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 of Vibrio fischeri are subject to an intrinsic demographic Allee effect. Populations subjected to predation by the bacterivore Cafeteria roenbergensis display 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. © 2016 The Author(s).

An Economic Framework of Microbial Trade

PubMed Central

Mee, Michael T.

2015-01-01

A large fraction of microbial life on earth exists in complex communities where metabolic exchange is vital. Microbes trade essential resources to promote their own growth in an analogous way to countries that exchange goods in modern economic markets. Inspired by these similarities, we developed a framework based on general equilibrium theory (GET) from economics to predict the population dynamics of trading microbial communities. Our biotic GET (BGET) model provides an a priori theory of the growth benefits of microbial trade, yielding several novel insights relevant to understanding microbial ecology and engineering synthetic communities. We find that the economic concept of comparative advantage is a necessary condition for mutualistic trade. Our model suggests that microbial communities can grow faster when species are unable to produce essential resources that are obtained through trade, thereby promoting metabolic specialization and increased intercellular exchange. Furthermore, we find that species engaged in trade exhibit a fundamental tradeoff between growth rate and relative population abundance, and that different environments that put greater pressure on group selection versus individual selection will promote varying strategies along this growth-abundance spectrum. We experimentally tested this tradeoff using a synthetic consortium of Escherichia coli cells and found the results match the predictions of the model. This framework provides a foundation to study natural and engineered microbial communities through a new lens based on economic theories developed over the past century. PMID:26222307

Theory of microbial genome evolution

NASA Astrophysics Data System (ADS)

Koonin, Eugene

Bacteria and archaea have small genomes tightly packed with protein-coding genes. This compactness is commonly perceived as evidence of adaptive genome streamlining caused by strong purifying selection in large microbial populations. In such populations, even the small cost incurred by nonfunctional DNA because of extra energy and time expenditure is thought to be sufficient for this extra genetic material to be eliminated by selection. However, contrary to the predictions of this model, there exists a consistent, positive correlation between the strength of selection at the protein sequence level, measured as the ratio of nonsynonymous to synonymous substitution rates, and microbial genome size. By fitting the genome size distributions in multiple groups of prokaryotes to predictions of mathematical models of population evolution, we show that only models in which acquisition of additional genes is, on average, slightly beneficial yield a good fit to genomic data. Thus, the number of genes in prokaryotic genomes seems to reflect the equilibrium between the benefit of additional genes that diminishes as the genome grows and deletion bias. New genes acquired by microbial genomes, on average, appear to be adaptive. Evolution of bacterial and archaeal genomes involves extensive horizontal gene transfer and gene loss. Many microbes have open pangenomes, where each newly sequenced genome contains more than 10% `ORFans', genes without detectable homologues in other species. A simple, steady-state evolutionary model reveals two sharply distinct classes of microbial genes, one of which (ORFans) is characterized by effectively instantaneous gene replacement, whereas the other consists of genes with finite, distributed replacement rates. These findings imply a conservative estimate of at least a billion distinct genes in the prokaryotic genomic universe.

Theory of prokaryotic genome evolution.

PubMed

Sela, Itamar; Wolf, Yuri I; Koonin, Eugene V

2016-10-11

Bacteria and archaea typically possess small genomes that are tightly packed with protein-coding genes. The compactness of prokaryotic genomes is commonly perceived as evidence of adaptive genome streamlining caused by strong purifying selection in large microbial populations. In such populations, even the small cost incurred by nonfunctional DNA because of extra energy and time expenditure is thought to be sufficient for this extra genetic material to be eliminated by selection. However, contrary to the predictions of this model, there exists a consistent, positive correlation between the strength of selection at the protein sequence level, measured as the ratio of nonsynonymous to synonymous substitution rates, and microbial genome size. Here, by fitting the genome size distributions in multiple groups of prokaryotes to predictions of mathematical models of population evolution, we show that only models in which acquisition of additional genes is, on average, slightly beneficial yield a good fit to genomic data. These results suggest that the number of genes in prokaryotic genomes reflects the equilibrium between the benefit of additional genes that diminishes as the genome grows and deletion bias (i.e., the rate of deletion of genetic material being slightly greater than the rate of acquisition). Thus, new genes acquired by microbial genomes, on average, appear to be adaptive. The tight spacing of protein-coding genes likely results from a combination of the deletion bias and purifying selection that efficiently eliminates nonfunctional, noncoding sequences.

Deposition and postdeposition mechanisms as possible drivers of microbial population variability in glacier ice.

PubMed

Xiang, Shu-Rong; Shang, Tian-Cui; Chen, Yong; Yao, Tan-Dong

2009-11-01

Glaciers accumulate airborne microorganisms year by year and thus are good archives of microbial communities and their relationship to climatic and environmental changes. Hypotheses have focused on two possible drivers of microbial community composition in glacier systems. One is aeolian deposition, in which the microbial load by aerosol, dust, and precipitation events directly determines the amount and composition of microbial species in glacier ice. The other is postdepositional selection, in which the metabolic activity in surface snow causes microbial community shifts in glacier ice. An additional possibility is that both processes occur simultaneously. Aeolian deposition initially establishes a microbial community in the ice, whereas postdeposition selection strengthens the deposition patterns of microorganisms with the development of tolerant species in surface snow, resulting in varying structures of microbial communities with depth. In this minireview, we examine these postulations through an analysis of physical-chemical and biological parameters from the Malan and Vostok ice cores, and the Kuytun 51 Glacial surface and deep snow. We discuss these and other recent results in the context of the hypothesized mechanisms driving microbial community succession in glaciers. We explore our current gaps in knowledge and point out future directions for research on microorganisms in glacial ecosystems.

Innovative MIOR Process Utilizing Indigenous Reservoir Constituents

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

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

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

Innovative MIOR Process Utilizing Indigenous Reservoir Constituents

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

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

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

Link between microbial composition and carbon substrate-uptake preferences in a PHA-storing community

PubMed Central

Albuquerque, Maria G E; Carvalho, Gilda; Kragelund, Caroline; Silva, Ana F; Barreto Crespo, Maria T; Reis, Maria A M; Nielsen, Per H

2013-01-01

The microbial community of a fermented molasses-fed sequencing batch reactor (SBR) operated under feast and famine conditions for production of polyhydroxyalkanoates (PHAs) was identified and quantified through a 16 S rRNA gene clone library and fluorescence in situ hybridization (FISH). The microbial enrichment was found to be composed of PHA-storing populations (84% of the microbial community), comprising members of the genera Azoarcus, Thauera and Paracoccus. The dominant PHA-storing populations ensured the high functional stability of the system (characterized by high PHA-storage efficiency, up to 60% PHA content). The fermented molasses contained primarily acetate, propionate, butyrate and valerate. The substrate preferences were determined by microautoradiography-FISH and differences in the substrate-uptake capabilities for the various probe-defined populations were found. The results showed that in the presence of multiple substrates, microbial populations specialized in different substrates were selected, thereby co-existing in the SBR by adapting to different niches. Azoarcus and Thauera, primarily consumed acetate and butyrate, respectively. Paracoccus consumed a broader range of substrates and had a higher cell-specific substrate uptake. The relative species composition and their substrate specialization were reflected in the substrate removal rates of different volatile fatty acids in the SBR reactor. PMID:22810062

Energy, ecology and the distribution of microbial life.

PubMed

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

2013-07-19

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

Energy, ecology and the distribution of microbial life

PubMed Central

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

2013-01-01

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

Innovative MIOR Process Utilizing Indigenous Reservoir Constituents

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

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

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

Intra-tumor heterogeneity: lessons from microbial evolution and clinical implications

PubMed Central

2013-01-01

Multiple subclonal populations of tumor cells can coexist within the same tumor. This intra-tumor heterogeneity will have clinical implications and it is therefore important to identify factors that drive or suppress such heterogeneous tumor progression. Evolutionary biology can provide important insights into this process. In particular, experimental evolution studies of microbial populations, which exist as clonal populations that can diversify into multiple subclones, have revealed important evolutionary processes driving heterogeneity within a population. There are transferrable lessons that can be learnt from these studies that will help us to understand the process of intra-tumor heterogeneity in the clinical setting. In this review, we summarize drivers of microbial diversity that have been identified, such as mutation rate and environmental influences, and discuss how knowledge gained from microbial experimental evolution studies may guide us to identify and understand important selective factors that promote intra-tumor heterogeneity. Furthermore, we discuss how these factors could be used to direct and optimize research efforts to improve patient care, focusing on therapeutic resistance. Finally, we emphasize the need for longitudinal studies to address the impact of these potential tumor heterogeneity-promoting factors on drug resistance, metastatic potential and clinical outcome. PMID:24267946

Beyond the bulk: disclosing the life of single microbial cells

PubMed Central

Rosenthal, Katrin; Oehling, Verena

2017-01-01

Abstract Microbial single cell analysis has led to discoveries that are beyond what can be resolved with population-based studies. It provides a pristine view of the mechanisms that organize cellular physiology, unbiased by population heterogeneity or uncontrollable environmental impacts. A holistic description of cellular functions at the single cell level requires analytical concepts beyond the miniaturization of existing technologies, defined but uncontrolled by the biological system itself. This review provides an overview of the latest advances in single cell technologies and demonstrates their potential. Opportunities and limitations of single cell microbiology are discussed using selected application-related examples. PMID:29029257

Towards a methodology for removing and reconstructing soil protists with intact soil microbial communities

NASA Astrophysics Data System (ADS)

Hu, Junwei; Tsegaye Gebremikael, Mesfin; Salehi Hosseini, Pezhman; De Neve, Stefaan

2017-04-01

Soil ecological theories on the role of soil fauna groups in soil functions are often tested in highly artificial conditions, i.e. on completely sterilized soils or pure quartz sand re-inoculated with a small selection of these fauna groups. Due to the variable sensitivity of different soil biota groups to gamma irradiation, the precise doses that can be administered, and the relatively small disturbance of soil physical and chemical properties (relative to e.g. autoclaving, freezing-thawing and chemical agents), gamma irradiation has been employed to selectively eliminate soil organisms. In recent research we managed to realistically estimate on the contribution of the entire nematode communities to C and N mineralization in soil, by selective removal of nematodes at 5 kGy gamma irradiation doses followed by reinoculation. However, we did not assess the population dynamics of protozoa in response to this irradiation, i.e. we could not assess the potential contribution of protists to the mineralization process. Selective removal of protists from soils with minimal disturbance of the soil microflora has never been attempted and constitutes a highly challenging but potentially groundbreaking technique in soil ecology. Accordingly, the objective of this research is to modify the successful methodology of selective elimination of nematodes, to selectively eliminate soil fauna including nematodes and protists with minimal effects on the soil microbial community and reconstruct soil protists and microbial communities in completely sterilized soil. To this end, we here compared two different approaches: 1) remove nematodes and protists while keeping the microbial community intact (through optimizing gamma irradiation doses); 2) reconstruct protists and microbial communities in sterilized soil (through adding multicellular fauna free pulverized soil). The experiment consists of 7 treatments with soil collected from 0 to 15 cm layer of an organically managed agricultural field: 1) non-irradiated (control); 2-6) irradiated with doses of 5, 7.5, 10, 12.5 and 15 kGy; 7) irradiated with 25 kGy followed by inoculation with multicellular fauna free soil powder. All treatments were incubated using Magenta™ vessels GA-7 which allow air exchange but exclude microbial infection, and we monitor nematode and protist populations after 0, 2, 4 and 8 weeks of incubation by destructive sampling. We also measure the degree of disturbance to the microbial community composition in all treatments as compared to the control soil at the end of incubation. The experiment is ongoing and the data will be presented at the conference.

Impact of Chloramination on the Development of Laboratory-Grown Biofilms Fed with Filter-Pretreated Groundwater

PubMed Central

Ling, Fangqiong; Liu, Wen-Tso

2013-01-01

This study evaluated the continuous impact of monochloramine disinfection on laboratory-grown biofilms through the characterization of biofilm architecture and microbial community structure. Biofilm development and disinfection were achieved using CDC (Centers for Disease Control and Prevention) biofilm reactor systems with polyvinyl chloride (PVC) coupons as the substratum and sand filter-pretreated groundwater as the source of microbial seeding and growth nutrient. After 2 weeks of growth, the biofilms were subjected to chloramination for 8 more weeks at concentrations of 7.5±1.4 to 9.1±0.4 mg Cl2 L−1. Control reactors received no disinfection during the development of biofilms. Confocal laser scanning microscopy and image analysis indicated that chloramination could lead to 81.4–83.5% and 86.3–95.6% reduction in biofilm biomass and thickness, respectively, but could not eliminate biofilm growth. 16S rRNA gene terminal restriction fragment length polymorphism analysis indicated that microbial community structures between chloraminated and non-chloraminated biofilms exhibited different successional trends. 16S rRNA gene pyrosequencing analysis further revealed that chloramination could select members of Actinobacteria and Acidobacteria as the dominant populations, whereas natural development leads to the selection of members of Nitrospira and Bacteroidetes as dominant biofilm populations. Overall, chloramination treatment could alter the growth of multi-species biofilms on the PVC surface, shape the biofilm architecture, and select a certain microbial community that can survive or proliferate under chloramination. PMID:23124766

Excess labile carbon promotes the expression of virulence factors in coral reef bacterioplankton.

PubMed

Cárdenas, Anny; Neave, Matthew J; Haroon, Mohamed Fauzi; Pogoreutz, Claudia; Rädecker, Nils; Wild, Christian; Gärdes, Astrid; Voolstra, Christian R

2018-01-01

Coastal pollution and algal cover are increasing on many coral reefs, resulting in higher dissolved organic carbon (DOC) concentrations. High DOC concentrations strongly affect microbial activity in reef waters and select for copiotrophic, often potentially virulent microbial populations. High DOC concentrations on coral reefs are also hypothesized to be a determinant for switching microbial lifestyles from commensal to pathogenic, thereby contributing to coral reef degradation, but evidence is missing. In this study, we conducted ex situ incubations to assess gene expression of planktonic microbial populations under elevated concentrations of naturally abundant monosaccharides (glucose, galactose, mannose, and xylose) in algal exudates and sewage inflows. We assembled 27 near-complete (>70%) microbial genomes through metagenomic sequencing and determined associated expression patterns through metatranscriptomic sequencing. Differential gene expression analysis revealed a shift in the central carbohydrate metabolism and the induction of metalloproteases, siderophores, and toxins in Alteromonas, Erythrobacter, Oceanicola, and Alcanivorax populations. Sugar-specific induction of virulence factors suggests a mechanistic link for the switch from a commensal to a pathogenic lifestyle, particularly relevant during increased algal cover and human-derived pollution on coral reefs. Although an explicit test remains to be performed, our data support the hypothesis that increased availability of specific sugars changes net microbial community activity in ways that increase the emergence and abundance of opportunistic pathogens, potentially contributing to coral reef degradation.

Evolution and population genomics of the Lyme borreliosis pathogen, Borrelia burgdorferi.

PubMed

Seifert, Stephanie N; Khatchikian, Camilo E; Zhou, Wei; Brisson, Dustin

2015-04-01

Population genomic studies have the potential to address many unresolved questions about microbial pathogens by facilitating the identification of genes underlying ecologically important traits, such as novel virulence factors and adaptations to humans or other host species. Additionally, this framework improves estimations of population demography and evolutionary history to accurately reconstruct recent epidemics and identify the molecular and environmental factors that resulted in the outbreak. The Lyme disease bacterium, Borrelia burgdorferi, exemplifies the power and promise of the application of population genomics to microbial pathogens. We discuss here the future of evolutionary studies in B. burgdorferi, focusing on the primary evolutionary forces of horizontal gene transfer, natural selection, and migration, as investigations transition from analyses of single genes to genomes. Copyright © 2015 Elsevier Ltd. All rights reserved.

Silage review: Using molecular approaches to define the microbial ecology of silage.

PubMed

McAllister, T A; Dunière, L; Drouin, P; Xu, S; Wang, Y; Munns, K; Zaheer, R

2018-05-01

Ensiling of forages was recognized as a microbial-driven process as early as the late 1800s, when it was associated with the production of "sweet" or "sour" silage. Classical microbiological plating techniques defined the epiphytic microbial populations associated with fresh forage, the pivotal role of lactic acid-producing bacteria in the ensiling process, and the contribution of clostridia, bacilli, yeast, and molds to the spoilage of silage. Many of these classical studies focused on the enumeration and characterization of a limited number of microbial species that could be readily isolated on selective media. Evidence suggested that many of the members of these microbial populations were viable but unculturable, resulting in classical studies underestimating the true microbial diversity associated with ensiling. Polymerase chain reaction-based techniques, including length heterogeneity PCR, terminal RFLP, denaturing gradient gel electrophoresis, and automated ribosomal intergenic spacer analysis, were the first molecular methods used to study silage microbial communities. Further advancements in whole comparative genomic, metagenomic, and metatranscriptomic sequencing have or are in the process of superseding these methods, enabling microbial communities during ensiling to be defined with a degree of detail that is impossible using classical microbiology. These methods have identified new microbial species in silage, as well as characterized shifts in microbial communities with forage type and composition, ensiling method, and in response to aerobic exposure. Strain- and species-specific primers have been used to track the persistence and contribution of silage inoculants to the ensiling process and the role of specific species of yeast and fungi in silage spoilage. Sampling and the methods used to isolate genetic materials for further molecular analysis can have a profound effect on results. Primer selection for PCR amplification and the presence of inhibitors can also lead to biases in the interpretation of sequence data. Bioinformatic analyses are reliant on the integrity and presence of sequence data within established databases and can be subject to low taxonomic resolution. Despite these limitations, advancements in molecular biology are poised to revolutionize our current understanding of the microbial ecology of silage. Published by FASS Inc. and Elsevier Inc. on behalf of the American Dairy Science Association®. All rights reserved.

Drift in ocean currents impacts intergenerational microbial exposure to temperature.

PubMed

Doblin, Martina A; van Sebille, Erik

2016-05-17

Microbes are the foundation of marine ecosystems [Falkowski PG, Fenchel T, Delong EF (2008) Science 320(5879):1034-1039]. Until now, the analytical framework for understanding the implications of ocean warming on microbes has not considered thermal exposure during transport in dynamic seascapes, implying that our current view of change for these critical organisms may be inaccurate. Here we show that upper-ocean microbes experience along-trajectory temperature variability up to 10 °C greater than seasonal fluctuations estimated in a static frame, and that this variability depends strongly on location. These findings demonstrate that drift in ocean currents can increase the thermal exposure of microbes and suggests that microbial populations with broad thermal tolerance will survive transport to distant regions of the ocean and invade new habitats. Our findings also suggest that advection has the capacity to influence microbial community assemblies, such that regions with strong currents and large thermal fluctuations select for communities with greatest plasticity and evolvability, and communities with narrow thermal performance are found where ocean currents are weak or along-trajectory temperature variation is low. Given that fluctuating environments select for individual plasticity in microbial lineages, and that physiological plasticity of ancestors can predict the magnitude of evolutionary responses of subsequent generations to environmental change [Schaum CE, Collins S (2014) Proc Biol Soc 281(1793):20141486], our findings suggest that microbial populations in the sub-Antarctic (∼40°S), North Pacific, and North Atlantic will have the most capacity to adapt to contemporary ocean warming.

Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations

DOE PAGES

Bendall, Matthew L.; Stevens, Sarah L.R.; Chan, Leong-Keat; ...

2016-01-08

Multiple models describe the formation and evolution of distinct microbial phylogenetic groups. These evolutionary models make different predictions regarding how adaptive alleles spread through populations and how genetic diversity is maintained. Processes predicted by competing evolutionary models, for example, genome-wide selective sweeps vs gene-specific sweeps, could be captured in natural populations using time-series metagenomics if the approach were applied over a sufficiently long time frame. Direct observations of either process would help resolve how distinct microbial groups evolve. Using a 9-year metagenomic study of a freshwater lake (2005–2013), we explore changes in single-nucleotide polymorphism (SNP) frequencies and patterns of genemore » gain and loss in 30 bacterial populations. SNP analyses revealed substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied by >1000-fold among populations. SNP allele frequencies also changed dramatically over time within some populations. Interestingly, nearly all SNP variants were slowly purged over several years from one population of green sulfur bacteria, while at the same time multiple genes either swept through or were lost from this population. Furthermore, these patterns were consistent with a genome-wide selective sweep in progress, a process predicted by the ‘ecotype model’ of speciation but not previously observed in nature. In contrast, other populations contained large, SNP-free genomic regions that appear to have swept independently through the populations prior to the study without purging diversity elsewhere in the genome. Finally, evidence for both genome-wide and gene-specific sweeps suggests that different models of bacterial speciation may apply to different populations coexisting in the same environment.« less

Selective whole genome amplification for resequencing target microbial species from complex natural samples.

PubMed

Leichty, Aaron R; Brisson, Dustin

2014-10-01

Population genomic analyses have demonstrated power to address major questions in evolutionary and molecular microbiology. Collecting populations of genomes is hindered in many microbial species by the absence of a cost effective and practical method to collect ample quantities of sufficiently pure genomic DNA for next-generation sequencing. Here we present a simple method to amplify genomes of a target microbial species present in a complex, natural sample. The selective whole genome amplification (SWGA) technique amplifies target genomes using nucleotide sequence motifs that are common in the target microbe genome, but rare in the background genomes, to prime the highly processive phi29 polymerase. SWGA thus selectively amplifies the target genome from samples in which it originally represented a minor fraction of the total DNA. The post-SWGA samples are enriched in target genomic DNA, which are ideal for population resequencing. We demonstrate the efficacy of SWGA using both laboratory-prepared mixtures of cultured microbes as well as a natural host-microbe association. Targeted amplification of Borrelia burgdorferi mixed with Escherichia coli at genome ratios of 1:2000 resulted in >10(5)-fold amplification of the target genomes with <6.7-fold amplification of the background. SWGA-treated genomic extracts from Wolbachia pipientis-infected Drosophila melanogaster resulted in up to 70% of high-throughput resequencing reads mapping to the W. pipientis genome. By contrast, 2-9% of sequencing reads were derived from W. pipientis without prior amplification. The SWGA technique results in high sequencing coverage at a fraction of the sequencing effort, thus allowing population genomic studies at affordable costs. Copyright © 2014 by the Genetics Society of America.

Allee effect: the story behind the stabilization or extinction of microbial ecosystem.

PubMed

Goswami, Madhurankhi; Bhattacharyya, Purnita; Tribedi, Prosun

2017-03-01

A population exhibiting Allee effect shows a positive correlation between population fitness and population size or density. Allee effect decides the extinction or conservation of a microbial population and thus appears to be an important criterion in population ecology. The underlying factor of Allee effect that decides the stabilization and extinction of a particular population density is the threshold or the critical density of their abundance. According to Allee, microbial populations exhibit a definite, critical or threshold density, beyond which the population fitness of a particular population increases with the rise in population density and below it, the population fitness goes down with the decrease in population density. In particular, microbial population displays advantageous traits such as biofilm formation, expression of virulence genes, spore formation and many more only at a high population density. It has also been observed that microorganisms exhibiting a lower population density undergo complete extinction from the residual microbial ecosystem. In reference to Allee effect, decrease in population density or size introduces deleterious mutations among the population density through genetic drift. Mutations are carried forward to successive generations resulting in its accumulation among the population density thus reducing its microbial fitness and thereby increasing the risk of extinction of a particular microbial population. However, when the microbial load is high, the chance of genetic drift is less, and through the process of biofilm formation, the cooperation existing among the microbial population increases that increases the microbial fitness. Thus, the high microbial population through the formation of microbial biofilm stabilizes the ecosystem by increasing fitness. Taken together, microbial fitness shows positive correlation with the ecosystem conservation and negative correlation with ecosystem extinction.

Evolutionary ecology of pungency in wild chilies

PubMed Central

Tewksbury, Joshua J.; Reagan, Karen M.; Machnicki, Noelle J.; Carlo, Tomás A.; Haak, David C.; Peñaloza, Alejandra Lorena Calderón; Levey, Douglas J.

2008-01-01

The primary function of fruit is to attract animals that disperse viable seeds, but the nutritional rewards that attract beneficial consumers also attract consumers that kill seeds instead of dispersing them. Many of these unwanted consumers are microbes, and microbial defense is commonly invoked to explain the bitter, distasteful, occasionally toxic chemicals found in many ripe fruits. This explanation has been criticized, however, due to a lack of evidence that microbial consumers influence fruit chemistry in wild populations. In the present study, we use wild chilies to show that chemical defense of ripe fruit reflects variation in the risk of microbial attack. Capsaicinoids are the chemicals responsible for the well known pungency of chili fruits. Capsicum chacoense is naturally polymorphic for the production of capsaicinoids and displays geographic variation in the proportion of individual plants in a population that produce capsaicinoids. We show that this variation is directly linked to variation in the damage caused by a fungal pathogen of chili seeds. We find that Fusarium fungus is the primary cause of predispersal chili seed mortality, and we experimentally demonstrate that capsaicinoids protect chili seeds from Fusarium. Further, foraging by hemipteran insects facilitates the entry of Fusarium into fruits, and we show that variation in hemipteran foraging pressure among chili populations predicts the proportion of plants in a population producing capsaicinoids. These results suggest that the pungency in chilies may be an adaptive response to selection by a microbial pathogen, supporting the influence of microbial consumers on fruit chemistry. PMID:18695236

Developing methanogenic microbial consortia from diverse coal sources and environments

DOE PAGES

Fuertez, John; Boakye, Richard; McLennan, John; ...

2017-08-18

Biogenic gas production is a promising alternative or supplement to conventional methane extraction from coalbeds. Adsorbed and free gas, generated over geologic time, can be supplemented with biogenic gas during short-term engineering operations. There are two generic protocols for doing this. The first is to contact the coal with nutrients to support native bacterial development. The second approach is to inject appropriately cultured ex-situ consortia into subsurface coal accumulations. Research has mainly focused on the former: in-situ stimulation of native microbial communities with added nutrients. Relatively few studies have been conducted on the strategies for enriching ex-situ microbial populations undermore » initial atmospheric exposure for subsequent injection into coal seams to stimulate biodegradation, and methanogenesis. In order to evaluate the feasibility of ex-situ cultivation, natural microbial populations were collected from various hydrocarbon-rich environments and locations characterized by natural methanogenesis. Different rank coals (i.e., lignite, sub-bituminous, bituminous), complex hydrocarbon sources (i.e., oil shale, waxy crude), hydrocarbon seeps, and natural biogenic environments were incorporated in the sampling. Three levels of screening (down-selection to high grade the most productive consortia) allowed selection of microbial populations, favorable nutrient amendments, sources of the microbial community, and quantification of methane produced from various coal types. Incubation periods of up to twenty-four weeks were evaluated at 23 °C. Headspace concentrations of CH 4 and CO 2 were analyzed by gas chromatography. After a two-week incubation period of the most promising microbes, generated headspace gas concentrations reached 873,400 ppm (154 sft 3/ton or 4.8 scm 3/g) for methane and 176,370 ppm (31 sft 3/ton or 0.9 scm 3/g) for carbon dioxide. Rudimentary statistical assessments – variance analysis (ANOVA) of a single factor - were used to identify trends and levels of significance or impact of the consortia enrichment. We then demonstrated that microbial communities from coal and lake sediments can be enriched and adapted to effectively generate methane under initial atmospheric exposure. The development and enrichment of these methanogenic consortia is described.« less

Developing methanogenic microbial consortia from diverse coal sources and environments

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

Fuertez, John; Boakye, Richard; McLennan, John

Biogenic gas production is a promising alternative or supplement to conventional methane extraction from coalbeds. Adsorbed and free gas, generated over geologic time, can be supplemented with biogenic gas during short-term engineering operations. There are two generic protocols for doing this. The first is to contact the coal with nutrients to support native bacterial development. The second approach is to inject appropriately cultured ex-situ consortia into subsurface coal accumulations. Research has mainly focused on the former: in-situ stimulation of native microbial communities with added nutrients. Relatively few studies have been conducted on the strategies for enriching ex-situ microbial populations undermore » initial atmospheric exposure for subsequent injection into coal seams to stimulate biodegradation, and methanogenesis. In order to evaluate the feasibility of ex-situ cultivation, natural microbial populations were collected from various hydrocarbon-rich environments and locations characterized by natural methanogenesis. Different rank coals (i.e., lignite, sub-bituminous, bituminous), complex hydrocarbon sources (i.e., oil shale, waxy crude), hydrocarbon seeps, and natural biogenic environments were incorporated in the sampling. Three levels of screening (down-selection to high grade the most productive consortia) allowed selection of microbial populations, favorable nutrient amendments, sources of the microbial community, and quantification of methane produced from various coal types. Incubation periods of up to twenty-four weeks were evaluated at 23 °C. Headspace concentrations of CH 4 and CO 2 were analyzed by gas chromatography. After a two-week incubation period of the most promising microbes, generated headspace gas concentrations reached 873,400 ppm (154 sft 3/ton or 4.8 scm 3/g) for methane and 176,370 ppm (31 sft 3/ton or 0.9 scm 3/g) for carbon dioxide. Rudimentary statistical assessments – variance analysis (ANOVA) of a single factor - were used to identify trends and levels of significance or impact of the consortia enrichment. We then demonstrated that microbial communities from coal and lake sediments can be enriched and adapted to effectively generate methane under initial atmospheric exposure. The development and enrichment of these methanogenic consortia is described.« less

Natural selection and infectious disease in human populations

PubMed Central

Karlsson, Elinor K.; Kwiatkowski, Dominic P.; Sabeti, Pardis C.

2015-01-01

The ancient biological 'arms race' between microbial pathogens and humans has shaped genetic variation in modern populations, and this has important implications for the growing field of medical genomics. As humans migrated throughout the world, populations encountered distinct pathogens, and natural selection increased the prevalence of alleles that are advantageous in the new ecosystems in both host and pathogens. This ancient history now influences human infectious disease susceptibility and microbiome homeostasis, and contributes to common diseases that show geographical disparities, such as autoimmune and metabolic disorders. Using new high-throughput technologies, analytical methods and expanding public data resources, the investigation of natural selection is leading to new insights into the function and dysfunction of human biology. PMID:24776769

Microbial ecological associations in the surface sediments of Bohai strait

NASA Astrophysics Data System (ADS)

Wang, Bin; Liu, Hongmei; Tang, Haitian; Hu, Xiaoke

2017-09-01

Microbial communities play key roles in the marine ecosystem. Despite a few studies on marine microbial communities in deep straits, ecological associations among microbial communities in the sediments of shallow straits have not been fully investigated. The Bohai Strait in northern China (average depth less than 20 m) separates the Bohai Sea from the Yellow Sea and has organic-rich sediments. In this study, in the summer of 2014, six stations across the strait were selected to explore the taxonomic composition of microbial communities and their ecological associations. The four most abundant classes were Gammaproteobacteria, Deltaproteobacteria, Bacilli and Flavobacteriia. Temperature, total carbon, depth, nitrate, fishery breeding and cold water masses influenced the microbial communities, as suggested by representational difference and composition analyses. Network analysis of microbial associations revealed that key families included Flavobacteriaceae, Pirellulaceae and Piscirickettsiaceae. Our findings suggest that the families with high phylogenetic diversity are key populations in the microbial association network that ensure the stability of microbial ecosystems. Our study contributes to a better understanding of microbial ecology in complex hydrological environments.

Patterns of Endemism and Habitat Selection in Coalbed Microbial Communities

PubMed Central

Lawson, Christopher E.; Strachan, Cameron R.; Williams, Dominique D.; Koziel, Susan; Hallam, Steven J.

2015-01-01

Microbially produced methane, a versatile, cleaner-burning alternative energy resource to fossil fuels, is sourced from a variety of natural and engineered ecosystems, including marine sediments, anaerobic digesters, shales, and coalbeds. There is a prevailing interest in developing environmental biotechnologies to enhance methane production. Here, we use small-subunit rRNA gene sequencing and metagenomics to better describe the interplay between coalbed methane (CBM) well conditions and microbial communities in the Alberta Basin. Our results show that CBM microbial community structures display patterns of endemism and habitat selection across the Alberta Basin, consistent with observations from other geographical locations. While some phylum-level taxonomic patterns were observed, relative abundances of specific taxonomic groups were localized to discrete wells, likely shaped by local environmental conditions, such as coal rank and depth-dependent physicochemical conditions. To better resolve functional potential within the CBM milieu, a metagenome from a deep volatile-bituminous coal sample was generated. This sample was dominated by Rhodobacteraceae genotypes, resolving a near-complete population genome bin related to Celeribacter sp. that encoded metabolic pathways for the degradation of a wide range of aromatic compounds and the production of methanogenic substrates via acidogenic fermentation. Genomic comparisons between the Celeribacter sp. population genome and related organisms isolated from different environments reflected habitat-specific selection pressures that included nitrogen availability and the ability to utilize diverse carbon substrates. Taken together, our observations reveal that both endemism and metabolic specialization should be considered in the development of biostimulation strategies for nonproductive wells or for those with declining productivity. PMID:26341214

Selective Pressure of Temperature on Competition and Cross-Feeding within Denitrifying and Fermentative Microbial Communities

PubMed Central

Hanke, Anna; Berg, Jasmine; Hargesheimer, Theresa; Tegetmeyer, Halina E.; Sharp, Christine E.; Strous, Marc

2016-01-01

In coastal marine sediments, denitrification and fermentation are important processes in the anaerobic decomposition of organic matter. Microbial communities performing these two processes were enriched from tidal marine sediments in replicated, long term chemostat incubations at 10 and 25°C. Whereas denitrification rates at 25°C were more or less stable over time, at 10°C denitrification activity was unstable and could only be sustained either by repeatedly increasing the amount of carbon substrates provided or by repeatedly decreasing the dilution rate. Metagenomic and transcriptomic sequencing was performed at different time points and provisional whole genome sequences (WGS) and gene activities of abundant populations were compared across incubations. These analyses suggested that a temperature of 10°C selected for populations related to Vibrionales/Photobacterium that contributed to both fermentation (via pyruvate/formate lyase) and nitrous oxide reduction. At 25°C, denitrifying populations affiliated with Rhodobacteraceae were more abundant. The latter performed complete denitrification, and may have used carbon substrates produced by fermentative populations (cross-feeding). Overall, our results suggest that a mixture of competition—for substrates between fermentative and denitrifying populations, and for electrons between both pathways active within a single population –, and cross feeding—between fermentative and denitrifying populations—controlled the overall rate of denitrification. Temperature was shown to have a strong selective effect, not only on the populations performing either process, but also on the nature of their ecological interactions. Future research will show whether these results can be extrapolated to the natural environment. PMID:26779132

Population densities of indigenous Acidobacteria change in the presence of plant growth promoting rhizobacteria (PGPR) in rhizosphere.

PubMed

Kalam, Sadaf; Das, Subha Narayan; Basu, Anirban; Podile, Appa Rao

2017-05-01

Rhizosphere microbial community has diverse metabolic capabilities and plays a crucial role in maintaining plant health. Oligotrophic plant growth promoting rhizobacteria (PGPR), along with difficult-to-culture microbial fractions, might be involved synergistically in microbe-microbe and plant-microbe interactions in the rhizosphere. Among the difficult-to-culture microbial fractions, Acidobacteria constitutes the most dominant phylum thriving in rhizospheric soils. We selected effective PGPR for tomato and black gram and studied their effect on population densities of acidobacterial members. Three facultatively oligotrophic PGPR were identified through 16S rRNA gene sequencing as Sphingobacterium sp. (P3), Variovorax sp. (P4), and Roseomonas sp. (A2); the latter being a new report of PGPR. In presence of selected PGPR strains, the changes in population densities of Acidobacteria were monitored in metagenomic DNA extracted from bulk and rhizospheric soils of tomato and black gram using real time qPCR. A gradual increase in equivalent cell numbers of Acidobacteria members was observed over time along with a simultaneous increase in plant growth promotion by test PGPR. We report characterization of three effective PGPR strains and their effects on indigenous, underexplored difficult-to-culture phylum-Acidobacteria. We suggest that putative interactions between these two bacterial groups thriving in rhizospheric soils could be beneficial for plant growth. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Clonality, genetic diversity and support for the diversifying selection hypothesis in natural populations of a flower-living yeast.

PubMed

Herrera, C M; Pozo, M I; Bazaga, P

2011-11-01

Vast amounts of effort have been devoted to investigate patterns of genetic diversity and structuring in plants and animals, but similar information is scarce for organisms of other kingdoms. The study of the genetic structure of natural populations of wild yeasts can provide insights into the ecological and genetic correlates of clonality, and into the generality of recent hypotheses postulating that microbial populations lack the potential for genetic divergence and allopatric speciation. Ninety-one isolates of the flower-living yeast Metschnikowia gruessii from southeastern Spain were DNA fingerprinted using amplified fragment length polymorphism (AFLP) markers. Genetic diversity and structuring was investigated with band-based methods and model- and nonmodel-based clustering. Linkage disequilibrium tests were used to assess reproduction mode. Microsite-dependent, diversifying selection was tested by comparing genetic characteristics of isolates from bumble bee vectors and different floral microsites. AFLP polymorphism (91%) and genotypic diversity were very high. Genetic diversity was spatially structured, as shown by amova (Φ(st)  = 0.155) and clustering. The null hypothesis of random mating was rejected, clonality seeming the prevailing reproductive mode in the populations studied. Genetic diversity of isolates declined from bumble bee mouthparts to floral microsites, and frequency of five AFLP markers varied significantly across floral microsites, thus supporting the hypothesis of diversifying selection on clonal lineages. Wild populations of clonal fungal microbes can exhibit levels of genetic diversity and spatial structuring that are not singularly different from those shown by sexually reproducing plants or animals. Microsite-dependent, divergent selection can maintain high local and regional genetic diversity in microbial populations despite extensive clonality. © 2011 Blackwell Publishing Ltd.

Allele Surfing Promotes Microbial Adaptation from Standing Variation

PubMed Central

Gralka, Matti; Stiewe, Fabian; Farrell, Fred; Möbius, Wolfram; Waclaw, Bartek; Hallatschek, Oskar

2016-01-01

The coupling of ecology and evolution during range expansions enables mutations to establish at expanding range margins and reach high frequencies. This phenomenon, called allele surfing, is thought to have caused revolutions in the gene pool of many species, most evidently in microbial communities. It has remained unclear, however, under which conditions allele surfing promotes or hinders adaptation. Here, using microbial experiments and simulations, we show that, starting with standing adaptive variation, range expansions generate a larger increase in mean fitness than spatially uniform population expansions. The adaptation gain results from ‘soft’ selective sweeps emerging from surfing beneficial mutations. The rate of these surfing events is shown to sensitively depend on the strength of genetic drift, which varies among strains and environmental conditions. More generally, allele surfing promotes the rate of adaptation per biomass produced, which could help developing biofilms and other resource-limited populations to cope with environmental challenges. PMID:27307400

Drift in ocean currents impacts intergenerational microbial exposure to temperature

PubMed Central

Doblin, Martina A.; van Sebille, Erik

2016-01-01

Microbes are the foundation of marine ecosystems [Falkowski PG, Fenchel T, Delong EF (2008) Science 320(5879):1034–1039]. Until now, the analytical framework for understanding the implications of ocean warming on microbes has not considered thermal exposure during transport in dynamic seascapes, implying that our current view of change for these critical organisms may be inaccurate. Here we show that upper-ocean microbes experience along-trajectory temperature variability up to 10 °C greater than seasonal fluctuations estimated in a static frame, and that this variability depends strongly on location. These findings demonstrate that drift in ocean currents can increase the thermal exposure of microbes and suggests that microbial populations with broad thermal tolerance will survive transport to distant regions of the ocean and invade new habitats. Our findings also suggest that advection has the capacity to influence microbial community assemblies, such that regions with strong currents and large thermal fluctuations select for communities with greatest plasticity and evolvability, and communities with narrow thermal performance are found where ocean currents are weak or along-trajectory temperature variation is low. Given that fluctuating environments select for individual plasticity in microbial lineages, and that physiological plasticity of ancestors can predict the magnitude of evolutionary responses of subsequent generations to environmental change [Schaum CE, Collins S (2014) Proc Biol Soc 281(1793):20141486], our findings suggest that microbial populations in the sub-Antarctic (∼40°S), North Pacific, and North Atlantic will have the most capacity to adapt to contemporary ocean warming. PMID:27140608

Leaf Treatments with a Protein-Based Resistance Inducer Partially Modify Phyllosphere Microbial Communities of Grapevine

PubMed Central

Cappelletti, Martina; Perazzolli, Michele; Antonielli, Livio; Nesler, Andrea; Torboli, Esmeralda; Bianchedi, Pier L.; Pindo, Massimo; Puopolo, Gerardo; Pertot, Ilaria

2016-01-01

Protein derivatives and carbohydrates can stimulate plant growth, increase stress tolerance, and activate plant defense mechanisms. However, these molecules can also act as a nutritional substrate for microbial communities living on the plant phyllosphere and possibly affect their biocontrol activity against pathogens. We investigated the mechanisms of action of a protein derivative (nutrient broth, NB) against grapevine downy mildew, specifically focusing on the effects of foliar treatments on plant defense stimulation and on the composition and biocontrol features of the phyllosphere microbial populations. NB reduced downy mildew symptoms and induced the expression of defense-related genes in greenhouse- and in vitro-grown plants, indicating the activation of grapevine resistance mechanisms. Furthermore, NB increased the number of culturable phyllosphere bacteria and altered the composition of bacterial and fungal populations on leaves of greenhouse-grown plants. Although, NB-induced changes on microbial populations were affected by the structure of indigenous communities originally residing on grapevine leaves, degrees of disease reduction and defense gene modulation were consistent among the experiments. Thus, modifications in the structure of phyllosphere populations caused by NB application could partially contribute to downy mildew control by competition for space or other biocontrol strategies. Particularly, changes in the abundance of phyllosphere microorganisms may provide a contribution to resistance induction, partially affecting the hormone-mediated signaling pathways involved. Modifying phyllosphere populations by increasing natural biocontrol agents with the application of selected nutritional factors can open new opportunities in terms of sustainable plant protection strategies. PMID:27486468

Excess of mutational jackpot events in expanding populations revealed by spatial Luria–Delbrück experiments

PubMed Central

Fusco, Diana; Gralka, Matti; Kayser, Jona; Anderson, Alex; Hallatschek, Oskar

2016-01-01

The genetic diversity of growing cellular populations, such as biofilms, solid tumours or developing embryos, is thought to be dominated by rare, exceptionally large mutant clones. Yet, the emergence of these mutational jackpot events is only understood in well-mixed populations, where they stem from mutations that arise during the first few cell divisions. To study jackpot events in spatially structured populations, we track mutant clones in microbial populations using fluorescence microscopy and population sequencing. High-frequency mutations are found to be massively enriched in microbial colonies compared with well-shaken liquid cultures, as a result of late-occurring mutations surfing at the edge of range expansions. Thus, jackpot events can be generated not only when mutations arise early but also when they occur at favourable locations, which exacerbates their role in adaptation and disease. In particular, because spatial competition with the wild type keeps most mutant clones in a quiescent state, strong selection pressures that kill the wild type promote drug resistance. PMID:27694797

Excess of mutational jackpot events in expanding populations revealed by spatial Luria-Delbrück experiments.

PubMed

Fusco, Diana; Gralka, Matti; Kayser, Jona; Anderson, Alex; Hallatschek, Oskar

2016-10-03

The genetic diversity of growing cellular populations, such as biofilms, solid tumours or developing embryos, is thought to be dominated by rare, exceptionally large mutant clones. Yet, the emergence of these mutational jackpot events is only understood in well-mixed populations, where they stem from mutations that arise during the first few cell divisions. To study jackpot events in spatially structured populations, we track mutant clones in microbial populations using fluorescence microscopy and population sequencing. High-frequency mutations are found to be massively enriched in microbial colonies compared with well-shaken liquid cultures, as a result of late-occurring mutations surfing at the edge of range expansions. Thus, jackpot events can be generated not only when mutations arise early but also when they occur at favourable locations, which exacerbates their role in adaptation and disease. In particular, because spatial competition with the wild type keeps most mutant clones in a quiescent state, strong selection pressures that kill the wild type promote drug resistance.

Greenhouse gas, animal performance, and bacterial population structure responses to dietary monensin fed to dairy cows.

PubMed

Hamilton, Scott W; DePeters, Edward J; McGarvey, Jeffery A; Lathrop, Jeremy; Mitloehner, Frank M

2010-01-01

The present study investigated the effects of a feed additive and rumen microbial modifier, monensin sodium (monensin), on selected variables in lactating dairy cows. Monensin fed cows (MON, 600 mg d(-1)) were compared with untreated control cows (CON, 0 mg d(-1)) with respect to the effects of monensin on the production of three greenhouse gases (GHG), methane (CH(4)), nitrous oxide (N(2)O), and carbon dioxide (CO(2)), along with animal performance (dry matter intake; DMI), milk production, milk components, plasma urea nitrogen (PUN), milk urea nitrogen (MUN), and the microbial population structure of fresh feces. Measurements of GHG were collected at Days 14 and 60 in an environmental chamber simulating commercial dairy freestall housing conditions. Milk production and DMI measurements were collected twice daily over the 60-d experimental period; milk components, PUN, and MUN were measured on Days 14 and 60. The microbial population structure of feces from 6 MON and 6 CON cows was examined on three different occasions (Days 14, 30, and 60). Monensin did not affect emissions of methane (CH(4)), nitrous oxide (N(2)O), and carbon dioxide (CO(2)). Over a 24-h period, emissions of CH(4), N(2)O, and CO(2) decreased in both MON and CON groups. Animal performance and the microbial population structure of the animal fresh waste were also unaffected for MON vs. CON cows.

Year-round shotgun metagenomes reveal stable microbial communities in agricultural soils and novel ammonia oxidizers responding to fertilization.

PubMed

Orellana, Luis H; Chee-Sanford, Joanne C; Sanford, Robert A; Löffler, Frank E; Konstantinidis, Konstantinos T

2017-11-03

The dynamics of individual microbial populations and their gene functions in agricultural soils, especially after major activities such as nitrogen (N) fertilization, remain elusive but are important for better understanding nutrient cycling. Here, we analyzed 20 short-read metagenomes collected at four time points across one year from two depths (0-5 and 20-30 cm) in two Midwestern agricultural sites representing contrasting soil textures (sandy versus silty-loam), with similar cropping histories. Although microbial community taxonomic and functional compositions differed between the two locations and depths, they were more stable within a depth/site throughout the year than communities in natural water-based ecosystems. For example, among the 69 population genomes assembled from the metagenomes, 75% showed less than 2-fold change in abundance between any two sampling points. Interestingly, six deep-branching Thaumarchaeota and three complete ammonia oxidizer (comammox) Nitrospira populations increased up to 5-fold in abundance upon the addition of N fertilizer. These results indicated that indigenous archaeal ammonia oxidizers may respond faster (more copiotrophic) to N fertilization than previously thought. None of 29 recovered putative denitrifier genomes encoded the complete denitrification pathway, suggesting that denitrification is carried out by a collection of different populations. Altogether, our study identified novel microbial populations and genes responding to seasonal and human-induced perturbations in agricultural soils that should facilitate future monitoring efforts and N-related studies. Importance Even though the impact of agricultural management on the microbial community structure has already been recognized, understanding of the dynamics of individual microbial populations and what functions each population encodes are limited. Yet, this information is important for better understanding nutrient cycling, with potentially important implications for preserving nitrogen in soils and sustainability. Here we show that reconstructed metagenome-assembled genomes (MAGs) are relatively stable in their abundance and functional gene content year-round, and seasonal nitrogen fertilization has selected for novel Thaumarchaeota and comammox Nitrospira nitrifiers that are potentially less oligotrophic compared to their marine counterparts previously studied. Copyright © 2017 American Society for Microbiology.

MOLECULAR DIVERSITY OF DRINKING WATER MICROBIAL COMMUNITIES: A PHYLOGENETIC APPROACH

EPA Science Inventory

Culture-based methods are traditionally used to determine microbiological quality of drinking water even though these methods are highly selective and tend to underestimate the densities and diversity bacterial populations inhabiting distribution systems. In order to better under...

Prospects for the Study of Evolution in the Deep Biosphere

PubMed Central

Biddle, Jennifer F.; Sylvan, Jason B.; Brazelton, William J.; Tully, Benjamin J.; Edwards, Katrina J.; Moyer, Craig L.; Heidelberg, John F.; Nelson, William C.

2012-01-01

Since the days of Darwin, scientists have used the framework of the theory of evolution to explore the interconnectedness of life on Earth and adaptation of organisms to the ever-changing environment. The advent of molecular biology has advanced and accelerated the study of evolution by allowing direct examination of the genetic material that ultimately determines the phenotypes upon which selection acts. The study of evolution has been furthered through examination of microbial evolution, with large population numbers, short generation times, and easily extractable DNA. Such work has spawned the study of microbial biogeography, with the realization that concepts developed in population genetics may be applicable to microbial genomes (Martiny et al., 2006; Manhes and Velicer, 2011). Microbial biogeography and adaptation has been examined in many different environments. Here we argue that the deep biosphere is a unique environment for the study of evolution and list specific factors that can be considered and where the studies may be performed. This publication is the result of the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) theme team on Evolution (www.darkenergybiosphere.org). PMID:22319515

Prospects for the study of evolution in the deep biosphere.

PubMed

Biddle, Jennifer F; Sylvan, Jason B; Brazelton, William J; Tully, Benjamin J; Edwards, Katrina J; Moyer, Craig L; Heidelberg, John F; Nelson, William C

2011-01-01

Since the days of Darwin, scientists have used the framework of the theory of evolution to explore the interconnectedness of life on Earth and adaptation of organisms to the ever-changing environment. The advent of molecular biology has advanced and accelerated the study of evolution by allowing direct examination of the genetic material that ultimately determines the phenotypes upon which selection acts. The study of evolution has been furthered through examination of microbial evolution, with large population numbers, short generation times, and easily extractable DNA. Such work has spawned the study of microbial biogeography, with the realization that concepts developed in population genetics may be applicable to microbial genomes (Martiny et al., 2006; Manhes and Velicer, 2011). Microbial biogeography and adaptation has been examined in many different environments. Here we argue that the deep biosphere is a unique environment for the study of evolution and list specific factors that can be considered and where the studies may be performed. This publication is the result of the NSF-funded Center for Dark Energy Biosphere Investigations (C-DEBI) theme team on Evolution (www.darkenergybiosphere.org).

Geographic parthenogenesis and plant-enemy interactions in the common dandelion.

