measures of ecological assets, commitment to learning, and academic procrastination. Structural equation modeling revealed that, as predicted, ecological assets were negatively associated with academic procrastination. In addition, commitment to learning fully mediated the association between ecological assets and academic procrastination. Implications of the present findings are discussed.

Ecological Assets and Academic Procrastination among Adolescents: The Mediating Role of Commitment to Learning

PubMed Central

Chen, Bin-Bin; Han, Wen

2017-01-01

Academic procrastination is defined as a purposive delay of academic tasks that must be completed. Within the framework of the ecological model of resiliency, this study examined how ecological assets were related to academic procrastination among adolescents. Participants in the study were 577 adolescents (53.5% boys) from Shanghai, China. They completed measures of ecological assets, commitment to learning, and academic procrastination. Structural equation modeling revealed that, as predicted, ecological assets were negatively associated with academic procrastination. In addition, commitment to learning fully mediated the association between ecological assets and academic procrastination. Implications of the present findings are discussed. PMID:29379451

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

Fluvial particle characterization using artificial neural network and spectral image processing

NASA Astrophysics Data System (ADS)

Shrestha, Bim Prasad; Gautam, Bijaya; Nagata, Masateru

2008-03-01

Sand, chemical waste, microbes and other solid materials flowing with the water bodies are of great significance to us as they cause substantial impact to different sectors including drinking water management, hydropower generation, irrigation, aquatic life preservation and various other socio-ecological factors. Such particles can't completely be avoided due to the high cost of construction and maintenance of the waste-treatment methods. A detailed understanding of solid particles in surface water system can have benefit in effective, economic, environmental and social management of water resources. This paper describes an automated system of fluvial particle characterization based on spectral image processing that lead to the development of devices for monitoring flowing particles in river. Previous research in coherent field has shown that it is possible to automatically classify shapes and sizes of solid particles ranging from 300-400 μm using artificial neural networks (ANN) and image processing. Computer facilitated with hyper spectral and multi spectral images using ANN can further classify fluvial materials into organic, inorganic, biodegradable, bio non degradable and microbes. This makes the method attractive for real time monitoring of particles, sand and microorganism in water bodies at strategic locations. Continuous monitoring can be used to determine the effect of socio-economic activities in upstream rivers, or to monitor solid waste disposal from treatment plants and industries or to monitor erosive characteristic of sand and its contribution to degradation of efficiency of hydropower plant or to identify microorganism, calculate their population and study the impact of their presence. Such system can also be used to characterize fluvial particles for planning effective utilization of water resources in micro-mega hydropower plant, irrigation, aquatic life preservation etc.

Exploring the microbially-mediated soil H2 sink: A lab-based study of the physiology and related H2 consumption of isolates from the Harvard Forest

NASA Astrophysics Data System (ADS)

Rao, D.; Meredith, L. K.; Bosak, T.; Hansel, C. M.; Ono, S.; Prinn, R. G.

2012-12-01

Atmospheric hydrogen (H2) is a secondary greenhouse gas because it attenuates the removal of methane (CH4) from the atmosphere. The largest and most uncertain term in the H2 biogeochemical cycle, microbe-mediated soil uptake, is responsible for about 80% of Earth's tropospheric H2 sink. Recently, the first H2-oxidizing soil microorganisms were discovered (genus Streptomyces) whose low-threshold, high-affinity NiFe-hydrogenase functions at ambient H2 levels (approx. 530 ppb). To better understand the ecological function of this hydrogenase, we conducted a controlled laboratory study of the H2 uptake behavior in accordance with the complex life cycle development of the streptomycetes. Several strains of the genus Streptomyces containing a high-affinity NiFe- hydrogenase were isolated from soil at the Harvard Forest. The presence of this hydrogenase, detected by PCR amplification of the hydrogenase large subunit, predicted H2 uptake behavior in wild-type streptomycetes and in phylogenetically different organisms containing more distantly related versions of the gene. H2 uptake depended on the streptomyces' life cycle, reaching a maximum during spore formation. These findings reveal connections between environmental conditions, organismal life cycle, and H2 uptake. With the rise of H2-based energy sources and a potential change in the tropospheric concentration of H2, understanding the sources and sinks of this trace gas is important for the future.

Linking microbial assemblages to paleoenvironmental conditions from the Holocene and Last Glacial Maximum times in Laguna Potrok Aike sediments, Argentina

NASA Astrophysics Data System (ADS)

Vuillemin, Aurele; Ariztegui, Daniel; Leavitt, Peter R.; Bunting, Lynda

2014-05-01

Laguna Potrok Aike is a closed basin located in the southern hemisphere's mid-latitudes (52°S) where paleoenvironmental conditions were recorded as temporal sedimentary sequences resulting from variations in the regional hydrological regime and geology of the catchment. The interpretation of the limnogeological multiproxy record developed during the ICDP-PASADO project allowed the identification of contrasting time windows associated with the fluctuations of Southern Westerly Winds. In the framework of this project, a 100-m-long core was also dedicated to a detailed geomicrobiological study which aimed at a thorough investigation of the lacustrine subsurface biosphere. Indeed, aquatic sediments do not only record past climatic conditions, but also provide a wide range of ecological niches for microbes. In this context, the influence of environmental features upon microbial development and survival remained still unexplored for the deep lacustrine realm. Therefore, we investigated living microbes throughout the sedimentary sequence using in situ ATP assays and DAPI cell count. These results, compiled with pore water analysis, SEM microscopy of authigenic concretions and methane and fatty acid biogeochemistry, provided evidence for a sustained microbial activity in deep sediments and pinpointed the substantial role of microbial processes in modifying initial organic and mineral fractions. Finally, because the genetic material associated with microorganisms can be preserved in sediments over millennia, we extracted environmental DNA from Laguna Potrok Aike sediments and established 16S rRNA bacterial and archaeal clone libraries to better define the use of DNA-based techniques in reconstructing past environments. We focused on two sedimentary horizons both displaying in situ microbial activity, respectively corresponding to the Holocene and Last Glacial Maximum periods. Sequences recovered from the productive Holocene record revealed a microbial community adapted to subsaline conditions producing methane with a high potential of organic matter degradation. In contrast, sediments rich in volcanic detritus from the Last Glacial Maximum showed a substantial presence of lithotrophic microorganisms and sulphate-reducing bacteria mediating authigenic minerals. Together, these features suggested that microbial communities developed in response to climatic control of lake and catchment productivity at the time of sediment deposition. Prevailing climatic conditions exerted a hierarchical control on the microbial composition of lake sediments by regulating the influx of organic and inorganic material to the lake basin, which in turn determined water column chemistry, production and sedimentation of particulate material, resulting in the different niches sheltering these microbial assemblages. Moreover, it demonstrated that environmental DNA can constitute sedimentary archives of phylogenetic diversity and diagenetic processes over tens of millennia.

Bacteria mediate oviposition by the black soldier fly, Hermetia illucens (L.), (Diptera: Stratiomyidae)

USDA-ARS?s Scientific Manuscript database

There can be substantial negative consequences for insects colonizing a resource in the presence of competitors. We hypothesized that microbes associated with an oviposition resource and resulting eggs deposited by insects serve as a mechanism regulating subsequent insect attraction, colonization, ...

A comparative study on effects of heterotrophic microbial activity on the stability of bivalve and coral carbonate during early diagenesis.

