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Sample records for microbial populations responsive

  1. Quantitative Modeling of Microbial Population Responses to Chronic Irradiation Combined with Other Stressors

    PubMed Central

    Shuryak, Igor; Dadachova, Ekaterina

    2016-01-01

    Microbial population responses to combined effects of chronic irradiation and other stressors (chemical contaminants, other sub-optimal conditions) are important for ecosystem functioning and bioremediation in radionuclide-contaminated areas. Quantitative mathematical modeling can improve our understanding of these phenomena. To identify general patterns of microbial responses to multiple stressors in radioactive environments, we analyzed three data sets on: (1) bacteria isolated from soil contaminated by nuclear waste at the Hanford site (USA); (2) fungi isolated from the Chernobyl nuclear-power plant (Ukraine) buildings after the accident; (3) yeast subjected to continuous γ-irradiation in the laboratory, where radiation dose rate and cell removal rate were independently varied. We applied generalized linear mixed-effects models to describe the first two data sets, whereas the third data set was amenable to mechanistic modeling using differential equations. Machine learning and information-theoretic approaches were used to select the best-supported formalism(s) among biologically-plausible alternatives. Our analysis suggests the following: (1) Both radionuclides and co-occurring chemical contaminants (e.g. NO2) are important for explaining microbial responses to radioactive contamination. (2) Radionuclides may produce non-monotonic dose responses: stimulation of microbial growth at low concentrations vs. inhibition at higher ones. (3) The extinction-defining critical radiation dose rate is dramatically lowered by additional stressors. (4) Reproduction suppression by radiation can be more important for determining the critical dose rate, than radiation-induced cell mortality. In conclusion, the modeling approaches used here on three diverse data sets provide insight into explaining and predicting multi-stressor effects on microbial communities: (1) the most severe effects (e.g. extinction) on microbial populations may occur when unfavorable environmental

  2. Quantitative Modeling of Microbial Population Responses to Chronic Irradiation Combined with Other Stressors.

    PubMed

    Shuryak, Igor; Dadachova, Ekaterina

    2016-01-01

    Microbial population responses to combined effects of chronic irradiation and other stressors (chemical contaminants, other sub-optimal conditions) are important for ecosystem functioning and bioremediation in radionuclide-contaminated areas. Quantitative mathematical modeling can improve our understanding of these phenomena. To identify general patterns of microbial responses to multiple stressors in radioactive environments, we analyzed three data sets on: (1) bacteria isolated from soil contaminated by nuclear waste at the Hanford site (USA); (2) fungi isolated from the Chernobyl nuclear-power plant (Ukraine) buildings after the accident; (3) yeast subjected to continuous γ-irradiation in the laboratory, where radiation dose rate and cell removal rate were independently varied. We applied generalized linear mixed-effects models to describe the first two data sets, whereas the third data set was amenable to mechanistic modeling using differential equations. Machine learning and information-theoretic approaches were used to select the best-supported formalism(s) among biologically-plausible alternatives. Our analysis suggests the following: (1) Both radionuclides and co-occurring chemical contaminants (e.g. NO2) are important for explaining microbial responses to radioactive contamination. (2) Radionuclides may produce non-monotonic dose responses: stimulation of microbial growth at low concentrations vs. inhibition at higher ones. (3) The extinction-defining critical radiation dose rate is dramatically lowered by additional stressors. (4) Reproduction suppression by radiation can be more important for determining the critical dose rate, than radiation-induced cell mortality. In conclusion, the modeling approaches used here on three diverse data sets provide insight into explaining and predicting multi-stressor effects on microbial communities: (1) the most severe effects (e.g. extinction) on microbial populations may occur when unfavorable environmental

  3. Microbial population dynamics in response to bioaugmentation in a constructed wetland system under 10°C.

    PubMed

    Zhao, Xinyue; Yang, Jixian; Bai, Shunwen; Ma, Fang; Wang, Li

    2016-04-01

    Compound microbial inocula were enriched and applied to a pilot-scale constructed wetland system to investigate their bioaugmentation effect on nitrogen removal under cold temperature (10°C). The results showed a 10% higher removal efficiency of ammonia and total nitrogen compared to a control (unbioaugmented) group. The microbial community structures before and after the bioaugmentation were analyzed through high throughput sequencing using Miseq Illumina platform. A variation of species richness and community equitability was observed in both systems. It is demonstrated that, based on the response of both the performance and microbial community, bioaugmentation using compound microbial inocula can fine tune the bacterial population and enhance the nitrogen removal efficiency of a constructed wetland system. PMID:26826956

  4. Microbial population dynamics in response to Pectobacterium atrosepticum infection in potato tubers

    PubMed Central

    Kõiv, Viia; Roosaare, Märt; Vedler, Eve; Ann Kivistik, Paula; Toppi, Kristel; Schryer, David W.; Remm, Maido; Tenson, Tanel; Mäe, Andres

    2015-01-01

    Endophytes are microbes and fungi that live inside plant tissues without damaging the host. Herein we examine the dynamic changes in the endophytic bacterial community in potato (Solanum tuberosum) tuber in response to pathogenic infection by Pectobacterium atrosepticum, which causes soft rot in numerous economically important crops. We quantified community changes using both cultivation and next-generation sequencing of the 16S rRNA gene and found that, despite observing significant variability in both the mass of macerated tissue and structure of the endophytic community between individual potato tubers, P. atrosepticum is always taken over by the endophytes during maceration. 16S rDNA sequencing revealed bacteria from the phyla Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Fusobacteria, Verrucomicrobia, Acidobacteria, TM7, and Deinococcus-Thermus. Prior to infection, Propionibacterium acnes is frequently among the dominant taxa, yet is out competed by relatively few dominant taxa as the infection proceeds. Two days post-infection, the most abundant sequences in macerated potato tissue are Gammaproteobacteria. The most dominant genera are Enterobacter and Pseudomonas. Eight days post-infection, the number of anaerobic pectolytic Clostridia increases, probably due to oxygen depletion. These results demonstrate that the pathogenesis is strictly initiated by the pathogen (sensu stricto) and proceeds with a major contribution from the endophytic community. PMID:26118792

  5. Microbial populations in contaminant plumes

    NASA Astrophysics Data System (ADS)

    Haack, Sheridan K.; Bekins, Barbara A.

    Efficient biodegradation of subsurface contaminants requires two elements: (1) microbial populations with the necessary degradative capabilities, and (2) favorable subsurface geochemical and hydrological conditions. Practical constraints on experimental design and interpretation in both the hydrogeological and microbiological sciences have resulted in limited knowledge of the interaction between hydrogeological and microbiological features of subsurface environments. These practical constraints include: (1) inconsistencies between the scales of investigation in the hydrogeological and microbiological sciences, and (2) practical limitations on the ability to accurately define microbial populations in environmental samples. However, advances in application of small-scale sampling methods and interdisciplinary approaches to site investigations are beginning to significantly improve understanding of hydrogeological and microbiological interactions. Likewise, culture-based and molecular analyses of microbial populations in subsurface contaminant plumes have revealed significant adaptation of microbial populations to plume environmental conditions. Results of recent studies suggest that variability in subsurface geochemical and hydrological conditions significantly influences subsurface microbial-community structure. Combined investigations of site conditions and microbial-community structure provide the knowledge needed to understand interactions between subsurface microbial populations, plume geochemistry, and contaminant biodegradation. La biodégradation efficace des polluants souterrains requiert deux éléments: des populations microbiennes possédant les aptitudes nécessaires à la dégradation, et des conditions géochimiques et hydrologiques souterraines favorables. Des contraintes pratiques sur la conception et l'interprétation des expériences à la fois en microbiologie et en hydrogéologie ont conduit à une connaissance limitée des interactions entre les

  6. Microbial population dynamics in response to increasing loadings of pre-hydrolyzed pig manure in an expanded granular sludge bed.

    PubMed

    Wang, Haoyu; Tao, Yu; Gao, Dawen; Liu, Gang; Chen, Chunhong; Ren, Nanqi; van Lier, Jules B; de Kreuk, Merle

    2015-12-15

    In recent years, pig manure (PM) has been regarded as a valuable substrate for energy and resource recovery via bioprocesses such as anaerobic digestion (AD), however, the efficiency of digesting raw PM is limited by the presence of refractory compounds. In this study, we applied a series of pretreatment on raw PM, consisting of subsequent thermochemical pretreatment, enzymatic hydrolysis, tyndallization and filtration. The liquid PM hydrolysates were fed to an expanded granular sludge bed (EGSB) for the production of biogas. The general performance and population dynamics of the EGSB reactor were assessed during an extended operational period of 339 days. An efficient and stable digestion process was achieved under high organic loading rates (OLRs) up to 21 kg-COD/(m(3)·d), agreeing with a sludge loading rate of 0.75 kg-COD/(kg-VSS·d), 1600 mg-NH4(+)-N/L and 17 mg/L of free ammonia nitrogen. The tyndallization decreased the total amount of active cells from 1 × 10(8) to 1 × 10(2) CFU/ml. Hence, bio-augmentation with pigs' intestinal microbiota was absent and the community dynamics were mainly credited to the composition of the substrate (i.e. PM hydrolysates) and the environmental conditions inside the reactor. The results showed the influence of both the seed community and the imposed loading rates on the evolutionary trajectory of the EGSB microbial community. Four bacterial genera (Clostridium, Cytophaga, Bacillus and Bacteroides) and two methanogenic genera (Methanosaeta and Methanobacterium) dominated the communities. An obvious shift from aceticlastic Methanosaeta to hydrogenotrophic Methanobacterium appeared when the OLR was increased to over 10 kg-COD/(m(3)·d). PMID:26378729

  7. Microbial response to triepthylphosphate

    SciTech Connect

    Hazen, T.C.; Santo Domingo, J.W.; Berry, C.J.

    1997-05-01

    The effect of triethylphosphate (TEP) on the activity of a landfill aquifer microbial community was evaluated using standard techniques and in situ hybridizations with phylogenetic probes. Benzene was used as an external carbon source to monitor degradation of an aromatic compound in TEP amended microcosms. Microscopical and viable counts were higher in TEP containing microcosms when compared to unamended controls. A significant increase in metabolic activity was also observed for TEP amended samples as determined by the number of cells hybridizing to an eubacterial probe. In addition, the number of beta and gamma Proteobacteria increased from undetectable levels prior to the study to 15-29% of the total bacteria in microcosms containing TEP and benzene. In these microcosms, nearly 40% of the benzene was degraded during the incubation period compared to less than 5% in unamended microcosms. While TEP has previously been used as an alternate phosphate source in the bioremediation of chlorinated aliphatics, this study shows that it can also stimulate the microbial degradation of aromatics in phosphate limited aquifers.

  8. Milk fatty acid composition, rumen microbial population, and animal performances in response to diets rich in linoleic acid supplemented with chestnut or quebracho tannins in dairy ewes.

    PubMed

    Buccioni, A; Pauselli, M; Viti, C; Minieri, S; Pallara, G; Roscini, V; Rapaccini, S; Marinucci, M Trabalza; Lupi, P; Conte, G; Mele, M

    2015-02-01

    The aim of the study was to evaluate milk fatty acid (FA) profile, animal performance, and rumen microbial population in response to diets containing soybean oil supplemented or not with chestnut and quebracho tannins in dairy ewes. Eighteen Comisana ewes at 122±6 d in milking were allotted into 3 experimental groups. Diets were characterized by chopped grass hay administered ad libitum and by 800 g/head and day of 3 experimental concentrates containing 84.5 g of soybean oil/kg of dry matter (DM) and 52.8 g/kg of DM of bentonite (control diet), chestnut tannin extract (CHT diet), or quebracho tannin extract (QUE diet). The trial lasted 4 wk. Milk yield was recorded daily, and milk composition and blood parameters were analyzed weekly. At the end of the experiment, samples of rumen fluid were collected to analyze pH, volatile fatty acid profile, and the relative proportions of Butyrivibrio fibrisolvens and Butyrivibrio proteoclasticus in the rumen microbial population. Hepatic functionality, milk yield, and gross composition were not affected by tannin extracts, whereas milk FA composition was characterized by significant changes in the concentration of linoleic acid (CHT +2.77% and QUE +9.23%), vaccenic acid (CHT +7.07% and QUE +13.88%), rumenic acid (CHT -1.88% and QUE +24.24%), stearic acid (CHT + 8.71% and QUE -11.45%), and saturated fatty acids (CHT -0.47% and QUE -3.38%). These differences were probably due to the ability of condensed versus hydrolyzable tannins to interfere with rumen microbial metabolism, as indirectly confirmed by changes in the relative proportions of B. fibrisolvens and B. proteoclasticus populations and by changes in the molar proportions of volatile fatty acids. The effect of the CHT diet on the milk FA profile and microbial species considered in this trial was intermediate between that of QUE and the control diet, suggesting a differential effect of condensed and hydrolyzable tannins on rumen microbes. Compared with control animals

  9. Monitoring microbial population dynamics at low densities

    NASA Astrophysics Data System (ADS)

    Julou, Thomas; Desprat, Nicolas; Bensimon, David; Croquette, Vincent

    2012-07-01

    We propose a new and simple method for the measurement of microbial concentrations in highly diluted cultures. This method is based on an analysis of the intensity fluctuations of light scattered by microbial cells under laser illumination. Two possible measurement strategies are identified and compared using simulations and measurements of the concentration of gold nanoparticles. Based on this comparison, we show that the concentration of Escherichia coli and Saccharomyces cerevisiae cultures can be easily measured in situ across a concentration range that spans five orders of magnitude. The lowest measurable concentration is three orders of magnitude (1000×) smaller than in current optical density measurements. We show further that this method can also be used to measure the concentration of fluorescent microbial cells. In practice, this new method is well suited to monitor the dynamics of population growth at early colonization of a liquid culture medium. The dynamic data thus obtained are particularly relevant for microbial ecology studies.

  10. MICROBIAL POPULATION ANALYSIS AS A MEASURE OF ECOSYSTEM RESTORATION

    EPA Science Inventory

    During a controlled oil spill study in a freshwater wetland, four methods were used to track changes in microbial populations in response to in situ remediation treatments, including nutrient amendments and the removal of surface vegetation. Most probable number (MPN) esimates o...

  11. Interval scanning photomicrography of microbial cell populations.

    NASA Technical Reports Server (NTRS)

    Casida, L. E., Jr.

    1972-01-01

    A single reproducible area of the preparation in a fixed focal plane is photographically scanned at intervals during incubation. The procedure can be used for evaluating the aerobic or anaerobic growth of many microbial cells simultaneously within a population. In addition, the microscope is not restricted to the viewing of any one microculture preparation, since the slide cultures are incubated separately from the microscope.

  12. Strongly Deterministic Population Dynamics in Closed Microbial Communities

    NASA Astrophysics Data System (ADS)

    Frentz, Zak; Kuehn, Seppe; Leibler, Stanislas

    2015-10-01

    Biological systems are influenced by random processes at all scales, including molecular, demographic, and behavioral fluctuations, as well as by their interactions with a fluctuating environment. We previously established microbial closed ecosystems (CES) as model systems for studying the role of random events and the emergent statistical laws governing population dynamics. Here, we present long-term measurements of population dynamics using replicate digital holographic microscopes that maintain CES under precisely controlled external conditions while automatically measuring abundances of three microbial species via single-cell imaging. With this system, we measure spatiotemporal population dynamics in more than 60 replicate CES over periods of months. In contrast to previous studies, we observe strongly deterministic population dynamics in replicate systems. Furthermore, we show that previously discovered statistical structure in abundance fluctuations across replicate CES is driven by variation in external conditions, such as illumination. In particular, we confirm the existence of stable ecomodes governing the correlations in population abundances of three species. The observation of strongly deterministic dynamics, together with stable structure of correlations in response to external perturbations, points towards a possibility of simple macroscopic laws governing microbial systems despite numerous stochastic events present on microscopic levels.

  13. Response of microbial community structure to microbial plugging in a mesothermic petroleum reservoir in China.

    PubMed

    Zhang, Fan; She, Yue Hui; Ma, Sha Sha; Hu, Ji Ming; Banat, Ibrahim M; Hou, Du Jie

    2010-12-01

    Microbial plugging, a microbial enhancement of oil recovery (MEOR) technique, has been applied in a candidate oil reservoir of Daqing Oil Field (China). The goal of this study is to monitor the survival of injected bacteria and reveal the response of microbial communities in field trial of microbial plugging through injection of selected microbial culture broth and nutrients. Culture-dependent enrichment and culture-independent 16S rDNA clone library methods were used. The results show that it was easy to activate targeted biopolymer-producing bacteria in a laboratory environment, and it was difficult for injected exogenous bacteria to survive. In addition, microbial communities in the oil reservoir also changed before and after the field trial. However, microbial communities, activated by fermentative medium for biopolymer-producing bacteria, appeared to show greater differences in the laboratory than in the natural reservoir. It was concluded that microbial populations monitoring was important to MEOR; results of response of microbial communities could provide a guide for the future field trials. PMID:20803140

  14. CRISPR-Induced Distributed Immunity in Microbial Populations

    PubMed Central

    Young, Mark J.; Weitz, Joshua S.; Whitaker, Rachel J.

    2014-01-01

    In bacteria and archaea, viruses are the primary infectious agents, acting as virulent, often deadly pathogens. A form of adaptive immune defense known as CRISPR-Cas enables microbial cells to acquire immunity to viral pathogens by recognizing specific sequences encoded in viral genomes. The unique biology of this system results in evolutionary dynamics of host and viral diversity that cannot be fully explained by the traditional models used to describe microbe-virus coevolutionary dynamics. Here, we show how the CRISPR-mediated adaptive immune response of hosts to invading viruses facilitates the emergence of an evolutionary mode we call distributed immunity - the coexistence of multiple, equally-fit immune alleles among individuals in a microbial population. We use an eco-evolutionary modeling framework to quantify distributed immunity and demonstrate how it emerges and fluctuates in multi-strain communities of hosts and viruses as a consequence of CRISPR-induced coevolution under conditions of low viral mutation and high relative numbers of viral protospacers. We demonstrate that distributed immunity promotes sustained diversity and stability in host communities and decreased viral population density that can lead to viral extinction. We analyze sequence diversity of experimentally coevolving populations of Streptococcus thermophilus and their viruses where CRISPR-Cas is active, and find the rapid emergence of distributed immunity in the host population, demonstrating the importance of this emergent phenomenon in evolving microbial communities. PMID:25000306

  15. Resilience vs. historical contingency in microbial responses to environmental change.

    PubMed

    Hawkes, Christine V; Keitt, Timothy H

    2015-07-01

    How soil processes such as carbon cycling will respond to future climate change depends on the responses of complex microbial communities, but most ecosystem models assume that microbial functional responses are resilient and can be predicted from simple parameters such as biomass and temperature. Here, we consider how historical contingencies might alter those responses because function depends on prior conditions or biota. Functional resilience can be driven by physiological, community or adaptive shifts; historical contingencies can result from the influence of historical environments or a combination of priority effects and biotic resistance. By modelling microbial population responses to environmental change, we demonstrate that historical environments can constrain soil function with the degree of constraint depending on the magnitude of change in the context of the prior environment. For example microbial assemblages from more constant environments were more sensitive to change leading to poorer functional acclimatisation compared to microbial assemblages from more fluctuating environments. Such historical contingencies can lead to deviations from expected functional responses to climate change as well as local variability in those responses. Our results form a set of interrelated hypotheses regarding soil microbial responses to climate change that warrant future empirical attention. PMID:25950733

  16. BIOSORPTION OF HYDROPHOBIC ORGANIC POLLUTANTS BY MIXED MICROBIAL POPULATIONS

    EPA Science Inventory

    In recognition of the need to estimate biosorption for natural microbial populations, the variability of partition coefficients for two hydrophobic pollutants to natural populations from a variety of aquatic systems was investigated. Biosorption partition coefficients for pyrene ...

  17. Linking Toluene Degradation with Specific Microbial Populations in Soil

    PubMed Central

    Hanson, Jessica R.; Macalady, Jennifer L.; Harris, David; Scow, Kate M.

    1999-01-01

    Phospholipid fatty acid (PLFA) analysis of a soil microbial community was coupled with 13C isotope tracer analysis to measure the community’s response to addition of 35 μg of [13C]toluene ml of soil solution−1. After 119 h of incubation with toluene, 96% of the incorporated 13C was detected in only 16 of the total 59 PLFAs (27%) extracted from the soil. Of the total 13C-enriched PLFAs, 85% were identical to the PLFAs contained in a toluene-metabolizing bacterium isolated from the same soil. In contrast, the majority of the soil PLFAs (91%) became labeled when the same soil was incubated with [13C]glucose. Our study showed that coupling 13C tracer analysis with PLFA analysis is an effective technique for distinguishing a specific microbial population involved in metabolism of a labeled substrate in complex environments such as soil. PMID:10583996

  18. Cooperation, cheating, and collapse in microbial populations

    NASA Astrophysics Data System (ADS)

    Gore, Jeff

    2012-02-01

    Natural populations can suffer catastrophic collapse in response to small changes in environmental conditions, and recovery after such a collapse can be exceedingly difficult. We have used laboratory yeast populations to study proposed early warning signals of impending extinction. Yeast cooperatively breakdown the sugar sucrose, meaning that there is a minimum number of cells required to sustain the population. We have demonstrated experimentally that the fluctuations in the population size increase in magnitude and become slower as the population approaches collapse. The cooperative nature of yeast growth on sucrose suggests that the population may be susceptible to cheater cells, which do not contribute to the public good and instead merely take advantage of the cooperative cells. We have confirmed this possibility experimentally by using a cheater yeast strain that lacks the gene encoding the cooperative behavior [1]. However, recent results in the lab demonstrate that the presence of a bacterial competitor may drive cooperation within the yeast population.[4pt] [1] Gore et al, Nature 459, 253 -- 256 (2009)

  19. Historical Contingencies in Microbial Responses to Drought

    NASA Astrophysics Data System (ADS)

    Hawkes, C.; Waring, B.; Rocca, J.; Kivlin, S.; Giauque, H.; Averill, C.

    2014-12-01

    Although water is a primary controller of microbial function and we expect climate change to alter water availability in the future, our understanding of how microbial communities respond to a change in moisture and what that means for soil carbon cycling remain poorly understood. In part, this uncertainty arises from a lack of understanding of microbial response mechanisms and how those lead to aggregate soil function. Environmental tracking would be facilitated if microbial communities respond to new climatic conditions via rapid physiological acclimatization, shifts in community composition, or adaptation. In contrast, historical contingencies could be created by dispersal limitation or local adaptation to previous conditions. To address environmental tracking vs. legacies, we examined how soil microbial communities were affected by precipitation at multiple scales and asked whether rainfall was a primary driver of the observed responses. We leveraged a local steep rainfall gradient with field surveys, lab incubations, reciprocal transplants, and rainfall manipulations to approach this problem. Across a steep rainfall gradient, we found that soil microbial communities were strongly associated with historical rainfall, with two-thirds of the variation in community composition explained by mean annual precipitation. In 12-month experimental lab manipulations of soil moisture, soil functional responses were constrained by historical rainfall, with greater activity in soils subjected to their original moisture condition. The constraints of historical rainfall held even after 18 months in reciprocal transplant common gardens along the rainfall gradient and with manipulated dispersal of regional microbial communities. Yet, when water was manipulated at a single site over 4 years, legacies did not develop. Overall, these findings are consistent with long-term rainfall acting as a strong habitat filter and resulting in a legacy of both microbial community composition

  20. Microbial Response to Carbon Dioxide Injection in a Shallow Aquifer

    NASA Astrophysics Data System (ADS)

    Rook, A.; Faehndrich, D.; O'Mullan, G.; Mailloux, B.; Matter, J.; Stute, M.; Goldberg, D.

    2007-12-01

    Extensive research is underway to investigate the geophysical and geochemical dynamics of subsurface carbon sequestration, but there has been only theoretical consideration of the microbial response. Microbial dynamics are capable of altering the range and rates of geochemical reactions in the subsurface. The goal of this field experiment is to link geochemical changes due to CO2 injection to alterations in the microbial community and to provide an initial characterization of the microbial response. A seven week push-pull experiment was conducted at the Lamont-Doherty Earth Observatory Test Well. 200L of groundwater was extracted, bubbled with carbon dioxide, augmented with a bromide tracer, and injected to 230m depth below ground surface. The hydraulically isolated injection zone marked the contact area between dolerite sill and sedimentary rock. Samples were taken on a weekly basis. Geochemically, a drop in pH from 9.4 to 4.5 at injection was coupled with a release of Fe2+ from the formation. As neutralization and mixing caused pH to return toward background levels, Fe2+ concentrations decreased. The aquifer remained anoxic throughout the experiment. DNA was successfully extracted and the gene encoding 16S ribosomal RNA was amplified from all samples with the exception of the injection fluid. Sequencing from clone libraries and tRFLP analyses were used to characterize microbial dynamics during the seven week study. Whereas the number of microbial groups detected remained relatively constant over the course of the experiment, changes were observed in both the dominant microbes phylogenetic identity and relative abundance. Methane concentrations increased from background levels (below 50 nM) to 4.2 nM after injection, but initial attempts to amplify archaeal and methanogen-specific genes were unsuccessful, bringing into question the presence of a significant methanogenic population. These results confirm that there is a microbial response to carbon dioxide

  1. Microbial nitrogen metabolism: response to warming and resource supply

    NASA Astrophysics Data System (ADS)

    Buckeridge, K. M.; Min, K.; Lehmeier, C.; Ballantyne, F.; Billings, S. A.

    2013-12-01

    Ecosystem nitrogen (N) dynamics are dependent on microbial metabolic responses to a changing climate. Most studies that investigate soil microbial N dynamics in response to temperature employ measurements reflective of many interacting and confounding phenomena, as altering soil temperature can simultaneously alter moisture regime, substrate availability, and competitive dynamics between microbial populations. As a result, it is difficult to discern how temperature alone can alter patterns of microbial N metabolism using whole soils. Without that knowledge, it is impossible to parse temperature effects on soil N fluxes from other drivers. We address this issue by exploring the sensitivity of microbial partitioning of N between assimilation (growing biomass) and dissimilation (releasing N to the environment) in response to changes in temperature and quality (C:N ratio) of substrate, using a chemostat approach in which a microbial population is maintained at steady state. We perform our experiments using a Gram-negative bacterium (Pseudomonas fluorescens), ubiquitous in soils and dependent on organic compounds to satisfy its resource demand. Individual chemostat runs, all conducted at similar microbial growth rates, generate data describing microbial biomass N, solution N pools and microbial biomass and solution d15N. With these data we can calculate d15N enrichment (d15N microbial biomass - d15N nutrient solution) a proxy for microbial N partitioning. From a recently published model of microbial biomass d15N drivers, fractionation of N occurs with both uptake and excretion of NH3+ so that microbes with a net dissimilation become 15N enriched relative to their source. Because a related study has demonstrated increased microbial C demand with temperature, we predict that in a warming environment microorganisms will become relatively C limited. Accordingly, we hypothesize that warming will enhance microbial dissimilation, and that this N release will be exacerbated as

  2. Induced polarization response of microbial induced sulfideprecipitation

    SciTech Connect

    Ntarlagiannis, Dimitrios; Williams, Kenneth Hurst; Slater, Lee; Hubbard, Susan

    2004-06-04

    A laboratory scale experiment was conducted to examine the use of induced polarization and electrical conductivity to monitor microbial induced sulfide precipitation under anaerobic conditions in sand filled columns. Three columns were fabricated; one for electrical measurements, one for geochemical sampling and a third non-inoculated column was used as a control. A continual upward flow of nutrients and metals in solution was established in each column. Desulfovibrio vulgaris microbes were injected into the middle of the geochemical and electrical columns. Iron and zinc sulfides precipitated along a microbial action front as a result of sulfate reduction due by Desulfovibrio vulgaris. The precipitation front initially developed near the microbial injection location, and subsequently migrated towards the nutrient inlet, as a result of chemotaxis by Desulfovibrio vulgaris. Sampling during and subsequent to the experiment revealed spatiotemporal changes in the biogeochemical measurements associated with microbial sulfate reduction. Conductivity measurements were insensitive to all biogeochemical changes occurred within the column. Changes in the IP response (of up to 14 mrad)were observed to coincide in place and in time with the active microbe respiration/sulfide precipitation front as determined from geochemical sampling. The IP response is correlated with the lactate concentration gradient, an indirect measurement of microbial metabolism, suggesting the potential of IP as a method for monitoring microbial respiration/activity. Post experimental destructive sample analysis and SEM imaging verified the geochemical results and supported our hypothesis that microbe induced sulfide precipitation is directly detectable using electrical methods. Although the processes not fully understood, the IP response appears to be sensitive to this anaerobic microbial precipitation, suggesting a possible novel application for the IP method.

  3. Microbial population responses to pH and salt shock during phenols degradation under high salt conditions revealed by RISA and AFDRA.

    PubMed

    Yan, Bin; Wang, Ping; Liao, Wenchao; Ye, Qian; Xu, Meilan; Zhou, Jiti

    2013-01-01

    The responses of microbial community to pH and salt shock during phenols degradation under high salt conditions were revealed by two DNA fingerprint methods, i.e. ribosomal intergenic spacer analysis (RISA) and amplified functional DNA restriction analysis (AFDRA), together with 16S rDNA clone library analysis. It was shown that the phenols removal rate was improved with increasing NaCl concentration from 0 to 50 mg/L, and could remain at a high level even in the presence of 100 mg/L NaCl. The degradation efficiency remained stable under neutral conditions (pH 7.0-9.0), but decreased sharply under acidic (below pH 5.0) or more alkaline conditions (above pH 10.0). The community structure was dramatically changed during salt fluctuations, with Halomonas sp. and Marinobacter sp. as the predominant salt-tolerant species. Meanwhile, Marinobacter sp. and Alcaligenes faecalis sp. were the major species which might play the key role for stabilizing the treatment systems under different pH conditions. Moreover, the changes of phenol hydroxylase genes were analyzed by AFDRA, which showed that these functional genes were substantially different under any shock conditions. PMID:23202556

  4. Multilevel Samplers to Assess Microbial Community Response to Biostimulation

    NASA Astrophysics Data System (ADS)

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

    2006-05-01

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

  5. Multilevel samplers as microcosms to assess microbial response to biostimulation.

    PubMed

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

    2008-01-01

    Passive multilevel samplers (MLS) containing a solid matrix for microbial colonization were used as in situ microcosms in conjunction with a push-pull biostimulation experiment designed to promote biological U(VI) and Tc(VII) reduction. MLS were deployed at 24 elevations in the injection well and two downgradient wells to investigate the spatial variability in microbial community composition and growth prior to and following biostimulation. The microbial community was characterized by real-time quantitative polymerase chain reaction (Q-PCR) quantification of bacteria, NO(3)(-)-reducing bacteria (nirS and nirK), delta-proteobacteria, Geobacter sp., and methanogens (mcrA). Pretest cell densities were low overall but varied substantially with significantly greater bacterial populations detected at circumneutral pH (t-test, alpha= 0.05), suggesting carbon substrate and low pH limitations of microbial activity. Although pretest cell densities were low, denitrifying bacteria were dominant members of the microbial community. Biostimulation with an ethanol-amended ground water resulted in concurrent NO(3)(-) and Tc(VII) reduction, followed by U(VI) reduction. Q-PCR analysis of MLS revealed significant (1 to 2 orders of magnitude, Mann-Whitney U-test, alpha= 0.05) increases in cell densities of bacteria, denitrifiers, delta-proteobacteria, Geobacter sp., and methanogens in response to biostimulation. Traditionally, characterization of sediment samples has been used to investigate the microbial community response to biostimulation; however, collection of sediment samples is expensive and not conducive to deep aquifers or temporal studies. The results presented demonstrate that push-pull tests with passive MLS provide an inexpensive approach to determine the effect of biostimulation on contaminant concentrations, geochemical conditions, and the microbial community composition and function. PMID:18194316

  6. Gut Microbial Metabolites Fuel Host Antibody Responses.

    PubMed

    Kim, Myunghoo; Qie, Yaqing; Park, Jeongho; Kim, Chang H

    2016-08-10

    Antibody production is a metabolically demanding process that is regulated by gut microbiota, but the microbial products supporting B cell responses remain incompletely identified. We report that short-chain fatty acids (SCFAs), produced by gut microbiota as fermentation products of dietary fiber, support host antibody responses. In B cells, SCFAs increase acetyl-CoA and regulate metabolic sensors to increase oxidative phosphorylation, glycolysis, and fatty acid synthesis, which produce energy and building blocks supporting antibody production. In parallel, SCFAs control gene expression to express molecules necessary for plasma B cell differentiation. Mice with low SCFA production due to reduced dietary fiber consumption or microbial insufficiency are defective in homeostatic and pathogen-specific antibody responses, resulting in greater pathogen susceptibility. However, SCFA or dietary fiber intake restores this immune deficiency. This B cell-helping function of SCFAs is detected from the intestines to systemic tissues and conserved among mouse and human B cells, highlighting its importance. PMID:27476413

  7. Waterborne microbial risk assessment : a population-based dose-response function for Giardia spp. (E.MI.R.A study)

    PubMed Central

    Zmirou-Navier, D; Gofti-Laroche, L; Hartemann, Ph

    2006-01-01

    Background Dose-response parameters based on clinical challenges are frequently used to assess the health impact of protozoa in drinking water. We compare the risk estimates associated with Giardia in drinking water derived from the dose-response parameter published in the literature and the incidence of acute digestive conditions (ADC) measured in the framework of an epidemiological study in a general population. Methods The study combined a daily follow-up of digestive morbidity among a panel of 544 volunteers and a microbiological surveillance of tap water. The relationship between incidence of ADC and concentrations of Giardia cysts was modeled with Generalized Estimating Equations, adjusting on community, age, tap water intake, presence of bacterial indicators, and genetic markers of viruses. The quantitative estimate of Giardia dose was the product of the declared amount of drinking water intake (in L) by the logarithm of cysts concentrations. Results The Odds Ratio for one unit of dose [OR = 1.76 (95% CI: 1.21, 2.55)] showed a very good consistency with the risk assessment estimate computed after the literature dose-response, provided application of a 20 % abatement factor to the cysts counts that were measured in the epidemiological study. Doing so, a daily water intake of 2 L and a Giardia concentration of 10 cysts/100 L, would yield an estimated relative excess risk of 12 % according to the Rendtorff model, against 11 % when multiplying the baseline rate of ADC by the corresponding OR. This abatement parameter encompasses uncertainties associated with germ viability, infectivity and virulence in natural settings. Conclusion The dose-response function for waterborne Giardia risk derived from clinical experiments is consistent with epidemiological data. However, much remains to be learned about key characteristics that may heavily influence quantitative risk assessment results. PMID:16672062

  8. Wetland Microbial Community Response to Restoration

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  9. Temporal variation in airborne microbial populations and microbially-derived allergens in a tropical urban landscape

    NASA Astrophysics Data System (ADS)

    Woo, Anthony C.; Brar, Manreetpal S.; Chan, Yuki; Lau, Maggie C. Y.; Leung, Frederick C. C.; Scott, James A.; Vrijmoed, Lilian L. P.; Zawar-Reza, Peyman; Pointing, Stephen B.

    2013-08-01

    The microbial component of outdoor aerosols was assessed along a gradient of urban development from inner-city to rural in the seasonal-tropical metropolis of Hong Kong. Sampling over a continuous one-year period was conducted, with molecular analyses to characterize bacterial and eukaryal microbial populations, immuno-assays to detect microbially-derived allergens and extensive environmental and meteorological observations. The data revealed bio-aerosol populations were not significantly impacted by the level of urban development as measured by anthropogenic pollutants and human population levels, but instead exhibited a strong seasonal trend related to general climatic variables. We applied back-trajectory analysis to establish sources of air masses and this allowed further explanation of urban bio-aerosols largely in terms of summer-marine and winter-continental origins. We also evaluated bio-aerosols for the potential to detect human health threats. Many samples supported bacterial and fungal phylotypes indicative of known pathogenic taxa, together with common indicators of human presence. The occurrence of allergenic endotoxins and beta-glucans generally tracked trends in microbial populations, with levels known to induce symptoms detected during summer months when microbial loading was higher. This strengthens calls for bio-aerosols to be considered in future risk assessments and surveillance of air quality, along with existing chemical and particulate indices.

  10. Microbial response to space environment, part B

    NASA Technical Reports Server (NTRS)

    Taylor, G. R.; Chassay, C. E.; Ellis, W. L.; Foster, B. G.; Volz, P. A.; Spizizen, J.; Buecker, H.; Wrenn, R. T.; Simmonds, R. C.; Long, R. A.

    1972-01-01

    The performance of the microbial response to space environment experiment is considered excellent by all investigators. For most microbial systems, only preliminary survival data are available at this time. None of the available data indicate space flight-mediated changes in cell viability or recovery. One quite important observation has been made at this early date, however. The eggs produced after mice had been infected with N. dubius larvae demonstrated a significant decrease in hatchability when compared to identical ground controls. Except for the fact that the Apollo 16 flight larvae had been on board the command module, treatment of the flown larvae and ground control larvae was the same; neither had been exposed to UV irradiation. The significance and implications of this finding are currently being studied.

  11. 2007 Microbial Population Biology (July 22-26, 2007)

    SciTech Connect

    Anthony M. Dean Nancy Ryan Gray

    2008-04-01

    Microbial Population Biology covers a diverse range of cutting edge issues in the microbial sciences and beyond. Firmly founded in evolutionary biology and with a strongly integrative approach, past meetings have covered topics ranging from the dynamics and genetics of adaptation to the evolution of mutation rate, community ecology, evolutionary genomics, altruism, and epidemiology. This meeting is never dull: some of the most significant and contentious issues in biology have been thrashed out here. We anticipate the 2007 meeting being no exception. The final form of the 2007 meeting is yet to be decided, but the following topics are likely to be included: evolutionary emergence of infectious disease and antibiotic resistance, genetic architecture and implications for the evolution of microbial populations, ageing in bacteria, biogeography, evolution of symbioses, the role of microbes in ecosystem function, and ecological genomics.