PubMed

Verhoeven, Koen J F; Biere, Arjen

2013-01-28

Many species with sexual and asexual variants show a pattern of geographic parthenogenesis where asexuals have broader and higher-latitude distribution than sexuals. Because sexual reproduction is often considered a costly evolutionary strategy that is advantageous in the face of selection by coevolving pests and pathogens, one possible explanation for geographic parthenogenesis is that populations at higher latitudes are exposed to fewer pests and pathogens. We tested this hypothesis in the common dandelion (Taraxacum officinale), a species with well-established geographic parthenogenesis, by screening prevalence and effects of several specialized pests and pathogens in natural dandelion populations. We did a population survey of 18 dandelion populations along a geographic transect that ranged from the area where sexual and asexual dandelions co-occur northward into the area where only asexuals occur. In addition we used four southern and four northern populations in a 8x8 cross-inoculation greenhouse experiment in which plants were exposed experimentally to each other's natural field soil microbial communities. The cross-inoculation experiment indicated a higher pathogenicity of soil microbial communities from the southern, mostly sexual, populations compared to soil microbial communities from the northern asexual populations. Northern dandelion populations also showed reduced infestation by a specialized seed-eating weevil. A similar trend of reduced rust fungus infection in northern populations was observed but this trend was not statistically significant. The prevalence of pests and pathogens decreased along the south-to-north axis of geographic parthenogenesis. This highlights the potential of biotic interactions in shaping patterns of geographic parthenogenesis.

Evaluation of microbial dynamics during post-consumption food waste composting.

PubMed

Awasthi, Sanjeev Kumar; Wong, Jonathan W C; Li, Jiao; Wang, Quan; Zhang, Zengqiang; Kumar, Sunil; Awasthi, Mukesh Kumar

2018-03-01

The objective of present study was to evaluate the efficacy of bacterial consortium to boost the microbial population and enzyme activities during post-consumption food waste (PCFWs) composting. Three treatments of PCFWs mixed with saw dust and 10% zeolite (dry weight basis) was design, where treatments T-2 and T-3 were applied with two distinctive bacterial consortium, respectively, while T-1 was served as control. The results showed that total aerobic proteolytic, amylolytic, cellulolytic, oil degrading and total aerobic bacteria populations were significantly higher in treatment T2 and T3 than T1. Consequently, the selected hydrolytic enzymes were also higher in T2 and T3 than T1, whose apparently gave the interesting information about rate of decomposition and end product stability. Furthermore, T2 and T3 showed significant correlations between the enzymatic activities and microbial population with other physico-chemical parameters. Based on germination assays and CO 2 -C evolution rate, T2 and T3 were considered phytotoxic free and highly stable final compost on day 56. Copyright © 2017 Elsevier Ltd. All rights reserved.

The impact of cotton growing practices on soil microbiology and its relation to plant and soil health

NASA Astrophysics Data System (ADS)

Pereg, Lily

2013-04-01

Crop production and agricultural practices heavily impact the soil microbial communities, which differ among varying types of soils and environmental conditions. Soil-borne microbial communities in cotton production systems, as in every other cropping system, consist of microbial populations that may either be pathogenic, beneficial or neutral with respect to the cotton crop. Crop production practices have major roles in determining the composition of microbial communities and function of microbial populations in soils. The structure and function of any given microbial community is determined by various factors, including those that are influenced by farming and those not controlled by farming activities. Examples of the latter are environmental conditions such as soil type, temperature, daylight length and UV radiation, air humidity, atmospheric pressure and some abiotic features of the soil. On the other hand, crop production practices may determine other abiotic soil properties, such as water content, density, oxygen levels, mineral and elemental nutrient levels and the load of other crop-related soil amendments. Moreover, crop production highly influences the biotic properties of the soil and has a major role in determining the fate of soil-borne microbial communities associated with the crop plant. Various microbial strains react differently to the presence of certain plants and plant exudates. Therefore, the type of plant and crop rotations are important factors determining microbial communities. In addition, practice management, e.g. soil cultivation versus crop stubble retention, have a major effect on the soil conditions and, thus, on microbial community structure and function. All of the above-mentioned factors can lead to preferential selection of certain microbial population over others. It may affect not only the composition of microbial communities (diversity and abundance of microbial members) but also the function of the community (the ability of different microbes to perform certain activities). Therefore, agricultural practices may determine the ability of beneficial microbes to realise their plant growth promoting potential or the pathogenic expression of others. This presentation will review the current knowledge about the impact of cotton growing practices on microbial communities and soil health in different environments as well as endeavour to identify gaps worthwhile exploring in future research for promoting plant growth in healthy soils.

Effects of triclosan on bacterial community composition and Vibrio populations in natural seawater microcosms

EPA Science Inventory

Pharmaceuticals and personal care products, including antimicrobials, can be found at trace levels in treated wastewater effluent. Impacts of chemical contaminants on coastal aquatic microbial community structure and pathogen abundance are unknown despite the potential for select...

Copolymers enhance selective bacterial community colonization for potential root zone applications.

PubMed

Pham, Vy T H; Murugaraj, Pandiyan; Mathes, Falko; Tan, Boon K; Truong, Vi Khanh; Murphy, Daniel V; Mainwaring, David E

2017-11-21

Managing the impact of anthropogenic and climate induced stress on plant growth remains a challenge. Here we show that polymeric hydrogels, which maintain their hydrous state, can be designed to exploit functional interactions with soil microorganisms. This microbial enhancement may mitigate biotic and abiotic stresses limiting productivity. The presence of mannan chains within synthetic polyacrylic acid (PAA) enhanced the dynamics and selectivity of bacterial ingress in model microbial systems and soil microcosms. Pseudomonas fluorescens exhibiting high mannan binding adhesins showed higher ingress and localised microcolonies throughout the polymeric network. In contrast, ingress of Bacillus subtilis, lacking adhesins, was unaltered by mannan showing motility comparable to bulk liquids. Incubation within microcosms of an agricultural soil yielded hydrogel populations significantly increased from the corresponding soil. Bacterial diversity was markedly higher in mannan containing hydrogels compared to both control polymer and soil, indicating enhanced selectivity towards microbial families that contain plant beneficial species. Here we propose functional polymers applied to the potential root zone which can positively influence rhizobacteria colonization and potentially plant growth as a new approach to stress tolerance.

Interplay Between Innate Immunity and the Plant Microbiota.

PubMed

Hacquard, Stéphane; Spaepen, Stijn; Garrido-Oter, Ruben; Schulze-Lefert, Paul

2017-08-04

The innate immune system of plants recognizes microbial pathogens and terminates their growth. However, recent findings suggest that at least one layer of this system is also engaged in cooperative plant-microbe interactions and influences host colonization by beneficial microbial communities. This immune layer involves sensing of microbe-associated molecular patterns (MAMPs) by pattern recognition receptors (PRRs) that initiate quantitative immune responses to control host-microbial load, whereas diversification of MAMPs and PRRs emerges as a mechanism that locally sculpts microbial assemblages in plant populations. This suggests a more complex microbial management role of the innate immune system for controlled accommodation of beneficial microbes and in pathogen elimination. The finding that similar molecular strategies are deployed by symbionts and pathogens to dampen immune responses is consistent with this hypothesis but implies different selective pressures on the immune system due to contrasting outcomes on plant fitness. The reciprocal interplay between microbiota and the immune system likely plays a critical role in shaping beneficial plant-microbiota combinations and maintaining microbial homeostasis.

Neutral theory, microbial practice: challenges in bacterial population genetics.

PubMed

Rocha, Eduardo P C

2018-04-19

Kimura's outstanding contributions to population genetics included many elegant theoretical results on the vagaries of alleles in populations. Once polymorphism data showed extensive variation in natural populations, these results led naturally to the Neutral Theory. In this article, I'll depart from some of these results to focus on four major open problems in microbial population genetics with direct implications to the study of molecular evolution: the lack of neutral polymorphism, the modeling of genetic exchanges, the population genetics of ill-defined populations, and the difficulty of untangling selection and demography in the light of the previous issues. Whilst studies in population genetics usually focus on single nucleotide polymorphism and allelic recombination, ignoring even small indels, a large fraction of genetic diversification in Bacteria results from horizontal gene transfer. Ignoring this fact defeats the purpose of population genetics: to characterize the genetic variation in populations and their adaptive effects. I'll argue that, following on Kimura's life work, one may need to develop new approaches to study microbes that reproduce asexually but are able to engage in gene exchanges with very distantly related organisms in a context where random sampling is often unachievable, populations are ill-defined, genetic linkage is strong, and random drift is rare.

Plants Rather than Mineral Fertilization Shape Microbial Community Structure and Functional Potential in Legacy Contaminated Soil.

PubMed

Ridl, Jakub; Kolar, Michal; Strejcek, Michal; Strnad, Hynek; Stursa, Petr; Paces, Jan; Macek, Tomas; Uhlik, Ondrej

2016-01-01

Plant-microbe interactions are of particular importance in polluted soils. This study sought to determine how selected plants (horseradish, black nightshade and tobacco) and NPK mineral fertilization shape the structure of soil microbial communities in legacy contaminated soil and the resultant impact of treatment on the soil microbial community functional potential. To explore these objectives, we combined shotgun metagenomics and 16S rRNA gene amplicon high throughput sequencing with data analysis approaches developed for RNA-seq. We observed that the presence of any of the selected plants rather than fertilization shaped the microbial community structure, and the microbial populations of the root zone of each plant significantly differed from one another and/or from the bulk soil, whereas the effect of the fertilizer proved to be insignificant. When we compared microbial diversity in root zones versus bulk soil, we observed an increase in the relative abundance of Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria or Bacteroidetes, taxa which are commonly considered copiotrophic. Our results thus align with the theory that fast-growing, copiotrophic, microorganisms which are adapted to ephemeral carbon inputs are enriched in the vegetated soil. Microbial functional potential indicated that some genetic determinants associated with signal transduction mechanisms, defense mechanisms or amino acid transport and metabolism differed significantly among treatments. Genetic determinants of these categories tend to be overrepresented in copiotrophic organisms. The results of our study further elucidate plant-microbe relationships in a contaminated environment with possible implications for the phyto/rhizoremediation of contaminated areas.

Microbial community composition along a 50 000-year lacustrine sediment sequence

PubMed Central

Ariztegui, Daniel; Horn, Fabian; Kallmeyer, Jens; Orsi, William D

2018-01-01

Abstract For decades, microbial community composition in subseafloor sediments has been the focus of extensive studies. In deep lacustrine sediments, however, the taxonomic composition of microbial communities remains undercharacterized. Greater knowledge on microbial diversity in lacustrine sediments would improve our understanding of how environmental factors, and resulting selective pressures, shape subsurface biospheres in marine and freshwater sediments. Using high-throughput sequencing of 16S rRNA genes across high-resolution climate intervals covering the last 50 000 years in Laguna Potrok Aike, Argentina, we identified changes in microbial populations in response to both past environmental conditions and geochemical changes of the sediment during burial. Microbial communities in Holocene sediments were most diverse, reflecting a layering of taxa linked to electron acceptors availability. In deeper intervals, the data show that salinity, organic matter and the depositional conditions over the Last Glacial-interglacial cycle were all selective pressures in the deep lacustrine assemblage resulting in a genetically distinct biosphere from the surface dominated primarily by Bathyarchaeota and Atribacteria groups. However, similar to marine sediments, some dominant taxa in the shallow subsurface persisted into the subsurface as minor fraction of the community. The subsequent establishment of a deep subsurface community likely results from a combination of paleoenvironmental factors that have shaped the pool of available substrates, together with substrate depletion and/or reworking of organic matter with depth. PMID:29471361

Sexual reproduction and the evolution of microbial pathogens.

PubMed

Heitman, Joseph

2006-09-05

Three common systemic human fungal pathogens--Cryptococcus neoformans, Candida albicans and Aspergillus fumigatus--have retained all the machinery to engage in sexual reproduction, and yet their populations are often clonal with limited evidence for recombination. Striking parallels have emerged with four protozoan parasites that infect humans: Toxoplasma gondii, Trypanosoma brucei, Trypanosoma cruzi and Plasmodium falciparum. Limiting sexual reproduction appears to be a common virulence strategy, enabling generation of clonal populations well adapted to host and environmental niches, yet retaining the ability to engage in sexual or parasexual reproduction and respond to selective pressure. Continued investigation of the sexual nature of microbial pathogens should facilitate both laboratory investigation and an understanding of the complex interplay between pathogens, hosts, vectors, and their environments.

Demographic noise can reverse the direction of deterministic selection

PubMed Central

Constable, George W. A.; Rogers, Tim; McKane, Alan J.; Tarnita, Corina E.

2016-01-01

Deterministic evolutionary theory robustly predicts that populations displaying altruistic behaviors will be driven to extinction by mutant cheats that absorb common benefits but do not themselves contribute. Here we show that when demographic stochasticity is accounted for, selection can in fact act in the reverse direction to that predicted deterministically, instead favoring cooperative behaviors that appreciably increase the carrying capacity of the population. Populations that exist in larger numbers experience a selective advantage by being more stochastically robust to invasions than smaller populations, and this advantage can persist even in the presence of reproductive costs. We investigate this general effect in the specific context of public goods production and find conditions for stochastic selection reversal leading to the success of public good producers. This insight, developed here analytically, is missed by the deterministic analysis as well as by standard game theoretic models that enforce a fixed population size. The effect is found to be amplified by space; in this scenario we find that selection reversal occurs within biologically reasonable parameter regimes for microbial populations. Beyond the public good problem, we formulate a general mathematical framework for models that may exhibit stochastic selection reversal. In this context, we describe a stochastic analog to r−K theory, by which small populations can evolve to higher densities in the absence of disturbance. PMID:27450085

Distinct Trajectories of Massive Recent Gene Gains and Losses in Populations of a Microbial Eukaryotic Pathogen

PubMed Central

Hartmann, Fanny E.; Croll, Daniel

2017-01-01

Abstract Differences in gene content are a significant source of variability within species and have an impact on phenotypic traits. However, little is known about the mechanisms responsible for the most recent gene gains and losses. We screened the genomes of 123 worldwide isolates of the major pathogen of wheat Zymoseptoria tritici for robust evidence of gene copy number variation. Based on orthology relationships in three closely related fungi, we identified 599 gene gains and 1,024 gene losses that have not yet reached fixation within the focal species. Our analyses of gene gains and losses segregating in populations showed that gene copy number variation arose preferentially in subtelomeres and in proximity to transposable elements. Recently lost genes were enriched in virulence factors and secondary metabolite gene clusters. In contrast, recently gained genes encoded mostly secreted protein lacking a conserved domain. We analyzed the frequency spectrum at loci segregating a gene presence–absence polymorphism in four worldwide populations. Recent gene losses showed a significant excess in low-frequency variants compared with genome-wide single nucleotide polymorphism, which is indicative of strong negative selection against gene losses. Recent gene gains were either under weak negative selection or neutral. We found evidence for strong divergent selection among populations at individual loci segregating a gene presence–absence polymorphism. Hence, gene gains and losses likely contributed to local adaptation. Our study shows that microbial eukaryotes harbor extensive copy number variation within populations and that functional differences among recently gained and lost genes led to distinct evolutionary trajectories. PMID:28981698

Geographic parthenogenesis and plant-enemy interactions in the common dandelion

PubMed Central

2013-01-01

Background Many species with sexual and asexual variants show a pattern of geographic parthenogenesis where asexuals have broader and higher-latitude distribution than sexuals. Because sexual reproduction is often considered a costly evolutionary strategy that is advantageous in the face of selection by coevolving pests and pathogens, one possible explanation for geographic parthenogenesis is that populations at higher latitudes are exposed to fewer pests and pathogens. We tested this hypothesis in the common dandelion (Taraxacum officinale), a species with well-established geographic parthenogenesis, by screening prevalence and effects of several specialized pests and pathogens in natural dandelion populations. Results We did a population survey of 18 dandelion populations along a geographic transect that ranged from the area where sexual and asexual dandelions co-occur northward into the area where only asexuals occur. In addition we used four southern and four northern populations in a 8x8 cross-inoculation greenhouse experiment in which plants were exposed experimentally to each other’s natural field soil microbial communities. The cross-inoculation experiment indicated a higher pathogenicity of soil microbial communities from the southern, mostly sexual, populations compared to soil microbial communities from the northern asexual populations. Northern dandelion populations also showed reduced infestation by a specialized seed-eating weevil. A similar trend of reduced rust fungus infection in northern populations was observed but this trend was not statistically significant. Conclusions The prevalence of pests and pathogens decreased along the south-to-north axis of geographic parthenogenesis. This highlights the potential of biotic interactions in shaping patterns of geographic parthenogenesis. PMID:23356700

Environmental drivers of differences in microbial community structure in crude oil reservoirs across a methanogenic gradient

USGS Publications Warehouse

Shelton, Jenna L.; Akob, Denise M.; McIntosh, Jennifer C.; Fierer, Noah; Spear, John R.; Warwick, Peter D.; McCray, John E.

2016-01-01

Stimulating in situ microbial communities in oil reservoirs to produce natural gas is a potentially viable strategy for recovering additional fossil fuel resources following traditional recovery operations. Little is known about what geochemical parameters drive microbial population dynamics in biodegraded, methanogenic oil reservoirs. We investigated if microbial community structure was significantly impacted by the extent of crude oil biodegradation, extent of biogenic methane production, and formation water chemistry. Twenty-two oil production wells from north central Louisiana, USA, were sampled for analysis of microbial community structure and fluid geochemistry. Archaea were the dominant microbial community in the majority of the wells sampled. Methanogens, including hydrogenotrophic and methylotrophic organisms, were numerically dominant in every well, accounting for, on average, over 98% of the total Archaea present. The dominant Bacteria groups were Pseudomonas, Acinetobacter, Enterobacteriaceae, and Clostridiales, which have also been identified in other microbially-altered oil reservoirs. Comparing microbial community structure to fluid (gas, water, and oil) geochemistry revealed that the relative extent of biodegradation, salinity, and spatial location were the major drivers of microbial diversity. Archaeal relative abundance was independent of the extent of methanogenesis, but closely correlated to the extent of crude oil biodegradation; therefore, microbial community structure is likely not a good sole predictor of methanogenic activity, but may predict the extent of crude oil biodegradation. However, when the shallow, highly biodegraded, low salinity wells were excluded from the statistical analysis, no environmental parameters could explain the differences in microbial community structure. This suggests that the microbial community structure of the 5 shallow, up-dip wells was different than the 17 deeper, down-dip wells. Also, the 17 down-dip wells had statistically similar microbial communities despite significant changes in environmental parameters between oil fields. Together, this implies that no single microbial population is a reliable indicator of a reservoir's ability to degrade crude oil to methane, and that geochemistry may be a more important indicator for selecting a reservoir suitable for microbial enhancement of natural gas generation.

Biogeography and organic matter removal shape long-term effects of timber harvesting on forest soil microbial communities.

PubMed

Wilhelm, Roland C; Cardenas, Erick; Maas, Kendra R; Leung, Hilary; McNeil, Larisa; Berch, Shannon; Chapman, William; Hope, Graeme; Kranabetter, J M; Dubé, Stephane; Busse, Matt; Fleming, Robert; Hazlett, Paul; Webster, Kara L; Morris, David; Scott, D Andrew; Mohn, William W

2017-11-01

The growing demand for renewable, carbon-neutral materials and energy is leading to intensified forest land-use. The long-term ecological challenges associated with maintaining soil fertility in managed forests are not yet known, in part due to the complexity of soil microbial communities and the heterogeneity of forest soils. This study determined the long-term effects of timber harvesting, accompanied by varied organic matter (OM) removal, on bacterial and fungal soil populations in 11- to 17-year-old reforested coniferous plantations at 18 sites across North America. Analysis of highly replicated 16 S rRNA gene and ITS region pyrotag libraries and shotgun metagenomes demonstrated consistent changes in microbial communities in harvested plots that included the expansion of desiccation- and heat-tolerant organisms and decline in diversity of ectomycorrhizal fungi. However, the majority of taxa, including the most abundant and cosmopolitan groups, were unaffected by harvesting. Shifts in microbial populations that corresponded to increased temperature and soil dryness were moderated by OM retention, which also selected for sub-populations of fungal decomposers. Biogeographical differences in the distribution of taxa as well as local edaphic and environmental conditions produced substantial variation in the effects of harvesting. This extensive molecular-based investigation of forest soil advances our understanding of forest disturbance and lays the foundation for monitoring long-term impacts of timber harvesting.

RELATIONSHIP BETWEEN THE CONCENTRATION OF DENITRIFIERS AND PSEUDOMONAS SPP. IN SOILS: IMPLICATIONS FOR BTX BIOREMEDIATION (R823420)

EPA Science Inventory

Aquifer microcosms were used to investigate the effect of stimulating denitrification on microbial population shifts and BTX degradation potential. Selective pressure
for facultative denitrifiers was applied to a treatment set by feeding acetate and nitrate, and cycling electr...

Genetic drift at expanding frontiers promotes gene segregation

PubMed Central

Hallatschek, Oskar; Hersen, Pascal; Ramanathan, Sharad; Nelson, David R.

2007-01-01

Competition between random genetic drift and natural selection play a central role in evolution: Whereas nonbeneficial mutations often prevail in small populations by chance, mutations that sweep through large populations typically confer a selective advantage. Here, however, we observe chance effects during range expansions that dramatically alter the gene pool even in large microbial populations. Initially well mixed populations of two fluorescently labeled strains of Escherichia coli develop well defined, sector-like regions with fractal boundaries in expanding colonies. The formation of these regions is driven by random fluctuations that originate in a thin band of pioneers at the expanding frontier. A comparison of bacterial and yeast colonies (Saccharomyces cerevisiae) suggests that this large-scale genetic sectoring is a generic phenomenon that may provide a detectable footprint of past range expansions. PMID:18056799

Kombucha Multimicrobial Community under Simulated Spaceflight and Martian Conditions

NASA Astrophysics Data System (ADS)

Podolich, O.; Zaets, I.; Kukharenko, O.; Orlovska, I.; Reva, O.; Khirunenko, L.; Sosnin, M.; Haidak, A.; Shpylova, S.; Rabbow, E.; Skoryk, M.; Kremenskoy, M.; Demets, R.; Kozyrovska, N.; de Vera, J.-P.

2017-05-01

Kombucha microbial community (KMC) produces a cellulose-based biopolymer of industrial importance and a probiotic beverage. KMC-derived cellulose-based pellicle film is known as a highly adaptive microbial macrocolony—a stratified community of prokaryotes and eukaryotes. In the framework of the multipurpose international astrobiological project "BIOlogy and Mars Experiment (BIOMEX)," which aims to study the vitality of prokaryotic and eukaryotic organisms and the stability of selected biomarkers in low Earth orbit and in a Mars-like environment, a cellulose polymer structural integrity will be assessed as a biomarker and biotechnological nanomaterial. In a preflight assessment program for BIOMEX, the mineralized bacterial cellulose did not exhibit significant changes in the structure under all types of tests. KMC members that inhabit the cellulose-based pellicle exhibited a high survival rate; however, the survival capacity depended on a variety of stressors such as the vacuum of space, a Mars-like atmosphere, UVC radiation, and temperature fluctuations. The critical limiting factor for microbial survival was high-dose UV irradiation. In the tests that simulated a 1-year mission of exposure outside the International Space Station, the core populations of bacteria and yeasts survived and provided protection against UV; however, the microbial density of the populations overall was reduced, which was revealed by implementation of culture-dependent and culture-independent methods. Reduction of microbial richness was also associated with a lower accumulation of chemical elements in the cellulose-based pellicle film, produced by microbiota that survived in the post-test experiments, as compared to untreated cultures that populated the film.

When everything is not everywhere but species evolve: an alternative method to model adaptive properties of marine ecosystems.

PubMed

Sauterey, Boris; Ward, Ben A; Follows, Michael J; Bowler, Chris; Claessen, David

2015-01-01

The functional and taxonomic biogeography of marine microbial systems reflects the current state of an evolving system. Current models of marine microbial systems and biogeochemical cycles do not reflect this fundamental organizing principle. Here, we investigate the evolutionary adaptive potential of marine microbial systems under environmental change and introduce explicit Darwinian adaptation into an ocean modelling framework, simulating evolving phytoplankton communities in space and time. To this end, we adopt tools from adaptive dynamics theory, evaluating the fitness of invading mutants over annual timescales, replacing the resident if a fitter mutant arises. Using the evolutionary framework, we examine how community assembly, specifically the emergence of phytoplankton cell size diversity, reflects the combined effects of bottom-up and top-down controls. When compared with a species-selection approach, based on the paradigm that "Everything is everywhere, but the environment selects", we show that (i) the selected optimal trait values are similar; (ii) the patterns emerging from the adaptive model are more robust, but (iii) the two methods lead to different predictions in terms of emergent diversity. We demonstrate that explicitly evolutionary approaches to modelling marine microbial populations and functionality are feasible and practical in time-varying, space-resolving settings and provide a new tool for exploring evolutionary interactions on a range of timescales in the ocean.

Electrosynthesis of Commodity Chemicals by an Autotrophic Microbial Community

PubMed Central

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

2012-01-01

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

An Algorithm of Association Rule Mining for Microbial Energy Prospection

PubMed Central

Shaheen, Muhammad; Shahbaz, Muhammad

2017-01-01

The presence of hydrocarbons beneath earth’s surface produces some microbiological anomalies in soils and sediments. The detection of such microbial populations involves pure bio chemical processes which are specialized, expensive and time consuming. This paper proposes a new algorithm of context based association rule mining on non spatial data. The algorithm is a modified form of already developed algorithm which was for spatial database only. The algorithm is applied to mine context based association rules on microbial database to extract interesting and useful associations of microbial attributes with existence of hydrocarbon reserve. The surface and soil manifestations caused by the presence of hydrocarbon oxidizing microbes are selected from existing literature and stored in a shared database. The algorithm is applied on the said database to generate direct and indirect associations among the stored microbial indicators. These associations are then correlated with the probability of hydrocarbon’s existence. The numerical evaluation shows better accuracy for non-spatial data as compared to conventional algorithms at generating reliable and robust rules. PMID:28393846

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 conditions (e.g. fluctuations of temperature and/or nutrient levels) coincide with radioactive contamination; (2) an organism’s radioresistance and bioremediation efficiency in rich laboratory media may be insufficient to carry out radionuclide bioremediation in the field—robustness against multiple stressors is needed. PMID:26808049

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

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

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

1999-06-01

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

A trait-based approach for examining microbial community assembly

NASA Astrophysics Data System (ADS)

Prest, T. L.; Nemergut, D.

2015-12-01

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

Prescreening of microbial populations for the assessment of sequencing potential.

PubMed

Hanning, Irene B; Ricke, Steven C

2011-01-01

Next-generation sequencing (NGS) is a powerful tool that can be utilized to profile and compare microbial populations. By amplifying a target gene present in all bacteria and subsequently sequencing amplicons, the bacteria genera present in the populations can be identified and compared. In some scenarios, little to no difference may exist among microbial populations being compared in which case a prescreening method would be practical to determine which microbial populations would be suitable for further analysis by NGS. Denaturing density-gradient electrophoresis (DGGE) is relatively cheaper than NGS and the data comparing microbial populations are ready to be viewed immediately after electrophoresis. DGGE follows essentially the same initial methodology as NGS by targeting and amplifying the 16S rRNA gene. However, as opposed to sequencing amplicons, DGGE amplicons are analyzed by electrophoresis. By prescreening microbial populations with DGGE, more efficient use of NGS methods can be accomplished. In this chapter, we outline the protocol for DGGE targeting the same gene (16S rRNA) that would be targeted for NGS to compare and determine differences in microbial populations from a wide range of ecosystems.

Transitory microbial habitat in the hyperarid Atacama Desert

PubMed Central

Schulze-Makuch, Dirk; Wagner, Dirk; Mangelsdorf, Kai; Devine, Kevin G.; de Vera, Jean-Pierre; Parro, Victor; Kaupenjohann, Martin; Galy, Albert; Schneider, Beate; Airo, Alessandro; Frösler, Jan; Davila, Alfonso F.; Arens, Felix L.; Cáceres, Luis; Cornejo, Francisco Solís; Carrizo, Daniel; Dartnell, Lewis; DiRuggiero, Jocelyne; Ganzert, Lars; Gessner, Mark O.; Grathwohl, Peter; Guan, Lisa; Heinz, Jacob; Hess, Matthias; Keppler, Frank; Maus, Deborah; McKay, Christopher P.; Meckenstock, Rainer U.; Montgomery, Wren; Oberlin, Elizabeth A.; Probst, Alexander J.; Sáenz, Johan S.; Sattler, Tobias; Schirmack, Janosch; Sephton, Mark A.; Schloter, Michael; Uhl, Jenny; Valenzuela, Bernardita; Vestergaard, Gisle; Wörmer, Lars; Zamorano, Pedro

2018-01-01

Traces of life are nearly ubiquitous on Earth. However, a central unresolved question is whether these traces always indicate an active microbial community or whether, in extreme environments, such as hyperarid deserts, they instead reflect just dormant or dead cells. Although microbial biomass and diversity decrease with increasing aridity in the Atacama Desert, we provide multiple lines of evidence for the presence of an at times metabolically active, microbial community in one of the driest places on Earth. We base this observation on four major lines of evidence: (i) a physico-chemical characterization of the soil habitability after an exceptional rain event, (ii) identified biomolecules indicative of potentially active cells [e.g., presence of ATP, phospholipid fatty acids (PLFAs), metabolites, and enzymatic activity], (iii) measurements of in situ replication rates of genomes of uncultivated bacteria reconstructed from selected samples, and (iv) microbial community patterns specific to soil parameters and depths. We infer that the microbial populations have undergone selection and adaptation in response to their specific soil microenvironment and in particular to the degree of aridity. Collectively, our results highlight that even the hyperarid Atacama Desert can provide a habitable environment for microorganisms that allows them to become metabolically active following an episodic increase in moisture and that once it decreases, so does the activity of the microbiota. These results have implications for the prospect of life on other planets such as Mars, which has transitioned from an earlier wetter environment to today’s extreme hyperaridity. PMID:29483268

Transitory microbial habitat in the hyperarid Atacama Desert.

PubMed

Schulze-Makuch, Dirk; Wagner, Dirk; Kounaves, Samuel P; Mangelsdorf, Kai; Devine, Kevin G; de Vera, Jean-Pierre; Schmitt-Kopplin, Philippe; Grossart, Hans-Peter; Parro, Victor; Kaupenjohann, Martin; Galy, Albert; Schneider, Beate; Airo, Alessandro; Frösler, Jan; Davila, Alfonso F; Arens, Felix L; Cáceres, Luis; Cornejo, Francisco Solís; Carrizo, Daniel; Dartnell, Lewis; DiRuggiero, Jocelyne; Flury, Markus; Ganzert, Lars; Gessner, Mark O; Grathwohl, Peter; Guan, Lisa; Heinz, Jacob; Hess, Matthias; Keppler, Frank; Maus, Deborah; McKay, Christopher P; Meckenstock, Rainer U; Montgomery, Wren; Oberlin, Elizabeth A; Probst, Alexander J; Sáenz, Johan S; Sattler, Tobias; Schirmack, Janosch; Sephton, Mark A; Schloter, Michael; Uhl, Jenny; Valenzuela, Bernardita; Vestergaard, Gisle; Wörmer, Lars; Zamorano, Pedro

2018-03-13

Traces of life are nearly ubiquitous on Earth. However, a central unresolved question is whether these traces always indicate an active microbial community or whether, in extreme environments, such as hyperarid deserts, they instead reflect just dormant or dead cells. Although microbial biomass and diversity decrease with increasing aridity in the Atacama Desert, we provide multiple lines of evidence for the presence of an at times metabolically active, microbial community in one of the driest places on Earth. We base this observation on four major lines of evidence: ( i ) a physico-chemical characterization of the soil habitability after an exceptional rain event, ( ii ) identified biomolecules indicative of potentially active cells [e.g., presence of ATP, phospholipid fatty acids (PLFAs), metabolites, and enzymatic activity], ( iii ) measurements of in situ replication rates of genomes of uncultivated bacteria reconstructed from selected samples, and ( iv ) microbial community patterns specific to soil parameters and depths. We infer that the microbial populations have undergone selection and adaptation in response to their specific soil microenvironment and in particular to the degree of aridity. Collectively, our results highlight that even the hyperarid Atacama Desert can provide a habitable environment for microorganisms that allows them to become metabolically active following an episodic increase in moisture and that once it decreases, so does the activity of the microbiota. These results have implications for the prospect of life on other planets such as Mars, which has transitioned from an earlier wetter environment to today's extreme hyperaridity. Copyright © 2018 the Author(s). Published by PNAS.

Transitory microbial habitat in the hyperarid Atacama Desert

NASA Astrophysics Data System (ADS)

Schulze-Makuch, Dirk; Wagner, Dirk; Kounaves, Samuel P.; Mangelsdorf, Kai; Devine, Kevin G.; de Vera, Jean-Pierre; Schmitt-Kopplin, Philippe; Grossart, Hans-Peter; Parro, Victor; Kaupenjohann, Martin; Galy, Albert; Schneider, Beate; Airo, Alessandro; Frösler, Jan; Davila, Alfonso F.; Arens, Felix L.; Cáceres, Luis; Solís Cornejo, Francisco; Carrizo, Daniel; Dartnell, Lewis; DiRuggiero, Jocelyne; Flury, Markus; Ganzert, Lars; Gessner, Mark O.; Grathwohl, Peter; Guan, Lisa; Heinz, Jacob; Hess, Matthias; Keppler, Frank; Maus, Deborah; McKay, Christopher P.; Meckenstock, Rainer U.; Montgomery, Wren; Oberlin, Elizabeth A.; Probst, Alexander J.; Sáenz, Johan S.; Sattler, Tobias; Schirmack, Janosch; Sephton, Mark A.; Schloter, Michael; Uhl, Jenny; Valenzuela, Bernardita; Vestergaard, Gisle; Wörmer, Lars; Zamorano, Pedro

2018-03-01

Traces of life are nearly ubiquitous on Earth. However, a central unresolved question is whether these traces always indicate an active microbial community or whether, in extreme environments, such as hyperarid deserts, they instead reflect just dormant or dead cells. Although microbial biomass and diversity decrease with increasing aridity in the Atacama Desert, we provide multiple lines of evidence for the presence of an at times metabolically active, microbial community in one of the driest places on Earth. We base this observation on four major lines of evidence: (i) a physico-chemical characterization of the soil habitability after an exceptional rain event, (ii) identified biomolecules indicative of potentially active cells [e.g., presence of ATP, phospholipid fatty acids (PLFAs), metabolites, and enzymatic activity], (iii) measurements of in situ replication rates of genomes of uncultivated bacteria reconstructed from selected samples, and (iv) microbial community patterns specific to soil parameters and depths. We infer that the microbial populations have undergone selection and adaptation in response to their specific soil microenvironment and in particular to the degree of aridity. Collectively, our results highlight that even the hyperarid Atacama Desert can provide a habitable environment for microorganisms that allows them to become metabolically active following an episodic increase in moisture and that once it decreases, so does the activity of the microbiota. These results have implications for the prospect of life on other planets such as Mars, which has transitioned from an earlier wetter environment to today’s extreme hyperaridity.

Microbial populations in contaminant plumes

USGS Publications Warehouse

Haack, S.K.; Bekins, B.A.

2000-01-01

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.

Distinct Trajectories of Massive Recent Gene Gains and Losses in Populations of a Microbial Eukaryotic Pathogen.

PubMed

Hartmann, Fanny E; Croll, Daniel

2017-11-01

Differences in gene content are a significant source of variability within species and have an impact on phenotypic traits. However, little is known about the mechanisms responsible for the most recent gene gains and losses. We screened the genomes of 123 worldwide isolates of the major pathogen of wheat Zymoseptoria tritici for robust evidence of gene copy number variation. Based on orthology relationships in three closely related fungi, we identified 599 gene gains and 1,024 gene losses that have not yet reached fixation within the focal species. Our analyses of gene gains and losses segregating in populations showed that gene copy number variation arose preferentially in subtelomeres and in proximity to transposable elements. Recently lost genes were enriched in virulence factors and secondary metabolite gene clusters. In contrast, recently gained genes encoded mostly secreted protein lacking a conserved domain. We analyzed the frequency spectrum at loci segregating a gene presence-absence polymorphism in four worldwide populations. Recent gene losses showed a significant excess in low-frequency variants compared with genome-wide single nucleotide polymorphism, which is indicative of strong negative selection against gene losses. Recent gene gains were either under weak negative selection or neutral. We found evidence for strong divergent selection among populations at individual loci segregating a gene presence-absence polymorphism. Hence, gene gains and losses likely contributed to local adaptation. Our study shows that microbial eukaryotes harbor extensive copy number variation within populations and that functional differences among recently gained and lost genes led to distinct evolutionary trajectories. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Field and Laboratory Evaluations of Insecticides for Southern Pine Beetle Control

Treesearch

Felton L. Hastings; Jack E. Coster; [Editors

1981-01-01

Reports results of laboratory screenings and field studies of insecticides for use against the southern pine beetle. Preventive as webas remedial efficacywere observed, along with phytotoxicity to pine and understory hardwood species, effects of insecticides on soil microbial and mesofaunal populations, and degradation of insecticides by selected soil microbes.

The Impact of Selection, Gene Conversion, and Biased Sampling on the Assessment of Microbial Demography.

PubMed

Lapierre, Marguerite; Blin, Camille; Lambert, Amaury; Achaz, Guillaume; Rocha, Eduardo P C

2016-07-01

Recent studies have linked demographic changes and epidemiological patterns in bacterial populations using coalescent-based approaches. We identified 26 studies using skyline plots and found that 21 inferred overall population expansion. This surprising result led us to analyze the impact of natural selection, recombination (gene conversion), and sampling biases on demographic inference using skyline plots and site frequency spectra (SFS). Forward simulations based on biologically relevant parameters from Escherichia coli populations showed that theoretical arguments on the detrimental impact of recombination and especially natural selection on the reconstructed genealogies cannot be ignored in practice. In fact, both processes systematically lead to spurious interpretations of population expansion in skyline plots (and in SFS for selection). Weak purifying selection, and especially positive selection, had important effects on skyline plots, showing patterns akin to those of population expansions. State-of-the-art techniques to remove recombination further amplified these biases. We simulated three common sampling biases in microbiological research: uniform, clustered, and mixed sampling. Alone, or together with recombination and selection, they further mislead demographic inferences producing almost any possible skyline shape or SFS. Interestingly, sampling sub-populations also affected skyline plots and SFS, because the coalescent rates of populations and their sub-populations had different distributions. This study suggests that extreme caution is needed to infer demographic changes solely based on reconstructed genealogies. We suggest that the development of novel sampling strategies and the joint analyzes of diverse population genetic methods are strictly necessary to estimate demographic changes in populations where selection, recombination, and biased sampling are present. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Among-Population Variation in Microbial Community Structure in the Floral Nectar of the Bee-Pollinated Forest Herb Pulmonaria officinalis L

PubMed Central

Jacquemyn, Hans; Lenaerts, Marijke; Brys, Rein; Willems, Kris; Honnay, Olivier; Lievens, Bart

2013-01-01

Background Microbial communities in floral nectar have been shown to be characterized by low levels of species diversity, yet little is known about among-plant population variation in microbial community composition. Methodology/Principal Findings We investigated the microbial community structure (yeasts and bacteria) in floral nectar of ten fragmented populations of the bee-pollinated forest herb Pulmonaria officinalis. We also explored possible relationships between plant population size and microbial diversity in nectar, and related microbial community composition to the distance separating plant populations. Culturable bacteria and yeasts occurring in the floral nectar of a total of 100 plant individuals were isolated and identified by partially sequencing the 16S rRNA gene and D1/D2 domains of the 26S rRNA gene, respectively. A total of 9 and 11 yeast and 28 and 39 bacterial OTUs was found, taking into account a 3% (OTU0.03) and 1% sequence dissimilarity cut-off (OTU0.01). OTU richness at the plant population level (i.e. the number of OTUs per population) was low for yeasts (mean: 1.7, range: 0–4 OTUs0.01/0.03 per population), whereas on average 6.9 (range: 2–13) OTUs0.03 and 7.9 (range 2–16) OTUs0.01 per population were found for bacteria. Both for yeasts and bacteria, OTU richness was not significantly related to plant population size. Similarity in community composition among populations was low (average Jaccard index: 0.14), and did not decline with increasing distance between populations. Conclusions/Significance We found low similarity in microbial community structure among populations, suggesting that the assembly of nectar microbiota is to a large extent context-dependent. Although the precise factors that affect variation in microbial community structure in floral nectar require further study, our results indicate that both local and regional processes may contribute to among-population variation in microbial community structure in nectar. PMID:23536759

Among-population variation in microbial community structure in the floral nectar of the bee-pollinated forest herb Pulmonaria officinalis L.

PubMed

Jacquemyn, Hans; Lenaerts, Marijke; Brys, Rein; Willems, Kris; Honnay, Olivier; Lievens, Bart

2013-01-01

Microbial communities in floral nectar have been shown to be characterized by low levels of species diversity, yet little is known about among-plant population variation in microbial community composition. We investigated the microbial community structure (yeasts and bacteria) in floral nectar of ten fragmented populations of the bee-pollinated forest herb Pulmonaria officinalis. We also explored possible relationships between plant population size and microbial diversity in nectar, and related microbial community composition to the distance separating plant populations. Culturable bacteria and yeasts occurring in the floral nectar of a total of 100 plant individuals were isolated and identified by partially sequencing the 16S rRNA gene and D1/D2 domains of the 26S rRNA gene, respectively. A total of 9 and 11 yeast and 28 and 39 bacterial OTUs was found, taking into account a 3% (OTU0.03) and 1% sequence dissimilarity cut-off (OTU0.01). OTU richness at the plant population level (i.e. the number of OTUs per population) was low for yeasts (mean: 1.7, range: 0-4 OTUs0.01/0.03 per population), whereas on average 6.9 (range: 2-13) OTUs0.03 and 7.9 (range 2-16) OTUs0.01 per population were found for bacteria. Both for yeasts and bacteria, OTU richness was not significantly related to plant population size. Similarity in community composition among populations was low (average Jaccard index: 0.14), and did not decline with increasing distance between populations. We found low similarity in microbial community structure among populations, suggesting that the assembly of nectar microbiota is to a large extent context-dependent. Although the precise factors that affect variation in microbial community structure in floral nectar require further study, our results indicate that both local and regional processes may contribute to among-population variation in microbial community structure in nectar.

The Utilization of the Microflora Indigenous to and present in Oil-Bearing Formations to Selectively Plug the More Porous Zones Thereby Increasing Oil Recovery During Waterflooding

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

Alex A. Vadie; Lewis R. Brown

1998-04-20

The use of indigenous microbes as a method of profile control in waterfloods is investigated. It is expected that as the microbial population is induced to increase the expanded biomass will selectively block the more permeable zones of the reservoir thereby forcing injection water to flow through the less permeable zones which will result in improved sweep efficiency.

Exogenous glucosinolate produced by Arabidopsis thaliana has an impact on microbes in the rhizosphere and plant roots.

PubMed

Bressan, Mélanie; Roncato, Marie-Anne; Bellvert, Floriant; Comte, Gilles; Haichar, Feth Zahar; Achouak, Wafa; Berge, Odile

2009-11-01

A specificity of Brassicaceous plants is the production of sulphur secondary metabolites called glucosinolates that can be hydrolysed into glucose and biocidal products. Among them, isothiocyanates are toxic to a wide range of microorganisms and particularly soil-borne pathogens. The aim of this study was to investigate the role of glucosinolates and their breakdown products as a factor of selection on rhizosphere microbial community associated with living Brassicaceae. We used a DNA-stable isotope probing approach to focus on the active microbial populations involved in root exudates degradation in rhizosphere. A transgenic Arabidopsis thaliana line producing an exogenous glucosinolate and the associated wild-type plant associated were grown under an enriched (13)CO(2) atmosphere in natural soil. DNA from the rhizospheric soil was separated by density gradient centrifugation. Bacterial (Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Acidobacteria), Archaea and fungal community structures were analysed by DGGE fingerprints of amplified 16S and 18S rRNA gene sequences. Specific populations were characterized by sequencing DGGE fragments. Roots of the transgenic plant line presented an altered profile of glucosinolates and other minor additional modifications. These modifications significantly influenced microbial community on roots and active populations in the rhizosphere. Alphaproteobacteria, particularly Rhizobiaceae, and fungal communities were mainly impacted by these Brassicaceous metabolites, in both structure and composition. Our results showed that even a minor modification in plant root could have important repercussions for soil microbial communities.

Kombucha Multimicrobial Community under Simulated Spaceflight and Martian Conditions.

PubMed

Podolich, O; Zaets, I; Kukharenko, O; Orlovska, I; Reva, O; Khirunenko, L; Sosnin, M; Haidak, A; Shpylova, S; Rabbow, E; Skoryk, M; Kremenskoy, M; Demets, R; Kozyrovska, N; de Vera, J-P

2017-05-01

Kombucha microbial community (KMC) produces a cellulose-based biopolymer of industrial importance and a probiotic beverage. KMC-derived cellulose-based pellicle film is known as a highly adaptive microbial macrocolony-a stratified community of prokaryotes and eukaryotes. In the framework of the multipurpose international astrobiological project "BIOlogy and Mars Experiment (BIOMEX)," which aims to study the vitality of prokaryotic and eukaryotic organisms and the stability of selected biomarkers in low Earth orbit and in a Mars-like environment, a cellulose polymer structural integrity will be assessed as a biomarker and biotechnological nanomaterial. In a preflight assessment program for BIOMEX, the mineralized bacterial cellulose did not exhibit significant changes in the structure under all types of tests. KMC members that inhabit the cellulose-based pellicle exhibited a high survival rate; however, the survival capacity depended on a variety of stressors such as the vacuum of space, a Mars-like atmosphere, UVC radiation, and temperature fluctuations. The critical limiting factor for microbial survival was high-dose UV irradiation. In the tests that simulated a 1-year mission of exposure outside the International Space Station, the core populations of bacteria and yeasts survived and provided protection against UV; however, the microbial density of the populations overall was reduced, which was revealed by implementation of culture-dependent and culture-independent methods. Reduction of microbial richness was also associated with a lower accumulation of chemical elements in the cellulose-based pellicle film, produced by microbiota that survived in the post-test experiments, as compared to untreated cultures that populated the film. Key Words: BIOlogy and Mars Experiment (BIOMEX)-Kombucha multimicrobial community-Biosignature-Biofilm-Bacterial cellulose. Astrobiology 17, 459-469.

Functionally Stable and Phylogenetically Diverse Microbial Enrichments from Microbial Fuel Cells during Wastewater Treatment

PubMed Central

Ishii, Shun'ichi; Suzuki, Shino; Norden-Krichmar, Trina M.; Nealson, Kenneth H.; Sekiguchi, Yuji; Gorby, Yuri A.; Bretschger, Orianna

2012-01-01

Microbial fuel cells (MFCs) are devices that exploit microorganisms as biocatalysts to recover energy from organic matter in the form of electricity. One of the goals of MFC research is to develop the technology for cost-effective wastewater treatment. However, before practical MFC applications are implemented it is important to gain fundamental knowledge about long-term system performance, reproducibility, and the formation and maintenance of functionally-stable microbial communities. Here we report findings from a MFC operated for over 300 days using only primary clarifier effluent collected from a municipal wastewater treatment plant as the microbial resource and substrate. The system was operated in a repeat-batch mode, where the reactor solution was replaced once every two weeks with new primary effluent that consisted of different microbial and chemical compositions with every batch exchange. The turbidity of the primary clarifier effluent solution notably decreased, and 97% of biological oxygen demand (BOD) was removed after an 8–13 day residence time for each batch cycle. On average, the limiting current density was 1000 mA/m2, the maximum power density was 13 mW/m2, and coulombic efficiency was 25%. Interestingly, the electrochemical performance and BOD removal rates were very reproducible throughout MFC operation regardless of the sample variability associated with each wastewater exchange. While MFC performance was very reproducible, the phylogenetic analyses of anode-associated electricity-generating biofilms showed that the microbial populations temporally fluctuated and maintained a high biodiversity throughout the year-long experiment. These results suggest that MFC communities are both self-selecting and self-optimizing, thereby able to develop and maintain functional stability regardless of fluctuations in carbon source(s) and regular introduction of microbial competitors. These results contribute significantly toward the practical application of MFC systems for long-term wastewater treatment as well as demonstrating MFC technology as a useful device to enrich for functionally stable microbial populations. PMID:22347379

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

PubMed Central

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

2015-01-01

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

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

PubMed

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

2015-05-07

Antibiotics leak constantly into environments due to widespread use in agriculture and human therapy. Although sublethal concentrations are well known to select for antibiotic-resistant bacteria, little is known about how bacterial evolution cascades through food webs, having indirect effect on species not directly affected by antibiotics (e.g. via population dynamics or pleiotropic effects). Here, we used an experimental evolution approach to test how temporal patterns of antibiotic stress, as well as migration within metapopulations, affect the evolution and ecology of microcosms containing one prey bacterium, one phage and two protist predators. We found that environmental variability, autocorrelation and migration had only subtle effects for population and evolutionary dynamics. However, unexpectedly, bacteria evolved greatest fitness increases to both antibiotics and enemies when the sublethal levels of antibiotics were highest, indicating positive pleiotropy. Crucially, bacterial adaptation cascaded through the food web leading to reduced predator-to-prey abundance ratio, lowered predator community diversity and increased instability of populations. Our results show that the presence of natural enemies can modify and even reverse the effects of antibiotics on bacteria, and that antibiotic selection can change the ecological properties of multitrophic microbial communities by having indirect effects on species not directly affected by antibiotics. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

The rhizosphere microbiota of plant invaders: an overview of recent advances in the microbiomics of invasive plants

PubMed Central

Coats, Vanessa C.; Rumpho, Mary E.

2014-01-01

Plants in terrestrial systems have evolved in direct association with microbes functioning as both agonists and antagonists of plant fitness and adaptability. As such, investigations that segregate plants and microbes provide only a limited scope of the biotic interactions that dictate plant community structure and composition in natural systems. Invasive plants provide an excellent working model to compare and contrast the effects of microbial communities associated with natural plant populations on plant fitness, adaptation, and fecundity. The last decade of DNA sequencing technology advancements opened the door to microbial community analysis, which has led to an increased awareness of the importance of an organism’s microbiome and the disease states associated with microbiome shifts. Employing microbiome analysis to study the symbiotic networks associated with invasive plants will help us to understand what microorganisms contribute to plant fitness in natural systems, how different soil microbial communities impact plant fitness and adaptability, specificity of host–microbe interactions in natural plant populations, and the selective pressures that dictate the structure of above-ground and below-ground biotic communities. This review discusses recent advances in invasive plant biology that have resulted from microbiome analyses as well as the microbial factors that direct plant fitness and adaptability in natural systems. PMID:25101069

Relative importance of evolutionary dynamics depends on the composition of microbial predator-prey community.