NASA Astrophysics Data System (ADS)

Lange, Skadi M.; Krause, Stefan; Immenhauser, Adrian; Ritter, Ann-Christin; Gorb, Stanislav N.; Kleinteich, Thomas; Treude, Tina

2016-04-01

Following deposition and shallow burial, marine biogenic carbonates are exposed to an environment that is geochemically affected by a manifold of bacterial metabolic redox processes. To allow for comparison of potential microbe-mediated alteration effects on carbonates, we used aragonitic bivalve shell samples and porous aragonitic coral fragments for incubation experiments in oxic- and anoxic seawater media. The media contained marine sediment slurries or bacterial cultures to mimic the natural processes in vitro. The results for anoxic experimental media containing bivalve shell samples or coral fragments displayed considerable changes in carbonate-system parameters (pH, AT, CA, DIC) and divalent-cation ratios (Mg/Ca, Mg/Sr, Sr/Ca) over time. Furthermore, incubated bivalve shell samples were altered in morphology, elemental composition and isotopic signature. Coral-fragment bearing oxic incubations were run at two temperature regimes and divalent-cation ratios of the high-temperature bacterial medium displayed withdrawal of Ca2+ and Sr2+ from the medium, thus indicating microbe-induced secondary aragonite precipitation. Analyses of coral fragments include electron-microprobe mapping and X-ray microtomography to resolve elemental sample composition and pore-space alteration features, respectively. Up to this point our results indicate that heterotrophic bacterial activity has the potential to affect surficial or open pore space in carbonate archives by increasing rates of alteration relative to sterile environments.

Microbial carbon pump and its significance for carbon sequestration in soils

NASA Astrophysics Data System (ADS)

Liang, Chao

2017-04-01

Studies of the decomposition, transformation and stabilization of soil organic carbon have dramatically increased in recent years due to growing interest in studying the global carbon cycle as it pertains to climate change. While it is readily accepted that the magnitude of the organic carbon reservoir in soils depends upon microbial involvement because soil carbon dynamics are ultimately the consequence of microbial growth and activity, it remains largely unknown how these microbe-mediated processes lead to soil carbon stabilization. Here, two pathways, ex vivo modification and in vivo turnover, were defined to jointly explain soil carbon dynamics driven by microbial catabolism and/or anabolism. Accordingly, a conceptual framework consisting of the raised concept of the soil "microbial carbon pump" (MCP) was demonstrated to describe how microbes act as an active player in soil carbon storage. The hypothesis is that the long-term microbial assimilation process may facilitate the formation of a set of organic compounds that are stabilized (whether via protection by physical interactions or a reduction in activation energy due to chemical composition), ultimately leading to the sequestration of microbial-derived carbon in soils. The need for increased efforts was proposed to seek to inspire new studies that utilize the soil MCP as a conceptual guideline for improving mechanistic understandings of the contributions of soil carbon dynamics to the responses of the terrestrial carbon cycle under global change.

Physics of phagocytosis of foreign versus self-tolerance

NASA Astrophysics Data System (ADS)

Tsai, Richard; Rodriguez, Pia; Discher, Dennis

2009-03-01

The first cells to `attack' an implanted or injected foreign material or microbe are phagocytic cells of the innate immune system. These cells actively and rapidly phagocytose foreign cells, surfaces, or particles, but the process that is inefficient when faced with ``self'' cells. We have examined the biochemistry and some of the physics of this decision to eat or not eat. One particular protein on all animal cell membranes, called CD47, seems to engage phagocytic cell couter-receptors, and deactivate the force-generating myosin machinery that otherwise makes phagocytosis efficient. We will map the phagocytic synapse between phagocytes and particles or cells and describe the physicochemical dynamics that mediate this key decision in compatability.

The biology of color.

PubMed

Cuthill, Innes C; Allen, William L; Arbuckle, Kevin; Caspers, Barbara; Chaplin, George; Hauber, Mark E; Hill, Geoffrey E; Jablonski, Nina G; Jiggins, Chris D; Kelber, Almut; Mappes, Johanna; Marshall, Justin; Merrill, Richard; Osorio, Daniel; Prum, Richard; Roberts, Nicholas W; Roulin, Alexandre; Rowland, Hannah M; Sherratt, Thomas N; Skelhorn, John; Speed, Michael P; Stevens, Martin; Stoddard, Mary Caswell; Stuart-Fox, Devi; Talas, Laszlo; Tibbetts, Elizabeth; Caro, Tim

2017-08-04

Coloration mediates the relationship between an organism and its environment in important ways, including social signaling, antipredator defenses, parasitic exploitation, thermoregulation, and protection from ultraviolet light, microbes, and abrasion. Methodological breakthroughs are accelerating knowledge of the processes underlying both the production of animal coloration and its perception, experiments are advancing understanding of mechanism and function, and measurements of color collected noninvasively and at a global scale are opening windows to evolutionary dynamics more generally. Here we provide a roadmap of these advances and identify hitherto unrecognized challenges for this multi- and interdisciplinary field. Copyright © 2017 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

NEON: High Frequency Monitoring Network for Watershed-Scale Processes and Aquatic Ecology

NASA Astrophysics Data System (ADS)

Vance, J. M.; Fitzgerald, M.; Parker, S. M.; Roehm, C. L.; Goodman, K. J.; Bohall, C.; Utz, R.

2014-12-01

Networked high frequency hydrologic and water quality measurements needed to investigate physical and biogeochemical processes at the watershed scale and create robust models are limited and lacking standardization. Determining the drivers and mechanisms of ecological changes in aquatic systems in response to natural and anthropogenic pressures is challenging due to the large amounts of terrestrial, aquatic, atmospheric, biological, chemical, and physical data it requires at varied spatiotemporal scales. The National Ecological Observatory Network (NEON) is a continental-scale infrastructure project designed to provide data to address the impacts of climate change, land-use, and invasive species on ecosystem structure and function. Using a combination of standardized continuous in situ measurements and observational sampling, the NEON Aquatic array will produce over 200 data products across its spatially-distributed field sites for 30 years to facilitate spatiotemporal analysis of the drivers of ecosystem change. Three NEON sites in Alabama were chosen to address linkages between watershed-scale processes and ecosystem changes along an eco-hydrological gradient within the Tombigbee River Basin. The NEON Aquatic design, once deployed, will include continuous measurements of surface water physical, chemical, and biological parameters, groundwater level, temperature and conductivity and local meteorology. Observational sampling will include bathymetry, water chemistry and isotopes, and a suite of organismal sampling from microbes to macroinvertebrates to vertebrates. NEON deployed a buoy to measure the temperature profile of the Black Warrior River from July - November, 2013 to determine the spatiotemporal variability across the water column from a daily to seasonal scale. In July 2014 a series of water quality profiles were performed to assess the contribution of physical and biogeochemical drivers over a diurnal cycle. Additional river transects were performed across our site reach to capture the spatial variability of surface water parameters. Our preliminary data show differing response times to precipitation events and diurnal processes informing our infrastructure designs and sampling protocols aimed at providing data to address the eco-hydrological gradient.

The Natural Biotic Environment of Caenorhabditis elegans.

PubMed

Schulenburg, Hinrich; Félix, Marie-Anne

2017-05-01

Organisms evolve in response to their natural environment. Consideration of natural ecological parameters are thus of key importance for our understanding of an organism's biology. Curiously, the natural ecology of the model species Caenorhabditis elegans has long been neglected, even though this nematode has become one of the most intensively studied models in biological research. This lack of interest changed ∼10 yr ago. Since then, an increasing number of studies have focused on the nematode's natural ecology. Yet many unknowns still remain. Here, we provide an overview of the currently available information on the natural environment of C. elegans We focus on the biotic environment, which is usually less predictable and thus can create high selective constraints that are likely to have had a strong impact on C. elegans evolution. This nematode is particularly abundant in microbe-rich environments, especially rotting plant matter such as decomposing fruits and stems. In this environment, it is part of a complex interaction network, which is particularly shaped by a species-rich microbial community. These microbes can be food, part of a beneficial gut microbiome, parasites and pathogens, and possibly competitors. C. elegans is additionally confronted with predators; it interacts with vector organisms that facilitate dispersal to new habitats, and also with competitors for similar food environments, including competitors from congeneric and also the same species. Full appreciation of this nematode's biology warrants further exploration of its natural environment and subsequent integration of this information into the well-established laboratory-based research approaches. Copyright © 2017 by the Genetics Society of America.