  12. Experimental demonstration of an Allee effect in microbial populations.

    PubMed

    Kaul, RajReni B; Kramer, Andrew M; Dobbs, Fred C; Drake, John M

    2016-04-01

    Microbial populations can be dispersal limited. However, microorganisms that successfully disperse into physiologically ideal environments are not guaranteed to establish. This observation contradicts the Baas-Becking tenet: 'Everything is everywhere, but the environment selects'. Allee effects, which manifest in the relationship between initial population density and probability of establishment, could explain this observation. Here, we experimentally demonstrate that small populations ofVibrio fischeriare subject to an intrinsic demographic Allee effect. Populations subjected to predation by the bacterivoreCafeteria roenbergensisdisplay both intrinsic and extrinsic demographic Allee effects. The estimated critical threshold required to escape positive density-dependence is around 5, 20 or 90 cells ml(-1)under conditions of high carbon resources, low carbon resources or low carbon resources with predation, respectively. This work builds on the foundations of modern microbial ecology, demonstrating that mechanisms controlling macroorganisms apply to microorganisms, and provides a statistical method to detect Allee effects in data. PMID:27048467

  13. Evolutionary Dynamics and Diversity in Microbial Populations

    NASA Astrophysics Data System (ADS)

    Thompson, Joel; Fisher, Daniel

    2013-03-01

    Diseases such as flu and cancer adapt at an astonishing rate. In large part, viruses and cancers are so difficult to prevent because they are continually evolving. Controlling such ``evolutionary diseases'' requires a better understanding of the underlying evolutionary dynamics. It is conventionally assumed that adaptive mutations are rare and therefore will occur and sweep through the population in succession. Recent experiments using modern sequencing technologies have illuminated the many ways in which real population sequence data does not conform to the predictions of conventional theory. We consider a very simple model of asexual evolution and perform simulations in a range of parameters thought to be relevant for microbes and cancer. Simulation results reveal complex evolutionary dynamics typified by competition between lineages with different sets of adaptive mutations. This dynamical process leads to a distribution of mutant gene frequencies different than expected under the conventional assumption that adaptive mutations are rare. Simulated gene frequencies share several conspicuous features with data collected from laboratory-evolved yeast and the worldwide population of influenza.

  14. Genetic Diversity Affects the Daily Transcriptional Oscillations of Marine Microbial Populations

    PubMed Central

    Shilova, Irina N.; Robidart, Julie C.; DeLong, Edward F.; Zehr, Jonathan P.

    2016-01-01

    Marine microbial communities are genetically diverse but have robust synchronized daily transcriptional patterns at the genus level that are similar across a wide variety of oceanic regions. We developed a microarray-inspired gene-centric approach to resolve transcription of closely-related but distinct strains/ecotypes in high-throughput sequence data. Applying this approach to the existing metatranscriptomics datasets collected from two different oceanic regions, we found unique and variable patterns of transcription by individual taxa within the abundant picocyanobacteria Prochlorococcus and Synechococcus, the alpha Proteobacterium Pelagibacter and the eukaryotic picophytoplankton Ostreococcus. The results demonstrate that marine microbial taxa respond differentially to variability in space and time in the ocean. These intra-genus individual transcriptional patterns underlie whole microbial community responses, and the approach developed here facilitates deeper insights into microbial population dynamics. PMID:26751368

  15. Responses to Microbial Challenges by SLAMF Receptors

    PubMed Central

    van Driel, Boaz Job; Liao, Gongxian; Engel, Pablo; Terhorst, Cox

    2016-01-01

    The SLAMF family (SLAMF) of cell surface glycoproteins is comprised of nine glycoproteins and while SLAMF1, 3, 5, 6, 7, 8, and 9 are self-ligand receptors, SLAMF2 and SLAMF4 interact with each other. Their interactions induce signal transduction networks in trans, thereby shaping immune cell–cell communications. Collectively, these receptors modulate a wide range of functions, such as myeloid cell and lymphocyte development, and T and B cell responses to microbes and parasites. In addition, several SLAMF receptors serve as microbial sensors, which either positively or negatively modulate the function of macrophages, dendritic cells, neutrophils, and NK cells in response to microbial challenges. The SLAMF receptor–microbe interactions contribute both to intracellular microbicidal activity as well as to migration of phagocytes to the site of inflammation. In this review, we describe the current knowledge on how the SLAMF receptors and their specific adapters SLAM-associated protein and EAT-2 regulate innate and adaptive immune responses to microbes. PMID:26834746

  16. Effect of Gamma radiation on microbial population of natural casings

    NASA Astrophysics Data System (ADS)

    Trigo, M. J.; Fraqueza, M. J.

    1998-06-01

    The high microbial load of fresh and dry natural casings increases the risk of meat product contamination with pathogenic microorganisms, agents of foodborn diseases. The aim of this work is to evaluate the killing effect of gamma radiation of the resident microbial population of pork and beef casings, to improve their hygiene and safety. Portions of fresh pork (small intestines and colon) and dry beef casings were irradiated in a Cobalt 60 source with with absorbed doses of 1,2,5 and 10 kGy. The D 10 values of total aerobic microorganisms in the pork casings were 1.65 kGy for colon and 1.54 kGy for small intestine. The D 10 value found in beef dry casings (small intestine) was 10.17 kGy. Radurization with 5 kGy was able to reduce, at least, 6 logs the coliform bacteria in pork casings. The killing effect over faecal Streptococci was 4 logs for pork fresh casings and 2 logs for beef dry casings. Gamma radiation with 5 kGy proved to be a convenient method to reduce substantially the microbial population of pork fresh casings. Otherwise, the microbial population of beef dry casings still resisted to 10 kGy.

  17. Comparing models of microbial-substrate interactions and their response to warming

    NASA Astrophysics Data System (ADS)

    Sihi, Debjani; Gerber, Stefan; Inglett, Patrick W.; Sharma Inglett, Kanika

    2016-03-01

    Recent developments in modelling soil organic carbon decomposition include the explicit incorporation of enzyme and microbial dynamics. A characteristic of these models is a positive feedback between substrate and consumers, which is absent in traditional first-order decay models. With sufficiently large substrate, this feedback allows an unconstrained growth of microbial biomass. We explore mechanisms that curb unrestricted microbial growth by including finite potential sites where enzymes can bind and by allowing microbial scavenging for enzymes. We further developed a model where enzyme synthesis is not scaled to microbial biomass but associated with a respiratory cost and microbial population adjusts enzyme production in order to optimise their growth. We then tested short- and long-term responses of these models to a step increase in temperature and find that these models differ in the long-term when short-term responses are harmonised. We show that several mechanisms, including substrate limitation, variable production of microbial enzymes, and microbes feeding on extracellular enzymes eliminate oscillations arising from a positive feedback between microbial biomass and depolymerisation. The model where enzyme production is optimised to yield maximum microbial growth shows the strongest reduction in soil organic carbon in response to warming, and the trajectory of soil carbon largely follows that of a first-order decomposition model. Modifications to separate growth and maintenance respiration generally yield short-term differences, but results converge over time because microbial biomass approaches a quasi-equilibrium with the new conditions of carbon supply and temperature.

  18. Molecular Characterization of Water Column Microbial Populations within the Northern Gulf of Mexico Hypoxic Zone

    NASA Astrophysics Data System (ADS)

    Mills, H. J.; Reese, B. K.; Romero, B.

    2012-12-01

    The Gulf of Mexico hypoxic zone displays spatial and temporal variability on seasonal, diurnal, and hourly timescales. The highly dynamic geochemistry can be a result of physical and chemical factors as well as pelagic microbial populations. As part of an ongoing project to determine the mechanisms controlling hypoxia and understand the biological factors within this region, shifts in the composition of the metabolically active microbial populations within the water column were characterized. Understanding these shifts provide information on microbial populations that have the potential to decrease oxygen concentrations through respiration and increase oxygen through photosynthesis. Temporal and spatial variations of metabolically active microbial populations were investigated along a well-studied 20 m isobath extending east of Terrebonne Bay to a location offshore from the Atchafalaya Bay. An RNA-based molecular characterization of the microbial population was used to determine the distribution of the metabolically active lineages. Bacterial SSU rRNA were pyrosequenced (Roche 454 FLX) providing over 700,000 sequences with an average read length of more than 400 bases. Known photosynthetic lineages varied in frequency of detection at depth and time of sampling, as was expected. Additional lineages with the capacity for suboxic metabolic processes were detected mid-water column associated with hypoxic water formation. These data suggest hypoxic conditions persist long enough in the mid-water to promote a physiological response within the microbial populations. In addition, temporal switches between photosynthesis and respiration should be considered when analyzing the extent of hypoxia. The techniques used provide a unique view of the biological mechanisms controlling hypoxia within the northern Gulf of Mexico.

  19. Self-Driven Jamming of Growing Microbial Populations

    NASA Astrophysics Data System (ADS)

    Schreck, Carl; Delarue, Morgan; Gneiwek, Pawel; Hallatschek, Oskar

    When cells grow in confined spaces, they assemble into dense populations that interact both chemically and physically. Although in recent years scientists have uncovered a previously hidden layer of mechanical regulation in mammalian tissues that impacts gene expression and development, little is known about the consequences of mechanical constraints on single-celled microbes. This is largely due to a lack of appropriate culturing techniques and accurate computational models. Using physically explicit computer models that are developed alongside microfluidic experiments, we address two fundamental questions: (1) what structures self-assemble in confined geometries due to the cell growth and division process? and (2) how do those structures and associated stresses feed back on to cell physiology? We find that microbial growth in confinement can lead to jamming, heterogeneous stress fields, and intermittent flow that in turn result in spatially and temporally heterogeneous physiological responses. With computer simulations, we further explore the differences between this 'active' flow that is driven internally by cell growth and 'inactive' flow, such as shear and hopper flow, that is driven externally.

  20. Self-driven jamming in growing microbial populations

    NASA Astrophysics Data System (ADS)

    Delarue, Morgan; Hartung, Jörn; Schreck, Carl; Gniewek, Pawel; Hu, Lucy; Herminghaus, Stephan; Hallatschek, Oskar

    2016-08-01

    In natural settings, microbes tend to grow in dense populations where they need to push against their surroundings to accommodate space for new cells. The associated contact forces play a critical role in a variety of population-level processes, including biofilm formation, the colonization of porous media, and the invasion of biological tissues. Although mechanical forces have been characterized at the single-cell level, it remains elusive how collective pushing forces result from the combination of single-cell forces. Here, we reveal a collective mechanism of confinement, which we call self-driven jamming, that promotes the build-up of large mechanical pressures in microbial populations. Microfluidic experiments on budding yeast populations in space-limited environments show that self-driven jamming arises from the gradual formation and sudden collapse of force chains driven by microbial proliferation, extending the framework of driven granular matter. The resulting contact pressures can become large enough to slow down cell growth, to delay the cell cycle in the G1 phase, and to strain or even destroy the micro-environment through crack propagation. Our results suggest that self-driven jamming and build-up of large mechanical pressures is a natural tendency of microbes growing in confined spaces, contributing to microbial pathogenesis and biofouling.

  1. Biogeography of Metabolically Active Microbial Populations within the Subseafloor Biosphere

    NASA Astrophysics Data System (ADS)

    Reese, B. K.; Shepard, A.; St. Peter, C.; Mills, H. J.

    2011-12-01

    Microbial life in deep marine sediments is widespread, metabolically active and diverse. Evidence of prokaryotic communities in sediments as deep as 800 m below the seafloor (mbsf) have been found. By recycling carbon and nutrients through biological and geochemical processes, the deep subsurface has the potential to remain metabolically active over geologic time scales. While a vast majority of the subsurface biosphere remains under studied, recent advances in molecular techniques and an increased focus on microbiological sampling during IODP expeditions have provided the initial steps toward better characterizations of the microbial communities. Coupling of geochemistry and RNA-based molecular analysis is essential to the description of the active microbial populations within the subsurface biosphere. Studies based on DNA may describe the taxa and metabolic pathways from the total microbial community within the sediment, whether the cells sampled were metabolically active, quiescent or dead. Due to a short lifespan within a cell, only an RNA-based analysis can be used to identify linkages between active populations and observed geochemistry. This study will coalesce and compare RNA sequence and geochemical data from Expeditions 316 (Nankai Trough), 320 (Pacific Equatorial Age Transect), 325 (Great Barrier Reef) and 329 (South Pacific Gyre) to evaluate the biogeography of microbial lineages actively altering the deep subsurface. The grouping of sediments allows for a wide range of geochemical environments to be compared, including two environments limited in organic carbon. Significant to this study is the use of similar extraction, amplification and simultaneous 454 pyrosequencing on all sediment populations allowing for robust comparisons with similar protocol strengths and biases. Initial trends support previously described reduction of diversity with increasing depth. The co-localization of active reductive and oxidative lineages suggests a potential cryptic

  2. Growth dynamics and the evolution of cooperation in microbial populations

    NASA Astrophysics Data System (ADS)

    Cremer, Jonas; Melbinger, Anna; Frey, Erwin

    2012-02-01

    Microbes providing public goods are widespread in nature despite running the risk of being exploited by free-riders. However, the precise ecological factors supporting cooperation are still puzzling. Following recent experiments, we consider the role of population growth and the repetitive fragmentation of populations into new colonies mimicking simple microbial life-cycles. Individual-based modeling reveals that demographic fluctuations, which lead to a large variance in the composition of colonies, promote cooperation. Biased by population dynamics these fluctuations result in two qualitatively distinct regimes of robust cooperation under repetitive fragmentation into groups. First, if the level of cooperation exceeds a threshold, cooperators will take over the whole population. Second, cooperators can also emerge from a single mutant leading to a robust coexistence between cooperators and free-riders. We find frequency and size of population bottlenecks, and growth dynamics to be the major ecological factors determining the regimes and thereby the evolutionary pathway towards cooperation.

  3. Facilitation as Attenuating of Environmental Stress among Structured Microbial Populations.

    PubMed

    Martins, Suzana Cláudia Silveira; Santaella, Sandra Tédde; Martins, Claudia Miranda; Martins, Rogério Parentoni

    2016-01-01

    There is currently an intense debate in microbial societies on whether evolution in complex communities is driven by competition or cooperation. Since Darwin, competition for scarce food resources has been considered the main ecological interaction shaping population dynamics and community structure both in vivo and in vitro. However, facilitation may be widespread across several animal and plant species. This could also be true in microbial strains growing under environmental stress. Pure and mixed strains of Serratia marcescens and Candida rugosa were grown in mineral culture media containing phenol. Growth rates were estimated as the angular coefficients computed from linearized growth curves. Fitness index was estimated as the quotient between growth rates computed for lineages grown in isolation and in mixed cultures. The growth rates were significantly higher in associated cultures than in pure cultures and fitness index was greater than 1 for both microbial species showing that the interaction between Serratia marcescens and Candida rugosa yielded more efficient phenol utilization by both lineages. This result corroborates the hypothesis that facilitation between microbial strains can increase their fitness and performance in environmental bioremediation. PMID:26904719

  4. Facilitation as Attenuating of Environmental Stress among Structured Microbial Populations

    PubMed Central

    Santaella, Sandra Tédde; Martins, Claudia Miranda; Martins, Rogério Parentoni

    2016-01-01

    There is currently an intense debate in microbial societies on whether evolution in complex communities is driven by competition or cooperation. Since Darwin, competition for scarce food resources has been considered the main ecological interaction shaping population dynamics and community structure both in vivo and in vitro. However, facilitation may be widespread across several animal and plant species. This could also be true in microbial strains growing under environmental stress. Pure and mixed strains of Serratia marcescens and Candida rugosa were grown in mineral culture media containing phenol. Growth rates were estimated as the angular coefficients computed from linearized growth curves. Fitness index was estimated as the quotient between growth rates computed for lineages grown in isolation and in mixed cultures. The growth rates were significantly higher in associated cultures than in pure cultures and fitness index was greater than 1 for both microbial species showing that the interaction between Serratia marcescens and Candida rugosa yielded more efficient phenol utilization by both lineages. This result corroborates the hypothesis that facilitation between microbial strains can increase their fitness and performance in environmental bioremediation. PMID:26904719

  5. Single gene-based distinction of individual microbial genomes from a mixed population of microbial cells

    PubMed Central

    Tamminen, Manu V.; Virta, Marko P. J.

    2015-01-01

    Recent progress in environmental microbiology has revealed vast populations of microbes in any given habitat that cannot be detected by conventional culturing strategies. The use of sensitive genetic detection methods such as CARD-FISH and in situ PCR have been limited by the cell wall permeabilization requirement that cannot be performed similarly on all cell types without lysing some and leaving some nonpermeabilized. Furthermore, the detection of low copy targets such as genes present in single copies in the microbial genomes, has remained problematic. We describe an emulsion-based procedure to trap individual microbial cells into picoliter-volume polyacrylamide droplets that provide a rigid support for genetic material and therefore allow complete degradation of cellular material to expose the individual genomes. The polyacrylamide droplets are subsequently converted into picoliter-scale reactors for genome amplification. The amplified genomes are labeled based on the presence of a target gene and differentiated from those that do not contain the gene by flow cytometry. Using the Escherichia coli strains XL1 and MC1061, which differ with respect to the presence (XL1), or absence (MC1061) of a single copy of a tetracycline resistance gene per genome, we demonstrate that XL1 genomes present at 0.1% of MC1061 genomes can be differentiated using this method. Using a spiked sediment microbial sample, we demonstrate that the method is applicable to highly complex environmental microbial communities as a target gene-based screen for individual microbes. The method provides a novel tool for enumerating functional cell populations in complex microbial communities. We envision that the method could be optimized for fluorescence-activated cell sorting to enrich genetic material of interest from complex environmental samples. PMID:25814987

  6. Comparing models of microbial-substrate interactions and their response to warming

    NASA Astrophysics Data System (ADS)

    Sihi, D.; Gerber, S.; Inglett, P. W.; Inglett, K. S.

    2015-07-01

    Recent developments in modelling soil organic carbon decomposition include the explicit incorporation of enzyme and microbial dynamics. A characteristic of these models is a positive feedback between substrate and consumers which is absent in traditional first order decay models. Under sufficient large substrate, this new feedback allows an unconstrained growth of microbial biomass. A second phenomenon incorporated in the microbial decomposition models is decreased carbon use efficiency (CUE) with increasing temperature. Here, first we analyse microbial decomposition models by parameterising changes in CUE based on the differentiation between growth and maintenance respiration. We then explore mechanisms that curb unrestricted microbial growth by including finite potential sites where enzymes can bind and by allowing microbial scavenging for enzymes. Finally, we propose a model where enzyme synthesis is associated with a respiratory cost and microbial population adjusts enzyme production in order to optimise their growth. When applying a step increase in temperature, we find fast responses that reflect adjustments to enzyme dynamics and maintenance respiration, a short-term adjustment in microbial growth, and the long-term change in carbon storage. We find that mechanisms that prevent unrestricted microbial growth lead to a similar response to warming as traditional first order decomposition models.

  7. The bacteriocin bactofencin A subtly modulates gut microbial populations.

    PubMed

    Guinane, Caitriona M; Lawton, Elaine M; O'Connor, Paula M; O'Sullivan, Órla; Hill, Colin; Ross, R Paul; Cotter, Paul D

    2016-08-01

    The diverse and dynamic microbiota of the gastrointestinal tract represents a vast source of bioactive substances. These include bacteriocins, which are antimicrobial peptides with the potential to modulate gut populations to impact positively on human health. Although several gut-derived bacteriocins have been isolated, there remain only a few exceptional studies in which their influence on microbial populations within the gut has been investigated. To facilitate such investigations, in vitro faecal fermentation systems can be used to simulate the anaerobic environment of the colon. In this instance, such a system was employed to explore the impact of bactofencin A, a novel broad spectrum class IId bacteriocin produced by gut isolates of Lactobacillus salivarius, on intestinal populations and overall microbial diversity. The study reveals that, although bactofencin A is a broad spectrum bacteriocin, it has a relatively subtle influence on intestinal communities, with a potentially positive impact on anaerobic populations such as Bacteroides, Clostridium and Bifidibacterium spp. The strategy taken is an important first step in investigating the merits of using bactofencin A to manipulate the gut microbiota in a beneficial way for health. PMID:27154638

  8. Microbial Responses to Environmentally Toxic Cadmium.

    PubMed

    Roane; Pepper

    1999-11-01

    We analyzed the soil microbial communities from one uncontaminated and two metal-impacted soils and found that while cadmium adversely affected the numbers of culturable bacteria in all soils, cadmium-resistant isolates were found from each of the soils. With exposure to 24 and 48 µg ml(-1) soluble cadmium, the metal-contaminated soil communities were more resistant than the uncontaminated soil community. In addition, in one metal-stressed soil, the resistant population became more resistant with increased cadmium levels. Ribosomal 16S DNA sequencing identified the isolates as Arthrobacter, Bacillus, or Pseudomonas spp. Further characterization demonstrated that two of the isolates were highly resistant to soluble cadmium with maximum resistance at 275 µg ml(-1) cadmium. These isolates were also resistant to a variety of antibiotics, namely ampicillin, gentamicin, penicillin, and streptomycin, but no overall correlation was found between enhanced antibiotic resistance and cadmium resistance. One Pseudomonas isolate H1 did become more resistant with increasing cadmium levels, suggesting a different resistance mechanism at high cadmium concentrations. PMID:10758182

  9. Metabolic Differences in Microbial Cell Populations Revealed by Nanophotonic Ionization

    SciTech Connect

    Walker, Bennett; Antonakos, Cory; Retterer, Scott T; Vertes, Akos

    2013-01-01

    ellular differences are linked to cell differentiation, the proliferation of cancer and to the development of drug resistance in microbial infections. Due to sensitivity limitations, however, large- scale metabolic analysis at the single cell level is only available for cells significantly larger in volume than Saccharomyces cerevisiae (~30 fL). Here we demonstrate that by a nanophotonic ionization platform and mass spectrometry, over one hundred up to 108 metabolites, or up to 18% of the known S. cerevisiae metabolome, can be identified in very small cell populations (n < 100). Under ideal conditions, r Relative quantitation of up to 4% of the metabolites is achieved at the single cell level.

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  11. Microbial Population Changes During Bioremediation of an Experimental Oil Spill

    SciTech Connect

    Chang, Y.J.; Davis, G.A.; Macnaughton, S.J.; Stephen, J.R.; Venosa, A.D.; White, D.C.

    1998-08-08

    A field experiment was conducted in Delaware (USA) to evaluate three crude oil bioremediation techniques. Four treatments were studied: no oil control, oil alone, oil + nutrients, and oil + nutrients + an indigenous inoculum. The microbial populations were monitored by standard MPN techniques, PLFA profile analysis, and 16S rDNA DGGE analysis for species definition. Viable MPN estimates showed high but steadily declining microbial numbers and no significant differences among treatments during the 14-weeks. Regarding the PLFA results, the communities shifted over the 14-week period from being composed primarily of eukaryotes to Gram-negative bacteria. The Gram-negative communities shifted from the exponential to the stationary phase of growth after week 0. All Gram-negative communities showed evidence of environmental stress. The 16S rDNA DGGE profile of all plots revealed eight prominent bands at time zero. The untreated control plots revealed a simple, dynamic dominant population structure throughout the experiment. The original banding pattern disappeared rapidly in all oiled plots, indicating that the dominant species diversity changed and increased substantially over 14 weeks. The nature of this change was altered by nutrient-addition and the addition of the indigenous inoculum.

  12. Population dynamics of microbial communities in the zebrafish gut

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  13. Matrix Effects and Measuring Microbial Responses to Xenobiotics in Soil

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Compartmentalization due to tortuous pore space promotes great diversity and functional redundancy in unsaturated soils. It is difficult to simultaneously expose discontiguous pore space (and organisms therein) to the same substance, which creates some challenges in measuring microbial responses to ...

  14. MICROBIAL RESPONSES TO WHEEL-TRAFFIC IN CONVENTIONAL AND NO-TILLAGE SYSTEMS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Traffic-induced soil compaction and tillage systems can impact the productivity and sustainability of agricultural soils. The objective of this study was to assess the response of soil microbial populations to wheel-traffic in two tillage systems on a Norfolk loamy sand (Typic Kandiudults; FAO clas...

  15. Characterization of Microbial Population Shifts during Sample Storage

    PubMed Central

    Mills, Heath J.; Reese, Brandi Kiel; Peter, Cruz St.

    2011-01-01

    The objective of this study was to determine shifts in the microbial community structure and potential function based on standard Integrated Ocean Drilling Program (IODP) storage procedures for sediment cores. Standard long-term storage protocols maintain sediment temperature at 4°C for mineralogy, geochemical, and/or geotechnical analysis whereas standard microbiological sampling immediately preserves sediments at −80°C. Storage at 4°C does not take into account populations may remain active over geologic time scales at temperatures similar to storage conditions. Identification of active populations within the stored core would suggest geochemical and geophysical conditions within the core change over time. To test this potential, the metabolically active fraction of the total microbial community was characterized from IODP Expedition 325 Great Barrier Reef sediment cores prior to and following a 3-month storage period. Total RNA was extracted from complementary 2, 20, and 40 m below sea floor sediment samples, reverse transcribed to complementary DNA and then sequenced using 454 FLX sequencing technology, yielding over 14,800 sequences from the six samples. Interestingly, 97.3% of the sequences detected were associated with lineages that changed in detection frequency during the storage period including key biogeochemically relevant lineages associated with nitrogen, iron, and sulfur cycling. These lineages have the potential to permanently alter the physical and chemical characteristics of the sediment promoting misleading conclusions about the in situ biogeochemical environment. In addition, the detection of new lineages after storage increases the potential for a wider range of viable lineages within the subsurface that may be underestimated during standard community characterizations. PMID:22363327

  16. Negative frequency-dependent interactions can underlie phenotypic heterogeneity in a clonal microbial population.

    PubMed

    Healey, David; Axelrod, Kevin; Gore, Jeff

    2016-01-01

    Genetically identical cells in microbial populations often exhibit a remarkable degree of phenotypic heterogeneity even in homogenous environments. Such heterogeneity is commonly thought to represent a bet-hedging strategy against environmental uncertainty. However, evolutionary game theory predicts that phenotypic heterogeneity may also be a response to negative frequency-dependent interactions that favor rare phenotypes over common ones. Here we provide experimental evidence for this alternative explanation in the context of the well-studied yeast GAL network. In an environment containing the two sugars glucose and galactose, the yeast GAL network displays stochastic bimodal activation. We show that in this mixed sugar environment, GAL-ON and GAL-OFF phenotypes can each invade the opposite phenotype when rare and that there exists a resulting stable mix of phenotypes. Consistent with theoretical predictions, the resulting stable mix of phenotypes is not necessarily optimal for population growth. We find that the wild-type mixed strategist GAL network can invade populations of both pure strategists while remaining uninvasible by either. Lastly, using laboratory evolution we show that this mixed resource environment can directly drive the de novo evolution of clonal phenotypic heterogeneity from a pure strategist population. Taken together, our results provide experimental evidence that negative frequency-dependent interactions can underlie the phenotypic heterogeneity found in clonal microbial populations. PMID:27487817

  17. Hydrological connectivity drives microbial responses to soil moisture (Invited)

    NASA Astrophysics Data System (ADS)

    Schimel, J.

    2013-12-01

    Biogeochemical models generally fit microbial responses to moisture with smooth functions--as soils dry, processes slow. Microbial physiology, in contrast, has focused on how cells synthesize organic solutes to remain hydrated. Increasingly, however, we recognize that drying affects soil processes through resource constraints that develop when hydrological connection breaks down and organisms and resources become isolated in disconnected water pockets. Thus, microbial activity is regulated by abrupt breaks in connectivity and resources become unavailable to synthesize organic osmolytes; i.e. both biogeochemical models and pure-culture physiology perspectives are flawed. Hydrological connectivity fails before microbes become substantially stressed and before extracellular enzymes become inactive. Thus, resources can accumulate in dry soils, even as microbial activity shuts down because of resource limitation. The differential moisture responses of enzymes, organisms, and transport explains why microbial biomass and extractable C pools increase through the dry summer in California annual grasslands, why the size of the respiration pulse on rewetting increases with the length of drought, and even why soils from a wide range of biomes show the same relative response to soil moisture. I will discuss the evidence that supports the hydrological connectivity hypothesis for soil microbial moisture responses, how it affects a range of ecosystem processes, and how we can use it to develop simple, yet mechanistically rich, models of soil dynamics.

  18. MICROBIAL DEGRADATION OF SEVEN AMIDES BY SUSPENDED BACTERIAL POPULATIONS

    EPA Science Inventory

    Microbial transformation rate constants were determined for seven amides in natural pond water. A second-order mathematical rate expression served as the model for describing the microbial transformation. Also investigated was the relationship between the infrared spectra and the...

  19. Spatial Shifts in Microbial Population Structure Within Poultry Litter Associated with Physicochemical Properties

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Microbial populations within poultry litter have been largely ignored with the exception of potential human or livestock pathogens. A better understanding of the community structure and identity of the microbial populations within poultry litter could aid in the development of management practices t...

  20. Demographic responses and population change.

    PubMed

    Friedlander, D

    1969-11-01

    Most Western societies have gone through a process of population change during the past 100-150 years. One important aspect is the socalled demographic transition: the shift from high to low birth and death rates, and accelerated growth resulting from the lag between falling mortality and falling fertility, in national populations. Equally important has been the "rural-to-urban" transition, which involved the migration of millions of people from rural areas. It is hypothesized, following the suggestion of Davis (Theory of the Multi-Phasic Demographic Response), that the adjustment in reproductive behavior made by a community in response to a rising "strain," such as that resulting from higher natural increase, is likely to differ depending upon the ease with which the community can relieve the strain through out migration. Relationships among such characteristics of modernization as intensity of industrialization, speed of urbanization, structural changes in the agricultural system, and declining fertility are implied. Case studies of England and Sweden lend support to the hypothesis: more rapid urban-industrial development, larger-scale movement from rural areas, and a delayed decline in the rural birth rate distinguish the English transition. PMID:21279792

  1. Microbial Population of Feedlot Waste and Associated Sites

    PubMed Central

    Rhodes, R. A.; Hrubant, G. R.

    1972-01-01

    A quantitative determination was made every 2 months for a year of the microflora of beef cattle waste and runoff at a medium-sized midwestern feedlot. Counts were obtained for selected groups of organisms in waste taken from paved areas of pens cleaned daily and, therefore, reflect the flora of raw waste. Overall, in terms of viable count per gram dry weight, the feedlot waste contained 1010 total organisms, 109 anaerobes, 108 gram-negative bacteria, 107 coliforms, 106 sporeformers, and 105 yeasts, fungi, and streptomycetes. The specific numbers and pattern of these groups of organisms varied only slightly during the study in spite of a wide variation in weather. Data indicate that little microbial growth occurs in the waste as it exists in the feedlot. Runoff from the pens contained the same general population pattern but with greater variation attributable to volume of liquid. Comparable determinations of an associated field disposal area (before and after cropping), stockpiled waste, and elevated dirt areas in the pens indicate that fungi, and especially streptomycetes, are the aerobic organisms most associated with final stabilization of the waste. Yeasts, which are the dominant type of organism in the ensiled corn fed the cattle, do not occur in large numbers in the animal waste. Large ditches receiving runoff and subsurface water from the fields have a population similar to the runoff but with fewer coliforms. PMID:16349931

  2. Microbial Responses to Microgravity and Other Low-Shear Environments

    PubMed Central

    Nickerson, Cheryl A.; Ott, C. Mark; Wilson, James W.; Ramamurthy, Rajee; Pierson, Duane L.

    2004-01-01

    Microbial adaptation to environmental stimuli is essential for survival. While several of these stimuli have been studied in detail, recent studies have demonstrated an important role for a novel environmental parameter in which microgravity and the low fluid shear dynamics associated with microgravity globally regulate microbial gene expression, physiology, and pathogenesis. In addition to analyzing fundamental questions about microbial responses to spaceflight, these studies have demonstrated important applications for microbial responses to a ground-based, low-shear stress environment similar to that encountered during spaceflight. Moreover, the low-shear growth environment sensed by microbes during microgravity of spaceflight and during ground-based microgravity analogue culture is relevant to those encountered during their natural life cycles on Earth. While no mechanism has been clearly defined to explain how the mechanical force of fluid shear transmits intracellular signals to microbial cells at the molecular level, the fact that cross talk exists between microbial signal transduction systems holds intriguing possibilities that future studies might reveal common mechanotransduction themes between these systems and those used to sense and respond to low-shear stress and changes in gravitation forces. The study of microbial mechanotransduction may identify common conserved mechanisms used by cells to perceive changes in mechanical and/or physical forces, and it has the potential to provide valuable insight for understanding mechanosensing mechanisms in higher organisms. This review summarizes recent and future research trends aimed at understanding the dynamic effects of changes in the mechanical forces that occur in microgravity and other low-shear environments on a wide variety of important microbial parameters. PMID:15187188

  3. Microbial Responses to Microgravity and Other Low-Shear Environments

    NASA Technical Reports Server (NTRS)

    Nickerson, Cheryl A.; Ott, C. Mark; Wilson, James W.; Ramamurthy, Rajee; Pierson, Duane L.

    2004-01-01

    Microbial adaptation to environmental stimuli is essential for survival. While several of these stimuli have been studied in detail, recent studies have demonstrated an important role for a novel environmental parameter in which microgravity and the low fluid shear dynamics associated with microgravity globally regulate microbial gene expression, physiology, and pathogenesis. In addition to analyzing fundamental questions about microbial responses to spaceflight, these studies have demonstrated important applications for microbial responses to a ground-based, low-shear stress environment similar to that encountered during spaceflight. Moreover, the low-shear growth environment sensed by microbes during microgravity of spaceflight and during ground-based microgravity analogue culture is relevant to those encountered during their natural life cycles on Earth. While no mechanism has been clearly defined to explain how the mechanical force of fluid shear transmits intracellular signals to microbial cells at the molecular level, the fact that cross talk exists between microbial signal transduction systems holds intriguing possibilities that future studies might reveal common mechanotransduction themes between these systems and those used to sense and respond to low-shear stress and changes in gravitation forces. The study of microbial mechanotransduction may identify common conserved mechanisms used by cells to perceive changes in mechanical and/or physical forces, and it has the potential to provide valuable insight for understanding mechanosensing mechanisms in higher organisms. This review summarizes recent and future research trends aimed at understanding the dynamic effects of changes in the mechanical forces that occur in microgravity and other low-shear environments on a wide variety of important microbial parameters.

  4. Alpine Microbial Community Responses to Summer Warming

    NASA Astrophysics Data System (ADS)

    Osborne, B. B.; Baron, J.; Wallenstein, M. D.

    2011-12-01

    Remote alpine ecosystems of the western US are vulnerable to anthropogenic drivers of change. Atmospheric nitrogen (N) deposition and a changing climate introduce nutrients, alter hydrological processes, and expose soils to novel temperature regimes. We asked whether terrestrial microbes, specifically nitrifiers that may contribute to already high lake and stream NO3- concentrations, may be responding to changes in important controls of community development and activity associated with a changing climate, namely temperature and moisture. In August 2010 we sampled three soils from the Loch Vale Watershed in Rocky Mountain National Park which fell along a gradient of succession commonly represented in deglaciated alpine catchments. These included well-developed meadow soils, poorly vegetated talus substrate, and newly-exposed glacial outwash. Outwash, talus, and meadow samples were all N-rich and contained NH4-N concentrations ~7 times higher than NO3-N. Soils were incubated for 45 days at 2.5, 10, and 25oC and three moisture levels based on initial field conditions. Nitrifier concentrations were greatest in outwash, intermediate in talus, and lowest in meadow samples. Bacterial nitrifier abundance greatly surpassed archaeal nitrifier levels. Net nitrification was also greatest in outwash, followed by meadow and talus respectively. Moisture, rather than temperature, was a dominant control over both nitrifier abundance and activity. Linking the influence of temperature and moisture on alpine microbial communities will provide insight into control thresholds, optima, and synergistic interactions. This research is part of a larger study of controls on headwater stream and lake NO3-. Characterizing microbial NO3- production in the alpine will help us evaluate the importance of biological, as opposed to physical, sources of stream NO3-. It will also inform our ability to forecast and mitigate consequences of anthropogenic drivers of change on these systems.

  5. Microbial responses to southward and northward Cambisol soil transplant

    SciTech Connect

    Wang, Mengmeng; Liu, Shanshan; Wang, Feng; Sun, Bo; Zhou, Jizhong; Yang, Yunfeng

    2015-10-26

    We report that soil transplant serves as a proxy to simulate climate changes. Recently, we have shown that southward transplant of black soil and northward transplant of red soil altered soil microbial communities and biogeochemical variables. However, fundamental differences in soil types have prevented direct comparison between southward and northward transplants. To tackle it, herein we report an analysis of microbial communities of Cambisol soil in an agriculture field after 4 years of adaptation to southward and northward soil transplants over large transects. Analysis of bare fallow soils revealed concurrent increase in microbial functional diversity and coarse-scale taxonomic diversity at both transplanted sites, as detected by GeoChip 3.0 and DGGE, respectively. Furthermore, a correlation between microbial functional diversity and taxonomic diversity was detected, which was masked in maize cropped soils. Mean annual temperature, soil moisture, and nitrate (NO3¯-N) showed strong correlations with microbial communities. In addition, abundances of ammonium-oxidizing genes (amoA) and denitrification genes were correlated with nitrification capacity and NO3¯-N contents, suggesting that microbial responses to soil transplant could alter microbe-mediated biogeochemical cycle at the ecosystem level.

  6. Microbial responses to southward and northward Cambisol soil transplant

    DOE PAGESBeta

    Wang, Mengmeng; Liu, Shanshan; Wang, Feng; Sun, Bo; Zhou, Jizhong; Yang, Yunfeng

    2015-10-26

    We report that soil transplant serves as a proxy to simulate climate changes. Recently, we have shown that southward transplant of black soil and northward transplant of red soil altered soil microbial communities and biogeochemical variables. However, fundamental differences in soil types have prevented direct comparison between southward and northward transplants. To tackle it, herein we report an analysis of microbial communities of Cambisol soil in an agriculture field after 4 years of adaptation to southward and northward soil transplants over large transects. Analysis of bare fallow soils revealed concurrent increase in microbial functional diversity and coarse-scale taxonomic diversity atmore » both transplanted sites, as detected by GeoChip 3.0 and DGGE, respectively. Furthermore, a correlation between microbial functional diversity and taxonomic diversity was detected, which was masked in maize cropped soils. Mean annual temperature, soil moisture, and nitrate (NO3¯-N) showed strong correlations with microbial communities. In addition, abundances of ammonium-oxidizing genes (amoA) and denitrification genes were correlated with nitrification capacity and NO3¯-N contents, suggesting that microbial responses to soil transplant could alter microbe-mediated biogeochemical cycle at the ecosystem level.« less

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

    NASA Astrophysics Data System (ADS)

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

    2013-09-01

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

  8. Microbial populations related to PAH biodegradation in an aged biostimulated creosote-contaminated soil.

    PubMed

    Lladó, Salvador; Jiménez, Nuria; Viñas, Marc; Solanas, Anna Maria

    2009-09-01

    A previous bioremediation survey on a creosote-contaminated soil showed that aeration and optimal humidity promoted depletion of three-ringed polycyclic aromatic hydrocarbons (PAHs), but residual concentrations of four-ringed benzo(a)anthracene (B(a)A) and chrysene (Chry) remained. In order to explain the lack of further degradation of heavier PAHs such as four-ringed PAHs and to analyze the microbial population responsible for PAH biodegradation, a chemical and microbial molecular approach was used. Using a slurry incubation strategy, soil in liquid mineral medium with and without additional B(a)A and Chry was found to contain a powerful PAH-degrading microbial community that eliminated 89% and 53% of the added B(a)A and Chry, respectively. It is hypothesized that the lack of PAH bioavailability hampered their further biodegradation in the unspiked soil. According to the results of the culture-dependent and independent techniques Mycobacterium parmense, Pseudomonas mexicana, and Sphingobacterials group could control B(a)A and Chry degradation in combination with several microorganisms with secondary metabolic activity. PMID:19153811

  9. Molecular Analysis of Surfactant-Driven Microbial Population Shifts in Hydrocarbon-Contaminated Soil†

    PubMed Central

    Colores, Gregory M.; Macur, Richard E.; Ward, David M.; Inskeep, William P.