PubMed

Friman, Ville-Petri; Dupont, Alessandra; Bass, David; Murrell, David J; Bell, Thomas

2016-06-01

Community dynamics are often studied in subsets of pairwise interactions. Scaling pairwise interactions back to the community level is, however, problematic because one given interaction might not reflect ecological and evolutionary outcomes of other functionally similar species interactions or capture the emergent eco-evolutionary dynamics arising only in more complex communities. Here we studied this experimentally by exposing Pseudomonas fluorescens SBW25 prey bacterium to four different protist predators (Tetrahymena pyriformis, Tetrahymena vorax, Chilomonas paramecium and Acanthamoeba polyphaga) in all possible single-predator, two-predator and four-predator communities for hundreds of prey generations covering both ecological and evolutionary timescales. We found that only T. pyriformis selected for prey defence in single-predator communities. Although T. pyriformis selection was constrained in the presence of the intraguild predator, T. vorax, T. pyriformis selection led to evolution of specialised prey defence strategies in the presence of C. paramecium or A. polyphaga. At the ecological level, adapted prey populations were phenotypically more diverse, less stable and less productive compared with non-adapted prey populations. These results suggest that predator community composition affects the relative importance of ecological and evolutionary processes and can crucially determine when rapid evolution has the potential to change ecological properties of microbial communities.

Relative importance of evolutionary dynamics depends on the composition of microbial predator–prey community

PubMed Central

Friman, Ville-Petri; Dupont, Alessandra; Bass, David; Murrell, David J; Bell, Thomas

2016-01-01

Community dynamics are often studied in subsets of pairwise interactions. Scaling pairwise interactions back to the community level is, however, problematic because one given interaction might not reflect ecological and evolutionary outcomes of other functionally similar species interactions or capture the emergent eco-evolutionary dynamics arising only in more complex communities. Here we studied this experimentally by exposing Pseudomonas fluorescens SBW25 prey bacterium to four different protist predators (Tetrahymena pyriformis, Tetrahymena vorax, Chilomonas paramecium and Acanthamoeba polyphaga) in all possible single-predator, two-predator and four-predator communities for hundreds of prey generations covering both ecological and evolutionary timescales. We found that only T. pyriformis selected for prey defence in single-predator communities. Although T. pyriformis selection was constrained in the presence of the intraguild predator, T. vorax, T. pyriformis selection led to evolution of specialised prey defence strategies in the presence of C. paramecium or A. polyphaga. At the ecological level, adapted prey populations were phenotypically more diverse, less stable and less productive compared with non-adapted prey populations. These results suggest that predator community composition affects the relative importance of ecological and evolutionary processes and can crucially determine when rapid evolution has the potential to change ecological properties of microbial communities. PMID:26684728

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

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

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

1999-06-01

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

Modeling the impact of the indigenous microbial population on the maximum population density of Salmonella on alfalfa.

PubMed

Rijgersberg, Hajo; Franz, Eelco; Nierop Groot, Masja; Tromp, Seth-Oscar

2013-07-01

Within a microbial risk assessment framework, modeling the maximum population density (MPD) of a pathogenic microorganism is important but often not considered. This paper describes a model predicting the MPD of Salmonella on alfalfa as a function of the initial contamination level, the total count of the indigenous microbial population, the maximum pathogen growth rate and the maximum population density of the indigenous microbial population. The model is parameterized by experimental data describing growth of Salmonella on sprouting alfalfa seeds at inoculum size, native microbial load and Pseudomonas fluorescens 2-79. The obtained model fits well to the experimental data, with standard errors less than ten percent of the fitted average values. The results show that the MPD of Salmonella is not only dictated by performance characteristics of Salmonella but depends on the characteristics of the indigenous microbial population like total number of cells and its growth rate. The model can improve the predictions of microbiological growth in quantitative microbial risk assessments. Using this model, the effects of preventive measures to reduce pathogenic load and a concurrent effect on the background population can be better evaluated. If competing microorganisms are more sensitive to a particular decontamination method, a pathogenic microorganism may grow faster and reach a higher level. More knowledge regarding the effect of the indigenous microbial population (size, diversity, composition) of food products on pathogen dynamics is needed in order to make adequate predictions of pathogen dynamics on various food products.

Effect of an essential oil-containing dentifrice on dental plaque microbial composition.

PubMed

Charles, C H; Vincent, J W; Borycheski, L; Amatnieks, Y; Sarina, M; Qaqish, J; Proskin, H M

2000-09-01

To determine the effect of 6 months use of an essential oil-containing (EO) antiplaque/antigingivitis fluoride dentifrice on the balance of the oral microbial flora and on the emergence of resistant microbial forms by analysis of dental plaque and saliva. The dentifrice essential oils consisted of a fixed combination of thymol, menthol, methyl salicylate, and eucalyptol. An identical fluoride-containing dentifrice without the essential oils served as the control. A subgroup of 66 subjects from a clinical trial population of 321 was randomly selected for characterization of their dental plaque microflora. Saliva was also cultured to monitor for the emergence of opportunistic pathogens. Supragingival plaque and saliva were harvested at baseline, after which subjects received a dental prophylaxis. Subjects were sampled again after 3 and 6 months of product use prior to clinical examination. Plaque was characterized for microbial content by phase contrast microscopy for recognizable cellular morphotypes and by cultivation on nonselective and selective culture media. Determination of the minimum inhibitory concentrations of the test agent against selected Actinomyces and Veillonella isolated bacterial species was conducted at all time points to monitor for the potential development of bacterial resistance. There were no statistically significant differences between the microbial flora obtained from subjects using the essential oil-containing dentifrice and the vehicle control for all parameters and time periods except for the percentage of spirochetes at 6 months and for percentage of "other" microorganisms at 3 months. The EO group exhibited a lower adjusted mean for both parameters. Additionally, there was no evidence of the development of bacterial resistance to the antimicrobial activity of the essential oils or the emergence of opportunistic pathogens.

Formaldehyde as a carbon and electron shuttle between autotroph and heterotroph populations in acidic hydrothermal vents of Norris Geyser Basin, Yellowstone National Park.

PubMed

Moran, James J; Whitmore, Laura M; Isern, Nancy G; Romine, Margaret F; Riha, Krystin M; Inskeep, William P; Kreuzer, Helen W

2016-05-01

The Norris Geyser Basin in Yellowstone National Park contains a large number of hydrothermal systems, which host microbial populations supported by primary productivity associated with a suite of chemolithotrophic metabolisms. We demonstrate that Metallosphaera yellowstonensis MK1, a facultative autotrophic archaeon isolated from a hyperthermal acidic hydrous ferric oxide (HFO) spring in Norris Geyser Basin, excretes formaldehyde during autotrophic growth. To determine the fate of formaldehyde in this low organic carbon environment, we incubated native microbial mat (containing M. yellowstonensis) from a HFO spring with (13)C-formaldehyde. Isotopic analysis of incubation-derived CO2 and biomass showed that formaldehyde was both oxidized and assimilated by members of the community. Autotrophy, formaldehyde oxidation, and formaldehyde assimilation displayed different sensitivities to chemical inhibitors, suggesting that distinct sub-populations in the mat selectively perform these functions. Our results demonstrate that electrons originally resulting from iron oxidation can energetically fuel autotrophic carbon fixation and associated formaldehyde excretion, and that formaldehyde is both oxidized and assimilated by different organisms within the native microbial community. Thus, formaldehyde can effectively act as a carbon and electron shuttle connecting the autotrophic, iron oxidizing members with associated heterotrophic members in the HFO community.

Formaldehyde as a carbon and electron shuttle between autotroph and heterotroph populations in acidic hydrothermal vents of Norris Geyser Basin, Yellowstone National Park

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

Moran, James J.; Whitmore, Laura M.; Isern, Nancy G.

The Norris Geyser Basin in Yellowstone National Park contains a large number of hydrothermal systems, which host microbial populations supported by primary productivity associated with a suite of chemolithotrophic metabolisms. We demonstrate that Metallosphaera yellowstonesis MK1, a facultative autotrophic archaeon isolated from a hyperthermal acidic hydrous ferric oxide (HFO) spring in Norris Geyser Basin, excretes formaldehyde during autotrophic growth. To determine the fate of formaldehyde in this low organic carbon environment, we incubated native microbial mat (containing M. yellowstonensis) from a HFO spring with 13C-formaldehyde. Isotopic analysis of incubation-derived CO2 and biomass showed that formaldehyde was both oxidized and assimilatedmore » by members of the community. Autotrophy, formaldehyde oxidation, and formaldehyde assimilation displayed different sensitivities to chemical inhibitors, suggesting that distinct sub-populations in the mat selectively perform these functions. Our results demonstrate that electrons originally resulting from iron oxidation can energetically fuel autotrophic carbon fixation and associated formaldehyde excretion, and that formaldehyde is both oxidized and assimilated by different organisms within the native microbial community. Thus, formaldehyde can effectively act as a carbon and electron shuttle connecting the autotrophic, iron oxidizing members with associated heterotrophic members in the HFO community.« less

High-sensitivity stable-isotope probing by a quantitative terminal restriction fragment length polymorphism protocol.

PubMed

Andeer, Peter; Strand, Stuart E; Stahl, David A

2012-01-01

Stable-isotope probing (SIP) has proved a valuable cultivation-independent tool for linking specific microbial populations to selected functions in various natural and engineered systems. However, application of SIP to microbial populations with relatively minor buoyant density increases, such as populations that utilize compounds as a nitrogen source, results in reduced resolution of labeled populations. We therefore developed a tandem quantitative PCR (qPCR)-TRFLP (terminal restriction fragment length polymorphism) protocol that improves resolution of detection by quantifying specific taxonomic groups in gradient fractions. This method combines well-controlled amplification with TRFLP analysis to quantify relative taxon abundance in amplicon pools of FAM-labeled PCR products, using the intercalating dye EvaGreen to monitor amplification. Method accuracy was evaluated using mixtures of cloned 16S rRNA genes, DNA extracted from low- and high-G+C bacterial isolates (Escherichia coli, Rhodococcus, Variovorax, and Microbacterium), and DNA from soil microcosms amended with known amounts of genomic DNA from bacterial isolates. Improved resolution of minor shifts in buoyant density relative to TRFLP analysis alone was confirmed using well-controlled SIP analyses.

Drivers of microbial community composition in mesophilic and thermophilic temperature-phased anaerobic digestion pre-treatment reactors.

PubMed

Pervin, Hasina M; Dennis, Paul G; Lim, Hui J; Tyson, Gene W; Batstone, Damien J; Bond, Philip L

2013-12-01

Temperature-phased anaerobic digestion (TPAD) is an emerging technology that facilitates improved performance and pathogen destruction in anaerobic sewage sludge digestion by optimising conditions for 1) hydrolytic and acidogenic organisms in a first-stage/pre-treatment reactor and then 2) methogenic populations in a second stage reactor. Pre-treatment reactors are typically operated at 55-65 °C and as such select for thermophilic bacterial communities. However, details of key microbial populations in hydrolytic communities and links to functionality are very limited. In this study, experimental thermophilic pre-treatment (TP) and control mesophilic pre-treatment (MP) reactors were operated as first-stages of TPAD systems treating activated sludge for 340 days. The TP system was operated sequentially at 50, 60 and 65 °C, while the MP rector was held at 35 °C for the entire period. The composition of microbial communities associated with the MP and TP pre-treatment reactors was characterised weekly using terminal-restriction fragment length polymorphism (T-RFLP) supported by clone library sequencing of 16S rRNA gene amplicons. The outcomes of this approach were confirmed using 454 pyrosequencing of gene amplicons and fluorescence in-situ hybridisation (FISH). TP associated bacterial communities were dominated by populations affiliated to the Firmicutes, Thermotogae, Proteobacteria and Chloroflexi. In particular there was a progression from Thermotogae to Lutispora and Coprothermobacter and diversity decreased as temperature and hydrolysis performance increased. While change in the composition of TP associated bacterial communities was attributable to temperature, that of MP associated bacterial communities was related to the composition of the incoming feed. This study determined processes driving the dynamics of key microbial populations that are correlated with an enhanced hydrolytic functionality of the TPAD system. Copyright © 2013 Elsevier Ltd. All rights reserved.

Microbial succession in an inflated lunar/Mars analog habitat during a 30-day human occupation.

PubMed

Mayer, Teresa; Blachowicz, Adriana; Probst, Alexander J; Vaishampayan, Parag; Checinska, Aleksandra; Swarmer, Tiffany; de Leon, Pablo; Venkateswaran, Kasthuri

2016-06-02

For potential future human missions to the Moon or Mars and sustained presence in the International Space Station, a safe enclosed habitat environment for astronauts is required. Potential microbial contamination of closed habitats presents a risk for crewmembers due to reduced human immune response during long-term confinement. To make future habitat designs safer for crewmembers, lessons learned from characterizing analogous habitats is very critical. One of the key issues is that how human presence influences the accumulation of microorganisms in the closed habitat. Molecular technologies, along with traditional microbiological methods, were utilized to catalog microbial succession during a 30-day human occupation of a simulated inflatable lunar/Mars habitat. Surface samples were collected at different time points to capture the complete spectrum of viable and potential opportunistic pathogenic bacterial population. Traditional cultivation, propidium monoazide (PMA)-quantitative polymerase chain reaction (qPCR), and adenosine triphosphate (ATP) assays were employed to estimate the cultivable, viable, and metabolically active microbial population, respectively. Next-generation sequencing was used to elucidate the microbial dynamics and community profiles at different locations of the habitat during varying time points. Statistical analyses confirm that occupation time has a strong influence on bacterial community profiles. The Day 0 samples (before human occupation) have a very different microbial diversity compared to the later three time points. Members of Proteobacteria (esp. Oxalobacteraceae and Caulobacteraceae) and Firmicutes (esp. Bacillaceae) were most abundant before human occupation (Day 0), while other members of Firmicutes (Clostridiales) and Actinobacteria (esp. Corynebacteriaceae) were abundant during the 30-day occupation. Treatment of samples with PMA (a DNA-intercalating dye for selective detection of viable microbial population) had a significant effect on the microbial diversity compared to non-PMA-treated samples. Statistical analyses revealed a significant difference in community structure of samples over time, particularly of the bacteriomes existing before human occupation of the habitat (Day 0 sampling) and after occupation (Day 13, Day 20, and Day 30 samplings). Actinobacteria (mainly Corynebacteriaceae) and Firmicutes (mainly Clostridiales Incertae Sedis XI and Staphylococcaceae) were shown to increase over the occupation time period. The results of this study revealed a strong relationship between human presence and succession of microbial diversity in a closed habitat. Consequently, it is necessary to develop methods and tools for effective maintenance of a closed system to enable safe human habitation in enclosed environments on Earth and beyond.

The role of lipids in host microbe interactions.

PubMed

Lang, Roland; Mattner, Jochen

2017-06-01

Lipids are one of the major subcellular constituents and serve as signal molecules, energy sources, metabolic precursors and structural membrane components in various organisms. The function of lipids can be modified by multiple biochemical processes such as (de-)phosphorylation or (de-)glycosylation, and the organization of fatty acids into distinct cellular pools and subcellular compartments plays a pivotal role for the morphology and function of various cell populations. Thus, lipids regulate, for example, phagosome formation and maturation within host cells and thus, are critical for the elimination of microbial pathogens. Vice versa, microbial pathogens can manipulate the lipid composition of phagosomal membranes in host cells, and thus avoid their delivery to phagolysosomes. Lipids of microbial origin belong also to the strongest and most versatile inducers of mammalian immune responses upon engagement of distinct receptors on myeloid and lymphoid cells. Furthermore, microbial lipid toxins can induce membrane injuries and cell death. Thus, we will review here selected examples for mutual host-microbe interactions within the broad and divergent universe of lipids in microbial defense, tissue injury and immune evasion.

Microbial Transformation of Esters of Chlorinated Carboxylic Acids

PubMed Central

Paris, D. F.; Wolfe, N. L.; Steen, W. C.

1984-01-01

Two groups of compounds were selected for microbial transformation studies. In the first group were carboxylic acid esters having a fixed aromatic moiety and an increasing length of the alkyl component. Ethyl esters of chlorine-substituted carboxylic acids were in the second group. Microorganisms from environmental waters and a pure culture of Pseudomonas putida U were used. The bacterial populations were monitored by plate counts, and disappearance of the parent compound was followed by gas-liquid chromatography as a function of time. The products of microbial hydrolysis were the respective carboxylic acids. Octanol-water partition coefficients (Kow) for the compounds were measured. These values spanned three orders of magnitude, whereas microbial transformation rate constants (kb) varied only 50-fold. The microbial rate constants of the carboxylic acid esters with a fixed aromatic moiety increased with an increasing length of alkyl substituents. The regression coefficient for the linear relationships between log kb and log Kow was high for group 1 compounds, indicating that these parameters correlated well. The regression coefficient for the linear relationships for group 2 compounds, however, was low, indicating that these parameters correlated poorly. PMID:16346459

Prediction of microbial growth in fresh-cut vegetables treated with acidic electrolyzed water during storage under various temperature conditions.

PubMed

Koseki, S; Itoh, K

2001-12-01

Effects of storage temperature (1, 5, and 10 degrees C) on growth of microbial populations (total aerobic bacteria, coliform bacteria, Bacillus cereus, and psychrotrophic bacteria) on acidic electrolyzed water (AcEW)-treated fresh-cut lettuce and cabbage were determined. A modified Gompertz function was used to describe the kinetics of microbial growth. Growth data were analyzed using regression analysis to generate "best-fit" modified Gompertz equations, which were subsequently used to calculate lag time, exponential growth rate, and generation time. The data indicated that the growth kinetics of each bacterium were dependent on storage temperature, except at 1 degrees C storage. At 1 degrees C storage, no increases were observed in bacterial populations. Treatment of vegetables with AcEW produced a decrease in initial microbial populations. However, subsequent growth rates were higher than on nontreated vegetables. The recovery time required by the reduced microbial population to reach the initial (treated with tap water [TW]) population was also determined in this study, with the recovery time of the microbial population at 10 degrees C being <3 days. The benefits of reducing the initial microbial populations on fresh-cut vegetables were greatly affected by storage temperature. Results from this study could be used to predict microbial quality of fresh-cut lettuce and cabbage throughout their distribution.

Impact of catch crop mixtures and soils on microbial diversity and nitrogen cycling communities in agroecosystems

NASA Astrophysics Data System (ADS)

Burbano, Claudia S.; Große, Julia; Hurek, Thomas; Reinhold-Hurek, Barbara

2017-04-01

In light of the projected world's population growth, food supplies will necessary have to increase. Soils are an essential component for achieving this expansion and its quality and fertility are crucial for bio-economic productivity. Catch crops can be an option to preserve or even improve soil productivity because of their effect on soil fertility and health. A long-term field experiment of the CATCHY project (Catch-cropping as an agrarian tool for continuing soil health and yield-increase) with two contrasting crop rotations was established in two different locations in Northern and Southern Germany. Single catch crops (white mustard, Egyptian clover, phacelia and bristle oat), catch crop mixtures (a mixture of the above and a commercial mixture) and main crops (wheat and maize) have been grown. To investigate how catch crops can affect the microbial diversity and particularly the microbial nitrogen cycling communities, we are studying first the short-term effect of different catch crop mixtures on the microbiomes associated with soils and roots. We compared these microbiomes with wheat plants, representing the microbial community before a catch crop treatment. Roots, rhizosphere and bulk soils were collected from representative samples of wheat plants from one field. The same compartments were also sampled from one fallow treatment and three catch crops variants from three fields each. The variants consisted of white mustard and the two catch crop mixtures. All fields were sampled by triplicate. Quantitative analyses were carried out by qPCR based on key functional marker genes for mineralization (ureC), nitrification (amoA), dissimilatory nitrate and nitrite reduction to ammonium -DNRA- (nrfA), denitrification (nirK, nirS, nosZ), and nitrogen fixation (nifH). These genes were targeted at the DNA and RNA level for the characterization of the microbial population and the actual transcription activity, respectively. We detected the presence and activity of microbial populations capable of performing all the main processes of the N-cycle except DNRA. In bulk soils the expression levels of genes for nitrification and denitrification were significantly higher in Northern than in Southern Germany. In contrast, the expression level of amoA genes in the rhizosphere were significantly higher in Southern than in Northern Germany, suggesting that amoA genes may be controlled by the plant and that this control is dependent on location as well. The microbial population structure was studied using rRNA and nifH amplicon sequencing of DNA extracts obtained from root, rhizosphere and bulk soils of wheat plants and catch crops. DNAs were sequenced using the Illumina platform (MiSeq platform). The OTU-based analysis showed that microbiomes from the three compartments studied were distinct in both locations. Additionally, the taxonomic-based analysis revealed also how plant roots selected for particular bacteria and excluded others. For example, wheat selected for β-Proteobacteria making up 35% of the bacterial community in roots but only 10% in bulk soil. These preliminary results indicate that location and catch crop treatments may have large effects on composition and activity of microbial communities and may be suitable to identify microbial functions which help to maintain or improve soil fertility and plant yield.

Population-Sequencing as a Biomarker of Burkholderia mallei and Burkholderia pseudomallei Evolution through Microbial Forensic Analysis.

PubMed

Jakupciak, John P; Wells, Jeffrey M; Karalus, Richard J; Pawlowski, David R; Lin, Jeffrey S; Feldman, Andrew B

2013-01-01

Large-scale genomics projects are identifying biomarkers to detect human disease. B. pseudomallei and B. mallei are two closely related select agents that cause melioidosis and glanders. Accurate characterization of metagenomic samples is dependent on accurate measurements of genetic variation between isolates with resolution down to strain level. Often single biomarker sensitivity is augmented by use of multiple or panels of biomarkers. In parallel with single biomarker validation, advances in DNA sequencing enable analysis of entire genomes in a single run: population-sequencing. Potentially, direct sequencing could be used to analyze an entire genome to serve as the biomarker for genome identification. However, genome variation and population diversity complicate use of direct sequencing, as well as differences caused by sample preparation protocols including sequencing artifacts and mistakes. As part of a Department of Homeland Security program in bacterial forensics, we examined how to implement whole genome sequencing (WGS) analysis as a judicially defensible forensic method for attributing microbial sample relatedness; and also to determine the strengths and limitations of whole genome sequence analysis in a forensics context. Herein, we demonstrate use of sequencing to provide genetic characterization of populations: direct sequencing of populations.

Population-Sequencing as a Biomarker of Burkholderia mallei and Burkholderia pseudomallei Evolution through Microbial Forensic Analysis

PubMed Central

Jakupciak, John P.; Wells, Jeffrey M.; Karalus, Richard J.; Pawlowski, David R.; Lin, Jeffrey S.; Feldman, Andrew B.

2013-01-01

Large-scale genomics projects are identifying biomarkers to detect human disease. B. pseudomallei and B. mallei are two closely related select agents that cause melioidosis and glanders. Accurate characterization of metagenomic samples is dependent on accurate measurements of genetic variation between isolates with resolution down to strain level. Often single biomarker sensitivity is augmented by use of multiple or panels of biomarkers. In parallel with single biomarker validation, advances in DNA sequencing enable analysis of entire genomes in a single run: population-sequencing. Potentially, direct sequencing could be used to analyze an entire genome to serve as the biomarker for genome identification. However, genome variation and population diversity complicate use of direct sequencing, as well as differences caused by sample preparation protocols including sequencing artifacts and mistakes. As part of a Department of Homeland Security program in bacterial forensics, we examined how to implement whole genome sequencing (WGS) analysis as a judicially defensible forensic method for attributing microbial sample relatedness; and also to determine the strengths and limitations of whole genome sequence analysis in a forensics context. Herein, we demonstrate use of sequencing to provide genetic characterization of populations: direct sequencing of populations. PMID:24455204

Rice rhizosphere soil and root surface bacterial community response to water management changes

USDA-ARS?s Scientific Manuscript database

Different water management practices could affect microbial populations in the rice rhizosphere. A field-scale study was conducted to evaluate microbial populations in the root plaque and rhizosphere of rice in response to continuous and intermittent flooding conditions. Microbial populations in rhi...

Community Structure and Function of Amphibian Skin Microbes: An Experiment with Bullfrogs Exposed to a Chytrid Fungus.

PubMed

Walke, Jenifer B; Becker, Matthew H; Loftus, Stephen C; House, Leanna L; Teotonio, Thais L; Minbiole, Kevin P C; Belden, Lisa K

2015-01-01

The vertebrate microbiome contributes to disease resistance, but few experiments have examined the link between microbiome community structure and disease resistance functions. Chytridiomycosis, a major cause of amphibian population declines, is a skin disease caused by the fungus, Batrachochytrium dendrobatidis (Bd). In a factorial experiment, bullfrog skin microbiota was reduced with antibiotics, augmented with an anti-Bd bacterial isolate (Janthinobacterium lividum), or unmanipulated, and individuals were then either exposed or not exposed to Bd. We found that the microbial community structure of individual frogs prior to Bd exposure influenced Bd infection intensity one week following exposure, which, in turn, was negatively correlated with proportional growth during the experiment. Microbial community structure and function differed among unmanipulated, antibiotic-treated, and augmented frogs only when frogs were exposed to Bd. Bd is a selective force on microbial community structure and function, and beneficial states of microbial community structure may serve to limit the impacts of infection.

Community Structure and Function of Amphibian Skin Microbes: An Experiment with Bullfrogs Exposed to a Chytrid Fungus

PubMed Central

Walke, Jenifer B.; Becker, Matthew H.; Loftus, Stephen C.; House, Leanna L.; Teotonio, Thais L.; Minbiole, Kevin P. C.; Belden, Lisa K.

2015-01-01

The vertebrate microbiome contributes to disease resistance, but few experiments have examined the link between microbiome community structure and disease resistance functions. Chytridiomycosis, a major cause of amphibian population declines, is a skin disease caused by the fungus, Batrachochytrium dendrobatidis (Bd). In a factorial experiment, bullfrog skin microbiota was reduced with antibiotics, augmented with an anti-Bd bacterial isolate (Janthinobacterium lividum), or unmanipulated, and individuals were then either exposed or not exposed to Bd. We found that the microbial community structure of individual frogs prior to Bd exposure influenced Bd infection intensity one week following exposure, which, in turn, was negatively correlated with proportional growth during the experiment. Microbial community structure and function differed among unmanipulated, antibiotic-treated, and augmented frogs only when frogs were exposed to Bd. Bd is a selective force on microbial community structure and function, and beneficial states of microbial community structure may serve to limit the impacts of infection. PMID:26445500

Microbial diversity in innovative mesophilic/thermophilic temperature-phased anaerobic digestion of sludge.

PubMed

Gagliano, M C; Braguglia, C M; Gallipoli, A; Gianico, A; Rossetti, S

2015-05-01

Anaerobic digestion (AD) is one of the few sustainable technologies that both produce energy and treat waste streams. Driven by a complex and diverse community of microbes, AD may be affected by different factors, many of which also influence the composition and activity of the microbial community. In this study, the biodiversity of microbial populations in innovative mesophilic/thermophilic temperature-phased AD of sludge was evaluated by means of fluorescence in situ hybridization (FISH). The increase of digestion temperature drastically affected the microbial composition and selected specialized biomass. Hydrogenotrophic Methanobacteriales and the protein fermentative bacterium Coprothermobacter spp. were identified in the thermophilic anaerobic biomass. Shannon-Weaver diversity (H') and evenness (E) indices were calculated using FISH data. Species richness was lower under thermophilic conditions compared with the values estimated in mesophilic samples, and it was flanked by similar trend of the evenness indicating that thermophilic communities may be therefore more susceptible to sudden changes and less prompt to adapting to operative variations.

Genome-wide Selective Sweeps in Natural Bacterial Populations Revealed by Time-series Metagenomics

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

Chan, Leong-Keat; Bendall, Matthew L.; Malfatti, Stephanie

2014-06-18

Multiple evolutionary models have been proposed to explain the formation of genetically and ecologically distinct bacterial groups. Time-series metagenomics enables direct observation of evolutionary processes in natural populations, and if applied over a sufficiently long time frame, this approach could capture events such as gene-specific or genome-wide selective sweeps. Direct observations of either process could help resolve how distinct groups form in natural microbial assemblages. Here, from a three-year metagenomic study of a freshwater lake, we explore changes in single nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in populations of Chlorobiaceae and Methylophilaceae. SNP analyses revealedmore » substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied considerably among closely related, co-occurring Methylophilaceae populations. SNP allele frequencies, as well as the relative abundance of certain genes, changed dramatically over time in each population. Interestingly, SNP diversity was purged at nearly every genome position in one of the Chlorobiaceae populations over the course of three years, while at the same time multiple genes either swept through or were swept from this population. These patterns were consistent with a genome-wide selective sweep, a process predicted by the ‘ecotype model’ of diversification, but not previously observed in natural populations.« less

Genome-wide Selective Sweeps in Natural Bacterial Populations Revealed by Time-series Metagenomics

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

Chan, Leong-Keat; Bendall, Matthew L.; Malfatti, Stephanie

2014-05-12

Multiple evolutionary models have been proposed to explain the formation of genetically and ecologically distinct bacterial groups. Time-series metagenomics enables direct observation of evolutionary processes in natural populations, and if applied over a sufficiently long time frame, this approach could capture events such as gene-specific or genome-wide selective sweeps. Direct observations of either process could help resolve how distinct groups form in natural microbial assemblages. Here, from a three-year metagenomic study of a freshwater lake, we explore changes in single nucleotide polymorphism (SNP) frequencies and patterns of gene gain and loss in populations of Chlorobiaceae and Methylophilaceae. SNP analyses revealedmore » substantial genetic heterogeneity within these populations, although the degree of heterogeneity varied considerably among closely related, co-occurring Methylophilaceae populations. SNP allele frequencies, as well as the relative abundance of certain genes, changed dramatically over time in each population. Interestingly, SNP diversity was purged at nearly every genome position in one of the Chlorobiaceae populations over the course of three years, while at the same time multiple genes either swept through or were swept from this population. These patterns were consistent with a genome-wide selective sweep, a process predicted by the ecotype model? of diversification, but not previously observed in natural populations.« less

Impact of an indigenous microbial enhanced oil recovery field trial on microbial community structure in a high pour-point oil reservoir.

PubMed

Zhang, Fan; She, Yue-Hui; Li, Hua-Min; Zhang, Xiao-Tao; Shu, Fu-Chang; Wang, Zheng-Liang; Yu, Long-Jiang; Hou, Du-Jie

2012-08-01

Based on preliminary investigation of microbial populations in a high pour-point oil reservoir, an indigenous microbial enhanced oil recovery (MEOR) field trial was carried out. The purpose of the study is to reveal the impact of the indigenous MEOR process on microbial community structure in the oil reservoir using 16Sr DNA clone library technique. The detailed monitoring results showed significant response of microbial communities during the field trial and large discrepancies of stimulated microorganisms in the laboratory and in the natural oil reservoir. More specifically, after nutrients injection, the original dominant populations of Petrobacter and Alishewanella in the production wells almost disappeared. The expected desirable population of Pseudomonas aeruginosa, determined by enrichment experiments in laboratory, was stimulated successfully in two wells of the five monitored wells. Unexpectedly, another potential population of Pseudomonas pseudoalcaligenes which were not detected in the enrichment culture in laboratory was stimulated in the other three monitored production wells. In this study, monitoring of microbial community displayed a comprehensive alteration of microbial populations during the field trial to remedy the deficiency of culture-dependent monitoring methods. The results would help to develop and apply more MEOR processes.

Taking chances and making mistakes: non-genetic phenotypic heterogeneity and its consequences for surviving in dynamic environments

PubMed Central

van Boxtel, Coco; van Heerden, Johan H.; Nordholt, Niclas; Schmidt, Phillipp

2017-01-01

Natural selection has shaped the strategies for survival and growth of microorganisms. The success of microorganisms depends not only on slow evolutionary tuning but also on the ability to adapt to unpredictable changes in their environment. In principle, adaptive strategies range from purely deterministic mechanisms to those that exploit the randomness intrinsic to many cellular and molecular processes. Depending on the environment and selective pressures, particular strategies can lie somewhere along this continuum. In recent years, non-genetic cell-to-cell differences have received a lot of attention, not least because of their potential impact on the ability of microbial populations to survive in dynamic environments. Using several examples, we describe the origins of spontaneous and induced mechanisms of phenotypic adaptation. We identify some of the commonalities of these examples and consider the potential role of chance and constraints in microbial phenotypic adaptation. PMID:28701503

Gut microbial communities of American pikas (Ochotona princeps): Evidence for phylosymbiosis and adaptations to novel diets.

PubMed

Kohl, Kevin D; Varner, Johanna; Wilkening, Jennifer L; Dearing, M Denise

2018-03-01

Gut microbial communities provide many physiological functions to their hosts, especially in herbivorous animals. We still lack an understanding of how these microbial communities are structured across hosts in nature, especially within a given host species. Studies on laboratory mice have demonstrated that host genetics can influence microbial community structure, but that diet can overwhelm these genetic effects. We aimed to test these ideas in a natural system, the American pika (Ochotona princeps). First, pikas are high-elevation specialists with significant population structure across various mountain ranges in the USA, allowing us to investigate whether similarities in microbial communities match host genetic differences. Additionally, pikas are herbivorous, with some populations exhibiting remarkable dietary plasticity and consuming high levels of moss, which is exceptionally high in fibre and low in protein. This allows us to investigate adaptations to an herbivorous diet, as well as to the especially challenging diet of moss. Here, we inventoried the microbial communities of pika caecal pellets from various populations using 16S rRNA sequencing to investigate structuring of microbial communities across various populations with different natural diets. Microbial communities varied significantly across populations, and differences in microbial community structure were congruent with genetic differences in host population structure, a pattern known as "phylosymbiosis." Several microbial members (Ruminococcus, Prevotella, Oxalobacter and Coprococcus) were detected across all samples, and thus likely represent a "core microbiome." These genera are known to perform a number of services for herbivorous hosts such as fibre fermentation and the degradation of plant defensive compounds, and thus are likely important for herbivory in pikas. Moreover, pikas that feed on moss harboured microbial communities highly enriched in Melainabacteria. This uncultivable candidate phylum has been proposed to ferment fibre for herbivores, and thus may contribute to the ability of some pika populations to consume high amounts of moss. These findings demonstrate that both host genetics and diet can influence the microbial communities of the American pika. These animals may be novel sources of fibre-degrading microbes. Last, we discuss the implications of population-specific microbial communities for conservation efforts in this species. © 2017 The Authors. Journal of Animal Ecology © 2017 British Ecological Society.

Comparative Study of Effects of CO 2 Concentration and pH on Microbial Communities from a Saline Aquifer, a Depleted Oil Reservoir, and a Freshwater Aquifer

DOE PAGES

Gulliver, Djuna M.; Lowry, Gregory V.; Gregory, Kelvin B.

2016-08-09

Injected CO 2 from geologic carbon storage is expected to impact the microbial communities of proposed storage sites, such as depleted oil reservoirs and deep saline aquifers, as well as overlying freshwater aquifers at risk of receiving leaking CO 2. Microbial community change in these subsurface sites may affect injectivity of CO 2, permanence of stored CO 2, and shallow subsurface water quality. The effect of CO 2 concentration on the microbial communities in fluid collected from a depleted oil reservoir and a freshwater aquifer was examined at subsurface pressures and temperatures. The community was exposed to 0%, 1%, 10%,more » and 100% pCO 2 for 56 days. Bacterial community structure was analyzed through 16S rRNA gene clone libraries, and total bacterial abundance was estimated through quantitative polymerase chain reaction. Changes in the microbial community observed in the depleted oil reservoir samples and freshwater samples were compared to previous results from CO 2-exposed deep saline aquifer fluids. Overall, results suggest that CO 2 exposure to microbial communities will result in pH-dependent population change, and the CO 2-selected microbial communities will vary among sites. In conclusion, this is the first study to compare the response of multiple subsurface microbial communities at conditions expected during geologic carbon storage, increasing the understanding of environmental drivers for microbial community changes in CO 2-exposed environments.« less

Comparative Study of Effects of CO 2 Concentration and pH on Microbial Communities from a Saline Aquifer, a Depleted Oil Reservoir, and a Freshwater Aquifer

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

Gulliver, Djuna M.; Lowry, Gregory V.; Gregory, Kelvin B.

Injected CO 2 from geologic carbon storage is expected to impact the microbial communities of proposed storage sites, such as depleted oil reservoirs and deep saline aquifers, as well as overlying freshwater aquifers at risk of receiving leaking CO 2. Microbial community change in these subsurface sites may affect injectivity of CO 2, permanence of stored CO 2, and shallow subsurface water quality. The effect of CO 2 concentration on the microbial communities in fluid collected from a depleted oil reservoir and a freshwater aquifer was examined at subsurface pressures and temperatures. The community was exposed to 0%, 1%, 10%,more » and 100% pCO 2 for 56 days. Bacterial community structure was analyzed through 16S rRNA gene clone libraries, and total bacterial abundance was estimated through quantitative polymerase chain reaction. Changes in the microbial community observed in the depleted oil reservoir samples and freshwater samples were compared to previous results from CO 2-exposed deep saline aquifer fluids. Overall, results suggest that CO 2 exposure to microbial communities will result in pH-dependent population change, and the CO 2-selected microbial communities will vary among sites. In conclusion, this is the first study to compare the response of multiple subsurface microbial communities at conditions expected during geologic carbon storage, increasing the understanding of environmental drivers for microbial community changes in CO 2-exposed environments.« less

Host population structure and treatment frequency maintain balancing selection on drug resistance

PubMed Central

Baskerville, Edward B.; Colijn, Caroline; Hanage, William; Fraser, Christophe; Lipsitch, Marc

2017-01-01

It is a truism that antimicrobial drugs select for resistance, but explaining pathogen- and population-specific variation in patterns of resistance remains an open problem. Like other common commensals, Streptococcus pneumoniae has demonstrated persistent coexistence of drug-sensitive and drug-resistant strains. Theoretically, this outcome is unlikely. We modelled the dynamics of competing strains of S. pneumoniae to investigate the impact of transmission dynamics and treatment-induced selective pressures on the probability of stable coexistence. We find that the outcome of competition is extremely sensitive to structure in the host population, although coexistence can arise from age-assortative transmission models with age-varying rates of antibiotic use. Moreover, we find that the selective pressure from antibiotics arises not so much from the rate of antibiotic use per se but from the frequency of treatment: frequent antibiotic therapy disproportionately impacts the fitness of sensitive strains. This same phenomenon explains why serotypes with longer durations of carriage tend to be more resistant. These dynamics may apply to other potentially pathogenic, microbial commensals and highlight how population structure, which is often omitted from models, can have a large impact. PMID:28835542

Natural selection for costly nutrient recycling in simulated microbial metacommunities.

PubMed

Boyle, Richard A; Williams, Hywel T P; Lenton, Timothy M

2012-11-07

Recycling of essential nutrients occurs at scales from microbial communities to global biogeochemical cycles, often in association with ecological interactions in which two or more species utilise each others' metabolic by-products. However, recycling loops may be unstable; sequences of reactions leading to net recycling may be parasitised by side-reactions causing nutrient loss, while some reactions in any closed recycling loop are likely to be costly to participants. Here we examine the stability of nutrient recycling loops in an individual-based ecosystem model based on microbial functional types that differ in their metabolism. A supplied nutrient is utilised by a "source" functional type, generating a secondary nutrient that is subsequently used by two other types-a "mutualist" that regenerates the initial nutrient at a growth rate cost, and a "parasite" that produces a refractory waste product but does not incur any additional cost. The three functional types are distributed across a metacommunity in which separate patches are linked by a stochastic diffusive migration process. Regions of high mutualist abundance feature high levels of nutrient recycling and increased local population density leading to greater export of individuals, allowing the source-mutualist recycling loop to spread across the system. Individual-level selection favouring parasites is balanced by patch-level selection for high productivity, indirectly favouring mutualists due to the synergistic productivity benefits of the recycling loop they support. This suggests that multi-level selection may promote nutrient cycling and thereby help to explain the apparent ubiquity and stability of nutrient recycling in nature.

The Utilization of the Microflora Indigenous to and Present in Oil-Bearing Formations to Selectively Plug the More Porous Zones Thereby Increasing Oil Recovery During Waterflooding

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

Brown, Lewis R.; Stephens, James O.; Vadie, Alex A.

The objective of this work is to demonstrate the use of indigenous microbes as a method of profile control in waterfloods. It is expected that as the microbial population is induced to increase, that the expanded biomass will selectively block the more permeable zones of the reservoir thereby forcing injection water to flow through the less permeable zones which will result in improved sweep efficiency. This increase in microbial population will be accomplished by injecting a nutrient solution into four injectors. Four other injectors will act as control wells. During Phase I, two wells will be cored through the zonemore » of interest. The core will be subjected to special core analyses in order to arrive at the optimum nutrient formulation. During Phase II, nutrient injection will begin, the results monitored, and adjustments to the nutrient composition made, if necessary. Phase II also will include the drilling of three wells for post-mortem core analysis. Phase III will focus on technology transfer of the results. It should be pointed out that one expected outcome of this new technology will be a prolongation of economical waterflooding operations, i.e. economical oil recovery should continue for much longer periods in the producing wells subjected to this selective plugging technique.« less

When everything is not everywhere but species evolve: an alternative method to model adaptive properties of marine ecosystems

PubMed Central

Sauterey, Boris; Ward, Ben A.; Follows, Michael J.; Bowler, Chris; Claessen, David

2015-01-01

The functional and taxonomic biogeography of marine microbial systems reflects the current state of an evolving system. Current models of marine microbial systems and biogeochemical cycles do not reflect this fundamental organizing principle. Here, we investigate the evolutionary adaptive potential of marine microbial systems under environmental change and introduce explicit Darwinian adaptation into an ocean modelling framework, simulating evolving phytoplankton communities in space and time. To this end, we adopt tools from adaptive dynamics theory, evaluating the fitness of invading mutants over annual timescales, replacing the resident if a fitter mutant arises. Using the evolutionary framework, we examine how community assembly, specifically the emergence of phytoplankton cell size diversity, reflects the combined effects of bottom-up and top-down controls. When compared with a species-selection approach, based on the paradigm that “Everything is everywhere, but the environment selects”, we show that (i) the selected optimal trait values are similar; (ii) the patterns emerging from the adaptive model are more robust, but (iii) the two methods lead to different predictions in terms of emergent diversity. We demonstrate that explicitly evolutionary approaches to modelling marine microbial populations and functionality are feasible and practical in time-varying, space-resolving settings and provide a new tool for exploring evolutionary interactions on a range of timescales in the ocean. PMID:25852217

Shifts in spinach microbial communities after chlorine washing and storage at compliant and abusive temperatures.

PubMed

Gu, Ganyu; Ottesen, Andrea; Bolten, Samantha; Ramachandran, Padmini; Reed, Elizabeth; Rideout, Steve; Luo, Yaguang; Patel, Jitendra; Brown, Eric; Nou, Xiangwu

2018-08-01

Fresh produce, like spinach, harbors diverse bacterial populations, including spoilage and potentially pathogenic bacteria. This study examined the effects of produce washing in chlorinated water and subsequent storage on the microbiota of spinach. Baby spinach leaves from a commercial fresh-cut produce processor were assessed before and after washing in chlorinated water, and then after one week's storage at 4, 10, and 15 °C. Microbial communities on spinach were analyzed by non-selective plating, qPCR, and 16S rDNA amplicon sequencing. Bacterial populations on spinach, averaging 6.12 ± 0.61 log CFU/g, were reduced by 1.33 ± 0.57 log after washing. However, populations increased by 1.77-3.24 log after storage, with larger increases occurring at higher temperature (15 > 10 > 4 °C). The predominant phylum identified on unwashed spinach leaves was Proteobacteria; dominant genera were Pseudomonas and Sphingomonas. Bacterial communities shifted significantly after chlorine washing and storage. Several Proteobacteria species, such as Stenotrophomonas sp. and Erwinia sp., were relatively tolerant of chlorine treatment, while species of Flavobacterium and Pedobacter (phylum Bacteroidetes) grew rapidly during storage, especially at abusive temperatures. Cupriavidus sp. and Ralstonia sp. showed significant increases after washing. After storage, microbial communities on spinach appeared to shift back toward the pre-washing distributions. Copyright © 2018. Published by Elsevier Ltd.

The Impact of Population Bottlenecks on Microbial Adaptation

NASA Astrophysics Data System (ADS)

LeClair, Joshua S.; Wahl, Lindi M.

2018-07-01

Population bottlenecks—sudden, severe reductions in population size—are ubiquitous in nature. Because of their critical implications for conservation genetics, the effects of population bottlenecks on the loss of genetic diversity have been well studied. Bottlenecks also have important implications for adaptation, however, and these effects have been addressed more recently, typically in microbial populations. In this short review, we survey both experimental and theoretical work describing the impact of population bottlenecks on microbial adaptation. Focusing on theoretical contributions, we highlight emerging insights and conclude with several open questions of interest in the field.

Active Marine Subsurface Bacterial Population Composition in Low Organic Carbon Environments from IODP Expedition 320

NASA Astrophysics Data System (ADS)

Shepard, A.; Reese, B. K.; Mills, H. J.; IODP Expedition 320 Shipboard Science Party

2011-12-01

The marine subsurface environment contains abundant and active microorganisms. These microbial populations are considered integral players in the marine subsurface biogeochemical system with significance in global geochemical cycles and reservoirs. However, variations in microbial community structure, activity and function associated with the wide-ranging sedimentary and geochemical environments found globally have not been fully resolved. Integrated Ocean Drilling Program Expedition 320 recovered sediments from site U1332. Two sampling depths were selected for analysis that spanned differing lithological units in the sediment core. Sediments were composed of mostly clay with zeolite minerals at 8 meters below sea floor (mbsf). At 27 mbsf, sediments were composed of alternating clayey radiolarian ooze and nannofossil ooze. The concentration of SO42- had little variability throughout the core and the concentration of Fe2+ remained close to, or below, detection limits (0.4 μM). Total organic carbon content ranged from a low of 0.03 wt% to a high of 0.07 wt% between 6 and 30 mbsf providing an opportunity to evaluate marine subsurface microbial communities under extreme electron donor limiting conditions. The metabolically active fraction of the bacterial population was isolated by the extraction and amplification of 16S ribosomal RNA. Pyrosequencing of 16S rRNA transcripts and subsequent bioinformatic analyses provided a robust data set (15,931 total classified sequences) to characterize the community at a high resolution. As observed in other subsurface environments, the overall diversity of active bacterial populations decreased with depth. The population shifted from a diverse but evenly distributed community at approximately 8 mbsf to a Firmicutes dominated population at 27 mbsf (80% of sequences). A total of 95% of the sequences at 27 mbsf were grouped into three genera: Lactobacillus (phylum Firmicutes) at 80% of the total sequences, Marinobacter (phylum Proteobacteria) at 8%, and Formosa (phylum Bacteroidetes) at 7%. These lineages support a paradigm suggesting the importance of fermentation in the subsurface. However, this study extends the predicted range for fermentation below the shallow subsurface and into organic carbon limited marine sediments. Other previously characterized subsurface active populations from environments with higher organic carbon concentrations do not show similar levels of reduced diversity or predominance of fermentative populations. This study further emphasizes the spatial variability of microbial populations in the deep subsurface and highlights the need for continued exploration.

Microbial Existence in Controlled Habitats and Their Resistance to Space Conditions

PubMed Central

Venkateswaran, Kasthuri; La Duc, Myron T.; Horneck, Gerda

2014-01-01

The National Research Council (NRC) has recently recognized the International Space Station (ISS) as uniquely suitable for furthering the study of microbial species in closed habitats. Answering the NRC’s call for the study, in particular, of uncommon microbial species in the ISS, and/or of those that have significantly increased or decreased in number, space microbiologists have begun capitalizing on the maturity, speed, and cost-effectiveness of molecular/genomic microbiological technologies to elucidate changes in microbial populations in the ISS and other closed habitats. Since investigators can only collect samples infrequently from the ISS itself due to logistical reasons, Earth analogs, such as spacecraft-assembly clean rooms, are used and extensively characterized for the presence of microbes. Microbiologists identify the predominant, problematic, and extremophilic microbial species in these closed habitats and use the ISS as a testbed to study their resistance to extreme extraterrestrial environmental conditions. Investigators monitor the microbes exposed to the real space conditions in order to track their genomic changes in response to the selective pressures present in outer space (external to the ISS) and the spaceflight (in the interior of the ISS). In this review, we discussed the presence of microbes in space research-related closed habitats and the resistance of some microbial species to the extreme environmental conditions of space. PMID:25130881

Microbial existence in controlled habitats and their resistance to space conditions.

PubMed

Venkateswaran, Kasthuri; La Duc, Myron T; Horneck, Gerda

2014-09-17

The National Research Council (NRC) has recently recognized the International Space Station (ISS) as uniquely suitable for furthering the study of microbial species in closed habitats. Answering the NRC's call for the study, in particular, of uncommon microbial species in the ISS, and/or of those that have significantly increased or decreased in number, space microbiologists have begun capitalizing on the maturity, speed, and cost-effectiveness of molecular/genomic microbiological technologies to elucidate changes in microbial populations in the ISS and other closed habitats. Since investigators can only collect samples infrequently from the ISS itself due to logistical reasons, Earth analogs, such as spacecraft-assembly clean rooms, are used and extensively characterized for the presence of microbes. Microbiologists identify the predominant, problematic, and extremophilic microbial species in these closed habitats and use the ISS as a testbed to study their resistance to extreme extraterrestrial environmental conditions. Investigators monitor the microbes exposed to the real space conditions in order to track their genomic changes in response to the selective pressures present in outer space (external to the ISS) and the spaceflight (in the interior of the ISS). In this review, we discussed the presence of microbes in space research-related closed habitats and the resistance of some microbial species to the extreme environmental conditions of space.

Why fruit rots: theoretical support for Janzen's theory of microbe-macrobe competition.