Draft Genome Sequence of Deep-Sea Alteromonas sp. Strain V450 Isolated from the Marine Sponge Leiodermatium sp.

PubMed Central

Barrett, Nolan H.; McCarthy, Peter J.

2017-01-01

ABSTRACT The proteobacterium Alteromonas sp. strain V450 was isolated from the Atlantic deep-sea sponge Leiodermatium sp. Here, we report the draft genome sequence of this strain, with a genome size of approx. 4.39 Mb and a G+C content of 44.01%. The results will aid deep-sea microbial ecology, evolution, and sponge-microbe association studies. PMID:28153886

Reconciling Pasteur and Darwin to control infectious diseases

PubMed Central

Méthot, Pierre-Olivier

2018-01-01

The continual emergence of new pathogens and the increased spread of antibiotic resistance in bacterial populations remind us that microbes are living entities that evolve at rates that impact public health interventions. Following the historical thread of the works of Pasteur and Darwin shows how reconciling clinical microbiology, ecology, and evolution can be instrumental to understanding pathology, developing new therapies, and prolonging the efficiency of existing ones. PMID:29346373

Soil Microbial Responses to Elevated CO2 and O3 in a Nitrogen-Aggrading Agroecosystem

PubMed Central

Cheng, Lei; Booker, Fitzgerald L.; Burkey, Kent O.; Tu, Cong; Shew, H. David; Rufty, Thomas W.; Fiscus, Edwin L.; Deforest, Jared L.; Hu, Shuijin

2011-01-01

Climate change factors such as elevated atmospheric carbon dioxide (CO2) and ozone (O3) can exert significant impacts on soil microbes and the ecosystem level processes they mediate. However, the underlying mechanisms by which soil microbes respond to these environmental changes remain poorly understood. The prevailing hypothesis, which states that CO2- or O3-induced changes in carbon (C) availability dominate microbial responses, is primarily based on results from nitrogen (N)-limiting forests and grasslands. It remains largely unexplored how soil microbes respond to elevated CO2 and O3 in N-rich or N-aggrading systems, which severely hinders our ability to predict the long-term soil C dynamics in agroecosystems. Using a long-term field study conducted in a no-till wheat-soybean rotation system with open-top chambers, we showed that elevated CO2 but not O3 had a potent influence on soil microbes. Elevated CO2 (1.5×ambient) significantly increased, while O3 (1.4×ambient) reduced, aboveground (and presumably belowground) plant residue C and N inputs to soil. However, only elevated CO2 significantly affected soil microbial biomass, activities (namely heterotrophic respiration) and community composition. The enhancement of microbial biomass and activities by elevated CO2 largely occurred in the third and fourth years of the experiment and coincided with increased soil N availability, likely due to CO2-stimulation of symbiotic N2 fixation in soybean. Fungal biomass and the fungi∶bacteria ratio decreased under both ambient and elevated CO2 by the third year and also coincided with increased soil N availability; but they were significantly higher under elevated than ambient CO2. These results suggest that more attention should be directed towards assessing the impact of N availability on microbial activities and decomposition in projections of soil organic C balance in N-rich systems under future CO2 scenarios. PMID:21731722

Interactive Effects of Nitrogen and Phosphorus on Soil Microbial Communities in a Tropical Forest

PubMed Central

Liu, Lei; Zhang, Tao; Gilliam, Frank S.; Gundersen, Per; Zhang, Wei; Chen, Hao; Mo, Jiangming

2013-01-01

Elevated nitrogen (N) deposition in humid tropical regions may exacerbate phosphorus (P) deficiency in forests on highly weathered soils. However, it is not clear how P availability affects soil microbes and soil carbon (C), or how P processes interact with N deposition in tropical forests. We examined the effects of N and P additions on soil microbes and soil C pools in a N-saturated old-growth tropical forest in southern China to test the hypotheses that (1) N and P addition will have opposing effects on soil microbial biomass and activity, (2) N and P addition will alter the composition of the microbial community, (3) the addition of N and P will have interactive effects on soil microbes and (4) addition-mediated changes in microbial communities would feed back on soil C pools. Phospholipid fatty acid (PLFA) analysis was used to quantify the soil microbial community following four treatments: Control, N addition (15 g N m−2 yr−1), P addition (15 g P m−2 yr−1), and N&P addition (15 g N m−2 yr−1 plus 15 g P m−2 yr−1). These were applied from 2007 to 2011. Whereas additions of P increased soil microbial biomass, additions of N reduced soil microbial biomass. These effects, however, were transient, disappearing over longer periods. Moreover, N additions significantly increased relative abundance of fungal PLFAs and P additions significantly increased relative abundance of arbuscular mycorrhizal (AM) fungi PLFAs. Nitrogen addition had a negative effect on light fraction C, but no effect on heavy fraction C and total soil C. In contrast, P addition significantly decreased both light fraction C and total soil C. However, there were no interactions between N addition and P addition on soil microbes. Our results suggest that these nutrients are not co-limiting, and that P rather than N is limiting in this tropical forest. PMID:23593427

Proposal and Research Direction of Soil Mass Organic Reorganization

NASA Astrophysics Data System (ADS)

Zhang, Lu; Han, Jichang

2018-01-01

Land engineering as a new discipline has been temporarily outrageous. The proposition of soil body organic reorganization undoubtedly enriches the research content for the construction of land engineering disciplines. Soil body organic reconstruction is designed to study how to realize the ecological ecology of the land by studying the external force of nature, to study the influence of sunlight, wind and water on soil body, how to improve the soil physical structure, to further strengthen the research of biological enzymes and microbes, and promote the release and utilization of beneficial inert elements in soil body. The emerging of frontier scientific research issues with soil body organic reorganization to indicate directions for the future development of soil engineering.

Ocean plankton. Structure and function of the global ocean microbiome.

PubMed

Sunagawa, Shinichi; Coelho, Luis Pedro; Chaffron, Samuel; Kultima, Jens Roat; Labadie, Karine; Salazar, Guillem; Djahanschiri, Bardya; Zeller, Georg; Mende, Daniel R; Alberti, Adriana; Cornejo-Castillo, Francisco M; Costea, Paul I; Cruaud, Corinne; d'Ovidio, Francesco; Engelen, Stefan; Ferrera, Isabel; Gasol, Josep M; Guidi, Lionel; Hildebrand, Falk; Kokoszka, Florian; Lepoivre, Cyrille; Lima-Mendez, Gipsi; Poulain, Julie; Poulos, Bonnie T; Royo-Llonch, Marta; Sarmento, Hugo; Vieira-Silva, Sara; Dimier, Céline; Picheral, Marc; Searson, Sarah; Kandels-Lewis, Stefanie; Bowler, Chris; de Vargas, Colomban; Gorsky, Gabriel; Grimsley, Nigel; Hingamp, Pascal; Iudicone, Daniele; Jaillon, Olivier; Not, Fabrice; Ogata, Hiroyuki; Pesant, Stephane; Speich, Sabrina; Stemmann, Lars; Sullivan, Matthew B; Weissenbach, Jean; Wincker, Patrick; Karsenti, Eric; Raes, Jeroen; Acinas, Silvia G; Bork, Peer

2015-05-22

Microbes are dominant drivers of biogeochemical processes, yet drawing a global picture of functional diversity, microbial community structure, and their ecological determinants remains a grand challenge. We analyzed 7.2 terabases of metagenomic data from 243 Tara Oceans samples from 68 locations in epipelagic and mesopelagic waters across the globe to generate an ocean microbial reference gene catalog with >40 million nonredundant, mostly novel sequences from viruses, prokaryotes, and picoeukaryotes. Using 139 prokaryote-enriched samples, containing >35,000 species, we show vertical stratification with epipelagic community composition mostly driven by temperature rather than other environmental factors or geography. We identify ocean microbial core functionality and reveal that >73% of its abundance is shared with the human gut microbiome despite the physicochemical differences between these two ecosystems. Copyright © 2015, American Association for the Advancement of Science.