    2000-01-01

    We analyzed the impact of surfactant addition on hydrocarbon mineralization kinetics and the associated population shifts of hydrocarbon-degrading microorganisms in soil. A mixture of radiolabeled hexadecane and phenanthrene was added to batch soil vessels. Witconol SN70 (a nonionic, alcohol ethoxylate) was added in concentrations that bracketed the critical micelle concentration (CMC) in soil (CMC′) (determined to be 13 mg g−1). Addition of the surfactant at a concentration below the CMC′ (2 mg g−1) did not affect the mineralization rates of either hydrocarbon. However, when surfactant was added at a concentration approaching the CMC′ (10 mg g−1), hexadecane mineralization was delayed and phenanthrene mineralization was completely inhibited. Addition of surfactant at concentrations above the CMC′ (40 mg g−1) completely inhibited mineralization of both phenanthrene and hexadecane. Denaturing gradient gel electrophoresis of 16S rRNA gene segments showed that hydrocarbon amendment stimulated Rhodococcus and Nocardia populations that were displaced by Pseudomonas and Alcaligenes populations at elevated surfactant levels. Parallel cultivation studies revealed that the Rhodococcus population can utilize hexadecane and that the Pseudomonas and Alcaligenes populations can utilize both Witconol SN70 and hexadecane for growth. The results suggest that surfactant applications necessary to achieve the CMC alter the microbial populations responsible for hydrocarbon mineralization. PMID:10877792

  10. Microbial Response to Microgravity and Other Low Shear Environments

    NASA Technical Reports Server (NTRS)

    Nickerson, C.; Ott, C. Mark; Wilson, James W.; Ramamurthy, Rajee; Pierson, Duane L.

    2004-01-01

    Microbial existence and survival requires the ability to sense and respond to environmental changes, including changes in physical forces. This is because microbes inhabit an amazingly diverse range of ecological niches and therefore must constantly adapt to a wide variety of changing environmental conditions, including alterations in temperature, pH, nutrient availability, oxygen levels, and osmotic pressure gradients. Microbes sense their environment through a variety of sensors and receptors which serve to integrate the different signals into the appropriate cellular response(s) that is optimal for survival. While numerous environmental stimuli have been examined for their effect on microorganisms, effects due to changes in mechanical and/or physical forces are also becoming increasingly apparent. Recently, several important studies have demonstrated a key role for microgravity and the low fluid shear dynamics associated with microgravity in the regulation of microbial gene expression, physiology and pathogenesis. The mechanosensory response of microorganisms to these environmental signals, which are relevant to those encountered during microbial life cycles on Earth, may provide insight into their adaptations to physiologically relevant conditions and may ultimately lead to eludicidation of the mechanisms important for mechanosensory transduction in living cells. This review summarizes the recent and potential future research trends aimed at understanding the effect of changes in mechanical forces that occur in microgravity and other low shear environments on different microbial parameters. The results of these studies provide an important step towards understanding how microbes integrate information from multiple mechanical stimuli to an appropriate physiological response.

  11. Molecular Characterization of Swine Manure Lagoon Microbial and Antibiotic Resistant Populations

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: The differences in swine manure lagoon effluent based on differing management styles or approaches such as different stages of swine rearing determines the presence of variable antibiotic resistance determinants and functional microbial populations. These concerns determine the suitabil...

  12. Innate immune responses to microbial agonist stimulations in heterophils and monocytes from young commercial turkeys

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The innate immune system recognizes microbial pathogens and pathogen associated molecular patterns and incites inflammatory immune responses to control the infection. Here, we examined functional innate immune responses of turkey heterophils and monocytes to microbial agonist stimulations by measur...

  13. Investigating the Response of Microbial Communities to Cyclodextrin

    NASA Astrophysics Data System (ADS)

    Szponar, N.; Slater, G.; Smith, J.

    2009-05-01

    Recent studies have found applications of hydroxypropyl-β-cyclodextrin (HPβCD) to be highly effective in removing DDT from soils in situ. However, the persistence of HPβCD within the soil and its impact on soil microbial communities is still unclear. It has been suggested that cyclodextrin might provide a substrate for microbial communities resulting in changes in the ongoing effectiveness of remediation and/or soil hydraulic properties. The potential exists that stimulation of the soil microbial community may contribute to removal of DDT, along with the solubilization effects normally associated with cyclodextrin treatment. This study investigated the response of soil microbial communities from a site undergoing remediation of DDT with HPβCD through microcosm and bench scale column studies. Phospholipid fatty acid (PLFA) analysis and their natural abundance 13C signatures can be used to identify in situ microbial metabolism of HPβCD. Heterotrophic organisms have PLFA with 13C signatures 3 to 6‰ depleted from their carbon source. Cyclodextrin was found to have a δ13C of -16‰ resulting from its formation via enzymatic degradation of cornstarch. In contrast, soil organic matter, had a predominantly C3 plant derived signature and a δ13C of -25‰. Incorporation of HPβCD by soil microbial communities would therefore cause a shift to a more enriched isotopic value. While microcosm studies demonstrated no noticeable change in biomass and few changes in PLFA distribution, column studies treated with a 10% solution of HPβCD demonstrated an approximate doubling of microbial biomass after 6 weeks of application based on PLFA concentrations. Concurrent changes in PLFA distribution further indicated a response to cyclodextrin. Changes in PLFA concentration and distribution were concurrent with isotopic enrichment of PLFA in treated columns. This isotopic enrichment provided direct evidence for microbial consumption of cyclodextrin. Incorporation of 13C enriched

  14. Genome-Centric Analysis of Microbial Populations Enriched by Hydraulic Fracture Fluid Additives in a Coal Bed Methane Production Well.

    PubMed

    Robbins, Steven J; Evans, Paul N; Parks, Donovan H; Golding, Suzanne D; Tyson, Gene W

    2016-01-01

    Coal bed methane (CBM) is generated primarily through the microbial degradation of coal. Despite a limited understanding of the microorganisms responsible for this process, there is significant interest in developing methods to stimulate additional methane production from CBM wells. Physical techniques including hydraulic fracture stimulation are commonly applied to CBM wells, however the effects of specific additives contained in hydraulic fracture fluids on native CBM microbial communities are poorly understood. Here, metagenomic sequencing was applied to the formation waters of a hydraulically fractured and several non-fractured CBM production wells to determine the effect of this stimulation technique on the in-situ microbial community. The hydraulically fractured well was dominated by two microbial populations belonging to the class Phycisphaerae (within phylum Planctomycetes) and candidate phylum Aminicenantes. Populations from these phyla were absent or present at extremely low abundance in non-fractured CBM wells. Detailed metabolic reconstruction of near-complete genomes from these populations showed that their high relative abundance in the hydraulically fractured CBM well could be explained by the introduction of additional carbon sources, electron acceptors, and biocides contained in the hydraulic fracture fluid. PMID:27375557

  15. Genome-Centric Analysis of Microbial Populations Enriched by Hydraulic Fracture Fluid Additives in a Coal Bed Methane Production Well

    PubMed Central

    Robbins, Steven J.; Evans, Paul N.; Parks, Donovan H.; Golding, Suzanne D.; Tyson, Gene W.

    2016-01-01

    Coal bed methane (CBM) is generated primarily through the microbial degradation of coal. Despite a limited understanding of the microorganisms responsible for this process, there is significant interest in developing methods to stimulate additional methane production from CBM wells. Physical techniques including hydraulic fracture stimulation are commonly applied to CBM wells, however the effects of specific additives contained in hydraulic fracture fluids on native CBM microbial communities are poorly understood. Here, metagenomic sequencing was applied to the formation waters of a hydraulically fractured and several non-fractured CBM production wells to determine the effect of this stimulation technique on the in-situ microbial community. The hydraulically fractured well was dominated by two microbial populations belonging to the class Phycisphaerae (within phylum Planctomycetes) and candidate phylum Aminicenantes. Populations from these phyla were absent or present at extremely low abundance in non-fractured CBM wells. Detailed metabolic reconstruction of near-complete genomes from these populations showed that their high relative abundance in the hydraulically fractured CBM well could be explained by the introduction of additional carbon sources, electron acceptors, and biocides contained in the hydraulic fracture fluid. PMID:27375557

  16. Ileal and cecal microbial populations in broilers given specific essential oil blends and probiotics in two consecutive grow-outs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Digestive microbial populations (MP) are key components for sustained healthy broiler production. Specific essential oil (EO) blends and probiotics used as feed additives have shown to promote healthy digestive microbials, resulting in improved poultry production. Two consecutive experiments were ...

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  18. Metagenomic Approach for Understanding Microbial Population from Petroleum Muck

    PubMed Central

    Joshi, M. N.; Dhebar, S. V.; Dhebar, S. V.; Bhargava, P.; Pandit, A. S.; Patel, R. P.; Saxena, A. K.

    2014-01-01

    Petroleum products play a major role in fueling the economy of the world but the pollution they create has become a critical issue. Understanding the diversity present in pipeline muck will help with the exploration of new microbial strains with better hydrocarbon degrading capacities for bioremediation of polluted sites. This study provides an analysis of petroleum muck using next generation sequencing. PMID:24874664

  19. Metagenomic approach for understanding microbial population from petroleum muck.

    PubMed

    Joshi, M N; Dhebar, S V; Dhebar, S V; Bhargava, P; Pandit, A S; Patel, R P; Saxena, A K; Bagatharia, S B

    2014-01-01

    Petroleum products play a major role in fueling the economy of the world but the pollution they create has become a critical issue. Understanding the diversity present in pipeline muck will help with the exploration of new microbial strains with better hydrocarbon degrading capacities for bioremediation of polluted sites. This study provides an analysis of petroleum muck using next generation sequencing. PMID:24874664

  20. MICROBIAL POPULATION CHANGES DURING BIOREMEDIATION OF AN EXPERIMENTAL OIL SPILL

    EPA Science Inventory

    Three crude oil bioremediation techniques were applied in a randomized block field experiment simulating a coastal oil-spill. Four treatments (no oil control, oil alone, oil + nutrients, and oil + nutrients + an indigenous inoculum) were applied. In-situ microbial community str...

  1. Response of microbial activities and diversity to PAHs contamination at coal tar contaminated land

    NASA Astrophysics Data System (ADS)

    Zhao, Xiaohui; Sun, Yujiao; Ding, Aizhong; Zhang, Dan; Zhang, Dayi

    2015-04-01

    Coal tar is one of the most hazardous and concerned organic pollutants and the main hazards are polycyclic aromatic hydrocarbons (PAHs). The indigenous microorganisms in soils are capable to degrade PAHs, with essential roles in biochemical process for PAHs natural attenuation. This study investigated 48 soil samples (from 8 depths of 6 boreholes) in Beijing coking and chemistry plant (China) and revealed the correlation between PAHs contamination, soil enzyme activities and microbial community structure, by 16S rRNA denaturing gradient gel electrophoresis (DGGE). At the site, the key contaminants were identified as naphthalene, acenaphthylene, acenaphthene, fluorene, phenanthrene and anthracene, and the total PAHs concentration ranged from 0.1 to 923.9 mg/kg dry soil. The total PAHs contamination level was positively correlated (p<0.05) with the bacteria count (0.9×107-14.2×107 CFU/mL), catalase activities (0.554-6.230 mL 0.02 M KMnO4/g•h) and dehydrogenase activities (1.9-30.4 TF μg/g•h soil), showing the significant response of microbial population and degrading functions to the organic contamination in soils. The PAHs contamination stimulated the PAHs degrading microbes and promoted their biochemical roles in situ. The positive relationship between bacteria count and dehydrogenase activities (p<0.05) suggested the dominancy of PAHs degrading bacteria in the microbial community. More interestingly, the microbial community deterioration was uncovered via the decline of microbial biodiversity (richness from 16S rRNA DGGE) against total PAHs concentration (p<0.05). Our research described the spatial profiles of PAHs contamination and soil microbial functions at the PAHs heavily contaminated sites, offering deeper understanding on the roles of indigenous microbial community in natural attenuation process.

  2. Microbial community response during the iron fertilization experiment LOHAFEX.

    PubMed

    Thiele, Stefan; Fuchs, Bernhard M; Ramaiah, Nagappa; Amann, Rudolf

    2012-12-01

    Iron fertilization experiments in high-nutrient, low-chlorophyll areas are known to induce phytoplankton blooms. However, little is known about the response of the microbial community upon iron fertilization. As part of the LOHAFEX experiment in the southern Atlantic Ocean, Bacteria and Archaea were monitored within and outside an induced bloom, dominated by Phaeocystis-like nanoplankton, during the 38 days of the experiment. The microbial production increased 1.6-fold (thymidine uptake) and 2.1-fold (leucine uptake), while total cell numbers increased only slightly over the course of the experiment. 454 tag pyrosequencing of partial 16S rRNA genes and catalyzed reporter deposition fluorescence in situ hybridization (CARD FISH) showed that the composition and abundance of the bacterial and archaeal community in the iron-fertilized water body were remarkably constant without development of typical bloom-related succession patterns. Members of groups usually found in phytoplankton blooms, such as Roseobacter and Gammaproteobacteria, showed no response or only a minor response to the bloom. However, sequence numbers and total cell numbers of the SAR11 and SAR86 clades increased slightly but significantly toward the end of the experiment. It seems that although microbial productivity was enhanced within the fertilized area, a succession-like response of the microbial community upon the algal bloom was averted by highly effective grazing. Only small-celled members like the SAR11 and SAR86 clades could possibly escape the grazing pressure, explaining a net increase of those clades in numbers. PMID:23064339

  3. Microbial population dynamics during sludge granulation in an A/O/A sequencing batch reactor.

    PubMed

    He, Qiulai; Zhou, Jun; Wang, Hongyu; Zhang, Jing; Wei, Li

    2016-08-01

    The evolution of the bacterial population during formation of denitrifying phosphorus removal granular sludge was investigated using high-throughput pyrosequencing. As a result, mature granules with a compact structure were obtained in an anaerobic/aerobic/anoxic (A/O/A) sequencing batch reactor under an organic loading rate as low as 0.3kg COD/(m(3)·d). Rod-shaped microbes were observed to cover with the outer surface of granules. Besides, reliable COD and simultaneous nitrogen and phosphorus removal efficiencies were achieved over the whole operation period. MiSeq pyrosequencing analysis illustrated that both the microbial diversity and richness increased sharply during the granulation process, whereas they stayed stable after the presence of granules. Some microorganisms seemed to contribute to the formation of granules, and some were identified as functional bacterial groups responsible for constructing the biological reactor. PMID:27115745

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

  6. Oxygen Effects on Thermophilic Microbial Populations in Biofilters Treating Nitric Oxide Containing Off-Gas Streams

    SciTech Connect

    Lee, Brady Douglas; Apel, William Arnold; Smith, William Aaron

    2004-04-01

    Electricity generation from coal has increased by an average of 51 billion kWh per year over the past 3 years. For this reason cost-effective strategies to control nitrogen oxides (NOx) from coal-fired power plant combustion gases must be developed. Compost biofilters operated at 55°C at an empty bed contact time (EBCT) of 13 seconds were shown to be feasible for removal of nitric oxide (NO) from synthetic flue gas. Denitrifying microbial populations in these biofilters were shown to reduce influent NO feeds by 90 to 95% at inlet NO concentrations of 500 ppmv. Oxygen was shown to have a significant effect on the NO removal efficiency demonstrated by these biofilters. Two biofilters were set up under identical conditions for the purpose of monitoring NO removal as well as changes in the microbial population in the bed medium under anaerobic and aerobic conditions. Changes in the microbial population were monitored to determine the maximum oxygen tolerance of a denitrifying biofilter as well as methods of optimizing microbial populations capable of denitrification in the presence of low oxygen concentrations. Nitric oxide removal dropped to between 10 and 20% when oxygen was present in the influent stream. The inactive compost used to pack the biofilters may have also caused the decreased NO removal efficiency compared to previous biofiltration experiments. Analysis of the bed medium microbial population using environmental scanning electron microscopy indicated significant increases in biomass populating the surface of the compost when compared to unacclimated compost.

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

    PubMed

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

    2011-10-01

    The relationships between vermicompost chemical features, enzyme activities, community-level physiological profiles (CLPPs), fungal community structures, and its microbial respiratory response to pesticides were investigated. Fungal community structure of vermicomposts produced from damaged tomato fruits (DT), winery wastes (WW), olive-mill waste and biosolids (OB), and cattle manure (CM) were determined by denaturing gradient gel electrophoresis of 18S rDNA. MicroResp™ was used for assessing vermicompost CLPPs and testing the microbial response to metalaxyl, imidacloprid, and diuron. Vermicompost enzyme activities and CLPPs indicated that WW, OB, and DT had higher microbial functional diversity than CM. The microbiota of the former tolerated all three pesticides whereas microbial respiration in CM was negatively affected by metalaxyl and imidacloprid. The response of vermicompost microbiota to the fungicide metalaxyl was correlated to its fungal community structure. The results suggest that vermicomposts with higher microbial functional diversity can be useful for the management of pesticide pollution in agriculture. PMID:21865033

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

    PubMed

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

    2014-10-23

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

  9. Long-term effects of timber harvesting on hemicellulolytic microbial populations in coniferous forest soils.

    PubMed

    Leung, Hilary T C; Maas, Kendra R; Wilhelm, Roland C; Mohn, William W

    2016-02-01

    Forest ecosystems need to be sustainably managed, as they are major reservoirs of biodiversity, provide important economic resources and modulate global climate. We have a poor knowledge of populations responsible for key biomass degradation processes in forest soils and the effects of forest harvesting on these populations. Here, we investigated the effects of three timber-harvesting methods, varying in the degree of organic matter removal, on putatively hemicellulolytic bacterial and fungal populations 10 or more years after harvesting and replanting. We used stable-isotope probing to identify populations that incorporated (13)C from labeled hemicellulose, analyzing (13)C-enriched phospholipid fatty acids, bacterial 16 S rRNA genes and fungal ITS regions. In soil microcosms, we identified 104 bacterial and 52 fungal hemicellulolytic operational taxonomic units (OTUs). Several of these OTUs are affiliated with taxa not previously reported to degrade hemicellulose, including the bacterial genera Methylibium, Pelomonas and Rhodoferax, and the fungal genera Cladosporium, Pseudeurotiaceae, Capronia, Xenopolyscytalum and Venturia. The effect of harvesting on hemicellulolytic populations was evaluated based on in situ bacterial and fungal OTUs. Harvesting treatments had significant but modest long-term effects on relative abundances of hemicellulolytic populations, which differed in strength between two ecozones and between soil layers. For soils incubated in microcosms, prior harvesting treatments did not affect the rate of incorporation of hemicellulose carbon into microbial biomass. In six ecozones across North America, distributions of the bacterial hemicellulolytic OTUs were similar, whereas distributions of fungal ones differed. Our work demonstrates that diverse taxa in soil are hemicellulolytic, many of which are differentially affected by the impact of harvesting on environmental conditions. However, the hemicellulolytic capacity of soil communities appears

  10. Midgut Microbial Community of Culex quinquefasciatus Mosquito Populations from India

    PubMed Central

    Chandel, Kshitij; Mendki, Murlidhar J.; Parikh, Rasesh Y.; Kulkarni, Girish; Tikar, Sachin N.; Sukumaran, Devanathan; Prakash, Shri; Parashar, Brahma D.; Shouche, Yogesh S.; Veer, Vijay

    2013-01-01

    The mosquito Culex quinquefasciatus is a ubiquitous species that serves as a major vector for west nile virus and lymphatic filariasis. Ingestion of bloodmeal by females triggers a series of physiological processes in the midgut and also exposes them to infection by these pathogens. The bacteria normally harbored in the midgut are known to influence physiology and can also alter the response to various pathogens. The midgut bacteria in female Cx. quinquefasciatus mosquitoes collected over a large geographical area from India was studied. Examination of 16S ribosomal DNA amplicons from culturable microflora revealed the presence of 83 bacterial species belonging to 31 bacterial genera. All of these species belong to three phyla i.e. Proteobacteria, Firmicutes and Actinobacteria. Phylum Proteobacteria was the most dominant phylum (37 species), followed by Firmicutes (33 species) and Actinobacteria (13 species). Phylum Proteobacteria, was dominated by members of γ-proteobacteria class. The genus Staphylococcus was the largest genus represented by 11 species whereas Enterobacter was the most prevalent genus and recovered from all the field stations except Leh. Highest bacterial prevalence was observed from Bhuj (22 species) followed by Nagrota (18 species), Masimpur (18 species) and Hathigarh (16 species). Whereas, least species were observed from Leh (8 species). It has been observed that individual mosquito harbor extremely diverse gut bacteria and have very small overlap bacterial taxa in their gut. This variation in midgut microbiota may be one of the factors responsible for variation in disease transmission rates or vector competence within mosquito population. The present data strongly encourage further investigations to verify the potential role of the detected bacteria in mosquito for the transmission of lymphatic filariasis and west nile virus. To the best of our knowledge this is the first study on midgut microbiota of wild Cx. quinquefasciatus from over a

  11. Integral structural-functional method for characterizing microbial populations

    NASA Astrophysics Data System (ADS)

    Yakushev, A. V.

    2015-04-01

    An original integral structural-functional method has been proposed for characterizing microbial communities. The novelty of the approach is the in situ study of microorganisms based on the growth kinetics of microbial associations in liquid nutrient broth media under selective conditions rather than on the level of taxa or large functional groups. The method involves the analysis of the integral growth model of a periodic culture. The kinetic parameters of such associations reflect their capacity of growing on different media, i.e., their physiological diversity, and the metabolic capacity of the microorganisms for growth on a nutrient medium. Therefore, the obtained parameters are determined by the features of the microbial ecological strategies. The inoculation of a dense medium from the original inoculate allows characterizing the taxonomic composition of the dominants in the soil community. The inoculation from the associations developed on selective media characterizes the composition of syntrophic groups, which fulfill a specific function in nature. This method is of greater information value than the classical methods of inoculation on selective media.

  12. The Biodiversity Changes in the Microbial Population of Soils Contaminated with Crude Oil.

    PubMed

    Abbasian, Firouz; Lockington, Robin; Megharaj, Mallavarapu; Naidu, Ravi

    2016-06-01

    Crude oil spills resulting from excavation, transportation and downstream processes can cause intensive damage to living organisms and result in changes in the microbial population of that environment. In this study, we used a pyrosequencing analysis to investigate changes in the microbial population of soils contaminated with crude oil. Crude oil contamination in soil resulted in the creation of a more homogenous population of microorganisms dominated by members of the Actinomycetales, Clostridiales and Bacillales (all belonging to Gram-positive bacteria) as well as Flavobacteriales, Pseudomonadales, Burkholderiales, Rhizobiales and Sphingomonadales (all belonging to Gram-negative bacteria). These changes in the biodiversity decreased the ratios of chemoheterotrophic bacteria at higher concentrations of crude oil contamination, with these being replaced by photoheterotrophic bacteria, mainly Rhodospirillales. Several of the dominant microbial orders in the crude oil contaminated soils are able to degrade crude oil hydrocarbons and therefore are potentially useful for remediation of crude oil in contaminated sites. PMID:26858133

  13. Large-scale distribution of microbial and viral populations in the South Atlantic Ocean.

    PubMed

    De Corte, Daniele; Sintes, Eva; Yokokawa, Taichi; Lekunberri, Itziar; Herndl, Gerhard J

    2016-04-01

    Viruses are abundant, diverse and dynamic components of the marine environments and play a significant role in the ocean biogeochemical cycles. To assess potential variations in the relation between viruses and microbes in different geographic regions and depths, viral and microbial abundance and production were determined throughout the water column along a latitudinal transect in the South Atlantic Ocean. Path analysis was used to examine the relationships between several abiotic and biotic parameters and the different microbial and viral populations distinguished by flow cytometry. The depth-integrated contribution of microbial and viral abundance to the total microbial and viral biomass differed significantly among the different provinces. Additionally, the virus-to-microbe ratio increased with depth and decreased laterally towards the more productive regions. Our data revealed that the abundance of phytoplankton and microbes is the main controlling factor of the viral populations in the euphotic and mesopelagic layers, whereas in the bathypelagic realm, viral abundance was only weakly related to the biotic and abiotic variables. The relative contribution of the three viral populations distinguished by flow cytometry showed a clear geographical pattern throughout the water column, suggesting that these populations are composed of distinct taxa able to infect specific hosts. Overall, our data indicate the presence of distinct microbial patterns along the latitudinal transect. This variability is not limited to the euphotic layer but also detectable in the meso- and bathypelagic layers. PMID:26765966

  14. Large‐scale distribution of microbial and viral populations in the South Atlantic Ocean

    PubMed Central

    Sintes, Eva; Yokokawa, Taichi; Lekunberri, Itziar; Herndl, Gerhard J.

    2016-01-01

    Summary Viruses are abundant, diverse and dynamic components of the marine environments and play a significant role in the ocean biogeochemical cycles. To assess potential variations in the relation between viruses and microbes in different geographic regions and depths, viral and microbial abundance and production were determined throughout the water column along a latitudinal transect in the South Atlantic Ocean. Path analysis was used to examine the relationships between several abiotic and biotic parameters and the different microbial and viral populations distinguished by flow cytometry. The depth‐integrated contribution of microbial and viral abundance to the total microbial and viral biomass differed significantly among the different provinces. Additionally, the virus‐to‐microbe ratio increased with depth and decreased laterally towards the more productive regions. Our data revealed that the abundance of phytoplankton and microbes is the main controlling factor of the viral populations in the euphotic and mesopelagic layers, whereas in the bathypelagic realm, viral abundance was only weakly related to the biotic and abiotic variables. The relative contribution of the three viral populations distinguished by flow cytometry showed a clear geographical pattern throughout the water column, suggesting that these populations are composed of distinct taxa able to infect specific hosts. Overall, our data indicate the presence of distinct microbial patterns along the latitudinal transect. This variability is not limited to the euphotic layer but also detectable in the meso‐ and bathypelagic layers. PMID:26765966

  15. Microbial Community Response to the Deepwater Horizon Oil Spill

    NASA Astrophysics Data System (ADS)

    Redmond, M. C.; Valentine, D. L.; Joye, S. B.

    2010-12-01

    The sinking of the Deepwater Horizon on April 22nd, 2010 led to one of the largest oil spills in history. The massive amounts of oil and natural gas leaking into the Gulf of Mexico led to development of distinct microbial communities dominated by hydrocarbon-degrading bacteria. To track this microbial response, we sampled hydrocarbon-laden surface water and deep plumes (1100-1200 m), as well as samples lacking hydrocarbon exposure. In samples collected in May /June 2010, deepwater plume 16S rRNA clone libraries were dominated by three groups of Gammaproteobacteria: unclassified members of the order Oceanospirillales, close relatives of the genus Colwellia, and relatives of the genus Cycloclasticus. These groups accounted for 90-100% of sequences in nine clone libraries and 50% of sequences in a tenth; this tenth sample was ~1 km from the wellhead and showed no detectable oxygen drawdown. In samples collected from above or below the plume, these three groups accounted for no more than 25% of clones. Surface samples were dominated by organisms most closely related to the genus Pseudoalteromonas. Ongoing cultivation and stable isotope probing experiments to identify and characterize the bacteria consuming specific hydrocarbon compounds will further our understanding of the microbial ecology of surface and deepwater hydrocarbon degrading microorganisms.

  16. Strain-level microbial epidemiology and population genomics from shotgun metagenomics.

    PubMed

    Scholz, Matthias; Ward, Doyle V; Pasolli, Edoardo; Tolio, Thomas; Zolfo, Moreno; Asnicar, Francesco; Truong, Duy Tin; Tett, Adrian; Morrow, Ardythe L; Segata, Nicola

    2016-05-01

    Identifying microbial strains and characterizing their functional potential is essential for pathogen discovery, epidemiology and population genomics. We present pangenome-based phylogenomic analysis (PanPhlAn; http://segatalab.cibio.unitn.it/tools/panphlan), a tool that uses metagenomic data to achieve strain-level microbial profiling resolution. PanPhlAn recognized outbreak strains, produced the largest strain-level population genomic study of human-associated bacteria and, in combination with metatranscriptomics, profiled the transcriptional activity of strains in complex communities. PMID:26999001

  17. Radiation resistance of the natural microbial population in buffer materials

    SciTech Connect

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

    1995-12-31

    The radiation sensitivity of naturally occurring microorganisms in buffer materials was investigated as well as the sensitivity of Bacillus subtillis spores and Acinetobacter radioresistens in a buffer matrix. The D{sub 10} values obtained in these radiation experiments varied from 0.34 to 1.68 kGy and it was calculated that the surface of a nuclear fuel waste container would be sterilized in 9 to 33 d after emplacement, depending on the type of container, and the initial bioburden. This suggests that formation of biofilms and microbially influenced corrosion would not be of concern of some time after emplacement. The results also indicated that sterilization throughout a 25 cm thick buffer layer is unlikely and that repopulation of the container surface after some time is a possibility, depending on the mobility of microbes in compacted buffer material.

  18. Controlling Salmonella infection in weanling pigs through water delivery of direct-fed microbials or organic acids; Part I. Effects on growth performance, microbial populations and immune status

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pigs (n=88) weaned at 19 ± 2 d of age were used in a 14 d study to evaluate the effects of water-delivered direct-fed microbials (DFM) or organic acids on immune status, Salmonella infection and shedding, and intestinal microbial populations following a Salmonella Typhimurium challenge. Pigs were ch...

  19. A meta-analysis of soil microbial biomass responses to forest disturbances

    PubMed Central

    Holden, Sandra R.; Treseder, Kathleen K.

    2013-01-01

    Climate warming is likely to increase the frequency and severity of forest disturbances, with uncertain consequences for soil microbial communities and their contribution to ecosystem C dynamics. To address this uncertainty, we conducted a meta-analysis of 139 published soil microbial responses to forest disturbances. These disturbances included abiotic (fire, harvesting, storm) and biotic (insect, pathogen) disturbances. We hypothesized that soil microbial biomass would decline following forest disturbances, but that abiotic disturbances would elicit greater reductions in microbial biomass than biotic disturbances. In support of this hypothesis, across all published studies, disturbances reduced soil microbial biomass by an average of 29.4%. However, microbial responses differed between abiotic and biotic disturbances. Microbial responses were significantly negative following fires, harvest, and storms (48.7, 19.1, and 41.7% reductions in microbial biomass, respectively). In contrast, changes in soil microbial biomass following insect infestation and pathogen-induced tree mortality were non-significant, although biotic disturbances were poorly represented in the literature. When measured separately, fungal and bacterial responses to disturbances mirrored the response of the microbial community as a whole. Changes in microbial abundance following disturbance were significantly positively correlated with changes in microbial respiration. We propose that the differential effect of abiotic and biotic disturbances on microbial biomass may be attributable to differences in soil disruption and organic C removal from forests among disturbance types. Altogether, these results suggest that abiotic forest disturbances may significantly decrease soil microbial abundance, with corresponding consequences for microbial respiration. Further studies are needed on the effect of biotic disturbances on forest soil microbial communities and soil C dynamics. PMID:23801985

  20. Soil Microbial Substrate Properties and Microbial Community Responses under Irrigated Organic and Reduced-Tillage Crop and Forage Production Systems

    PubMed Central

    Ghimire, Rajan; Norton, Jay B.; Stahl, Peter D.; Norton, Urszula

    2014-01-01

    Changes in soil microbiotic properties such as microbial biomass and community structure in response to alternative management systems are driven by microbial substrate quality and substrate utilization. We evaluated irrigated crop and forage production in two separate four-year experiments for differences in microbial substrate quality, microbial biomass and community structure, and microbial substrate utilization under conventional, organic, and reduced-tillage management systems. The six different management systems were imposed on fields previously under long-term, intensively tilled maize production. Soils under crop and forage production responded to conversion from monocropping to crop rotation, as well as to the three different management systems, but in different ways. Under crop production, four years of organic management resulted in the highest soil organic C (SOC) and microbial biomass concentrations, while under forage production, reduced-tillage management most effectively increased SOC and microbial biomass. There were significant increases in relative abundance of bacteria, fungi, and protozoa, with two- to 36-fold increases in biomarker phospholipid fatty acids (PLFAs). Under crop production, dissolved organic C (DOC) content was higher under organic management than under reduced-tillage and conventional management. Perennial legume crops and organic soil amendments in the organic crop rotation system apparently favored greater soil microbial substrate availability, as well as more microbial biomass compared with other management systems that had fewer legume crops in rotation and synthetic fertilizer applications. Among the forage production management systems with equivalent crop rotations, reduced-tillage management had higher microbial substrate availability and greater microbial biomass than other management systems. Combined crop rotation, tillage management, soil amendments, and legume crops in rotations considerably influenced soil

  1. Contrasting response to nutrient manipulation in Arctic mesocosms are reproduced by a minimum microbial food web model

    PubMed Central

    Larsen, Aud; Egge, Jorun K; Nejstgaard, Jens C; Di Capua, Iole; Thyrhaug, Runar; Bratbak, Gunnar; Thingstad, T Frede

    2015-01-01

    A minimum mathematical model of the marine pelagic microbial food web has previously shown to be able to reproduce central aspects of observed system response to different bottom-up manipulations in a mesocosm experiment Microbial Ecosystem Dynamics (MEDEA) in Danish waters. In this study, we apply this model to two mesocosm experiments (Polar Aquatic Microbial Ecology (PAME)-I and PAME-II) conducted at the Arctic location Kongsfjorden, Svalbard. The different responses of the microbial community to similar nutrient manipulation in the three mesocosm experiments may be described as diatom-dominated (MEDEA), bacteria-dominated (PAME-I), and flagellated-dominated (PAME-II). When allowing ciliates to be able to feed on small diatoms, the model describing the diatom-dominated MEDEA experiment give a bacteria-dominated response as observed in PAME I in which the diatom community comprised almost exclusively small-sized cells. Introducing a high initial mesozooplankton stock as observed in PAME-II, the model gives a flagellate-dominated response in accordance with the observed response also of this experiment. The ability of the model originally developed for temperate waters to reproduce population dynamics in a 10°C colder Arctic fjord, does not support the existence of important shifts in population balances over this temperature range. Rather, it suggests a quite resilient microbial food web when adapted to in situ temperature. The sensitivity of the model response to its mesozooplankton component suggests, however, that the seasonal vertical migration of Arctic copepods may be a strong forcing factor on Arctic microbial food webs. PMID:26074626

  2. Metamorphosis of a scleractinian coral in response to microbial biofilms.

    PubMed

    Webster, Nicole S; Smith, Luke D; Heyward, Andrew J; Watts, Joy E M; Webb, Richard I; Blackall, Linda L; Negri, Andrew P

    2004-02-01

    Microorganisms have been reported to induce settlement and metamorphosis in a wide range of marine invertebrate species. However, the primary cue reported for metamorphosis of coral larvae is calcareous coralline algae (CCA). Herein we report the community structure of developing coral reef biofilms and the potential role they play in triggering the metamorphosis of a scleractinian coral. Two-week-old biofilms induced metamorphosis in less than 10% of larvae, whereas metamorphosis increased significantly on older biofilms, with a maximum of 41% occurring on 8-week-old microbial films. There was a significant influence of depth in 4- and 8-week biofilms, with greater levels of metamorphosis occurring in response to shallow-water communities. Importantly, larvae were found to settle and metamorphose in response to microbial biofilms lacking CCA from both shallow and deep treatments, indicating that microorganisms not associated with CCA may play a significant role in coral metamorphosis. A polyphasic approach consisting of scanning electron microscopy, fluorescence in situ hybridization (FISH), and denaturing gradient gel electrophoresis (DGGE) revealed that coral reef biofilms were comprised of complex bacterial and microalgal communities which were distinct at each depth and time. Principal-component analysis of FISH data showed that the Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, and Cytophaga-Flavobacterium of Bacteroidetes had the largest influence on overall community composition. A low abundance of Archaea was detected in almost all biofilms, providing the first report of Archaea associated with coral reef biofilms. No differences in the relative densities of each subdivision of Proteobacteria were observed between slides that induced larval metamorphosis and those that did not. Comparative cluster analysis of bacterial DGGE patterns also revealed that there were clear age and depth distinctions in biofilm community structure; however, no

  3. Soil microbial responses to nitrogen addition in arid ecosystems.

    PubMed

    Sinsabaugh, Robert L; Belnap, Jayne; Rudgers, Jennifer; Kuske, Cheryl R; Martinez, Noelle; Sandquist, Darren

    2015-01-01

    The N cycle of arid ecosystems is influenced by low soil organic matter, high soil pH, and extremes in water potential and temperature that lead to open canopies and development of biological soil crusts (biocrusts). We investigated the effects of N amendment on soil microbial dynamics in a Larrea tridentata-Ambrosia dumosa shrubland site in southern Nevada USA. Sites were fertilized with a NO3-NH4 mix at 0, 7, and 15 kg N ha(-1) y(-1) from March 2012 to March 2013. In March 2013, biocrust (0-0.5 cm) and bulk soils (0-10 cm) were collected beneath Ambrosia canopies and in the interspaces between plants. Biomass responses were assessed as bacterial and fungal SSU rRNA gene copy number and chlorophyll a concentration. Metabolic responses were measured by five ecoenzyme activities and rates of N transformation. By most measures, nutrient availability, microbial biomass, and process rates were greater in soils beneath the shrub canopy compared to the interspace between plants, and greater in the surface biocrust horizon compared to the deeper 10 cm soil profile. Most measures responded positively to experimental N addition. Effect sizes were generally greater for bulk soil than biocrust. Results were incorporated into a meta-analysis of arid ecosystem responses to N amendment that included data from 14 other studies. Effect sizes were calculated for biomass and metabolic responses. Regressions of effect sizes, calculated for biomass, and metabolic responses, showed similar trends in relation to N application rate and N load (rate × duration). The critical points separating positive from negative treatment effects were 88 kg ha(-1) y(-1) and 159 kg ha(-1), respectively, for biomass, and 70 kg ha(-1) y(-1) and 114 kg ha(-1), respectively, for metabolism. These critical values are comparable to those for microbial biomass, decomposition rates and respiration reported in broader meta-analyses of N amendment effects in mesic ecosystems. However, large effect sizes at low N