PubMed

Ruxton, Graeme D; Wilkinson, David M; Schaefer, H Martin; Sherratt, Thomas N

2014-05-07

We present a formal model of Janzen's influential theory that competition for resources between microbes and vertebrates causes microbes to be selected to make these resources unpalatable to vertebrates. That is, fruit rots, seeds mould and meat spoils, in part, because microbes gain a selective advantage if they can alter the properties of these resources to avoid losing the resources to vertebrate consumers. A previous model had failed to find circumstances in which such a costly spoilage trait could flourish; here, we present a simple analytic model of a general situation where costly microbial spoilage is selected and persists. We argue that the key difference between the two models lies in their treatments of microbial dispersal. If microbial dispersal is sufficiently spatially constrained that different resource items can have differing microbial communities, then spoilage will be selected; however, if microbial dispersal has a strong homogenizing effect on the microbial community then spoilage will not be selected. We suspect that both regimes will exist in the natural world, and suggest how future empirical studies could explore the influence of microbial dispersal on spoilage.

Ecological feedback in quorum-sensing microbial populations can induce heterogeneous production of autoinducers

PubMed Central

Bauer, Matthias; Knebel, Johannes; Lechner, Matthias; Pickl, Peter; Frey, Erwin

2017-01-01

Autoinducers are small signaling molecules that mediate intercellular communication in microbial populations and trigger coordinated gene expression via ‘quorum sensing’. Elucidating the mechanisms that control autoinducer production is, thus, pertinent to understanding collective microbial behavior, such as virulence and bioluminescence. Recent experiments have shown a heterogeneous promoter activity of autoinducer synthase genes, suggesting that some of the isogenic cells in a population might produce autoinducers, whereas others might not. However, the mechanism underlying this phenotypic heterogeneity in quorum-sensing microbial populations has remained elusive. In our theoretical model, cells synthesize and secrete autoinducers into the environment, up-regulate their production in this self-shaped environment, and non-producers replicate faster than producers. We show that the coupling between ecological and population dynamics through quorum sensing can induce phenotypic heterogeneity in microbial populations, suggesting an alternative mechanism to stochastic gene expression in bistable gene regulatory circuits. DOI: http://dx.doi.org/10.7554/eLife.25773.001 PMID:28741470

Long-term Spatial Distribution Patterns of Protozoa in Connected Microhabitats

NASA Astrophysics Data System (ADS)

Taghon, G. L.; Tuorto, S. J.

2016-02-01

Studies of microbial ecosystems usually assume habitat homogeneity. Recent research, however, indicates that habitat structure varies at millimeter scales and that this patchiness affects abundance and behavior of microbes. In this study, two species of ciliated protozoa were maintained, together, for multiple generations in microfluidic devices consisting of arrays of interconnected microhabitats with differing resource availability. The species differed in their population dynamics and tendency to disperse among microhabitats. Both species coexisted for over 45 days, and their coexistence likely resulted from habitat selection at millimeter scales. We demonstrate that it is not only possible, but imperative, that detailed ecological phenomena of microbial systems be studied at the relevant spatial and temporal scales.

Diversity and physiology of polyhydroxyalkanoate-producing and -degrading strains in microbial mats.

PubMed

Villanueva, Laura; Del Campo, Javier; Guerrero, Ricardo

2010-10-01

Photosynthetic microbial mats are sources of microbial diversity and physiological strategies that reflect the physical and metabolic interactions between their resident species. This study focused on the diversity and activity of polyhydroxyalkanoate-producing and -degrading bacteria and their close partnership with cyanobacteria in an estuarine and a hypersaline microbial mat. The aerobic heterotrophic population was characterized on the basis of lipid biomarkers (respiratory quinones, sphingoid bases), polyhydroxyalkanoate determination, biochemical analysis of the isolates, and interaction assays. Most of the polyhydroxyalkanoate-producing isolates obtained from an estuarine mat belonged to the Halomonas and Labrenzia genera, while species of Sphingomonas and Bacillus were more prevalent in the hypersaline mat. Besides, the characterization of heterotrophic bacteria coisolated with filamentous cyanobacteria after selection suggested a specific association between them and diversification of the heterotrophic partner belonging to the Halomonas genus. Preliminary experiments suggested that syntrophic associations between strains of the Pseudoalteromonas and Halomonas genera explain the dynamics of polyhydroxyalkanoate accumulation in some microbial mats. These metabolic interactions and the diversity of the bacteria that participate in them are most likely supported by the strong mutual dependence of the partners. © 2010 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Microbial community composition and endolith colonization at an Arctic thermal spring are driven by calcite precipitation

USGS Publications Warehouse

Starke, Verena; Kirshtein, Julie; Fogel, Marilyn L.; Steele, Andrew

2013-01-01

Environmental conditions shape community composition. Arctic thermal springs provide an opportunity to study how environmental gradients can impose strong selective pressures on microbial communities and provide a continuum of niche opportunities. We use microscopic and molecular methods to conduct a survey of microbial community composition at Troll Springs on Svalbard, Norway, in the high Arctic. Microorganisms there exist under a wide range of environmental conditions: in warm water as periphyton, in moist granular materials, and in cold, dry rock as endoliths. Troll Springs has two distinct ecosystems, aquatic and terrestrial, together in close proximity, with different underlying environmental factors shaping each microbial community. Periphyton are entrapped during precipitation of calcium carbonate from the spring's waters, providing microbial populations that serve as precursors for the development of endolithic communities. This process differs from most endolith colonization, in which the rock predates the communities that colonize it. Community composition is modulated as environmental conditions change within the springs. At Troll, the aquatic environments show a small number of dominant operational taxonomic units (OTUs) that are specific to each sample. The terrestrial environments show a more even distribution of OTUs common to multiple samples.

Overproduction of laccase and pectinase by microbial associations in solid substrate fermentation.

PubMed

Stoilova, Ivanka; Krastanov, Albert

2008-04-01

The growth and the enzymatic production of two microbial fungal associations were studied: Aspergillus niger and Fusarium moniliforme and Trametes versicolor and Aspergillus niger. The synergistic interrelations between the species of the first mixed culture increased the biosynthesis of alpha-amylase and pectinase. T. versicolor and A. niger proved to be compatible partners in the overproduction of the enzyme laccase, whose synthesis surpassed 8.4 times the enzymatic level in the monoculture, with both of the mixed microbial populations cocultivation facilitating the amplified synthesis of enzymes rather than their growth acceleration. A further proof of the presence of synergism established by the cultures was the enzyme volumetric productivities in both of the mixed microbial cultures, which increased parallel to the rise in the combined biomass synthesis. The competent selection of compatible partners can adjust the desired enzymatic levels and compositions in mixed fungal systems aimed at a number of specified designations. Thus, a very high level of laccase production (97,600 IU/g dry weight) was achieved. The chosen fungal strains produce a variety of different enzymes, but first microbial association produces mainly amylase and pectinase, necessary for their growth, and second association produces mainly laccase and pectinase.

INNOVATIVE MIOR PROCESS UTILIZING INDIGENOUS RESERVOIR CONSTITUENTS

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

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

This research program was directed at improving the knowledge of reservoir ecology and developing practical microbial solutions and technologies for improving oil production. The goal was to identify and utilize indigenous microbial populations which can produce beneficial metabolic products and develop a methodology to stimulate those select microbes with nutrient amendments to increase oil recovery. This microbial technology has the capability of producing multiple oil-releasing agents. Experimental laboratory work in model sandpack cores was conducted using microbial cultures isolated from produced water samples. Comparative laboratory studies demonstrating in situ production of microbial products as oil recovery agents were conducted inmore » sand packs with natural field waters using cultures and conditions representative of oil reservoirs. Increased oil recovery in multiple model sandpack systems was achieved and the technology and results were verified by successful field studies. Direct application of the research results has lead to the development of a feasible, practical, successful, and cost-effective technology which increases oil recovery. This technology is now being commercialized and applied in numerous field projects to increase oil recovery. Two field applications of the developed technology reported production increases of 21% and 24% in oil recovery.« less

Response of anaerobes to methyl fluoride, 2-bromoethanesulfonate and hydrogen during acetate degradation.

PubMed

Hao, Liping; Lü, Fan; Li, Lei; Shao, Liming; He, Pinjing

2013-05-01

To use the selective inhibition method for quantitative analysis of acetate metabolism in methanogenic systems, the responses of microbial communities and metabolic activities, which were involved in anaerobic degradation of acetate, to the addition of methyl fluoride (CH3F), 2-bromoethanesulfonate (BES) and hydrogen were investigated in a thermophilic batch experiment. Both the methanogenic inhibitors, i.e., CH3F and BES, showed their effectiveness on inhibiting CH4 production, whereas acetate metabolism other than acetoclastic methanogenesis was stimulated by BES, as reflected by the fluctuated acetate concentration. Syntrophic acetate oxidation was thermodynamically blocked by hydrogen (H2), while H2-utilizing reactions as hydrogenotrophic methanogenesis and homoacetogenesis were correspondingly promoted. Results of PCR-DGGE fingerprinting showed that, CH3F did not influence the microbial populations significantly. However, the BES and hydrogen notably altered the bacterial community structures and increased the diversity. BES gradually changed the methanogenic community structure by affecting the existence of different populations to different levels, whilst H2 greatly changed the abundance of different methanogenic populations, and induced growth of new species.

Ecology and exploration of the rare biosphere.

PubMed

Lynch, Michael D J; Neufeld, Josh D

2015-04-01

The profound influence of microorganisms on human life and global biogeochemical cycles underlines the value of studying the biogeography of microorganisms, exploring microbial genomes and expanding our understanding of most microbial species on Earth: that is, those present at low relative abundance. The detection and subsequent analysis of low-abundance microbial populations—the 'rare biosphere'—have demonstrated the persistence, population dynamics, dispersion and predation of these microbial species. We discuss the ecology of rare microbial populations, and highlight molecular and computational methods for targeting taxonomic 'blind spots' within the rare biosphere of complex microbial communities.

A fosmid cloning strategy for detecting the widest possible spectrum of microbes from the international space station drinking water system.

PubMed

Choi, Sangdun; Chang, Mi Sook; Stuecker, Tara; Chung, Christine; Newcombe, David A; Venkateswaran, Kasthuri

2012-12-01

In this study, fosmid cloning strategies were used to assess the microbial populations in water from the International Space Station (ISS) drinking water system (henceforth referred to as Prebiocide and Tank A water samples). The goals of this study were: to compare the sensitivity of the fosmid cloning strategy with that of traditional culture-based and 16S rRNA-based approaches and to detect the widest possible spectrum of microbial populations during the water purification process. Initially, microbes could not be cultivated, and conventional PCR failed to amplify 16S rDNA fragments from these low biomass samples. Therefore, randomly primed rolling-circle amplification was used to amplify any DNA that might be present in the samples, followed by size selection by using pulsed-field gel electrophoresis. The amplified high-molecular-weight DNA from both samples was cloned into fosmid vectors. Several hundred clones were randomly selected for sequencing, followed by Blastn/Blastx searches. Sequences encoding specific genes from Burkholderia, a species abundant in the soil and groundwater, were found in both samples. Bradyrhizobium and Mesorhizobium, which belong to rhizobia, a large community of nitrogen fixers often found in association with plant roots, were present in the Prebiocide samples. Ralstonia, which is prevalent in soils with a high heavy metal content, was detected in the Tank A samples. The detection of many unidentified sequences suggests the presence of potentially novel microbial fingerprints. The bacterial diversity detected in this pilot study using a fosmid vector approach was higher than that detected by conventional 16S rRNA gene sequencing.

Preliminary characterization of the oral microbiota of Chinese adults with and without gingivitis

PubMed Central

2011-01-01

Background Microbial communities inhabiting human mouth are associated with oral health and disease. Previous studies have indicated the general prevalence of adult gingivitis in China to be high. The aim of this study was to characterize in depth the oral microbiota of Chinese adults with or without gingivitis, by defining the microbial phylogenetic diversity and community-structure using highly paralleled pyrosequencing. Methods Six non-smoking Chinese, three with and three without gingivitis (age range 21-39 years, 4 females and 2 males) were enrolled in the present cross-sectional study. Gingival parameters of inflammation and bleeding on probing were characterized by a clinician using the Mazza Gingival Index (MGI). Plaque (sampled separately from four different oral sites) and salivary samples were obtained from each subject. Sequences and relative abundance of the bacterial 16 S rDNA PCR-amplicons were determined via pyrosequencing that produced 400 bp-long reads. The sequence data were analyzed via a computational pipeline customized for human oral microbiome analyses. Furthermore, the relative abundances of selected microbial groups were validated using quantitative PCR. Results The oral microbiomes from gingivitis and healthy subjects could be distinguished based on the distinct community structures of plaque microbiomes, but not the salivary microbiomes. Contributions of community members to community structure divergence were statistically accessed at the phylum, genus and species-like levels. Eight predominant taxa were found associated with gingivitis: TM7, Leptotrichia, Selenomonas, Streptococcus, Veillonella, Prevotella, Lautropia, and Haemophilus. Furthermore, 98 species-level OTUs were identified to be gingivitis-associated, which provided microbial features of gingivitis at a species resolution. Finally, for the two selected genera Streptococcus and Fusobacterium, Real-Time PCR based quantification of relative bacterial abundance validated the pyrosequencing-based results. Conclusions This methods study suggests that oral samples from this patient population of gingivitis can be characterized via plaque microbiome by pyrosequencing the 16 S rDNA genes. Further studies that characterize serial samples from subjects (longitudinal study design) with a larger population size may provide insight into the temporal and ecological features of oral microbial communities in clinically-defined states of gingivitis. PMID:22152152

Effectiveness of a full-scale horizontal slow sand filter for controlling phytopathogens in recirculating hydroponics: From microbial isolation to full microbiome assessment.

PubMed

Prenafeta-Boldú, Francesc X; Trillas, Isabel; Viñas, Marc; Guivernau, Miriam; Cáceres, Rafaela; Marfà, Oriol

2017-12-01

The microbial disinfestation efficiency of an innovative horizontal-flow slow sand filter (HSSF) for treating nutrient solution spent from an experimental closed-loop nursery was evaluated by means of a combination of culture-dependent and independent molecular techniques. A dense inoculum of the fungal plant pathogen Fusarium oxysporum f.sp. lycopersici was applied in the fertigation system (10 6 cells per mL). Indigenous and introduced populations of eubacteria and fungi were assessed in the nutrient solution, the HSSF influent/effluent, and a sand bed transect by isolation on selective media, as well as by quantitative qPCR and next-generation sequencing (NGS) on target ribosomal genes. The HSSF effectively reduced viable Fusarium propagules and fungal gene content with an efficiency consistently above 99.9% (5 orders of magnitude down). On the other hand, Fusarium cells accumulated in the sand bed, indicating that physical entrapment was the main removal mechanism. The viability of retained Fusarium cells tended to decrease in time, so that treatment efficiency might be enhanced by antagonistic species from the genera Bacillus, Pseudomonas, and Trichoderma, also identified in the sand bed. Indigenous bacterial populations from the HSSF effluent were reduced by 87.2% and 99.9% in terms of colony forming units and gene counts, respectively, when compared to the influent. Furthermore, microbial populations from the HSSF effluent were different from those observed in the sand bed and the influent. In summary, the HSSF microbial disinfestation efficiency is comparable to that reported for other more intensive and costly methodologies, while allowing a significant recovery of water and nutrients. Copyright © 2017 Elsevier B.V. All rights reserved.

Microbial Successions Are Associated with Changes in Chemical Profiles of a Model Refrigerated Fresh Pork Sausage during an 80-Day Shelf Life Study

PubMed Central

David, Jairus R. D.; Gilbreth, Stefanie Evans; Smith, Gordon; Nietfeldt, Joseph; Legge, Ryan; Kim, Jaehyoung; Sinha, Rohita; Duncan, Christopher E.; Ma, Junjie; Singh, Indarpal

2014-01-01

Fresh pork sausage is produced without a microbial kill step and therefore chilled or frozen to control microbial growth. In this report, the microbiota in a chilled fresh pork sausage model produced with or without an antimicrobial combination of sodium lactate and sodium diacetate was studied using a combination of traditional microbiological methods and deep pyrosequencing of 16S rRNA gene amplicons. In the untreated system, microbial populations rose from 102 to 106 CFU/g within 15 days of storage at 4°C, peaking at nearly 108 CFU/g by day 30. Pyrosequencing revealed a complex community at day 0, with taxa belonging to the Bacilli, Gammaproteobacteria, Betaproteobacteria, Actinobacteria, Bacteroidetes, and Clostridia. During storage at 4°C, the untreated system displayed a complex succession, with species of Weissella and Leuconostoc that dominate the product at day 0 being displaced by species of Pseudomonas (P. lini and P. psychrophila) within 15 days. By day 30, a second wave of taxa (Lactobacillus graminis, Carnobacterium divergens, Buttiauxella brennerae, Yersinia mollaretti, and a taxon of Serratia) dominated the population, and this succession coincided with significant chemical changes in the matrix. Treatment with lactate-diacetate altered the dynamics dramatically, yielding a monophasic growth curve of a single species of Lactobacillus (L. graminis), followed by a uniform selective die-off of the majority of species in the population. Of the six species of Lactobacillus that were routinely detected, L. graminis became the dominant member in all samples, and its origins were traced to the spice blend used in the formulation. PMID:24928886

Microbial Properties Database Editor Tutorial

EPA Science Inventory

A Microbial Properties Database Editor (MPDBE) has been developed to help consolidate microbial-relevant data to populate a microbial database and support a database editor by which an authorized user can modify physico-microbial properties related to microbial indicators and pat...

INNOVATIVE MIOR PROCESS UTILIZING INDIGENOUS RESERVOIR CONSTITUENTS

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

D.O. Hitzman; S.A. Bailey

This research program is directed at improving the knowledge of reservoir ecology and developing practical microbial solutions for improving oil production. The goal is to identify indigenous microbial populations which can produce beneficial metabolic products and develop a methodology to stimulate those select microbes with inorganic nutrient amendments to increase oil recovery.This microbial technology has the capability of producing multiple oil releasing agents. The potential of the system will be illustrated and demonstrated by the example of biopolymer production on oil recovery. Research has begun on the program and experimental laboratory work is underway. Polymer-producing cultures have been isolated frommore » produced water samples and initially characterized. Concurrently, a microcosm scale sand-packed column has been designed and developed for testing cultures of interest, including polymer-producing strains. In research that is planned to begin in future work, comparative laboratory studies demonstrating in situ production of microbial products as oil recovery agents will be conducted in sand pack and cores with synthetic and natural field waters at concentrations, flooding rates, and with cultures and conditions representative of oil reservoirs.« less

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.

Understanding of polyhydroxybutyrate production under carbon and phosphorus-limited growth conditions in non-axenic continuous culture.

PubMed

Cavaillé, Laëtitia; Albuquerque, Maria; Grousseau, Estelle; Lepeuple, Anne-Sophie; Uribelarrea, Jean-Louis; Hernandez-Raquet, Guillermina; Paul, Etienne

2016-02-01

In a waste into resource strategy, a selection of polyhydroxybutyrate (PHB)-accumulating organisms from activated sludge was achieved in an open continuous culture under acetic acid and phosphorus limitation. Once the microbial population was selected at a dilution rate (D), an increase in phosphorus limitation degree was applied in order to study the intracellular phosphorus plasticity of selected bacteria and the resulting capacity to produce PHB. Whatever D, all selected populations were able to produce PHB. At a D, the phosphorus availability determined the phosphorus-cell content which in turn fixed the amount of cell. All the remaining carbon was thus directed toward PHB. By decreasing D, microorganisms adapted more easily to higher phosphorus limitation leading to higher PHB content. A one-stage continuous reactor operated at D=0.023h(-)(1) gave reliable high PHB productivity with PHB content up to 80%. A two-stage reactor could ensure better productivity while allowing tuning product quality. Copyright © 2015 Elsevier Ltd. All rights reserved.

Noise and Epigenetic Inheritance of Single-Cell Division Times Influence Population Fitness.

PubMed

Cerulus, Bram; New, Aaron M; Pougach, Ksenia; Verstrepen, Kevin J

2016-05-09

The fitness effect of biological noise remains unclear. For example, even within clonal microbial populations, individual cells grow at different speeds. Although it is known that the individuals' mean growth speed can affect population-level fitness, it is unclear how or whether growth speed heterogeneity itself is subject to natural selection. Here, we show that noisy single-cell division times can significantly affect population-level growth rate. Using time-lapse microscopy to measure the division times of thousands of individual S. cerevisiae cells across different genetic and environmental backgrounds, we find that the length of individual cells' division times can vary substantially between clonal individuals and that sublineages often show epigenetic inheritance of division times. By combining these experimental measurements with mathematical modeling, we find that, for a given mean division time, increasing heterogeneity and epigenetic inheritance of division times increases the population growth rate. Furthermore, we demonstrate that the heterogeneity and epigenetic inheritance of single-cell division times can be linked with variation in the expression of catabolic genes. Taken together, our results reveal how a change in noisy single-cell behaviors can directly influence fitness through dynamics that operate independently of effects caused by changes to the mean. These results not only allow a better understanding of microbial fitness but also help to more accurately predict fitness in other clonal populations, such as tumors. Copyright © 2016 Elsevier Ltd. All rights reserved.

Nitrification rates in Arctic soils are associated with functionally distinct populations of ammonia-oxidizing archaea

NASA Astrophysics Data System (ADS)

Alves, Ricardo J. E.; Wanek, Wolfgang; Zappe, Anna; Richter, Andreas; Svenning, Mette M.; Schleper, Christa; Urich, Tim

2014-05-01

The functioning of Arctic soil ecosystems is crucially important for global climate, although basic knowledge regarding their biogeochemical processes is lacking. Nitrogen (N) is the major limiting nutrient in these environments, and therefore it is particularly important to gain a better understanding of the microbial populations catalyzing transformations that influence N bioavailability. However, microbial communities driving this process remain largely uncharacterized in Arctic soils, namely those catalyzing the rate-limiting step of ammonia (NH3) oxidation. Eleven Arctic soils from Svalbard were analyzed through a polyphasic approach, including determination of gross nitrification rates through a 15N pool dilution method, qualitative and quantitative analyses of ammonia-oxidizing archaea (AOA) and bacteria (AOB) populations based on the functional marker gene amoA (encoding the ammonia monooxygenase subunit A), and enrichment of AOA in laboratory cultures. AOA were the only NH3 oxidizers detected in five out of 11 soils, and outnumbered AOB by 1 to 3 orders of magnitude in most others. AOA showed a great overall phylogenetic diversity that was differentially distributed across soil ecosystems, and exhibited an uneven population composition that reflected the dominance of a single AOA phylotype in each population. Moreover, AOA populations showed a multifactorial association with the soil properties, which reflected an overall distribution associated with tundra type and with several physico-chemical parameters combined, namely pH and soil moisture and N contents (i.e., NO3- and dissolved organic N). Remarkably, the different gross in situ and potential nitrification rates between soils were associated with distinct AOA phylogenetic clades, suggesting differences in their nitrifying potential, both under the native NH3 conditions and as a response to higher NH3 availability. This was further supported by the selective enrichment of two AOA clades that exhibited different NH3 oxidation rates. In addition, the enrichment cultures provided the first direct evidence for NH3 oxidation by an AOA from an uncharacterized Thaumarchaeota-AOA lineage. Our results indicate that AOA are functionally heterogeneous, and that the selection of distinct AOA populations by the environment can be determinant for nitrification activity and N availability in soils. Furthermore, our observations emphasize the fact that, disturbances in populations of specific microbial functional groups, such as nitrifiers, constitute potential response mechanisms to environmental changes. These findings are not only relevant for Arctic environments, but have implications for the role of AOA in nitrification in all soils.

Evaluating digestion efficiency in full-scale anaerobic digesters by identifying active microbial populations through the lens of microbial activity

NASA Astrophysics Data System (ADS)

Mei, Ran; Narihiro, Takashi; Nobu, Masaru K.; Kuroda, Kyohei; Liu, Wen-Tso

2016-09-01

Anaerobic digestion is a common technology to biologically stabilize wasted solids produced in municipal wastewater treatment. Its efficiency is usually evaluated by calculating the reduction in volatile solids, which assumes no biomass growth associated with digestion. To determine whether this assumption is valid and further evaluate digestion efficiency, this study sampled 35 digester sludge from different reactors at multiple time points together with the feed biomass in a full-scale water reclamation plant at Chicago, Illinois. The microbial communities were characterized using Illumina sequencing technology based on 16S rRNA and 16S rRNA gene (rDNA). 74 core microbial populations were identified and represented 58.7% of the entire digester community. Among them, active populations were first identified using the ratio of 16S rRNA and 16S rDNA (rRNA/rDNA) for individual populations, but this approach failed to generate consistent results. Subsequently, a recently proposed mass balance model was applied to calculate the specific growth rate (μ), and this approach successfully identified active microbial populations in digester (positive μ) that could play important roles than those with negative μ. It was further estimated that 82% of microbial populations in the feed sludge were digested in comparison with less than 50% calculated using current equations.

Microbial electrosynthetic cells

DOEpatents

May, Harold D.; Marshall, Christopher W.; Labelle, Edward V.

2018-01-30

Methods are provided for microbial electrosynthesis of H.sub.2 and organic compounds such as methane and acetate. Method of producing mature electrosynthetic microbial populations by continuous culture is also provided. Microbial populations produced in accordance with the embodiments as shown to efficiently synthesize H.sub.2, methane and acetate in the presence of CO.sub.2 and a voltage potential. The production of biodegradable and renewable plastics from electricity and carbon dioxide is also disclosed.

ATP as a biomarker of viable microorganisms in clean-room facilities

NASA Technical Reports Server (NTRS)

Venkateswaran, Kasthuri; Hattori, Noriaki; La Duc, Myron T.; Kern, Roger

2003-01-01

A new firefly luciferase bioluminescence assay method that differentiates free extracellular ATP (dead cells, etc.) from intracellular ATP (viable microbes) was used to determine the viable microbial cleanliness of various clean-room facilities. For comparison, samples were taken from both clean-rooms, where the air was filtered to remove particles >0.5 microm, and ordinary rooms with unfiltered air. The intracellular ATP was determined after enzymatically degrading the sample's free ATP. Also for comparison, cultivable microbial populations were counted on nutrient-rich trypticase soy agar (TSA) plates. Both the cultivable and ATP-based determinations indicate that the microbial burden was lower in clean-room facilities than in ordinary rooms. However, there was no direct correlation between the two sets of measurements because the two assays measured very different populations. A large fraction of the samples yielded no colony formers on TSA, but were positive for intracellular ATP. Subsequently, genomic DNA was isolated directly from selected samples and 16S rDNA fragments were cloned and sequenced, identifying nearest neighbors, many of which are known to be noncultivable in the media employed. It was concluded that viable microbial contamination can be reliably monitored by measurement of intracellular ATP, and that this method may be considered superior to cultivable colony counts due to its speed and its ability to report the presence of viable but noncultivable organisms. When the detection of nonviable microbes is of interest, the ATP assay can be supplemented with DNA analysis.

ATP as a biomarker of viable microorganisms in clean-room facilities.

PubMed

Venkateswaran, Kasthuri; Hattori, Noriaki; La Duc, Myron T; Kern, Roger

2003-03-01

A new firefly luciferase bioluminescence assay method that differentiates free extracellular ATP (dead cells, etc.) from intracellular ATP (viable microbes) was used to determine the viable microbial cleanliness of various clean-room facilities. For comparison, samples were taken from both clean-rooms, where the air was filtered to remove particles >0.5 microm, and ordinary rooms with unfiltered air. The intracellular ATP was determined after enzymatically degrading the sample's free ATP. Also for comparison, cultivable microbial populations were counted on nutrient-rich trypticase soy agar (TSA) plates. Both the cultivable and ATP-based determinations indicate that the microbial burden was lower in clean-room facilities than in ordinary rooms. However, there was no direct correlation between the two sets of measurements because the two assays measured very different populations. A large fraction of the samples yielded no colony formers on TSA, but were positive for intracellular ATP. Subsequently, genomic DNA was isolated directly from selected samples and 16S rDNA fragments were cloned and sequenced, identifying nearest neighbors, many of which are known to be noncultivable in the media employed. It was concluded that viable microbial contamination can be reliably monitored by measurement of intracellular ATP, and that this method may be considered superior to cultivable colony counts due to its speed and its ability to report the presence of viable but noncultivable organisms. When the detection of nonviable microbes is of interest, the ATP assay can be supplemented with DNA analysis.

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

USDA-ARS?s Scientific Manuscript database

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 ...

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...

Tillage system affects microbiological properties of soil

NASA Astrophysics Data System (ADS)

Delgado, A.; de Santiago, A.; Avilés, M.; Perea, F.

2012-04-01

Soil tillage significantly affects organic carbon accumulation, microbial biomass, and subsequently enzymatic activity in surface soil. Microbial activity in soil is a crucial parameter contributing to soil functioning, and thus a basic quality factor for soil. Since enzymes remain soil after excretion by living or disintegrating cells, shifts in their activities reflect long-term fluctuations in microbial biomass. In order to study the effects of no-till on biochemical and microbiological properties in comparison to conventional tillage in a representative soil from South Spain, an experiment was conducted since 1982 on the experimental farm of the Institute of Agriculture and Fisheries Research of Andalusia (IFAPA) in Carmona, SW Spain (37o24'07''N, 5o35'10''W). The soil at the experimental site was a very fine, montomorillonitic, thermic Chromic Haploxerert (Soil Survey Staff, 2010). A randomized complete block design involving three replications and the following two tillage treatments was performed: (i) Conventional tillage, which involved mouldboard plowing to a depth of 50 cm in the summer (once every three years), followed by field cultivation to a depth of 15 cm before sowing; crop residues being burnt, (ii) No tillage, which involved controlling weeds before sowing by spraying glyphosate and sowing directly into the crop residue from the previous year by using a planter with double-disk openers. For all tillage treatments, the crop rotation (annual crops) consisted of winter wheat, sunflower, and legumes (pea, chickpea, or faba bean, depending on the year), which were grown under rainfed conditions. Enzymatic activities (ß-glucosidase, dehydrogenase, aryl-sulphatase, acid phosphatase, and urease), soil microbial biomass by total viable cells number by acridine orange direct count, the density of cultivable groups of bacteria and fungi by dilution plating on semi-selective media, the physiological profiles of the microbial communities by BiologR, and the Shannon (H') and Gini (1-G) diversity index of microbial communities were determined in soil samples (0-10 cm depth) taken in autumn 2009. All the enzymatic activities and the biomass estimated by viable cell counting were significantly higher under no-till than under conventional tillage. However, only fluorescents pseudomonas population was increased under no-till, meanwhile oligotrophic bacteria and actinomycetes populations were higher with conventional tillage than with no-till. Overall, there was a higher use all the group of carbon sources used in the BiologR test with conventional tillage than with no-till, by except amines and phenols which showed non-significant differences. This reveals different physiological profiles in the microbial communities under both tillage systems. The Gini diversity was significantly lower with no-till than with conventional tillage. It can be concluded that no-till increases microbial biomass in soil and subsequently enzymatic activities likely ascribed to an increased organic matter content. Under low availability of hydrocarbon sources in soil due to conventional tillage, which promotes a decrease in the organic matter content of the soil, populations of oligotrophods and the diversity of microbial communities are increased. Under these conditions, there must not be dominant carbon sources promoting the selection of microorganisms with a given physiological profile. The reduced hydrocarbon availability and the higher diversity contribute to explain the increased use of carbon sources used in Biolog with conventional tillage than with no-till.

Microbial Populations in Naked Neck Chicken Ceca Raised on Pasture Flock Fed with Commercial Yeast Cell Wall Prebiotics via an Illumina MiSeq Platform

PubMed Central

Park, Si Hong; Lee, Sang In; Ricke, Steven C.

2016-01-01

Prebiotics are non-digestible carbohydrate dietary supplements that selectively stimulate the growth of one or more beneficial bacteria in the gastrointestinal tract of the host. These bacteria can inhibit colonization of pathogenic bacteria by producing antimicrobial substances such as short chain fatty acids (SCFAs) and competing for niches with pathogens within the gut. Pasture flock chickens are generally raised outdoors with fresh grass, sunlight and air, which represents different environmental growth conditions compared to conventionally raised chickens. The purpose of this study was to evaluate the difference in microbial populations from naked neck chicken ceca fed with commercial prebiotics derived from brewer’s yeast cell wall via an Illumina MiSeq platform. A total of 147 day-of-hatch naked neck chickens were distributed into 3 groups consisted of 1) C: control (no prebiotic), 2) T1: Biolex® MB40 with 0.2%, and 3) T2: Leiber® ExCel with 0.2%, consistently supplemented prebiotics during the experimental period. At 8 weeks, a total of 15 birds from each group were randomly selected and ceca removed for DNA extraction. The Illumina Miseq platform based on V4 region of 16S rRNA gene was applied for microbiome analysis. Both treatments exhibited limited impact on the microbial populations at the phylum level, with no significant differences in the OTU number of Bacteroidetes among groups and an increase of Proteobacteria OTUs for the T1 (Biolex® MB40) group. In addition there was a significant increase of genus Faecalibacterium OTU, phylum Firmicutes. According to the development of next generation sequencing (NGS), microbiome analysis based on 16S rRNA gene proved to be informative on the prebiotic impact on poultry gut microbiota in pasture-raised naked neck birds. PMID:26992104

Microbial Populations in Naked Neck Chicken Ceca Raised on Pasture Flock Fed with Commercial Yeast Cell Wall Prebiotics via an Illumina MiSeq Platform.

PubMed

Park, Si Hong; Lee, Sang In; Ricke, Steven C

2016-01-01

Prebiotics are non-digestible carbohydrate dietary supplements that selectively stimulate the growth of one or more beneficial bacteria in the gastrointestinal tract of the host. These bacteria can inhibit colonization of pathogenic bacteria by producing antimicrobial substances such as short chain fatty acids (SCFAs) and competing for niches with pathogens within the gut. Pasture flock chickens are generally raised outdoors with fresh grass, sunlight and air, which represents different environmental growth conditions compared to conventionally raised chickens. The purpose of this study was to evaluate the difference in microbial populations from naked neck chicken ceca fed with commercial prebiotics derived from brewer's yeast cell wall via an Illumina MiSeq platform. A total of 147 day-of-hatch naked neck chickens were distributed into 3 groups consisted of 1) C: control (no prebiotic), 2) T1: Biolex® MB40 with 0.2%, and 3) T2: Leiber® ExCel with 0.2%, consistently supplemented prebiotics during the experimental period. At 8 weeks, a total of 15 birds from each group were randomly selected and ceca removed for DNA extraction. The Illumina Miseq platform based on V4 region of 16S rRNA gene was applied for microbiome analysis. Both treatments exhibited limited impact on the microbial populations at the phylum level, with no significant differences in the OTU number of Bacteroidetes among groups and an increase of Proteobacteria OTUs for the T1 (Biolex® MB40) group. In addition there was a significant increase of genus Faecalibacterium OTU, phylum Firmicutes. According to the development of next generation sequencing (NGS), microbiome analysis based on 16S rRNA gene proved to be informative on the prebiotic impact on poultry gut microbiota in pasture-raised naked neck birds.

Metagenomic Approaches to Investigate the Contribution of the Vineyard Environment to the Quality of Wine Fermentation: Potentials and Difficulties

PubMed Central

Stefanini, Irene; Cavalieri, Duccio

2018-01-01

The winemaking is a complex process that begins in the vineyard and ends at consumption moment. Recent reports have shown the relevance of microbial populations in the definition of the regional organoleptic and sensory characteristics of a wine. Metagenomic approaches, allowing the exhaustive identification of microorganisms present in complex samples, have recently played a fundamental role in the dissection of the contribution of the vineyard environment to wine fermentation. Systematic approaches have explored the impact of agronomical techniques, vineyard topologies, and climatic changes on bacterial and fungal populations found in the vineyard and in fermentations, also trying to predict or extrapolate the effects on the sensorial characteristics of the resulting wine. This review is aimed at highlighting the major technical and experimental challenges in dissecting the contribution of the vineyard and native environments microbiota to the wine fermentation process, and how metagenomic approaches can help in understanding microbial fluxes and selections across the environments and specimens related to wine fermentation. PMID:29867889

Coupling Spatiotemporal Community Assembly Processes to Changes in Microbial Metabolism.

PubMed

Graham, Emily B; Crump, Alex R; Resch, Charles T; Fansler, Sarah; Arntzen, Evan; Kennedy, David W; Fredrickson, Jim K; Stegen, James C

2016-01-01

Community assembly processes generate shifts in species abundances that influence ecosystem cycling of carbon and nutrients, yet our understanding of assembly remains largely separate from ecosystem-level functioning. Here, we investigate relationships between assembly and changes in microbial metabolism across space and time in hyporheic microbial communities. We pair sampling of two habitat types (i.e., attached and planktonic) through seasonal and sub-hourly hydrologic fluctuation with null modeling and temporally explicit multivariate statistics. We demonstrate that multiple selective pressures-imposed by sediment and porewater physicochemistry-integrate to generate changes in microbial community composition at distinct timescales among habitat types. These changes in composition are reflective of contrasting associations of Betaproteobacteria and Thaumarchaeota with ecological selection and with seasonal changes in microbial metabolism. We present a conceptual model based on our results in which metabolism increases when oscillating selective pressures oppose temporally stable selective pressures. Our conceptual model is pertinent to both macrobial and microbial systems experiencing multiple selective pressures and presents an avenue for assimilating community assembly processes into predictions of ecosystem-level functioning.

Genomic variation of subseafloor archaeal and bacterial populations from venting fluids at the Mid-Cayman Rise

NASA Astrophysics Data System (ADS)

Anderson, R. E.; Eren, A. M.; Stepanauskas, R.; Huber, J. A.; Reveillaud, J.

2015-12-01

Deep-sea hydrothermal vent systems serve as windows to a dynamic, gradient-dominated deep biosphere that is home to a wide diversity of archaea, bacteria, and viruses. Until recently the majority of these microbial lineages were uncultivated, resulting in a poor understanding of how the physical and geochemical context shapes microbial evolution in the deep subsurface. By comparing metagenomes, metatranscriptomes and single-cell genomes between geologically distinct vent fields, we can better understand the relationship between the environment and the evolution of subsurface microbial communities. An ideal setting in which to use this approach is the Mid-Cayman Rise, located on the world's deepest and slowest-spreading mid-ocean ridge, which hosts both the mafic-influenced Piccard and ultramafic-influenced Von Damm vent fields. Previous work has shown that Von Damm has higher taxonomic and metabolic diversity than Piccard, consistent with geochemical model expectations, and the fluids from all vents are enriched in hydrogen (Reveillaud et al., submitted). Mapping of both metagenomes and metatranscriptomes to a combined assembly showed very little overlap among the Von Damm samples, indicating substantial variability that is consistent with the diversity of potential metabolites in this ultramafic vent field. In contrast, the most consistently abundant and active lineage across the Piccard samples was Sulfurovum, a sulfur-oxidizing chemolithotroph that uses nitrate or oxygen as an electron acceptor. Moreover, analysis of point mutations within individual lineages suggested that Sulfurovumat Piccard is under strong selection, whereas microbial genomes at Von Damm were more variable. These results are consistent with the hypothesis that the subsurface environment at Piccard supports the emergence of a dominant lineage that is under strong selection pressure, whereas the more geochemically diverse microbial habitat at Von Damm creates a wider variety of stable ecological niches, facilitating higher diversity both within and between microbial lineages. By examining how the environment is imprinted into microbial genomes, we hope to gain insight into how subsurface microbial communities co-evolve with their environment in both the present and the deep past.

Rethinking the evolution of specialization: A model for the evolution of phenotypic heterogeneity.

PubMed

Rubin, Ilan N; Doebeli, Michael

2017-12-21

Phenotypic heterogeneity refers to genetically identical individuals that express different phenotypes, even when in the same environment. Traditionally, "bet-hedging" in fluctuating environments is offered as the explanation for the evolution of phenotypic heterogeneity. However, there are an increasing number of examples of microbial populations that display phenotypic heterogeneity in stable environments. Here we present an evolutionary model of phenotypic heterogeneity of microbial metabolism and a resultant theory for the evolution of phenotypic versus genetic specialization. We use two-dimensional adaptive dynamics to track the evolution of the population phenotype distribution of the expression of two metabolic processes with a concave trade-off. Rather than assume a Gaussian phenotype distribution, we use a Beta distribution that is capable of describing genotypes that manifest as individuals with two distinct phenotypes. Doing so, we find that environmental variation is not a necessary condition for the evolution of phenotypic heterogeneity, which can evolve as a form of specialization in a stable environment. There are two competing pressures driving the evolution of specialization: directional selection toward the evolution of phenotypic heterogeneity and disruptive selection toward genetically determined specialists. Because of the lack of a singular point in the two-dimensional adaptive dynamics and the fact that directional selection is a first order process, while disruptive selection is of second order, the evolution of phenotypic heterogeneity dominates and often precludes speciation. We find that branching, and therefore genetic specialization, occurs mainly under two conditions: the presence of a cost to maintaining a high phenotypic variance or when the effect of mutations is large. A cost to high phenotypic variance dampens the strength of selection toward phenotypic heterogeneity and, when sufficiently large, introduces a singular point into the evolutionary dynamics, effectively guaranteeing eventual branching. Large mutations allow the second order disruptive selection to dominate the first order selection toward phenotypic heterogeneity. Copyright © 2017 Elsevier Ltd. All rights reserved.

An Exogenous Surfactant-Producing Bacillus subtilis Facilitates Indigenous Microbial Enhanced Oil Recovery

PubMed Central

Gao, Peike; Li, Guoqiang; Li, Yanshu; Li, Yan; Tian, Huimei; Wang, Yansen; Zhou, Jiefang; Ma, Ting

2016-01-01

This study used an exogenous lipopeptide-producing Bacillus subtilis to strengthen the indigenous microbial enhanced oil recovery (IMEOR) process in a water-flooded reservoir in the laboratory. The microbial processes and driving mechanisms were investigated in terms of the changes in oil properties and the interplay between the exogenous B. subtilis and indigenous microbial populations. The exogenous B. subtilis is a lipopeptide producer, with a short growth cycle and no oil-degrading ability. The B. subtilis facilitates the IMEOR process through improving oil emulsification and accelerating microbial growth with oil as the carbon source. Microbial community studies using quantitative PCR and high-throughput sequencing revealed that the exogenous B. subtilis could live together with reservoir microbial populations, and did not exert an observable inhibitory effect on the indigenous microbial populations during nutrient stimulation. Core-flooding tests showed that the combined exogenous and indigenous microbial flooding increased oil displacement efficiency by 16.71%, compared with 7.59% in the control where only nutrients were added, demonstrating the application potential in enhanced oil recovery in water-flooded reservoirs, in particular, for reservoirs where IMEOR treatment cannot effectively improve oil recovery. PMID:26925051

An Exogenous Surfactant-Producing Bacillus subtilis Facilitates Indigenous Microbial Enhanced Oil Recovery.

PubMed

Gao, Peike; Li, Guoqiang; Li, Yanshu; Li, Yan; Tian, Huimei; Wang, Yansen; Zhou, Jiefang; Ma, Ting

2016-01-01

This study used an exogenous lipopeptide-producing Bacillus subtilis to strengthen the indigenous microbial enhanced oil recovery (IMEOR) process in a water-flooded reservoir in the laboratory. The microbial processes and driving mechanisms were investigated in terms of the changes in oil properties and the interplay between the exogenous B. subtilis and indigenous microbial populations. The exogenous B. subtilis is a lipopeptide producer, with a short growth cycle and no oil-degrading ability. The B. subtilis facilitates the IMEOR process through improving oil emulsification and accelerating microbial growth with oil as the carbon source. Microbial community studies using quantitative PCR and high-throughput sequencing revealed that the exogenous B. subtilis could live together with reservoir microbial populations, and did not exert an observable inhibitory effect on the indigenous microbial populations during nutrient stimulation. Core-flooding tests showed that the combined exogenous and indigenous microbial flooding increased oil displacement efficiency by 16.71%, compared with 7.59% in the control where only nutrients were added, demonstrating the application potential in enhanced oil recovery in water-flooded reservoirs, in particular, for reservoirs where IMEOR treatment cannot effectively improve oil recovery.

Detailed analysis of the microbial population in Malaysian spontaneous cocoa pulp fermentations reveals a core and variable microbiota.

PubMed

Meersman, Esther; Steensels, Jan; Mathawan, Melissa; Wittocx, Pieter-Jan; Saels, Veerle; Struyf, Nore; Bernaert, Herwig; Vrancken, Gino; Verstrepen, Kevin J

2013-01-01

The fermentation of cocoa pulp is one of the few remaining large-scale spontaneous microbial processes in today's food industry. The microbiota involved in cocoa pulp fermentations is complex and variable, which leads to inconsistent production efficiency and cocoa quality. Despite intensive research in the field, a detailed and comprehensive analysis of the microbiota is still lacking, especially for the expanding Asian production region. Here, we report a large-scale, comprehensive analysis of four spontaneous Malaysian cocoa pulp fermentations across two time points in the harvest season and two fermentation methods. Our results show that the cocoa microbiota consists of a "core" and a "variable" part. The bacterial populations show a remarkable consistency, with only two dominant species, Lactobacillus fermentum and Acetobacter pasteurianus. The fungal diversity is much larger, with four dominant species occurring in all fermentations ("core" yeasts), and a large number of yeasts that only occur in lower numbers and specific fermentations ("variable" yeasts). Despite this diversity, a clear pattern emerges, with early dominance of apiculate yeasts and late dominance of Saccharomyces cerevisiae. Our results provide new insights into the microbial diversity in Malaysian cocoa pulp fermentations and pave the way for the selection of starter cultures to increase efficiency and consistency.

Implications of streamlining theory for microbial ecology

PubMed Central

Giovannoni, Stephen J; Cameron Thrash, J; Temperton, Ben

2014-01-01

Whether a small cell, a small genome or a minimal set of chemical reactions with self-replicating properties, simplicity is beguiling. As Leonardo da Vinci reportedly said, ‘simplicity is the ultimate sophistication'. Two diverging views of simplicity have emerged in accounts of symbiotic and commensal bacteria and cosmopolitan free-living bacteria with small genomes. The small genomes of obligate insect endosymbionts have been attributed to genetic drift caused by small effective population sizes (Ne). In contrast, streamlining theory attributes small cells and genomes to selection for efficient use of nutrients in populations where Ne is large and nutrients limit growth. Regardless of the cause of genome reduction, lost coding potential eventually dictates loss of function. Consequences of reductive evolution in streamlined organisms include atypical patterns of prototrophy and the absence of common regulatory systems, which have been linked to difficulty in culturing these cells. Recent evidence from metagenomics suggests that streamlining is commonplace, may broadly explain the phenomenon of the uncultured microbial majority, and might also explain the highly interdependent (connected) behavior of many microbial ecosystems. Streamlining theory is belied by the observation that many successful bacteria are large cells with complex genomes. To fully appreciate streamlining, we must look to the life histories and adaptive strategies of cells, which impose minimum requirements for complexity that vary with niche. PMID:24739623

Detailed Analysis of the Microbial Population in Malaysian Spontaneous Cocoa Pulp Fermentations Reveals a Core and Variable Microbiota

PubMed Central

Mathawan, Melissa; Wittocx, Pieter-Jan; Saels, Veerle; Struyf, Nore; Bernaert, Herwig; Vrancken, Gino; Verstrepen, Kevin J.

2013-01-01

The fermentation of cocoa pulp is one of the few remaining large-scale spontaneous microbial processes in today's food industry. The microbiota involved in cocoa pulp fermentations is complex and variable, which leads to inconsistent production efficiency and cocoa quality. Despite intensive research in the field, a detailed and comprehensive analysis of the microbiota is still lacking, especially for the expanding Asian production region. Here, we report a large-scale, comprehensive analysis of four spontaneous Malaysian cocoa pulp fermentations across two time points in the harvest season and two fermentation methods. Our results show that the cocoa microbiota consists of a “core” and a “variable” part. The bacterial populations show a remarkable consistency, with only two dominant species, Lactobacillus fermentum and Acetobacter pasteurianus. The fungal diversity is much larger, with four dominant species occurring in all fermentations (“core” yeasts), and a large number of yeasts that only occur in lower numbers and specific fermentations (“variable” yeasts). Despite this diversity, a clear pattern emerges, with early dominance of apiculate yeasts and late dominance of Saccharomyces cerevisiae. Our results provide new insights into the microbial diversity in Malaysian cocoa pulp fermentations and pave the way for the selection of starter cultures to increase efficiency and consistency. PMID:24358116

PCR-DGGE analysis of lactic acid bacteria and yeast dynamics during the production processes of three varieties of Panettone.

PubMed

Garofalo, C; Silvestri, G; Aquilanti, L; Clementi, F

2008-07-01

To study lactic acid bacteria (LAB) and yeast dynamics during the production processes of sweet-leavened goods manufactured with type I sourdoughs. Fourteen sourdough and dough samples were taken from a baking company in central Italy during the production lines of three varieties of Panettone. The samples underwent pH measurements and plating analysis on three solid media. The microbial DNA was extracted from both the (sour)doughs and the viable LAB and yeast cells collected in bulk, and subjected to PCR-denaturing gradient gel electrophoresis (DGGE) analysis. The molecular fingerprinting of the cultivable plus noncultivable microbial populations provide evidence of the dominance of Lactobacillus sanfranciscensis, Lactobacillus brevis and Candida humilis in the three fermentation processes. The DGGE profiles of the cultivable communities reveal a bacterial shift in the final stages of two of the production processes, suggesting an effect of technological parameters on the selection of the dough microflora. Our findings confirm the importance of using a combined analytical approach to explore microbial communities that develop during the leavening process of sweet-leavened goods. In-depth studies of sourdough biodiversity and population dynamics occurring during sourdough fermentation are fundamental for the control of the leavening process and the manufacture of standardized, high-quality products.

Remediation aspect of microbial changes of plant rhizosphere in mercury contaminated soil.

PubMed

Sas-Nowosielska, Aleksandra; Galimska-Stypa, Regina; Kucharski, Rafał; Zielonka, Urszula; Małkowski, Eugeniusz; Gray, Laymon

2008-02-01

Phytoremediation, an approach that uses plants to remediate contaminated soil through degradation, stabilization or accumulation, may provide an efficient solution to some mercury contamination problems. This paper presents growth chamber experiments that tested the ability of plant species to stabilize mercury in soil. Several indigenous herbaceous species and Salix viminalis were grown in soil collected from a mercury-contaminated site in southern Poland. The uptake and distribution of mercury by these plants were investigated, and the growth and vitality of the plants through a part of one vegetative cycle were assessed. The highest concentrations of mercury were found at the roots, but translocation to the aerial part also occurred. Most of the plant species tested displayed good growth on mercury contaminated soil and sustained a rich microbial population in the rhizosphere. The microbial populations of root-free soil and rhizosphere soil from all species were also examined. An inverse correlation between the number of sulfur amino acid decomposing bacteria and root mercury content was observed. These results indicate the potential for using some species of plants to treat mercury contaminated soil through stabilization rather than extraction. The present investigation proposes a practical cost-effective temporary solution for phytostabilization of soil with moderate mercury contamination as well as the basis for plant selection.