Fragile skin microbiomes in megacities are assembled by a predominantly niche-based process

PubMed Central

Kim, Hye-Jin; Kim, Hanbyul; Kim, Jin Ju; Myeong, Nu Ri; Kim, Taeyune; Park, Taehun; Kim, Eunjoo; Choi, Ji-yei; Lee, Johnhwan; An, Susun; Sul, Woo Jun

2018-01-01

Given the higher incidence of skin diseases in more urbanized populations and its association with the skin microbiome, we questioned how the skin microbiome differed depending on the degree of urbanization. Skin microbiomes of 231 healthy subjects in five large cities in China varied mainly with environment and socioeconomic status of the cities in question. The differences among microbiomes could be explained by the predominantly niche-based assembly of microbial communities, which was supported by a dominance test, β-null deviation, and edge-length abundance distribution. Networks among microbes in larger cities were more fragile, which may contribute to the higher incidence of skin diseases in more urbanized environments. These results suggest that microbial ecological theory can provide a framework for understanding crucial health-associated features of the human microbiome. PMID:29532031

Defining the Molecular-Cellular-Field Continuum of Mercury Detoxification

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

Summers, Anne O.

Hg is of special interest to DOE due to past intensive use in manufacture of nuclear weapons at the Oak Ridge Reservation (ORR). Because of its facile oxidation/reduction [Hg(II)/Hg(0)] chemistry, ability to bond to carbon [as in highly toxic methylmercury: MeHg(I)] and its unique physical properties [e.g., volatility of Hg(0)], Hg has a complex environmental cycle involving soils, sediments, waterways and the atmosphere and including biotic and abiotic chemical and physical transport and transformations.1 Understanding such processes well enough to design stewardship plans that minimize negative impacts in diverse ecological settings requires rich knowledge of the contributing abiotic and bioticmore » processes. Prokaryotes are major players in the global Hg cycle. Facultative and anaerobic bacteria can form MeHg(I) with consequent intoxication of wildlife and humans. Sustainable stewardship of Hg-contaminated sites requires eliminating not only MeHg(I) but also the Hg(II) substrate for methylation. Fortunately, a variety of mercury resistant (HgR) aerobic and facultative bacteria and archaea can do both things. Prokaryotes harboring narrow or broad Hg resistance (mer) loci detoxify Hg(II) or RHg(I), respectively, to relatively inert, less toxic, volatile Hg(0). HgR microbes are enriched in highly contaminated sites and extensive field data show they depress levels of MeHg >500-fold in such zones2. So, enhancing the natural capacity of indigenous HgR microbes to remove Hg(II) and RHg(I) from soils, sediments and waterways is a logical component of a comprehensive plan for clean up and stewardship of contaminated sites.« less

Molecular Mechanisms of Bacterial Mercury Transformation

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

Summers, Anne O.; Smith, Jeremy C.

Hg is of special interest to DOE due to past intensive use in manufacture of nuclear weapons at the Oak Ridge Reservation (ORR). Because of its facile oxidation/reduction [Hg(II)/Hg(0)] chemistry, ability to bond to carbon [as in highly toxic methylmercury: MeHg(I)] and its unique physical properties [e.g., volatility of Hg(0)], Hg has a complex environmental cycle involving soils, sediments, waterways and the atmosphere and including biotic and abiotic chemical and physical transport and transformations. Understanding such processes well enough to design stewardship plans that minimize negative impacts in diverse ecological settings requires rich knowledge of the contributing abiotic and bioticmore » processes. Prokaryotes are major players in the global Hg cycle. Facultative and anaerobic bacteria can form MeHg(I) with consequent intoxication of wildlife and humans. Sustainable stewardship of Hg-contaminated sites requires eliminating not only MeHg(I) but also the Hg(II) substrate for methylation. Fortunately, a variety of mercury resistant (HgR) aerobic and facultative bacteria and archaea can do both things. Prokaryotes harboring narrow or broad Hg resistance (mer) loci detoxify Hg(II) or RHg(I), respectively, to relatively inert, less toxic, volatile Hg(0). HgR microbes are enriched in highly contaminated sites and extensive field data show they depress levels of MeHg >500-fold in such zones. So, enhancing the natural capacity of indigenous HgR microbes to remove Hg(II) and RHg(I) from soils, sediments and waterways is a logical component of a comprehensive plan for clean up and stewardship of contaminated sites.« less

Free-Living Nematodes in the Freshwater Food Web: A Review

PubMed Central

Majdi, Nabil; Traunspurger, Walter

2015-01-01

Free-living nematodes are well-recognized as an abundant and ubiquitous component of benthic communities in inland waters. Compelling evidence from soil and marine ecosystems has highlighted the importance of nematodes as trophic intermediaries between microbial production and higher trophic levels. However, the paucity of empirical evidence of their role in freshwater ecosystems has hampered their inclusion in our understanding of freshwater food web functioning. This literature survey provides an overview of research efforts in the field of freshwater nematode ecology and of the complex trophic interactions between free-living nematodes and microbes, other meiofauna, macro-invertebrates, and fishes. Based on an analysis of the relevant literature and an appreciation of the potential of emerging approaches for the evaluation of nematode trophic ecology, we point out research gaps and recommend relevant directions for further research. The latter include (i) interactions of nematodes with protozoans and fungi; (ii) nonconsumptive effects of nematodes on microbial activity and the effects of nematodes on associated key ecosystem processes (decomposition, primary production); and (iii) the feeding selectivity and intraspecific feeding variability of nematodes and their potential impacts on the structure of benthic communities. PMID:25861114

MICROBES IN DRINKING WATER: RECENT EPIDEMIOLOGIC RESEARCH TO ASSESS WATERBORNE RISKS

EPA Science Inventory

Microbial caused diarrhea continues to be a major cause of death in many countries. The transmission of these organisms to humans is often mediated by drinking water. These enteric illnesses occur in epidemic form (the occurrence of disease in excess of normal expectancy) an...

Contextualizing Community Violence and Its Effects: An Ecological Model of Parent-Child Interdependent Coping

ERIC Educational Resources Information Center

Aisenberg, Eugene; Ell, Kathleen

2005-01-01

This article presents an integrated conceptual framework that contextualizes exposure to community violence and the interpersonal and interdependent processes of parent and child response to community violence. This model posits that parental distress, including post-traumatic stress disorder (PTSD) and depression, is a significant mediator of…

Novel Insights into Insect-Microbe Interactions—Role of Epigenomics and Small RNAs

PubMed Central

Kim, Dohyup; Thairu, Margaret W.; Hansen, Allison K.

2016-01-01

It has become increasingly clear that microbes form close associations with the vast majority of animal species, especially insects. In fact, an array of diverse microbes is known to form shared metabolic pathways with their insect hosts. A growing area of research in insect-microbe interactions, notably for hemipteran insects and their mutualistic symbionts, is to elucidate the regulation of this inter-domain metabolism. This review examines two new emerging mechanisms of gene regulation and their importance in host-microbe interactions. Specifically, we highlight how the incipient areas of research on regulatory “dark matter” such as epigenomics and small RNAs, can play a pivotal role in the evolution of both insect and microbe gene regulation. We then propose specific models of how these dynamic forms of gene regulation can influence insect-symbiont-plant interactions. Future studies in this area of research will give us a systematic understanding of how these symbiotic microbes and animals reciprocally respond to and regulate their shared metabolic processes. PMID:27540386

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Monitoring for conservation

USGS Publications Warehouse

Nichols, J.D.; Williams, B.K.

2006-01-01

Human-mediated environmental changes have resulted in appropriate concern for the conservation of ecological systems and have led to the development of many ecological monitoring programs worldwide. Many programs that are identified with the purpose of `surveillance? represent an inefficient use of conservation funds and effort. Here, we revisit the 1964 paper by Platt and argue that his recommendations about the conduct of science are equally relevant to the conduct of ecological monitoring programs. In particular, we argue that monitoring should not be viewed as a stand-alone activity, but instead as a component of a larger process of either conservation-oriented science or management. Corresponding changes in monitoring focus and design would lead to substantial increases in the efficiency and usefulness of monitoring results in conservation.