  4. Soil microbial responses to nitrogen addition in arid ecosystems

    DOE PAGESBeta

    Sinsabaugh, Robert L.; Belnap, Jayne; Rudgers, Jennifer; Kuske, Cheryl R.; Martinez, Noelle; Sandquist, Darren

    2015-08-14

    The N cycle of arid ecosystems is influenced by low soil organic matter, high soil pH, and extremes in water potential and temperature that lead to open canopies and development of biological soil crusts (biocrusts). We investigated the effects of N amendment on soil microbial dynamics in a Larrea tridentata-Ambrosia dumosa shrubland site in southern Nevada USA. Sites were fertilized with a NO3-NH4 mix at 0, 7, and 15 kg N ha-1 y-1 from March 2012 to March 2013. In March 2013, biocrust (0–0.5 cm) and bulk soils (0–10 cm) were collected beneath Ambrosia canopies and in the interspaces betweenmore » plants. Biomass responses were assessed as bacterial and fungal SSU rRNA gene copy number and chlorophyll a concentration. Metabolic responses were measured by five ecoenzyme activities and rates of N transformation. With most measures, nutrient availability, microbial biomass, and process rates were greater in soils beneath the shrub canopy compared to the interspace between plants, and greater in the surface biocrust horizon compared to the deeper 10 cm soil profile. Most measures responded positively to experimental N addition. Effect sizes were generally greater for bulk soil than biocrust. Results were incorporated into a meta-analysis of arid ecosystem responses to N amendment that included data from 14 other studies. Effect sizes were calculated for biomass and metabolic responses. Regressions of effect sizes, calculated for biomass, and metabolic responses, showed similar trends in relation to N application rate and N load (rate × duration). The critical points separating positive from negative treatment effects were 88 kg ha-1 y-1 and 159 kg ha-1, respectively, for biomass, and 70 kg ha-1 y-1 and 114 kg ha-1, respectively, for metabolism. These critical values are comparable to those for microbial biomass, decomposition rates and respiration reported in broader meta-analyses of N amendment effects in mesic ecosystems. The large effect sizes at low N

  5. Soil microbial responses to nitrogen addition in arid ecosystems

    PubMed Central

    Sinsabaugh, Robert L.; Belnap, Jayne; Rudgers, Jennifer; Kuske, Cheryl R.; Martinez, Noelle; Sandquist, Darren

    2015-01-01

    The N cycle of arid ecosystems is influenced by low soil organic matter, high soil pH, and extremes in water potential and temperature that lead to open canopies and development of biological soil crusts (biocrusts). We investigated the effects of N amendment on soil microbial dynamics in a Larrea tridentata-Ambrosia dumosa shrubland site in southern Nevada USA. Sites were fertilized with a NO3-NH4 mix at 0, 7, and 15 kg N ha-1 y-1 from March 2012 to March 2013. In March 2013, biocrust (0–0.5 cm) and bulk soils (0–10 cm) were collected beneath Ambrosia canopies and in the interspaces between plants. Biomass responses were assessed as bacterial and fungal SSU rRNA gene copy number and chlorophyll a concentration. Metabolic responses were measured by five ecoenzyme activities and rates of N transformation. By most measures, nutrient availability, microbial biomass, and process rates were greater in soils beneath the shrub canopy compared to the interspace between plants, and greater in the surface biocrust horizon compared to the deeper 10 cm soil profile. Most measures responded positively to experimental N addition. Effect sizes were generally greater for bulk soil than biocrust. Results were incorporated into a meta-analysis of arid ecosystem responses to N amendment that included data from 14 other studies. Effect sizes were calculated for biomass and metabolic responses. Regressions of effect sizes, calculated for biomass, and metabolic responses, showed similar trends in relation to N application rate and N load (rate × duration). The critical points separating positive from negative treatment effects were 88 kg ha-1 y-1 and 159 kg ha-1, respectively, for biomass, and 70 kg ha-1 y-1 and 114 kg ha-1, respectively, for metabolism. These critical values are comparable to those for microbial biomass, decomposition rates and respiration reported in broader meta-analyses of N amendment effects in mesic ecosystems. However, large effect sizes at low N addition

  6. Soil microbial responses to nitrogen addition in arid ecosystems

    SciTech Connect

    Sinsabaugh, Robert L.; Belnap, Jayne; Rudgers, Jennifer; Kuske, Cheryl R.; Martinez, Noelle; Sandquist, Darren

    2015-08-14

    The N cycle of arid ecosystems is influenced by low soil organic matter, high soil pH, and extremes in water potential and temperature that lead to open canopies and development of biological soil crusts (biocrusts). We investigated the effects of N amendment on soil microbial dynamics in a Larrea tridentata-Ambrosia dumosa shrubland site in southern Nevada USA. Sites were fertilized with a NO3-NH4 mix at 0, 7, and 15 kg N ha-1 y-1 from March 2012 to March 2013. In March 2013, biocrust (0–0.5 cm) and bulk soils (0–10 cm) were collected beneath Ambrosia canopies and in the interspaces between plants. Biomass responses were assessed as bacterial and fungal SSU rRNA gene copy number and chlorophyll a concentration. Metabolic responses were measured by five ecoenzyme activities and rates of N transformation. With most measures, nutrient availability, microbial biomass, and process rates were greater in soils beneath the shrub canopy compared to the interspace between plants, and greater in the surface biocrust horizon compared to the deeper 10 cm soil profile. Most measures responded positively to experimental N addition. Effect sizes were generally greater for bulk soil than biocrust. Results were incorporated into a meta-analysis of arid ecosystem responses to N amendment that included data from 14 other studies. Effect sizes were calculated for biomass and metabolic responses. Regressions of effect sizes, calculated for biomass, and metabolic responses, showed similar trends in relation to N application rate and N load (rate × duration). The critical points separating positive from negative treatment effects were 88 kg ha-1 y-1 and 159 kg ha-1, respectively, for biomass, and 70 kg ha-1 y-1 and 114 kg ha-1, respectively, for metabolism. These critical values are comparable to those for microbial biomass, decomposition rates and respiration

  7. Constraining Microbial Community Response During Oil Sands Reclamation via Lipid and Isotope Biosignatures

    NASA Astrophysics Data System (ADS)

    Bradford, L. M.; Ziolkowski, L. A.; Ngonadi, N.; Warren, L. A.; Slater, G. F.

    2013-12-01

    A pilot scale reclamation project in the Athabasca oil sands region (Fort McMurray, Alberta, Canada) has created an artificial freshwater fen typical of the boreal forest region in which the oil sands occur. At this site, composite tailings (CT) residue was overlain with a thick sand cap and a freshwater fen constructed on top. This project began in 2009, with most wetland development occurring over the summer of 2012. It is recognized that the response of microbial communities to reclamation activities has the potential to play a significant role in the outcome of reclamation. Microbial biodegradation of petroleum residues may improve reclamation outcomes, while production of by-products, particularly hydrogen sulphide gas (H2S) via bacterial sulphate reduction, must be assessed to manage any potential negative impacts. Phospholipid fatty acid (PLFA) concentration and isotopic analysis were used to characterize the response of in situ microbial communities within the reclamation fen system. Increases in PLFA concentrations were observed in sediment taken from the sand layer at sample sites within the fen from during its establishment. Initial values equivalent to circa 106 cells/gram in July 2011 increased to values equivalent to 107cells/gram in August 2012 and then to 108 cells/gram in November 2012. Analysis of the radiocarbon (Δ14C) content of total organic carbon shows an increase in Δ14C from highly depleted values (-983×2‰) in July 2011, consistent with petroleum hydrocarbons dominating the total organic carbon, to more 14C enriched values as fen development progressed (-423×2.1‰ in August 2012 and -417×1.4‰ in November 2012). This indicates inputs of more modern organic matter potentially associated with the peat used to construct the fen and/or inputs from recent photosynthesis. The correlation between the observed PLFA increases and this increase in modern carbon inputs suggests that reclamation activities have stimulated the increase in the

  8. Profiling the Change in Fecal Microbial Populations of Mares and Foals Over Time

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The gastrointestinal tract of the mature horse contains a complex community of microorganisms, many of which aid in digestion. Little information is available concerning the establishment of these microbial populations in young horses. The limited research that has been conducted has utilized cultur...

  9. USE OF ARISA TO MONITOR SHIFTS IN RUMEN MICROBIAL POPULATIONS CAUSED BY CHANGES IN DIET

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective was to determine whether automated ribosomal intergenic spacer analysis (ARISA) is sensitive enough to detect shifts in rumen microbial populations caused by dietary changes. Six ruminally cannulated, non-lactating, non-pregnant Holstein cows were sampled for rumen contents in a random...

  10. IN SITU APPARENT CONDUCTIVITY MEASUREMENTS AND MICROBIAL POPULATION DISTRIBUTION AT A HYDROCARBON CONTAMINATED SITE

    EPA Science Inventory

    We investigated the bulk electrical conductivity and microbial population distribution in sediments at a site contaminated with light non-aqueous phase liquid (LNAPL). The bulk conductivity was measured using in situ vertical resistivity probes, while the most probable number met...

  11. Aerobic Microbial Community of Insectary Population of Phlebotomus papatasi

    PubMed Central

    Maleki-Ravasan, Naseh; Oshaghi, Mohammad Ali; Hajikhani, Sara; Saeidi, Zahra; Akhavan, Amir Ahmad; Gerami-Shoar, Mohsen; Shirazi, Mohammad Hasan; Yakhchali, Bagher; Rassi, Yavar; Afshar, Davoud

    2014-01-01

    Background: Microbes particularly bacteria presenting in the gut of haematophagous insects may have an important role in the epidemiology of human infectious disease. Methods: The microbial flora of gut and surrounding environmental of a laboratory strain of Phlebotomus papatasi, the main vector of Zoonotic Cutaneous Leishmaniasis (ZCL) in the old world, was investigated. Biochemical reactions and 16s rDNA sequencing of the isolated bacteria against 24 sugars and amino acids were used for bacteria species identification. Common mycological media used for fungi identification as well. Results: Most isolates belonged to the Enterobacteriaceae, a large, heterogeneous group of gram-negative rods whose natural habitat is the intestinal tract of humans and animals. Enterobacteriaceae groups included Edwardsiella, Enterobacter, Escherichia, Klebsiella, Kluyvera, Leminorella, Pantoea, Proteus, Providencia, Rahnella, Serratia, Shigella, Tatumella, and Yersinia and non Enterobacteriaceae groups included Bacillus, Staphylococcus and Pseudomonas. The most prevalent isolates were Proteus mirabilis and P. vulgaris. These saprophytic and swarming motile bacteria were isolated from all immature, pupae, and mature fed or unfed male or female sand flies as well as from larval and adult food sources. Five fungi species were also isolated from sand flies, their food sources and colonization materials where Candida sp. was common in all mentioned sources. Conclusion: Midgut microbiota are increasingly seen as an important factor for modulating vector competence in insect vectors so their possible effects of the mirobiota on the biology of P. papatasi and their roles in the sandfly-Leishmania interaction are discussed. PMID:25629067

  12. Chronic impact of sulfamethoxazole on acetate utilization kinetics and population dynamics of fast growing microbial culture.

    PubMed

    Kor-Bicakci, G; Pala-Ozkok, I; Rehman, A; Jonas, D; Ubay-Cokgor, E; Orhon, D

    2014-08-01

    The study evaluated the chronic impact of sulfamethoxazole on metabolic activities of fast growing microbial culture. It focused on changes induced on utilization kinetics of acetate and composition of the microbial community. The experiments involved a fill and draw reactor, fed with acetate and continuous sulfamethoxazole dosing of 50 mg/L. The evaluation relied on model evaluation of the oxygen uptake rate profiles, with parallel assessment of microbial community structure by 454-pyrosequencing. Continuous sulfamethoxazole dosing inflicted a retardation effect on acetate utilization in a way commonly interpreted as competitive inhibition, blocked substrate storage and accelerated endogenous respiration. A fraction of acetate was utilized at a much lower rate with partial biodegradation of sulfamethoxazole. Results of pyrosequencing with a replacement mechanism within a richer more diversified microbial culture, through inactivation of vulnerable fractions in favor of species resistant to antibiotic, which made them capable of surviving and competing even with a slower metabolic response. PMID:24908607

  13. A new device for real time monitoring of microbial population dynamics during in situ and ex situ bioremediation

    SciTech Connect

    Woodward, R.E.; Malone, R.W.

    1995-12-31

    Monitoring of microbial population dynamics is an important operating parameter for successful bioremediation projects. The traditional method of plate counts or most probable number (MPN) requires 2 to 7 days for development and therefore provides a historical measurement of little real-time operational significance. Selected enzyme activity is directly proportional to microbial population density and is linear in the population range from 10{sub 4} to 10{sup 8} CFU/mL. This paper summarizes the use of this enzyme based, real-time measurement of microbial population dynamics for the management of four bioremediation projects: (1) differentiation of assimilation from nitrification during the metabolism of ammonia in an industrial waste stream, (2) treatability assessment and management of activated sludge processes during the treatment of a hazardous, petrochemical waste, (3) measurement of intrinsic microbial activity in soil cores at a spill site, and (4) non-invasive monitoring of microbial populations during in situ bioremediation of two aquifers.

  14. Effect of hybrid poplar trees on microbial populations important to hazardous waste bioremediation

    SciTech Connect

    Jordahl, J.L.; Foster, L.; Schnoor, J.L.; Alvarez, P.J.J.

    1997-06-01

    Microbial concentrations of denitrifiers, pseudomonads, and monoaromatic petroleum hydrocarbon (BTX) degraders were significantly higher (p < 0.1) in soil samples from the rhizosphere of poplar trees than in adjacent agricultural soils, and atrazine degraders were found only in one rhizosphere sample. The relative abundance of these phenotypes (as a fraction of total heterotrophs) was not significantly different between rhizosphere and surrounding soils. Therefore, the poplar rhizosphere enhanced the growth of microbial populations that participate in natural bioremediation without exerting selective pressure for them.

  15. Microbial Dioxygenase Gene Population Shifts during Polycyclic Aromatic Hydrocarbon Biodegradation

    PubMed Central

    Ní Chadhain, Sinéad M.; Norman, R. Sean; Pesce, Karen V.; Kukor, Jerome J.; Zylstra, Gerben J.

    2006-01-01

    The degradation of polycyclic aromatic hydrocarbons (PAHs) by bacteria has been widely studied. While many pure cultures have been isolated and characterized for their ability to grow on PAHs, limited information is available on the diversity of microbes involved in PAH degradation in the environment. We have designed generic PCR primers targeting the gene fragment encoding the Rieske iron sulfur center common to all PAH dioxygenase enzymes. These Rieske primers were employed to track dioxygenase gene population shifts in soil enrichment cultures following exposure to naphthalene, phenanthrene, or pyrene. PAH degradation was monitored by gas chromatograph with flame ionization detection. DNA was extracted from the enrichment cultures following PAH degradation. 16S rRNA and Rieske gene fragments were PCR amplified from DNA extracted from each enrichment culture and an unamended treatment. The PCR products were cloned and sequenced. Molecular monitoring of the enrichment cultures before and after PAH degradation using denaturing gradient gel electrophoresis and 16S rRNA gene libraries suggests that specific phylotypes of bacteria were associated with the degradation of each PAH. Sequencing of the cloned Rieske gene fragments showed that different suites of genes were present in soil microbe populations under each enrichment culture condition. Many of the Rieske gene fragment sequences fell into clades which are distinct from the reference dioxygenase gene sequences used to design the PCR primers. The ability to profile not only the bacterial community but also the dioxygenases which they encode provides a powerful tool for both assessing bioremediation potential in the environment and for the discovery of novel dioxygenase genes. PMID:16751518

  16. Changes in the Size of the Active Microbial Pool Explain Short-Term Soil Respiratory Responses to Temperature and Moisture

    PubMed Central

    Salazar-Villegas, Alejandro; Blagodatskaya, Evgenia; Dukes, Jeffrey S.

    2016-01-01

    Heterotrophic respiration contributes a substantial fraction of the carbon flux from soil to atmosphere, and responds strongly to environmental conditions. However, the mechanisms through which short-term changes in environmental conditions affect microbial respiration still remain unclear. Microorganisms cope with adverse environmental conditions by transitioning into and out of dormancy, a state in which they minimize rates of metabolism and respiration. These transitions are poorly characterized in soil and are generally omitted from decomposition models. Most current approaches to model microbial control over soil CO2 production relate responses to total microbial biomass (TMB) and do not differentiate between microorganisms in active and dormant physiological states. Indeed, few data for active microbial biomass (AMB) exist with which to compare model output. Here, we tested the hypothesis that differences in soil microbial respiration rates across various environmental conditions are more closely related to differences in AMB (e.g., due to activation of dormant microorganisms) than in TMB. We measured basal respiration (SBR) of soil incubated for a week at two temperatures (24 and 33°C) and two moisture levels (10 and 20% soil dry weight [SDW]), and then determined TMB, AMB, microbial specific growth rate, and the lag time before microbial growth (tlag) using the Substrate-Induced Growth Response (SIGR) method. As expected, SBR was more strongly correlated with AMB than with TMB. This relationship indicated that each g active biomass C contributed ~0.04 g CO2-C h−1 of SBR. TMB responded very little to short-term changes in temperature and soil moisture and did not explain differences in SBR among the treatments. Maximum specific growth rate did not respond to environmental conditions, suggesting that the dominant microbial populations remained similar. However, warmer temperatures and increased soil moisture both reduced tlag, indicating that favorable

  17. Changes in the Size of the Active Microbial Pool Explain Short-Term Soil Respiratory Responses to Temperature and Moisture.

    PubMed

    Salazar-Villegas, Alejandro; Blagodatskaya, Evgenia; Dukes, Jeffrey S

    2016-01-01

    Heterotrophic respiration contributes a substantial fraction of the carbon flux from soil to atmosphere, and responds strongly to environmental conditions. However, the mechanisms through which short-term changes in environmental conditions affect microbial respiration still remain unclear. Microorganisms cope with adverse environmental conditions by transitioning into and out of dormancy, a state in which they minimize rates of metabolism and respiration. These transitions are poorly characterized in soil and are generally omitted from decomposition models. Most current approaches to model microbial control over soil CO2 production relate responses to total microbial biomass (TMB) and do not differentiate between microorganisms in active and dormant physiological states. Indeed, few data for active microbial biomass (AMB) exist with which to compare model output. Here, we tested the hypothesis that differences in soil microbial respiration rates across various environmental conditions are more closely related to differences in AMB (e.g., due to activation of dormant microorganisms) than in TMB. We measured basal respiration (SBR) of soil incubated for a week at two temperatures (24 and 33°C) and two moisture levels (10 and 20% soil dry weight [SDW]), and then determined TMB, AMB, microbial specific growth rate, and the lag time before microbial growth (t lag ) using the Substrate-Induced Growth Response (SIGR) method. As expected, SBR was more strongly correlated with AMB than with TMB. This relationship indicated that each g active biomass C contributed ~0.04 g CO2-C h(-1) of SBR. TMB responded very little to short-term changes in temperature and soil moisture and did not explain differences in SBR among the treatments. Maximum specific growth rate did not respond to environmental conditions, suggesting that the dominant microbial populations remained similar. However, warmer temperatures and increased soil moisture both reduced t lag , indicating that favorable

  18. Population-expression models of immune response

    NASA Astrophysics Data System (ADS)

    Stromberg, Sean P.; Antia, Rustom; Nemenman, Ilya

    2013-06-01

    The immune response to a pathogen has two basic features. The first is the expansion of a few pathogen-specific cells to form a population large enough to control the pathogen. The second is the process of differentiation of cells from an initial naive phenotype to an effector phenotype which controls the pathogen, and subsequently to a memory phenotype that is maintained and responsible for long-term protection. The expansion and the differentiation have been considered largely independently. Changes in cell populations are typically described using ecologically based ordinary differential equation models. In contrast, differentiation of single cells is studied within systems biology and is frequently modeled by considering changes in gene and protein expression in individual cells. Recent advances in experimental systems biology make available for the first time data to allow the coupling of population and high dimensional expression data of immune cells during infections. Here we describe and develop population-expression models which integrate these two processes into systems biology on the multicellular level. When translated into mathematical equations, these models result in non-conservative, non-local advection-diffusion equations. We describe situations where the population-expression approach can make correct inference from data while previous modeling approaches based on common simplifying assumptions would fail. We also explore how model reduction techniques can be used to build population-expression models, minimizing the complexity of the model while keeping the essential features of the system. While we consider problems in immunology in this paper, we expect population-expression models to be more broadly applicable.

  19. Predicting fish population response to instream flows

    SciTech Connect

    Studley, T.K.; Baldridge, J.E.; Railsback, S.F.

    1996-10-01

    A cooperative research program initiated by Pacific Gas and Electric is described. The goals of the project are to determine if trout populations respond to changes in base streamflows in a predictible manner, and to evaluate and improve the methods used to predict rainbow and brown trout population responses under altered flow regimes. Predictive methods based on computer models of the Physical Habitat Simulation System are described, and predictions generated for four diversions and creeks are tabulated. Baseline data indicates that instream flow assessments can be improved by using guild criteria in streams with competing species and including additional limiting factors (low recruitment, high winter flow, and high stream temperatures) in the analyses.

  20. Microbial Genomics of a Host-Associated Commensal Bacterium in Fragmented Populations of Endangered Takahe.

    PubMed

    Grange, Zoë L; Gartrell, Brett D; Biggs, Patrick J; Nelson, Nicola J; Anderson, Marti; French, Nigel P

    2016-05-01

    Isolation of wildlife into fragmented populations as a consequence of anthropogenic-mediated environmental change may alter host-pathogen relationships. Our understanding of some of the epidemiological features of infectious disease in vulnerable populations can be enhanced by the use of commensal bacteria as a proxy for invasive pathogens in natural ecosystems. The distinctive population structure of a well-described meta-population of a New Zealand endangered flightless bird, the takahe (Porphyrio hochstetteri), provided a unique opportunity to investigate the influence of host isolation on enteric microbial diversity. The genomic epidemiology of a prevalent rail-associated endemic commensal bacterium was explored using core genome and ribosomal multilocus sequence typing (rMLST) of 70 Campylobacter sp. nova 1 isolated from one third of the takahe population resident in multiple locations. While there was evidence of recombination between lineages, bacterial divergence appears to have occurred and multivariate analysis of 52 rMLST genes revealed location-associated differentiation of C. sp. nova 1 sequence types. Our results indicate that fragmentation and anthropogenic manipulation of populations can influence host-microbial relationships, with potential implications for niche adaptation and the evolution of micro-organisms in remote environments. This study provides a novel framework in which to explore the complex genomic epidemiology of micro-organisms in wildlife populations. PMID:26707136

  1. Long Live Rock! Exploring Active Microbial Populations in North Pond Subsurface Basalt

    NASA Astrophysics Data System (ADS)

    Mills, H. J.; Lehne, J.

    2014-12-01

    Microbial life should be considered as an active source for subsurface alterations of crustal material. Over the past several decades, microbial populations have been qualitatively and quantitatively characterized in marine sediments from the near shore to gyre centers, from the surface to two kilometers below the surface. Recent exploration of the underlying basement has revealed bacterial populations within the basalt. Initial cultivation-based and in situ analysis of subsurface basalt has produced some structural identification of populations that have the potential to alter the crust. Within this study, we have advanced this understanding by characterizing the metabolically active fraction of these populations. A 16S rRNA gene transcript approach was conducted using high throughput sequencing on RNA extracted from breccia, glass basalts and ultramafic basalts of the western flank of the Mid-Atlantic Ridge. Previous research has shown that the fluid within the basement is oxic. As expected, populations associated with aerobic metabolism were detected. In addition, iron-utilizing populations were observed to be metabolically active within the basalt samples characterized. Future characterization will reveal overlap between previous studies to determine the total versus metabolically active populations.

  2. Effect of oenological practices on microbial populations using culture-independent techniques.

    PubMed

    Andorrà, Imma; Landi, Sara; Mas, Albert; Guillamón, José M; Esteve-Zarzoso, Braulio

    2008-10-01

    Sulphur dioxide (SO(2)) addition and yeast inoculation are well-established practices in winemaking for restricting the growth of indigenous yeasts and bacterial populations. The effect of these oenological practices on wine microbial populations has been evaluated using culture-independent methods. These are quantitative PCR (qPCR) for the enumeration of yeasts, lactic acid bacteria (LAB) and acetic acid bacteria (AAB), and PCR-DGGE to determine the yeast and bacteria species diversity. The PCR-DGGE method detected a low yeast and bacteria species diversity. On the contrary, the specificity of the primers designed for the qPCR allowed that minor microbial groups such as Hanseniaspora were accurately quantified regardless of a large presence of other microbial groups such as Saccharomyces. From an oenological point of view, inoculation increased the proportion of Saccharomyces vs. non-Saccharomyces in a shorter time. Hanseniaspora increased during the first phase and decreased during the latter phases of the process, especially in the sulphited fermentations. Both yeast inoculation and SO(2) kept the LAB populations at very low level, while the AAB populations were hardly affected by these two practices. PMID:18721672

  3. Population-reaction model and microbial experimental ecosystems for understanding hierarchical dynamics of ecosystems.

    PubMed

    Hosoda, Kazufumi; Tsuda, Soichiro; Kadowaki, Kohmei; Nakamura, Yutaka; Nakano, Tadashi; Ishii, Kojiro

    2016-02-01

    Understanding ecosystem dynamics is crucial as contemporary human societies face ecosystem degradation. One of the challenges that needs to be recognized is the complex hierarchical dynamics. Conventional dynamic models in ecology often represent only the population level and have yet to include the dynamics of the sub-organism level, which makes an ecosystem a complex adaptive system that shows characteristic behaviors such as resilience and regime shifts. The neglect of the sub-organism level in the conventional dynamic models would be because integrating multiple hierarchical levels makes the models unnecessarily complex unless supporting experimental data are present. Now that large amounts of molecular and ecological data are increasingly accessible in microbial experimental ecosystems, it is worthwhile to tackle the questions of their complex hierarchical dynamics. Here, we propose an approach that combines microbial experimental ecosystems and a hierarchical dynamic model named population-reaction model. We present a simple microbial experimental ecosystem as an example and show how the system can be analyzed by a population-reaction model. We also show that population-reaction models can be applied to various ecological concepts, such as predator-prey interactions, climate change, evolution, and stability of diversity. Our approach will reveal a path to the general understanding of various ecosystems and organisms. PMID:26747638

  4. Milankovitch-scale correlations between deeply buried microbial populations and biogenic ooze lithology

    USGS Publications Warehouse

    Aiello, I.W.; Bekins, B.A.

    2010-01-01

    The recent discoveries of large, active populations of microbes in the subseafloor of the world's oceans supports the impact of the deep biosphere biota on global biogeochemical cycles and raises important questions concerning the functioning of these extreme environments for life. These investigations demonstrated that subseafloor microbes are unevenly distributed and that cell abundances and metabolic activities are often independent from sediment depths, with increased prokaryotic activity at geochemical and/or sedimentary interfaces. In this study we demonstrate that microbial populations vary at the scale of individual beds in the biogenic oozes of a drill site in the eastern equatorial Pacific (Ocean Drilling Program Leg 201, Site 1226). We relate bedding-scale changes in biogenic ooze sediment composition to organic carbon (OC) and microbial cell concentrations using high-resolution color reflectance data as proxy for lithology. Our analyses demonstrate that microbial concentrations are an order of magnitude higher in the more organic-rich diatom oozes than in the nannofossil oozes. The variations mimic small-scale variations in diatom abundance and OC, indicating that the modern distribution of microbial biomass is ultimately controlled by Milankovitch-frequency variations in past oceanographic conditions. ?? 2010 Geological Society of America.

  5. Microbial Diversity and Population Structure of Extremely Acidic Sulfur-Oxidizing Biofilms From Sulfidic Caves

    NASA Astrophysics Data System (ADS)

    Jones, D.; Stoffer, T.; Lyon, E. H.; Macalady, J. L.

    2005-12-01

    Extremely acidic (pH 0-1) microbial biofilms called snottites form on the walls of sulfidic caves where gypsum replacement crusts isolate sulfur-oxidizing microorganisms from the buffering action of limestone host rock. We investigated the phylogeny and population structure of snottites from sulfidic caves in central Italy using full cycle rRNA methods. A small subunit rRNA bacterial clone library from a Frasassi cave complex snottite sample contained a single sequence group (>60 clones) similar to Acidithiobacillus thiooxidans. Bacterial and universal rRNA clone libraries from other Frasassi snottites were only slightly more diverse, containing a maximum of 4 bacterial species and probably 2 archaeal species. Fluorescence in situ hybridization (FISH) of snottites from Frasassi and from the much warmer Rio Garrafo cave complex revealed that all of the communities are simple (low-diversity) and dominated by Acidithiobacillus and/or Ferroplasma species, with smaller populations of an Acidimicrobium species, filamentous fungi, and protists. Our results suggest that sulfidic cave snottites will be excellent model microbial ecosystems suited for ecological and metagenomic studies aimed at elucidating geochemical and ecological controls on microbial diversity, and at mapping the spatial history of microbial evolutionary events such as adaptations, recombinations and gene transfers.

  6. Monomethylhydrazine degradation and its effect on carbon dioxide evolution and microbial populations in soil

    SciTech Connect

    Ou, L.T.; Street, J.J.

    1988-09-01

    Monomethylhydrazine (MMH), along with hydrazine and 1,1-dimethylhydrazine are the main components of hydrazine fuels. Information on the fate of MMH in soil and its overall effect on soil microbial activity is not known, though MMH is known to be toxic to a number of soil bacteria. Despite the fact that axenic bacterial cultures are inhibited by the three hydrazines, Ou and Street reported that soil respiration, and total bacterial and fungal populations in soil, were not inhibited by hydrazine at concentrations of 100 ..mu..g/g and lower. Even at 500 ..mu..g/g, only total bacterial populations in soil were inhibited by the presence of hydrazine. They also reported that hydrazine rapidly disappeared in soil. The authors initiated this study to investigate the effect of MMH on soil microbial activity and on degradation of the chemical in soil.

  7. Mapping Microbial Response Metabolomes for Induced Natural Product Discovery.

    PubMed

    Derewacz, Dagmara K; Covington, Brett C; McLean, John A; Bachmann, Brian O

    2015-09-18

    Intergeneric microbial interactions may originate a significant fraction of secondary metabolic gene regulation in nature. Herein, we expose a genomically characterized Nocardiopsis strain, with untapped polyketide biosynthetic potential, to intergeneric interactions via coculture with low inoculum exposure to Escherichia, Bacillus, Tsukamurella, and Rhodococcus. The challenge-induced responses of extracted metabolites were characterized via multivariate statistical and self-organizing map (SOM) analyses, revealing the magnitude and selectivity engendered by the limiting case of low inoculum exposure. The collected inventory of cocultures revealed substantial metabolomic expansion in comparison to monocultures with nearly 14% of metabolomic features in cocultures undetectable in monoculture conditions and many features unique to coculture genera. One set of SOM-identified responding features was isolated, structurally characterized by multidimensional NMR, and revealed to comprise previously unreported polyketides containing an unusual pyrrolidinol substructure and moderate and selective cytotoxicity. Designated ciromicin A and B, they are detected across mixed cultures with intergeneric preferences under coculture conditions. The structural novelty of ciromicin A is highlighted by its ability to undergo a diastereoselective photochemical 12-π electron rearrangement to ciromicin B at visible wavelengths. This study shows how organizing trends in metabolomic responses under coculture conditions can be harnessed to characterize multipartite cultures and identify previously silent secondary metabolism. PMID:26039241

  8. Gut melatonin response to microbial infection in carp Catla catla.

    PubMed

    Pal, Palash Kumar; Hasan, Kazi Nurul; Maitra, Saumen Kumar

    2016-04-01

    The purpose of present study was to demonstrate the response of gut melatoninergic system to Aeromonas hydrophila infection for 3 or 6 days and search for its correlation with the activity of different antioxidative and digestive enzymes to focus their interplay under pathophysiological conditions in carp (Catla catla). Microscopic study of gut in infected fish revealed degenerative changes in the tunica mucosa and lamina propria layers with sloughed off epithelial cells in the lumen. The activity of each digestive enzyme was reduced, but the levels of melatonin, arylalkylamine-N-acetyl transferase protein, the key regulator of melatonin biosynthesis, and different enzymatic antioxidants in gut were gradually and significantly increased with the progress of infection. Gut melatonin concentrations in A. hydrophila challenged carp by showing a positive correlation with the activity of each antioxidative enzyme, and a negative correlation with different digestive enzymes argued in favor of their functional relation, at least, during pathological stress. Moreover, parallel changes in the gut and serum melatonin titers indicated possible contribution of gut to circulating melatonin. Collectively, present carp study provided the first data to suggest that endogenous gut melatonin may be implicated to the mechanism of response to microbial infections in any fish species. PMID:26563281

  9. Microbial influences on the small intestinal response to radiation injury

    PubMed Central

    Packey, Christopher D.; Ciorba, Matthew A.

    2014-01-01

    Purpose of review Injury to the small bowel from ionizing radiation occurs commonly in patients undergoing cancer therapy and less commonly in instances of accidental radiation overexposure. Several lines of evidence now suggest that dynamic interactions between the host’s enteric microbiota and innate immune system are important in modulating the intestinal response to radiation. Here, we will review recent developments in the area of acute radiation enteropathy and examine the current state of knowledge regarding the impact of host–microbial interactions in the process. Recent findings There is promise in the development and testing of new clinical biomarkers including serum citrulline. Toll-like receptor agonists and innate immune system signaling pathways including nuclear factor-kappa B profoundly alter intestinal epithelial cell apoptosis and crypt survival after radiation exposure. Germ-free conditions, probiotics and antibiotics are each identified as modifiers of disease development and course. A human study suggested that luminal microbiota composition may influence the host’s intestinal response to radiation and may change in those developing postradiation diarrhea. Summary New knowledge implies that investigations aimed at deciphering the microbiome–host interactions before and after small bowl radiation injury may eventually allow prediction of disease course and offer opportunities for the development of novel therapeutic or prophylactic strategies. PMID:20040865

  10. Management and control of microbial populations' development in LSS of missions of different durations.

    PubMed

    Somova, L A; Pechurkin, N S

    2005-01-01

    The problem of interaction between man and microorganisms in closed habitats is an inextricable part of the whole problem of co-existence between macro- and microorganisms. Concerning the support of human life in closed habitat, we can, conventionally, divide microorganisms, acting in life support system (LSS) into three groups: useful, neutral and harmful. The tasks, for human beings for optimal coexistence with microhabitants seem to be trivial: (1) to increase the activity of useful forms, (2) decrease the activity harmful forms, (3) not allow the neutral forms to become the harmful ones and even to help them to gain useful activity. The task of efficient management and control of microbial population's development in LSS highly depends on mission duration. As for short-term missions without recycling, the proper hygienic procedures are developed. For longer missions, the probability of transformation of the neutral forms into the harmful ones is becoming more dangerous. The LSS for long-term missions are to use cycling-recycling systems, including system with biological recycling. In these systems, microbial populations as regenerative link should be useful and active agents. Some problems of microbial populations control and management are discussed in the paper. PMID:16175696

  11. Dynamics of organic matter and microbial populations in amended soil: a multidisciplinary approach

    NASA Astrophysics Data System (ADS)

    Gigliotti, Giovanni; Pezzolla, Daniela; Zadra, Claudia; Albertini, Emidio; Marconi, Gianpiero; Turchetti, Benedetta; Buzzini, Pietro

    2013-04-01

    The application of organic amendments to soils, such as pig slurry, sewage sludge and compost is considered a tool for improving soil fertility and enhancing C stock. The addition of these different organic materials allows a good supply of nutrients for plants but also contributes to C sequestration, affects the microbial activity and the transformation of soil organic matter (SOM). Moreover, the addition of organic amendment has gained importance as a source of greenhouse gas (GHG) emissions and then as a cause of the "Global Warming". Therefore, it is important to investigate the factors controlling the SOM mineralization in order to improve soil C sequestration and decreasing at the same time the GHG emissions. The quality of organic matter added to the soil will play an important role in these dynamics, affecting the microbial activity and the changes in microbial community structure. A laboratory, multidisciplinary experiment was carried out to test the effect of the amendment by anaerobic digested livestock-derived organic materials on labile organic matter evolution and on dynamics of microbial population, this latter both in terms of consistence of microbial biomass, as well as in terms of microbial biodiversity. Different approaches were used to study the microbial community structure: chemical (CO2 fluxes, WEOC, C-biomass, PLFA), microbiological (microbial enumeration) and molecular (DNA extraction and Roche 454, Next Generation Sequencing, NGS). The application of fresh digestate, derived from the anaerobic treatment of animal wastes, affected the short-term dynamics of microbial community, as reflected by the increase of CO2 emissions immediately after the amendment compared to the control soil. This is probably due to the addition of easily available C added with the digestate, demonstrating that this organic material was only partially stabilized by the anaerobic process. In fact, the digestate contained a high amounts of available C, which led to

  12. Microbial community response to the CO2 injection and storage in the saline aquifer, Ketzin, Germany

    NASA Astrophysics Data System (ADS)

    Morozova, Daria; Zettlitzer, Michael; Vieth, Andrea; Würdemann, Hilke

    2010-05-01

    The concept of CO2 capture and storage in the deep underground is currently receiving great attention as a consequence of the effects of global warming due to the accumulation of carbon dioxide gas in the atmosphere. The EU funded CO2SINK project is aimed as a pilot storage of CO2 in a saline aquifer located near Ketzin, Germany. One of the main aims of the project is to develop efficient monitoring procedures for assessing the processes that are triggered in the reservoir by CO2 injection. This study reveals analyses of the composition and activity of the microbial community of a saline CO2 storage aquifer and its response to CO2 injection. The availability of CO2 has an influence on the metabolism of both heterotrophic microorganisms, which are involved in carbon cycle, and lithoautotrophic microorganisms, which are able to use CO2 as the sole carbon source and electron acceptor. Injection of CO2 in the supercritical state (temperature above 31.1 °C, pressure above 72.9 atm) may induce metabolic shifts in the microbial communities. Furthermore, bacterial population and activity can be strongly influenced by changes in pH value, pressure, temperature, salinity and other abiotic factors, which will be all influenced by CO2 injection into the deep subsurface. Analyses of the composition of microbial communities and its changes should contribute to an evaluation of the effectiveness and reliability of the long-term CO2 storage technique. The interactions between microorganisms and the minerals of both the reservoir and the cap rock may cause major changes to the structure and chemical composition of the rock formations, which would influence the permeability within the reservoir. In addition, precipitation and corrosion may occur around the well affecting the casing and the casing cement. By using Fluorescence in situ Hybridisation (FISH) and molecular fingerprinting such as Polymerase-Chain-Reaction Single-Strand-Conformation Polymorphism (PCR-SSCP) and Denaturing

  13. Methane Inhibition Alters the Microbial Community, Hydrogen Flow, and Fermentation Response in the Rumen of Cattle.

    PubMed

    Martinez-Fernandez, Gonzalo; Denman, Stuart E; Yang, Chunlei; Cheung, Jane; Mitsumori, Makoto; McSweeney, Christopher S

    2016-01-01

    Management of metabolic hydrogen ([H]) in the rumen has been identified as an important consideration when reducing ruminant CH4 emissions. However, little is known about hydrogen flux and microbial rumen population responses to CH4 inhibition when animals are fed with slowly degradable diets. The effects of the anti-methanogenic compound, chloroform, on rumen fermentation, microbial ecology, and H2/CH4 production were investigated in vivo. Eight rumen fistulated Brahman steers were fed a roughage hay diet (Rhode grass hay) or roughage hay:concentrate diet (60:40) with increasing levels (low, mid, and high) of chloroform in a cyclodextrin matrix. The increasing levels of chloroform resulted in an increase in H2 expelled as CH4 production decreased with no effect on dry matter intakes. The amount of expelled H2 per mole of decreased methane, was lower for the hay diet suggesting a more efficient redirection of hydrogen into other microbial products compared with hay:concentrate diet. A shift in rumen fermentation toward propionate and branched-chain fatty acids was observed for both diets. Animals fed with the hay:concentrate diet had both higher formate concentration and H2 expelled than those fed only roughage hay. Metabolomic analyses revealed an increase in the concentration of amino acids, organic, and nucleic acids in the fluid phase for both diets when methanogenesis was inhibited. These changes in the rumen metabolism were accompanied by a shift in the microbiota with an increase in Bacteroidetes:Firmicutes ratio and a decrease in Archaea and Synergistetes for both diets. Within the Bacteroidetes family, some OTUs assigned to Prevotella were promoted under chloroform treatment. These bacteria may be partly responsible for the increase in amino acids and propionate in the rumen. No significant changes were observed for abundance of fibrolytic bacteria, protozoa, and fungi, which suggests that fiber degradation was not impaired. The observed 30% decrease in

  14. Methane Inhibition Alters the Microbial Community, Hydrogen Flow, and Fermentation Response in the Rumen of Cattle

    PubMed Central

    Martinez-Fernandez, Gonzalo; Denman, Stuart E.; Yang, Chunlei; Cheung, Jane; Mitsumori, Makoto; McSweeney, Christopher S.