Microbial properties database editor tutorial

USDA-ARS?s Scientific Manuscript database

A Microbial Properties Database Editor (MPDBE) has been developed to help consolidate microbialrelevant data to populate a microbial database and support a database editor by which an authorized user can modify physico-microbial properties related to microbial indicators and pathogens. Physical prop...

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

PubMed

Whittaker, Kerry A; Rynearson, Tatiana A

2017-03-07

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

Spatial and Temporal Variation in Enterococcal Abundance and Its Relationship to the Microbial Community in Hawaii Beach Sand and Water

PubMed Central

Cui, Henglin; Yang, Kun; Pagaling, Eulyn

2013-01-01

Recent studies have reported high levels of fecal indicator enterococci in marine beach sand. This study aimed to determine the spatial and temporal variation of enterococcal abundance and to evaluate its relationships with microbial community parameters in Hawaii beach sand and water. Sampling at 23 beaches on the Island of Oahu detected higher levels of enterococci in beach foreshore sand than in beach water on a mass unit basis. Subsequent 8-week consecutive samplings at two selected beaches (Waialae and Kualoa) consistently detected significantly higher levels of enterococci in backshore sand than in foreshore/nearshore sand and beach water. Comparison between the abundance of enterococci and the microbial communities showed that enterococci correlated significantly with total Vibrio in all beach zones but less significantly with total bacterial density and Escherichia coli. Samples from the different zones of Waialae beach were sequenced by 16S rRNA gene pyrosequencing to determine the microbial community structure and diversity. The backshore sand had a significantly more diverse community and contained different major bacterial populations than the other beach zones, which corresponded to the spatial distribution pattern of enterococcal abundance. Taken together, multiple lines of evidence support the possibility of enterococci as autochthonous members of the microbial community in Hawaii beach sand. PMID:23563940

A Fosmid Cloning Strategy for Detecting the Widest Possible Spectrum of Microbes from the International Space Station Drinking Water System

PubMed Central

Choi, Sangdun; Chang, Mi Sook; Stuecker, Tara; Chung, Christine; Newcombe, David A.; Venkateswaran, Kasthuri

2012-01-01

In this study, fosmid cloning strategies were used to assess the microbial populations in water from the International Space Station (ISS) drinking water system (henceforth referred to as Prebiocide and Tank A water samples). The goals of this study were: to compare the sensitivity of the fosmid cloning strategy with that of traditional culture-based and 16S rRNA-based approaches and to detect the widest possible spectrum of microbial populations during the water purification process. Initially, microbes could not be cultivated, and conventional PCR failed to amplify 16S rDNA fragments from these low biomass samples. Therefore, randomly primed rolling-circle amplification was used to amplify any DNA that might be present in the samples, followed by size selection by using pulsed-field gel electrophoresis. The amplified high-molecular-weight DNA from both samples was cloned into fosmid vectors. Several hundred clones were randomly selected for sequencing, followed by Blastn/Blastx searches. Sequences encoding specific genes from Burkholderia, a species abundant in the soil and groundwater, were found in both samples. Bradyrhizobium and Mesorhizobium, which belong to rhizobia, a large community of nitrogen fixers often found in association with plant roots, were present in the Prebiocide samples. Ralstonia, which is prevalent in soils with a high heavy metal content, was detected in the Tank A samples. The detection of many unidentified sequences suggests the presence of potentially novel microbial fingerprints. The bacterial diversity detected in this pilot study using a fosmid vector approach was higher than that detected by conventional 16S rRNA gene sequencing. PMID:23346038

An Insight into Phage Diversity at Environmental Habitats using Comparative Metagenomics Approach.

PubMed

Parmar, Krupa; Dafale, Nishant; Pal, Rajesh; Tikariha, Hitesh; Purohit, Hemant

2018-02-01

Bacteriophages play significant role in driving microbial diversity; however, little is known about the diversity of phages in different ecosystems. A dynamic predator-prey mechanism called "kill the winner" suggests the elimination of most active bacterial populations through phages. Thus, interaction between phage and host has an effect on the composition of microbial communities in ecosystems. In this study, secondary phage metagenome data from aquatic habitats: wastewater treatment plant (WWTP), fresh, marine, and hot water spring habitat were analyzed using MG-RAST and STAMP tools to explore the diversity of the viruses. Differential relative abundance of phage families-Siphoviridae (34%) and Myoviridae (26%) in WWTP, Myoviridae (30%) and Podoviridae (23%) in fresh water, and Myoviridae (41%) and Podoviridae (8%) in marine-was found to be a discriminating factor among four habitats while Rudiviridae (9%), Globuloviridae (8%), and Lipothrixviridae (1%) were exclusively observed in hot water spring. Subsequently, at genera level, Bpp-1-like virus, Chlorovirus, and T4-like virus were found abundant in WWTP, fresh, and marine habitat, respectively. PCA analysis revealed completely disparate composition of phage in hot water spring from other three ecosystems. Similar analysis of relative abundance of functional features corroborated observations from taxa analysis. Functional features corresponding to phage packaging machinery, replication, integration and excision, and gene transfer discriminated among four habitats. The comparative metagenomics approach exhibited genetically distinct phage communities among four habitats. Results revealed that selective distribution of phage communities would help in understanding the role of phages in food chains, nutrient cycling, and microbial ecology. Study of specific phages would also help in controlling environmental pathogens including MDR bacterial populations using phage therapy approach by selective mining and isolation of phages against specific pathogens persisting in a given environment.

Adaptive laboratory evolution -- principles and applications for biotechnology.

PubMed

Dragosits, Martin; Mattanovich, Diethard

2013-07-01

Adaptive laboratory evolution is a frequent method in biological studies to gain insights into the basic mechanisms of molecular evolution and adaptive changes that accumulate in microbial populations during long term selection under specified growth conditions. Although regularly performed for more than 25 years, the advent of transcript and cheap next-generation sequencing technologies has resulted in many recent studies, which successfully applied this technique in order to engineer microbial cells for biotechnological applications. Adaptive laboratory evolution has some major benefits as compared with classical genetic engineering but also some inherent limitations. However, recent studies show how some of the limitations may be overcome in order to successfully incorporate adaptive laboratory evolution in microbial cell factory design. Over the last two decades important insights into nutrient and stress metabolism of relevant model species were acquired, whereas some other aspects such as niche-specific differences of non-conventional cell factories are not completely understood. Altogether the current status and its future perspectives highlight the importance and potential of adaptive laboratory evolution as approach in biotechnological engineering.

Confirmation of putative stormwater impact on water quality at a Florida beach by microbial source tracking methods and structure of indicator organism populations.

PubMed

Brownell, M J; Harwood, V J; Kurz, R C; McQuaig, S M; Lukasik, J; Scott, T M

2007-08-01

The effect of a stormwater conveyance system on indicator bacteria levels at a Florida beach was assessed using microbial source tracking methods, and by investigating indicator bacteria population structure in water and sediments. During a rain event, regulatory standards for both fecal coliforms and Enterococcus spp. were exceeded, contrasting with significantly lower levels under dry conditions. Indicator bacteria levels were high in sediments under all conditions. The involvement of human sewage in the contamination was investigated using polymerase chain reaction (PCR) assays for the esp gene of Enterococcus faecium and for the conserved T antigen of human polyomaviruses, all of which were negative. BOX-PCR subtyping of Escherichia coli and Enterococcus showed higher population diversity during the rain event; and higher population similarity during dry conditions, suggesting that without fresh inputs, only a subset of the population survives the selective pressure of the secondary habitat. These data indicate that high indicator bacteria levels were attributable to a stormwater system that acted as a reservoir and conduit, flushing high levels of indicator bacteria to the beach during a rain event. Such environmental reservoirs of indicator bacteria further complicate the already questionable relationship between indicator organisms and human pathogens, and call for a better understanding of the ecology, fate and persistence of indicator bacteria.

Combination of sodium chlorite and calcium propionate reduces enzymatic browning and microbial population of fresh-cut ‘Granny Smith’ apples

USDA-ARS?s Scientific Manuscript database

Tissue browning and microbial growth are the main concerns associated with fresh-cut apples. In this study, effects of sodium chlorite (SC) and calcium propionate (CP), individually and combined, on quality and microbial population of apple slices were investigated. ‘Granny Smith’ apple slices, dipp...

Programmable removal of bacterial strains by use of genome-targeting CRISPR-Cas systems.

PubMed

Gomaa, Ahmed A; Klumpe, Heidi E; Luo, Michelle L; Selle, Kurt; Barrangou, Rodolphe; Beisel, Chase L

2014-01-28

CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems in bacteria and archaea employ CRISPR RNAs to specifically recognize the complementary DNA of foreign invaders, leading to sequence-specific cleavage or degradation of the target DNA. Recent work has shown that the accidental or intentional targeting of the bacterial genome is cytotoxic and can lead to cell death. Here, we have demonstrated that genome targeting with CRISPR-Cas systems can be employed for the sequence-specific and titratable removal of individual bacterial strains and species. Using the type I-E CRISPR-Cas system in Escherichia coli as a model, we found that this effect could be elicited using native or imported systems and was similarly potent regardless of the genomic location, strand, or transcriptional activity of the target sequence. Furthermore, the specificity of targeting with CRISPR RNAs could readily distinguish between even highly similar strains in pure or mixed cultures. Finally, varying the collection of delivered CRISPR RNAs could quantitatively control the relative number of individual strains within a mixed culture. Critically, the observed selectivity and programmability of bacterial removal would be virtually impossible with traditional antibiotics, bacteriophages, selectable markers, or tailored growth conditions. Once delivery challenges are addressed, we envision that this approach could offer a novel means to quantitatively control the composition of environmental and industrial microbial consortia and may open new avenues for the development of "smart" antibiotics that circumvent multidrug resistance and differentiate between pathogenic and beneficial microorganisms. Controlling the composition of microbial populations is a critical aspect in medicine, biotechnology, and environmental cycles. While different antimicrobial strategies, such as antibiotics, antimicrobial peptides, and lytic bacteriophages, offer partial solutions, what remains elusive is a generalized and programmable strategy that can distinguish between even closely related microorganisms and that allows for fine control over the composition of a microbial population. This study demonstrates that RNA-directed immune systems in bacteria and archaea called CRISPR-Cas systems can provide such a strategy. These systems can be employed to selectively and quantitatively remove individual bacterial strains based purely on sequence information, creating opportunities in the treatment of multidrug-resistant infections, the control of industrial fermentations, and the study of microbial consortia.

High-throughput screening to identify selective inhibitors of microbial sulfate reduction (and beyond)

NASA Astrophysics Data System (ADS)

Carlson, H. K.; Coates, J. D.; Deutschbauer, A. M.

2015-12-01

The selective perturbation of complex microbial ecosystems to predictably influence outcomes in engineered and industrial environments remains a grand challenge for geomicrobiology. In some industrial ecosystems, such as oil reservoirs, sulfate reducing microorganisms (SRM) produce hydrogen sulfide which is toxic, explosive and corrosive. Current strategies to selectively inhibit sulfidogenesis are based on non-specific biocide treatments, bio-competitive exclusion by alternative electron acceptors or sulfate-analogs which are competitive inhibitors or futile/alternative substrates of the sulfate reduction pathway. Despite the economic cost of sulfidogenesis, there has been minimal exploration of the chemical space of possible inhibitory compounds, and very little work has quantitatively assessed the selectivity of putative souring treatments. We have developed a high-throughput screening strategy to target SRM, quantitatively ranked the selectivity and potency of hundreds of compounds and identified previously unrecognized SRM selective inhibitors and synergistic interactions between inhibitors. Once inhibitor selectivity is defined, high-throughput characterization of microbial community structure across compound gradients and identification of fitness determinants using isolate bar-coded transposon mutant libraries can give insights into the genetic mechanisms whereby compounds structure microbial communities. The high-throughput (HT) approach we present can be readily applied to target SRM in diverse environments and more broadly, could be used to identify and quantify the potency and selectivity of inhibitors of a variety of microbial metabolisms. Our findings and approach are relevant for engineering environmental ecosystems and also to understand the role of natural gradients in shaping microbial niche space.

Degradation of metalaxyl and folpet by filamentous fungi isolated from Portuguese (Alentejo) vineyard soils.

PubMed

Martins, M Rosário; Pereira, Pablo; Lima, Nelson; Cruz-Morais, Júlio

2013-07-01

Degradation of xenobiotics by microbial populations is a potential method to enhance the effectiveness of ex situ or in situ bioremediation. The purpose of this study was to evaluate the impact of repeated metalaxyl and folpet treatments on soil microbial communities and to select soil fungal strains able to degrade these fungicides. Results showed enhanced degradation of metalaxyl and folpet in vineyards soils submitted to repeated treatments with these fungicides. Indeed, the greatest degradation ability was observed in vineyard soil samples submitted to greater numbers of treatments. Respiration activities, as determined in the presence of selective antibiotics in soil suspensions amended with metalaxyl and folpet, showed that the fungal population was the microbiota community most active in the degradation process. Batch cultures performed with a progressive increase of fungicide concentrations allowed the selection of five tolerant fungal strains: Penicillium sp. 1 and Penicillium sp. 2, mycelia sterila 1 and 3, and Rhizopus stolonifer. Among these strains, mycelium sterila 3 and R. stolonifer presented only in vineyard soils treated with repeated application of these fungicides and showed tolerance >1,000 mg l(-1) against commercial formulations of metalaxyl (10 %) plus folpet (40 %). Using specific methods for inducing sporulation, mycelium sterila 3 was identified as Gongronella sp. Because this fungus is rare, it was compared using csM13-polymerase chain reaction (PCR) with the two known species, Gongronella butleri and G. lacrispora. The high tolerance to metalaxyl and folpet shown by Gongronella sp. and R. stolonifer might be correlated with their degradation ability. Our results point out that selected strains have potential for the bioremediation of metalaxyl and folpet in polluted soil sites.

Biodiversity within hot spring microbial mat communities: molecular monitoring of enrichment cultures

NASA Technical Reports Server (NTRS)

Ward, D. M.; Santegoeds, C. M.; Nold, S. C.; Ramsing, N. B.; Ferris, M. J.; Bateson, M. M.

1997-01-01

We have begun to examine the basis for incongruence between hot spring microbial mat populations detected by cultivation or by 16S rRNA methods. We used denaturing gradient gel electrophoresis (DGGE) to monitor enrichments and isolates plated therefrom. At near extincting inoculum dilutions we observed Chloroflexus-like and cyanobacterial populations whose 16S rRNA sequences have been detected in the 'New Pit' Spring Chloroflexus mat and the Octopus Spring cyanobacterial mat. Cyanobacterial populations enriched from 44 to 54 degrees C and 56 to 63 degrees C samples at near habitat temperatures were similar to those previously detected in mat samples of comparable temperatures. However, a lower temperature enrichment from the higher temperature sample selected for the populations found in the lower temperature sample. Three Thermus populations detected by both DGGE and isolation exemplify even more how enrichment may bias our view of community structure. The most abundant population was adapted to the habitat temperature (50 degrees C), while populations adapted to 65 degrees C and 70 degrees C were 10(2)- and 10(4)-fold less abundant, respectively. However, enrichment at 70 degrees C favored the least abundant strain. Inoculum dilution and incubation at the habitat temperature favored the more numerically relevant populations. We enriched many other aerobic chemoorganotrophic populations at various inoculum dilutions and substrate concentrations, most of whose 16S rRNA sequences have not been detected in mats. A common feature of numerically relevant cyanobacterial, Chloroflexus-like and aerobic chemorganotrophic populations, is that they grow poorly and resist cultivation on solidified medium, suggesting plating bias, and that the medium composition and incubation conditions may not reflect the natural microenvironments these populations inhabit.

Modelling the competition of planktonic and sessile aerobic heterotrophs for complementary nutrients in biofilm reactor.

PubMed

Lu, T; Saikaly, P E; Oerther, D B

2007-01-01

A comprehensive, simplified microbial biofilm model was developed to evaluate the impact of bioreactor operating parameters on changes in microbial population abundance. Biofilm simulations were conducted using three special cases: fully penetrated, internal mass transfer resistance and external mass transfer resistance. The results of model simulations showed that for certain operating conditions, competition for growth limiting nutrients generated oscillations in the abundance of planktonic and sessile microbial populations. These oscillations resulted in the violation of the competitive exclusion principle where the number of microbial populations was greater than the number of growth limiting nutrients. However, the operating conditions which impacted microbial community diversity were different for the three special cases. Comparing the results of model simulations for dispersed-growth, biofilms and bioflocs showed that oscillations and microbial community diversity were a function of competition as well as other key features of the ecosystem. The significance of the current study is that it is the first to examine competition as a mechanism for controlling microbial community diversity in biofilm reactors.

Dynamics of Marine Microbial Metabolism and Physiology at Station ALOHA

NASA Astrophysics Data System (ADS)

Casey, John R.

Marine microbial communities influence global biogeochemical cycles by coupling the transduction of free energy to the transformation of Earth's essential bio-elements: H, C, N, O, P, and S. The web of interactions between these processes is extraordinarily complex, though fundamental physical and thermodynamic principles should describe its dynamics. In this collection of 5 studies, aspects of the complexity of marine microbial metabolism and physiology were investigated as they interact with biogeochemical cycles and direct the flow of energy within the Station ALOHA surface layer microbial community. In Chapter 1, and at the broadest level of complexity discussed, a method to relate cell size to metabolic activity was developed to evaluate allometric power laws at fine scales within picoplankton populations. Although size was predictive of metabolic rates, within-population power laws deviated from the broader size spectrum, suggesting metabolic diversity as a key determinant of microbial activity. In Chapter 2, a set of guidelines was proposed by which organic substrates are selected and utilized by the heterotrophic community based on their nitrogen content, carbon content, and energy content. A hierarchical experimental design suggested that the heterotrophic microbial community prefers high nitrogen content but low energy density substrates, while carbon content was not important. In Chapter 3, a closer look at the light-dependent dynamics of growth on a single organic substrate, glycolate, suggested that growth yields were improved by photoheterotrophy. The remaining chapters were based on the development of a genome-scale metabolic network reconstruction of the cyanobacterium Prochlorococcus to probe its metabolic capabilities and quantify metabolic fluxes. Findings described in Chapter 4 pointed to evolution of the Prochlorococcus metabolic network to optimize growth at low phosphate concentrations. Finally, in Chapter 5 and at the finest scale of complexity, a method was developed to predict hourly changes in both physiology and metabolic fluxes in Prochlorococcus by incorporating gene expression time-series data within the metabolic network model. Growth rates predicted by this method more closely matched experimental data, and diel changes in elemental composition and the energy content of biomass were predicted. Collectively, these studies identify and quantify the potential impact of variations in metabolic and physiological traits on the melee of microbial community interactions.

Estimating and mapping ecological processes influencing microbial community assembly

PubMed Central

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

2015-01-01

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

Microevolutionary dynamics in Methanothermococcus populations from deep-sea hydrothermal vents in the Mid-Cayman Rise

NASA Astrophysics Data System (ADS)

Hoffert, M.; Anderson, R. E.; Stepanauskas, R.; Huber, J. A.

2017-12-01

Deep-sea hydrothermal vents sustain diverse communities of microorganisms. The effects of geochemical and biological interactions on the process of evolution in these ecosystems remains poorly understood because the majority of subsurface microorganisms remain uncultivated. By examining metagenomic samples from hydrothermal fluids and mapping the samples to closely-related genomes found in vent sites, we can better understand how the process of evolution is affected by the geochemical and environmental context in deep-sea vents. The Mid-Cayman Rise is a spreading ridge that hosts both mafic-influenced and ultramafic-influenced vent fields. Previous research on metagenomic samples from sites in the Mid-Cayman Rise has shown that these vents contain metabolically and taxonomically diverse microbial communities. Here, we investigate five single cell amplified Methanothermococcus genomes (SAGs) to investigate patterns in pangenomic variation and molecular evolution in these methanogens. Mappings of metagenomic reads from 15 sample sites to the SAGs reveal substantial variation in Methanothermococcus population abundance, nucleotide variability and selection pressure among the 15 geochemically distinct sample sites. Within each sample site, we observed distinct patterns of single nucleotide variant (SNV) accumulation and selection pressure within the SAG populations. Closely related genomes showed similar patterns of SNV accumulation. Analysis of open reading frames (ORFs) from the SAGs indicated that homologous genes accumulated variation at the same rate. For example, a genomic island for Nif genes was identified in three of the five genomes with significantly elevated SNV counts. dN/dS analyses revealed evidence for frequency-dependent selection, in which genes unique to individual SAGs displayed elevated diversifying selection relative to other genes. These results indicate that different strains of Methanothermococcus outcompete others in specific environmental settings, and that these fitness advantages may result from variation in the pangenome, as revealed by dN/dS and SNV analyses. By examining variation and the scale of nucleotide and genes, we aim to gain insight into the roles of genetic diversity and environmental selection on microbial evolution in these ecosystems.

Microbiome dynamics during ensiling of corn with and without Lactobacillus plantarum inoculant.

PubMed

Keshri, Jitendra; Chen, Yaira; Pinto, Riky; Kroupitski, Yulia; Weinberg, Zwi G; Sela Saldinger, Shlomo

2018-05-01

Microbial population dynamics associated with corn silage, with and without Lactobacillus plantarum treatment, was studied. Whole crop corn was ensiled using laboratory silos and sampled at different times, up to 3 months. The dominant bacteria, before ensiling, were Acinetobacter (38.5%) and Klebsiella (16.3%), while the dominant fungi were Meyerozyma (53.5%) and Candida (27.7%). During ensiling, the microbial population shifted considerably, and Lactobacillus (> 94%) and Candida (> 74%) became the most dominant microbial genera in both treated and untreated silages. Yet, lactic acid content was higher in the treated silage, while the microbial diversity was lower than in the untreated silage. Upon aerobic exposure, spoilage occurred more rapidly in the treated silage, possibly due to the higher abundance of lactic acid-assimilating fungi, such as Candida. Our study is the first to describe microbial population dynamics during whole-crop corn ensiling and the results indicate that microbial diversity may be an indicator of aerobic stability.

Drastic changes in aquatic bacterial populations from the Cuatro Cienegas Basin (Mexico) in response to long-term environmental stress.

PubMed

Pajares, Silvia; Eguiarte, Luis E; Bonilla-Rosso, German; Souza, Valeria

2013-12-01

Understanding the changes of aquatic microbial community composition in response to changes in temperature and ultraviolet irradiation is relevant for predicting biogeochemical modifications in the functioning of natural microbial communities under global climate change scenarios. Herein we investigate shifts in the bacterioplankton composition in response to long-term changes in temperature and UV radiation. For this purpose, 15 mesocosms were seeded with composite aquatic microbial communities from natural pools within the Cuatro Cienegas Basin (Mexican Chihuahuan desert) and were subject to different temperatures and UV conditions. 16S rRNA gene clone libraries were obtained from water samples at the mid-point (4 months) and the end of the experiment (8 months). An increase in bacterial diversity over time was found in the treatment of constant temperature and UV protection, which suggests that stable environments promote the establishment of complex and diverse bacterial community. Drastic changes in the phylogenetic bacterioplankton composition and structure were observed in response to fluctuating temperature and increasing UV radiation and temperature. Fluctuating temperature induced the largest decrease of bacterial richness during the experiment, indicating that frequent temperature changes drive the reduction in abundance of several species, most notably autotrophs. The long-term impact of these environmental stresses reduced diversity and selected for generalist aquatic bacterial populations, such as Porphyrobacter. These changes at the community level occur at an ecological time scale, suggesting that under global warming scenarios cascade effects on the food web are possible if the microbial diversity is modified.

Effects of dietary cooked navy bean on the fecal microbiome of healthy companion dogs.

PubMed

Kerr, Katherine R; Forster, Genevieve; Dowd, Scot E; Ryan, Elizabeth P; Swanson, Kelly S

2013-01-01

Cooked bean powders are a promising novel protein and fiber source for dogs, which have demonstrated potential to alter microbial composition and function for chronic disease control and prevention. This study aimed to determine the impact of cooked navy bean powder fed as a staple food ingredient on the fecal microbiome of healthy adult pet dogs. Fecal samples from healthy dogs prior to dietary control and after 4 wk of dietary treatment with macro- and micronutrient matched diets containing either 0 or 25% cooked navy beans (n = 11 and n = 10, respectively) were analyzed by 454-pyrosequencing of the 16S rRNA gene. There were few differences between dogs fed the control and navy bean diets after 4 wk of treatment. These data indicate that there were no major effects of navy bean inclusion on microbial populations. However, significant differences due to dietary intervention onto both research diets were observed (i.e., microbial populations at baseline versus 4 wk of intervention with 0 or 25% navy bean diets). After 4 wk of dietary intervention on either control or navy bean diet, the Phylum Firmicutes was increased and the Phyla Actinobacteria and Fusobacteria were decreased compared to baseline. No negative alterations of microbial populations occurred following cooked navy bean intake in dogs, indicating that bean powders may be a viable protein and fiber source for commercial pet foods. The highly variable microbial populations observed in these healthy adult pet dogs at baseline is one potential reason for the difficulty to detect alterations in microbial populations following dietary changes. Given the potential physiological benefits of bean intake in humans and dogs, further evaluation of the impacts of cooked navy bean intake on fecal microbial populations with higher power or more sensitive methods are warranted.

Increased survival of experimentally evolved antimicrobial peptide-resistant Staphylococcus aureus in an animal host

PubMed Central

Dobson, Adam J; Purves, Joanne; Rolff, Jens

2014-01-01

Antimicrobial peptides (AMPs) have been proposed as new class of antimicrobial drugs, following the increasing prevalence of bacteria resistant to antibiotics. Synthetic AMPs are functional analogues of highly evolutionarily conserved immune effectors in animals and plants, produced in response to microbial infection. Therefore, the proposed therapeutic use of AMPs bears the risk of ‘arming the enemy’: bacteria that evolve resistance to AMPs may be cross-resistant to immune effectors (AMPs) in their hosts. We used a panel of populations of Staphylococcus aureus that were experimentally selected for resistance to a suite of individual AMPs and antibiotics to investigate the ‘arming the enemy’ hypothesis. We tested whether the selected strains showed higher survival in an insect model (Tenebrio molitor) and cross-resistance against other antimicrobials in vitro. A population selected for resistance to the antimicrobial peptide iseganan showed increased in vivo survival, but was not more virulent. We suggest that increased survival of AMP-resistant bacteria almost certainly poses problems to immune-compromised hosts. PMID:25469169

Phylogenetically conserved resource partitioning in the coastal microbial loop

PubMed Central

Bryson, Samuel; Li, Zhou; Chavez, Francisco; Weber, Peter K; Pett-Ridge, Jennifer; Hettich, Robert L; Pan, Chongle; Mayali, Xavier; Mueller, Ryan S

2017-01-01

Resource availability influences marine microbial community structure, suggesting that population-specific resource partitioning defines discrete niches. Identifying how resources are partitioned among populations, thereby characterizing functional guilds within the communities, remains a challenge for microbial ecologists. We used proteomic stable isotope probing (SIP) and NanoSIMS analysis of phylogenetic microarrays (Chip-SIP) along with 16S rRNA gene amplicon and metagenomic sequencing to characterize the assimilation of six 13C-labeled common metabolic substrates and changes in the microbial community structure within surface water collected from Monterey Bay, CA. Both sequencing approaches indicated distinct substrate-specific community shifts. However, observed changes in relative abundance for individual populations did not correlate well with directly measured substrate assimilation. The complementary SIP techniques identified assimilation of all six substrates by diverse taxa, but also revealed differential assimilation of substrates into protein and ribonucleotide biomass between taxa. Substrate assimilation trends indicated significantly conserved resource partitioning among populations within the Flavobacteriia, Alphaproteobacteria and Gammaproteobacteria classes, suggesting that functional guilds within marine microbial communities are phylogenetically cohesive. However, populations within these classes exhibited heterogeneity in biosynthetic activity, which distinguished high-activity copiotrophs from low-activity oligotrophs. These results indicate distinct growth responses between populations that is not apparent by genome sequencing alone. PMID:28800138

Slightly acidic electrolyzed water for reducing airborne microorganisms in a layer breeding house.

PubMed

Hao, Xiaoxia; Cao, Wei; Li, Baoming; Zhang, Qiang; Wang, Chaoyuan; Ge, Liangpeng

2014-04-01

Reducing airborne microorganisms may potentially improve the environment in layer breeding houses. The effectiveness of slightly acidic electrolyzed water (SAEW; pH 5.29-6.30) in reducing airborne microorganisms was investigated in a commercial layer house in northern China. The building had a tunnel-ventilation system, with an evaporative cooling. The experimental area was divided into five zones along the length of the house, with zone 1 nearest to an evaporative cooling pad and zone 5 nearest to the fans. The air temperature, relative humidity, dust concentration, and microbial population were measured at the sampling points in the five zones during the study period. The SAEW was sprayed by workers in the whole house. A six-stage air microbial sampler was used to measure airborne microbial population. Results showed that the population of airborne bacteria and fungi were sharply reduced by 0.71 x 10(5) and 2.82 x 10(3) colony-forming units (CFU) m(-3) after 30 min exposure to SAEW, respectively. Compared with the benzalkonium chloride (BC) solution and povidone-iodine (PVP-I) solution treatments, the population reductions of airborne fungi treated by SAEW were significantly (P < 0.05) more, even though the three disinfectants can decrease both the airborne bacteria and fungi significantly (P < 0.05) 30 min after spraying. There are no effective methods for reducing airborne microbial levels in tunnel-ventilated layer breeding houses; additionally, there is limited information available on airborne microorganism distribution. This research investigated the spatial distribution of microbial population, and the effectiveness of spraying slightly acidic electrolyzed water in reducing microbial levels. The research revealed that slightly acidic electrolyzed water spray was a potential method for reducing microbial presence in layer houses. The knowledge gained in this research about the microbial population variations in the building may assist producers in managing the bird housing environment and engineers in designing poultry houses.

Population genomics of a symbiont in the early stages of a pest invasion.

PubMed

Brown, Amanda M V; Huynh, Lynn Y; Bolender, Caitlin M; Nelson, Kelly G; McCutcheon, John P

2014-03-01

Invasive species often depend on microbial symbionts, but few studies have examined the evolutionary dynamics of symbionts during the early stages of an invasion. The insect Megacopta cribraria and its bacterial nutritional symbiont Candidatus Ishikawaella capsulata invaded the southeastern US in 2009. While M. cribraria was initially discovered on wild kudzu plants, it was found as a pest on soybeans within 1 year of infestation. Because prior research suggests Ishikawaella confers the pest status--that is, the ability to thrive on soybeans--in some Megacopta species, we performed a genomic study on Ishikawaella from US. Megacopta cribraria populations to understand the role of the symbiont in driving host plant preferences. We included Ishikawaella samples collected in the first days of the invasion in 2009 and from 23 locations across the insect's 2011 US range. The 0.75 Mb symbiont genome revealed only 47 fixed differences from the pest-conferring Ishikawaella in Japan, with only one amino acid change in a nutrition-provisioning gene. This similarity, along with a lack of fixed substitutions in the US symbiont population, indicates that Ishikawella likely arrived in the US capable of being a soybean pest. Analyses of allele frequency changes between 2009 and 2011 uncover signatures of both positive and negative selection and suggest that symbionts on soybeans and kudzu experience differential selection for genes related to nutrient provisioning. Our data reveal the evolutionary trajectory of an important insect-bacteria symbiosis in the early stages of an invasion, highlighting the role microbial symbionts may play in the spread of invasive species. © 2013 John Wiley & Sons Ltd.

Profile of microflora of the posterior intestine of Chinook salmon before, during, and after administration of rations with and without erythromycin

USGS Publications Warehouse

Moffitt, C.M.; Mobin, S.M.A.

2006-01-01

We describe the resident heterotrophic aerobic microflora of the salmonid posterior intestine before, during, and after the administration of rations with erythromycin in a hatchery raceway environment. We compare the profiles of medicated Chinook salmon Oncorhynchus tshawytscha with those of control fish that were not fed erythromycin. The combined counts of bacteria and yeasts per gram of fish intestine originating from four upstream raceways ranged from 3.0 ?? 102 to 9.6 ?? 105 colony-forming units (CFU) over the study period. Yeasts were commonly identified in the gut, and abundances ranged from 0% to more than 80% of the CFU. Erythromycin therapy decreased the total microbial population and altered the bacterial diversity in the gut during treatment. The intestinal microbial populations in fish medicated with erythromycin increased rapidly after treatment ceased, and by 25 d after treatment the CFU were similar in samples from both medicated and control fish populations. Of 325 isolates from fish selected for biochemical profiles, we identified a total of eight gram-positive and eight gram-negative genera. Bacillus spp. were common throughout sampling and were identified in samples of fish feed. Erythromycin-resistant, gram-positive bacteria were observed throughout the sampling in medicated and control fish. We identified seven gram-positive and two gram-negative genera in 74 selected isolates from control and erythromycin feeds. Our studies suggest that the aerobic microflora of the posterior intestine varies over time, and it is likely that few resistant genera of concern to human health are present.

Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances.

PubMed

Xu, Jianping

2006-06-01

Microbial ecology examines the diversity and activity of micro-organisms in Earth's biosphere. In the last 20 years, the application of genomics tools have revolutionized microbial ecological studies and drastically expanded our view on the previously underappreciated microbial world. This review first introduces the basic concepts in microbial ecology and the main genomics methods that have been used to examine natural microbial populations and communities. In the ensuing three specific sections, the applications of the genomics in microbial ecological research are highlighted. The first describes the widespread application of multilocus sequence typing and representational difference analysis in studying genetic variation within microbial species. Such investigations have identified that migration, horizontal gene transfer and recombination are common in natural microbial populations and that microbial strains can be highly variable in genome size and gene content. The second section highlights and summarizes the use of four specific genomics methods (phylogenetic analysis of ribosomal RNA, DNA-DNA re-association kinetics, metagenomics, and micro-arrays) in analysing the diversity and potential activity of microbial populations and communities from a variety of terrestrial and aquatic environments. Such analyses have identified many unexpected phylogenetic lineages in viruses, bacteria, archaea, and microbial eukaryotes. Functional analyses of environmental DNA also revealed highly prevalent, but previously unknown, metabolic processes in natural microbial communities. In the third section, the ecological implications of sequenced microbial genomes are briefly discussed. Comparative analyses of prokaryotic genomic sequences suggest the importance of ecology in determining microbial genome size and gene content. The significant variability in genome size and gene content among strains and species of prokaryotes indicate the highly fluid nature of prokaryotic genomes, a result consistent with those from multilocus sequence typing and representational difference analyses. The integration of various levels of ecological analyses coupled to the application and further development of high throughput technologies are accelerating the pace of discovery in microbial ecology.

Flow cytometric monitoring of bacterioplankton phenotypic diversity predicts high population-specific feeding rates by invasive dreissenid mussels.

PubMed

Props, Ruben; Schmidt, Marian L; Heyse, Jasmine; Vanderploeg, Henry A; Boon, Nico; Denef, Vincent J

2018-02-01

Species invasion is an important disturbance to ecosystems worldwide, yet knowledge about the impacts of invasive species on bacterial communities remains sparse. Using a novel approach, we simultaneously detected phenotypic and derived taxonomic change in a natural bacterioplankton community when subjected to feeding pressure by quagga mussels, a widespread aquatic invasive species. We detected a significant decrease in diversity within 1 h of feeding and a total diversity loss of 11.6 ± 4.1% after 3 h. This loss of microbial diversity was caused by the selective removal of high nucleic acid populations (29 ± 5% after 3 h). We were able to track the community diversity at high temporal resolution by calculating phenotypic diversity estimates from flow cytometry (FCM) data of minute amounts of sample. Through parallel FCM and 16S rRNA gene amplicon sequencing analysis of environments spanning a broad diversity range, we showed that the two approaches resulted in highly correlated diversity measures and captured the same seasonal and lake-specific patterns in community composition. Based on our results, we predict that selective feeding by invasive dreissenid mussels directly impacts the microbial component of the carbon cycle, as it may drive bacterioplankton communities toward less diverse and potentially less productive states. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Antimicrobial activity of ceftaroline and other anti-infective agents against microbial pathogens recovered from the surgical intensive care patient population: a prevalence analysis.

PubMed

Edmiston, Charles E; Krepel, Candace J; Leaper, David; Ledeboer, Nathan A; Mackey, Tami-Lea; Graham, Mary Beth; Lee, Cheong; Rossi, Peter J; Brown, Kellie R; Lewis, Brian D; Seabrook, Gary R

2014-12-01

Ceftaroline is a new parenteral cephalosporin agent with excellent activity against methicillin-sensitive (MSSA) and resistant strains of Staphylococcus aureus (MRSA). Critically ill surgical patients are susceptible to infection, often by multi-drug-resistant pathogens. The activity of ceftaroline against such pathogens has not been described. Three hundred thirty-five consecutive microbial isolates were collected from surgical wounds or abscesses, respiratory, urine, and blood cultures from patients in the surgical intensive care unit (SICU) of a major tertiary medical center. Using Clinical and Laboratory Standards Institute (CLSI) standard methodology and published breakpoints, all aerobic, facultative anaerobic isolates were tested against ceftaroline and selected comparative antimicrobial agents. All staphylococcal isolates were susceptible to ceftaroline at a breakpoint of ≤1.0 mcg/mL. In addition, ceftaroline exhibited excellent activity against all streptococcal clinical isolates and non-ESBL-producing strains of Enterobacteriaceae (93.5%) recovered from SICU patients. Ceftaroline was inactive against ESBL-producing Enterobacteriaceae, Pseudomonas aeruginosa, vancomycin-resistant enterococci, and selective gram-negative anaerobic bacteria. At present, ceftaroline is the only cephalosporin agent that is active against community and healthcare-associated MRSA. Further studies are needed to validate the benefit of this novel broad-spectrum anti-infective agent for the treatment of susceptible serious infections in the SICU patient population.

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

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

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

Mineralogic control on abundance and diversity of surface-adherent microbial communities

USGS Publications Warehouse

Mauck, Brena S.; Roberts, Jennifer A.

2007-01-01

In this study, we investigated the role of mineral-bound P and Fe in defining microbial abundance and diversity in a carbon-rich groundwater. Field colonization experiments of initially sterile mineral surfaces were combined with community structure characterization of the attached microbial population. Silicate minerals containing varying concentrations of P (∼1000 ppm P) and Fe (∼4 wt % Fe 2 O3), goethite (FeOOH), and apatite [Ca5(PO4)3(OH)] were incubated for 14 months in three biogeochemically distinct zones within a petroleum-contaminated aquifer. Phospholipid fatty acid analysis of incubated mineral surfaces and groundwater was used as a measure of microbial community structure and biomass. Microbial biomass on minerals exhibited distinct trends as a function of mineralogy depending on the environment of incubation. In the carbon-rich, aerobic groundwater attached biomass did not correlate to the P- or Fe- content of the mineral. In the methanogenic groundwater, however, biomass was most abundant on P-containing minerals. Similarly, in the Fe-reducing groundwater a correlation between Fe-content and biomass was observed. The community structure of the mineral-adherent microbial population was compared to the native groundwater community. These two populations were significantly different regardless of mineralogy, suggesting differentiation of the planktonic community through attachment, growth, and death of colonizing cells. Biomarkers specific for dissimilatory Fe-reducing bacteria native to the aquifer were identified only on Fe-containing minerals in the Fe-reducing groundwater. These results demonstrate that the trace nutrient content of minerals affects both the abundance and diversity of surface-adherent microbial communities. This behavior may be a means to access limiting nutrients from the mineral, creating a niche for a particular microbial population. These results suggest that heterogeneity of microbial populations and their associated activities in subsurface environments extend to the microscale and cautions over-interpretation of highly sample-dependent measurements in the context of interpreting field data.

mRNA-Based Parallel Detection of Active Methanotroph Populations by Use of a Diagnostic Microarray

PubMed Central

Bodrossy, Levente; Stralis-Pavese, Nancy; Konrad-Köszler, Marianne; Weilharter, Alexandra; Reichenauer, Thomas G.; Schöfer, David; Sessitsch, Angela

2006-01-01

A method was developed for the mRNA-based application of microbial diagnostic microarrays to detect active microbial populations. DNA- and mRNA-based analyses of environmental samples were compared and confirmed via quantitative PCR. Results indicated that mRNA-based microarray analyses may provide additional information on the composition and functioning of microbial communities. PMID:16461725

16S rRNA analysis of diversity of manure microbial community in dairy farm environment

PubMed Central

Miao, Max; Wang, Yi; Settles, Matthew; del Rio, Noelia Silva; Castillo, Alejandro; Souza, Alex; Pereira, Richard

2018-01-01

Dairy farms generate a considerable amount of manure, which is applied in cropland as fertilizer. While the use of manure as fertilizer reduces the application of chemical fertilizers, the main concern with regards to manure application is microbial pollution. Manure is a reservoir of a broad range of microbial populations, including pathogens, which have potential to cause contamination and pose risks to public and animal health. Despite the widespread use of manure fertilizer, the change in microbial diversity of manure under various treatment processes is still not well-understood. We hypothesize that the microbial population of animal waste changes with manure handling used in a farm environment. Consequential microbial risk caused by animal manure may depend on manure handling. In this study, a reconnaissance effort for sampling dairy manure in California Central Valley followed by 16S rRNA analysis of content and diversity was undertaken to understand the microbiome of manure after various handling processes. The microbial community analysis of manure revealed that the population in liquid manure differs from that in solid manure. For instance, the bacteria of genus Sulfuriomonas were unique in liquid samples, while the bacteria of genus Thermos were observed only in solid samples. Bacteria of genus Clostridium were present in both solid and liquid samples. The population among liquid samples was comparable, as was the population among solid samples. These findings suggest that the mode of manure application (i.e., liquid versus solid) could have a potential impact on the microbiome of cropland receiving manure as fertilizers. PMID:29304047

Associations between Ectomycorrhizal Fungi and Bacterial Needle Endophytes in Pinus radiata: Implications for Biotic Selection of Microbial Communities

PubMed Central

Rúa, Megan A.; Wilson, Emily C.; Steele, Sarah; Munters, Arielle R.; Hoeksema, Jason D.; Frank, Anna C.

2016-01-01

Studies of the ecological and evolutionary relationships between plants and their associated microbes have long been focused on single microbes, or single microbial guilds, but in reality, plants associate with a diverse array of microbes from a varied set of guilds. As such, multitrophic interactions among plant-associated microbes from multiple guilds represent an area of developing research, and can reveal how complex microbial communities are structured around plants. Interactions between coniferous plants and their associated microbes provide a good model system for such studies, as conifers host a suite of microorganisms including mutualistic ectomycorrhizal (ECM) fungi and foliar bacterial endophytes. To investigate the potential role ECM fungi play in structuring foliar bacterial endophyte communities, we sampled three isolated, native populations of Monterey pine (Pinus radiata), and used constrained analysis of principal coordinates to relate the community matrices of the ECM fungi and bacterial endophytes. Our results suggest that ECM fungi may be important factors for explaining variation in bacterial endophyte communities but this effect is influenced by population and environmental characteristics, emphasizing the potential importance of other factors — biotic or abiotic — in determining the composition of bacterial communities. We also classified ECM fungi into categories based on known fungal traits associated with substrate exploration and nutrient mobilization strategies since variation in these traits allows the fungi to acquire nutrients across a wide range of abiotic conditions and may influence the outcome of multi-species interactions. Across populations and environmental factors, none of the traits associated with fungal foraging strategy types significantly structured bacterial assemblages, suggesting these ECM fungal traits are not important for understanding endophyte-ECM interactions. Overall, our results suggest that both biotic species interactions and environmental filtering are important for structuring microbial communities but emphasize the need for more research into these interactions. PMID:27065966

Bacterial Profile of Dentine Caries and the Impact of pH on Bacterial Population Diversity

PubMed Central

Kianoush, Nima; Adler, Christina J.; Nguyen, Ky-Anh T.; Browne, Gina V.; Simonian, Mary; Hunter, Neil

2014-01-01

Dental caries is caused by the release of organic acids from fermentative bacteria, which results in the dissolution of hydroxyapatite matrices of enamel and dentine. While low environmental pH is proposed to cause a shift in the consortium of oral bacteria, favouring the development of caries, the impact of this variable has been overlooked in microbial population studies. This study aimed to detail the zonal composition of the microbiota associated with carious dentine lesions with reference to pH. We used 454 sequencing of the 16S rRNA gene (V3–V4 region) to compare microbial communities in layers ranging in pH from 4.5–7.8 from 25 teeth with advanced dentine caries. Pyrosequencing of the amplicons yielded 449,762 sequences. Nine phyla, 97 genera and 409 species were identified from the quality-filtered, de-noised and chimera-free sequences. Among the microbiota associated with dentinal caries, the most abundant taxa included Lactobacillus sp., Prevotella sp., Atopobium sp., Olsenella sp. and Actinomyces sp. We found a disparity between microbial communities localised at acidic versus neutral pH strata. Acidic conditions were associated with low diversity microbial populations, with Lactobacillus species including L. fermentum, L. rhamnosus and L. crispatus, being prominent. In comparison, the distinctive species of a more diverse flora associated with neutral pH regions of carious lesions included Alloprevotella tanerrae, Leptothrix sp., Sphingomonas sp. and Streptococcus anginosus. While certain bacteria were affected by the pH gradient, we also found that ∼60% of the taxa associated with caries were present across the investigated pH range, representing a substantial core. We demonstrated that some bacterial species implicated in caries progression show selective clustering with respect to pH gradient, providing a basis for specific therapeutic strategies. PMID:24675997

The microbial community structure in petroleum-contaminated sediments corresponds to geophysical signatures

USGS Publications Warehouse

Allen, J.P.; Atekwana, E.A.; Duris, J.W.; Werkema, D.D.; Rossbach, S.

2007-01-01

The interdependence between geoelectrical signatures at underground petroleum plumes and the structures of subsurface microbial communities was investigated. For sediments contaminated with light non-aqueousphase liquids, anomalous high conductivity values have been observed. Vertical changes in the geoelectrical properties of the sediments were concomitant with significant changes in the microbial community structures as determined by the construction and evaluation of 16S rRNA gene libraries. DNA sequencing of clones from four 16S rRNA gene libraries from different depths of a contaminated field site and two libraries from an uncontaminated background site revealed spatial heterogeneity in the microbial community structures. Correspondence analysis showed that the presence of distinct microbial populations, including the various hydrocarbon-degrading, syntrophic, sulfate-reducing, and dissimilatory-iron-reducing populations, was a contributing factor to the elevated geoelectrical measurements. Thus, through their growth and metabolic activities, microbial populations that have adapted to the use of petroleum as a carbon source can strongly influence their geophysical surroundings. Since changes in the geophysical properties of contaminated sediments parallel changes in the microbial community compositions, it is suggested that geoelectrical measurements can be a cost-efficient tool to guide microbiological sampling for microbial ecology studies during the monitoring of natural or engineered bioremediation processes. Copyright ?? 2007, American Society for Microbiology. All Rights Reserved.

Evolutionary consequences of antibiotic use for the resistome, mobilome and microbial pangenome

PubMed Central

Gillings, Michael R.

2013-01-01

The widespread use and abuse of antibiotic therapy has evolutionary and ecological consequences, some of which are only just beginning to be examined. One well known consequence is the fixation of mutations and lateral gene transfer (LGT) events that confer antibiotic resistance. Sequential selection events, driven by different classes of antibiotics, have resulted in the assembly of diverse resistance determinants and mobile DNAs into novel genetic elements of ever-growing complexity and flexibility. These novel plasmids, integrons, and genomic islands have now become fixed at high frequency in diverse cell lineages by human antibiotic use. Consequently they can be regarded as xenogenetic pollutants, analogous to xenobiotic compounds, but with the critical distinction that they replicate rather than degrade when released to pollute natural environments. Antibiotics themselves must also be regarded as pollutants, since human production overwhelms natural synthesis, and a major proportion of ingested antibiotic is excreted unchanged into waste streams. Such antibiotic pollutants have non-target effects, raising the general rates of mutation, recombination, and LGT in all the microbiome, and simultaneously providing the selective force to fix such changes. This has the consequence of recruiting more genes into the resistome and mobilome, and of increasing the overlap between these two components of microbial genomes. Thus the human use and environmental release of antibiotics is having second order effects on the microbial world, because these small molecules act as drivers of bacterial evolution. Continued pollution with both xenogenetic elements and the selective agents that fix such elements in populations has potentially adverse consequences for human welfare. PMID:23386843

Evolutionary consequences of antibiotic use for the resistome, mobilome and microbial pangenome.

PubMed

Gillings, Michael R

2013-01-01

The widespread use and abuse of antibiotic therapy has evolutionary and ecological consequences, some of which are only just beginning to be examined. One well known consequence is the fixation of mutations and lateral gene transfer (LGT) events that confer antibiotic resistance. Sequential selection events, driven by different classes of antibiotics, have resulted in the assembly of diverse resistance determinants and mobile DNAs into novel genetic elements of ever-growing complexity and flexibility. These novel plasmids, integrons, and genomic islands have now become fixed at high frequency in diverse cell lineages by human antibiotic use. Consequently they can be regarded as xenogenetic pollutants, analogous to xenobiotic compounds, but with the critical distinction that they replicate rather than degrade when released to pollute natural environments. Antibiotics themselves must also be regarded as pollutants, since human production overwhelms natural synthesis, and a major proportion of ingested antibiotic is excreted unchanged into waste streams. Such antibiotic pollutants have non-target effects, raising the general rates of mutation, recombination, and LGT in all the microbiome, and simultaneously providing the selective force to fix such changes. This has the consequence of recruiting more genes into the resistome and mobilome, and of increasing the overlap between these two components of microbial genomes. Thus the human use and environmental release of antibiotics is having second order effects on the microbial world, because these small molecules act as drivers of bacterial evolution. Continued pollution with both xenogenetic elements and the selective agents that fix such elements in populations has potentially adverse consequences for human welfare.

Rapid estimation of microbial populations in fish samples by using terminal restriction fragment length polymorphism analysis of 16S rDNA.