Predator attack rate evolution in space: the role of ecology mediated by complex emergent spatial structure and self-shading.

PubMed

Messinger, Susanna M; Ostling, Annette

2013-11-01

Predation interactions are an important element of ecological communities. Population spatial structure has been shown to influence predator evolution, resulting in the evolution of a reduced predator attack rate; however, the evolutionary role of traits governing predator and prey ecology is unknown. The evolutionary effect of spatial structure on a predator's attack rate has primarily been explored assuming a fixed metapopulation spatial structure, and understood in terms of group selection. But endogenously generated, emergent spatial structure is common in nature. Furthermore, the evolutionary influence of ecological traits may be mediated through the spatial self-structuring process. Drawing from theory on pathogens, the evolutionary effect of emergent spatial structure can be understood in terms of self-shading, where a voracious predator limits its long-term invasion potential by reducing local prey availability. Here we formalize the effects of self-shading for predators using spatial moment equations. Then, through simulations, we show that in a spatial context self-shading leads to relationships between predator-prey ecology and the predator's attack rate that are not expected in a non-spatial context. Some relationships are analogous to relationships already shown for host-pathogen interactions, but others represent new trait dimensions. Finally, since understanding the effects of ecology using existing self-shading theory requires simplifications of the emergent spatial structure that do not apply well here, we also develop metrics describing the complex spatial structure of the predator and prey populations to help us explain the evolutionary effect of predator and prey ecology in the context of self-shading. The identification of these metrics may provide a step towards expansion of the predictive domain of self-shading theory to more complex spatial dynamics. Copyright © 2013 Elsevier Inc. All rights reserved.

Microbial interspecies electron transfer via electric currents through conductive minerals

PubMed Central

Kato, Souichiro; Hashimoto, Kazuhito; Watanabe, Kazuya

2012-01-01

In anaerobic biota, reducing equivalents (electrons) are transferred between different species of microbes [interspecies electron transfer (IET)], establishing the basis of cooperative behaviors and community functions. IET mechanisms described so far are based on diffusion of redox chemical species and/or direct contact in cell aggregates. Here, we show another possibility that IET also occurs via electric currents through natural conductive minerals. Our investigation revealed that electrically conductive magnetite nanoparticles facilitated IET from Geobacter sulfurreducens to Thiobacillus denitrificans, accomplishing acetate oxidation coupled to nitrate reduction. This two-species cooperative catabolism also occurred, albeit one order of magnitude slower, in the presence of Fe ions that worked as diffusive redox species. Semiconductive and insulating iron-oxide nanoparticles did not accelerate the cooperative catabolism. Our results suggest that microbes use conductive mineral particles as conduits of electrons, resulting in efficient IET and cooperative catabolism. Furthermore, such natural mineral conduits are considered to provide ecological advantages for users, because their investments in IET can be reduced. Given that conductive minerals are ubiquitously and abundantly present in nature, electric interactions between microbes and conductive minerals may contribute greatly to the coupling of biogeochemical reactions. PMID:22665802

Phylogenetic characterization of culturable bacteria and fungi associated with tarballs from Betul beach, Goa, India.

PubMed

Shinde, Varsha Laxman; Meena, Ram Murti; Shenoy, Belle Damodara

2018-03-01

Tarballs are semisolid blobs of crude oil, normally formed due to weathering of crude-oil in the sea after any kind of oil spills. Microorganisms are believed to thrive on hydrocarbon-rich tarballs and possibly assist in biodegradation. The taxonomy of ecologically and economically important tarball-associated microbes, however, needs improvement as DNA-based identification and phylogenetic characterization have been scarcely incorporated into it. In this study, bacteria and fungi associated with tarballs from touristic Betul beach in Goa, India were isolated, followed by phylogenetic analyses of 16S rRNA gene and the ITS sequence-data to decipher their clustering patterns with closely-related taxa. The gene-sequence analyses identified phylogenetically diverse 20 bacterial genera belonging to the phyla Proteobacteria (14), Actinobacteria (3), Firmicutes (2) and Bacteroidetes (1), and 8 fungal genera belonging to the classes Eurotiomycetes (6), Sordariomycetes (1) and Leotiomycetes (1) associated with the Betul tarball samples. Future studies employing a polyphasic approach, including multigene sequence-data, are needed for species-level identification of culturable tarball-associated microbes. This paper also discusses potentials of tarball-associated microbes to degrade hydrocarbons. Copyright © 2018 Elsevier Ltd. All rights reserved.

Biodiversity of genes encoding anti-microbial traits within plant associated microbes

PubMed Central

Mousa, Walaa K.; Raizada, Manish N.

2015-01-01

The plant is an attractive versatile home for diverse associated microbes. A subset of these microbes produces a diversity of anti-microbial natural products including polyketides, non-ribosomal peptides, terpenoids, heterocylic nitrogenous compounds, volatile compounds, bacteriocins, and lytic enzymes. In recent years, detailed molecular analysis has led to a better understanding of the underlying genetic mechanisms. New genomic and bioinformatic tools have permitted comparisons of orthologous genes between species, leading to predictions of the associated evolutionary mechanisms responsible for diversification at the genetic and corresponding biochemical levels. The purpose of this review is to describe the biodiversity of biosynthetic genes of plant-associated bacteria and fungi that encode selected examples of antimicrobial natural products. For each compound, the target pathogen and biochemical mode of action are described, in order to draw attention to the complexity of these phenomena. We review recent information of the underlying molecular diversity and draw lessons through comparative genomic analysis of the orthologous coding sequences (CDS). We conclude by discussing emerging themes and gaps, discuss the metabolic pathways in the context of the phylogeny and ecology of their microbial hosts, and discuss potential evolutionary mechanisms that led to the diversification of biosynthetic gene clusters. PMID:25914708

The Evolutionary Ecology of Plant Disease: A Phylogenetic Perspective.

PubMed

Gilbert, Gregory S; Parker, Ingrid M

2016-08-04

An explicit phylogenetic perspective provides useful tools for phytopathology and plant disease ecology because the traits of both plants and microbes are shaped by their evolutionary histories. We present brief primers on phylogenetic signal and the analytical tools of phylogenetic ecology. We review the literature and find abundant evidence of phylogenetic signal in pathogens and plants for most traits involved in disease interactions. Plant nonhost resistance mechanisms and pathogen housekeeping functions are conserved at deeper phylogenetic levels, whereas molecular traits associated with rapid coevolutionary dynamics are more labile at branch tips. Horizontal gene transfer disrupts the phylogenetic signal for some microbial traits. Emergent traits, such as host range and disease severity, show clear phylogenetic signals. Therefore pathogen spread and disease impact are influenced by the phylogenetic structure of host assemblages. Phylogenetically rare species escape disease pressure. Phylogenetic tools could be used to develop predictive tools for phytosanitary risk analysis and reduce disease pressure in multispecies cropping systems.