    2016-01-01

    Management of metabolic hydrogen ([H]) in the rumen has been identified as an important consideration when reducing ruminant CH4 emissions. However, little is known about hydrogen flux and microbial rumen population responses to CH4 inhibition when animals are fed with slowly degradable diets. The effects of the anti-methanogenic compound, chloroform, on rumen fermentation, microbial ecology, and H2/CH4 production were investigated in vivo. Eight rumen fistulated Brahman steers were fed a roughage hay diet (Rhode grass hay) or roughage hay:concentrate diet (60:40) with increasing levels (low, mid, and high) of chloroform in a cyclodextrin matrix. The increasing levels of chloroform resulted in an increase in H2 expelled as CH4 production decreased with no effect on dry matter intakes. The amount of expelled H2 per mole of decreased methane, was lower for the hay diet suggesting a more efficient redirection of hydrogen into other microbial products compared with hay:concentrate diet. A shift in rumen fermentation toward propionate and branched-chain fatty acids was observed for both diets. Animals fed with the hay:concentrate diet had both higher formate concentration and H2 expelled than those fed only roughage hay. Metabolomic analyses revealed an increase in the concentration of amino acids, organic, and nucleic acids in the fluid phase for both diets when methanogenesis was inhibited. These changes in the rumen metabolism were accompanied by a shift in the microbiota with an increase in Bacteroidetes:Firmicutes ratio and a decrease in Archaea and Synergistetes for both diets. Within the Bacteroidetes family, some OTUs assigned to Prevotella were promoted under chloroform treatment. These bacteria may be partly responsible for the increase in amino acids and propionate in the rumen. No significant changes were observed for abundance of fibrolytic bacteria, protozoa, and fungi, which suggests that fiber degradation was not impaired. The observed 30% decrease in

  15. Microbial Populations Associated with Treatment of an Industrial Dye Effluent in an Anaerobic Baffled Reactor

    PubMed Central

    Plumb, Jason J.; Bell, Joanne; Stuckey, David C.

    2001-01-01

    Fluorescent in situ hybridization (FISH) using 16S and 23S rRNA-targeted probes together with construction of an archaeal 16S ribosomal DNA (rDNA) clone library was used to characterize the microbial populations of an anaerobic baffled reactor successfully treating industrial dye waste. Wastewater produced during the manufacture of food dyes containing several different azo and other dye compounds was decolorized and degraded under sulfidogenic and methanogenic conditions. Use of molecular methods to describe microbial populations showed that a diverse group of Bacteria and Archaea was involved in this treatment process. FISH enumeration showed that members of the gamma subclass of the class Proteobacteria and bacteria in the Cytophaga-Flexibacter-Bacteroides phylum, together with sulfate-reducing bacteria, were prominent members of a mixed bacterial population. A combination of FISH probing and analysis of 98 archaeal 16S rDNA clone inserts revealed that together with the bacterial population, a methanogenic population dominated by Methanosaeta species and containing species of Methanobacterium and Methanospirillum and a relatively unstudied methanogen, Methanomethylovorans hollandica, contributed to successful anaerobic treatment of the industrial waste. We suggest that sulfate reducers, or more accurately sulfidogenic bacteria, together with M. hollandica contribute considerably to the treatment process through metabolism of dye-associated sulfonate groups and subsequent conversion of sulfur compounds to carbon dioxide and methane. PMID:11425746

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

    PubMed

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

    2015-06-01

    Four Thai native beef cattle with initial body weight (BW) of 91.8 ± 4.75 kg were randomly assigned according to a 4 × 4 Latin square design to receive four concentrates replacement levels of soybean meal (SBM) by dried rumen digesta (DRD) at 0, 33, 67, and 100 % on dry matter (DM) basis. All cattle were fed rice straw ad libitum while additional concentrate was fed at 0.5 % BW daily. The experiment was conducted for four periods of 21 days. Rumen fluid was analyzed for predominant cellulolytic bacterial population by using real-time PCR technique. Increasing levels of DRD did not alter total feed intake, ruminal pH and temperature, and plasma urea nitrogen (P > 0.05). Protozoa and fungal population were not differed by DRD supplementation while population of bacteria at 4 h post feeding was increased when SBM was replaced with DRD at 66 and 100 % DM. Population of total bacteria and R. flavefaciens at 4 h post feeding were significantly highest with inclusion of 100 % of DRD in the ration. The experimental diets has no effect on excretion and absorption of purine derivatives (P > 0.05), while microbial crude protein and efficiency of microbial N synthesis were significantly increased with DRD inclusion in the diet and highest with 100 % DRD replacement (P > 0.05). Replacement of SBM by DRD at 100 % DM improved the rumen ecology and microbial population in beef cattle fed on rice straw. PMID:25851930

  17. Response of the microbial metallome to arsenic stress

    NASA Astrophysics Data System (ADS)

    Wolfe-Simon, F.; Lancaster, W. A.; Menon, A. L.; Yannone, S. M.; Adams, M. W.; Tainer, J. A.

    2012-12-01

    Life depends on access to nutrients in the environment. While elements such as nitrogen, carbon, sulfur and phosphorus are fundamental to microbial survival, trace nutrient elements like iron, molybdenum and copper show dramatically different profiles depending on environmental conditions. These elements are known nutrients but also can be toxic at higher concentrations. For low or limiting concentrations of one nutrient element, microbes may utilize another element to serve similar functions often, but not always, in similar macromolecular structures. Well-characterized elemental exchanges include manganese for iron and tungsten for molybdenum. Here we report on our preliminary metallomic analyses of the Gammaproteobacterium Halomonas sp. str. GFAJ-1 grown under severe arsenic stress. We analyzed 53 elements by ICP-MS, in order to determine which elements are tightly, weakly or not bound to soluble macromolecules (> 3 kDa). We specifically investigated the changes to the metallome of GFAJ-1cells that were grown in the synthetic minimal medium AML60 supplemented with 50 mM arsenate (As(V)), 50 μM phosphate (P) or 50 mM As(V) plus 50 μM P. Further studies will identify which macromolecules are associated with the various elements. This research extends our understanding of metal assimilation in microbes in response to tandem phosphorus limitation coupled to extreme arsenic concentrations and furthermore contributes to the expanding set of chemical elements utilized by microbes in unusual environmental niches.

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

    ERIC Educational Resources Information Center

    Stromberger, Mary E.

    2005-01-01

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

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

    SciTech Connect

    Firestone, Mary

    2015-01-14

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

  20. Geochemical Attributes and Gradients Within Geothermal Systems Define the Distribution of Specific Microbial Populations

    NASA Astrophysics Data System (ADS)

    Inskeep, W. P.; Macur, R. E.; Korf, S.; Taylor, W. P.; Ackerman, G.; Kozubal, M.; Nagy, A.

    2006-12-01

    Microorganisms in natural habitats interact with mineral surfaces in many different respects. For example, microorganisms are known to enhance the dissolution rates of some minerals via the production of organic acids and other exudates, but at the same time, may mineralize solid phases as a direct or indirect result of metabolic processes. It is also well-established that many microorganisms form biofilms on mineral surfaces, and may preferentially attach to surfaces rich in necessary nutrients or in elements used for energy conservation. In part due to the complexity of natural soil, water and sediments systems, it is generally difficult to ascertain mechanisms controlling the distribution of organisms on mineral surfaces and their role in mineral precipitation-dissolution reactions. Geothermal microbial communities are often less diverse than surface soils and sediments and offer opportunities for understanding relationships among specific microbial populations and geochemical processes that define the biogeochemical cycles of individual elements. We have investigated numerous acidic and near-neutral geothermal sites in Yellowstone National Park, and have performed a number of complimentary chemical and microbiological analyses to ascertain the role of microorganisms in S, Fe, As and Sb cycling in geothermal systems. Our results demonstrate the importance of microbiota in the formation of various Fe(III) oxide phases with variable anion chemistry, and the importance of chemolithotrophic metabolisms in Fe, S and As cycling. Where possible, these metabolisms are linked to specific microbial populations identified via molecular methods, and in some cases confirmed using isolation and characterization of individual organisms.

  1. Effects of Flavonoids on Rumen Fermentation Activity, Methane Production, and Microbial Population

    PubMed Central

    Abdullah, Norhani; Oskoueian, Armin

    2013-01-01

    This research was carried out to evaluate the effects of flavone, myricetin, naringin, catechin, rutin, quercetin, and kaempferol at the concentration of 4.5% of the substrate (dry matter basis) on the rumen microbial activity in vitro. Mixture of guinea grass and concentrate (60 : 40) was used as the substrate. The results showed that all the flavonoids except naringin and quercetin significantly (P < 0.05) decreased the dry matter degradability. The gas production significantly (P < 0.05) decreased by flavone, myricetin, and kaempferol, whereas naringin, rutin, and quercetin significantly (P < 0.05) increased the gas production. The flavonoids suppressed methane production significantly (P < 0.05). The total VFA concentration significantly (P < 0.05) decreased in the presence of flavone, myricetin, and kaempferol. All flavonoids except naringin and quercetin significantly (P < 0.05) reduced the carboxymethyl cellulase, filter paperase, xylanase, and β-glucosidase activities, purine content, and the efficiency of microbial protein synthesis. Flavone, myricetin, catechin, rutin, and kaempferol significantly (P < 0.05) reduced the population of rumen microbes. Total populations of protozoa and methanogens were significantly (P < 0.05) suppressed by naringin and quercetin. The results of this research demonstrated that naringin and quercetin at the concentration of 4.5% of the substrate (dry matter basis) were potential metabolites to suppress methane production without any negative effects on rumen microbial fermentation. PMID:24175289

  2. Microbial population dynamics in a thermophilic methane digester fed with garbage.

    PubMed

    Cheon, J; Hong, F; Hidaka, T; Koshikawa, H; Tsuno, H

    2007-01-01

    The diversity of microbial communities in three full-scale thermophilic anaerobic digesters which treated garbage, sewage sludge and livestock wastes (hereafter called TGD, TSD and TLD, respectively) was investigated using 16S rDNA clone libraries in triplicate. The population dynamics of TGD were also studied. The purposes were to show the microbial diversity in each reactor and to suggest which key microbes in a thermophilic methane digester fed with garbage, including a check of reproducibility and the suggestion of an error range in this molecular biology method. 736 clones were identified, and the maximum error was estimated to be around +/-10% for the same OTU (operational taxonomic unit) and for most detected OTUs. The most frequently detected OTU shows a close relationship to Uncultured bacterium clone MBA08, Unidentified bacterium clone TUG22 and Uncultured archaeal symbiont PA204 in TGD, TSD and TLD, respectively. The microbial population dynamics in TGD were studied over a period of 90 days, and the occupying ratios of Bacillus infernus and Methanothermobacter wolfeii were shown to change with the change in VFA concentration. From the dynamic change and characteristics of the microbes, it is concluded that Bacillus infernus and Methanothermobacter wolfeii played an important role and were recommended as key microbes in TGD. PMID:17564383

  3. [Nutrient contents and microbial populations of aeolian sandy soil in Sanjiangyuan region of Qinghai Province].

    PubMed

    Lin, Chao-feng; Chen, Zhan-quan; Xue, Quan-hong; Lai, Hang-xian; Chen, Lai-sheng; Zhang, Deng-shan

    2007-01-01

    Sanjiangyuan region (the headstream of three rivers) in Qinghai Province of China is the highest and largest inland alpine wetland in the world. The study on the nutrient contents and microbial populations of aeolian sandy soils in this region showed that soil organic matter content increased with the evolution of aeolian sand dunes from un-stabilized to stabilized state, being 5.9 and 3.8 times higher in stabilized sand dune than in mobile and semi-stabilized sand dunes, respectively. Soil nitrogen and phosphorus contents increased in line with the amount of organic matter, while potassium content and pH value varied slightly. The microbial populations changed markedly with the development of vegetation, fixing of mobile sand, and increase of soil nutrients. The quantities of soil bacteria, fungi and actinomycetes were 4.0 and 2.8 times, 19.6 and 6.3 times, and 12.4 and 2.6 times higher in stabilized and semi-stabilized sand dunes than in mobile sand dune, respectively, indicating that soil microbial bio-diversity was increased with the evolution of aeolian sand dunes from mobile to stabilized state. In addition, the quantities of soil microbes were closely correlated with the contents of soil organic matter, total nitrogen, and available nitrogen and phosphorus, but not correlated with soil total phosphorus, total and available potassium, or pH value. PMID:17396507

  4. Activity and growth of microbial populations in pressurized deep-sea sediment and animal gut samples.

    PubMed

    Tabor, P S; Deming, J W; Ohwada, K; Colwell, R R

    1982-08-01

    Benthic animals and sediment samples were collected at deep-sea stations in the northwest (3,600-m depth) and southeast (4,300- and 5200-m depths) Atlantic Ocean. Utilization rates of [14C]glutamate (0.67 to 0.74 nmol) in sediment suspensions incubated at in situ temperatures and pressures (3 to 5 degrees C and 360, 430, or 520 atmospheres) were relatively slow, ranging from 0.09 to 0.39 nmol g-1 day-1, whereas rates for pressurized samples of gut suspensions varied widely, ranging from no detectable activity to a rapid rate of 986 nmol g-1 day-1. Gut flora from a holothurian specimen and a fish demonstrated rapid, barophilic substrate utilization, based on relative rates calculated for pressurized samples and samples held at 1 atm (101.325 kPa). Substrate utilization by microbial populations in several sediment samples was not inhibited by in situ pressure. Deep-sea pressures did not restrict growth, measured as doubling time, of culturable bacteria present in a northwest Atlantic sediment sample and in a gut suspension prepared from an abyssal scavenging amphipod. From the results of this study, it was concluded that microbial populations in benthic environments can demonstrate significant metabolic activity under deep-ocean conditions of temperature and pressure. Furthermore, rates of microbial activity in the guts of benthic macrofauna are potentially more rapid than in surrounding deep-sea sediments. PMID:6127054

  5. Activity and growth of microbial populations in pressurized deep-sea sediment and animal gut samples.

    PubMed Central

    Tabor, P S; Deming, J W; Ohwada, K; Colwell, R R

    1982-01-01

    Benthic animals and sediment samples were collected at deep-sea stations in the northwest (3,600-m depth) and southeast (4,300- and 5200-m depths) Atlantic Ocean. Utilization rates of [14C]glutamate (0.67 to 0.74 nmol) in sediment suspensions incubated at in situ temperatures and pressures (3 to 5 degrees C and 360, 430, or 520 atmospheres) were relatively slow, ranging from 0.09 to 0.39 nmol g-1 day-1, whereas rates for pressurized samples of gut suspensions varied widely, ranging from no detectable activity to a rapid rate of 986 nmol g-1 day-1. Gut flora from a holothurian specimen and a fish demonstrated rapid, barophilic substrate utilization, based on relative rates calculated for pressurized samples and samples held at 1 atm (101.325 kPa). Substrate utilization by microbial populations in several sediment samples was not inhibited by in situ pressure. Deep-sea pressures did not restrict growth, measured as doubling time, of culturable bacteria present in a northwest Atlantic sediment sample and in a gut suspension prepared from an abyssal scavenging amphipod. From the results of this study, it was concluded that microbial populations in benthic environments can demonstrate significant metabolic activity under deep-ocean conditions of temperature and pressure. Furthermore, rates of microbial activity in the guts of benthic macrofauna are potentially more rapid than in surrounding deep-sea sediments. PMID:6127054

  6. 2012 MICROBIAL STRESS RESPONSE GORDON RESEARCH CONFERENCE, JULY 20-25, 2012

    SciTech Connect

    Timothy Donohue

    2012-07-25

    The Gordon Research Conference on MICROBIAL STRESS RESPONSE was held at Mount Holyoke College, South Hadley, Massachusetts, July 15-20, 2012. The Conference was well-attended with 180 participants. The 2012 Microbial Stress Responses Gordon Research Conference will provide a forum for the open reporting of recent discoveries on the diverse mechanisms employed by microbes to respond to stress. Approaches range from analysis at the molecular level (how are signals perceived and transmitted to change gene expression or function) to cellular and microbial community responses. Gordon Research Conferences does not permit publication of meeting proceedings.

  7. Variation in microbial population during composting of agro-industrial waste.

    PubMed

    Coelho, Luísa; Reis, Mário; Dionísio, Lídia

    2013-05-01

    Two compost piles were prepared, using two ventilation systems: forced ventilation and ventilation through mechanical turning. The material to compost was a mixture of orange waste, olive pomace, and grass clippings (2:1:1 v/v). During the composting period (375 days), samples were periodically taken from both piles, and the enumeration of fungi, actinomycetes, and heterotrophic bacteria was carried out. All studied microorganisms were incubated at 25 and 55 °C after inoculation in appropriate growth media. Fungi were dominant in the early stages of both composting processes; heterotrophic bacteria proliferated mainly during the thermophilic stage, and actinomycetes were more abundant in the final stage of the composting process. Our results showed that the physical and chemical parameters: temperature, pH, moisture, and aeration influenced the variation of the microbial population along the composting process. This study demonstrated that composting of these types of wastes, despite the prolonged mesophilic stage, provided an expected microbial variation. PMID:22699450

  8. Unlocking the biogeochemical black box: What drives microbial response to climate forcing in semi-arid soils?

    NASA Astrophysics Data System (ADS)

    Moravec, B. G.; McLain, J. E.; Lohse, K. A.

    2009-12-01

    Microbial mediated cycling of carbon (C) and nitrogen (N) and their loss from soils are closely linked to soil moisture and temperature. Yet, it is unclear how microbial communities will respond to climatic forcing (namely increased inter-annual precipitation variability and severe drought) and to what extent parent material controls these responses. We used Real Time Polymerase Chain Reaction (RT-PCR) and C utilization assays to determine the relative abundance and diversity of microbial populations during pre-, mid- and post-monsoon time intervals at four sites along a steep elevation gradient (temperature and precipitation range of >10°C and >50 cm, respectively) in the Santa Catalina Mountains, AZ. Contrasting parent materials (schist and granite) were paired at elevations. RT-PCR results showed large increases of bacterial and fungal biomarkers at high elevations with the onset of precipitation (pre- to mid- monsoon conditions) (as much as 824%). In contrast, bacteria biomarkers did not change at low elevation granite site as a result of the onset of precipitation whereas fungal biomarkers increased by 177% at this site. Both bacteria and fungal biomarkers increased substantially at low elevation schist sites with the onset of precipitation. Finally, C utilization assays indicated that high elevation sites had a relatively high diversity of C utilization compared to low elevation soils. We hypothesize that increased bacterial and fungal abundance in low elevation schist-derived soils relative to granite soils after the onset of monsoon rains may be a function of soil texture, with higher clay content in schist soils leading to higher soil moisture availability. Alternatively, differences in microbial responses may be due to higher C availability in schist soils compared to granite soils. Higher C utilization diversity as well as similar bacteria and fungal biomarker responses found at high elevation sites (both granite and schist soils) in response to

  9. New Methods for Analysis of Spatial Distribution and Coaggregation of Microbial Populations in Complex Biofilms

    PubMed Central

    Almstrand, Robert; Daims, Holger; Persson, Frank; Sörensson, Fred

    2013-01-01

    In biofilms, microbial activities form gradients of substrates and electron acceptors, creating a complex landscape of microhabitats, often resulting in structured localization of the microbial populations present. To understand the dynamic interplay between and within these populations, quantitative measurements and statistical analysis of their localization patterns within the biofilms are necessary, and adequate automated tools for such analyses are needed. We have designed and applied new methods for fluorescence in situ hybridization (FISH) and digital image analysis of directionally dependent (anisotropic) multispecies biofilms. A sequential-FISH approach allowed multiple populations to be detected in a biofilm sample. This was combined with an automated tool for vertical-distribution analysis by generating in silico biofilm slices and the recently developed Inflate algorithm for coaggregation analysis of microbial populations in anisotropic biofilms. As a proof of principle, we show distinct stratification patterns of the ammonia oxidizers Nitrosomonas oligotropha subclusters I and II and the nitrite oxidizer Nitrospira sublineage I in three different types of wastewater biofilms, suggesting niche differentiation between the N. oligotropha subclusters, which could explain their coexistence in the same biofilms. Coaggregation analysis showed that N. oligotropha subcluster II aggregated closer to Nitrospira than did N. oligotropha subcluster I in a pilot plant nitrifying trickling filter (NTF) and a moving-bed biofilm reactor (MBBR), but not in a full-scale NTF, indicating important ecophysiological differences between these phylogenetically closely related subclusters. By using high-resolution quantitative methods applicable to any multispecies biofilm in general, the ecological interactions of these complex ecosystems can be understood in more detail. PMID:23892743

  10. Effect of temperature decrease on the microbial population and process performance of a mesophilic anaerobic bioreactor.

    PubMed

    Bohn, I; Björnsson, L; Mattiasson, B

    2007-08-01

    The effect of a temperature decrease from 33 degrees C to 12 degrees C was investigated for anaerobic digestion of crop residues. A laboratory-scale reactor (R0) was inoculated with mesophilic sludge and operated as continuously stirred fed-batch system at temperatures of 12 degrees C, 18 degrees C and 33 degrees C. Changes in the microbial populations of the sludge were followed by means of fluorescence in situ hybridization analysis. Methane was produced in R0 at all temperatures. Stable long-term operation at 18 degress C was achieved yielding 151 mlCH4 gVS(added(-1) at a rate of 108 mlCH4 l(R)(-1)d(-1) once the microbial populations of the sludge had adapted to this temperature. After operation at 18 degrees C, the contents of R0 was mixed and distributed into three smaller reactors, which were operated at 18 degrees C (R18), 25 degrees C (R25) and 37 degrees C (R37), respectively. Methane production rates for R37 and R25 were 366 and 310 mlCH4 l(R)(-1)d(-1), respectively, which were higher than the 215 mlCH4 l(R)(-1)d(-1) obtained in R0 when this was operated at 33 degrees C. Hydrolysis was found to decrease when temperature was decreased and especially below 25 degrees C. At temperatures below 16 degrees C, acidogenesis and methanogenesis were the rate-limiting steps. Adaptation of the mesophilic sludge to 18 degrees C was indicated by an increase in the ratio of Bacteria to total prokaryotes (sum of Archaea and Bacteria). This was thought to be caused by enrichment of Bacteria in the sludge, which appeared to be an important adaptation mechanism. During the adaptation, the Methanomicrobiales and Methanosarcinaceae populations increased relative to the total Archaea population whereas the Methanosaeta population decreased. The population changes were reflected by reactor performance. PMID:17879853

  11. Functional responses and adaptation of mesophilic microbial communities to psychrophilic anaerobic digestion.

    PubMed

    Gunnigle, Eoin; Nielsen, Jeppe L; Fuszard, Matthew; Botting, Catherine H; Sheahan, Jerome; O'Flaherty, Vincent; Abram, Florence

    2015-12-01

    Psychrophilic (<20°C) anaerobic digestion (AD) represents an attractive alternative to mesophilic wastewater treatment. In order to investigate the AD microbiome response to temperature change, with particular emphasis on methanogenic archaea, duplicate laboratory-scale AD bioreactors were operated at 37°C followed by a temperature drop to 15°C. A volatile fatty acid-based wastewater (composed of propionic acid, butyric acid, acetic acid and ethanol) was used to provide substrates representing the later stages of AD. Community structure was monitored using 16S rRNA gene clone libraries, as well as DNA and cDNA-based DGGE analysis, while the abundance of relevant methanogens was followed using qPCR. In addition, metaproteomics, microautoradiography-fluorescence in situ hybridization, and methanogenic activity measurements were employed to investigate microbial activities and functions. Methanomicrobiales abundance increased at low temperature, which correlated with an increased contribution of CH4 production from hydrogenotrophic methanogenesis at 15°C. Methanosarcinales utilized acetate and H2/CO2 as CH4 precursors at both temperatures and a partial shift from acetoclastic to hydrogenotrophic methanogenesis was observed for this archaeal population at 15°C. An upregulation of protein expression was reported at low temperature as well as the detection of chaperones indicating that mesophilic communities experienced stress during long-term exposure to 15°C. Overall, changes in microbial community structure and function were found to underpin the adaptation of mesophilic sludge to psychrophilic AD. PMID:26507125

  12. ECOLOGICALLY SIGNIFICANT EFFECTS OF #PSEUDOMONAS PUTIDA# PP0103 (PR0103), GENETICALLY ENGINEERED TO DEGRADE 2,4-DICHLOROPHENOXYACETATE, ON MICROBIAL POPULATIONS AND PROCESSES IN SOIL

    EPA Science Inventory

    Genetically engineered microorganisms (GEMS) released to the environment may perturb microbial populations and their processes in soil. hanges in microbial communities, biogeochemical processes, and the physiochemical characteristics of soil might result from the introduction of ...

  13. Characterization of Microbial Population Structures in Recreational Waters and Primary Sources of Fecal Pollution with a Next-Generation Sequencing Approach

    EPA Science Inventory

    The invention of new approaches to DNA sequencing commonly referred to as next generation sequencing technologies is revolutionizing the study of microbial diversity. In this chapter, we discuss the characterization of microbial population structures in recreational waters and p...

  14. Unsupervised discovery of microbial population structure within metagenomes using nucleotide base composition

    PubMed Central

    Saeed, Isaam; Tang, Sen-Lin; Halgamuge, Saman K.

    2012-01-01

    An approach to infer the unknown microbial population structure within a metagenome is to cluster nucleotide sequences based on common patterns in base composition, otherwise referred to as binning. When functional roles are assigned to the identified populations, a deeper understanding of microbial communities can be attained, more so than gene-centric approaches that explore overall functionality. In this study, we propose an unsupervised, model-based binning method with two clustering tiers, which uses a novel transformation of the oligonucleotide frequency-derived error gradient and GC content to generate coarse groups at the first tier of clustering; and tetranucleotide frequency to refine these groups at the secondary clustering tier. The proposed method has a demonstrated improvement over PhyloPythia, S-GSOM, TACOA and TaxSOM on all three benchmarks that were used for evaluation in this study. The proposed method is then applied to a pyrosequenced metagenomic library of mud volcano sediment sampled in southwestern Taiwan, with the inferred population structure validated against complementary sequencing of 16S ribosomal RNA marker genes. Finally, the proposed method was further validated against four publicly available metagenomes, including a highly complex Antarctic whale-fall bone sample, which was previously assumed to be too complex for binning prior to functional analysis. PMID:22180538

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

    PubMed

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

    1997-01-01

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

  16. Highly variable functional response of microbial communities to experimental temperature disturbances

    NASA Astrophysics Data System (ADS)

    Wanek, Wolfgang; Mooshammer, Maria; Hofhansl, Florian; Frank, Alexander H.; Leitner, Sonja; Schnecker, Jörg; Wild, Birgit; Watzka, Margarete; Keiblinger, Katharina M.; Zechmeister-Boltenstern, Sophie; Richter, Andreas

    2015-04-01

    Climate change is expected to alter the frequency and intensity of climate excursions, such as heat, drought and freeze-thaw events, requiring a thorough mechanistic understanding of the response of microbially-mediated nutrient cycling processes to such transient but severe disturbances. Here, we investigated the resistance and resilience of major gross processes of microbial carbon (C), nitrogen (N) and phosphorus (P) cycling, determined by isotope pool dilution assays, as well as potential enzyme activities in decomposing beech litter to two contrasting temperature disturbances (freeze-thaw and heat treatment for 9 days) in four different litter types. Microbial processes were substantially altered by the temperature disturbances but both the magnitude and direction of the disturbance effect varied among them. Phosphorus processes and hydrolytic enzyme activities showed lowest resistance as well as resilience, whereas N processes were more resistant and C processes intermediate. In general, responses of microbial processes were mainly consistent across disturbances but partially dependent on litter-specific microbial communities. The transient disturbances affected the relative availability of essential nutrients through a decoupling of microbial C, N and P cycling processes. Understanding the underlying mechanisms through which a decoupling of the supply of these elements as a result of microbial responses to environmental disturbances occurs will help to better predicting ecosystem responses to global change.

  17. Study on Biodegradation Process of Polyethylene Glycol with Exponential Glowth of Microbial Population

    NASA Astrophysics Data System (ADS)

    Watanabe, Masaji; Kawai, Fusako

    Biodegradation of polyethylene glycol is studied mathematically. A mathematical model for depolymerization process of exogenous type is described. When a degradation rate is a product of a time factor and a molecular factor, a time dependent model can be transformed into a time independent model, and techniques developed in previous studies can be applied to the time independent model to determine the molecular factor. The time factor can be determined assuming the exponential growth of the microbial population. Those techniques are described, and numerical results are presented. A comparison between a numerical result and an experimental result shows that the mathematical method is appropriate for practical applications.

  18. Changes in Microbial Community Structure and Carbon Utilization Patterns in Response to Woody Encroachment into Grasslands

    NASA Astrophysics Data System (ADS)

    Creamer, C. A.; Filley, T. R.; Boutton, T. W.

    2012-12-01

    Land cover changes occurring in dryland ecosystems, such as woody encroachment, can moderate microbial activity and alter the flow of C and N between litter and soil, ultimately impacting soil organic carbon (SOC) dynamics. We analyzed the quantity and isotopic composition of microbial phospholipids along a grassland-to-woodland successional chronosequence in southern Texas to determine how microbial community structure and SOC utilization patterns responded to the extent of woody encroachment across two sampling seasons (Spring and Fall). Woody encroachment resulted in significant increases in total microbial biomass and fungal:bacterial ratios along with significant decreases in the ratio of gram-positive:gram-negative bacteria. Compound-specific 13C analysis of microbial phospholipids revealed that gram-negative bacteria and fungi were preferentially utilizing newer, C3-derived inputs, while other microbial groups generally showed no preferential incorporation of newer or older C. This preferential use of newer C in gram-negative bacteria and fungi, combined with their increasing relative abundance, reveals that these microbial groups are most responsive to biogeochemical changes elicited by woody encroachment, potentially to enhanced rhizosphere development or changes in the chemical stability of C inputs. This research provides important information regarding the links between changing plant cover, SOC accrual, and microbial activity in response to a globally relevant environmental perturbation.

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

    SciTech Connect

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

    2010-01-01

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

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

    PubMed Central

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

    2010-01-01

    An important challenge in microbial ecology is developing methods that simultaneously examine the physiology of organisms at the molecular level and their ecosystem level interactions in complex natural systems. We integrated extensive proteomic, geochemical, and biological information from 28 microbial communities collected from an acid mine drainage environment and representing a range of biofilm development stages and geochemical conditions to evaluate how the physiologies of the dominant and less abundant organisms change along environmental gradients. The initial colonist dominates across all environments, but its proteome changes between two stable states as communities diversify, implying that interspecies interactions affect this organism's metabolism. Its overall physiology is robust to abiotic environmental factors, but strong correlations exist between these factors and certain subsets of proteins, possibly accounting for its wide environmental distribution. Lower abundance populations are patchier in their distribution, and proteomic data indicate that their environmental niches may be constrained by specific sets of abiotic environmental factors. This research establishes an effective strategy to investigate ecological relationships between microbial physiology and the environment for whole communities in situ. PMID:20531404

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

    USGS Publications Warehouse

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

    2010-01-01

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

  2. Temperature sensitivity of soil respiration rates enhanced by microbial community response.

    PubMed

    Karhu, Kristiina; Auffret, Marc D; Dungait, Jennifer A J; Hopkins, David W; Prosser, James I; Singh, Brajesh K; Subke, Jens-Arne; Wookey, Philip A; Agren, Göran I; Sebastià, Maria-Teresa; Gouriveau, Fabrice; Bergkvist, Göran; Meir, Patrick; Nottingham, Andrew T; Salinas, Norma; Hartley, Iain P

    2014-09-01

    Soils store about four times as much carbon as plant biomass, and soil microbial respiration releases about 60 petagrams of carbon per year to the atmosphere as carbon dioxide. Short-term experiments have shown that soil microbial respiration increases exponentially with temperature. This information has been incorporated into soil carbon and Earth-system models, which suggest that warming-induced increases in carbon dioxide release from soils represent an important positive feedback loop that could influence twenty-first-century climate change. The magnitude of this feedback remains uncertain, however, not least because the response of soil microbial communities to changing temperatures has the potential to either decrease or increase warming-induced carbon losses substantially. Here we collect soils from different ecosystems along a climate gradient from the Arctic to the Amazon and investigate how microbial community-level responses control the temperature sensitivity of soil respiration. We find that the microbial community-level response more often enhances than reduces the mid- to long-term (90 days) temperature sensitivity of respiration. Furthermore, the strongest enhancing responses were observed in soils with high carbon-to-nitrogen ratios and in soils from cold climatic regions. After 90 days, microbial community responses increased the temperature sensitivity of respiration in high-latitude soils by a factor of 1.4 compared to the instantaneous temperature response. This suggests that the substantial carbon stores in Arctic and boreal soils could be more vulnerable to climate warming than currently predicted. PMID:25186902

  3. Development of a microbial population within a hot-drinks vending machine and the microbial load of vended hot chocolate drink.

    PubMed

    Hall, A; Short, K; Saltmarsh, M; Fielding, L; Peters, A

    2007-09-01

    In order to understand the development of the microbial population within a hot-drinks vending machine a new machine was placed in a staff area of a university campus vending only hot chocolate. The machine was cleaned weekly using a detergent based protocol. Samples from the mixing bowl, dispense area, and drink were taken over a 19-wk period and enumerated using plate count agar. Bacillus cereus was identified using biochemical methods. Vended drinks were sampled at 0, 3, 6, and 9 min after vending; the hot chocolate powder was also sampled. Over the 1st 8 wk, a significant increase in the microbial load of the machine components was observed. By the end of the study, levels within the vended drink had also increased significantly. Inactivation of the automatic flush over a subsequent 5-wk period led to a statistically but not operationally significant increase in the microbial load of the dispense area and vended drink. The simple weekly clean had a significant impact on the microbial load of the machine components and the vended drink. This study demonstrated that a weekly, detergent-based cleaning protocol was sufficient to maintain the microbial population of the mixing bowl and dispense point in a quasi-steady state below 3.5 log CFU/cm2 ensuring that the microbial load of the vended drinks was maintained below 3.4 log CFU/mL. The microbial load of the drinks showed no significant changes over 9 min after vending, suggesting only spores are present in the final product. PMID:17995650

  4. Effect of fly ash application on soil microbial response and heavy metal accumulation in soil and rice plant.

    PubMed

    Nayak, A K; Raja, R; Rao, K S; Shukla, A K; Mohanty, Sangita; Shahid, Mohammad; Tripathi, R; Panda, B B; Bhattacharyya, P; Kumar, Anjani; Lal, B; Sethi, S K; Puri, C; Nayak, D; Swain, C K

    2015-04-01

    Fly ash (FA), a byproduct of coal combustion in thermal power plants, has been considered as a problematic solid waste and its safe disposal is a cause of concern. Several studies proposed that FA can be used as a soil additive; however its effect on microbial response, soil enzymatic activities and heavy metal accumulation in soil and grain of rice (cv. Naveen) to fly ash (FA) application was studied in a pot experiment during dry season 2011 in an Inceptisol. Fly ash was applied at a rate of zero per cent (FS), five per cent (FA5), ten per cent (FA10), twenty per cent (FA20), 40 per cent (FA40) and 100 per cent (FA100) on soil volume basis with nitrogen (N), phosphorus (P) and potassium (K) (40:20:20mg N:P:Kkg(-1) soil) with six replications. Heavy metals contents in soil and plant parts were analysed after harvest of crop. On the other hand, microbial population and soil enzymatic activities were analysed at panicle initiation stage (PI, 65 days after transplanting) of rice. There was no significant change in the concentration of zinc (Zn), iron (Fe), copper (Cu), manganese (Mn), cadmium (Cd) and chromium (Cr) with application of fly ash up to FA10. However, at FA100 there was significant increase of all metals concentration in soil than other treatments. Microorganisms differed in their response to the rate of FA application. Population of both fungi and actinomycetes decreased with the application of fly ash, while aerobic heterotrophic bacterial population did not change significantly up to FA40. On the other hand, total microbial activity measured in terms of Fluorescein diacetate (FDA) assay, and denitrifiers showed an increased trend up to FA40. However, activities of both alkaline and acid phosphatase were decreased with the application of FA. Application of FA at lower levels (ten to twenty per cent on soil volume basis) in soil enhanced micronutrients content, microbial activities and crop yield. PMID:24836933

  5. Long- and short-term temperature responses of microbially-mediated boreal soil organic matter transformations

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

    Microorganisms use exoenzymes to decay soil organic matter into assimilable substrates, some of which are transformed into CO2. Microbial CO2 efflux contributes up to 60% of soil respiration, a feature that can change with temperature due to altered exoenzyme activities (short-term) and microbial communities producing different exoenzymes (longer-term). Often, however, microbial temperature responses are masked by factors that also change with temperature in soil, making accurate projections of microbial CO2 efflux with warming challenging. Using soils along a natural climate gradient similar in most respects except for temperature regime (Newfoundland Labrador Boreal Ecosystem Latitudinal Transect), we investigated short-vs. long-term temperature responses of microbially-mediated organic matter transformations. While incubating soils at 5, 15, and 25°C for 84 days, we measured exoenzyme activities, CO2 efflux rates and biomass, and extracted DNA at multiple times. We hypothesized that short-term, temperature-induced increases in exoenzyme activities and CO2 losses would be smaller in soils from warmer regions, because microbes presumably adapted to warmer regions should use assimilable substrates more efficiently and thus produce exoenzymes at a lower rate. While incubation temperature generally induced greater exoenzyme activities (p<0.001), exoenzymes' temperature responses depended on enzymes and regions (p<0.001). Rate of CO2 efflux was affected by incubation temperature (P<0.001), but not by region. Microbial biomass and DNA sequencing will reveal how microbial community abundance and composition change with short-vs. longer-term temperature change. Though short-term microbial responses to temperature suggest higher CO2 efflux and thus lower efficiency of resource use with warming, longer-term adaptations of microbial communities to warmer climates remain unknown; this work helps fill that knowledge gap.