PubMed

Tanaka, Yuichiro; Takahashi, Hajime; Kitazawa, Nao; Kimura, Bon

2010-01-01

A rapid system using terminal restriction fragment length polymorphism (T-RFLP) analysis targeting 16S rDNA is described for microbial population analysis in edible fish samples. The defined terminal restriction fragment database was constructed by collecting 102 strains of bacteria representing 53 genera that are associated with fish. Digestion of these 102 strains with two restriction enzymes, HhaI and MspI, formed 54 pattern groups with discrimination to the genus level. This T-RFLP system produced results comparable to those from a culture-based method in six natural fish samples with a qualitative correspondence of 71.4 to 92.3%. Using the T-RFLP system allowed an estimation of the microbial population within 7 h. Rapid assay of the microbial population is advantageous for food manufacturers and testing laboratories; moreover, the strategy presented here allows adaptation to specific testing applications.

Population density controls on microbial pollution across the Ganga catchment.

PubMed

Milledge, D G; Gurjar, S K; Bunce, J T; Tare, V; Sinha, R; Carbonneau, P E

2018-01-01

For millions of people worldwide, sewage-polluted surface waters threaten water security, food security and human health. Yet the extent of the problem and its causes are poorly understood. Given rapid widespread global urbanisation, the impact of urban versus rural populations is particularly important but unknown. Exploiting previously unpublished archival data for the Ganga (Ganges) catchment, we find a strong non-linear relationship between upstream population density and microbial pollution, and predict that these river systems would fail faecal coliform standards for irrigation waters available to 79% of the catchment's 500 million inhabitants. Overall, this work shows that microbial pollution is conditioned by the continental-scale network structure of rivers, compounded by the location of cities whose growing populations contribute c. 100 times more microbial pollutants per capita than their rural counterparts. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Range expansion promotes cooperation in an experimental microbial metapopulation

PubMed Central

Datta, Manoshi Sen; Korolev, Kirill S.; Cvijovic, Ivana; Dudley, Carmel; Gore, Jeff

2013-01-01

Natural populations throughout the tree of life undergo range expansions in response to changes in the environment. Recent theoretical work suggests that range expansions can have a strong effect on evolution, even leading to the fixation of deleterious alleles that would normally be outcompeted in the absence of migration. However, little is known about how range expansions might influence alleles under frequency- or density-dependent selection. Moreover, there is very little experimental evidence to complement existing theory, since expanding populations are difficult to study in the natural environment. In this study, we have used a yeast experimental system to explore the effect of range expansions on the maintenance of cooperative behaviors, which commonly display frequency- and density-dependent selection and are widespread in nature. We found that range expansions favor the maintenance of cooperation in two ways: (i) through the enrichment of cooperators at the front of the expanding population and (ii) by allowing cooperators to “outrun” an invading wave of defectors. In this system, cooperation is enhanced through the coupling of population ecology and evolutionary dynamics in expanding populations, thus providing experimental evidence for a unique mechanism through which cooperative behaviors could be maintained in nature. PMID:23569263

Insights into recent and ancient trends in the co-evolution of Earth and life as revealed by microbial genomics

NASA Astrophysics Data System (ADS)

Anderson, R. E.; Huber, J. A.; Parsons, C.; Stüeken, E.

2017-12-01

Since the origin of life over 4 billion years ago, life has fundamentally altered the habitability of Earth. Similarly, the environment molds the evolutionary trajectory of life itself through natural selection. Microbial genomes retain a "memory" of the co-evolution of life and Earth and can be analyzed to better understand trends and events in both the recent and distant past. To examine evolutionary trends in the more recent past, we have used metagenomics analyses to investigate which environmental factors play the strongest role in driving the evolution of microbes in deep-sea hydrothermal vents, which are thought to have been important habitats in the earliest stages of life's evolution. We have shown that microbial populations in a deep, basalt-hosted system appear to be under stronger purifying selection than populations inhabiting a cooler serpentinizing system less than 20 km away, suggesting that environmental context and geochemistry have an important impact on evolutionary rates and trends. We also found evidence that viruses play an important role in driving evolution in these habitats. Changing environmental conditions may also effect long-term evolutionary trends in Earth's distant past, as revealed by comparative genomics. By reconciling phylogenetic trees for microbial species with trees of metabolic genes, we can determine approximately when crucial metabolic genes began to spread across the tree of life through horizontal gene transfer. Using these methods, we conducted an analysis of the relative timing of the spread of genes related to the nitrogen cycle. Our results indicate that the rate of horizontal gene transfer for important genes related to denitrification increased after the Great Oxidation Event, concurrent with geochemical evidence for increasing availability of nitrate, suggesting that the oxygenation of the atmosphere and surface ocean may have been an important determining factor for the spread of denitrification genes across the tree of life. In contrast, genes related to nitrogen fixation display much more consistent rates of horizontal gene transfer throughout Earth's history. Studies that couple genomics approaches with geochemistry have the potential to reveal insights into the co-evolution of life and Earth both in the recent and distant past.

Sources of Variation in the Gut Microbial Community of Lycaeides melissa Caterpillars.

PubMed

Chaturvedi, Samridhi; Rego, Alexandre; Lucas, Lauren K; Gompert, Zachariah

2017-09-12

Microbes can mediate insect-plant interactions and have been implicated in major evolutionary transitions to herbivory. Whether microbes also play a role in more modest host shifts or expansions in herbivorous insects is less clear. Here we evaluate the potential for gut microbial communities to constrain or facilitate host plant use in the Melissa blue butterfly (Lycaeides melissa). We conducted a larval rearing experiment where caterpillars from two populations were fed plant tissue from two hosts. We used 16S rRNA sequencing to quantify the relative effects of sample type (frass versus whole caterpillar), diet (plant species), butterfly population and development (caterpillar age) on the composition and diversity of the caterpillar gut microbial communities, and secondly, to test for a relationship between microbial community and larval performance. Gut microbial communities varied over time (that is, with caterpillar age) and differed between frass and whole caterpillar samples. Diet (host plant) and butterfly population had much more limited effects on microbial communities. We found no evidence that gut microbe community composition was associated with caterpillar weight, and thus, our results provide no support for the hypothesis that variation in microbial community affects performance in L. melissa.

Modeling evolution of spatially distributed bacterial communities: a simulation with the haploid evolutionary constructor

PubMed Central

2015-01-01

Background Multiscale approaches for integrating submodels of various levels of biological organization into a single model became the major tool of systems biology. In this paper, we have constructed and simulated a set of multiscale models of spatially distributed microbial communities and study an influence of unevenly distributed environmental factors on the genetic diversity and evolution of the community members. Results Haploid Evolutionary Constructor software http://evol-constructor.bionet.nsc.ru/ was expanded by adding the tool for the spatial modeling of a microbial community (1D, 2D and 3D versions). A set of the models of spatially distributed communities was built to demonstrate that the spatial distribution of cells affects both intensity of selection and evolution rate. Conclusion In spatially heterogeneous communities, the change in the direction of the environmental flow might be reflected in local irregular population dynamics, while the genetic structure of populations (frequencies of the alleles) remains stable. Furthermore, in spatially heterogeneous communities, the chemotaxis might dramatically affect the evolution of community members. PMID:25708911

Noninvasive methods for dynamic mapping of microbial populations across the landscape

NASA Astrophysics Data System (ADS)

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

2017-12-01

Soil microorganisms drive key ecosystem processes, and yet characterizing their distribution and activity in soil has been notoriously difficult. This is due, in part, to the heterogeneous nature of their response to changing environmental and nutrient conditions across time and space. These dynamics are challenging to constrain in both natural and experimental systems because of sampling difficulty and constraints. For example, soil microbial sampling at the Landscape Evolution Observatory (LEO) infrastructure in Biosphere 2 is limited in efforts to minimize soil disruption to the long term experiment that aims to characterize the interacting biological, hydrological, and geochemical processes driving soil evolution. In this and other systems, new methods are needed to monitor soil microbial communities and their genetic potential over time. In this study, we take advantage of the well-defined boundary conditions on hydrological flow at LEO to develop a new method to nondestructively characterize in situ microbial populations. In our approach, we sample microbes from the seepage flow at the base of each of three replicate LEO hillslopes and use hydrological models to `map back' in situ microbial populations. Over the course of a 3-month periodic rainfall experiment we collected samples from the LEO outflow for DNA and extraction and microbial community composition analysis. These data will be used to describe changes in microbial community composition over the course of the experiment. In addition, we will use hydrological flow models to identify the changing source region of discharge water over the course of periodic rainfall pulses, thereby mapping back microbial populations onto their geographic origin in the slope. These predictions of in situ microbial populations will be ground-truthed against those derived from destructive soil sampling at the beginning and end of the rainfall experiment. Our results will show the suitability of this method for long-term, non-destructive monitoring of the microbial communities that contribute to soil evolution in this large-scale model system. Furthermore, this method may be useful for other study systems with limitations to destructive sampling including other model infrastructures and natural landscapes.

Importance of positioning for microbial evolution

PubMed Central

Kim, Wook; Racimo, Fernando; Schluter, Jonas; Levy, Stuart B.; Foster, Kevin R.

2014-01-01

Microbes commonly live in dense surface-attached communities where cells layer on top of one another such that only those at the edges have unimpeded access to limiting nutrients and space. Theory predicts that this simple spatial effect, akin to plants competing for light in a forest, generates strong natural selection on microbial phenotypes. However, we require direct empirical tests of the importance of this spatial structuring. Here we show that spontaneous mutants repeatedly arise, push their way to the surface, and dominate colonies of the bacterium Pseudomonas fluorescens Pf0-1. Microscopy and modeling suggests that these mutants use secretions to expand and push themselves up to the growth surface to gain the best access to oxygen. Physically mixing the cells in the colony, or introducing space limitations, largely removes the mutant’s advantage, showing a key link between fitness and the ability of the cells to position themselves in the colony. We next follow over 500 independent adaptation events and show that all occur through mutation of a single repressor of secretions, RsmE, but that the mutants differ in competitiveness. This process allows us to map the genetic basis of their adaptation at high molecular resolution and we show how evolutionary competitiveness is explained by the specific effects of each mutation. By combining population level and molecular analyses, we demonstrate how living in dense microbial communities can generate strong natural selection to reach the growing edge. PMID:24715732

HYGIENE PRACTICES IN URBAN RESTAURANTS AND CHALLENGES TO IMPLEMENTING FOOD SAFETY AND HAZARD ANALYSIS CRITICAL CONTROL POINTS (HACCP) PROGRAMMES IN THIKA TOWN, KENYA.

PubMed

Muinde, R K; Kiinyukia, C; Rombo, G O; Muoki, M A

2012-12-01

To determine the microbial load in food, examination of safety measures and possibility of implementing an Hazard Analysis Critical Control Points (HACCP) system. The target population for this study consisted of restaurants owners in Thika. Municipality (n = 30). Simple randomsamples of restaurantswere selected on a systematic sampling method of microbial analysis in cooked, non-cooked, raw food and water sanitation in the selected restaurants. Two hundred and ninety eight restaurants within Thika Municipality were selected. Of these, 30 were sampled for microbiological testing. From the study, 221 (74%) of the restaurants were ready to eat establishments where food was prepared early enough to hold and only 77(26%) of the total restaurants, customers made an order of food they wanted. 118(63%) of the restaurant operators/staff had knowledge on quality control on food safety measures, 24 (8%) of the restaurants applied these knowledge while 256 (86%) of the restaurants staff showed that food contains ingredients that were hazard if poorly handled. 238 (80%) of the resultants used weighing and sorting of food materials, 45 (15%) used preservation methods and the rest used dry foods as critical control points on food safety measures. The study showed that there was need for implementation of Hazard Analysis Critical Control Points (HACCP) system to enhance food safety. Knowledge of HACCP was very low with 89 (30%) of the restaurants applying some of quality measures to the food production process systems. There was contamination with Coliforms, Escherichia coli and Staphylococcus aureus microbial though at very low level. The means of Coliforms, Escherichia coli and Staphylococcus aureas microbial in sampled food were 9.7 x 103CFU/gm, 8.2 x 103 CFU/gm and 5.4 x 103 CFU/gm respectively with Coliforms taking the highest mean.

The link of feast-phase dissolved oxygen (DO) with substrate competition and microbial selection in PHA production.

PubMed

Wang, Xiaofei; Oehmen, Adrian; Freitas, Elisabete B; Carvalho, Gilda; Reis, Maria A M

2017-04-01

Polyhydroxyalkanoates (PHAs) are biobased and biodegradable polyesters with the potential to replace conventional plastics. Aeration requires large amounts of energy in PHA production by mixed microbial cultures (MMCs), particularly during the feast phase due to substrate uptake. The objective of this study was to investigate the impact of DO concentrations on microbial selection, substrate competition and PHA production performance by MMCs. This represents the first study investigating DO impact on PHA production while feeding the multiple volatile fatty acids (VFAs) typically encountered in real fermented feedstocks, as well as the substrate preferences at different DO levels. Efficient microbial cultures were enriched under both high (3.47 ± 1.12 mg/L) and low (0.86 ± 0.50 mg/L) DO conditions in the feast phase containing mostly the same populations but with different relative abundance. The most abundant microorganisms in the two MMCs were Plasticicumulans, Zoogloea, Paracoccus, and Flavobacterium. Butyrate and valerate were found to be the preferred substrates as compared to acetate and propionate regardless of DO concentrations. In the accumulation step, the PHA storage capacity and yield were less affected by the change of DO levels when applying the culture selected under low DO in the feast phase (PHA storage capacity >60% and yield > 0.9 Cmol PHA/Cmol VFA). A high DO level is required for maximal PHA accumulation rates with the four VFAs (acetate, propionate, butyrate and valerate) present, due to the lower specific uptake rates of acetate and propionate under low DO conditions. However, butyrate and valerate specific uptake rates were less impacted by DO levels and hence low DO for PHA accumulation may be effective when feed is composed of these substrates only. Copyright © 2017 Elsevier Ltd. All rights reserved.

Microbial Response in Peat Overlying Kimberlite Pipes in The Attawapiskat Area, Northern Ontario

NASA Astrophysics Data System (ADS)

Donkervoort, L. J.; Southam, G.

2009-05-01

Exploration for ore deposits occurring under thick, post-mineralized cover requires innovative methods and instrumentation [1]. Buried kimberlite pipes 'produce' geochemical conditions such as increased pH and decreased Eh in overlying peat [2] that intuitively select for bacterial populations that are best able to grow and, which in turn affect the geochemistry producing a linked signal. A microbiological study of peat was conducted over the Zulu kimberlite in the Attawapiskat area of the James Bay Lowlands to determine if the type of underlying rock influences the diversity and populations of microorganisms living in the overlying peat. Peat was sampled along an 800 m transect across the Zulu kimberlite, including samples underlain by limestone. Microbial populations and carbon source utilization patterns of peat samples were compared between the two underlying rock types. Results demonstrate an inverse relationship of increased anaerobic populations and lower biodiversity directly above the kimberlite pipe. These results support a reduced 'column' consistent with the model presented by Hamilton [3]. The combination of traditional bacterial enumeration and community- level profiling represents a cost-effective and efficient exploration technique that can serve to compliment both geophysical and geochemical surveys. [1] Goldberg (1998) J. Geochem. Explor. 61, 191-202 [2] Hattori and Hamilton (2008) Appl. Geochem. 23, 3767-3782 [3] Hamilton (1998) J. Geochem. Explor. 63, 155-172

Reestablishment of recipient-associated microbiota in the lung allograft is linked to reduced risk of bronchiolitis obliterans syndrome.

PubMed

Willner, Dana L; Hugenholtz, Philip; Yerkovich, Stephanie T; Tan, Maxine E; Daly, Joshua N; Lachner, Nancy; Hopkins, Peter M; Chambers, Daniel C

2013-03-15

Bronchiolitis obliterans syndrome (BOS) is the primary limiting factor for long-term survival after lung transplantation, and has previously been associated with microbial infections. To cross-sectionally and longitudinally characterize microbial communities in allografts from transplant recipients with and without BOS using a culture-independent method based on high-throughput sequencing. Allografts were sampled by bronchoalveolar lavage, and microbial communities were profiled using 16S rRNA gene amplicon pyrosequencing. Community profiles were compared using the weighted Unifrac metric and the relationship between microbial populations, BOS, and other covariates was explored using PERMANOVA and logistic regression. Microbial communities in transplant patients fell into two main groups: those dominated by Pseudomonas or those dominated by Streptococcus and Veillonella, which seem to be mutually exclusive lung microbiomes. Aspergillus culture was also negatively correlated with the Pseudomonas-dominated group. The reestablishment of dominant populations present in patients pretransplant, notably Pseudomonas in individuals with cystic fibrosis, was negatively correlated with BOS. Recolonization of the allograft by Pseudomonas in individuals with cystic fibrosis is not associated with BOS. In general, reestablishment of pretransplant lung populations in the allograft seems to have a protective effect against BOS, whereas de novo acquisition of microbial populations often belonging to the same genera may increase the risk of BOS.

Digestive enzymes of human and nonhuman primates.

PubMed

Janiak, Mareike Cora

2016-09-01

All living organisms need to consume nutrients to grow, survive, and reproduce, making the successful acquisition of food resources a powerful selective pressure. However, acquiring food is only part of the challenge. While all animals spend much of their daily activity budget hunting, searching for, or otherwise procuring food, a large part of what is involved in overall nutrition occurs once the meal has been swallowed. Most nutritional components are too complex for immediate use and must be broken down into simpler compounds, which can then be absorbed by the body. This process, digestion, is catalyzed by enzymes that are either endogenous or produced by the host's microbial population. 1 Research shows that the nutritional value of food is partially constrained by the digestive abilities of the microbial community present in the host's gut and that these microbes rapidly adapt to changes in diet and other environmental pressures. 2 An accumulating body of evidence suggests that endogenously produced digestive enzymes also have been, and still are, common targets of natural selection, further cementing their crucial role in an organism's digestive system. 3-5 . © 2016 Wiley Periodicals, Inc.

Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases.

PubMed

Citorik, Robert J; Mimee, Mark; Lu, Timothy K

2014-11-01

Current antibiotics tend to be broad spectrum, leading to indiscriminate killing of commensal bacteria and accelerated evolution of drug resistance. Here, we use CRISPR-Cas technology to create antimicrobials whose spectrum of activity is chosen by design. RNA-guided nucleases (RGNs) targeting specific DNA sequences are delivered efficiently to microbial populations using bacteriophage or bacteria carrying plasmids transmissible by conjugation. The DNA targets of RGNs can be undesirable genes or polymorphisms, including antibiotic resistance and virulence determinants in carbapenem-resistant Enterobacteriaceae and enterohemorrhagic Escherichia coli. Delivery of RGNs significantly improves survival in a Galleria mellonella infection model. We also show that RGNs enable modulation of complex bacterial populations by selective knockdown of targeted strains based on genetic signatures. RGNs constitute a class of highly discriminatory, customizable antimicrobials that enact selective pressure at the DNA level to reduce the prevalence of undesired genes, minimize off-target effects and enable programmable remodeling of microbiota.

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

DOE PAGES

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

2017-08-04

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

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

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

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

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

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. © 2016 The Authors. Environmental Microbiology Reports published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Demonstration Bulletin: Aqueous Biological Treatment System (Fixed-Film Biodegradation), Biotrol, Inc

EPA Science Inventory

This patented biological treatment system, called the BioTrol Aqueous Treatment System (BATS)., uses an amended microbial population to achieve biological degradation. The system is considered amended when a specific microorganism is added to the indigenous microbial population ...

Phylogenetically conserved resource partitioning in the coastal microbial loop

DOE PAGES

Bryson, Samuel; Li, Zhou; Chavez, Francisco; ...

2017-08-11

Resource availability influences marine microbial community structure, suggesting that population-specific resource partitioning defines discrete niches. Identifying how resources are partitioned among populations, thereby characterizing functional guilds within the communities, remains a challenge for microbial ecologists. We used proteomic stable isotope probing (SIP) and NanoSIMS analysis of phylogenetic microarrays (Chip-SIP) along with 16S rRNA gene amplicon and metagenomic sequencing to characterize the assimilation of six 13C-labeled common metabolic substrates and changes in the microbial community structure within surface water collected from Monterey Bay, CA. Both sequencing approaches indicated distinct substrate-specific community shifts. However, observed changes in relative abundance for individual populationsmore » did not correlate well with directly measured substrate assimilation. The complementary SIP techniques identified assimilation of all six substrates by diverse taxa, but also revealed differential assimilation of substrates into protein and ribonucleotide biomass between taxa. Substrate assimilation trends indicated significantly conserved resource partitioning among populations within the Flavobacteriia, Alphaproteobacteria and Gammaproteobacteria classes, suggesting that functional guilds within marine microbial communities are phylogenetically cohesive. However, populations within these classes exhibited heterogeneity in biosynthetic activity, which distinguished high-activity copiotrophs from low-activity oligotrophs. These results indicate distinct growth responses between populations that is not apparent by genome sequencing alone.« less

Phylogenetically conserved resource partitioning in the coastal microbial loop

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

Bryson, Samuel; Li, Zhou; Chavez, Francisco

Resource availability influences marine microbial community structure, suggesting that population-specific resource partitioning defines discrete niches. Identifying how resources are partitioned among populations, thereby characterizing functional guilds within the communities, remains a challenge for microbial ecologists. We used proteomic stable isotope probing (SIP) and NanoSIMS analysis of phylogenetic microarrays (Chip-SIP) along with 16S rRNA gene amplicon and metagenomic sequencing to characterize the assimilation of six 13C-labeled common metabolic substrates and changes in the microbial community structure within surface water collected from Monterey Bay, CA. Both sequencing approaches indicated distinct substrate-specific community shifts. However, observed changes in relative abundance for individual populationsmore » did not correlate well with directly measured substrate assimilation. The complementary SIP techniques identified assimilation of all six substrates by diverse taxa, but also revealed differential assimilation of substrates into protein and ribonucleotide biomass between taxa. Substrate assimilation trends indicated significantly conserved resource partitioning among populations within the Flavobacteriia, Alphaproteobacteria and Gammaproteobacteria classes, suggesting that functional guilds within marine microbial communities are phylogenetically cohesive. However, populations within these classes exhibited heterogeneity in biosynthetic activity, which distinguished high-activity copiotrophs from low-activity oligotrophs. These results indicate distinct growth responses between populations that is not apparent by genome sequencing alone.« less

Microbial DNA records historical delivery of anthropogenic mercury

PubMed Central

Poulain, Alexandre J; Aris-Brosou, Stéphane; Blais, Jules M; Brazeau, Michelle; Keller, Wendel (Bill); Paterson, Andrew M

2015-01-01

Mercury (Hg) is an anthropogenic pollutant that is toxic to wildlife and humans, but the response of remote ecosystems to globally distributed Hg is elusive. Here, we use DNA extracted from a dated sediment core to infer the response of microbes to historical Hg delivery. We observe a significant association between the mercuric reductase gene (merA) phylogeny and the timing of Hg deposition. Using relaxed molecular clock models, we show a significant increase in the scaled effective population size of the merA gene beginning ~200 years ago, coinciding with the Industrial Revolution and a coincident strong signal for positive selection acting on residues in the terminal region of the mercuric reductase. This rapid evolutionary response of microbes to changes in the delivery of anthropogenic Hg indicates that microbial genomes record ecosystem response to pollutant deposition in remote regions. PMID:26057844

Microbial growth associated with granular activated carbon in a pilot water treatment facility.

PubMed Central

Wilcox, D P; Chang, E; Dickson, K L; Johansson, K R

1983-01-01

The microbial dynamics associated with granular activated carbon (GAC) in a pilot water treatment plant were investigated over a period of 16 months. Microbial populations were monitored in the influent and effluent waters and on the GAC particles by means of total plate counts and ATP assays. Microbial populations between the influent and effluent waters of the GAC columns generally increased, indicating microbial growth. The dominant genera of microorganisms isolated from interstitial waters and GAC particles were Achromobacter, Acinetobacter, Aeromonas, Alcaligenes, Bacillus, Chromobacterium, Corynebacterium, Micrococcus, Microcyclus, Paracoccus, and Pseudomonas. Coliform bacteria were found in small numbers in the effluents from some of the GAC columns in the later months of the study. Oxidation of influent waters with ozone and maintenance of aerobic conditions on the GAC columns failed to appreciably enhance the microbial growth on GAC. PMID:6625567

Effects of vegetation type on microbial biomass carbon and nitrogen in subalpine mountain forest soils.

PubMed

Ravindran, Anita; Yang, Shang-Shyng

2015-08-01

Microbial biomass plays an important role in nutrient transformation and conservation of forest and grassland ecosystems. The objective of this study was to determine the microbial biomass among three vegetation types in subalpine mountain forest soils of Taiwan. Tatachia is a typical high-altitude subalpine temperate forest ecosystem in Taiwan with an elevation of 1800-3952 m and consists of three vegetation types: spruce, hemlock, and grassland. Three plots were selected in each vegetation type. Soil samples were collected from the organic layer, topsoil, and subsoil. Microbial biomass carbon (Cmic) was determined by the chloroform fumigation-extraction method, and microbial biomass nitrogen (Nmic) was determined from the total nitrogen (Ntot) released during fumigation-extraction. Bacteria, actinomycetes, fungi, cellulolytic microbes, phosphate-solubilizing microbes, and nitrogen-fixing microbes were also counted. The Cmic and Nmic were highest in the surface soil and declined with the soil depth. These were also highest in spruce soils, followed by in hemlock soils, and were lowest in grassland soils. Cmic and Nmic had the highest values in the spring season and the lowest values in the winter season. Cmic and Nmic had significantly positive correlations with total organic carbon (Corg) and Ntot. Contributions of Cmic and Nmic, respectively, to Corg and Ntot indicated that the microbial biomass was immobilized more in spruce and hemlock soils than in grassland soils. Microbial populations of the tested vegetation types decreased with increasing soil depth. Cmic and Nmic were high in the organic layer and decreased with the depth of layers. These values were higher for spruce and hemlock soils than for grassland soils. Positive correlations were observed between Cmic and Nmic and between Corg and Ntot. Copyright © 2014. Published by Elsevier B.V.

Body Mass Index and Sex Affect Diverse Microbial Niches within the Gut

PubMed Central

Borgo, Francesca; Garbossa, Stefania; Riva, Alessandra; Severgnini, Marco; Luigiano, Carmelo; Benetti, Albero; Pontiroli, Antonio E.; Morace, Giulia; Borghi, Elisa

2018-01-01

Gut microbiota is considered a separate organ with endocrine capabilities, actively contributing to tissue homeostasis. It consists of at least two separate microbial populations, the lumen-associated (LAM) and the mucosa-associated microbiota (MAM). In the present study, we compared LAM and MAM, by collecting stools and sigmoid brush samples of forty adults without large-bowel symptoms, and through a 16S rRNA gene next-generation sequencing (NGS) approach. MAM sample analysis revealed enrichment in aerotolerant Proteobacteria, probably selected by a gradient of oxygen that decreases from tissue to lumen, and in Streptococcus and Clostridium spp., highly fermenting bacteria. On the other hand, LAM microbiota showed an increased abundance in Bacteroides, Prevotella, and Oscillospira, genera able to digest and to degrade biopolymers in the large intestine. Predicted metagenomic analysis showed LAM to be enriched in genes encoding enzymes mostly involved in energy extraction from carbohydrates and lipids, whereas MAM in amino acid and vitamin metabolism. Moreover, LAM and MAM communities seemed to be influenced by different host factors, such as diet and sex. LAM is affected by body mass index (BMI) status. Indeed, BMI negatively correlates with Faecalibacterium prausnitzii and Flavonifractor plautii abundance, putative biomarkers of healthy status. In contrast, MAM microbial population showed a significant grouping according to sex. Female MAM was enriched in Actinobacteria (with an increased trend of the genus Bifidobacterium), and a significant depletion in Veillonellaceae. Interestingly, we found the species Gemmiger formicilis to be associated with male and Bifidobacterium adolescentis, with female MAM samples. In conclusion, our results suggest that gut harbors microbial niches that differ in both composition and host factor susceptibility, and their richness and diversity may be overlooked evaluating only fecal samples. PMID:29491857

Assessment of the horizontal transfer of functional genes as a suitable approach for evaluation of the bioremediation potential of petroleum-contaminated sites: a mini-review.

PubMed

Shahi, Aiyoub; Ince, Bahar; Aydin, Sevcan; Ince, Orhan

2017-06-01

Petroleum sludge contains recalcitrant residuals. These compounds because of being toxic to humans and other organism are of the major concerns. Therefore, petroleum sludge should be safely disposed. Physicochemical methods which are used by this sector are mostly expensive and need complex devices. Bioremediation methods because of being eco-friendly and cost-effective overcome most of the limitations of physicochemical treatments. Microbial strains capable to degrade petroleum hydrocarbons are practically present in all soils and sediments and their population density increases in contact with contaminants. Bacterial strains cannot degrade alone all kinds of petroleum hydrocarbons, rather microbial consortium should collaborate with each other for degradation of petroleum hydrocarbon mixtures. Horizontal transfer of functional genes between bacteria plays an important role in increasing the metabolic potential of the microbial community. Therefore, selecting a suitable degrading gene and tracking its horizontal transfer would be a useful approach to evaluate the bioremediation process and to assess the bioremediation potential of contaminated sites.

Adaptive laboratory evolution – principles and applications for biotechnology

PubMed Central

2013-01-01

Adaptive laboratory evolution is a frequent method in biological studies to gain insights into the basic mechanisms of molecular evolution and adaptive changes that accumulate in microbial populations during long term selection under specified growth conditions. Although regularly performed for more than 25 years, the advent of transcript and cheap next-generation sequencing technologies has resulted in many recent studies, which successfully applied this technique in order to engineer microbial cells for biotechnological applications. Adaptive laboratory evolution has some major benefits as compared with classical genetic engineering but also some inherent limitations. However, recent studies show how some of the limitations may be overcome in order to successfully incorporate adaptive laboratory evolution in microbial cell factory design. Over the last two decades important insights into nutrient and stress metabolism of relevant model species were acquired, whereas some other aspects such as niche-specific differences of non-conventional cell factories are not completely understood. Altogether the current status and its future perspectives highlight the importance and potential of adaptive laboratory evolution as approach in biotechnological engineering. PMID:23815749

Estimating and mapping ecological processes influencing microbial community assembly

DOE PAGES

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

2015-05-01

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

Microbial protein synthesis, ruminal digestion, microbial populations, and nitrogen balance in sheep fed diets varying in forage-to-concentrate ratio and type of forage.

PubMed

Ramos, S; Tejido, M L; Martínez, M E; Ranilla, M J; Carro, M D

2009-09-01

Six ruminally and duodenally cannulated sheep were used in a partially replicated 4 x 4 Latin square to evaluate the effects of 4 diets on microbial synthesis, microbial populations, and ruminal digestion. The experimental diets had forage to concentrate ratios (F:C; DM basis) of 70:30 (HF) or 30:70 (HC) with alfalfa hay (A) or grass hay (G) as forage and were designated as HFA, HCA, HFG, and HCG. The concentrate was based on barley, gluten feed, wheat middlings, soybean meal, palmkern meal, wheat, corn, and mineral-vitamin premix in the proportions of 22, 20, 20, 13, 12, 5, 5, and 3%, respectively (as-is basis). Sheep were fed the diets at a daily rate of 56 g/kg of BW(0.75) to minimize feed selection. High-concentrate diets resulted in greater (P < 0.001) total tract apparent OM digestibility compared with HF diets, but no differences were detected in NDF digestibility. Ruminal digestibility of OM, NDF, and ADF was decreased by increasing the proportion of concentrate, but no differences between forages were detected. Compared with sheep fed HF diets, sheep receiving HC diets had less ruminal pH values and acetate proportions, but greater butyrate proportions. No differences among diets were detected in numbers of cellulolytic bacteria, but protozoa numbers were less (P = 0.004) and total bacteria numbers tended (P = 0.08) to be less for HC diets. Carboxymethylcellulase, xylanase, and amylase activities were greater for HC compared with HF diets, with A diets showing greater (P = 0.008) carboxymethylcellulase activities than G diets. Retained N ranged from 28.7 to 37.9% of N intake and was not affected by F:C (P = 0.62) or the type of forage (P = 0.31). Microbial N synthesis and its efficiency was greater (P < 0.001) for HC diets compared with HF diets. The results indicate that concentrates with low cereal content can be included in the diet of sheep up to 70% of the diet without detrimental effects on ruminal activity, microbial synthesis efficiency, and N losses.

Effects of Dietary Cooked Navy Bean on the Fecal Microbiome of Healthy Companion Dogs

PubMed Central

Kerr, Katherine R.; Forster, Genevieve; Dowd, Scot E.; Ryan, Elizabeth P.; Swanson, Kelly S.

2013-01-01

Background Cooked bean powders are a promising novel protein and fiber source for dogs, which have demonstrated potential to alter microbial composition and function for chronic disease control and prevention. This study aimed to determine the impact of cooked navy bean powder fed as a staple food ingredient on the fecal microbiome of healthy adult pet dogs. Methodology/Principal Findings Fecal samples from healthy dogs prior to dietary control and after 4 wk of dietary treatment with macro- and micronutrient matched diets containing either 0 or 25% cooked navy beans (n = 11 and n = 10, respectively) were analyzed by 454-pyrosequencing of the 16S rRNA gene. There were few differences between dogs fed the control and navy bean diets after 4 wk of treatment. These data indicate that there were no major effects of navy bean inclusion on microbial populations. However, significant differences due to dietary intervention onto both research diets were observed (i.e., microbial populations at baseline versus 4 wk of intervention with 0 or 25% navy bean diets). After 4 wk of dietary intervention on either control or navy bean diet, the Phylum Firmicutes was increased and the Phyla Actinobacteria and Fusobacteria were decreased compared to baseline. Conclusions No negative alterations of microbial populations occurred following cooked navy bean intake in dogs, indicating that bean powders may be a viable protein and fiber source for commercial pet foods. The highly variable microbial populations observed in these healthy adult pet dogs at baseline is one potential reason for the difficulty to detect alterations in microbial populations following dietary changes. Given the potential physiological benefits of bean intake in humans and dogs, further evaluation of the impacts of cooked navy bean intake on fecal microbial populations with higher power or more sensitive methods are warranted. PMID:24040374

Genome surfing as driver of microbial genomic diversity

USDA-ARS?s Scientific Manuscript database

Historical changes in population size, such as those caused by demographic range expansions, can produce nonadaptive changes in genomic diversity through mechanisms such as gene surfing. We propose that demographic range expansion of a microbial population capable of horizontal gene exchange can res...

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...

Molecular Characterization of Swine Manure Lagoon Microbial and Antibiotic Resistant Populations

USDA-ARS?s Scientific Manuscript database

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...

Microbial shifts in the swine distal gut in response to the treatment with antimicrobial growth promoter, tylosin

PubMed Central

Kim, Hyeun Bum; Borewicz, Klaudyna; White, Bryan A.; Singer, Randall S.; Sreevatsan, Srinand; Tu, Zheng Jin; Isaacson, Richard E.

2012-01-01

Antimicrobials have been used extensively as growth promoters (AGPs) in agricultural animal production. However, the specific mechanism of action for AGPs has not yet been determined. The work presented here was to determine and characterize the microbiome of pigs receiving one AGP, tylosin, compared with untreated pigs. We hypothesized that AGPs exerted their growth promoting effect by altering gut microbial population composition. We determined the fecal microbiome of pigs receiving tylosin compared with untreated pigs using pyrosequencing of 16S rRNA gene libraries. The data showed microbial population shifts representing both microbial succession and changes in response to the use of tylosin. Quantitative and qualitative analyses of sequences showed that tylosin caused microbial population shifts in both abundant and less abundant species. Our results established a baseline upon which mechanisms of AGPs in regulation of health and growth of animals can be investigated. Furthermore, the data will aid in the identification of alternative strategies to improve animal health and consequently production. PMID:22955886

Microbial activity and diversity in long-term mixed contaminated soils with respect to polyaromatic hydrocarbons and heavy metals.

PubMed

Thavamani, Palanisami; Malik, Seidu; Beer, Michael; Megharaj, Mallavarapu; Naidu, Ravi

2012-05-30

The co-occurrence of polyaromatic hydrocarbons (PAHs) with heavy metals and their effect on soil microbial activity have not been systematically investigated. In this study a holistic approach was employed by combining physico-chemical, biological and advanced molecular methods to determine the soil microbial activities of long-term mixed contaminated soils collected from a former manufactured gas plant (MGP) site. Concentrations of PAHs in MGP soils ranged from 335 to 8645 mg/kg. Of the potentially toxic metals, concentrations of lead were found to be highest, ranging from 88 to 671 mg/kg, cadmium 8 to 112 mg/kg, while zinc varied from 64 to 488 mg/kg. The enzyme activities were severely inhibited in soils that were contaminated with both PAHs and heavy metals. The presence of heavy metals in PAH-contaminated soils not only reduced the diversity of microbial population but also showed a few distinctive species by exerting selective pressure. The multivariate analysis revealed that there is an association between PAHs and heavy metals which influenced biological properties in mixed contaminated soils. The findings of this study have major implications for the bioremediation of organic pollutants in metal-organic mixed contaminated sites. Copyright © 2012 Elsevier Ltd. All rights reserved.

Bacterial Diversity Across a Turbidite-Stranded Sediment-Water Interface, La Jolla Canyon, CA

NASA Astrophysics Data System (ADS)

Harrison, B. K.; Flood, B.; Myrbo, A.; Bailey, J.

2016-12-01

The emplacement of gravity-driven sediment flows imposes a significant physical and geochemical impact on underlying sediment and microbial communities. Although previous studies have established lasting mineralogical (e.g., McKay and Pederson, 2014) and biological signatures (e.g., Anschutz et al., 2002) of turbidite deposition, the response of prokaryotes within and beneath debris flows remains poorly constrained. Both bacterial cells associated with the underlying sediment and allocthonous material must respond to substantially altered selective pressures. As a consequence, turbidites and underlying sediments provide an exceptional opportunity to examine 1) microbial community response to sedimentation 2) preservation and identification of microbial dispersal mechanisms. We collected Illumina MiSeq sequence libraries across an intact marine turbidite boundary at 25cm sediment depth in La Jolla canyon off the coast of California. 16S rRNA gene signatures of relict and active bacterial populations exhibit persistent differences attributable to turbidite deposition. In particular, the sedimentary boundary is sharply demarcated at the cm scale by the diversity and abundance of Chloroflexi, Planctomycetes, and Actinobacteria. Variations in the abundance of putative dissimilatory sulfate-reducing Deltaproteobacteria across the stranded sediment-water interface reflect persistent turbidite-induced changes to the geochemical environment. This work raises the possibility that abrupt sedimentological events may alter the microbial community in a manner that persists with burial.

The canine and feline skin microbiome in health and disease.

PubMed

Weese, J Scott

2013-02-01

The skin harbours a diverse and abundant, yet inadequately investigated, microbial population. The population is believed to play an important role in both the pathophysiology and the prevention of disease, through a variety of poorly explored mechanisms. Early studies of the skin microbiota in dogs and cats reported a minimally diverse microbial composition of low overall abundance, most probably as a reflection of the limitations of testing methodology. Despite these limitations, it was clear that the bacterial population of the skin plays an important role in disease and in changes in response to both infectious and noninfectious diseases. Recent advances in technology are challenging some previous assumptions about the canine and feline skin microbiota and, with preliminary application of next-generation sequenced-based methods, it is apparent that the diversity and complexity of the canine skin microbiome has been greatly underestimated. A better understanding of this complex microbial population is critical for elucidation of the pathophysiology of various dermatological (and perhaps systemic) diseases and to develop novel ways to manipulate this microbial population to prevent or treat disease. © 2013 The Author. Veterinary Dermatology © 2013 ESVD and ACVD.

Multiwall carbon nanotubes increase the microbial community in crude oil contaminated fresh water sediments.

PubMed

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

2016-01-01

Since crude oil contamination is one of the biggest environmental concerns, its removal from contaminated sites is of interest for both researchers and industries. In situ bioremediation is a promising technique for decreasing or even eliminating crude oil and hydrocarbon contamination. However, since these compounds are potentially toxic for many microorganisms, high loads of contamination can inhibit the microbial community and therefore reduce the removal rate. Therefore, any strategy with the ability to increase the microbial population in such circumstances can be of promise in improving the remediation process. In this study, multiwall carbon nanotubes were employed to support microbial growth in sediments contaminated with crude oil. Following spiking of fresh water sediments with different concentrations of crude oil alone and in a mixture with carbon nanotubes for 30days, the microbial profiles in these sediments were obtained using FLX-pyrosequencing. Next, the ratios of each member of the microbial population in these sediments were compared with those values in the untreated control sediment. This study showed that combination of crude oil and carbon nanotubes can increase the diversity of the total microbial population. Furthermore, these treatments could increase the ratios of several microorganisms that are known to be effective in the degradation of hydrocarbons. Copyright © 2015 Elsevier B.V. All rights reserved.

Concepts and tools for predictive modeling of microbial dynamics.

PubMed

Bernaerts, Kristel; Dens, Els; Vereecken, Karen; Geeraerd, Annemie H; Standaert, Arnout R; Devlieghere, Frank; Debevere, Johan; Van Impe, Jan F

2004-09-01

Description of microbial cell (population) behavior as influenced by dynamically changing environmental conditions intrinsically needs dynamic mathematical models. In the past, major effort has been put into the modeling of microbial growth and inactivation within a constant environment (static models). In the early 1990s, differential equation models (dynamic models) were introduced in the field of predictive microbiology. Here, we present a general dynamic model-building concept describing microbial evolution under dynamic conditions. Starting from an elementary model building block, the model structure can be gradually complexified to incorporate increasing numbers of influencing factors. Based on two case studies, the fundamentals of both macroscopic (population) and microscopic (individual) modeling approaches are revisited. These illustrations deal with the modeling of (i) microbial lag under variable temperature conditions and (ii) interspecies microbial interactions mediated by lactic acid production (product inhibition). Current and future research trends should address the need for (i) more specific measurements at the cell and/or population level, (ii) measurements under dynamic conditions, and (iii) more comprehensive (mechanistically inspired) model structures. In the context of quantitative microbial risk assessment, complexity of the mathematical model must be kept under control. An important challenge for the future is determination of a satisfactory trade-off between predictive power and manageability of predictive microbiology models.

Microbial assessment of cabin air quality on commercial airliners

NASA Technical Reports Server (NTRS)

La Duc, Myron T.; Stuecker, Tara; Bearman, Gregory; Venkateswaran, Kasthuri

2005-01-01

The microbial burdens of 69 cabin air samples collected from commercial airliners were assessed via conventional culture-dependent, and molecular-based microbial enumeration assays. Cabin air samples from each of four separate flights aboard two different carriers were collected via air-impingement. Microbial enumeration techniques targeting DNA, ATP, and endotoxin were employed to estimate total microbial burden. The total viable microbial population ranged from 0 to 3.6 x10 4 cells per 100 liters of air, as assessed by the ATP-assay. When these same samples were plated on R2A minimal medium, anywhere from 2% to 80% of these viable populations were cultivable. Five of the 29 samples examined exhibited higher cultivable counts than ATP derived viable counts, perhaps a consequence of the dormant nature (and thus lower concentration of intracellular ATP) of cells inhabiting these air cabin samples. Ribosomal RNA gene sequence analysis showed these samples to consist of a moderately diverse group of bacteria, including human pathogens. Enumeration of ribosomal genes via quantitative-PCR indicated that population densities ranged from 5 x 10 1 ' to IO 7 cells per 100 liters of air. Each of the aforementioned strategies for assessing overall microbial burden has its strengths and weaknesses; this publication serves as a testament to the power of their use in concert.

Screening For Alcohol-Producing Microbes

NASA Technical Reports Server (NTRS)

Schubert, Wayne W.

1988-01-01

Dye reaction rapidly identifies alcohol-producing microbial colonies. Method visually detects alcohol-producing micro-organisms, and distinguishes them from other microbial colonies that do not produce alcohol. Method useful for screening mixed microbial populations in environmental samples.

Sulfolobus islandicus meta-populations in Yellowstone National Park hot springs

USGS Publications Warehouse

Campbell, Kate M.; Kouris, Angela; England, Whitney; Anderson, Rika E.; McCleskey, R. Blaine; Nordstrom, D. Kirk; Whitaker, Rachel J.

2017-01-01

Abiotic and biotic forces shape the structure and evolution of microbial populations. We investigated forces that shape the spatial and temporal population structure of Sulfolobus islandicus by comparing geochemical and molecular analysis from seven hot springs in five regions sampled over 3 years in Yellowstone National Park. Through deep amplicon sequencing, we uncovered 148 unique alleles at two loci whose relative frequency provides clear evidence for independent populations in different hot springs. Although geography controls regional geochemical composition and population differentiation, temporal changes in population were not explained by corresponding variation in geochemistry. The data suggest that the influence of extinction, bottleneck events and/or selective sweeps within a spring and low migration between springs shape these populations. We suggest that hydrologic events such as storm events and surface snowmelt runoff destabilize smaller hot spring environments with smaller populations and result in high variation in the S. islandicus population over time. Therefore, physical abiotic features such as hot spring size and position in the landscape are important factors shaping the stability and diversity of the S. islandicus meta-population within Yellowstone National Park.

Optimization of heat and relative humidity conditions to reduce Escherichia coli O157:H7 contamination and maximize the germination of radish seeds.

PubMed

Song, M K; Kim, H W; Rhee, M S

2016-06-01

We previously reported that a combination of heat and relative humidity (RH) had a marked bactericidal effect on Escherichia coli O157:H7 on radish seeds. Here, response surface methodology with a Box-Behnken design was used to build a model to predict reductions in E. coli O157:H7 populations based on three independent variables: heating temperature (55 °C, 60 °C, or 65 °C), RH (40%, 60%, and 80%), and holding time (8, 15, or 22 h). Optimum treatment conditions were selected using a desirability function. The predictive model for microbial reduction had a high regression coefficient (R(2) = 0.97), and the accuracy of the model was verified using validation data (R(2) = 0.95). Among the three variables examined, heating temperature (P < 0.0001) and RH (P = 0.004) were the most significant in terms of bacterial reduction and seed germination, respectively. The optimum conditions for microbial reduction (6.6 log reduction) determined by ridge analysis were as follows: 64.5 °C and 63.2% RH for 17.7 h. However, when both microbial reduction and germination rate were taken into consideration, the desirability function yielded optimal conditions of 65 °C and 40% RH for 8 h (6.6 log reduction in the bacterial population; 94.4% of seeds germinated). This study provides comprehensive data that improve our understanding of the effects of heating temperature, RH, and holding time on the E. coli O157:H7 population on radish seeds. Radish seeds can be exposed to these conditions before sprouting, which greatly increases the microbiological safety of the products. Copyright © 2015 Elsevier Ltd. All rights reserved.

Phylogenetic Profiles of In-House Microflora in Drains at a Food Production Facility: Comparison and Biocontrol Implications of Listeria-Positive and -Negative Bacterial Populations

PubMed Central

Solomon, Katie; Moore, John E.; Wall, Patrick G.; Fanning, Séamus

2014-01-01

Listeria species experience complex interactions with other microorganisms, which may promote growth and colonization of the organism in local environments or negatively affect them. This study investigated the microbial community at a food production facility, examining interactions between Listeria and the associated microbiome. Listeria species can be transferred between zones in the production environment by individuals or equipment, and drains may act as a reservoir for the organism, reflecting the microbial flora potentially in the production environment. Drains that were colonized by Listeria species and those determined to be free of Listeria were examined. In each case, 16S rRNA gene analysis was performed using the PhyloChip platform. Some general similarities in bacterial population structure were observed when Listeria-negative and -positive drain communities were compared, with some distinct differences also noted. These included increased populations of the genera Prevotella and Janthinobacterium associated with the absence of Listeria species, whereas Enterococcus and Rhodococcus were in higher abundance in drains colonized by Listeria species. Based on these results, a selection of bacterial species were grown in coculture biofilm with a Listeria monocytogenes strain identified as having colonized a drain at the facility. Mixed-species biofilm experiments showed that Janthinobacterium inhibited attachment and subsequent biofilm formation of L. monocytogenes; however, Enterococcus gallinarum significantly increased it. The results of this study suggest the microbial community in food processing facilities can impact the colonization of Listeria species and that influencing the microbiome in favor of antilisterial species may reduce the colonization of Listeria species and limit the likelihood of product/process contamination. PMID:24657862

Dynamic Succession of Soil Bacterial Community during Continuous Cropping of Peanut (Arachis hypogaea L.)

PubMed Central

Chen, Mingna; Li, Xiao; Yang, Qingli; Chi, Xiaoyuan; Pan, Lijuan; Chen, Na; Yang, Zhen; Wang, Tong; Wang, Mian; Yu, Shanlin

2014-01-01

Plant health and soil fertility are affected by plant–microbial interactions in soils. Peanut is an important oil crop worldwide and shows considerable adaptability, but growth and yield are negatively affected by continuous cropping. In this study, 16S rRNA gene clone library analyses were used to study the succession of soil bacterial communities under continuous peanut cultivation. Six libraries were constructed for peanut over three continuous cropping cycles and during its seedling and pod-maturing growth stages. Cluster analyses indicated that soil bacterial assemblages obtained from the same peanut cropping cycle were similar, regardless of growth period. The diversity of bacterial sequences identified in each growth stage library of the three peanut cropping cycles was high and these sequences were affiliated with 21 bacterial groups. Eight phyla: Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Gemmatimonadetes, Planctomycetes, Proteobacteria and Verrucomicrobia were dominant. The related bacterial phylotypes dynamic changed during continuous cropping progress of peanut. This study demonstrated that the bacterial populations especially the beneficial populations were positively selected. The simplification of the beneficial microbial communities such as the phylotypes of Alteromonadales, Burkholderiales, Flavobacteriales, Pseudomonadales, Rhizobiales and Rhodospirillales could be important factors contributing to the decline in peanut yield under continuous cropping. The microbial phylotypes that did not successively changed with continuous cropping, such as populations related to Rhizobiales and Rhodospirillales, could potentially resist stress due to continuous cropping and deserve attention. In addition, some phylotypes, such as Acidobacteriales, Chromatiales and Gemmatimonadales, showed a contrary tendency, their abundance or diversity increased with continuous peanut cropping progress. Some bacterial phylotypes including Acidobacteriales, Burkholderiales, Bdellovibrionales, and so on, also were affected by plant age. PMID:25010658

Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris

DOE PAGES

Zhou, Aifen; Hillesland, Kristina L.; He, Zhili; ...