The coastal environment and human health: microbial indicators, pathogens, sentinels and reservoirs

PubMed Central

Stewart, Jill R; Gast, Rebecca J; Fujioka, Roger S; Solo-Gabriele, Helena M; Meschke, J Scott; Amaral-Zettler, Linda A; del Castillo, Erika; Polz, Martin F; Collier, Tracy K; Strom, Mark S; Sinigalliano, Christopher D; Moeller, Peter DR; Holland, A Fredrick

2008-01-01

Innovative research relating oceans and human health is advancing our understanding of disease-causing organisms in coastal ecosystems. Novel techniques are elucidating the loading, transport and fate of pathogens in coastal ecosystems, and identifying sources of contamination. This research is facilitating improved risk assessments for seafood consumers and those who use the oceans for recreation. A number of challenges still remain and define future directions of research and public policy. Sample processing and molecular detection techniques need to be advanced to allow rapid and specific identification of microbes of public health concern from complex environmental samples. Water quality standards need to be updated to more accurately reflect health risks and to provide managers with improved tools for decision-making. Greater discrimination of virulent versus harmless microbes is needed to identify environmental reservoirs of pathogens and factors leading to human infections. Investigations must include examination of microbial community dynamics that may be important from a human health perspective. Further research is needed to evaluate the ecology of non-enteric water-transmitted diseases. Sentinels should also be established and monitored, providing early warning of dangers to ecosystem health. Taken together, this effort will provide more reliable information about public health risks associated with beaches and seafood consumption, and how human activities can affect their exposure to disease-causing organisms from the oceans. PMID:19025674

Multiple hypotheses testing of fish incidence patterns in an urbanized ecosystem

USGS Publications Warehouse

Chizinski, C.J.; Higgins, C.L.; Shavlik, C.E.; Pope, K.L.

2006-01-01

Ecological and evolutionary theories have focused traditionally on natural processes with little attempt to incorporate anthropogenic influences despite the fact that humans are such an integral part of virtually all ecosystems. A series of alternate models that incorporated anthropogenic factors and traditional ecological mechanisms of invasion to account for fish incidence patterns in urban lakes was tested. The models were based on fish biology, human intervention, and habitat characteristics. However, the only models to account for empirical patterns were those that included fish invasiveness, which incorporated species-specific information about overall tolerance and fecundity. This suggests that species-specific characteristics are more important in general distributional patterns than human-mediated dispersal. Better information of illegal stocking activities is needed to improve human-mediated models, and more insight into basic life history of ubiquitous species is needed to truly understand underlying mechanisms of biotic homogenization. ?? Springer 2005.

Bioactive Molecules in Soil Ecosystems: Masters of the Underground

PubMed Central

Zhuang, Xuliang; Gao, Jie; Ma, Anzhou; Fu, Shenglei; Zhuang, Guoqiang

2013-01-01

Complex biological and ecological processes occur in the rhizosphere through ecosystem-level interactions between roots, microorganisms and soil fauna. Over the past decade, studies of the rhizosphere have revealed that when roots, microorganisms and soil fauna physically contact one another, bioactive molecular exchanges often mediate these interactions as intercellular signal, which prepare the partners for successful interactions. Despite the importance of bioactive molecules in sustainable agriculture, little is known of their numerous functions, and improving plant health and productivity by altering ecological processes remains difficult. In this review, we describe the major bioactive molecules present in below-ground ecosystems (i.e., flavonoids, exopolysaccharides, antibiotics and quorum-sensing signals), and we discuss how these molecules affect microbial communities, nutrient availability and plant defense responses. PMID:23615474

Development of Microbial and Enzymatic Fuel Cells for Bio-Inspired Power Sources

DTIC Science & Technology

2009-03-01

that of the oxidation of NADH as possible.[30] A variety of organic mediators have been studied for the anode, including phenazines ,[38] dyes,[39,40...glucose-6-phosphate dehydrogenase on the rotating graphite disc electrode modified with phenazine methosulfate. Enzyme Microb. Technol. 1993, 15 (6), 525

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Auxin and the integration of environmental signals into plant root development

PubMed Central

Kazan, Kemal

2013-01-01

Background Auxin is a versatile plant hormone with important roles in many essential physiological processes. In recent years, significant progress has been made towards understanding the roles of this hormone in plant growth and development. Recent evidence also points to a less well-known but equally important role for auxin as a mediator of environmental adaptation in plants. Scope This review briefly discusses recent findings on how plants utilize auxin signalling and transport to modify their root system architecture when responding to diverse biotic and abiotic rhizosphere signals, including macro- and micro-nutrient starvation, cold and water stress, soil acidity, pathogenic and beneficial microbes, nematodes and neighbouring plants. Stress-responsive transcription factors and microRNAs that modulate auxin- and environment-mediated root development are also briefly highlighted. Conclusions The auxin pathway constitutes an essential component of the plant's biotic and abiotic stress tolerance mechanisms. Further understanding of the specific roles that auxin plays in environmental adaptation can ultimately lead to the development of crops better adapted to stressful environments. PMID:24136877

Auxin and the integration of environmental signals into plant root development.

PubMed

Kazan, Kemal

2013-12-01

Auxin is a versatile plant hormone with important roles in many essential physiological processes. In recent years, significant progress has been made towards understanding the roles of this hormone in plant growth and development. Recent evidence also points to a less well-known but equally important role for auxin as a mediator of environmental adaptation in plants. This review briefly discusses recent findings on how plants utilize auxin signalling and transport to modify their root system architecture when responding to diverse biotic and abiotic rhizosphere signals, including macro- and micro-nutrient starvation, cold and water stress, soil acidity, pathogenic and beneficial microbes, nematodes and neighbouring plants. Stress-responsive transcription factors and microRNAs that modulate auxin- and environment-mediated root development are also briefly highlighted. The auxin pathway constitutes an essential component of the plant's biotic and abiotic stress tolerance mechanisms. Further understanding of the specific roles that auxin plays in environmental adaptation can ultimately lead to the development of crops better adapted to stressful environments.

Hyperglycemia Impairs Neutrophil-Mediated Bacterial Clearance in Mice Infected with the Lyme Disease Pathogen.

PubMed

Javid, Ashkan; Zlotnikov, Nataliya; Pětrošová, Helena; Tang, Tian Tian; Zhang, Yang; Bansal, Anil K; Ebady, Rhodaba; Parikh, Maitry; Ahmed, Mijhgan; Sun, Chunxiang; Newbigging, Susan; Kim, Yae Ram; Santana Sosa, Marianna; Glogauer, Michael; Moriarty, Tara J

2016-01-01

Insulin-insufficient type 1 diabetes is associated with attenuated bactericidal function of neutrophils, which are key mediators of innate immune responses to microbes as well as pathological inflammatory processes. Neutrophils are central to immune responses to the Lyme pathogen Borrelia burgdorferi. The effect of hyperglycemia on host susceptibility to and outcomes of B. burgdorferi infection has not been examined. The present study investigated the impact of sustained obesity-independent hyperglycemia in mice on bacterial clearance, inflammatory pathology and neutrophil responses to B. burgdorferi. Hyperglycemia was associated with reduced arthritis incidence but more widespread tissue colonization and reduced clearance of bacterial DNA in multiple tissues including brain, heart, liver, lung and knee joint. B. burgdorferi uptake and killing were impaired in neutrophils isolated from hyperglycemic mice. Thus, attenuated neutrophil function in insulin-insufficient hyperglycemia was associated with reduced B. burgdorferi clearance in target organs. These data suggest that investigating the effects of comorbid conditions such as diabetes on outcomes of B. burgdorferi infections in humans may be warranted.

Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession.

PubMed

Dini-Andreote, Francisco; Stegen, James C; van Elsas, Jan Dirk; Salles, Joana Falcão

2015-03-17

Ecological succession and the balance between stochastic and deterministic processes are two major themes within microbial ecology, but these conceptual domains have mostly developed independent of each other. Here we provide a framework that integrates shifts in community assembly processes with microbial primary succession to better understand mechanisms governing the stochastic/deterministic balance. Synthesizing previous work, we devised a conceptual model that links ecosystem development to alternative hypotheses related to shifts in ecological assembly processes. Conceptual model hypotheses were tested by coupling spatiotemporal data on soil bacterial communities with environmental conditions in a salt marsh chronosequence spanning 105 years of succession. Analyses within successional stages showed community composition to be initially governed by stochasticity, but as succession proceeded, there was a progressive increase in deterministic selection correlated with increasing sodium concentration. Analyses of community turnover among successional stages--which provide a larger spatiotemporal scale relative to within stage analyses--revealed that changes in the concentration of soil organic matter were the main predictor of the type and relative influence of determinism. Taken together, these results suggest scale-dependency in the mechanisms underlying selection. To better understand mechanisms governing these patterns, we developed an ecological simulation model that revealed how changes in selective environments cause shifts in the stochastic/deterministic balance. Finally, we propose an extended--and experimentally testable--conceptual model integrating ecological assembly processes with primary and secondary succession. This framework provides a priori hypotheses for future experiments, thereby facilitating a systematic approach to understand assembly and succession in microbial communities across ecosystems.

Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession

PubMed Central

Dini-Andreote, Francisco; Stegen, James C.; van Elsas, Jan Dirk; Salles, Joana Falcão

2015-01-01

Ecological succession and the balance between stochastic and deterministic processes are two major themes within microbial ecology, but these conceptual domains have mostly developed independent of each other. Here we provide a framework that integrates shifts in community assembly processes with microbial primary succession to better understand mechanisms governing the stochastic/deterministic balance. Synthesizing previous work, we devised a conceptual model that links ecosystem development to alternative hypotheses related to shifts in ecological assembly processes. Conceptual model hypotheses were tested by coupling spatiotemporal data on soil bacterial communities with environmental conditions in a salt marsh chronosequence spanning 105 years of succession. Analyses within successional stages showed community composition to be initially governed by stochasticity, but as succession proceeded, there was a progressive increase in deterministic selection correlated with increasing sodium concentration. Analyses of community turnover among successional stages—which provide a larger spatiotemporal scale relative to within stage analyses—revealed that changes in the concentration of soil organic matter were the main predictor of the type and relative influence of determinism. Taken together, these results suggest scale-dependency in the mechanisms underlying selection. To better understand mechanisms governing these patterns, we developed an ecological simulation model that revealed how changes in selective environments cause shifts in the stochastic/deterministic balance. Finally, we propose an extended—and experimentally testable—conceptual model integrating ecological assembly processes with primary and secondary succession. This framework provides a priori hypotheses for future experiments, thereby facilitating a systematic approach to understand assembly and succession in microbial communities across ecosystems. PMID:25733885

Soil Minerals: AN Overlooked Mediator of Plant-Microbe Competition for Organic Nitrogen in the Rhizosphere

NASA Astrophysics Data System (ADS)

Grandy, S.; Jilling, A.; Keiluweit, M.

2016-12-01

Recent research on the rate limiting steps in soil nitrogen (N) availability have shifted in focus from mineralization to soil organic matter (SOM) depolymerization. To that end, Schimel and Bennett (2004) argued that together with enzymatic breakdown of polymers to monomers, microsite processes and plant-microbial competition collectively drive N cycling. Here we present new conceptual models arguing that while depolymerization is a critical first step, mineral-organic associations may ultimately regulate the provisioning of bioavailable organic N, especially in the rhizosphere. Mineral-associated organic matter (MAOM) is a rich reservoir for N in soils and often holds 5-7x more N than particulate or labile fractions. However, MAOM is considered largely unavailable to plants as a source of N due to the physicochemical forces on mineral surfaces that stabilize organic matter. We argue that in rhizosphere hotspots, MAOM is in fact a potentially mineralizable and important source of nitrogen for plants. Several biochemical strategies enable plants and microbes to compete with mineral-organic interactions and effectively access MAOM. In particular, root-deposited low molecular weight compounds in the form of root exudates facilitate the biotic and abiotic destabilization and subsequent bioavailability of MAOM. We believe that the competitive balance between the potential fates of assimilable organic N — bound to mineral surfaces or dissolved and available for assimilation — depends on the specific interaction between and properties of the clay, soil solution, mineral-bound organic matter, and microbial community. For this reason, the plant-soil-MAOM interplay is enhanced in rhizosphere hotspots relative to non-rhizosphere environments, and likely strongly regulates plant-microbe competition for N. If these hypotheses are true, we need to reconsider potential soil N cycle responses to changes in climate and land use intensity, focusing on the processes by which management and other anthropogenic stressors can alter MAOM's N-supplying capacity.

Friends with social benefits: host-microbe interactions as a driver of brain evolution and development?

PubMed Central

Stilling, Roman M.; Bordenstein, Seth R.; Dinan, Timothy G.; Cryan, John F.

2014-01-01

The tight association of the human body with trillions of colonizing microbes that we observe today is the result of a long evolutionary history. Only very recently have we started to understand how this symbiosis also affects brain function and behavior. In this hypothesis and theory article, we propose how host-microbe associations potentially influenced mammalian brain evolution and development. In particular, we explore the integration of human brain development with evolution, symbiosis, and RNA biology, which together represent a “social triangle” that drives human social behavior and cognition. We argue that, in order to understand how inter-kingdom communication can affect brain adaptation and plasticity, it is inevitable to consider epigenetic mechanisms as important mediators of genome-microbiome interactions on an individual as well as a transgenerational time scale. Finally, we unite these interpretations with the hologenome theory of evolution. Taken together, we propose a tighter integration of neuroscience fields with host-associated microbiology by taking an evolutionary perspective. PMID:25401092

Aspergillus fumigatus Copper Export Machinery and Reactive Oxygen Intermediate Defense Counter Host Copper-Mediated Oxidative Antimicrobial Offense.

PubMed

Wiemann, Philipp; Perevitsky, Adi; Lim, Fang Yun; Shadkchan, Yana; Knox, Benjamin P; Landero Figueora, Julio A; Choera, Tsokyi; Niu, Mengyao; Steinberger, Andrew J; Wüthrich, Marcel; Idol, Rachel A; Klein, Bruce S; Dinauer, Mary C; Huttenlocher, Anna; Osherov, Nir; Keller, Nancy P

2017-05-02

The Fenton-chemistry-generating properties of copper ions are considered a potent phagolysosome defense against pathogenic microbes, yet our understanding of underlying host/microbe dynamics remains unclear. We address this issue in invasive aspergillosis and demonstrate that host and fungal responses inextricably connect copper and reactive oxygen intermediate (ROI) mechanisms. Loss of the copper-binding transcription factor AceA yields an Aspergillus fumigatus strain displaying increased sensitivity to copper and ROI in vitro, increased intracellular copper concentrations, decreased survival in challenge with murine alveolar macrophages (AMΦs), and reduced virulence in a non-neutropenic murine model. ΔaceA survival is remediated by dampening of host ROI (chemically or genetically) or enhancement of copper-exporting activity (CrpA) in A. fumigatus. Our study exposes a complex host/microbe multifactorial interplay that highlights the importance of host immune status and reveals key targetable A. fumigatus counter-defenses. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation

PubMed Central

Agler, Matthew T.; Ruhe, Jonas; Kroll, Samuel; Morhenn, Constanze; Kim, Sang-Tae; Weigel, Detlef; Kemen, Eric M.

2016-01-01

Plant-associated microorganisms have been shown to critically affect host physiology and performance, suggesting that evolution and ecology of plants and animals can only be understood in a holobiont (host and its associated organisms) context. Host-associated microbial community structures are affected by abiotic and host factors, and increased attention is given to the role of the microbiome in interactions such as pathogen inhibition. However, little is known about how these factors act on the microbial community, and especially what role microbe–microbe interaction dynamics play. We have begun to address this knowledge gap for phyllosphere microbiomes of plants by simultaneously studying three major groups of Arabidopsis thaliana symbionts (bacteria, fungi and oomycetes) using a systems biology approach. We evaluated multiple potential factors of microbial community control: we sampled various wild A. thaliana populations at different times, performed field plantings with different host genotypes, and implemented successive host colonization experiments under lab conditions where abiotic factors, host genotype, and pathogen colonization was manipulated. Our results indicate that both abiotic factors and host genotype interact to affect plant colonization by all three groups of microbes. Considering microbe–microbe interactions, however, uncovered a network of interkingdom interactions with significant contributions to community structure. As in other scale-free networks, a small number of taxa, which we call microbial “hubs,” are strongly interconnected and have a severe effect on communities. By documenting these microbe–microbe interactions, we uncover an important mechanism explaining how abiotic factors and host genotypic signatures control microbial communities. In short, they act directly on “hub” microbes, which, via microbe–microbe interactions, transmit the effects to the microbial community. We analyzed two “hub” microbes (the obligate biotrophic oomycete pathogen Albugo and the basidiomycete yeast fungus Dioszegia) more closely. Albugo had strong effects on epiphytic and endophytic bacterial colonization. Specifically, alpha diversity decreased and beta diversity stabilized in the presence of Albugo infection, whereas they otherwise varied between plants. Dioszegia, on the other hand, provided evidence for direct hub interaction with phyllosphere bacteria. The identification of microbial “hubs” and their importance in phyllosphere microbiome structuring has crucial implications for plant–pathogen and microbe–microbe research and opens new entry points for ecosystem management and future targeted biocontrol. The revelation that effects can cascade through communities via “hub” microbes is important to understand community structure perturbations in parallel fields including human microbiomes and bioprocesses. In particular, parallels to human microbiome “keystone” pathogens and microbes open new avenues of interdisciplinary research that promise to better our understanding of functions of host-associated microbiomes. PMID:26788878