  6. Analysis of the respiratory response of soil microbial biomass to different substrates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The criticism of the microbial biomass analysis using respiratory response to glucose has centered on the fact that only glucose sensitive organisms will respond. Thus only glucose utilizing organisms will contribute to the respiration response. In addition, all of the respiration response does no...

  7. Microbial populations stimulated for hexavalent uranium reduction in uranium mine sediment.

    SciTech Connect

    Suzuki, Y.; Kelly, S. D.; Kemner, K. M.; Banfield, J. F.; Environmental Research; Univ. of Wisconsin-Madison; Univ. of California-Berkeley

    2003-03-01

    Uranium-contaminated sediment and water collected from an inactive uranium mine were incubated anaerobically with organic substrates. Stimulated microbial populations removed U almost entirely from solution within 1 month. X-ray absorption near-edge structure analysis showed that U(VI) was reduced to U(IV) during the incubation. Observations by transmission electron microscopy, selected area diffraction pattern analysis, and energy-dispersive X-ray spectroscopic analysis showed two distinct types of prokaryotic cells that precipitated only a U(IV) mineral uraninite (UO{sub 2}) or both uraninite and metal sulfides. Prokaryotic cells associated with uraninite and metal sulfides were inferred to be sulfate-reducing bacteria. Phylogenetic analysis of 16S ribosomal DNA obtained from the original and incubated sediments revealed that microbial populations were changed from microaerophilic Proteobacteria to anaerobic low-G+C gram-positive sporeforming bacteria by the incubation. Forty-two out of 94 clones from the incubated sediment were related to sulfate-reducing Desulfosporosinus spp., and 23 were related to fermentative Clostridium spp. The results suggest that, if in situ bioremediation were attempted in the uranium mine ponds, Desulfosporosinus spp. would be a major contributor to U(VI) and sulfate reduction and Clostridium spp. to U(VI) reduction.

  8. Microbial Populations Stimulated for Hexavalent Uranium Reduction in Uranium Mine Sediment

    PubMed Central

    Suzuki, Yohey; Kelly, Shelly D.; Kemner, Kenneth M.; Banfield, Jillian F.

    2003-01-01

    Uranium-contaminated sediment and water collected from an inactive uranium mine were incubated anaerobically with organic substrates. Stimulated microbial populations removed U almost entirely from solution within 1 month. X-ray absorption near-edge structure analysis showed that U(VI) was reduced to U(IV) during the incubation. Observations by transmission electron microscopy, selected area diffraction pattern analysis, and energy-dispersive X-ray spectroscopic analysis showed two distinct types of prokaryotic cells that precipitated only a U(IV) mineral uraninite (UO2) or both uraninite and metal sulfides. Prokaryotic cells associated with uraninite and metal sulfides were inferred to be sulfate-reducing bacteria. Phylogenetic analysis of 16S ribosomal DNA obtained from the original and incubated sediments revealed that microbial populations were changed from microaerophilic Proteobacteria to anaerobic low-G+C gram-positive sporeforming bacteria by the incubation. Forty-two out of 94 clones from the incubated sediment were related to sulfate-reducing Desulfosporosinus spp., and 23 were related to fermentative Clostridium spp. The results suggest that, if in situ bioremediation were attempted in the uranium mine ponds, Desulfosporosinus spp. would be a major contributor to U(VI) and sulfate reduction and Clostridium spp. to U(VI) reduction. PMID:12620814

  9. Temporal variation of microbial population in a thermophilic biofilter for SO₂ removal.

    PubMed

    Zhang, Jingying; Li, Lin; Liu, Junxin

    2016-01-01

    The performance of a biofilter relies on the activity of microorganisms during the gas contaminant treatment process. In this study, SO2 was treated using a laboratory-scale biofilter packed with polyurethane foam cubes (PUFC), on which thermophilic desulfurization bacteria were attached. The thermophilic biofilter effectively reduced SO2 within 10months of operation time, with a maximum elimination capacity of 48.29 g/m(3)/hr. Temporal shifts in the microbial population in the thermophilic biofilter were determined through polymerase chain reaction-denaturing gradient gel electrophoresis and deoxyribonucleic acid (DNA) sequence analysis. The substrate species and environmental conditions in the biofilter influenced the microbial population. Oxygen distribution in the PUFC was analyzed using a microelectrode. When the water-containing rate in PUFC was over 98%, the oxygen distribution presented aerobic-anoxic-aerobic states along the test route on the PUFC. The appearance of sulfate-reducing bacteria was caused by the anaerobic conditions and sulfate formation after 4months of operation. PMID:26899638

  10. Effects of different sources of physically effective fiber on rumen microbial populations.

    PubMed

    Shaw, C N; Kim, M; Eastridge, M L; Yu, Z

    2016-03-01

    Physically effective fiber is needed by dairy cattle to prevent ruminal acidosis. This study aimed to examine the effects of different sources of physically effective fiber on the populations of fibrolytic bacteria and methanogens. Five ruminally cannulated Holstein cows were each fed five diets differing in physically effective fiber sources over 15 weeks (21 days/period) in a Latin Square design: (1) 44.1% corn silage, (2) 34.0% corn silage plus 11.5% alfalfa hay, (3) 34.0% corn silage plus 5.1% wheat straw, (4) 36.1% corn silage plus 10.1% wheat straw, and (5) 34.0% corn silage plus 5.5% corn stover. The impact of the physically effective fiber sources on total bacteria and archaea were examined using denaturing gradient gel electrophoresis. Specific real-time PCR assays were used to quantify total bacteria, total archaea, the genus Butyrivibrio, Fibrobacter succinogenes, Ruminococcus albus, Ruminococcus flavefaciens and three uncultured rumen bacteria that were identified from adhering ruminal fractions in a previous study. No significant differences were observed among the different sources of physical effective fiber with respect to the microbial populations quantified. Any of the physically effective fiber sources may be fed to dairy cattle without negative impact on the ruminal microbial community. PMID:26365790

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

    PubMed Central

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

    2015-01-01

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

  12. 2010 MICROBIAL STRESS RESPONSE GORDON RESEARCH CONFERENCE, JULY 18-23, 2010

    SciTech Connect

    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. A 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.

  13. Microbial Biomass and Population Densities of Non-Sorted Circles in High Arctic Ecosystems

    NASA Astrophysics Data System (ADS)

    Rivera-Figueroa, F.; González, G.; Gould, W. A.; Cantrell, S.; Pérez, J.

    2006-12-01

    Non-sorted circles are small patterned-ground features that occur in arctic soils as a result of intensive frost heave action. This tundra feature has been extensively described. However, little is known about the ecological relationships between this pattern and above- and belowground organisms. In this study, we compare the biomass and populaton densities of microbes in non-sorted circles and the vegetated surrounding soils (inter-circles) in the High Arctic. We collected soil samples during the summer of 2004 and 2005 on Banks and Prince Patrick and Ellef Ringnes Islands, Canada. Soil samples (0-10 cm) were gathered from non- sorted circles and inter-circles along a topographic sequence: dry (ridge), mesic (mid slope) and wet (valley) and along three transects in zonal (mesic) sites on each island. We estimated total microbial biomass and bacterial population densities using substrate induce respiration (SIR) and the most probable number method (MPN), respectively. We also isolated soil fungi using Rose Bengal and Saboraud Dextrose culture media. We are in the process of analyzing the catena samples using a terminal restriction fragment length polymorphism (TRFLP) technique of PCR-amplified 16S rRNA. Based on the SIR trials, the average microbial biomass at the mid slope position in the Banks site (Green Cabin) was 0.49 mg C g-1 dry soil in the non- sorted circles and 0.95 mg C g-1 dry soil in the inter-circles. At Prince Patrick Island (Mould Bay) the microbial biomass was 0.54 mg C g-1 dry soil in the non-sorted circles and 0.74 mg C g-1 dry soil in the inter-circles. In Ellef Ringnes (Isachsen) the microbial biomass was 0.09 mg C g-1 dry soil in the non- sorted circles and 0.14 mg C g-1 dry soil in the inter-circles. At the mesic site at Green Cabin, bacteria vary from 2.92 x 106 cell g-1 dry soil in the non-sorted circles to 6.74 x 106 cell g-1 dry soil in the inter-circles. At Mould Bay the range was 7.67 x 105 cells g-1 dry soil in the non-sorted circles

  14. Specific microbial populations thrive under fluctuating redox conditions in tropical soils

    NASA Astrophysics Data System (ADS)

    Deangelis, K. M.; Silver, W. L.; Thompson, A.; Firestone, M. K.

    2008-12-01

    The highly weathered soils of upland humid tropical forests are characterized by rapidly fluctuating redox conditions, dominated by Fe-oxide mineralogy, and have relatively low sulfate availability. To assess how fluctuating redox conditions and accompanying biogeochemistry impact microbial community structure and function, we collected soil cores from the Luquillo LTER forest in Puerto Rico and incubated them for 32 days under one of three redox regimes: static oxic, static anoxic, and 4-day fluctuating redox. Over this time course we measured CO2, CH4, and N2O production, amorphous iron and Fe(II), and microbial community structure by high density microarray (PhyloChip) analysis. Static oxic, anoxic, and fluctuating redox soils all had statistically indistinguishable respiration rates over the course of the experiment. Fluctuating redox conditions permitted simultaneous methanogenesis, N2O production, and iron reduction, all accompanied by steady CO2 production. We analyzed the standing and active microbial community using the 16S ribosomal DNA and RNA biomarkers, identifying 2489 taxa in these soils. Ordination analysis showed significant separation between the active (RNA-based) and standing (DNA-based) communities, with much more variation in the active community compared to the standing community. Fluctuating redox conditions maintained a microbial community structure similar to that of the pre-incubation samples, while static anaerobic conditions had the most profound effect on the communities. Finally, there was considerable overlap between the taxa that were the most highly correlated with production of CH4 and Fe(II). Association of groups of taxa with specific biogeochemical processes begins to identify organisms potentially responsible for field biogeochemical processing.

  15. Water regime history drives responses of soil Namib Desert microbial communities to wetting events

    PubMed Central

    Frossard, Aline; Ramond, Jean-Baptiste; Seely, Mary; Cowan, Don A.

    2015-01-01

    Despite the dominance of microorganisms in arid soils, the structures and functional dynamics of microbial communities in hot deserts remain largely unresolved. The effects of wetting event frequency and intensity on Namib Desert microbial communities from two soils with different water-regime histories were tested over 36 days. A total of 168 soil microcosms received wetting events mimicking fog, light rain and heavy rainfall, with a parallel “dry condition” control. T-RFLP data showed that the different wetting events affected desert microbial community structures, but these effects were attenuated by the effects related to the long-term adaptation of both fungal and bacterial communities to soil origins (i.e. soil water regime histories). The intensity of the water pulses (i.e. the amount of water added) rather than the frequency of wetting events had greatest effect in shaping bacterial and fungal community structures. In contrast to microbial diversity, microbial activities (enzyme activities) showed very little response to the wetting events and were mainly driven by soil origin. This experiment clearly demonstrates the complexity of microbial community responses to wetting events in hyperarid hot desert soil ecosystems and underlines the dynamism of their indigenous microbial communities. PMID:26195343

  16. Water regime history drives responses of soil Namib Desert microbial communities to wetting events.

    PubMed

    Frossard, Aline; Ramond, Jean-Baptiste; Seely, Mary; Cowan, Don A

    2015-01-01

    Despite the dominance of microorganisms in arid soils, the structures and functional dynamics of microbial communities in hot deserts remain largely unresolved. The effects of wetting event frequency and intensity on Namib Desert microbial communities from two soils with different water-regime histories were tested over 36 days. A total of 168 soil microcosms received wetting events mimicking fog, light rain and heavy rainfall, with a parallel "dry condition" control. T-RFLP data showed that the different wetting events affected desert microbial community structures, but these effects were attenuated by the effects related to the long-term adaptation of both fungal and bacterial communities to soil origins (i.e. soil water regime histories). The intensity of the water pulses (i.e. the amount of water added) rather than the frequency of wetting events had greatest effect in shaping bacterial and fungal community structures. In contrast to microbial diversity, microbial activities (enzyme activities) showed very little response to the wetting events and were mainly driven by soil origin. This experiment clearly demonstrates the complexity of microbial community responses to wetting events in hyperarid hot desert soil ecosystems and underlines the dynamism of their indigenous microbial communities. PMID:26195343

  17. Water regime history drives responses of soil Namib Desert microbial communities to wetting events

    NASA Astrophysics Data System (ADS)

    Frossard, Aline; Ramond, Jean-Baptiste; Seely, Mary; Cowan, Don A.

    2015-07-01

    Despite the dominance of microorganisms in arid soils, the structures and functional dynamics of microbial communities in hot deserts remain largely unresolved. The effects of wetting event frequency and intensity on Namib Desert microbial communities from two soils with different water-regime histories were tested over 36 days. A total of 168 soil microcosms received wetting events mimicking fog, light rain and heavy rainfall, with a parallel “dry condition” control. T-RFLP data showed that the different wetting events affected desert microbial community structures, but these effects were attenuated by the effects related to the long-term adaptation of both fungal and bacterial communities to soil origins (i.e. soil water regime histories). The intensity of the water pulses (i.e. the amount of water added) rather than the frequency of wetting events had greatest effect in shaping bacterial and fungal community structures. In contrast to microbial diversity, microbial activities (enzyme activities) showed very little response to the wetting events and were mainly driven by soil origin. This experiment clearly demonstrates the complexity of microbial community responses to wetting events in hyperarid hot desert soil ecosystems and underlines the dynamism of their indigenous microbial communities.

  18. Soil Bacteria Population Dynamics Following Stimulation for Ureolytic Microbial-Induced CaCO3 Precipitation.

    PubMed

    Gat, Daniella; Ronen, Zeev; Tsesarsky, Michael

    2016-01-19

    Microbial-induced CaCO3 precipitation (MICP) via urea-hydrolysis (ureolysis) is an emerging soil improvement technique for various civil engineering and environmental applications. In-situ application of MICP in soils is performed either by augmenting the site with ureolytic bacteria or by stimulating indigenous ureolytic bacteria. Both of these approaches may lead to changes in the indigenous bacterial population composition and to the accumulation of large quantities of ammonium. In this batch study, effective ureolysis was stimulated in coastal sand from a semiarid environment, with low initial ureolytic bacteria abundance. Two different carbon sources were used: yeast-extract and molasses. No ureolysis was observed in their absence. Ureolysis was achieved using both carbon sources, with a higher rate in the yeast-extract enrichment resulting from increased bacterial growth. The changes to the indigenous bacterial population following biostimulation of ureolysis were significant: Bacilli class abundancy increased from 5% in the native sand up to 99% in the yeast-extract treatment. The sand was also enriched with ammonium-chloride, where ammonia-oxidation was observed after 27 days, but was not reflected in the bacterial population composition. These results suggest that biostimulation of ureolytic bacteria can be applied even in a semiarid and nutrient-poor environment using a simple carbon source, that is, molasses. The significant changes to bacterial population composition following ureolysis stimulation could result in a decrease in trophic activity and diversity in the treated site, thus they require further attention. PMID:26689904

  19. Microbial population dynamics during fed-batch operation of commercially available garbage composters.

    PubMed

    Narihiro, T; Abe, T; Yamanaka, Y; Hiraishi, A

    2004-09-01

    Microbial populations in terms of quantity, quality, and activity were monitored during 2 months of start-up operation of commercially available composters for fed-batch treatment of household biowaste. All the reactors, operated at a waste-loading rate of 0.7 kg day(-1) (wet wt), showed a mass reduction efficiency of 88-93%. The core temperature in the reactors fluctuated between 31 degrees C and 58 degrees C due to self-heating. The pH declined during the early stage of operation and steadied at pH 7.4-9.3 during the fully acclimated stage. The moisture content was 48-63% early in the process and 30-40% at the steady state. Both direct total counts and plate counts of bacteria increased via two phases (designated phases I, II) and reached an order of magnitude of 10(11) cells g(-1) (dry wt) at the steady state. Microbial community changes during the start-up period were studied by culture-independent quinone profiling and denatured gradient gel electrophoresis (DGGE) of PCR-amplified 16S rDNA. In all the reactors, ubiquinones predominated during phase I, whereas partially saturated menaquinones became predominant during phase II. This suggested that there was a drastic population shift from ubiquinone-containing Proteobacteria to Actinobacteria during the start-up period. The DGGE analysis of the bacterial community in one of the reactors also demonstrated a drastic population shift during phase I and the predominance of members of the phyla Proteobacteria and Bacteroidetes during the overall period. But this molecular analysis failed to detect actinobacterial clones from the reactor at any stage. PMID:15480624

  20. Low-frequency electrical response to microbial induced sulfide precipitation

    NASA Astrophysics Data System (ADS)

    Ntarlagiannis, Dimitrios; Williams, Kenneth Hurst; Slater, Lee; Hubbard, Susan

    2005-12-01

    We investigated the sensitivity of low-frequency electrical measurements to microbe-induced metal sulfide precipitation. Three identical sand-packed monitoring columns were used; a geochemical column, an electrical column and a control column. In the first experiment, continuous upward flow of nutrients and metals in solution was established in each column. Cells of Desulfovibrio vulgaris (D. vulgaris) were injected into the center of the geochemical and electrical columns. Geochemical sampling and post-experiment destructive analysis showed that microbial induced sulfate reduction led to metal precipitation on bacteria cells, forming motile biominerals. Precipitation initially occurred in the injection zone, followed by chemotactic migration of D. vulgaris and ultimate accumulation around the nutrient source at the column base. Results from this experiment conducted with metals show (1) polarization anomalies, up to 14 mrad, develop at the bacteria injection and final accumulation areas, (2) the onset of polarization increase occurs concurrently with the onset of lactate consumption, (3) polarization profiles are similar to calculated profiles of the rate of lactate consumption, and (4) temporal changes in polarization and conduction correlate with a geometrical rearrangement of metal-coated bacterial cells. In a second experiment, the same biogeochemical conditions were established except that no metals were added to the flow solution. Polarization anomalies were absent when the experiment was replicated without metals in solution. We therefore attribute the polarization increase observed in the first experiment to a metal-fluid interfacial mechanism that develops as metal sulfides precipitate onto microbial cells and form biominerals. Temporal changes in polarization and conductivity reflect changes in (1) the amount of metal-fluid interfacial area, and (2) the amount of electronic conduction resulting from microbial growth, chemotactic movement and final

  1. Soil microbial response to photo-degraded C60 fullerenes.

    PubMed

    Berry, Timothy D; Clavijo, Andrea P; Zhao, Yingcan; Jafvert, Chad T; Turco, Ronald F; Filley, Timothy R

    2016-04-01

    Recent studies indicate that while unfunctionalized carbon nanomaterials (CNMs) exhibit very low decomposition rates in soils, even minor surface functionalization (e.g., as a result of photochemical weathering) may accelerate microbial decay. We present results from a C60 fullerene-soil incubation study designed to investigate the potential links between photochemical and microbial degradation of photo-irradiated C60. Irradiating aqueous (13)C-labeled C60 with solar-wavelength light resulted in a complex mixture of intermediate products with decreased aromaticity. Although addition of irradiated C60 to soil microcosms had little effect on net soil respiration, excess (13)C in the respired CO2 demonstrates that photo-irradiating C60 enhanced its degradation in soil, with ∼ 0.78% of 60 day photo-irradiated C60 mineralized. Community analysis by DGGE found that soil microbial community structure was altered and depended on the photo-treatment duration. These findings demonstrate how abiotic and biotic transformation processes can couple to influence degradation of CNMs in the natural environment. PMID:26774781

  2. Distribution of microbial populations and their relationship with environmental variables in the North Yellow Sea, China

    NASA Astrophysics Data System (ADS)

    Bai, Xiaoge; Wang, Min; Liang, Yantao; Zhang, Zhifeng; Wang, Fang; Jiang, Xuejiao

    2012-03-01

    In order to understand the large-scale spatial distribution characteristics of picoplankton, nanophytoplankton and virioplankton and their relationship with environmental variables in coastal and offshore waters, flow cytometry (FCM) was used to analyze microbial abundance of samples collected in summer from four depths at 36 stations in the North Yellow Sea (NYS). The data revealed spatial heterogeneity in microbial populations in the offshore and near-shore waters of the NYS during the summer. For the surface layer, picoeukaryotes were abundant in the near-shore waters, Synechococcus was abundant in the offshore areas, and bacterial and viral abundances were high in the near-shore waters around the Liaodong peninsula. In the near-shore waters, no significant vertical variation of picophytoplankton (0.2-2μm) abundance was found. However, the nanophytoplankton abundance was higher in the upper layers (from the surface to 10 m depth) than in the bottom layer. For the offshore waters, both pico- and nanophytoplankton (2-20μm) abundance decreased sharply with depth in the North Yellow Sea Cold Water Mass (NYSCWM). But, for the vertical distribution of virus and bacteria abundance, no significant variation was observed in both near-shore and offshore waters. Autotrophic microbes were more sensitive to environmental change than heterotrophic microbes and viruses. Viruses showed a positive correlation with bacterial abundance, suggesting that the bacteriophage might be prominent for virioplankton (about 0.45μm) in summer in the NYS and that viral abundance might play an important role in microbial loop functions.

  3. High throughput sequencing reveals distinct microbial populations within the mucosal and luminal niches in healthy individuals

    PubMed Central

    Ringel, Yehuda; Maharshak, Nitsan; Ringel-Kulka, Tamar; Wolber, Elizabeth Ashley; Sartor, R Balfour; Carroll, Ian M

    2015-01-01

    Background: The intestinal microbiota is associated with human health and diseases. The luminal microbiota (LM) and the mucosal-associated microbiota (MAM) are 2 distinct ecosystems with different metabolic and immunological functions. Aim: To characterize the intestinal LM and MAM in humans using high throughput sequencing of the 16S rRNA gene. Methods: Fresh fecal samples and distal colonic mucosal biopsies collected from 24 healthy subjects before (fecal) and during (mucosa) a flexible sigmoidoscopy of an un-prepared bowel. High throughput sequencing of the 16S rRNA gene was used to characterize bacterial communities. Sequences were processed using the QIIME pipeline. Results: LM and MAM populations were significantly different (ANOSIM: R = 0.49, P = 0.001). The LM displayed tighter clustering compared to the MAM (average weighted UniFrac distances 0.27 ± 0.05 vs. 0.43 ± 0.09, P < 0.001, respectively), and showed higher diversity (Shannon diversity index: 4.96 ± 0.37 vs 4.14 ± 0.56, respectively, P < 0.001). The dominant phyla in the LM and MAM were significantly different: Firmicutes (41.4% vs. 29.1%, FDR < 0.0001, respectively), Bacteroidetes (20.2% vs. 26.3%, FDR < 0.05, respectively), Actinobacteria (22% vs. 12.6%, FDR < 0.0001, respectively) and Proteobacteria (9.3% vs. 19.3%, FDR < 0.0001, respectively). The abundance of 56 genera differed significantly (FDR < 0.1) between the 2 niches. All of the genera in the fecal microbiota were present in the MAM while 10 genera were found to be unique to the MAM. Conclusion: The LM and MAM are distinct microbial ecosystems that differ significantly from each other in microbial diversity and composition. These two microbial niches should be investigated independently to better understand the role of the intestinal microbiota in health and disease. PMID:25915459

  4. The Abundance and Activity of Nitrate-Reducing Microbial Populations in Estuarine Sediments

    NASA Astrophysics Data System (ADS)

    Cardarelli, E.; Francis, C. A.

    2014-12-01

    Estuaries are productive ecosystems that ameliorate nutrient and metal contaminants from surficial water supplies. At the intersection of terrestrial and aquatic environments, estuarine sediments host major microbially-mediated geochemical transformations. These include denitrification (the conversion of nitrate to nitrous oxide and/or dinitrogen) and dissimilatory nitrate reduction to ammonium (DNRA). Denitrification has historically been seen as the predominant nitrate attenuation process and functions as an effective sink for nitrate. DNRA has previously been believed to be a minor nitrate reduction process and transforms nitrate within the ecosystem to ammonium, a more biologically available N species. Recent studies have compared the two processes in coastal environments and determined fluctuating environmental conditions may suppress denitrification, supporting an increased role for DNRA in the N cycle. Nitrate availability and salinity are factors thought to influence the membership of the microbial communities present, and the nitrate reduction process that predominates. The aim of this study is to investigate how nitrate concentration and salinity alter the transcript abundances of N cycling functional gene markers for denitrification (nirK, nirS) and DNRA (nrfA) in estuarine sediments at the mouth of the hypernutrified Old Salinas River, CA. Short-term whole core incubations amended with artificial freshwater/artificial seawater (2 psu, 35 psu) and with varying NO3- concentrations (200mM, 2000mM) were conducted to assess the activity as well as the abundance of the nitrate-reducing microbial populations present. Gene expression of nirK, nirS, and nrfA at the conclusion of the incubations was quantified using reverse transcription quantitative polymerase chain reaction (RT-qPCR). High abundances of nirK, nirS, and nrfA under particular conditions coupled with the resulting geochemical data ultimately provides insight onto how the aforementioned factors

  5. Acinetobacter, Aeromonas, and Trichococcus populations dominate the microbial community within urban sewer infrastructure

    PubMed Central

    VandeWalle, J. L.; Goetz, G.W.; Huse, S.M.; Morrison, H. G.; Sogin, M.L.; Hoffmann, R.G.; Yan, K.; McLellan, S.L.

    2012-01-01

    We evaluated the population structure and temporal dynamics of the dominant community members within sewage influent from two wastewater treatment plants (WWTPs) in Milwaukee, WI. We generated >1.1M bacterial pyrotag sequences from the V6 hypervariable region of 16S rRNA genes from 38 influent samples and two samples taken upstream in the sanitary sewer system. Only a small fraction of pyrotags from influent samples (~15%) matched sequences from human fecal samples. The fecal components of the sewage samples included enriched pyrotag populations from Lactococcus and Enterobacteriaceae relative to their fractional representation in human fecal samples. In contrast to the large number of distinct pyrotags that represent fecal bacteria such as Lachnospiraceae and Bacteroides, only one or two unique V6 sequences represented Acinetobacter, Trichococcus and Aeromonas, which collectively account for nearly 35% of the total sewage community. Two dominant Acinetobacter V6 pyrotags (designated Acineto tag 1 and Acineto tag 2) fluctuated inversely with a seasonal pattern over a 3-year period, suggesting two distinct Acinetobacter populations respond differently to ecological forcings in the system. A single nucleotide change in the V6 pyrotags accounted for the difference in these populations and corresponded to two phylogenically distinct clades based on full-length sequences. Analysis of wavelet functions, derived from a mathematical model of temporal fluctuations, demonstrated that other abundant sewer associated populations including Trichococcus and Aeromonas had temporal patterns similar to either Acineto tag 1 or Acineto tag 2. Populations with related temporal fluctuations were found to significantly correlate with the same WWTP variables (5-day BOD, flow, ammonia, total phosphorous, and suspended solids). These findings illustrate that small differences in V6 sequences can represent phylogenetically and ecologically distinct taxa. This work provides insight into

  6. 2009 MICROBIAL POPULATION BIOLOGY GORDON RESEARCH CONFERENCES JULY 19-24,2009

    SciTech Connect

    ANTHONY DEAN

    2009-07-24

    The 2009 Gordon Conference on Microbial Population Biology will cover a diverse range of cutting edge issues in the microbial sciences and beyond. Firmly founded in evolutionary biology and with a strongly integrative approach, past Conferences have covered a range of topics from the dynamics and genetics of adaptation to the evolution of mutation rate, community ecology, evolutionary genomics, altruism, and epidemiology. The 2009 Conference is no exception, and will include sessions on the evolution of infectious diseases, social evolution, the evolution of symbioses, experimental evolution, adaptive landscapes, community dynamics, and the evolution of protein structure and function. While genomic approaches continue to make inroads, broadening our knowledge and encompassing new questions, the conference will also emphasize the use of experimental approaches to test hypotheses decisively. As in the past, this Conference provides young scientists and graduate students opportunities to present their work in poster format and exchange ideas with leading investigators from a broad spectrum of disciplines. This meeting is never dull: some of the most significant and contentious issues in biology have been thrashed out here. The 2009 meeting will be no exception.

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

    PubMed

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

    2016-09-01

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

  8. Visualizing the population dynamics of microbial communities in the larval zebrafish gut

    NASA Astrophysics Data System (ADS)

    Parthasarathy, Raghuveer

    In each of our digestive tracts, trillions of microbes representing hundreds of different species colonize local environments, reproduce, and compete with one another. The resulting ecosystems influence many aspects their host's development and health. Little is known about how gut microbial communities vary in space and time: how they grow, fluctuate, and respond to various perturbations. To address this and investigate microbial colonization of the vertebrate gut, we apply light sheet fluorescence microscopy to a model system that combines a realistic in vivo environment with a high degree of experimental control: larval zebrafish with defined subsets of commensal bacterial species. Light sheet microscopy enables three-dimensional imaging with high resolution over the entire intestine, providing visualizations that would be difficult or impossible to achieve with other techniques. Quantitative analysis of image data enables measurement of bacterial abundances and distributions. I will describe this approach and focus especially on recent experiments in which a colonizing bacterial species is challenged by the invasion of a second species, which leads to the decline of the first group. Imaging reveals dramatic population collapses that differentially affect the two species due to their different biogeographies and morphologies. The collapses are driven by the peristaltic motion of the zebrafish intestine, indicating that the physical activity of the host environment can play a major role in mediating inter-species competition. role in mediating inter-species competition. Supported by the National Science Foundation under Grant No. 0922951 and the National Institutes of Health under Award Number 1P50GM098911.

  9. Microbial population, activity, and phylogenetic diversity in the subseafloor core sediment from the Sea of Okhotsk

    NASA Astrophysics Data System (ADS)

    Inagaki, F.; Suzuki, M.; Takai, K.; Nealson, K. H.; Horikoshi, K.

    2002-12-01

    Subseafloor environments has already been recognized as the largest biosphere on the planet Earth, however, the microbial diversity and activity has been still poorly understood, even in their impacts on biogeochemical processes, tectonic settings, and paleoenvironmental events. We demonstrate here the evaluation of microbial community structure and active habitats in deeply buried cold marine sediments collected from the Sea of Okhotsk by a combined use of molecular ecological surveys and culturing assays. The piston core sediment (MD01-2412) was collected by IMAGES (International Marine Global Change Study) Project from the southeastern Okhotsk Sea, June 2001. The total recovered length was about 58m. The lithology of the core sediment was mainly constructed from pelagic clay (PC) and volcanic ash layers (Ash). We collected aseptically the most inside core parts from 16 sections at different depths for microbiological study. The direct count of DAPI-stained cells revealed that the cells in Ash samples were present 1.2 to 2.2 times higher than in PC samples. The quantitative-PCR of 16S rDNA between bacterial and archaeal rDNA suggested that the increased population density in Ash layers was caused by the bacterial components. We studied approximately 650 and 550 sequences from bacterial and archaeal rDNA clone libraries, respectively. The similarity and phylogenetic analyses revealed that the microbial community structures were apparently different between in Ash layers and PC samples. From bacterial rDNA clone libraries, the members within gamma-Proteobacteria such as genera Halomonas, Shewanella, Psychromonas and Methylosinus were predominantly detected in Ash layers whereas the Dehalococcoides group and delta-Proteobacteria were major bacterial components in PC samples. From archaeal libraries, the sequences from Ash and PC samples were affiliated into the clusters represented by the environmental sequences obtained from terrestrial and deep-sea environments

  10. Effect of feed starvation on side-stream anammox activity and key microbial populations.

    PubMed

    Reeve, Petra J; Mouilleron, Irina; Chuang, Hui-Ping; Thwaites, Ben; Hyde, Kylie; Dinesh, Nirmala; Krampe, Joerg; Lin, Tsair-Fuh; van den Akker, Ben

    2016-04-15

    The anaerobic ammonium oxidation (anammox) process is widely acknowledged to be susceptible to a wide range of environmental factors given the slow growth rate of the anammox bacteria. Surprisingly there is limited experimental data regarding the susceptibility of the anammox process to feed starvations which may be encountered in full-scale applications. Therefore, a study was established to investigate the impact of feed starvations on nitritation and anammox activity in a demonstration-scale sequencing batch reactor. Three starvation periods were trialled, lasting one fortnight (15 d), one month (33 d) and two months (62 d). Regardless of the duration of the starvation period, assessment of the ammonia removal performance demonstrated nitritation and anammox activity were reinstated within one day of recovery operation. Characterisation of the community structure using 16S rRNA and functional genes specific for nitrogen-related microbes showed there was no clear impact or shift in the microbial populations between starvation and recovery phases. PMID:26861222

  11. Comparative effects of Aroclor 1254 (polychlorinated biphenyls) and phenanthrene on glucose uptake by freshwater microbial populations.

    PubMed Central

    Sayler, G S; Lund, L C; Shiaris, M P; Sherrill, T W; Perkins, R E

    1979-01-01

    The effects of polychlorinated biphenyl (PCB) and phenanthrene stress on glucose uptake by natural microbial populations were examined by the heterotrophic potential technique. Temporal and spatial distributions in glucose uptake velocities were examined for natural samples as well as PCB- and phenanthrene-stressed samples. Statistical analysis indicated significant variability among the various samples. It was demonstrated that the environmental variables contributed significantly to the variability in uptake kinetics. Although general trends indicated a PCB-induced stimulation in uptake velocities, these trends were in part masked by sample variability. Data analysis indicated no statistically significant PCB or phenanthrene effect on either total glucose uptake velocities or the proportion of 14CO2 evolved, as compared to natural unstressed samples. PMID:114110

  12. Survey of microbial populations within Lake Michigan nearshore waters at two Chicago public beaches.

    PubMed

    Malki, Kema; Bruder, Katherine; Putonti, Catherine

    2015-12-01

    Lake Michigan is a critical resource for the residents of Chicago, providing drinking water to its 9+ million area residents. Along Chicago׳s 26 miles of public beaches the populous urban environment and this freshwater environment meet. While city-led monitoring initiatives investigate pathogenic bacteria in these nearshore waters, very little is known about other microbial species present. We collected surface water samples from two Chicago public beaches - Montrose Beach and 57th Street Beach - every ten days from June 5 through August 4, 2013 as well as once in early Fall (October 4, 2013). Sixteen bacterial communities in total were surveyed through targeted sequencing of the V4 16S rRNA gene. Taxa were identified using Mothur. Raw sequence data is available via NCBI׳s SRA database (part of BioProject PRJNA245802). OTU calls for each read are also available at our online repository: www.lakemichiganmicrobes.com/bacteria/. PMID:26958608

  13. Selective progressive response of soil microbial community to wild oat roots

    SciTech Connect

    DeAngelis, K.M.; Brodie, E.L.; DeSantis, T.Z.; Andersen, G.L.; Lindow, S.E.; Firestone, M.K.

    2008-10-01

    Roots moving through soil enact physical and chemical changes that differentiate rhizosphere from bulk soil, and the effects of these changes on soil microorganisms have long been a topic of interest. Use of a high-density 16S rRNA microarray (PhyloChip) for bacterial and archaeal community analysis has allowed definition of the populations that respond to the root within the complex grassland soil community; this research accompanies previously reported compositional changes, including increases in chitinase and protease specific activity, cell numbers and quorum sensing signal. PhyloChip results showed a significant change in 7% of the total rhizosphere microbial community (147 of 1917 taxa); the 7% response value was confirmed by16S rRNA T-RFLP analysis. This PhyloChip-defined dynamic subset was comprised of taxa in 17 of the 44 phyla detected in all soil samples. Expected rhizosphere-competent phyla, such as Proteobacteria and Firmicutes, were well represented, as were less-well-documented rhizosphere colonizers including Actinobacteria, Verrucomicrobia and Nitrospira. Richness of Bacteroidetes and Actinobacteria decreased in soil near the root tip compared to bulk soil, but then increased in older root zones. Quantitative PCR revealed {beta}-Proteobacteria and Actinobacteria present at about 10{sup 8} copies of 16S rRNA genes g{sup -1} soil, with Nitrospira having about 10{sup 5} copies g{sup -1} soil. This report demonstrates that changes in a relatively small subset of the soil microbial community are sufficient to produce substantial changes in function in progressively more mature rhizosphere zones.