2015-04-07

To investigate the genetic basis of microbial evolutionary adaptation to salt (NaCl) stress, populations of Desulfovibrio vulgaris Hildenborough (DvH), a sulfate-reducing bacterium important for the biogeochemical cycling of sulfur, carbon and nitrogen, and potentially the bioremediation of toxic heavy metals and radionuclides, were propagated under salt stress or non-stress conditions for 1200 generations. Whole-genome sequencing revealed 11 mutations in salt stress-evolved clone ES9-11 and 14 mutations in non-stress-evolved clone EC3-10. Whole-population sequencing data suggested the rapid selective sweep of the pre-existing polymorphisms under salt stress within the first 100 generations and the slow fixation of new mutations. Population genotyping datamore » demonstrated that the rapid selective sweep of pre-existing polymorphisms was common in salt stress-evolved populations. In contrast, the selection of pre-existing polymorphisms was largely random in EC populations. Consistently, at 100 generations, stress-evolved population ES9 showed improved salt tolerance, namely increased growth rate (2.0-fold), higher biomass yield (1.8-fold) and shorter lag phase (0.7-fold) under higher salinity conditions. The beneficial nature of several mutations was confirmed by site-directed mutagenesis. All four tested mutations contributed to the shortened lag phases under higher salinity condition. In particular, compared with the salt tolerance improvement in ES9-11, a mutation in a histidine kinase protein gene lytS contributed 27% of the growth rate increase and 23% of the biomass yield increase while a mutation in hypothetical gene DVU2472 contributed 24% of the biomass yield increase. In conclusion, our results suggested that a few beneficial mutations could lead to dramatic improvements in salt tolerance.« less

Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris

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

Zhou, Aifen; Hillesland, Kristina L.; He, Zhili

To investigate the genetic basis of microbial evolutionary adaptation to salt (NaCl) stress, populations of Desulfovibrio vulgaris Hildenborough (DvH), a sulfate-reducing bacterium important for the biogeochemical cycling of sulfur, carbon and nitrogen, and potentially the bioremediation of toxic heavy metals and radionuclides, were propagated under salt stress or non-stress conditions for 1200 generations. Whole-genome sequencing revealed 11 mutations in salt stress-evolved clone ES9-11 and 14 mutations in non-stress-evolved clone EC3-10. Whole-population sequencing data suggested the rapid selective sweep of the pre-existing polymorphisms under salt stress within the first 100 generations and the slow fixation of new mutations. Population genotyping datamore » demonstrated that the rapid selective sweep of pre-existing polymorphisms was common in salt stress-evolved populations. In contrast, the selection of pre-existing polymorphisms was largely random in EC populations. Consistently, at 100 generations, stress-evolved population ES9 showed improved salt tolerance, namely increased growth rate (2.0-fold), higher biomass yield (1.8-fold) and shorter lag phase (0.7-fold) under higher salinity conditions. The beneficial nature of several mutations was confirmed by site-directed mutagenesis. All four tested mutations contributed to the shortened lag phases under higher salinity condition. In particular, compared with the salt tolerance improvement in ES9-11, a mutation in a histidine kinase protein gene lytS contributed 27% of the growth rate increase and 23% of the biomass yield increase while a mutation in hypothetical gene DVU2472 contributed 24% of the biomass yield increase. In conclusion, our results suggested that a few beneficial mutations could lead to dramatic improvements in salt tolerance.« less

Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris

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

Zhou, Aifen; Hillesland, Kristina L.; He, Zhili

To investigate the genetic basis of microbial evolutionary adaptation to salt (NaCl) stress, populations of Desulfovibrio vulgaris Hildenborough (DvH), a sulfate-reducing bacterium important for the biogeochemical cycling of sulfur, carbon and nitrogen, and potentially the bioremediation of toxic heavy metals and radionuclides, were propagated under salt stress or non-stress conditions for 1200 generations. Whole-genome sequencing revealed 11 mutations in salt stress-evolved clone ES9-11 and 14 mutations in non-stress-evolved clone EC3-10. Whole-population sequencing data suggested the rapid selective sweep of the pre-existing polymorphisms under salt stress within the first 100 generations and the slow fixation of new mutations. Population genotyping datamore » demonstrated that the rapid selective sweep of pre-existing polymorphisms was common in salt stress-evolved populations. In contrast, the selection of pre-existing polymorphisms was largely random in EC populations. Consistently, at 100 generations, stress-evolved population ES9 showed improved salt tolerance, namely increased growth rate (2.0-fold), higher biomass yield (1.8-fold) and shorter lag phase (0.7-fold) under higher salinity conditions. The beneficial nature of several mutations was confirmed by site-directed mutagenesis. All four tested mutations contributed to the shortened lag phases under higher salinity condition. In particular, compared with the salt tolerance improvement in ES9-11, a mutation in a histidine kinase protein gene lytS contributed 27% of the growth rate increase and 23% of the biomass yield increase while a mutation in hypothetical gene DVU2472 contributed 24% of the biomass yield increase. Our results suggested that a few beneficial mutations could lead to dramatic improvements in salt tolerance.« less

Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris.

PubMed

Zhou, Aifen; Hillesland, Kristina L; He, Zhili; Schackwitz, Wendy; Tu, Qichao; Zane, Grant M; Ma, Qiao; Qu, Yuanyuan; Stahl, David A; Wall, Judy D; Hazen, Terry C; Fields, Matthew W; Arkin, Adam P; Zhou, Jizhong

2015-11-01

To investigate the genetic basis of microbial evolutionary adaptation to salt (NaCl) stress, populations of Desulfovibrio vulgaris Hildenborough (DvH), a sulfate-reducing bacterium important for the biogeochemical cycling of sulfur, carbon and nitrogen, and potentially the bioremediation of toxic heavy metals and radionuclides, were propagated under salt stress or non-stress conditions for 1200 generations. Whole-genome sequencing revealed 11 mutations in salt stress-evolved clone ES9-11 and 14 mutations in non-stress-evolved clone EC3-10. Whole-population sequencing data suggested the rapid selective sweep of the pre-existing polymorphisms under salt stress within the first 100 generations and the slow fixation of new mutations. Population genotyping data demonstrated that the rapid selective sweep of pre-existing polymorphisms was common in salt stress-evolved populations. In contrast, the selection of pre-existing polymorphisms was largely random in EC populations. Consistently, at 100 generations, stress-evolved population ES9 showed improved salt tolerance, namely increased growth rate (2.0-fold), higher biomass yield (1.8-fold) and shorter lag phase (0.7-fold) under higher salinity conditions. The beneficial nature of several mutations was confirmed by site-directed mutagenesis. All four tested mutations contributed to the shortened lag phases under higher salinity condition. In particular, compared with the salt tolerance improvement in ES9-11, a mutation in a histidine kinase protein gene lytS contributed 27% of the growth rate increase and 23% of the biomass yield increase while a mutation in hypothetical gene DVU2472 contributed 24% of the biomass yield increase. Our results suggested that a few beneficial mutations could lead to dramatic improvements in salt tolerance.

Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris

PubMed Central

Zhou, Aifen; Hillesland, Kristina L; He, Zhili; Schackwitz, Wendy; Tu, Qichao; Zane, Grant M; Ma, Qiao; Qu, Yuanyuan; Stahl, David A; Wall, Judy D; Hazen, Terry C; Fields, Matthew W; Arkin, Adam P; Zhou, Jizhong

2015-01-01

To investigate the genetic basis of microbial evolutionary adaptation to salt (NaCl) stress, populations of Desulfovibrio vulgaris Hildenborough (DvH), a sulfate-reducing bacterium important for the biogeochemical cycling of sulfur, carbon and nitrogen, and potentially the bioremediation of toxic heavy metals and radionuclides, were propagated under salt stress or non-stress conditions for 1200 generations. Whole-genome sequencing revealed 11 mutations in salt stress-evolved clone ES9-11 and 14 mutations in non-stress-evolved clone EC3-10. Whole-population sequencing data suggested the rapid selective sweep of the pre-existing polymorphisms under salt stress within the first 100 generations and the slow fixation of new mutations. Population genotyping data demonstrated that the rapid selective sweep of pre-existing polymorphisms was common in salt stress-evolved populations. In contrast, the selection of pre-existing polymorphisms was largely random in EC populations. Consistently, at 100 generations, stress-evolved population ES9 showed improved salt tolerance, namely increased growth rate (2.0-fold), higher biomass yield (1.8-fold) and shorter lag phase (0.7-fold) under higher salinity conditions. The beneficial nature of several mutations was confirmed by site-directed mutagenesis. All four tested mutations contributed to the shortened lag phases under higher salinity condition. In particular, compared with the salt tolerance improvement in ES9-11, a mutation in a histidine kinase protein gene lytS contributed 27% of the growth rate increase and 23% of the biomass yield increase while a mutation in hypothetical gene DVU2472 contributed 24% of the biomass yield increase. Our results suggested that a few beneficial mutations could lead to dramatic improvements in salt tolerance. PMID:25848870

Plasma discharge and time-dependence of its effect to bacteria.

PubMed

Justan, I; Cernohorska, L; Dvorak, Z; Slavicek, P

2014-07-01

Several types of plasma discharge have been proven to have a capacity for sterilization. Our goal is to introduce new nonthermal plasma pencil. We used it to sterilize different microbial populations with differing ages. We used a plasma discharge of the following characteristics: radio frequency barrier discharger at atmospheric pressure with a working frequency of 13.56 MHz, and the working gas used was argon. We performed 110 tests with the following microbial populations: Pseudomonas aeruginosa, Staphylococcus aureus, Proteus species, and Klebsiella pneumoniae. All populations were inoculated on the previous day and also on the day of our experiment. We made our evaluations the following day and also after 5 days, with all our microbial populations. Eradication of microbial populations is dependent on the plasma discharge exposure time in all cases. With regard to freshly inoculated microbes, we were able to sterilize agar with intensive exposure lasting for 10 s of colonies Pseudomonas, Proteus, and Klebsiella. The most resistant microbe seems to be S. aureus, which survives 5 s of coherent exposure in half of the cases. Using the lightest plasma discharge exposure, we achieved a maximum of 10(4)-10(5) CFU/mL (colony-forming unit - CFU). Regarding older microbial populations inoculated the day before the experiment, we can only decrease population growth to 10(5) CFU/mL approximately, but never completely sterilize. The plasma discharge with our characteristics could be used for the sterilization of the aforementioned superficially growing microbes, but does not sufficiently affect deeper layers and thus seems to be a limitation for eradication of the already erupted colonies.

GEOELECTRICAL EVIDENCE OF MICROBIAL DEGRADATION OF DIESEL CONTAMINATED SEDIMENTS

EPA Science Inventory

The alteration of physical properties by microbial activity in petroleum contaminated sediments was investigated using geophysical techniques in laboratory column experiments. Microbial population growth was determined by the Most Probable Number technique (MPN), community dynami...

Evolution and stability of altruist strategies in microbial games

NASA Astrophysics Data System (ADS)

Adami, Christoph; Schossau, Jory; Hintze, Arend

2012-01-01

When microbes compete for limited resources, they often engage in chemical warfare using bacterial toxins. This competition can be understood in terms of evolutionary game theory (EGT). We study the predictions of EGT for the bacterial “suicide bomber” game in terms of the phase portraits of population dynamics, for parameter combinations that cover all interesting games for two-players, and seven of the 38 possible phase portraits of the three-player game. We compare these predictions to simulations of these competitions in finite well-mixed populations, but also allowing for probabilistic rather than pure strategies, as well as Darwinian adaptation over tens of thousands of generations. We find that Darwinian evolution of probabilistic strategies stabilizes games of the rock-paper-scissors type that emerge for parameters describing realistic bacterial populations, and point to ways in which the population fixed point can be selected by changing those parameters.

Habitat generalists and specialists in microbial communities across a terrestrial-freshwater gradient

NASA Astrophysics Data System (ADS)

Monard, C.; Gantner, S.; Bertilsson, S.; Hallin, S.; Stenlid, J.

2016-11-01

Observations of distributions of microorganisms and their differences in community composition across habitats provide evidence of biogeographical patterns. However, little is known about the processes controlling transfers across habitat gradients. By analysing the overall microbial community composition (bacteria, fungi, archaea) across a terrestrial-freshwater gradient, the aim of this study was to understand the spatial distribution patterns of populations and identify taxa capable of crossing biome borders. Barcoded 454 pyrosequencing of taxonomic gene markers was used to describe the microbial communities in adjacent soil, freshwater and sediment samples and study the role of biotic and spatial factors in shaping their composition. Few habitat generalists but a high number of specialists were detected indicating that microbial community composition was mainly regulated by species sorting and niche partitioning. Biotic interactions within microbial groups based on an association network underlined the importance of Actinobacteria, Sordariomycetes, Agaricomycetes and Nitrososphaerales in connecting among biomes. Even if dispersion seemed limited, the shore of the lake represented a transition area, allowing populations to cross the biome boundaries. In finding few broadly distributed populations, our study points to biome specialization within microbial communities with limited potential for dispersal and colonization of new habitats along the terrestrial-freshwater continuum.

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...

Managing microbial communities for sequentially reconstruct genomes from complex metagenomes

NASA Astrophysics Data System (ADS)

Delmont, Tom O.; Vogel, Timothy M.; Simonet, Pascal

2013-04-01

Global understanding on environmental microbial communities is currently limited by the bottleneck of genome reconstruction. Soil is a typical example where individual cells are currently mostly uncultured and metagenomic datasets unassembled. In this study, the microbial community composition of a natural grassland soil was managed under several controlled selective pressures to experiment a "multi-evenness" stratagem for sequentially attempt to reconstruct genomes from a complex metagenome. While lowly represented in the natural community, several newly dominant genomes (an enrichment attaining 105 in some cases) were successfully reconstructed under various "harsh" tested conditions. These genomes belong to several genera including (but not restricted to) Leifsonia, Rhodanobacter, Bacillus, Ktedonobacter, Xanthomonas, Streptomyces and Burkholderia. So far, from 10 to 78% of generated metagenomic datasets were reconstructed, so providing access to more than 88 000 genes of known or unknown functions and to their genetic environment. Adaptative genes directly related to selective pressures were found, mostly in large plasmids. Functions of potential industrial interest (e.g., novel polyketide synthase modules in Streptomyces) were also discovered. Furthermore, an important phage infection snapshot (>1500X of coverage for the most represented phage) was observed among the Streptomyces population (three distinct genomes reconstructed) of a particular enrichment (mercury, 0.02g/kg) during the fourth month of incubation. This "divide and conquer" strategy could be applied to other environments and using auxiliary sequencing approaches like single cell to detect, connect and mine taxa and functions of interest while creating an extensive set of reference genomes from across the planet. Next limit could turn out to become our imagination defining novel selective pressures to sequentially make dominant the 1030 cells of the biosphere.

Amphibian skin may select for rare environmental microbes

PubMed Central

Walke, Jenifer B; Becker, Matthew H; Loftus, Stephen C; House, Leanna L; Cormier, Guy; Jensen, Roderick V; Belden, Lisa K

2014-01-01

Host-microbe symbioses rely on the successful transmission or acquisition of symbionts in each new generation. Amphibians host a diverse cutaneous microbiota, and many of these symbionts appear to be mutualistic and may limit infection by the chytrid fungus, Batrachochytrium dendrobatidis, which has caused global amphibian population declines and extinctions in recent decades. Using bar-coded 454 pyrosequencing of the 16S rRNA gene, we addressed the question of symbiont transmission by examining variation in amphibian skin microbiota across species and sites and in direct relation to environmental microbes. Although acquisition of environmental microbes occurs in some host-symbiont systems, this has not been extensively examined in free-living vertebrate-microbe symbioses. Juvenile bullfrogs (Rana catesbeiana), adult red-spotted newts (Notophthalmus viridescens), pond water and pond substrate were sampled at a single pond to examine host-specificity and potential environmental transmission of microbiota. To assess population level variation in skin microbiota, adult newts from two additional sites were also sampled. Cohabiting bullfrogs and newts had distinct microbial communities, as did newts across the three sites. The microbial communities of amphibians and the environment were distinct; there was very little overlap in the amphibians' core microbes and the most abundant environmental microbes, and the relative abundances of OTUs that were shared by amphibians and the environment were inversely related. These results suggest that, in a host species-specific manner, amphibian skin may select for microbes that are generally in low abundance in the environment. PMID:24858782

Spatial Distribution of Bacterial Communities and Phenanthrene Degradation in the Rhizosphere of Lolium perenne L.

PubMed Central

Corgié, S. C.; Beguiristain, T.; Leyval, C.

2004-01-01

Rhizodegradation of organic pollutants, such as polycyclic aromatic hydrocarbons, is based on the effect of root-produced compounds, known as exudates. These exudates constitute an important and constant carbon source that selects microbial populations in the plant rhizosphere, modifying global as well as specific microbial activities. We conducted an experiment in two-compartment devices to show the selection of bacterial communities by root exudates and phenanthrene as a function of distance to roots. Using direct DNA extraction, PCR amplification, and thermal gradient gel electrophoresis screening, bacterial population profiles were analyzed in parallel to bacterial counts and quantification of phenanthrene biodegradation in three layers (0 to 3, 3 to 6, and 6 to 9 mm from root mat) of unplanted-polluted (phenanthrene), planted-polluted, and planted-unpolluted treatments. Bacterial community differed as a function of the distance to roots, in both the presence and the absence of phenanthrene. In the planted and polluted treatment, biodegradation rates showed a strong gradient with higher values near the roots. In the nonplanted treatment, bacterial communities were comparable in the three layers and phenanthrene biodegradation was high. Surprisingly, no biodegradation was detected in the section of planted polluted treatment farthest from the roots, where the bacterial community structure was similar to those of the nonplanted treatment. We conclude that root exudates and phenanthrene induce modifications of bacterial communities in polluted environments and spatially modify the activity of degrading bacteria. PMID:15184156

Continental-level population differentiation and environmental adaptation in the mushroom Suillus brevipes

PubMed Central

Branco, Sara; Bi, Ke; Liao, Hui-Ling; Gladieux, Pierre; Badouin, Hélène; Ellison, Christopher E.; Nguyen, Nhu H.; Vilgalys, Rytas; Peay, Kabir G.; Taylor, John W.; Bruns, Thomas D.

2016-01-01

Recent advancements in sequencing technology allowed researchers to better address the patterns and mechanisms involved in microbial environmental adaptation at large spatial scales. Here we investigated the genomic basis of adaptation to climate at the continental scale in Suillus brevipes, an ectomycorrhizal fungus symbiotically associated with the roots of pine trees. We used genomic data from 55 individuals in seven locations across North America to perform genome scans to detect signatures of positive selection and assess whether temperature and precipitation were associated with genetic differentiation. We found that S. brevipes exhibited overall strong population differentiation, with potential admixture in Canadian populations. This species also displayed genomic signatures of positive selection as well as genomic sites significantly associated with distinct climatic regimes and abiotic environmental parameters. These genomic regions included genes involved in transmembrane transport of substances and helicase activity potentially involved in cold stress response. Our study sheds light on large-scale environmental adaptation in fungi by identifying putative adaptive genes and providing a framework to further investigate the genetic basis of fungal adaptation. PMID:27761941

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.

Can biowarfare agents be defeated with light?

PubMed

Vatansever, Fatma; Ferraresi, Cleber; de Sousa, Marcelo Victor Pires; Yin, Rui; Rineh, Ardeshir; Sharma, Sulbha K; Hamblin, Michael R

2013-11-15

Biological warfare and bioterrorism is an unpleasant fact of 21st century life. Highly infectious and profoundly virulent diseases may be caused in combat personnel or in civilian populations by the appropriate dissemination of viruses, bacteria, spores, fungi, or toxins. Dissemination may be airborne, waterborne, or by contamination of food or surfaces. Countermeasures may be directed toward destroying or neutralizing the agents outside the body before infection has taken place, by destroying the agents once they have entered the body before the disease has fully developed, or by immunizing susceptible populations against the effects. A range of light-based technologies may have a role to play in biodefense countermeasures. Germicidal UV (UVC) is exceptionally active in destroying a wide range of viruses and microbial cells, and recent data suggests that UVC has high selectivity over host mammalian cells and tissues. Two UVA mediated approaches may also have roles to play; one where UVA is combined with titanium dioxide nanoparticles in a process called photocatalysis, and a second where UVA is combined with psoralens (PUVA) to produce "killed but metabolically active" microbial cells that may be particularly suitable for vaccines. Many microbial cells are surprisingly sensitive to blue light alone, and blue light can effectively destroy bacteria, fungi, and Bacillus spores and can treat wound infections. The combination of photosensitizing dyes such as porphyrins or phenothiaziniums and red light is called photodynamic therapy (PDT) or photoinactivation, and this approach cannot only kill bacteria, spores, and fungi, but also inactivate viruses and toxins. Many reports have highlighted the ability of PDT to treat infections and stimulate the host immune system. Finally pulsed (femtosecond) high power lasers have been used to inactivate pathogens with some degree of selectivity. We have pointed to some of the ways light-based technology may be used to defeat biological warfare in the future.

Can biowarfare agents be defeated with light?

PubMed Central

Vatansever, Fatma; Ferraresi, Cleber; de Sousa, Marcelo Victor Pires; Yin, Rui; Rineh, Ardeshir; Sharma, Sulbha K; Hamblin, Michael R

2013-01-01

Biological warfare and bioterrorism is an unpleasant fact of 21st century life. Highly infectious and profoundly virulent diseases may be caused in combat personnel or in civilian populations by the appropriate dissemination of viruses, bacteria, spores, fungi, or toxins. Dissemination may be airborne, waterborne, or by contamination of food or surfaces. Countermeasures may be directed toward destroying or neutralizing the agents outside the body before infection has taken place, by destroying the agents once they have entered the body before the disease has fully developed, or by immunizing susceptible populations against the effects. A range of light-based technologies may have a role to play in biodefense countermeasures. Germicidal UV (UVC) is exceptionally active in destroying a wide range of viruses and microbial cells, and recent data suggests that UVC has high selectivity over host mammalian cells and tissues. Two UVA mediated approaches may also have roles to play; one where UVA is combined with titanium dioxide nanoparticles in a process called photocatalysis, and a second where UVA is combined with psoralens (PUVA) to produce “killed but metabolically active” microbial cells that may be particularly suitable for vaccines. Many microbial cells are surprisingly sensitive to blue light alone, and blue light can effectively destroy bacteria, fungi, and Bacillus spores and can treat wound infections. The combination of photosensitizing dyes such as porphyrins or phenothiaziniums and red light is called photodynamic therapy (PDT) or photoinactivation, and this approach cannot only kill bacteria, spores, and fungi, but also inactivate viruses and toxins. Many reports have highlighted the ability of PDT to treat infections and stimulate the host immune system. Finally pulsed (femtosecond) high power lasers have been used to inactivate pathogens with some degree of selectivity. We have pointed to some of the ways light-based technology may be used to defeat biological warfare in the future. PMID:24067444

Fecal indicator organism modeling and microbial source tracking in environmental waters: Chapter 3.4.6

USGS Publications Warehouse

Nevers, Meredith; Byappanahalli, Muruleedhara; Phanikumar, Mantha S.; Whitman, Richard L.

2016-01-01

Mathematical models have been widely applied to surface waters to estimate rates of settling, resuspension, flow, dispersion, and advection in order to calculate movement of particles that influence water quality. Of particular interest are the movement, survival, and persistence of microbial pathogens or their surrogates, which may contaminate recreational water, drinking water, or shellfish. Most models devoted to microbial water quality have been focused on fecal indicator organisms (FIO), which act as a surrogate for pathogens and viruses. Process-based modeling and statistical modeling have been used to track contamination events to source and to predict future events. The use of these two types of models require different levels of expertise and input; process-based models rely on theoretical physical constructs to explain present conditions and biological distribution while data-based, statistical models use extant paired data to do the same. The selection of the appropriate model and interpretation of results is critical to proper use of these tools in microbial source tracking. Integration of the modeling approaches could provide insight for tracking and predicting contamination events in real time. A review of modeling efforts reveals that process-based modeling has great promise for microbial source tracking efforts; further, combining the understanding of physical processes influencing FIO contamination developed with process-based models and molecular characterization of the population by gene-based (i.e., biological) or chemical markers may be an effective approach for locating sources and remediating contamination in order to protect human health better.

Microbial population and functional dynamics associated with surface potential and carbon metabolism

PubMed Central

Ishii, Shun'ichi; Suzuki, Shino; Norden-Krichmar, Trina M; Phan, Tony; Wanger, Greg; Nealson, Kenneth H; Sekiguchi, Yuji; Gorby, Yuri A; Bretschger, Orianna

2014-01-01

Microbial extracellular electron transfer (EET) to solid surfaces is an important reaction for metal reduction occurring in various anoxic environments. However, it is challenging to accurately characterize EET-active microbial communities and each member's contribution to EET reactions because of changes in composition and concentrations of electron donors and solid-phase acceptors. Here, we used bioelectrochemical systems to systematically evaluate the synergistic effects of carbon source and surface redox potential on EET-active microbial community development, metabolic networks and overall electron transfer rates. The results indicate that faster biocatalytic rates were observed under electropositive electrode surface potential conditions, and under fatty acid-fed conditions. Temporal 16S rRNA-based microbial community analyses showed that Geobacter phylotypes were highly diverse and apparently dependent on surface potentials. The well-known electrogenic microbes affiliated with the Geobacter metallireducens clade were associated with lower surface potentials and less current generation, whereas Geobacter subsurface clades 1 and 2 were associated with higher surface potentials and greater current generation. An association was also observed between specific fermentative phylotypes and Geobacter phylotypes at specific surface potentials. When sugars were present, Tolumonas and Aeromonas phylotypes were preferentially associated with lower surface potentials, whereas Lactococcus phylotypes were found to be closely associated with Geobacter subsurface clades 1 and 2 phylotypes under higher surface potential conditions. Collectively, these results suggest that surface potentials provide a strong selective pressure, at the species and strain level, for both solid surface respirators and fermentative microbes throughout the EET-active community development. PMID:24351938

Impact of Ferrous Iron on Microbial Community of the Biofilm in Microbial Fuel Cells.

PubMed

Liu, Qian; Liu, Bingfeng; Li, Wei; Zhao, Xin; Zuo, Wenjing; Xing, Defeng

2017-01-01

The performance of microbial electrochemical cells depends upon microbial community structure and metabolic activity of the electrode biofilms. Iron as a signal affects biofilm development and enrichment of exoelectrogenic bacteria. In this study, the effect of ferrous iron on microbial communities of the electrode biofilms in microbial fuel cells (MFCs) was investigated. Voltage production showed that ferrous iron of 100 μM facilitated MFC start-up compared to 150 μM, 200 μM, and without supplement of ferrous iron. However, higher concentration of ferrous iron had an inhibitive influence on current generation after 30 days of operation. Illumina Hiseq sequencing of 16S rRNA gene amplicons indicated that ferrous iron substantially changed microbial community structures of both anode and cathode biofilms. Principal component analysis showed that the response of microbial communities of the anode biofilms to higher concentration of ferrous iron was more sensitive. The majority of predominant populations of the anode biofilms in MFCs belonged to Geobacter , which was different from the populations of the cathode biofilms. An obvious shift of community structures of the cathode biofilms occurred after ferrous iron addition. This study implied that ferrous iron influenced the power output and microbial community of MFCs.

EVIDENCE FOR MICROBIAL ENHANCED ELECTRICAL CONDUCTIVITY IN HYDROCARBON-CONTAMINATED SEDIMENTS

EPA Science Inventory

Electrical conductivity of sediments during microbial mineralization of diesel was investigated in a mesoscale column experiment consisting of biotic contaminated and uncontaminated columns. Microbial population numbers increased with a clear pattern of depth zonation within the ...

Microbial ecology of watery kimchi.

PubMed

Kyung, Kyu Hang; Medina Pradas, Eduardo; Kim, Song Gun; Lee, Yong Jae; Kim, Kyong Ho; Choi, Jin Joo; Cho, Joo Hyong; Chung, Chang Ho; Barrangou, Rodolphe; Breidt, Frederick

2015-05-01

The biochemistry and microbial ecology of 2 similar types of watery (mul) kimchi, containing sliced and unsliced radish and vegetables (nabak and dongchimi, respectively), were investigated. Samples from kimchi were fermented at 4, 10, and 20 °C were analyzed by plating on differential and selective media, high-performance liquid chromatography, and high-throughput DNA sequencing of 16S rDNA. Nabak kimchi showed similar trends as dongchimi, with increasing lactic and acetic acids and decreasing pH for each temperature, but differences in microbiota were apparent. Interestingly, bacteria from the Proteobacterium phylum, including Enterobacteriaceae, decreased more rapidly during fermentation at 4 °C in nabak cabbage fermentations compared with dongchimi. Although changes for Proteobacterium and Enterobacteriaceae populations were similar during fermentation at 10 and 20 °C, the homolactic stage of fermentation did not develop for the 4 and 10 °C samples of both nabak and dongchimi during the experiment. These data show the differences in biochemistry and microbial ecology that can result from preparation method and fermentation conditions of the kimchi, which may impact safety (Enterobacteriaceae populations may include pathogenic bacteria) and quality (homolactic fermentation can be undesirable, if too much acid is produced) of the product. In addition, the data also illustrate the need for improved methods for identifying and differentiating closely related lactic acid bacteria species using high-throughput sequencing methods. © 2015 Institute of Food Technologists®. This article has been contributed by US Government employees and their work is in the public domain in the USA.

Review: Microbial Analysis in Dielectrophoretic Microfluidic Systems

PubMed Central

Fernandez, Renny E.; Rohani, Ali; Farmehini, Vahid; Swami, Nathan S.

2017-01-01

Infections caused by various known and emerging pathogenic microorganisms, including antibiotic-resistant strains, are a major threat to global health and well-being. This highlights the urgent need for detection systems for microbial identification, quantification and characterization towards assessing infections, prescribing therapies and understanding the dynamic cellular modifications. Current state-of-the-art microbial detection systems exhibit a trade-off between sensitivity and assay time, which could be alleviated by selective and label-free microbial capture onto the sensor surface from dilute samples. AC electrokinetic methods, such as dielectrophoresis, enable frequency-selective capture of viable microbial cells and spores due to polarization based on their distinguishing size, shape and sub-cellular compositional characteristics, for downstream coupling to various detection modalities. Following elucidation of the polarization mechanisms that distinguish bacterial cells from each other, as well as from mammalian cells, this review compares the microfluidic platforms for dielectrophoretic manipulation of microbials and their coupling to various detection modalities, including immuno-capture, impedance measurement, Raman spectroscopy and nucleic acid amplification methods, as well as for phenotypic assessment of microbial viability and antibiotic susceptibility. Based on the urgent need within point-of-care diagnostics towards reducing assay times and enhancing capture of the target organism, as well as the emerging interest in isolating intact microbials based on their phenotype and subcellular features, we envision widespread adoption of these label-free and selective electrokinetic techniques. PMID:28372723

Determination of succession of rumen bacterial species in nursing beef calves

USDA-ARS?s Scientific Manuscript database

Ruminants are typically born with a non-functional rumen essentially devoid of microorganisms. The succession of the microbial population in the rumen from birth to animal maturity is of interest due to the key role that the rumen microbial population plays in the overall health and productivity of ...

Environment of care: Is it time to reassess microbial contamination of the operating room air as a risk factor for surgical site infection in total joint arthroplasty?

PubMed

Parvizi, Javad; Barnes, Sue; Shohat, Noam; Edmiston, Charles E

2017-11-01

In the modern operating room (OR), traditional surgical mask, frequent air exchanges, and architectural barriers are viewed as effective in reducing airborne microbial populations. Intraoperative sampling of airborne particulates is rarely performed in the OR because of technical difficulties associated with sampling methodologies and a common belief that airborne contamination is infrequently associated with surgical site infections (SSIs). Recent studies suggest that viable airborne particulates are readily disseminated throughout the OR, placing patients at risk for postoperative SSI. In 2017, virtually all surgical disciplines are engaged in the implantation of selective biomedical devices, and these implants have been documented to be at high risk for intraoperative contamination. Approximately 1.2 million arthroplasties are performed annually in the United States, and that number is expected to increase to 3.8 million by the year 2030. The incidence of periprosthetic joint infection is perceived to be low (<2.5%); however, the personal and fiscal morbidity is significant. Although the pharmaceutic and computer industries enforce stringent air quality standards on their manufacturing processes, there is currently no U.S. standard for acceptable air quality within the OR environment. This review documents the contribution of air contamination to the etiology of periprosthetic joint infection, and evidence for selective innovative strategies to reduce the risk of intraoperative microbial aerosols. Copyright © 2017 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Elsevier Inc. All rights reserved.

Toxicity of zero-valent iron nanoparticles to a trichloroethylene-degrading groundwater microbial community.

PubMed

Zabetakis, Kara M; Niño de Guzmán, Gabriela T; Torrents, Alba; Yarwood, Stephanie

2015-01-01

The microbiological impact of zero-valent iron used in the remediation of groundwater was investigated by exposing a trichloroethylene-degrading anaerobic microbial community to two types of iron nanoparticles. Changes in total bacterial and archaeal population numbers were analyzed using qPCR and were compared to results from a blank and negative control to assess for microbial toxicity. Additionally, the results were compared to those of samples exposed to silver nanoparticles and iron filings in an attempt to discern the source of toxicity. Statistical analysis revealed that the three different iron treatments were equally toxic to the total bacteria and archaea populations, as compared with the controls. Conversely, the silver nanoparticles had a limited statistical impact when compared to the controls and increased the microbial populations in some instances. Therefore, the findings suggest that zero-valent iron toxicity does not result from a unique nanoparticle-based effect.

Bioremediation of uranium-contaminated groundwater: a systems approach to subsurface biogeochemistry.

PubMed

Williams, Kenneth H; Bargar, John R; Lloyd, Jonathan R; Lovley, Derek R

2013-06-01

Adding organic electron donors to stimulate microbial reduction of highly soluble U(VI) to less soluble U(IV) is a promising strategy for immobilizing uranium in contaminated subsurface environments. Studies suggest that diagnosing the in situ physiological status of the subsurface community during uranium bioremediation with environmental transcriptomic and proteomic techniques can identify factors potentially limiting U(VI) reduction activity. Models which couple genome-scale in silico representations of the metabolism of key microbial populations with geochemical and hydrological models may be able to predict the outcome of bioremediation strategies and aid in the development of new approaches. Concerns remain about the long-term stability of sequestered U(IV) minerals and the release of co-contaminants associated with Fe(III) oxides, which might be overcome through targeted delivery of electrons to select microorganisms using in situ electrodes. Copyright © 2012 Elsevier Ltd. All rights reserved.

Exposure to vancomycin causes a shift in the microbial community structure without affecting nitrate reduction rates in river sediments.

PubMed

Laverman, Anniet M; Cazier, Thibaut; Yan, Chen; Roose-Amsaleg, Céline; Petit, Fabienne; Garnier, Josette; Berthe, Thierry

2015-09-01

Antibiotics and antibiotic resistance genes have shown to be omnipresent in the environment. In this study, we investigated the effect of vancomycin (VA) on denitrifying bacteria in river sediments of a Waste Water Treatment Plant, receiving both domestic and hospital waste. We exposed these sediments continuously in flow-through reactors to different VA concentrations under denitrifying conditions (nitrate addition and anoxia) in order to determine potential nitrate reduction rates and changes in sedimentary microbial community structures. The presence of VA had no effect on sedimentary nitrate reduction rates at environmental concentrations, whereas a change in bacterial (16S rDNA) and denitrifying (nosZ) community structures was observed (determined by polymerase chain reaction-denaturing gradient gel electrophoresis). The bacterial and denitrifying community structure within the sediment changed upon VA exposure indicating a selection of a non-susceptible VA population.

The Utilization of the Microflora Indigenous to and Present in Oil-Bearing Formations to Selectively Plug the More Porous Zones Thereby Increasing Oil Recovery During Waterflooding

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

Brown, Lewis R.; Byrnes, Martin J.; Stephens, James O.

This project was designed to demonstrate that a microbially enhanced oil recovery process (MEOR), developed in part under DOE Contract No. DE-AC22-90BC14665, will increase oil recovery from fluvial dominated deltaic oil reservoirs. The process involves stimulating the in-situ indigenous microbial population in the reservoir to grow in the more permeable zones, thus diverting flow to other areas of the reservoir, thereby increasing the effectiveness of the waterflood. This five and a half year project is divided into three phases, Phase I, Planning and Analysis (9 months), Phase II, Implementation (45 months), and Phase III, Technology Transfer (12 months). Phase Imore » was completed and reported in the first annual report. This fifth annual report covers the completion of Phase II and the first six months of Phase III.« less

Deterministic processes guide long-term synchronised population dynamics in replicate anaerobic digesters

PubMed Central

Vanwonterghem, Inka; Jensen, Paul D; Dennis, Paul G; Hugenholtz, Philip; Rabaey, Korneel; Tyson, Gene W

2014-01-01

A replicate long-term experiment was conducted using anaerobic digestion (AD) as a model process to determine the relative role of niche and neutral theory on microbial community assembly, and to link community dynamics to system performance. AD is performed by a complex network of microorganisms and process stability relies entirely on the synergistic interactions between populations belonging to different functional guilds. In this study, three independent replicate anaerobic digesters were seeded with the same diverse inoculum, supplied with a model substrate, α-cellulose, and operated for 362 days at a 10-day hydraulic residence time under mesophilic conditions. Selective pressure imposed by the operational conditions and model substrate caused large reproducible changes in community composition including an overall decrease in richness in the first month of operation, followed by synchronised population dynamics that correlated with changes in reactor performance. This included the synchronised emergence and decline of distinct Ruminococcus phylotypes at day 148, and emergence of a Clostridium and Methanosaeta phylotype at day 178, when performance became stable in all reactors. These data suggest that many dynamic functional niches are predictably filled by phylogenetically coherent populations over long time scales. Neutral theory would predict that a complex community with a high degree of recognised functional redundancy would lead to stochastic changes in populations and community divergence over time. We conclude that deterministic processes may play a larger role in microbial community dynamics than currently appreciated, and under controlled conditions it may be possible to reliably predict community structural and functional changes over time. PMID:24739627

Identification of Some of the Major Groups of Bacteria in Efficient and Nonefficient Biological Phosphorus Removal Activated Sludge Systems

PubMed Central

Bond, Philip L.; Erhart, Robert; Wagner, Michael; Keller, Jürg; Blackall, Linda L.

1999-01-01

To investigate the bacteria that are important to phosphorus (P) removal in activated sludge, microbial populations were analyzed during the operation of a laboratory-scale reactor with various P removal performances. The bacterial population structure, analyzed by fluorescence in situ hybridization (FISH) with oligonucleotides probes complementary to regions of the 16S and 23S rRNAs, was associated with the P removal performance of the reactor. At one stage of the reactor operation, chemical characterization revealed that extremely poor P removal was occurring. However, like in typical P-removing sludges, complete anaerobic uptake of the carbon substrate occurred. Bacteria inhibiting P removal overwhelmed the reactor, and according to FISH, bacteria of the β subclass of the class Proteobacteria other than β-1 or β-2 were dominant in the sludge (58% of the population). Changes made to the operation of the reactor led to the development of a biomass population with an extremely good P removal capacity. The biochemical transformations observed in this sludge were characteristic of typical P-removing activated sludge. The microbial population analysis of the P-removing sludge indicated that bacteria of the β-2 subclass of the class Proteobacteria and actinobacteria were dominant (55 and 35%, respectively), therefore implicating bacteria from these groups in high-performance P removal. The changes in operation that led to the improved performance of the reactor included allowing the pH to rise during the anaerobic period, which promoted anaerobic phosphate release and possibly caused selection against non-phosphate-removing bacteria. PMID:10473419

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...

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

EPA Science Inventory

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

Status of microbial diversity in agroforestry systems in Tamil Nadu, India.

PubMed

Radhakrishnan, Srinivasan; Varadharajan, Mohan

2016-06-01

Soil is a complex and dynamic biological system. Agroforestry systems are considered to be an alternative land use option to help and prevent soil degradation, improve soil fertility, microbial diversity, and organic matter status. An increasing interest has emerged with respect to the importance of microbial diversity in soil habitats. The present study deals with the status of microbial diversity in agroforestry systems in Tamil Nadu. Eight soil samples were collected from different fields in agroforestry systems in Cuddalore, Villupuram, Tiruvanamalai, and Erode districts, Tamil Nadu. The number of microorganisms and physico-chemical parameters of soils were quantified. Among different microbial population, the bacterial population was recorded maximum (64%), followed by actinomycetes (23%) and fungi (13%) in different samples screened. It is interesting to note that the microbial population was positively correlated with the physico-chemical properties of different soil samples screened. Total bacterial count had positive correlation with soil organic carbon (C), moisture content, pH, nitrogen (N), and micronutrients such as Iron (Fe), copper (Cu), and zinc (Zn). Similarly, the total actinomycete count also showed positive correlations with bulk density, moisture content, pH, C, N, phosphorus (P), potassium (K), calcium (Ca), copper (Cu), magnesium (Mg), manganese (Mn), and zinc (Zn). It was also noticed that the soil organic matter, vegetation, and soil nutrients altered the microbial community under agroforestry systems. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Experimental demonstration of an Allee effect in microbial populations

PubMed Central

Kramer, Andrew M.; Dobbs, Fred C.; Drake, John M.

2016-01-01

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 of Vibrio fischeri are subject to an intrinsic demographic Allee effect. Populations subjected to predation by the bacterivore Cafeteria roenbergensis display 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

Septic tank additive impacts on microbial populations.

PubMed

Pradhan, S; Hoover, M T; Clark, G H; Gumpertz, M; Wollum, A G; Cobb, C; Strock, J

2008-01-01

Environmental health specialists, other onsite wastewater professionals, scientists, and homeowners have questioned the effectiveness of septic tank additives. This paper describes an independent, third-party, field scale, research study of the effects of three liquid bacterial septic tank additives and a control (no additive) on septic tank microbial populations. Microbial populations were measured quarterly in a field study for 12 months in 48 full-size, functioning septic tanks. Bacterial populations in the 48 septic tanks were statistically analyzed with a mixed linear model. Additive effects were assessed for three septic tank maintenance levels (low, intermediate, and high). Dunnett's t-test for tank bacteria (alpha = .05) indicated that none of the treatments were significantly different, overall, from the control at the statistical level tested. In addition, the additives had no significant effects on septic tank bacterial populations at any of the septic tank maintenance levels. Additional controlled, field-based research iswarranted, however, to address additional additives and experimental conditions.

Standing variation in spatially growing populations

NASA Astrophysics Data System (ADS)

Fusco, Diana; Gralka, Matti; Kayser, Jona; Hallatschek, Oskar

Patterns of genetic diversity not only reflect the evolutionary history of a species but they can also determine the evolutionary response to environmental change. For instance, the standing genetic diversity of a microbial population can be key to rescue in the face of an antibiotic attack. While genetic diversity is in general shaped by both demography and evolution, very little is understood when both factors matter, as e.g. for biofilms with pronounced spatial organization. Here, we quantitatively explore patterns of genetic diversity by using microbial colonies and well-mixed test tube populations as antipodal model systems with extreme and very little spatial structure, respectively. We find that Eden model simulations and KPZ theory can remarkably reproduce the genetic diversity in microbial colonies obtained via population sequencing. The excellent agreement allows to draw conclusions on the resilience of spatially-organized populations and to uncover new strategies to contain antibiotic resistance.

Social interaction in synthetic and natural microbial communities.

PubMed

Xavier, Joao B

2011-04-12

Social interaction among cells is essential for multicellular complexity. But how do molecular networks within individual cells confer the ability to interact? And how do those same networks evolve from the evolutionary conflict between individual- and population-level interests? Recent studies have dissected social interaction at the molecular level by analyzing both synthetic and natural microbial populations. These studies shed new light on the role of population structure for the evolution of cooperative interactions and revealed novel molecular mechanisms that stabilize cooperation among cells. New understanding of populations is changing our view of microbial processes, such as pathogenesis and antibiotic resistance, and suggests new ways to fight infection by exploiting social interaction. The study of social interaction is also challenging established paradigms in cancer evolution and immune system dynamics. Finding similar patterns in such diverse systems suggests that the same 'social interaction motifs' may be general to many cell populations.

Succession of microbial communities and changes of incremental oil in a post-polymer flooded reservoir with nutrient stimulation.

PubMed

Gao, Peike; Li, Guoqiang; Le, Jianjun; Liu, Xiaobo; Liu, Fang; Ma, Ting

2018-02-01

Further exploitation of the residual oil underground in post-polymer flooded reservoirs is attractive and challengeable. In this study, indigenous microbial enhanced oil recovery (IMEOR) in a post-polymer flooded reservoir was performed. The succession of microbial communities was revealed by high-throughput sequencing of 16S rRNA genes and changes of incremental oil were analyzed. The results indicated that the abundances of reservoir microorganisms significantly increased, with alpha diversities decreased in the IMEOR process. With the intermittent nutrient injection, microbial communities showed a regular change and were alternately dominated by minority populations: Pseudomonas and Acinetobacter significantly increased when nutrients were injected; Thauera, Azovibrio, Arcobacter, Helicobacter, Desulfitobacterium, and Clostridium increased in the following water-flooding process. Accompanied by the stimulated populations, higher oil production was obtained. However, these populations did not contribute a persistent level of incremental oil in the reservoir. In summary, this study revealed the alternative succession of microbial communities and the changes of incremental oil in a post-polymer flooded reservoir with intermittent nutrient stimulation process.

Microbial Diversity of Impact-Generated Habitats

NASA Astrophysics Data System (ADS)

Pontefract, Alexandra; Osinski, Gordon R.; Cockell, Charles S.; Southam, Gordon; McCausland, Phil J. A.; Umoh, Joseph; Holdsworth, David W.

2016-10-01

Impact-generated lithologies have recently been identified as viable and important microbial habitats, especially within cold and arid regions such as the polar deserts on Earth. These unique habitats provide protection from environmental stressors, such as freeze-thaw events, desiccation, and UV radiation, and act to trap aerially deposited detritus within the fissures and pore spaces, providing necessary nutrients for endoliths. This study provides the first culture-independent analysis of the microbial community structure within impact-generated lithologies in a Mars analog environment, involving the analysis of 44,534 16S rRNA sequences from an assemblage of 21 rock samples that comprises three shock metamorphism categories. We find that species diversity increases (H = 2.4-4.6) with exposure to higher shock pressures, which leads to the development of three distinct populations. In each population, Actinobacteria were the most abundant (41%, 65%, and 59%), and the dominant phototrophic taxa came from the Chloroflexi. Calculated porosity (a function of shock metamorphism) for these samples correlates (R2 = 0.62) with inverse Simpson indices, accounting for overlap in populations in the higher shock levels. The results of our study show that microbial diversity is tied to the amount of porosity in the target substrate (as a function of shock metamorphism), resulting in the formation of distinct microbial populations.

The Environment and the Microbial Ecology of Human Skin

PubMed Central

McBride, Mollie E.; Duncan, W. Christopher; Knox, J. M.

1977-01-01

Microbial flora of the skin of three human population groups representing different natural environments was examined quantitatively and qualitatively to determine whether environmental differences in temperature and humidity can influence the microbial flora of normal skin. Five anatomical skin sites - hands, back, axillae, groin, and feet - were sampled from 10 subjects working in a high-humidity, high-temperature environment, 10 subjects from a low-temperature, high-humidity environment, and 10 subjects working in a moderate-temperature and low-humidity environment. Bacterial populations were significantly larger from the back, axillae, and feet in individuals from the high-temperature and high-humidity environment as compared to the moderate-temperature, low-humidity environment. High humidity and low temperature had no significant effect on total populations, but this group showed a higher frequency of isolation of fungi, and gram-negative bacteria from the back and feet. Although there was an indication that increase in the environmental humidity could result in an increased frequency of isolation of gram-negative bacteria, there was no evidence that an increase in either temperature or humidity altered the relative proportions of gram-negative bacteria in the predominantly gram-positive microbial flora found on normal skin. It was concluded that, although climatic changes may cause fluctation in microbial populations from certain sites, they are not a major influence on the ecology of the microbial flora of normal skin in the natural environment. The variables introduced by studying individuals in their natural environment and the influence of these on the results are discussed. PMID:16345214

What is microbial community ecology?

PubMed

Konopka, Allan

2009-11-01

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

Fine-scale phylogenetic architecture of a complex bacterial community.

PubMed

Acinas, Silvia G; Klepac-Ceraj, Vanja; Hunt, Dana E; Pharino, Chanathip; Ceraj, Ivica; Distel, Daniel L; Polz, Martin F

2004-07-29

Although molecular data have revealed the vast scope of microbial diversity, two fundamental questions remain unanswered even for well-defined natural microbial communities: how many bacterial types co-exist, and are such types naturally organized into phylogenetically discrete units of potential ecological significance? It has been argued that without such information, the environmental function, population biology and biogeography of microorganisms cannot be rigorously explored. Here we address these questions by comprehensive sampling of two large 16S ribosomal RNA clone libraries from a coastal bacterioplankton community. We show that compensation for artefacts generated by common library construction techniques reveals fine-scale patterns of community composition. At least 516 ribotypes (unique rRNA sequences) were detected in the sample and, by statistical extrapolation, at least 1,633 co-existing ribotypes in the sampled population. More than 50% of the ribotypes fall into discrete clusters containing less than 1% sequence divergence. This pattern cannot be accounted for by interoperon variation, indicating a large predominance of closely related taxa in this community. We propose that such microdiverse clusters arise by selective sweeps and persist because competitive mechanisms are too weak to purge diversity from within them.

Successive range expansion promotes diversity and accelerates evolution in spatially structured microbial populations.

PubMed

Goldschmidt, Felix; Regoes, Roland R; Johnson, David R

2017-09-01

Successive range expansions occur within all domains of life, where one population expands first (primary expansion) and one or more secondary populations then follow (secondary expansion). In general, genetic drift reduces diversity during range expansion. However, it is not clear whether the same effect applies during successive range expansion, mainly because the secondary population must expand into space occupied by the primary population. Here we used an experimental microbial model system to show that, in contrast to primary range expansion, successive range expansion promotes local population diversity. Because of mechanical constraints imposed by the presence of the primary population, the secondary population forms fractal-like dendritic structures. This divides the advancing secondary population into many small sub-populations and promotes intermixing between the primary and secondary populations. We further developed a mathematical model to simulate the formation of dendritic structures in the secondary population during succession. By introducing mutations in the primary or dendritic secondary populations, we found that mutations are more likely to accumulate in the dendritic secondary populations. Our results thus show that successive range expansion can promote intermixing over the short term and increase genetic diversity over the long term. Our results therefore have potentially important implications for predicting the ecological processes and evolutionary trajectories of microbial communities.