A Mesocosm of Lactobacillus johnsonii, Bifidobacterium longum, and Escherichia coli in the mouse gut.

PubMed

Denou, Emmanuel; Rezzonico, Enea; Panoff, Jean-Michel; Arigoni, Fabrizio; Brüssow, Harald

2009-08-01

The relative contribution of competition and cooperation at the microbe-microbe level is not well understood for the bacteria constituting the gut microbiota. The high number and variability of human gut commensals have hampered the analysis. To get some insight into the question how so many different bacterial species can coexist in the mammalian gut, we studied the interaction between three human gut commensals (Escherichia coli K-12, Lactobacillus johnsonii NCC533, and Bifidobacterium longum NCC2705) in the intestine of gnotobiotic mice. The bacterial titers and their anatomical distribution were studied in the colonized mice. L. johnsonii achieved the highest cell counts in the stomach, while B. longum dominated the colon. The colon was also the intestinal location in which B. longum displayed the highest number of expressed genes, followed by the cecum and the small intestine. Addition of further bacterial strains led to strikingly different results. A Lactobacillus paracasei strain coexisted, while a second B. longum strain was excluded from the system. Notably, this strain lacked an operon involved in the degradation, import, and metabolism of mannosylated glycans. Subsequent introduction of the E. coli Nissle strain resulted in the elimination of L. johnsonii NCC533 and E. coli K-12, while B. longum NCC2705 showed a transient decrease in population size, demonstrating the dynamic nature of microbe-microbe interactions. The study of such simple interacting bacterial systems might help to derive some basic rules governing microbial ecology within the mammalian gut.

Microbe-Induced Inflammatory Signals Triggering Acquired Bone Marrow Failure Syndromes.

PubMed

Espinoza, J Luis; Kotecha, Ritesh; Nakao, Shinji

2017-01-01

Acquired bone marrow failure syndromes encompass a unique set of disorders characterized by a reduction in the effective production of mature cells by the bone marrow (BM). In the majority of cases, these syndromes are the result of the immune-mediated destruction of hematopoietic stem cells or their progenitors at various stages of differentiation. Microbial infection has also been associated with hematopoietic stem cell injury and may lead to associated transient or persistent BM failure, and recent evidence has highlighted the potential impact of commensal microbes and their metabolites on hematopoiesis. We summarize the interactions between microorganisms and the host immune system and emphasize how they may impact the development of acquired BM failure.

Microbe-Induced Inflammatory Signals Triggering Acquired Bone Marrow Failure Syndromes

PubMed Central

Espinoza, J. Luis; Kotecha, Ritesh; Nakao, Shinji

2017-01-01

Acquired bone marrow failure syndromes encompass a unique set of disorders characterized by a reduction in the effective production of mature cells by the bone marrow (BM). In the majority of cases, these syndromes are the result of the immune-mediated destruction of hematopoietic stem cells or their progenitors at various stages of differentiation. Microbial infection has also been associated with hematopoietic stem cell injury and may lead to associated transient or persistent BM failure, and recent evidence has highlighted the potential impact of commensal microbes and their metabolites on hematopoiesis. We summarize the interactions between microorganisms and the host immune system and emphasize how they may impact the development of acquired BM failure. PMID:28286502

Designing Autonomy: Opportunities for New Wildness in the Anthropocene.

PubMed

Cantrell, Bradley; Martin, Laura J; Ellis, Erle C

2017-03-01

Maintaining wild places increasingly involves intensive human interventions. Several recent projects use semi-automated mediating technologies to enact conservation and restoration actions, including re-seeding and invasive species eradication. Could a deep-learning system sustain the autonomy of nonhuman ecological processes at designated sites without direct human interventions? We explore here the prospects for automated curation of wild places, as well as the technical and ethical questions that such co-creation poses for ecologists, conservationists, and designers. Our goal is to foster innovative approaches to creating and maintaining the autonomy of evolving ecological systems. Copyright © 2016 Elsevier Ltd. All rights reserved.

Draft Genome Sequence of Deep-Sea Alteromonas sp. Strain V450 Isolated from the Marine Sponge Leiodermatium sp.

PubMed

Wang, Guojun; Barrett, Nolan H; McCarthy, Peter J

2017-02-02

The proteobacterium Alteromonas sp. strain V450 was isolated from the Atlantic deep-sea sponge Leiodermatium sp. Here, we report the draft genome sequence of this strain, with a genome size of approx. 4.39 Mb and a G+C content of 44.01%. The results will aid deep-sea microbial ecology, evolution, and sponge-microbe association studies. Copyright © 2017 Wang et al.

[Origin of the plague microbe Yersinia pestis: structure of the process of speciation].

PubMed

Suntsov, V V

2012-01-01

The origin and evolution of the plague microbe Yersinia pestis are considered in the context of propositions of modern Darwinism. It was shown that the plague pathogen diverged from the pseudotuberculous microbe Yersinia pseudotuberculosis O:1b in the mountain steppe landscapes of Central Asia in the Sartan: 22000-15000 years ago. Speciation occurred in the tarbagan (Marmota sibirica)--flea (Oropsylla silantiewi) parasitic system. The structure of the speciation process included six stages: isolation, genetic drift, enhancement of intrapopulational polymorphism, the beginning of pesticin synthesis (genetic conflict and emergence of hiatus), specialization (stabilization of characteristics), and adaptive irradiation (transformation of the monotypic species Y. pestis tarbagani into a polytypic species). The scenario opens up wide prospects for construction of the molecular phylogeny of the plague microbe Y. pestis and for investigation of the biochemical and molecular-genetic aspects of "Darwinian" evolution of pathogens from many other nature-focal infections.

Plant Responses to Pathogen Attack: Small RNAs in Focus.

PubMed

Islam, Waqar; Noman, Ali; Qasim, Muhammad; Wang, Liande

2018-02-08

Small RNAs (sRNA) are a significant group of gene expression regulators for multiple biological processes in eukaryotes. In plants, many sRNA silencing pathways produce extensive array of sRNAs with specialized roles. The evidence on record advocates for the functions of sRNAs during plant microbe interactions. Host sRNAs are reckoned as mandatory elements of plant defense. sRNAs involved in plant defense processes via different pathways include both short interfering RNA (siRNA) and microRNA (miRNA) that actively regulate immunity in response to pathogenic attack via tackling pathogen-associated molecular patterns (PAMPs) and other effectors. In response to pathogen attack, plants protect themselves with the help of sRNA-dependent immune systems. That sRNA-mediated plant defense responses play a role during infections is an established fact. However, the regulations of several sRNAs still need extensive research. In this review, we discussed the topical advancements and findings relevant to pathogen attack and plant defense mediated by sRNAs. We attempted to point out diverse sRNAs as key defenders in plant systems. It is hoped that sRNAs would be exploited as a mainstream player to achieve food security by tackling different plant diseases.