  14. Microbial community responses to temperature increase the potential for soil carbon losses under climate change.

    NASA Astrophysics Data System (ADS)

    Hartley, Iain; Karhu, Kristiina; Auffret, Marc; Hopkins, David; Prosser, Jim; Singh, Brajesh; Subke, Jens-Arne; Wookey, Philip; Ågren, Göran

    2014-05-01

    There are concerns that global warming may stimulate decomposition rates in soils, with the extra CO2 released representing a positive feedback to climate change. However, there is growing recognition that adaptation of soil microbial communities to temperature changes may alter the potential rate of carbon release. Critically, recent studies have produced conflicting results in terms of whether the medium-term soil microbial community response to temperature reduces (compensatory thermal adaptation) or enhances (enhancing thermal adaptation) the instantaneous direct positive effects of temperature on microbial activity. This lack of understanding adds considerably to uncertainty in predictions of the magnitude and direction of carbon-cycle feedbacks to climate change. In this talk, I present results from one of the most extensive investigations ever undertaken into the role that microbial adaptation plays in controlling the temperature sensitivity of decomposition. Soils were collected from a range of ecosystem types, representing a thermal gradient from the Arctic to the Amazon. Our novel soil-cooling approach minimises issues associated with substrate depletion in warming studies, but still tests whether adaptation enhances or reduces the direct impact of temperature changes on microbial activity. We also investigated the mechanisms underlying changes in microbial respiration by quantifying changes in microbial community composition, microbial biomass, mass-specific activity, carbon-use efficiency, and enzyme activities. Our results indicate that enhancing responses are much more common than compensatory thermal acclimation, with the latter being observed in less than 10% of cases. However, identifying the mechanisms underlying enhancing and compensatory adaptation remained elusive. No consistent changes were observed in terms of mass-specific activity, biomass or enzyme activity, indicating that current theory is inadequate in explaining observed patterns

  15. Heterotrophic activity and biodegradation of labile and refractory compounds by groundwater and stream microbial populations.

    PubMed Central

    Ladd, T I; Ventullo, R M; Wallis, P M; Costerton, J W

    1982-01-01

    The bacteriology and heterotrophic activity of a stream and of nearby groundwater in Marmot Basin, Alberta, Canada, were studied. Acridine orange direct counts indicated that bacterial populations in the groundwater were greater than in the stream. Bacteria that were isolated from the groundwater were similar to species associated with soils. Utilization of labile dissolved organic material as measured by the heterotrophic potential technique with glutamic acid, phenylalanine, and glycolic acid as substrates was generally greater in the groundwater. In addition, specific activity indices for the populations suggested greater metabolic activity per bacterium in the groundwater. 14C-labeled lignocellulose, preferentially labeled in the lignin fraction by feeding Picea engelmannii [14C]phenylalanine, was mineralized by microorganisms in both the groundwater and the stream, but no more than 4% of the added radioactivity was lost as 14CO2 within 960 h. Up to 20% of [3'-14C]cinnamic acid was mineralized by microorganisms in both environments within 500 h. Both microbial populations appear to influence the levels of labile and recalcitrant dissolved organic material in mountain streams. PMID:7125651

  16. Range expansions transition from pulled to pushed waves with increasing cooperativity in an experimental microbial population

    NASA Astrophysics Data System (ADS)

    Gandhi, Saurabh; Yurtsev, Eugene; Korolev, Kirill; Gore, Jeff

    Range expansions are becoming more frequent due to environmental changes and rare long distance dispersal, often facilitated by anthropogenic activities. Simple models in theoretical ecology explain many emergent properties of range expansions, such as a constant expansion velocity, in terms of organism-level properties such as growth and dispersal rates. Testing these quantitative predictions in natural populations is difficult because of large environmental variability. Here, we used a controlled microbial model system to study range expansions of populations with and without intra-specific cooperativity. For non-cooperative growth, the expansion dynamics were dominated by population growth at the low-density front, which pulled the expansion forward. We found these expansions to be in close quantitative agreement with the classical theory of pulled waves by Fisher and Skellam, suitably adapted to our experimental system. However, as cooperativity increased, the expansions transitioned to being pushed, i.e. controlled by growth in the bulk as well as in the front. Although both pulled and pushed waves expand at a constant velocity and appear otherwise similar, their distinct dynamics leads to very different evolutionary consequences. Given the prevalence of cooperative growth in nature, understanding the effects of cooperativity is essential to managing invading species and understanding their evolution.

  17. Short-term precipitation exclusion alters microbial responses to soil moisture in a wet tropical forest.

    PubMed

    Waring, Bonnie G; Hawkes, Christine V

    2015-05-01

    Many wet tropical forests, which contain a quarter of global terrestrial biomass carbon stocks, will experience changes in precipitation regime over the next century. Soil microbial responses to altered rainfall are likely to be an important feedback on ecosystem carbon cycling, but the ecological mechanisms underpinning these responses are poorly understood. We examined how reduced rainfall affected soil microbial abundance, activity, and community composition using a 6-month precipitation exclusion experiment at La Selva Biological Station, Costa Rica. Thereafter, we addressed the persistent effects of field moisture treatments by exposing soils to a controlled soil moisture gradient in the lab for 4 weeks. In the field, compositional and functional responses to reduced rainfall were dependent on initial conditions, consistent with a large degree of spatial heterogeneity in tropical forests. However, the precipitation manipulation significantly altered microbial functional responses to soil moisture. Communities with prior drought exposure exhibited higher respiration rates per unit microbial biomass under all conditions and respired significantly more CO2 than control soils at low soil moisture. These functional patterns suggest that changes in microbial physiology may drive positive feedbacks to rising atmospheric CO2 concentrations if wet tropical forests experience longer or more intense dry seasons in the future. PMID:24889286

  18. Responses of soil microbial community to experimental warming and precipitation manipulation

    NASA Astrophysics Data System (ADS)

    Li, G.; Kim, S.; Park, M. J.; Han, S. H.; Lee, J.; Son, Y.

    2015-12-01

    An experimental nursery was established with two-year-old Pinus densiflora seedlings at Korea University to study soil microbial community responses to air warming (+3°C) and precipitation manipulation (-30% and +30%). Soil samplings were collected monthly from July to November, 2014. Substrate utilization profile of microbial community was examined using BIOLOG EcoPlate. Microbial community composition was assessed by high-throughput sequencing technology. The results showed that warming significantly affected the substrate utilization profile of microbial community (P<0.05), which labile substrates were degraded more quickly in warming plots than unwarmed plots. Only significant effects of warming on fungal community richness and abundance were observed (all P<0.05). Compared with unwarmed and precipitation control treatment, fungal community richness in the others were significantly decreased by 1.22%-15.27% (P<0.05), but community diversity in those treatments were slightly increased (P>0.05). In contrast, compared with unwarmed and precipitation control treatment, the bacterial community richness in the others were increased, but community abundance and diversity in those treatments were decreased (all P>0.05). These changes in microbial community structure resulted in the changes in community functional composition, which microbial metabolic functions were higher in warming plots than unwarmed plots. Since microorganisms differ in their susceptibility to stressors, changes in the soil environment affect the microbial community. Therefore, the results indicated that effects of warming and precipitation manipulation on soil microbial community might be related to warming and precipitation manipulation-induced changes in soil moisture. We suggested that shifts in the microbial community may be important implications for soil carbon and nitrogen dynamics in a warmer world. This study was supported by National Research Foundation of Korea (NRF-2013R1A1A2012242).

  19. Stream microbial diversity in response to environmental changes: review and synthesis of existing research

    PubMed Central

    Zeglin, Lydia H.

    2015-01-01

    The importance of microbial activity to ecosystem function in aquatic ecosystems is well established, but microbial diversity has been less frequently addressed. This review and synthesis of 100s of published studies on stream microbial diversity shows that factors known to drive ecosystem processes, such as nutrient availability, hydrology, metal contamination, contrasting land-use and temperature, also cause heterogeneity in bacterial diversity. Temporal heterogeneity in stream bacterial diversity was frequently observed, reflecting the dynamic nature of both stream ecosystems and microbial community composition. However, within-stream spatial differences in stream bacterial diversity were more commonly observed, driven specifically by different organic matter (OM) compartments. Bacterial phyla showed similar patterns in relative abundance with regard to compartment type across different streams. For example, surface water contained the highest relative abundance of Actinobacteria, while epilithon contained the highest relative abundance of Cyanobacteria and Bacteroidetes. This suggests that contrasting physical and/or nutritional habitats characterized by different stream OM compartment types may select for certain bacterial lineages. When comparing the prevalence of physicochemical effects on stream bacterial diversity, effects of changing metal concentrations were most, while effects of differences in nutrient concentrations were least frequently observed. This may indicate that although changing nutrient concentrations do tend to affect microbial diversity, other environmental factors are more likely to alter stream microbial diversity and function. The common observation of connections between ecosystem process drivers and microbial diversity suggests that microbial taxonomic turnover could mediate ecosystem-scale responses to changing environmental conditions, including both microbial habitat distribution and physicochemical factors. PMID:26042102

  20. Metagenomic analysis of permafrost microbial community response to thaw

    SciTech Connect

    Mackelprang, R.; Waldrop, M.P.; DeAngelis, K.M.; David, M.M.; Chavarria, K.L.; Blazewicz, S.J.; Rubin, E.M.; Jansson, J.K.

    2011-07-01

    We employed deep metagenomic sequencing to determine the impact of thaw on microbial phylogenetic and functional genes and related this data to measurements of methane emissions. Metagenomics, the direct sequencing of DNA from the environment, allows for the examination of whole biochemical pathways and associated processes, as opposed to individual pieces of the metabolic puzzle. Our metagenome analyses revealed that during transition from a frozen to a thawed state there were rapid shifts in many microbial, phylogenetic and functional gene abundances and pathways. After one week of incubation at 5°C, permafrost metagenomes converged to be more similar to each other than while they were frozen. We found that multiple genes involved in cycling of C and nitrogen shifted rapidly during thaw. We also constructed the first draft genome from a complex soil metagenome, which corresponded to a novel methanogen. Methane previously accumulated in permafrost was released during thaw and subsequently consumed by methanotrophic bacteria. Together these data point towards the importance of rapid cycling of methane and nitrogen in thawing permafrost.

  1. Effect of Plants Containing Secondary Compounds with Palm Oil on Feed Intake, Digestibility, Microbial Protein Synthesis and Microbial Population in Dairy Cows

    PubMed Central

    Anantasook, N.; Wanapat, M.; Cherdthong, A.; Gunun, P.

    2013-01-01

    The objective of this study was to determine the effect of rain tree pod meal with palm oil supplementation on feed intake, digestibility, microbial protein synthesis and microbial populations in dairy cows. Four, multiparous early-lactation Holstein-Friesian crossbred (75%) lactating dairy cows with an initial body weight (BW) of 405±40 kg and 36±8 DIM were randomly assigned to receive dietary treatments according to a 4×4 Latin square design. The four dietary treatments were un-supplementation (control), supplementation with rain tree pod meal (RPM) at 60 g/kg, supplementation with palm oil (PO) at 20 g/kg, and supplementation with RPM at 60 g/kg and PO at 20 g/kg (RPO), of total dry matter intake. The cows were offered concentrates, at a ratio of concentrate to milk production of 1:2, and chopped 30 g/kg of urea treated rice straw was fed ad libitum. The RPM contained condensed tannins and crude saponins at 88 and 141 g/kg of DM, respectively. It was found that supplementation with RPM and/or PO to dairy cows diets did not show negative effects on feed intake and ruminal pH and BUN at any times of sampling (p>0.05). However, RPM supplementation resulted in lower crude protein digestibility, NH3-N concentration and number of proteolytic bacteria. It resulted in greater allantoin absorption and microbial crude protein (p<0.05). In addition, dairy cows showed a higher efficiency of microbial N supply (EMNS) in both RPM and RPO treatments. Moreover, NDF digestibility and cellulolytic bacteria numbers were highest in RPO supplementation (p<0.05) while, supplementation with RPM and/or PO decreased the protozoa population in dairy cows. Based on this study, supplementation with RPM and/or PO in diets could improve fiber digestibility, microbial protein synthesis in terms of quantity and efficiency and microbial populations in dairy cows. PMID:25049855

  2. Effect of plants containing secondary compounds with palm oil on feed intake, digestibility, microbial protein synthesis and microbial population in dairy cows.

    PubMed

    Anantasook, N; Wanapat, M; Cherdthong, A; Gunun, P

    2013-06-01

    The objective of this study was to determine the effect of rain tree pod meal with palm oil supplementation on feed intake, digestibility, microbial protein synthesis and microbial populations in dairy cows. Four, multiparous early-lactation Holstein-Friesian crossbred (75%) lactating dairy cows with an initial body weight (BW) of 405±40 kg and 36±8 DIM were randomly assigned to receive dietary treatments according to a 4×4 Latin square design. The four dietary treatments were un-supplementation (control), supplementation with rain tree pod meal (RPM) at 60 g/kg, supplementation with palm oil (PO) at 20 g/kg, and supplementation with RPM at 60 g/kg and PO at 20 g/kg (RPO), of total dry matter intake. The cows were offered concentrates, at a ratio of concentrate to milk production of 1:2, and chopped 30 g/kg of urea treated rice straw was fed ad libitum. The RPM contained condensed tannins and crude saponins at 88 and 141 g/kg of DM, respectively. It was found that supplementation with RPM and/or PO to dairy cows diets did not show negative effects on feed intake and ruminal pH and BUN at any times of sampling (p>0.05). However, RPM supplementation resulted in lower crude protein digestibility, NH3-N concentration and number of proteolytic bacteria. It resulted in greater allantoin absorption and microbial crude protein (p<0.05). In addition, dairy cows showed a higher efficiency of microbial N supply (EMNS) in both RPM and RPO treatments. Moreover, NDF digestibility and cellulolytic bacteria numbers were highest in RPO supplementation (p<0.05) while, supplementation with RPM and/or PO decreased the protozoa population in dairy cows. Based on this study, supplementation with RPM and/or PO in diets could improve fiber digestibility, microbial protein synthesis in terms of quantity and efficiency and microbial populations in dairy cows. PMID:25049855

  3. Microbial nitrogen cycling response to forest-based bioenergy production.

    PubMed

    Minick, Kevan J; Strahm, Brian D; Fox, Thomas R; Sucre, Eric B; Leggett, Zakiya H

    2015-12-01

    Concern over rising atmospheric CO2 and other greenhouse gases due to fossil fuel combustion has intensified research into carbon-neutral energy production. Approximately 15.8 million ha of pine plantations exist across the southeastern United States, representing a vast land area advantageous for bioenergy production without significant landuse change or diversion of agricultural resources from food production. Furthermore, intercropping of pine with bioenergy grasses could provide annually harvestable, lignocellulosic biomass feedstocks along with production of traditional wood products. Viability of such a system hinges in part on soil nitrogen (N) availability and effects of N competition between pines and grasses on ecosystem productivity. We investigated effects of intercropping loblolly pine (Pinus taeda) with switchgrass (Panicum virgatum) on microbial N cycling processes in the Lower Coastal Plain of North Carolina, USA. Soil samples were collected from bedded rows of pine and interbed space of two treatments, composed of either volunteer native woody and herbaceous vegetation (pine-native) or pure switchgrass (pine-switchgrass) in interbeds. An in vitro 15N pool-dilution technique was employed to quantify gross N transformations at two soil depths (0-5 and 5-15 cm) on four dates in 2012-2013. At the 0-5 cm depth in beds of the pine-switchgrass treatment, gross N mineralization was two to three times higher in November and February compared to the pine-native treatment, resulting in increased NH4(+) availability. Gross and net nitrification were also significantly higher in February in the same pine beds. In interbeds of the pine-switchgrass treatment, gross N mineralization was lower from April to November, but higher in February, potentially reflecting positive effects of switchgrass root-derived C inputs during dormancy on microbial activity. These findings indicate soil N cycling and availability has increased in pine beds of the pine

  4. RELATIONSHIPS BETWEEN CULTURABLE SOIL MICROBIAL POPULATIONS AND GROSS NITROGEN TRANSFORMATION PROCESSES IN A CLAY LOAM SOIL ACROSS ECOSYSTEMS

    EPA Science Inventory

    The size and quality of soil organic matter (SOM) pool can vary between ecosystems and can affect many soil properties. The objective of this study was to examine the relationship between gross N transformation rates and microbial populations and to investigate the role that SOM...

  5. Soil microbial response to waste potassium silicate drilling fluid.

    PubMed

    Yao, Linjun; Naeth, M Anne; Jobson, Allen

    2015-03-01

    Potassium silicate drilling fluids (PSDF) are a waste product of the oil and gas industry with potential for use in land reclamation. Few studies have examined the influence of PSDF on abundance and composition of soil bacteria and fungi. Soils from three representative locations for PSDF application in Alberta, Canada, with clay loam, loam and sand textures were studied with applications of unused, used once and used twice PSDF. For all three soils, applying ≥40 m3/ha of used PSDF significantly affected the existing soil microbial flora. No microbiota was detected in unused PSDF without soil. Adding used PSDF to soil significantly increased total fungal and aerobic bacterial colony forming units in dilution plate counts, and anaerobic denitrifying bacteria numbers in serial growth experiments. Used PSDF altered bacterial and fungal colony forming unit ratios of all three soils. PMID:25766028

  6. Low-frequency Electrical Response to Microbial Induced Sulfide Precipitation

    SciTech Connect

    Ntarlagiannis, Dimitrios; Williams, Kenneth H.; Slater, Lee D.; Hubbard, Susan S.

    2005-11-19

    We investigated the sensitivity of low-frequency electrical measurements to microbeinduced metal sulfide precipitation. Three identical sand-packed monitoring columns were used; a geochemical column, an electrical column and a control column. In the first experiment, continuous upward flow of nutrients and metals in solution was established in each column. Cells of Desulfovibrio vulgaris (D. vulgaris) were injected into the center of the geochemical and electrical columns. Geochemical sampling and post-experiment destructive analysis showed that microbial induced sulfate reduction led to metal precipitation on bacteria cells, forming motile biominerals. Precipitation initially occurred in the injection zone, followed by chemotactic migration of D. vulgaris and ultimate accumulation around the nutrient source at the column base.

  7. Response of Microbial Soil Carbon Mineralization Rates to Oxygen Limitations

    NASA Astrophysics Data System (ADS)

    Keiluweit, M.; Denney, A.; Nico, P. S.; Fendorf, S. E.

    2014-12-01

    The rate of soil organic matter (SOM) mineralization is known to be controlled by climatic factors as well as molecular structure, mineral-organic associations, and physical protection. What remains elusive is to what extent oxygen (O2) limitations impact overall rates of microbial SOM mineralization (oxidation) in soils. Even within upland soils that are aerobic in bulk, factors limiting O2 diffusion such as texture and soil moisture can result in an abundance of anaerobic microsites in the interior of soil aggregates. Variation in ensuing anaerobic respiration pathways can further impact SOM mineralization rates. Using a combination of (first) aggregate model systems and (second) manipulations of intact field samples, we show how limitations on diffusion and carbon bioavailability interact to impose anaerobic conditions and associated respiration constraints on SOM mineralization rates. In model aggregates, we examined how particle size (soil texture) and amount of dissolved organic carbon (bioavailable carbon) affect O2 availability and distribution. Monitoring electron acceptor profiles (O2, NO3-, Mn and Fe) and SOM transformations (dissolved, particulate, mineral-associated pools) across the resulting redox gradients, we then determined the distribution of operative microbial metabolisms and their cumulative impact on SOM mineralization rates. Our results show that anaerobic conditions decrease SOM mineralization rates overall, but those are partially offset by the concurrent increases in SOM bioavailability due to transformations of protective mineral phases. In intact soil aggregates collected from soils varying in texture and SOM content, we mapped the spatial distribution of anaerobic microsites. Optode imaging, microsensor profiling and 3D tomography revealed that soil texture regulates overall O2 availability in aggregate interiors, while particulate SOM in biopores appears to control the fine-scale distribution of anaerobic microsites. Collectively, our

  8. Response of sediment microbial community structure in a freshwater reservoir to manipulations in oxygen availability.

    PubMed

    Bryant, Lee D; Little, John C; Bürgmann, Helmut

    2012-04-01

    Hypolimnetic oxygenation systems (HOx) are being increasingly used in freshwater reservoirs to elevate dissolved oxygen levels in the hypolimnion and suppress sediment-water fluxes of soluble metals (e.g. Fe and Mn) which are often microbially mediated. We assessed changes in sediment microbial community structure and corresponding biogeochemical cycling on a reservoir-wide scale as a function of HOx operations. Sediment microbial biomass as quantified by DNA concentration was increased in regions most influenced by the HOx. Following an initial decrease in biomass in the upper sediment while oxygen concentrations were low, biomass typically increased at all depths as the 4-month-long oxygenation season progressed. A distinct shift in microbial community structure was only observed at the end of the season in the upper sediment near the HOx. While this shift was correlated to HOx-enhanced oxygen availability, increased TOC levels and precipitation of Fe- and Mn-oxides, abiotic controls on Fe and Mn cycling, and/or the adaptability of many bacteria to variations in prevailing electron acceptors may explain the delayed response and the comparatively limited changes at other locations. While the sediment microbial community proved remarkably resistant to relatively short-term changes in HOx operations, HOx-induced variation in microbial structure, biomass, and activity was observed after a full season of oxygenation. PMID:22224595

  9. Soil microbial respiration and PICT responses to an industrial and historic lead pollution: a field study.

    PubMed

    Bérard, Annette; Capowiez, Line; Mombo, Stéphane; Schreck, Eva; Dumat, Camille; Deola, Frédéric; Capowiez, Yvan

    2016-03-01

    We performed a field investigation to study the long-term impacts of Pb soil contamination on soil microbial communities and their catabolic structure in the context of an industrial site consisting of a plot of land surrounding a secondary lead smelter. Microbial biomass, catabolic profiles, and ecotoxicological responses (PICT) were monitored on soils sampled at selected locations along 110-m transects established on the site. We confirmed the high toxicity of Pb on respirations and microbial and fungal biomasses by measuring positive correlations with distance from the wall factory and negative correlation with total Pb concentrations. Pb contamination also induced changes in microbial and fungal catabolic structure (from carbohydrates to amino acids through carboxylic malic acid). Moreover, PICT measurement allowed to establish causal linkages between lead and its effect on biological communities taking into account the contamination history of the ecosystem at community level. The positive correlation between qCO2 (based on respiration and substrate use) and PICT suggested that the Pb stress-induced acquisition of tolerance came at a greater energy cost for microbial communities in order to cope with the toxicity of the metal. In this industrial context of long-term polymetallic contamination dominated by Pb in a field experiment, we confirmed impacts of this metal on soil functioning through microbial communities, as previously observed for earthworm communities. PMID:26233741

  10. Microbial succession in response to pollutants in batch-enrichment culture.

    PubMed

    Jiao, Shuo; Chen, Weimin; Wang, Entao; Wang, Junman; Liu, Zhenshan; Li, Yining; Wei, Gehong

    2016-01-01

    As a global problem, environmental pollution is an important factor to shape the microbial communities. The elucidation of the succession of microbial communities in response to pollutants is essential for developing bioremediation procedures. In the present study, ten batches of soil-enrichment subcultures were subjected to four treatments: phenanthrene, n-octadecane, phenanthrene + n-octadecane, or phenanthrene + n-octadecane + CdCl2. Forty pollutant-degrading consortia, corresponding to each batch of the four treatments were obtained. High-throughput sequencing of the 16S rRNA gene revealed that the diversity, richness and evenness of the consortia decreased throughout the subculturing procedure. The well-known hydrocarbon degraders Acinetobacter, Gordonia, Sphingobium, Sphingopyxis, and Castellaniella and several other genera, including Niabella and Naxibacter, were detected in the enriched consortia. The predominant microbes varied and the microbial community in the consortia gradually changed during the successive subculturing depending on the treatment, indicating that the pollutants influenced the microbial successions. Comparison of the networks in the treatments indicated that organic pollutants and CdCl2 affected the co-occurrence patterns in enriched consortia. In conclusion, single environmental factors, such as the addition of nutrients or selection pressure, can shape microbial communities and partially explain the extensive differences in microbial community structures among diverse environments. PMID:26905741

  11. Microbial succession in response to pollutants in batch-enrichment culture

    PubMed Central

    Jiao, Shuo; Chen, Weimin; Wang, Entao; Wang, Junman; Liu, Zhenshan; Li, Yining; Wei, Gehong

    2016-01-01

    As a global problem, environmental pollution is an important factor to shape the microbial communities. The elucidation of the succession of microbial communities in response to pollutants is essential for developing bioremediation procedures. In the present study, ten batches of soil-enrichment subcultures were subjected to four treatments: phenanthrene, n-octadecane, phenanthrene + n-octadecane, or phenanthrene + n-octadecane + CdCl2. Forty pollutant-degrading consortia, corresponding to each batch of the four treatments were obtained. High-throughput sequencing of the 16S rRNA gene revealed that the diversity, richness and evenness of the consortia decreased throughout the subculturing procedure. The well-known hydrocarbon degraders Acinetobacter, Gordonia, Sphingobium, Sphingopyxis, and Castellaniella and several other genera, including Niabella and Naxibacter, were detected in the enriched consortia. The predominant microbes varied and the microbial community in the consortia gradually changed during the successive subculturing depending on the treatment, indicating that the pollutants influenced the microbial successions. Comparison of the networks in the treatments indicated that organic pollutants and CdCl2 affected the co-occurrence patterns in enriched consortia. In conclusion, single environmental factors, such as the addition of nutrients or selection pressure, can shape microbial communities and partially explain the extensive differences in microbial community structures among diverse environments. PMID:26905741

  12. Monitoring microbial populations of sulfate-reducing bacteria using an impedimetric immunosensor based on agglutination assay.

    PubMed

    Wan, Yi; Zhang, Dun; Hou, Baorong

    2009-11-15

    An impedimetric immunosensor was fabricated for rapid and non-labeled detection of sulfate-reducing bacteria, Desulforibrio caledoiensis (SRB) by immobilizing lectin-Concanavalin A using an agglutination assay. The immobilization of lectin was conducted using amine coupling on the surface of a gold (Au) electrode assembled with 11-Mercaptoundecanoic acid. Electrochemical impedance spectroscopy (EIS) was used to verify the stepwise assembly of the sensor system. The work conditions of the impedimetric immunosensor, such as pH of the buffer solutions and the incubation time of lectin, were optimized. Faradic impedance spectra for charge transfer for the redox probe Fe(CN)(6)(3-/4-)were measured to determine SRB concentrations. The diameter of the Nyquist diagram that is equal to the charge-transfer resistance (R(ct)) increased with increasing SRB concentration. A linear relationship between R(ct) and SRB concentration was obtained in SRB concentration range of 1.8 to 1.8 x 10(7)cfu/ml. The variation of the SRB population during the growth process was also monitored using the impedimetric immunosensor. This approach has great potential for simple, low-cost, and time-saving monitoring of microbial populations. PMID:19782217

  13. Assessment of partial nitrification reactor performance through microbial population shift using quinone profile, FISH and SEM.

    PubMed

    Sinha, B; Annachhatre, A P

    2007-12-01

    In engineered systems, biological nitrogen removal through partial nitrification to nitrite is of great interest. Accordingly, effect of operating parameters such as pH, DO and temperature on the accumulation of ammonia-oxidizers was investigated. pH of 8, DO of 0.3-0.5mg/l and temperature of 35 degrees C yielded a ratio of 0.9-1.5 of NO(2)N:NH(4)N in the effluent suitable as a feed for Anammox reactor. Microbial population shift during start-up was assessed using quinone profile, SEM and FISH. UQ-8 in the biomass, which is the predominant quinone in ammonia-oxidizers, increased from 24.8% on Day 1 to 61.2% on Day 136. Fluorescence in situ hybridization analysis in the reactor showed that ammonia-oxidizing bacteria gradually outcompeted other bacteria and was the dominant population. The morphology and inner structure of the granular sludge was observed using SEM and the photographs indicated that the aerobic granular sludge showed a shift towards spherical and small rod-shaped clusters. PMID:17257833

  14. Influence of packaging conditions on natural microbial population growth of endive.

    PubMed

    Charles, Florence; Rugani, Nathalie; Gontard, Nathalie

    2005-05-01

    The influence of three packaging conditions, i.e., unmodified atmosphere packaging (UAP), passive modified atmosphere packaging (MAP), and active MAP, on the natural microbial population growth of endive was investigated at 20 degrees C. For UAP, endive was placed in macroperforated oriented polypropylene pouches that maintained gas composition close to that of air (21 kPa O2 and 0 kPa CO2) but also limited superficial product dehydration. For MAP, endive was placed in low-density polyethylene pouches that induced a 3 kPa O2 and 5 kPa CO2 equilibrium atmosphere composition. Steady state was reached after 25 h of storage with an oxygen absorbing packet (active MAP) compared with 100 h without the packet (passive MAP) and was maintained for 200 h. After 312 h of storage, both active and passive MAP reduced total aerobic mesophile, yeast, and mold population growth compared with endive in UAP. Active MAP accelerated and improved the inhibition of Pseudomonas spp. and Enterobacteriaceae, respectively, probably because of the rapid O2 depletion during the transition period. A shift in the Enterobacteriaceae subpopulation from Rhanella aquatilis to Enterobacter agglomerans was observed for both passive and active MAP. PMID:15895736

  15. The Microbial Opsin Homolog Sop1 is involved in Sclerotinia sclerotiorum Development and Environmental Stress Response

    PubMed Central

    Lyu, Xueliang; Shen, Cuicui; Fu, Yanping; Xie, Jiatao; Jiang, Daohong; Li, Guoqing; Cheng, Jiasen

    2016-01-01

    Microbial opsins play a crucial role in responses to various environmental signals. Here, we report that the microbial opsin homolog gene sop1 from the necrotrophic phytopathogenic fungus Sclerotinia sclerotiorum was dramatically up-regulated during infection and sclerotial development compared with the vegetative growth stage. Further, study showed that sop1 was essential for growth, sclerotial development and full virulence of S. sclerotiorum. Sop1-silenced transformants were more sensitive to high salt stress, fungicides and high osmotic stress. However, they were more tolerant to oxidative stress compared with the wild-type strain, suggesting that sop1 is involved in different stress responses and fungicide resistance, which plays a role in the environmental adaptability of S. sclerotiorum. Furthermore, a Delta blast search showed that microbial opsins are absent from the genomes of animals and most higher plants, indicating that sop1 is a potential drug target for disease control of S. sclerotiorum. PMID:26779159

  16. Response of soil microbial communities to fire and fire-fighting chemicals.

    PubMed

    Barreiro, A; Martín, A; Carballas, T; Díaz-Raviña, M

    2010-11-15

    Worldwide, fire-fighting chemicals are rapidly gaining acceptance as an effective and efficient tool in wildfires control and in prescribed burns for habitat management. However, despite its widespread use as water additives to control and/or slow the spread of fire, information concerning the impact of these compounds on soil ecosystems is scarce. In the present work we examine, under field conditions, the response of the microbial communities to three different fire-chemicals at normal doses of application. The study was performed with a Humic Cambisol over granite under heath, located in the temperate humid zone (Galicia, NW Spain) with the following treatments: unburned soil (US) and burned soil added with water alone (BS) or mixed with the foaming agent Auxquímica RFC-88 at 1% (BS+Fo), Firesorb at 1.5% (BS+Fi) and FR Cross ammonium polyphosphate at 20% (BS+Ap). The microbial mass (microbial C), activity (β-glucosidase, urease) and community structure [phospholipids fatty acids (PLFA) pattern] were measured on soil samples collected at different sampling times during a 5year period after a prescribed fire. The results showed a negative short-term effect of the fire on the microbial properties. The microbial biomass and activity levels tended to recover with time; however, changes in the microbial community structure (PLFA pattern) were still detected 5years after the prescribed fire. Compared to the burned soil added with water, the ammonium polyphosphate and the Firesorb treatments were the fire-fighting chemicals that showed a higher influence on the microbial communities over the whole study period. Our data indicated the usefulness of the PLFAs analysis to detect the long-term impact of both fire and fire-fighting chemicals on the soil microbial communities and hence on the soil quality of forest ecosystems. PMID:20888616

  17. Microbial Community Response to Carbon Substrate Amendment in Mercury Impacted Sediments: Implications on Microbial Methylation of Mercury.

    NASA Astrophysics Data System (ADS)

    Elias, D. A.; Somenahally, A. C.; Moberly, J. G.; Hurt, R. A., Jr.; Brown, S. D.; Podar, M.; Palumbo, A. V.; Gilmour, C. C.

    2015-12-01

    Methylmercury (MeHg) is a neurotoxic and bio-accumulative product of the microbial methylation of inorganic mercury (Hg(II)). Methylating organisms are now known to exist in almost all anaerobic niches including fermentation, Fe(III)- and sulfate- reduction as well as methanogenesis. The study objective was to determine the effect of different carbon sources on the microbial community and methylating populations in particular along a Hg contaminated creek. Sediment cores from upstream and downstream at the Hg contaminated East Fork Poplar Creek (EFPC), Oak Ridge TN, and a background site were sectioned by depth, and Hg-methylation potential (HgMP) assays were performed using stable isotope spikes. Sediments from the lowest depth possessed the highest in-situ activity. Replicate samples were amended with different carbon substrates (cellulose, acetate, propionate, lactate, ethanol and methanol), spiked with stable isotopes for HgMP assays and incubated for 24hrs. Sequencing of the 16S rRNA gene was performed to determine alterations in Bacterial and Archaeal population dynamics. Additionally, bioinformatics and our new qualitative and quantitative hgcAB primers were utilized to determine microbial community structure alterations and correlate organism and gene abundance with altered MeHg generation. HgMP was significantly reduced in cellulose amended sediments while acetate and propionate slightly decreased HgMP in both sites. Methanol, ethanol and lactate increased the HgMP in EFPC downstream while cellulose amendment significantly decreased the Proteobacteria, and the Firmicutes increased but none are currently known to produce MeHg. Geobacter bemidjiensis in particular significantly decreased in cellulose amended sediments in all three sites from being predominant in-situ. This suggests that in EFPC downstream and background sites, the prevalent Hg-methyaltors might be Deltaprotebacteria, since upstream, cellulose amendment did not reduce HgMP even though

  18. Microbial population dynamics and changes in main nutrients during the acidification process of pig manures.

    PubMed

    Zhang, Dongdong; Yuan, Xufeng; Guo, Peng; Suo, Yali; Wang, Xiaofen; Wang, Weidong; Cui, Zongjun

    2011-01-01

    This study evaluated the impact of pig manure acidification on anaerobic treatment and composition of the fecal microbial community. According to the different chemical oxygen demand (COD) in the anaerobic treatment processes, pig manure was diluted 4 times (x4), 16 times (x16), or 64 times (x64) and subjected to acidification. During the acidification process, pH, soluble chemical oxygen demand (SCOD), volatile fatty acids (VFAs), nitrogen (N), phosphorus (P) and potassium (K) were determined along with microbial population dynamics. The pH of the three dilutions first declined, and then slowly increased. The total VFAs of x4 and x16 dilutions peaked on day 15 and 20, respectively. The content of acetic acid, propanoic acid, butanoic acid and valeric acid of the x4 dilution were 23.6, 11.4, 8.8 and 0.6 g/L respectively, and that of the x16 dilution was 5.6, 2.3, 0.9 and 0.2 g/L respectively. Only acetic acid was detected in the x64 dilution, and its level peaked on day 10. The results showed that the liquid pig manure was more suitable to enter the anaerobic methanogenic bioreactors after two weeks of acidification. During the acidification process, total P concentration increased during the first ten days, then dropped sharply, and rose again to a relatively high final concentration, while total N concentration rose initially and then declined. Based on the analysis of denaturing gradient gel electrophoresis (DGGE) and 16S rRNA gene clone library, we concluded that the acidification process reduced the number of pathogenic bacteria species in pig manure. PMID:21520820

  19. Responses of oxidation rate and microbial communities to methane in simulated landfill cover soil microcosms.

    PubMed

    He, Ruo; Ruan, Aidong; Jiang, Chenjing; Shen, Dong-Sheng

    2008-10-01

    CH4 oxidation capacities and microbial community structures developed in response to the presence of CH4 were investigated in two types of landfill cover soil microcosms, waste soil (fine material in stabilized waste) and clay soil. CH4 emission fluxes were lower in the waste soil cover over the course of the experiment. After exposure to CH4 flow for 120 days, the waste soil developed CH4 oxidation capacity from 0.53 to 11.25-13.48micromol CH4gd.w.(-1)h(-1), which was ten times higher than the clay soil. The topsoils of the two soil covers were observed dried and inhibited CH4 oxidation. The maximum CH4 oxidation rate occurred at the depth of 10-20cm in the waste soil cover (the middle layer), whereas it took place mainly at the depth of 20-30cm in the clay soil cover (the bottom layer). The amounts of the phospholipid fatty acid (PLFA) biomarks 16:1omega8c and 18:1omega8c for type I and II methanotrophs, respectively, showed that type I methanotrophic bacteria predominated in the clay soil, while the type II methanotrophic bacteria were abundant in the waste soil, and the highest population in the middle layer. The results also indicated that a greater active methanotrophic community was developed in the waste soil relative to the clay soil. PMID:18294841

  20. Effects of cowpea (Vigna unguiculata) root mucilage on microbial community response and capacity for phenanthrene remediation.

    PubMed

    Sun, Ran; Belcher, Richard W; Liang, Jianqiang; Wang, Li; Thater, Brian; Crowley, David E; Wei, Gehong

    2015-07-01

    Biodegradation of polycyclic aromatic hydrocarbons (PAHs) is normally limited by their low solubility and poor bioavailability. Prior research suggests that biosurfactants are synthesized as intermediates during the production of mucilage at the root tip. To date the effects of mucilage on PAH degradation and microbial community response have not been directly examined. To address this question, our research compared 3 cowpea breeding lines (Vigna unguiculata) that differed in mucilage production for their effects on phenanthrene (PHE) degradation in soil. The High Performance Liquid Chromatography results indicated that the highest PHE degradation rate was achieved in soils planted with mucilage producing cowpea line C1, inoculated with Bradyrhizobium, leading to 91.6% PHE disappearance in 5 weeks. In root printing tests, strings treated with mucilage and bacteria produced larger clearing zones than those produced on mucilage treated strings with no bacteria or bacteria inoculated strings. Experiments with 14C-PHE and purified mucilage in soil slurry confirmed that the root mucilage significantly enhanced PHE mineralization (82.7%), which is 12% more than the control treatment without mucilage. The profiles of the PHE degraders generated by Denaturing gradient gel electrophoresis suggested that cowpea C1, producing a high amount of root mucilage, selectively enriched the PHE degrading bacteria population in rhizosphere. These findings indicate that root mucilage may play a significant role in enhancing PHE degradation and suggests that differences in mucilage production may be an important criterion for selection of the best plant species for use in phytoremediation of PAH contaminated soils. PMID:26141877

  1. Soil microbial community response to precipitation change in a semi-arid ecosystem

    SciTech Connect

    Cregger, Melissa; Schadt, Christopher Warren; McDowell, Nathan; Pockman, William; Classen, Aimee T

    2012-01-01

    Microbial communities regulate many belowground carbon cycling processes; thus, the impact of climate change on the struc- ture and function of soil microbial communities could, in turn, impact the release or storage of carbon in soils. Here we used a large-scale precipitation manipulation ( 18%, 50%, or ambient) in a pi on-juniper woodland (Pinus edulis-Juniperus mono- sperma) to investigate how changes in precipitation amounts altered soil microbial communities as well as what role seasonal variation in rainfall and plant composition played in the microbial community response. Seasonal variability in precipitation had a larger role in determining the composition of soil microbial communities in 2008 than the direct effect of the experimental precipitation treatments. Bacterial and fungal communities in the dry, relatively moisture-limited premonsoon season were compositionally distinct from communities in the monsoon season, when soil moisture levels and periodicity varied more widely across treatments. Fungal abundance in the drought plots during the dry premonsoon season was particularly low and was 4.7 times greater upon soil wet-up in the monsoon season, suggesting that soil fungi were water limited in the driest plots, which may result in a decrease in fungal degradation of carbon substrates. Additionally, we found that both bacterial and fungal communities beneath pi on pine and juniper were distinct, suggesting that microbial functions beneath these trees are different. We conclude that predicting the response of microbial communities to climate change is highly dependent on seasonal dynam- ics, background climatic variability, and the composition of the associated aboveground community.

  2. Diethyl phthalate in compost: ecotoxicological effects and response of the microbial community.

    PubMed

    Kapanen, A; Stephen, J R; Brüggemann, J; Kiviranta, A; White, D C; Itävaara, M

    2007-05-01

    There is a great need to understand the environmental impacts of organic pollutants on soil health. Phthalates are widely used in consumables and can be found extensively. We studied the toxicity of diethyl phthalate (DEP), spiked in a compost plant growth substrate, by means of the acute toxicity Flash test and on the basis of the germination and plant growth of radish seedlings. The response of the microbial community to DEP in the growth substrate was studied by PCR-DGGE (denaturing gradient gel electrophoresis). In the acute toxicity test, DEP was found to be less toxic as a pure compound than when mixed with the compost mixture. This suggests the synergistic effect of unknown toxic compounds or the release of compounds due to DEP addition. The same DEP concentration level in compost substrate induced toxic response in both plant test and microbial community analysis. The diversity of the major microbial community was reduced from a broad community to only 10 major species at toxic concentrations of DEP. Several of the identified microbial species are known to be able to degrade phthalates, which means that the suppression of other microbial species might be due to the substrate availability and toxicity. The major species identified included Sphingomonas sp., Pseudomonas sp., Actinomycetes sp. PMID:17258270

  3. An integrated insight into the response of sedimentary microbial communities to heavy metal contamination

    PubMed Central

    Yin, Huaqun; Niu, Jiaojiao; Ren, Youhua; Cong, Jing; Zhang, Xiaoxia; Fan, Fenliang; Xiao, Yunhua; Zhang, Xian; Deng, Jie; Xie, Ming; He, Zhili; Zhou, Jizhong; Liang, Yili; Liu, Xueduan

    2015-01-01

    Response of biological communities to environmental stresses is a critical issue in ecology, but how microbial communities shift across heavy metal gradients remain unclear. To explore the microbial response to heavy metal contamination (e.g., Cr, Mn, Zn), the composition, structure and functional potential of sedimentary microbial community were investigated by sequencing of 16S rRNA gene amplicons and a functional gene microarray. Analysis of 16S rRNA sequences revealed that the composition and structure of sedimentary microbial communities changed significantly across a gradient of heavy metal contamination, and the relative abundances were higher for Firmicutes, Chloroflexi and Crenarchaeota, but lower for Proteobacteria and Actinobacteria in highly contaminated samples. Also, molecular ecological network analysis of sequencing data indicated that their possible interactions might be enhanced in highly contaminated communities. Correspondently, key functional genes involved in metal homeostasis (e.g., chrR, metC, merB), carbon metabolism, and organic remediation showed a higher abundance in highly contaminated samples, indicating that bacterial communities in contaminated areas may modulate their energy consumption and organic remediation ability. This study indicated that the sedimentary indigenous microbial community may shift the composition and structure as well as function priority and interaction network to increase their adaptability and/or resistance to environmental contamination. PMID:26391875

  4. Microbial response to single-cell protein production and brewery wastewater treatment

    PubMed Central

    Lee, Jackson Z; Logan, Andrew; Terry, Seth; Spear, John R

    2015-01-01

    As global fisheries decline, microbial single-cell protein (SCP) produced from brewery process water has been highlighted as a potential source of protein for sustainable animal feed. However, biotechnological investigation of SCP is difficult because of the natural variation and complexity of microbial ecology in wastewater bioreactors. In this study, we investigate microbial response across a full-scale brewery wastewater treatment plant and a parallel pilot bioreactor modified to produce an SCP product. A pyrosequencing survey of the brewery treatment plant showed that each unit process selected for a unique microbial community. Notably, flow equalization basins were dominated by Prevotella, methanogenesis effluent had the highest levels of diversity, and clarifier wet-well samples were sources of sequences for the candidate bacterial phyla of TM7 and BD1-5. Next, the microbial response of a pilot bioreactor producing SCP was tracked over 1 year, showing that two different production trials produced two different communities originating from the same starting influent. However, SCP production resulted generally in enrichment of several clades of rhizospheric diazotrophs of Alphaproteobacteria and Betaproteobacteria in the bioreactor and even more so in the final product. These diazotrophs are potentially useful as the basis of a SCP product for commercial feed production. PMID:24837420

  5. Microbial response to single-cell protein production and brewery wastewater treatment.

    PubMed

    Lee, Jackson Z; Logan, Andrew; Terry, Seth; Spear, John R

    2015-01-01

    As global fisheries decline, microbial single-cell protein (SCP) produced from brewery process water has been highlighted as a potential source of protein for sustainable animal feed. However, biotechnological investigation of SCP is difficult because of the natural variation and complexity of microbial ecology in wastewater bioreactors. In this study, we investigate microbial response across a full-scale brewery wastewater treatment plant and a parallel pilot bioreactor modified to produce an SCP product. A pyrosequencing survey of the brewery treatment plant showed that each unit process selected for a unique microbial community. Notably, flow equalization basins were dominated by Prevotella, methanogenesis effluent had the highest levels of diversity, and clarifier wet-well samples were sources of sequences for the candidate bacterial phyla of TM7 and BD1-5. Next, the microbial response of a pilot bioreactor producing SCP was tracked over 1 year, showing that two different production trials produced two different communities originating from the same starting influent. However, SCP production resulted generally in enrichment of several clades of rhizospheric diazotrophs of Alphaproteobacteria and Betaproteobacteria in the bioreactor and even more so in the final product. These diazotrophs are potentially useful as the basis of a SCP product for commercial feed production. PMID:24837420

  6. An integrated insight into the response of sedimentary microbial communities to heavy metal contamination.

    PubMed

    Yin, Huaqun; Niu, Jiaojiao; Ren, Youhua; Cong, Jing; Zhang, Xiaoxia; Fan, Fenliang; Xiao, Yunhua; Zhang, Xian; Deng, Jie; Xie, Ming; He, Zhili; Zhou, Jizhong; Liang, Yili; Liu, Xueduan

    2015-01-01

    Response of biological communities to environmental stresses is a critical issue in ecology, but how microbial communities shift across heavy metal gradients remain unclear. To explore the microbial response to heavy metal contamination (e.g., Cr, Mn, Zn), the composition, structure and functional potential of sedimentary microbial community were investigated by sequencing of 16S rRNA gene amplicons and a functional gene microarray. Analysis of 16S rRNA sequences revealed that the composition and structure of sedimentary microbial communities changed significantly across a gradient of heavy metal contamination, and the relative abundances were higher for Firmicutes, Chloroflexi and Crenarchaeota, but lower for Proteobacteria and Actinobacteria in highly contaminated samples. Also, molecular ecological network analysis of sequencing data indicated that their possible interactions might be enhanced in highly contaminated communities. Correspondently, key functional genes involved in metal homeostasis (e.g., chrR, metC, merB), carbon metabolism, and organic remediation showed a higher abundance in highly contaminated samples, indicating that bacterial communities in contaminated areas may modulate their energy consumption and organic remediation ability. This study indicated that the sedimentary indigenous microbial community may shift the composition and structure as well as function priority and interaction network to increase their adaptability and/or resistance to environmental contamination. PMID:26391875

  7. Comparisons of ruminal fermentation characteristics and microbial populations in bison and cattle.

    PubMed Central

    Towne, G; Nagaraja, T G; Cochran, R C; Harmon, D L; Owensby, C E; Kaufman, D W

    1988-01-01

    Ruminal microbial populations, fermentation characteristics, digestibility, and liquid flow rates in two ruminally cannulated bison and two ruminally cannulated Hereford steers fed a prairie hay diet were compared. No significant differences in anaerobic bacterial counts, volatile fatty acid concentrations, or ruminal pHs were evident between bison and cattle. Also, no significant differences in neutral detergent fiber digestibility, indigestible fiber retention time, or intake were detected between bison and cattle, although cattle had higher levels (P less than 0.08) of ruminal dry matter and indigestible fiber than bison. Bison had a smaller (P = .02) ruminoreticular volume, faster liquid dilution rates, and faster liquid turnover times than cattle. The average ruminal ammonia nitrogen concentration was higher (P = 0.02) in bison (1.17 mg/dl) than in cattle (0.79 mg/dl). Total ciliate protozoal counts and cell volume were greater (P = 0.07) in bison (32.8 x 10(4)/g and 407.1 x 10(-4) ml/g, respectively) than in cattle (15.7 x 10(4)/g and 162.2 x 10(-4) ml/g, respectively). Bison harbored higher (P less than 0.02) numbers of Dasytricha spp., Eudiplodinium maggii, Eudiplodinium bursa, and Epidinium spp. than cattle and possessed a type B protozoan population. The cattle possessed a mixed type A-type B population that was characterized by Ophryoscolex spp. and Polyplastron spp. in association with low concentrations of Epidinium spp. and Eudiplodinium maggii. PMID:3272131

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

    PubMed

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

    2015-01-01

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

  9. RESPONSE OF SOIL MICROBIAL BIOMASS AND COMMUNITY COMPOSITION TO CHRONIC NITROGEN ADDITIONS AT HARVARD FOREST

    EPA Science Inventory

    Soil microbial communities may respond to anthropogenic increases in ecosystem nitrogen (N) availability, and their response may ultimately feedback on ecosystem carbon and N dynamics. We examined the long-term effects of chronic N additions on soil microbes by measuring soil mi...

  10. CATALASE FROM A FUNGAL MICROBIAL PESTICIDE INDUCES A UNIQUE IGE RESPONSE.

    EPA Science Inventory

    BALB/c mice exposed by involuntary aspiration to Metarhizium anisopliae extract (MACA), a microbial pesticide, have shown responses characteristic of human allergic lung disease/asthma. IgE-binding proteins have been identified in MACA by Western blot analysis, 2-dimensio...

  11. Soil microbial responses to a subambient to elevated gradient of atmospheric CO2

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Increasing atmospheric CO2 has been shown to significantly affect terrestrial ecosystems through increased primary production. This response is thought to be mitigated by changes to the soil microbial community, which can alter nutrient availability in these systems. In this study we examine the e...

  12. Immune response and gut microbial community structure in bumblebees after microbiota transplants.

    PubMed

    Näpflin, Kathrin; Schmid-Hempel, Paul

    2016-05-25

    Microbial communities are a key component of host health. As the microbiota is initially 'foreign' to a host, the host's immune system should respond to its acquisition. Such variation in the response should relate not only to host genetic background, but also to differences in the beneficial properties of the microbiota. However, little is known about such interactions. Here, we investigate the gut microbiota of the bumblebee, Bombus terrestris, which has a protective function against the bee's natural trypanosome gut parasite, Crithidia bombi We transplanted 'resistant' and 'susceptible' microbiota into 'resistant' and 'susceptible' host backgrounds, and studied the activity of the host immune system. We found that bees from different resistance backgrounds receiving a microbiota differed in aspects of their immune response. At the same time, the elicited immune response also depended on the received microbiota's resistance phenotype. Furthermore, the microbial community composition differed between microbiota resistance phenotypes (resistant versus susceptible). Our results underline the complex feedback between the host's ability to potentially exert selection on the establishment of a microbial community and the influence of the microbial community on the host immune response in turn. PMID:27226466

  13. Triclosan Alters Anti-microbial and Inflammatory Responses of Epithelial Cells

    PubMed Central

    Wallet, Mark A.; Calderon, Nadia L.; Alonso, Tess R.; Choe, Christina S.; Catalfamo, Dana L.; Lalane, Charles J.; Neiva, Kathleen G.; Panagakos, Foti; Wallet, Shannon M.

    2012-01-01

    Periodontal diseases are a class of pathologies wherein oral microbes induce harmful immune responses in a susceptible host. Therefore, an agent which can both reduce microbial burden and lessen pathogenesis of localized inflammation would have beneficial effects in periodontal disease. 2,4,4-trichloro-2-hydroxydiphenyl-ether [triclosan] is currently used in oral care products due to broad spectrum anti-microbial and anti-inflammatory properties. Objective To determine effects of triclosan on the response of oral epithelial cells to stimulation with the inflammatory microbial product lipopolysaccharide [LPS], a ligand for toll-like receptor 4 [TLR4]. Materials/Methods Primary human oral epithelial cells were stimulated with LPS in the presence and/or absence of triclosan after which expression of pro-inflammatory cytokines, β-defensins, micro-RNAs [miRNAs] or TLR signaling pathway proteins were evaluated. Results Here we demonstrate that triclosan is a potent inhibitor of oral epithelial cell LPS-induced pro-inflammatory responses by inducing miRNA regulation of the TLR-signaling pathway. Triclosan was not a pan-suppresser of oral epithelial cell responses as β-defensin 2 [βD2] and βD3 were upregulated by triclosan following LPS-stimulation. Conclusions These data demonstrate both a novel anti-microbial mechanism by which triclosan improves plaque control and an additional anti-inflammatory property which could have beneficial effects in periodontal disease resolution. PMID:24079913

  14. Microbial Composition in Decomposing Pine Litter Shifts in Response to Common Soil Secondary Minerals

    NASA Astrophysics Data System (ADS)

    Welty-Bernard, A. T.; Heckman, K.; Vazquez, A.; Rasmussen, C.; Chorover, J.; Schwartz, E.

    2011-12-01

    A range of environmental and biotic factors have been identified that drive microbial community structure in soils - carbon substrates, redox conditions, mineral nutrients, salinity, pH, and species interactions. However, soil mineralogy has been largely ignored as a candidate in spite of recent studies that indicate that minerals have a substantial impact on soil organic matter stores and subsequent fluxes from soils. Given that secondary minerals and organic colloids govern a soil's biogeochemical activity due to surface area and electromagnetic charge, we propose that secondary minerals are a strong determinant of the communities that are responsible for process rates. To test this, we created three microcosms to study communities during decomposition using pine forest litter mixed with two common secondary minerals in soils (goethite and gibbsite) and with quartz as a control. Changes in bacterial and fungal communities were tracked over the 154-day incubation by pyrosequencing fragments of the bacterial 16S and fungal 18S rRNA genes. Ordination using nonmetric multidimensional scaling showed that bacterial communities separated on the basis of minerals. Overall, a single generalist - identified as an Acidobacteriaceae isolate - dominated all treatments over the course of the experiment, representing roughly 25% of all communities. Fungal communities discriminated between the quartz control alone and mineral treatments as a whole. Again, several generalists dominated the community. Coniochaeta ligniaria dominated communities with abundances ranging from 29 to 40%. The general stability of generalist populations may explain the similarities between treatment respiration rates. Variation between molecular fingerprints, then, were largely a function of unique minor members with abundances ranging from 0.01 to 8%. Carbon availability did not surface as a possible mechanism responsible for shifts in fingerprints due to the relatively large mass of needles in the

  15. Response of Antarctic cryoconite microbial communities to light

    PubMed Central

    Bagshaw, Elizabeth A.; Wadham, Jemma L.; Tranter, Martyn; Perkins, Rupert; Morgan, Alistair; Williamson, Christopher J.; Fountain, Andrew G.; Fitzsimons, Sean; Dubnick, Ashley

    2016-01-01

    Microbial communities on polar glacier surfaces are found dispersed on the ice surface, or concentrated in cryoconite holes and cryolakes, which are accumulations of debris covered by a layer of ice for some or all of the year. The ice lid limits the penetration of photosynthetically available radiation (PAR) to the sediment layer, since the ice attenuates up to 99% of incoming radiation. This suite of field and laboratory experiments demonstrates that PAR is an important control on primary production in cryoconite and cryolake ecosystems. Increased light intensity increased efficiency of primary production in controlled laboratory incubations of debris from the surface of Joyce Glacier, McMurdo Dry Valleys, Antarctica. However, when light intensity was increased to levels near that received on the ice surface, without the protection of an ice lid, efficiency decreased and measurements of photophysiology showed that the communities suffered light stress. The communities are therefore well adapted to low light levels. Comparison with Arctic cryoconite communities, which are typically not covered by an ice lid for the majority of the ablation season, showed that these organisms were also stressed by high light, so they must employ strategies to protect against photodamage. PMID:27095815

  16. Response of Antarctic cryoconite microbial communities to light.

    PubMed

    Bagshaw, Elizabeth A; Wadham, Jemma L; Tranter, Martyn; Perkins, Rupert; Morgan, Alistair; Williamson, Christopher J; Fountain, Andrew G; Fitzsimons, Sean; Dubnick, Ashley

    2016-06-01

    Microbial communities on polar glacier surfaces are found dispersed on the ice surface, or concentrated in cryoconite holes and cryolakes, which are accumulations of debris covered by a layer of ice for some or all of the year. The ice lid limits the penetration of photosynthetically available radiation (PAR) to the sediment layer, since the ice attenuates up to 99% of incoming radiation. This suite of field and laboratory experiments demonstrates that PAR is an important control on primary production in cryoconite and cryolake ecosystems. Increased light intensity increased efficiency of primary production in controlled laboratory incubations of debris from the surface of Joyce Glacier, McMurdo Dry Valleys, Antarctica. However, when light intensity was increased to levels near that received on the ice surface, without the protection of an ice lid, efficiency decreased and measurements of photophysiology showed that the communities suffered light stress. The communities are therefore well adapted to low light levels. Comparison with Arctic cryoconite communities, which are typically not covered by an ice lid for the majority of the ablation season, showed that these organisms were also stressed by high light, so they must employ strategies to protect against photodamage. PMID:27095815

  17. Response of Antarctic cryoconite microbial communities to light

    PubMed Central

    Bagshaw, Elizabeth A.; Wadham, Jemma L.; Tranter, Martyn; Perkins, Rupert; Morgan, Alistair; Williamson, Christopher J.; Fountain, Andrew G.; Fitzsimons, Sean; Dubnick, Ashley

    2016-01-01

    Microbial communities on polar glacier surfaces are found dispersed on the ice surface, or concentrated in cryoconite holes and cryolakes, which are accumulations of debris covered by a layer of ice for some or all of the year. The ice lid limits the penetration of photosynthetically available radiation (PAR) to the sediment layer, since the ice attenuates up to 99% of incoming radiation. This suite of field and laboratory experiments demonstrates that PAR is an important control on primary production in cryoconite and cryolake ecosystems. Increased light intensity increased efficiency of primary production in controlled laboratory incubations of debris from the surface of Joyce Glacier, McMurdo Dry Valleys, Antarctica. However, when light intensity was increased to levels near that received on the ice surface, without the protection of an ice lid, efficiency decreased and measurements of photophysiology showed that the communities suffered light stress. The communities are therefore well adapted to low light levels. Comparison with Arctic cryoconite communities, which are typically not covered by an ice lid for the majority of the ablation season, showed that these organisms were also stressed by high light, so they must employ strategies to protect against photodamage.

  18. Microbial responses to changes in flow status in temporary headwater streams: a cross-system comparison

    PubMed Central

    Febria, Catherine M.; Hosen, Jacob D.; Crump, Byron C.; Palmer, Margaret A.; Williams, D. Dudley

    2015-01-01

    Microbial communities are responsible for the bulk of biogeochemical processing in temporary headwater streams, yet there is still relatively little known about how community structure and function respond to periodic drying. Moreover, the ability to sample temporary habitats can be a logistical challenge due to the limited capability to measure and predict the timing, intensity and frequency of wet-dry events. Unsurprisingly, published datasets on microbial community structure and function are limited in scope and temporal resolution and vary widely in the molecular methods applied. We compared environmental and microbial community datasets for permanent and temporary tributaries of two different North American headwater stream systems: Speed River (Ontario, Canada) and Parkers Creek (Maryland, USA). We explored whether taxonomic diversity and community composition were altered as a result of flow permanence and compared community composition amongst streams using different 16S microbial community methods (i.e., T-RFLP and Illumina MiSeq). Contrary to our hypotheses, and irrespective of method, community composition did not respond strongly to drying. In both systems, community composition was related to site rather than drying condition. Additional network analysis on the Parkers Creek dataset indicated a shift in the central microbial relationships between temporary and permanent streams. In the permanent stream at Parkers Creek, associations of methanotrophic taxa were most dominant, whereas associations with taxa from the order Nitrospirales were more dominant in the temporary stream, particularly during dry conditions. We compared these results with existing published studies from around the world and found a wide range in community responses to drying. We conclude by proposing three hypotheses that may address contradictory results and, when tested across systems, may expand understanding of the responses of microbial communities in temporary streams to

  19. Microbial Population Analysis of the Salivary Glands of Ticks; A Possible Strategy for the Surveillance of Bacterial Pathogens

    PubMed Central

    Qiu, Yongjin; Nakao, Ryo; Ohnuma, Aiko; Kawamori, Fumihiko; Sugimoto, Chihiro

    2014-01-01

    Ticks are one of the most important blood-sucking vectors for infectious microorganisms in humans and animals. When feeding they inject saliva, containing microbes, into the host to facilitate the uptake of blood. An understanding of the microbial populations within their salivary glands would provide a valuable insight when evaluating the vectorial capacity of ticks. Three tick species (Ixodes ovatus, I. persulcatus and Haemaphysalis flava) were collected in Shizuoka Prefecture of Japan between 2008 and 2011. Each tick was dissected and the salivary glands removed. Bacterial communities in each salivary gland were characterized by 16S amplicon pyrosequencing using a 454 GS-Junior Next Generation Sequencer. The Ribosomal Database Project (RDP) Classifier was used to classify sequence reads at the genus level. The composition of the microbial populations of each tick species were assessed by principal component analysis (PCA) using the Metagenomics RAST (MG-RAST) metagenomic analysis tool. Rickettsia-specific PCR was used for the characterization of rickettsial species. Almost full length of 16S rDNA was amplified in order to characterize unclassified bacterial sequences obtained in I. persulcatus female samples. The numbers of bacterial genera identified for the tick species were 71 (I. ovatus), 127 (I. persulcatus) and 59 (H. flava). Eighteen bacterial genera were commonly detected in all tick species. The predominant bacterial genus observed in all tick species was Coxiella. Spiroplasma was detected in Ixodes, and not in H. flava. PCA revealed that microbial populations in tick salivary glands were different between tick species, indicating that host specificities may play an important role in determining the microbial complement. Four female I. persulcatus samples contained a high abundance of several sequences belonging to Alphaproteobacteria symbionts. This study revealed the microbial populations within the salivary glands of three species of ticks, and the

  20. Effects of Population Type on Mail Survey Response Rates and on the Efficacy of Response Enhancers.

    ERIC Educational Resources Information Center

    Green, Kathy E.; And Others

    Experimental studies of response rates to mail surveys were reviewed and differences in response by population type were described. Cases were selected for review if they were experimental studies that manipulated a response enhancement factor. Results suggest significant differences in typical response rates for different populations. Higher…

  1. Brain Microbial Populations in HIV/AIDS: α-Proteobacteria Predominate Independent of Host Immune Status

    PubMed Central

    Branton, William G.; Ellestad, Kristofor K.; Maingat, Ferdinand; Wheatley, B. Matt; Rud, Erling; Warren, René L.; Holt, Robert A.; Surette, Michael G.; Power, Christopher

    2013-01-01

    The brain is assumed to be a sterile organ in the absence of disease although the impact of immune disruption is uncertain in terms of brain microbial diversity or quantity. To investigate microbial diversity and quantity in the brain, the profile of infectious agents was examined in pathologically normal and abnormal brains from persons with HIV/AIDS [HIV] (n = 12), other disease controls [ODC] (n = 14) and in cerebral surgical resections for epilepsy [SURG] (n = 6). Deep sequencing of cerebral white matter-derived RNA from the HIV (n = 4) and ODC (n = 4) patients and SURG (n = 2) groups revealed bacterially-encoded 16 s RNA sequences in all brain specimens with α-proteobacteria representing over 70% of bacterial sequences while the other 30% of bacterial classes varied widely. Bacterial rRNA was detected in white matter glial cells by in situ hybridization and peptidoglycan immunoreactivity was also localized principally in glia in human brains. Analyses of amplified bacterial 16 s rRNA sequences disclosed that Proteobacteria was the principal bacterial phylum in all human brain samples with similar bacterial rRNA quantities in HIV and ODC groups despite increased host neuroimmune responses in the HIV group. Exogenous viruses including bacteriophage and human herpes viruses-4, -5 and -6 were detected variably in autopsied brains from both clinical groups. Brains from SIV- and SHIV-infected macaques displayed a profile of bacterial phyla also dominated by Proteobacteria but bacterial sequences were not detected in experimentally FIV-infected cat or RAG1−/− mouse brains. Intracerebral implantation of human brain homogenates into RAG1−/− mice revealed a preponderance of α-proteobacteria 16 s RNA sequences in the brains of recipient mice at 7 weeks post-implantation, which was abrogated by prior heat-treatment of the brain homogenate. Thus, α-proteobacteria represented the major bacterial component of the primate brain

  2. Response to selection and evolvability of invasive populations.

    PubMed

    Lee, Carol Eunmi; Remfert, Jane Louise; Chang, Yu-Mei

    2007-02-01

    While natural selection might in some cases facilitate invasions into novel habitats, few direct measurements of selection response exist for invasive populations. This study examined selection response to changes in salinity using the copepod Eurytemora affinis. This copepod has invaded fresh water from saline habitats multiple times independently throughout the Northern Hemisphere. Selection response to a constant intermediate salinity (5 PSU) was measured in the laboratory for saline source and freshwater invading populations from the St. Lawrence drainage (North America). These populations were reared under three conditions: (1) native salinities (0 or 15 PSU) for at least two generations, (2) 5 PSU for two generations, and (3) 5 PSU for six generations. Full-sib clutches taken from populations reared under these three conditions were split across four salinities (0, 5, 15, and 25 PSU) to determine reaction norms for survival and development time. Contrasts in survival and development time across the three rearing conditions were treated as the selection response. Selection at 5 PSU resulted in a significant decline in freshwater (0 PSU) tolerance for both the saline and freshwater populations. Yet, evolutionary differences in freshwater tolerance persisted between the saline and freshwater populations. The saline and freshwater populations converged in their high-salinity (25 PSU) tolerance, with an increase in the freshwater population and decline in the saline population. Development time did not shift greatly in response to selection at 5 PSU. For all three rearing conditions, the freshwater population exhibited retarded larval development and accelerated juvenile development relative to the saline population. Results from this study indicate that both the saline and freshwater populations exhibit significant responses to selection for a fitness-related trait critical for invasions into a novel habitat. PMID:16915512

  3. Precipitation regime drives soil microbial responses to warming in temperate steppes

    NASA Astrophysics Data System (ADS)

    Liu, W.; Xia, J.; Liu, L.; Wan, S.

    2014-12-01

    Although numerous warming experiments have been done to examine the impacts of elevated temperature on soil microbial actives, most of them were based on responses from a single site. To investigate how precipitation regime regulate warming's effects on carbon cycle, field manipulative warming experiments were conducted at 3 types of steppes (desert, typical and meadow steppe) along a precipitation gradient in northern China. Soil temperature, moisture, dissolved organic C (DOC), inorganic nitrogen (N) concentration, microbial biomass C (MBC), N (MBN) and respiration (MR) were measured once a year from 2006 to 2009. The results showed that soil moisture was significantly decreased in the typical steppe whereas not affected in the desert and meadow steppe, respectively. Across the 4 years, warming decreased MBC and MR in the desert and typical steppe while did not affect them in the meadow steppe. The magnitude of reductions in warming-induced MBC and MR declined with increasing precipitation gradient at a regional scale. Across the precipitation gradient, all changes in soil MBC, MBN and MR were positively correlated with both annual precipitation and changes in belowground net primary productivity (BNPP), suggesting that soil microbial responses to warming may be regulated by annual precipitation and substrate availability. However, the lab-incubation revealed that soil moisture is more important in regulating soil microbial activities than substrate across the 3 steppes. In addition, soil microbial responses to warming showed year-to-year variations during the first 4 years coincided with the fluctuations in annual precipitation across the 3 steppes. Our results suggested that precipitation regime controls the spatial and interannual responses of soil microbes to warming, mainly by regulating soil moisture and substrate availability. With the increase in precipitation, the positive responses of soil microbes to warming started to outweigh the negative impacts

  4. Phospholipids fatty acids of drinking water reservoir sedimentary microbial community: Structure and function responses to hydrostatic pressure and other physico-chemical properties.

    PubMed

    Chai, Bei-Bei; Huang, Ting-Lin; Zhao, Xiao-Guang; Li, Ya-Jiao

    2015-07-01

    Microbial communities in three drinking water reservoirs, with different depth in Xi'an city, were quantified by phospholipids fatty acids analysis and multivariate statistical analysis was employed to interpret their response to different hydrostatic pressure and other physico-chemical properties of sediment and overlying water. Principle component analyses of sediment characteristics parameters showed that hydrostatic pressure was the most important effect factor to differentiate the overlying water quality from three drinking water reservoirs from each other. NH4+ content in overlying water was positive by related to hydrostatic pressure, while DO in water-sediment interface and sediment OC in sediment were negative by related with it. Three drinking water reservoir sediments were characterized by microbial communities dominated by common and facultative anaerobic Gram-positive bacteria, as well as, by sulfur oxidizing bacteria. Hydrostatic pressure and physico-chemical properties of sediments (such as sediment OC, sediment TN and sediment TP) were important effect factors to microbial community structure, especially hydrostatic pressure. It is also suggested that high hydrostatic pressure and low dissolved oxygen concentration stimulated Gram-positive and sulfate-reducing bacteria (SRB) bacterial population in drinking water reservoir sediment. This research supplied a successful application of phospholipids fatty acids and multivariate analysis to investigate microbial community composition response to different environmental factors. Thus, few physico-chemical factors can be used to estimate composition microbial of community as reflected by phospholipids fatty acids, which is difficult to detect. PMID:26387360

  5. Microbial population dynamics during start-up and overload conditions of anaerobic digesters treating municipal solid waste and sewage sludge.

    PubMed

    McMahon, Katherine D; Zheng, Dandan; Stams, Alfons J M; Mackie, Roderick I; Raskin, Lutgarde

    2004-09-30

    Microbial population dynamics were investigated during start-up and during periods of overload conditions in anaerobic co-digesters treating municipal solid waste and sewage sludge. Changes in community structure were monitored using ribosomal RNA-based oligonucleotide probe hybridization to measure the abundance of syntrophic propionate-oxidizing bacteria (SPOB), saturated fatty acid-beta-oxidizing syntrophs (SFAS), and methanogens. These changes were linked to traditional performance parameters such as biogas production and volatile fatty acid (VFA) concentrations. Digesters with high levels of Archaea started up successfully. Methanosaeta concilii was the dominant aceticlastic methanogen in these systems. In contrast, digesters that experienced a difficult start-up period had lower levels of Archaea with proportionally more abundant Methanosarcina spp. Syntrophic propionate-oxidizing bacteria and saturated fatty acid-beta-oxidizing syntrophs were present at low levels in all digesters, and SPOB appeared to play a role in stabilizing propionate levels during start-up of one digester. Digesters with a history of poor performance tolerated a severe organic overload event better than digesters that had previously performed well. It is hypothesized that higher levels of SPOB and SFAS and their methanogenic partners in previously unstable digesters are responsible for this behavior. PMID:15334409

  6. Particulate DNA in smoker fluids: Evidence for existence of microbial populations in hot hydrothermal systems

    SciTech Connect

    Straube, W.L.; Colwell, R.R. Univ. of Maryland, Baltimore ); Deming, J.W.; Baross, J.A. ); Somerville, C.C. )

    1990-05-01

    As part of an interdisciplinary study of hydrothermal vents on the Endeavour Segment of the Juan de Fuca Ridge, we used the submersible ALVIN to collect 57 fluid samples from 17 different hot vents (smokers and flanges) and their environs for the purpose of extracting particulate DNA. Particulate material concentrated from these samples was lysed enzymatically (enz) and by a combination of enzyme and French press treatment (fp). Concentrations of partially purified DNA recovered from these lysates were determined spectrofluorometrically. Ambient seawater surrounding the vents was found to contain low DNA concentrations, 0.18 to 0.32 ng of DNA per ml, while low-temperature vent samples yielded significantly higher concentrations of 0.37 to 2.12 ng of DNA per ml. Although DNA recovery values from superheated (210 to 345{degree}C) flange samples were not significantly different from ambient seawater values, most of the superheated (174 to 357{degree}C) smoker fluid samples contained particulate DNA in concentrations too high to be attributable to entrained seawater. Detailed sampling at one smoker site demonstrated not only the existence of significant levels of particulate DNA in the superheated smoker fluids but also the presence of an elevated microbial population in the buoyant plume 20 to 100 m above the smoker. These results underscore the heterogeneity of smoker environments within a given hydrothermal vent fluid and indicate that microorganisms exist in some superheated fluids.

  7. Microbial population index and community structure in saline-alkaline soil using gene targeted metagenomics.

    PubMed

    Keshri, Jitendra; Mishra, Avinash; Jha, Bhavanath

    2013-03-30

    Population indices of bacteria and archaea were investigated from saline-alkaline soil and a possible microbe-environment pattern was established using gene targeted metagenomics. Clone libraries were constructed using 16S rRNA and functional gene(s) involved in carbon fixation (cbbL), nitrogen fixation (nifH), ammonia oxidation (amoA) and sulfur metabolism (apsA). Molecular phylogeny revealed the dominance of Actinobacteria, Firmicutes and Proteobacteria along with archaeal members of Halobacteraceae. The library consisted of novel bacterial (20%) and archaeal (38%) genera showing ≤95% similarity to previously retrieved sequences. Phylogenetic analysis indicated ability of inhabitant to survive in stress condition. The 16S rRNA gene libraries contained novel gene sequences and were distantly homologous with cultured bacteria. Functional gene libraries were found unique and most of the clones were distantly related to Proteobacteria, while clones of nifH gene library also showed homology with Cyanobacteria and Firmicutes. Quantitative real-time PCR exhibited that bacterial abundance was two orders of magnitude higher than archaeal. The gene(s) quantification indicated the size of the functional guilds harboring relevant key genes. The study provides insights on microbial ecology and different metabolic interactions occurring in saline-alkaline soil, possessing phylogenetically diverse groups of bacteria and archaea, which may be explored further for gene cataloging and metabolic profiling. PMID:23083746

  8. Effects of Environmental Factors on Microbial Populations in Brackish Waters off the Southern Coast of Finland

    PubMed Central

    Väätänen, Pentti

    1980-01-01

    The roles played by environmental factors in seasonal changes in microbial populations were investigated in the Tvärminne area, off the southern coast of Finland. Surface-layer samples were collected at 1- or 2-week intervals in 1976-78, and 14 microbiological and 10 environmental parameters were determined. Stepwise multiple regression analysis was used to explain seasonal variation in the microbiological parameters. Separate analyses were made of the data from the open-water and ice-cover periods. In analyses of data from both periods, the environmental factors included accounted for a significant proportion of the variation in the parameters for community respiration (90%) and bacterial spores (80%), and a smaller proportion (60 to 65%) of the variation in total counts of bacteria and plate counts of psychrophiles and yeasts. Lower values (40 to 55%) were obtained for the variation in the other microbiological parameters. The environmental factors with maximal contributions were organic matter, water temperature, chlorophyll a, and salinity, but rainfall and winds also explained part of the variation in some microbiological parameters. In the winter analysis the results differed from those obtained for the other seasons, the variation being governed by parameters indicating freshwater outflows, namely, humic matter, salinity, water temperature (positive regression coefficient), and rainfall (negative regression coefficient). PMID:16345595

  9. Fermentation and microbial population dynamics during the ensiling of native grass and subsequent exposure to air.

    PubMed

    Zhang, Qing; Wu, Baiyila; Nishino, Naoki; Wang, Xianguo; Yu, Zhu

    2016-03-01

    To study the microbial population and fermentation dynamics of large needlegrass (LN) and Chinese leymus (CL) during ensiling and subsequent exposure to air, silages were sampled and analyzed using culture-based techniques and denaturing gradient gel electrophoresis (DGGE). A total of 112 lactic acid bacteria (LAB) strains were isolated and identified using the 16S rRNA sequencing method. Lactic acid was not detected in the first 20 days in LN silage and the pH decreased to 6.13 after 45 days of ensiling. The temperature of the LN silage increased after approximately 30 h of air exposure and the CL silage showed a slight temperature variation. Enterococcus spp. were mainly present in LN silage. The proportion of Lactobacillus brevis in CL silage increased after exposure to air. LN silage with a higher proportion of Enterococcus spp. and propionic acid concentration did not show higher fermentation quality or aerobic stability than CL silage, which had a higher concentration of acetic acid, butyric acid and increased proportion of L. brevis after exposure to air. PMID:26950516

  10. Soil Microbial Community Responses to Long-Term Global Change Factors in a California Grassland

    NASA Astrophysics Data System (ADS)

    Qin, K.; Peay, K.

    2015-12-01

    Soil fungal and bacterial communities act as mediators of terrestrial carbon and nutrient cycling, and interact with the aboveground plant community as both pathogens and mutualists. However, these soil microbial communities are sensitive to changes in their environment. A better understanding of the response of soil microbial communities to global change may help to predict future soil microbial diversity, and assist in creating more comprehensive models of terrestrial carbon and nutrient cycles. This study examines the effects of four global change factors (increased temperature, increased variability in precipitation, nitrogen deposition, and CO2 enrichment) on soil microbial communities at the Jasper Ridge Global Change Experiment (JRGCE), a full-factorial global change manipulative experiment on three hectares of California grassland. While similar studies have examined the effects of global change on soil microbial communities, few have manipulated more factors or been longer in duration than the JRGCE, which began field treatments in 1998. We find that nitrogen deposition, CO2 enrichment, and increased variability in precipitation significantly affect the structure of both fungal and bacterial communities, and explain more of the variation in the community structures than do local soil chemistry or aboveground plant community. Fungal richness is correlated positively with soil nitrogen content and negatively with soil water content. Arbuscular mycorrhizal fungi (AMF), which associate closely with herbaceous plants' roots and assist in nutrient uptake, decrease in both richness and relative abundance in elevated CO2 treatments.