Molecular characterization of microbial population dynamics during sildenafil citrate degradation.

PubMed

De Felice, Bruna; Argenziano, Carolina; Guida, Marco; Trifuoggi, Marco; Russo, Francesca; Condorelli, Valerio; Inglese, Mafalda

2009-02-01

Little is known about pharmaceutical and personal care products pollutants (PPCPs), but there is a growing interest in how they might impact the environment and microbial communities. The widespread use of Viagra (sildenafil citrate) has attracted great attention because of the high usage rate, the unpredictable disposal and the unknown potential effects on wildlife and the environment. Until now information regarding the impact of Viagra on microbial community in water environment has not been reported. In this research, for the first time, the genetic profile of the microbial community, developing in a Viagra polluted water environment, was evaluated by means of the 16S and 18S rRNA genes, for bacteria and fungi, respectively, amplified by polymerase chain reaction (PCR) and separated using the denaturing gradient gel electrophoresis (DGGE) technique. The DGGE results revealed a complex microbial community structure with most of the population persisting throughout the experimental period. DNA sequences from bands observed in the different denaturing gradient gel electrophoresis profiles exhibited the highest degree of identity to uncultured bacteria and fungi found previously mainly in polluted environmental and treating bioreactors. Biotransformation ability of sildenafil citrate by the microbial pool was studied and the capability of these microorganisms to detoxify a polluted water ecosystem was assessed. The bacterial and fungal population was able to degrade sildenafil citrate entirely. Additionally, assays conducted on Daphnia magna, algal growth inhibition assay and cell viability determination on HepG2 human cells showed that biotransformation products obtained from the bacterial growth was not toxic. The higher removal efficiency for sildenafil citrate and the lack of toxicity by the biotransformation products obtained showed that the microbial community identified here represented a composite population that might have biotechnological relevance to retrieve sildenafil citrate contaminated sites.

High-Throughput Screening To Identify Potent and Specific Inhibitors of Microbial Sulfate Reduction.

PubMed

Carlson, Hans K; Mullan, Mark R; Mosqueda, Lorraine A; Chen, Steven; Arkin, Michelle R; Coates, John D

2017-06-20

The selective perturbation of complex microbial ecosystems to predictably influence outcomes in engineered and industrial environments remains a grand challenge for geomicrobiology. In some industrial ecosystems, such as oil reservoirs, sulfate reducing microorganisms (SRM) produce hydrogen sulfide which is toxic, explosive, and corrosive. Despite the economic cost of sulfidogenesis, there has been minimal exploration of the chemical space of possible inhibitory compounds, and very little work has quantitatively assessed the selectivity of putative souring treatments. We have developed a high-throughput screening strategy to identify potent and selective inhibitors of SRM, quantitatively ranked the selectivity and potency of hundreds of compounds and identified previously unrecognized SRM selective inhibitors and synergistic interactions between inhibitors. Zinc pyrithione is the most potent inhibitor of sulfidogenesis that we identified, and is several orders of magnitude more potent than commonly used industrial biocides. Both zinc and copper pyrithione are also moderately selective against SRM. The high-throughput (HT) approach we present can be readily adapted to target SRM in diverse environments and similar strategies could be used to quantify the potency and selectivity of inhibitors of a variety of microbial metabolisms. Our findings and approach are relevant to efforts to engineer environmental ecosystems and also to understand the role of natural gradients in shaping microbial niche space.

Are Microbial Nanowires Responsible for Geoelectrical Changes at Hydrocarbon Contaminated Sites?

NASA Astrophysics Data System (ADS)

Hager, C.; Atekwana, E. A.; Gorby, Y. A.; Duris, J. W.; Allen, J. P.; Atekwana, E. A.; Ownby, C.; Rossbach, S.

2007-05-01

Significant advances in near-surface geophysics and biogeophysics in particular, have clearly established a link between geoelectrical response and the growth and enzymatic activities of microbes in geologic media. Recent studies from hydrocarbon contaminated sites suggest that the activities of distinct microbial populations, specifically syntrophic, sulfate reducing, and dissimilatory iron reducing microbial populations are a contributing factor to elevated sediment conductivity. However, a fundamental mechanistic understanding of the processes and sources resulting in the measured electrical response remains uncertain. The recent discovery of bacterial nanowires and their electron transport capabilities suggest that if bacterial nanowires permeate the subsurface, they may in part be responsible for the anomalous conductivity response. In this study we investigated the microbial population structure, the presence of nanowires, and microbial-induced alterations of a hydrocarbon contaminated environment and relate them to the sediments' geoelectrical response. Our results show that microbial communities varied substantially along the vertical gradient and at depths where hydrocarbons saturated the sediments, ribosomal intergenic spacer analysis (RISA) revealed signatures of microbial communities adapted to hydrocarbon impact. In contrast, RISA profiles from a background location showed little community variations with depth. While all sites showed evidence of microbial activity, a scanning electron microscope (SEM) study of sediment from the contaminated location showed pervasive development of "nanowire-like structures" with morphologies consistent with nanowires from laboratory experiments. SEM analysis suggests extensive alteration of the sediments by microbial Activity. We conclude that, excess organic carbon (electron donor) but limited electron acceptors in these environments cause microorganisms to produce nanowires to shuttle the electrons as they seek for distant electron acceptors. Hence, electron flow via bacterial nanowires may contribute to the geoelectrical response.

Genome-centric metatranscriptomes and ecological roles of the active microbial populations during cellulosic biomass anaerobic digestion.

PubMed

Jia, Yangyang; Ng, Siu-Kin; Lu, Hongyuan; Cai, Mingwei; Lee, Patrick K H

2018-01-01

Although anaerobic digestion for biogas production is used worldwide in treatment processes to recover energy from carbon-rich waste such as cellulosic biomass, the activities and interactions among the microbial populations that perform anaerobic digestion deserve further investigations, especially at the population genome level. To understand the cellulosic biomass-degrading potentials in two full-scale digesters, this study examined five methanogenic enrichment cultures derived from the digesters that anaerobically digested cellulose or xylan for more than 2 years under 35 or 55 °C conditions. Metagenomics and metatranscriptomics were used to capture the active microbial populations in each enrichment culture and reconstruct their meta-metabolic network and ecological roles. 107 population genomes were reconstructed from the five enrichment cultures using a differential coverage binning approach, of which only a subset was highly transcribed in the metatranscriptomes. Phylogenetic and functional convergence of communities by enrichment condition and phase of fermentation was observed for the highly transcribed populations in the metatranscriptomes. In the 35 °C cultures grown on cellulose, Clostridium cellulolyticum -related and Ruminococcus -related bacteria were identified as major hydrolyzers and primary fermenters in the early growth phase, while Clostridium leptum -related bacteria were major secondary fermenters and potential fatty acid scavengers in the late growth phase. While the meta-metabolism and trophic roles of the cultures were similar, the bacterial populations performing each function were distinct between the enrichment conditions. Overall, a population genome-centric view of the meta-metabolism and functional roles of key active players in anaerobic digestion of cellulosic biomass was obtained. This study represents a major step forward towards understanding the microbial functions and interactions at population genome level during the microbial conversion of lignocellulosic biomass to methane. The knowledge of this study can facilitate development of potential biomarkers and rational design of the microbiome in anaerobic digesters.

Localized electron transfer rates and microelectrode-based enrichment of microbial communities within a phototrophic microbial mat.

PubMed

Babauta, Jerome T; Atci, Erhan; Ha, Phuc T; Lindemann, Stephen R; Ewing, Timothy; Call, Douglas R; Fredrickson, James K; Beyenal, Haluk

2014-01-01

Phototrophic microbial mats frequently exhibit sharp, light-dependent redox gradients that regulate microbial respiration on specific electron acceptors as a function of depth. In this work, a benthic phototrophic microbial mat from Hot Lake, a hypersaline, epsomitic lake located near Oroville in north-central Washington, was used to develop a microscale electrochemical method to study local electron transfer processes within the mat. To characterize the physicochemical variables influencing electron transfer, we initially quantified redox potential, pH, and dissolved oxygen gradients by depth in the mat under photic and aphotic conditions. We further demonstrated that power output of a mat fuel cell was light-dependent. To study local electron transfer processes, we deployed a microscale electrode (microelectrode) with tip size ~20 μm. To enrich a subset of microorganisms capable of interacting with the microelectrode, we anodically polarized the microelectrode at depth in the mat. Subsequently, to characterize the microelectrode-associated community and compare it to the neighboring mat community, we performed amplicon sequencing of the V1-V3 region of the 16S gene. Differences in Bray-Curtis beta diversity, illustrated by large changes in relative abundance at the phylum level, suggested successful enrichment of specific mat community members on the microelectrode surface. The microelectrode-associated community exhibited substantially reduced alpha diversity and elevated relative abundances of Prosthecochloris, Loktanella, Catellibacterium, other unclassified members of Rhodobacteraceae, Thiomicrospira, and Limnobacter, compared with the community at an equivalent depth in the mat. Our results suggest that local electron transfer to an anodically polarized microelectrode selected for a specific microbial population, with substantially more abundance and diversity of sulfur-oxidizing phylotypes compared with the neighboring mat community.

Localized electron transfer rates and microelectrode-based enrichment of microbial communities within a phototrophic microbial mat

PubMed Central

Babauta, Jerome T.; Atci, Erhan; Ha, Phuc T.; Lindemann, Stephen R.; Ewing, Timothy; Call, Douglas R.; Fredrickson, James K.; Beyenal, Haluk

2014-01-01

Phototrophic microbial mats frequently exhibit sharp, light-dependent redox gradients that regulate microbial respiration on specific electron acceptors as a function of depth. In this work, a benthic phototrophic microbial mat from Hot Lake, a hypersaline, epsomitic lake located near Oroville in north-central Washington, was used to develop a microscale electrochemical method to study local electron transfer processes within the mat. To characterize the physicochemical variables influencing electron transfer, we initially quantified redox potential, pH, and dissolved oxygen gradients by depth in the mat under photic and aphotic conditions. We further demonstrated that power output of a mat fuel cell was light-dependent. To study local electron transfer processes, we deployed a microscale electrode (microelectrode) with tip size ~20 μm. To enrich a subset of microorganisms capable of interacting with the microelectrode, we anodically polarized the microelectrode at depth in the mat. Subsequently, to characterize the microelectrode-associated community and compare it to the neighboring mat community, we performed amplicon sequencing of the V1–V3 region of the 16S gene. Differences in Bray-Curtis beta diversity, illustrated by large changes in relative abundance at the phylum level, suggested successful enrichment of specific mat community members on the microelectrode surface. The microelectrode-associated community exhibited substantially reduced alpha diversity and elevated relative abundances of Prosthecochloris, Loktanella, Catellibacterium, other unclassified members of Rhodobacteraceae, Thiomicrospira, and Limnobacter, compared with the community at an equivalent depth in the mat. Our results suggest that local electron transfer to an anodically polarized microelectrode selected for a specific microbial population, with substantially more abundance and diversity of sulfur-oxidizing phylotypes compared with the neighboring mat community. PMID:24478768

Localized electron transfer rates and microelectrode-based enrichment of microbial communities within a phototrophic microbial mat

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

Babauta, Jerome T.; Atci, Erhan; Ha, Phuc T.

2014-01-01

Phototrophic microbial mats frequently exhibit sharp, light-dependent redox gradients that regulate microbial respiration on specific electron acceptors as a function of depth. In this work, a benthic phototrophic microbial mat from Hot Lake, a hypersaline, epsomitic lake located near Oroville in north-central Washington, was used to develop a microscale electrochemical method to study local electron transfer processes within the mat. To characterize the physicochemical variables influencing electron transfer, we initially quantified redox potential, pH, and dissolved oxygen gradients by depth in the mat under photic and aphotic conditions. We further demonstrated that power output of a mat fuel cell wasmore » light-dependent. To study local electron transfer processes, we deployed a microscale electrode (microelectrode) with tip size ~20 μm. To enrich a subset of microorganisms capable of interacting with the microelectrode, we anodically polarized the microelectrode at depth in the mat. Subsequently, to characterize the microelectrode- associated community and compare it to the neighboring mat community, we performed amplicon sequencing of the V1-V3 region of the 16S gene. Differences in Bray-Curtis beta diversity, illustrated by large changes in relative abundance at the phylum level, suggested successful enrichment of specific mat community members on the microelectrode surface. The microelectrode-associated community exhibited substantially reduced alpha diversity and elevated relative abundances of Prosthecochloris, Loktanella, Catellibacterium, other unclassified members of Rhodobacteraceae, Thiomicrospira, and Limnobacter, compared with the community at an equivalent depth in the mat. Our results suggest that local electron transfer to an anodically polarized microelectrode selected for a specific microbial population, with substantially more abundance and diversity of sulfur-oxidizing phylotypes compared with the neighboring mat community.« less

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:25767468

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...

The effect of wheat prebiotics on the gut bacterial population and iron status of iron deficient broiler chickens

USDA-ARS?s Scientific Manuscript database

In recent years, there is a lot of interest in improving the intestinal health, and consequently increasing minerals as iron absorption, by managing the intestinal microbial population. This is traditionally done by the consumption of probiotics, which are live microbial food supplements. However, a...

Succession of ruminal bacterial species and fermentation characteristics in nursing Brangus calves

USDA-ARS?s Scientific Manuscript database

Ruminants are typically born with a non-functional rumen essentially devoid of microorganism. The succession of the microbial population in the rumen from birth to animal maturity is of interest due to the key role the rumen microbial population plays in the overall health and productivity of the ho...

Season mediates herbivore effects on litter and soil microbial abundance and activity in a semi-arid woodland

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

Classen, Aimee T; Overby, Stephen; Hart, Stephen C

2007-01-01

Herbivores can directly impact ecosystem function by altering litter quality entering an ecosystem or indirectly by affecting a shift in the microbial community that mediate nutrient processes. We examine herbivore susceptibility and resistance effects on litter microarthropod and soil microbial communities to test the general hypothesis that herbivore driven changes in litter inputs will feedback to the microbial community. Our study population consisted of individual trees that are susceptible or resistant to the stem-boring moth (Dioryctria albovittella) and trees that herbivores have been manually removed since 1982. Moth herbivory increased pi on litter nitrogen concentrations (16%) and canopy precipitation infiltrationmore » (28%), both significant factors influencing litter and soil microbial populations. Our research resulted in three major conclusions: 1) In spite of an increase in litter quality, herbivory does not change litter microarthropod abundance or species richness. 2) Herbivore susceptibility alters bulk soil microbial communities, but not soil properties. 3) Season has a strong influence on microbial communities, and their response to herbivore inputs, in this semi-arid ecosystem.« less

Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials.

PubMed

Bikard, David; Euler, Chad W; Jiang, Wenyan; Nussenzweig, Philip M; Goldberg, Gregory W; Duportet, Xavier; Fischetti, Vincent A; Marraffini, Luciano A

2014-11-01

Antibiotics target conserved bacterial cellular pathways or growth functions and therefore cannot selectively kill specific members of a complex microbial population. Here, we develop programmable, sequence-specific antimicrobials using the RNA-guided nuclease Cas9 (refs.1,2) delivered by a bacteriophage. We show that Cas9, reprogrammed to target virulence genes, kills virulent, but not avirulent, Staphylococcus aureus. Reprogramming the nuclease to target antibiotic resistance genes destroys staphylococcal plasmids that harbor antibiotic resistance genes and immunizes avirulent staphylococci to prevent the spread of plasmid-borne resistance genes. We also show that CRISPR-Cas9 antimicrobials function in vivo to kill S. aureus in a mouse skin colonization model. This technology creates opportunities to manipulate complex bacterial populations in a sequence-specific manner.

Urban aerosols harbor diverse and dynamic bacterial populations

PubMed Central

Brodie, Eoin L.; DeSantis, Todd Z.; Parker, Jordan P. Moberg; Zubietta, Ingrid X.; Piceno, Yvette M.; Andersen, Gary L.

2007-01-01

Considering the importance of its potential implications for human health, agricultural productivity, and ecosystem stability, surprisingly little is known regarding the composition or dynamics of the atmosphere's microbial inhabitants. Using a custom high-density DNA microarray, we detected and monitored bacterial populations in two U.S. cities over 17 weeks. These urban aerosols contained at least 1,800 diverse bacterial types, a richness approaching that of some soil bacterial communities. We also reveal the consistent presence of bacterial families with pathogenic members including environmental relatives of select agents of bioterrorism significance. Finally, using multivariate regression techniques, we demonstrate that temporal and meteorological influences can be stronger factors than location in shaping the biological composition of the air we breathe. PMID:17182744

Molecular Technique to Understand Deep Microbial Diversity

NASA Technical Reports Server (NTRS)

Vaishampayan, Parag A.; Venkateswaran, Kasthuri J.

2012-01-01

Current sequencing-based and DNA microarray techniques to study microbial diversity are based on an initial PCR (polymerase chain reaction) amplification step. However, a number of factors are known to bias PCR amplification and jeopardize the true representation of bacterial diversity. PCR amplification of the minor template appears to be suppressed by the exponential amplification of the more abundant template. It is widely acknowledged among environmental molecular microbiologists that genetic biosignatures identified from an environment only represent the most dominant populations. The technological bottleneck has overlooked the presence of the less abundant minority population, and underestimated their role in the ecosystem maintenance. To generate PCR amplicons for subsequent diversity analysis, bacterial l6S rRNA genes are amplified by PCR using universal primers. Two distinct PCR regimes are employed in parallel: one using normal and the other using biotinlabeled universal primers. PCR products obtained with biotin-labeled primers are mixed with streptavidin-labeled magnetic beads and selectively captured in the presence of a magnetic field. Less-abundant DNA templates that fail to amplify in this first round of PCR amplification are subjected to a second round of PCR using normal universal primers. These PCR products are then subjected to downstream diversity analyses such as conventional cloning and sequencing. A second round of PCR amplified the minority population and completed the deep diversity picture of the environmental sample.

Response of the microbial community structure of biofilms to ferric iron in microbial fuel cells.

PubMed

Liu, Qian; Yang, Yang; Mei, Xiaoxue; Liu, Bingfeng; Chen, Chuan; Xing, Defeng

2018-08-01

Ferric iron can affect the current generation of microbial electrochemical system (MES); however, how it influences microbial biofilm formation and metabolic activity has not been reported. Here, we describe the response of microbial electrode biofilm communities to insoluble ferric iron (Fe 3+ ) at different concentrations in microbial fuel cells (MFCs). Insoluble ferric iron (200μM) improved electrochemical activity of the MFCs microbial biofilms during start-up and resulted in a higher maximum power density of 0.95W/m 2 , compared with the control (0.76W/m 2 ), 500μM Fe 3+ (0.83W/m 2 ), 1000μM Fe 3+ (0.73W/m 2 ), and 2000μM Fe 3+ (0.59W/m 2 ) treatments. Illumina Hiseq sequencing of 16S rRNA gene amplicons indicated that the predominant populations in the anode biofilms of the MFCs belonged to Geobacter, with relative abundance of 66-75%. Microbial cathode biofilm communities were more susceptible to Fe 3+ , as an obvious shift in the cathode biofilm community structures occurred as Fe 3+ concentration was increased. The most predominant populations in the MFC cathode biofilms without Fe 3+ and with 200μM Fe 3+ were affiliated with Thauera (46% and 35%), whereas no absolutely predominant populations were present in the MFC cathode biofilm with 1000μM Fe 3+ . The results demonstrate that a low concentration of Fe 3+ facilitated the power output of MFCs and shaped community structures of the electrode biofilm. Copyright © 2018 Elsevier B.V. All rights reserved.

Impacts of chemical gradients on microbial community structure

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

Chen, Jianwei; Hanke, Anna; Tegetmeyer, Halina E.

Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the ‘redox tower’. Here, we investigated whether redox sorting of microbial processes explains microbial community structure at low-oxygen concentrations. We subjected a diverse microbial community sampled from a coastal marine sediment to 100 days of tidal cycling in a laboratory chemostat. Oxygen gradients (both in space and time) led to the assembly of a microbial community dominated by populations that each performed aerobicmore » and anaerobic metabolism in parallel. This was shown by metagenomics, transcriptomics, proteomics and stable isotope incubations. Effective oxygen consumption combined with the formation of microaggregates sustained the activity of oxygen-sensitive anaerobic enzymes, leading to braiding of unsorted redox processes, within and between populations. Analyses of available metagenomic data sets indicated that the same ecological strategies might also be successful in some natural ecosystems.« less

Study of the diversity of microbial communities in a sequencing batch reactor oxic-settling-anaerobic process and its modified process.

PubMed

Sun, Lianpeng; Chen, Jianfan; Wei, Xiange; Guo, Wuzhen; Lin, Meishan; Yu, Xiaoyu

2016-05-01

To further reveal the mechanism of sludge reduction in the oxic-settling-anaerobic (OSA) process, the polymerase chain reaction - denaturing gradient gel electrophoresis protocol was used to study the possible difference in the microbial communities between a sequencing batch reactor (SBR)-OSA process and its modified process, by analyzing the change in the diversity of the microbial communities in each reactor of both systems. The results indicated that the structure of the microbial communities in aerobic reactors of the 2 processes was very different, but the predominant microbial populations in anaerobic reactors were similar. The predominant microbial population in the aerobic reactor of the SBR-OSA belonged to Burkholderia cepacia, class Betaproteobacteria, while those of the modified process belonged to the classes Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. These 3 types of microbes had a cryptic growth characteristic, which was the main cause of a greater sludge reduction efficiency achieved by the modified process.

Impacts of chemical gradients on microbial community structure

DOE PAGES

Chen, Jianwei; Hanke, Anna; Tegetmeyer, Halina E.; ...

2017-01-17

Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the ‘redox tower’. Here, we investigated whether redox sorting of microbial processes explains microbial community structure at low-oxygen concentrations. We subjected a diverse microbial community sampled from a coastal marine sediment to 100 days of tidal cycling in a laboratory chemostat. Oxygen gradients (both in space and time) led to the assembly of a microbial community dominated by populations that each performed aerobicmore » and anaerobic metabolism in parallel. This was shown by metagenomics, transcriptomics, proteomics and stable isotope incubations. Effective oxygen consumption combined with the formation of microaggregates sustained the activity of oxygen-sensitive anaerobic enzymes, leading to braiding of unsorted redox processes, within and between populations. Analyses of available metagenomic data sets indicated that the same ecological strategies might also be successful in some natural ecosystems.« less

Impacts of chemical gradients on microbial community structure

PubMed Central

Chen, Jianwei; Hanke, Anna; Tegetmeyer, Halina E; Kattelmann, Ines; Sharma, Ritin; Hamann, Emmo; Hargesheimer, Theresa; Kraft, Beate; Lenk, Sabine; Geelhoed, Jeanine S; Hettich, Robert L; Strous, Marc

2017-01-01

Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the ‘redox tower'. Here, we investigated whether redox sorting of microbial processes explains microbial community structure at low-oxygen concentrations. We subjected a diverse microbial community sampled from a coastal marine sediment to 100 days of tidal cycling in a laboratory chemostat. Oxygen gradients (both in space and time) led to the assembly of a microbial community dominated by populations that each performed aerobic and anaerobic metabolism in parallel. This was shown by metagenomics, transcriptomics, proteomics and stable isotope incubations. Effective oxygen consumption combined with the formation of microaggregates sustained the activity of oxygen-sensitive anaerobic enzymes, leading to braiding of unsorted redox processes, within and between populations. Analyses of available metagenomic data sets indicated that the same ecological strategies might also be successful in some natural ecosystems. PMID:28094795

Impacts of chemical gradients on microbial community structure.

PubMed

Chen, Jianwei; Hanke, Anna; Tegetmeyer, Halina E; Kattelmann, Ines; Sharma, Ritin; Hamann, Emmo; Hargesheimer, Theresa; Kraft, Beate; Lenk, Sabine; Geelhoed, Jeanine S; Hettich, Robert L; Strous, Marc

2017-04-01

Succession of redox processes is sometimes assumed to define a basic microbial community structure for ecosystems with oxygen gradients. In this paradigm, aerobic respiration, denitrification, fermentation and sulfate reduction proceed in a thermodynamically determined order, known as the 'redox tower'. Here, we investigated whether redox sorting of microbial processes explains microbial community structure at low-oxygen concentrations. We subjected a diverse microbial community sampled from a coastal marine sediment to 100 days of tidal cycling in a laboratory chemostat. Oxygen gradients (both in space and time) led to the assembly of a microbial community dominated by populations that each performed aerobic and anaerobic metabolism in parallel. This was shown by metagenomics, transcriptomics, proteomics and stable isotope incubations. Effective oxygen consumption combined with the formation of microaggregates sustained the activity of oxygen-sensitive anaerobic enzymes, leading to braiding of unsorted redox processes, within and between populations. Analyses of available metagenomic data sets indicated that the same ecological strategies might also be successful in some natural ecosystems.

Molecular Tools for Investigating the Gut Microbiota

NASA Astrophysics Data System (ADS)

Lay, Christophe

The “microbial world within us” (Zoetendal et al., 2006) is populated by a complex society of indigenous microorganisms that feature different “ethnic” populations. Those microbial cells thriving within us are estimated to outnumber human body cells by a factor of ten to one. Insights into the relation between the intestinal microbial community and its host have been gained through gnotobiology. Indeed, the influence of the gut microbiota upon human development, physiology, immunity, and nutrition has been inferred by comparing gnotoxenic and axenic murine models (Hooper et al., 1998, 2002, 2003; Hooper and Gordon, 2001).

Effects of Variety and Postharvest Handling Practices on Microbial Population at Different Stages of the Value Chain of Fresh Tomato (Solanum lycopersicum) in Western Terai of Nepal.

PubMed

Khadka, Ram B; Marasini, Madan; Rawal, Ranjana; Gautam, Durga M; Acedo, Antonio L

2017-01-01

Background . Fresh vegetables such as tomato should have low microbial population for safe consumption and long storage life. The aerobic bacterial count (ABC) and coliform bacterial count (CBC), yeast, and mold population are the most widely used microbial indicators in fresh vegetables which should be lower than 4 log CFU g -1 for safe consumption. The stages of the supply chain, postharvest handling methods, and crop varieties had significant effects on microbial population. ABC, CBC, yeast, and mold population were significantly highest ( P < 0.05) at retail market (5.59, 4.38, 2.60, and 3.14 log CFU g -1 , resp.), followed by wholesale market (4.72, 4.71, 2.43, and 2.44 log CFU g -1 , resp.), and were least at farm gate (3.89, 3.63, 2.38, and 2.03 log CFU g -1 , resp.). Improved postharvest practices (washing in clean water and grading and packaging in clean plastic crate) helped to reduce ABC, CBC, and mold population by 2.51, 32.70, and 29.86 percentage as compared to the conventional method (no washing and no grading and packaging in mud plastered bamboo baskets). Among varieties, Pusa ruby had the lowest microbial load of 2.58, 4.53, 0.96, and 1.77 log CFU g -1 for ABC, CBC, yeast, and mold count, respectively. Significantly negative correlation ( P < 0.05) was observed between fruit pH & ABC and pH & mold count. Although the microbial quality of fresh tomato is safe in the local market of western Terai of Nepal both in conventional and in improved practices however still it is essential to follow improved postharvest handling practices in production and marketing of newly introduced tomato cultivars (high-pH cultivars) for ensuring the safe availability of fresh tomato in the market.

Effects of Variety and Postharvest Handling Practices on Microbial Population at Different Stages of the Value Chain of Fresh Tomato (Solanum lycopersicum) in Western Terai of Nepal

PubMed Central

Marasini, Madan; Rawal, Ranjana; Gautam, Durga M.; Acedo, Antonio L.

2017-01-01

Background. Fresh vegetables such as tomato should have low microbial population for safe consumption and long storage life. The aerobic bacterial count (ABC) and coliform bacterial count (CBC), yeast, and mold population are the most widely used microbial indicators in fresh vegetables which should be lower than 4 log CFU g−1 for safe consumption. The stages of the supply chain, postharvest handling methods, and crop varieties had significant effects on microbial population. ABC, CBC, yeast, and mold population were significantly highest (P < 0.05) at retail market (5.59, 4.38, 2.60, and 3.14 log CFU g−1, resp.), followed by wholesale market (4.72, 4.71, 2.43, and 2.44 log CFU g−1, resp.), and were least at farm gate (3.89, 3.63, 2.38, and 2.03 log CFU g−1, resp.). Improved postharvest practices (washing in clean water and grading and packaging in clean plastic crate) helped to reduce ABC, CBC, and mold population by 2.51, 32.70, and 29.86 percentage as compared to the conventional method (no washing and no grading and packaging in mud plastered bamboo baskets). Among varieties, Pusa ruby had the lowest microbial load of 2.58, 4.53, 0.96, and 1.77 log CFU g−1 for ABC, CBC, yeast, and mold count, respectively. Significantly negative correlation (P < 0.05) was observed between fruit pH & ABC and pH & mold count. Although the microbial quality of fresh tomato is safe in the local market of western Terai of Nepal both in conventional and in improved practices however still it is essential to follow improved postharvest handling practices in production and marketing of newly introduced tomato cultivars (high-pH cultivars) for ensuring the safe availability of fresh tomato in the market. PMID:29124068

Molecular Technique to Reduce PCR Bias for Deeper Understanding of Microbial Diversity

NASA Technical Reports Server (NTRS)

Vaishampayan, Parag A.; Venkateswaran, Kasthuri J.

2012-01-01

Current planetary protection policies require that spacecraft targeted to sensitive solar system bodies be assembled and readied for launch in controlled cleanroom environments. A better understanding of the distribution and frequency at which high-risk contaminant microbes are encountered on spacecraft surfaces would significantly aid in assessing the threat of forward contamination. However, despite a growing understanding of the diverse microbial populations present in cleanrooms, less abundant microbial populations are probably not adequately taken into account due to technological limitations. This novel approach encompasses a wide spectrum of microbial species and will represent the true picture of spacecraft cleanroom-associated microbial diversity. All of the current microbial diversity assessment techniques are based on an initial PCR amplification step. However, a number of factors are known to bias PCR amplification and jeopardize the true representation of bacterial diversity. PCR amplification of a minor template appears to be suppressed by the amplification of a more abundant template. It is widely acknowledged among environmental molecular microbiologists that genetic biosignatures identified from an environment only represent the most dominant populations. The technological bottleneck overlooks the presence of the less abundant minority population and may underestimate their role in the ecosystem maintenance. DNA intercalating agents such as propidium monoazide (PMA) covalently bind with DNA molecules upon photolysis using visible light, and make it unavailable for DNA polymerase enzyme during polymerase chain reaction (PCR). Environmental DNA samples will be treated with suboptimum PMA concentration, enough to intercalate with 90 99% of the total DNA. The probability of PMA binding with DNA from abundant bacterial species will be much higher than binding with DNA from less abundant species. This will increase the relative DNA concentration of previously "shadowed" less abundant species available for PCR amplification. These PCR products obtained with and without PMA treatment will then be subjected to downstream diversity analyses such as sequencing and DNA microarray. It is expected that PMA-coupled PCR will amplify the "minority population" and help in understanding microbial diversity spectrum of an environmental sample at a much deeper level. This new protocol aims to overcome the major potential biases faced when analyzing microbial 16S rRNA gene diversity. This study will lead to a technological advancement and a commercial product that will aid microbial ecologists in understanding microbial diversity from various environmental niches. Implementation of this technique may lead to discoveries of novel microbes and their functions in sustenance of the ecosystem.

Microbial Biosensors for Selective Detection of Disaccharides

USDA-ARS?s Scientific Manuscript database

Seven microbial strains were screened for their ability to detect disaccharides as components of Clark-type oxygen biosensors. Sensors responded to varying degrees to maltose, cellobiose, sucrose, and melibiose, but none responded strongly to lactose. Although microbial sensors are relatively nons...

Microbial degradation of hydrocarbons in the environment.

PubMed Central

Leahy, J G; Colwell, R R

1990-01-01

The ecology of hydrocarbon degradation by microbial populations in the natural environment is reviewed, emphasizing the physical, chemical, and biological factors that contribute to the biodegradation of petroleum and individual hydrocarbons. Rates of biodegradation depend greatly on the composition, state, and concentration of the oil or hydrocarbons, with dispersion and emulsification enhancing rates in aquatic systems and absorption by soil particulates being the key feature of terrestrial ecosystems. Temperature and oxygen and nutrient concentrations are important variables in both types of environments. Salinity and pressure may also affect biodegradation rates in some aquatic environments, and moisture and pH may limit biodegradation in soils. Hydrocarbons are degraded primarily by bacteria and fungi. Adaptation by prior exposure of microbial communities to hydrocarbons increases hydrocarbon degradation rates. Adaptation is brought about by selective enrichment of hydrocarbon-utilizing microorganisms and amplification of the pool of hydrocarbon-catabolizing genes. The latter phenomenon can now be monitored through the use of DNA probes. Increases in plasmid frequency may also be associated with genetic adaptation. Seeding to accelerate rates of biodegradation has been shown to be effective in some cases, particularly when used under controlled conditions, such as in fermentors or chemostats. PMID:2215423

[Spring water quality assessment regarding the problem of endemic fluorosis].

PubMed

Leshchenko, D V; Mialo, O A; Beliakova, M B; Beliaeva, E A; Samoukina, A M; Chervinets, Iu V; Ivanova, O V

2013-01-01

A possible variant for reducing the consumption of fluoride by population of Tver region is the use of water with low fluoride content, such as spring water. Assessment of drinking suitability of spring water (the content of physiologically important mineral elements and microbial purity) is relevant to our region. Water samples from 6 spring-water source of Tver region were studied during the year. The content of fluoride and calcium were measured by using an ion-selective electrodes. Microbiological purity tested by the presence of total coliform bacteria, thermotolerant coliform bacteria, coliphages and total microbial numbers. The analysis of some mineral components in spring water of Tver region showed that calcium content was in range 33-88 mg/l, that satisfied the recommended value; fluoride concentration is less then 0.5 mg/l. In all spring water samples total coliforms, thermotolerant coliforms and coliphages were absent. The total microbial number was in standard range, except of two spring-water source in the autumn and summer. The data suppose that spring water of Tver region can be used as a component of diet normalizing the fluoride consumption at risk of dental fluorosis in children.

PCB126 modulates fecal microbial fermentation of the dietary fiber inulin

USDA-ARS?s Scientific Manuscript database

Exposure to environmental pollutants can alter gut microbial populations. Short-chain fatty acids (SCFAs), produced from gut microbial fermentation of dietary fibers such as inulin, exert numerous effects on host energy metabolism. SCFAs are also linked to health promoting effects, including a red...

Maximizing power generation from dark fermentation effluents in microbial fuel cell by selective enrichment of exoelectrogens and optimization of anodic operational parameters.

PubMed

Varanasi, Jhansi L; Sinha, Pallavi; Das, Debabrata

2017-05-01

To selectively enrich an electrogenic mixed consortium capable of utilizing dark fermentative effluents as substrates in microbial fuel cells and to further enhance the power outputs by optimization of influential anodic operational parameters. A maximum power density of 1.4 W/m 3 was obtained by an enriched mixed electrogenic consortium in microbial fuel cells using acetate as substrate. This was further increased to 5.43 W/m 3 by optimization of influential anodic parameters. By utilizing dark fermentative effluents as substrates, the maximum power densities ranged from 5.2 to 6.2 W/m 3 with an average COD removal efficiency of 75% and a columbic efficiency of 10.6%. A simple strategy is provided for selective enrichment of electrogenic bacteria that can be used in microbial fuel cells for generating power from various dark fermentative effluents.

Unravelling the active microbial community in a thermophilic anaerobic digester-microbial electrolysis cell coupled system under different conditions.

PubMed

Cerrillo, Míriam; Viñas, Marc; Bonmatí, August

2017-03-01

Thermophilic anaerobic digestion (AD) of pig slurry coupled to a microbial electrolysis cell (MEC) with a recirculation loop was studied at lab-scale as a strategy to increase AD stability when submitted to organic and nitrogen overloads. The system performance was studied, with the recirculation loop both connected and disconnected, in terms of AD methane production, chemical oxygen demand removal (COD) and volatile fatty acid (VFA) concentrations. Furthermore, the microbial population was quantitatively and qualitatively assessed through DNA and RNA-based qPCR and high throughput sequencing (MiSeq), respectively to identify the RNA-based active microbial populations from the total DNA-based microbial community composition both in the AD and MEC reactors under different operational conditions. Suppression of the recirculation loop reduced the AD COD removal efficiency (from 40% to 22%) and the methane production (from 0.32 to 0.03 m 3  m -3  d -1 ). Restoring the recirculation loop led to a methane production of 0.55 m 3  m -3  d -1 concomitant with maximum MEC COD and ammonium removal efficiencies of 29% and 34%, respectively. Regarding microbial analysis, the composition of the AD and MEC anode populations differed from really active microorganisms. Desulfuromonadaceae was revealed as the most active family in the MEC (18%-19% of the RNA relative abundance), while hydrogenotrophic methanogens (Methanobacteriaceae) dominated the AD biomass. Copyright © 2016 Elsevier Ltd. All rights reserved.

Inferring Microbial Fitness Landscapes

DTIC Science & Technology

2016-02-25

infer from data the determinants of microbial evolution with sufficient resolution that we can quantify 1. REPORT DATE (DD-MM-YYYY) 4. TITLE AND...Distribution Unlimited UU UU UU UU 25-02-2016 1-Oct-2012 30-Sep-2015 Final Report: Inferring Microbial Fitness Landscapes The views, opinions and/or findings...Triangle Park, NC 27709-2211 evolution, fitness landscapes, epistasis, microbial populations REPORT DOCUMENTATION PAGE 11. SPONSOR/MONITOR’S REPORT

Microbial activity discovered in previously ice-entombed Arctic ecosystems

NASA Astrophysics Data System (ADS)

Welker, J. M.; Fahnestock, J. T.; Henry, G. H. R.; 0'Dea, K. W.; Piper, R. E.

One of the more intriguing discoveries in the biogeochemical sciences in recent years is the tremendous capacity of microbial populations to occupy and flourish in extreme habitats [Rothschild and Mancinelli 2001]. Microbial populations survive and multiply under a diversity of harsh conditions, including the hot springs of Yellowstone National Park, Wyoming, and on the ocean floor around thermal vents. At the other extreme, active microbial communities occupy some of the coldest and driest habitats on Earth. For instance, a variety of bacterial and fungal species have been found in the Dry Valleys of Antarctica, and there is evidence that microbes are also present beneath the Antarctic Ice Sheet in Lake Vostok, a system that has not been exposed to the atmosphere for thousands of years.

Microbial populations of crude oil spill polluted soils at the Jordan-Iraq desert (the Badia region).

PubMed

Saadoun, Ismail; Mohammad, Munir J; Hameed, Khalid M; Shawaqfah, Mo'ayyad

2008-07-01

Microbial populations' inhabitants in crude petroleum contaminated soils were analyzed in relation with the soil characteristics. A noticeable greater decline of bacterial counts and diversity but a prevalence of the genus Pseudomonas over the other identified genera in the fresh contaminated soils as compared to the old ones was observed.

Linkages among geophysical facies, microbial composition, biogeochemical rates, and seasonal hydrology in the hyporheic zone

NASA Astrophysics Data System (ADS)

Stegen, J.

2016-12-01

The hyporheic zone is a critical ecosystem transition that links terrestrial, aquatic, and subsurface domains. To understand connections among physical, microbial, and biogeochemical components of the hyporheic zone, we obtained freeze cores along the Columbia River in the Hanford 300 Area and performed geologic, molecular, and microbial assays. Mud and sand content were found to be the primary drivers of microbial community attributes (in particular, of nitrite and carbon oxidizers). Microbial community analysis revealed an abundance of nitrifying Archaea (Thaumarchaea) and an absence of nitrifiying Bacteria. Network analysis revealed significant negative correlations between sand content and some statistical modules of microbial taxa, perhaps indicating the importance of pore water residence time on community composition. A similar set of microbial modules was positively correlated with total organic carbon. One such module that also positively correlated with aerobic metabolic rates was dominated by Thaumarchaea and Nitrospira, suggesting that ammonia oxidation was the dominant aerobic process. We also examined temporal changes in hyporheic microbial structure and activity through repeated sampling of attached and pore water microbes across a spatial gradient. We found that microbial communities remained distinct in river, hyporheic, and inland zones across seasonal variation in hydrologic mixing conditions. One reason was temperature-driven increases in microbial species richness in the hyporheic zone. We show that the relative importance of ecological selection and dispersal varied across environments and across geographic zones. Our results also indicated that while selection imposed short-term constraints on microbial community structure, hyporheic sediment communities did not respond to short-term hydrologic variation. Importantly, we demonstrated that the influence of selective pressures varied with phylogenetic affiliation, which may have been responsible for seasonal increases in Thaumarchaea and aerobic activity. Our results elucidate spatiotemporal shifts in composition and activity of hyporheic microbes across sedimentary and seasonal gradients in pore water environments that correlate with the contribution of Thaumarchaea to aerobic processes.

Coupling Spatiotemporal Community Assembly Processes to Changes in Microbial Metabolism

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

Graham, Emily B.; Crump, Alex R.; Resch, Charles T.

Community assembly processes govern shifts in species abundances in response to environmental change, yet our understanding of assembly remains largely decoupled from ecosystem function. Here, we test hypotheses regarding assembly and function across space and time using hyporheic microbial communities as a model system. We pair sampling of two habitat types through hydrologic fluctuation with null modeling and multivariate statistics. We demonstrate that dual selective pressures assimilate to generate compositional changes at distinct timescales among habitat types, resulting in contrasting associations of Betaproteobacteria and Thaumarchaeota with selection and with seasonal changes in aerobic metabolism. Our results culminate in a conceptualmore » model in which selection from contrasting environments regulates taxon abundance and ecosystem function through time, with increases in function when oscillating selection opposes stable selective pressures. Our model is applicable within both macrobial and microbial ecology and presents an avenue for assimilating community assembly processes into predictions of ecosystem function.« less

Plant-based strategies towards minimising 'livestock's long shadow'.

PubMed

Kingston-Smith, Alison H; Edwards, Joan E; Huws, Sharon A; Kim, Eun J; Abberton, Michael

2010-11-01

Ruminant farming is an important component of the human food chain. Ruminants can use offtake from land unsuitable for cereal crop cultivation via interaction with the diverse microbial population in their rumens. The rumen is a continuous flow fermenter for the digestion of ligno-cellulose, with microbial protein and fermentation end-products incorporated by the animal directly or during post-ruminal digestion. However, ruminal fermentation is inefficient in capturing the nutrient resource presented, resulting in environmental pollution and generation of greenhouse gases. Methane is generated as a consequence of ruminal fermentation and poor retention of ingested forage nitrogen causes nitrogenous pollution of water and land and contributes to the generation of nitrous oxide. One possible cause is the imbalanced provision of dietary substrates to the rumen micro-organisms. Deamination of amino acids by ammonia-producing bacteria liberates ammonia which can be assimilated by the rumen bacteria and used for microbial protein synthesis. However, when carbohydrate is limiting, microbial growth is slow, meaning low demand for ammonia for microbial protein synthesis and excretion of the excess. Protein utilisation can therefore be improved by increasing the availability of readily fermentable sugars in forage or by making protein unavailable for proteolysis through complexing with plant secondary products. Alternatively, realisation that grazing cattle ingest living cells has led to the discovery that plant cells undergo endogenous, stress-mediated protein degradation due to the exposure to rumen conditions. This presents the opportunity to decrease the environmental impact of livestock farming by using decreased proteolysis as a selection tool for the development of improved pasture grass varieties.

Patterns in bacterial and archaeal community structure and diversity in western Beaufort Sea sediments and waters

NASA Astrophysics Data System (ADS)

Hamdan, L. J.; Sikaroodi, M.; Coffin, R. B.; Gillevet, P. M.

2010-12-01

A culture-independent phylogenetic study of microbial communities in water samples and sediment cores recovered from the Beaufort Sea slope east of Point Barrow, Alaska was conducted. The goal of the work was to describe community composition in sediment and water samples and determine the influence of local environmental conditions on microbial populations. Archaeal and bacterial community composition was studied using length heterogeneity-polymerase chain reaction (LH-PCR) and multitag pyrosequencing (MTPS). Sediment samples were obtained from three piston cores on the slope (~1000m depth) arrayed along an east-west transect and one core from a depth of approximately 2000m. Discrete water samples were obtained using a CTD-rosette from three locations adjacent to piston core sites. Water sample were selected at three discrete depths within a vertically stratified (density) water column. The microbial community in near surface waters was distinct from the community observed in deeper stratified layers of the water column. Multidimensional scaling analysis (MDS) revealed that water samples from mid and deep stratified layers bore high similarity to communities in cores collected in close proximity. Overall, the highest diversity (bacteria and archaea) was observed in a core which had elevated methane concentration relative to other locations. Geochemical (e.g., bulk organic and inorganic carbon pools, nutrients, metabolites) and physical data (e.g. depth, water content) were used to reveal the abiotic factors structuring microbial communities. The analysis indicates that sediment water content (porosity) and inorganic carbon concentration are the most significant structuring elements on Beaufort shelf sedimentary microbial communities.

EVAPORITE MICROBIAL FILMS, MATS, MICROBIALITES AND STROMATOLITES

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

Brigmon, R; Penny Morris, P; Garriet Smith, G

2008-01-28

Evaporitic environments are found in a variety of depositional environments as early as the Archean. The depositional settings, microbial community and mineralogical composition vary significantly as no two settings are identical. The common thread linking all of the settings is that evaporation exceeds precipitation resulting in elevated concentrations of cations and anions that are higher than in oceanic systems. The Dead Sea and Storrs Lake are examples of two diverse modern evaporitic settings as the former is below sea level and the latter is a coastal lake on an island in the Caribbean. Each system varies in water chemistry asmore » the Dead Sea dissolved ions originate from surface weathered materials, springs, and aquifers while Storrs Lake dissolved ion concentration is primarily derived from sea water. Consequently some of the ions, i.e., Sr, Ba are found at significantly lower concentrations in Storrs Lake than in the Dead Sea. The origin of the dissolved ions are ultimately responsible for the pH of each system, alkaline versus mildly acidic. Each system exhibits unique biogeochemical properties as the extreme environments select certain microorganisms. Storrs Lake possesses significant biofilms and stromatolitic deposits and the alkalinity varies depending on rainfall and storm activity. The microbial community Storrs Lake is much more diverse and active than those observed in the Dead Sea. The Dead Sea waters are mildly acidic, lack stromatolites, and possess a lower density of microbial populations. The general absence of microbial and biofilm fossilization is due to the depletion of HCO{sub 3} and slightly acidic pH.« less

Mnemiopsis leidyi Gut Harbors Seasonally Variant and Commensal Microbial Assemblages

NASA Astrophysics Data System (ADS)

Mariita, R. M.; Hossain, M. J.; Liles, M. R.; Moss, A.

2016-02-01

Studies have shown that with widespread use of antibiotics in human and domestic animal populations, antibiotic resistance becomes increasingly common in the environment. Estuaries provide ideal conditions for acquisition and dissemination of drug resistance genes because they serve as sinks for pollution. This study aimed to identify M. leidyi microbial diversity and richness and their potential to act as vectors for antibiotic resistance determinants (ARDs). M. leidyi, although native to study area are highly invasive. Metagenomic analyses indicate that there are temporal variations of bacterioplankton assemblages in M. leidyi gut. Overall, Proteobacteria and Actinobacteria are the most abundant phyla. Despite the temporal dynamics in the microbial assemblages in M. leidyi gut, they seem to retain Propionibacterium acnes (gut microbiota in some insects) and select proteobacteria across all seasons. The results contradict previous studies that suggest that M. leidyi does not have constant a microbiota, but only seasonally variant microbial assemblages. Here we reveal the presence of M. leidyi gut ARDs in winter and summer, probably because of the ctenophores' positive geotaxis during rough surface conditions. Genes responsible for resistance to fluoroquinolones, multidrug resistance efflux pumps, mercuric reductase, copper homeostasis and blaR1 genes were observed. This is the first study to demonstrate that M. leidyi harbors constant microbiota and provides a baseline for understanding M. leidyi gut microbial and ARDs ecology. It also suggests that M. leidyi bacterial taxonomic and functional dynamics is influenced by season. Funding: Alabama EPSCoR GRSP fellowship, AU-CMB fellowship, NSF EPS-1158862, USDA-Hatch 370225-310100 (AGM, ML).

Investigating bacterial populations in styrene-degrading biofilters by 16S rDNA tag pyrosequencing.

PubMed

Portune, Kevin J; Pérez, M Carmen; Álvarez-Hornos, F Javier; Gabaldón, Carmen

2015-01-01

Microbial biofilms are essential components in the elimination of pollutants within biofilters, yet still little is known regarding the complex relationships between microbial community structure and biodegradation function within these engineered ecosystems. To further explore this relationship, 16S rDNA tag pyrosequencing was applied to samples taken at four time points from a styrene-degrading biofilter undergoing variable operating conditions. Changes in microbial structure were observed between different stages of biofilter operation, and the level of styrene concentration was revealed to be a critical factor affecting these changes. Bacterial genera Azoarcus and Pseudomonas were among the dominant classified genera in the biofilter. Canonical correspondence analysis (CCA) and correlation analysis revealed that the genera Brevundimonas, Hydrogenophaga, and Achromobacter may play important roles in styrene degradation under increasing styrene concentrations. No significant correlations (P > 0.05) could be detected between biofilter operational/functional parameters and biodiversity measurements, although biological heterogeneity within biofilms and/or technical variability within pyrosequencing may have considerably affected these results. Percentages of selected bacterial taxonomic groups detected by fluorescence in situ hybridization (FISH) were compared to results from pyrosequencing in order to assess the effectiveness and limitations of each method for identifying each microbial taxon. Comparison of results revealed discrepancies between the two methods in the detected percentages of numerous taxonomic groups. Biases and technical limitations of both FISH and pyrosequencing, such as the binding of FISH probes to non-target microbial groups and lack of classification of sequences for defined taxonomic groups from pyrosequencing, may partially explain some differences between the two methods.

Prospects of Astromicrobiology

NASA Astrophysics Data System (ADS)

Galchenko, Valery

Accepting the potential for carbon-based extraterrestrial life as an axiom, the scientific commu-nity has assigned the task of obtaining supportive evidence. Since planetary life is dependent on microbial activity, the evidence gathering activities should include missions and sampling for obtaining of the microbial component. These are several tasks that may need to be ad-dressed in the case of successful sampling: (1) detection of microbial cells by direct methods; (2) updating of the methods used for revival (reactivation) of microorganisms when carrying out studies under a special regime; (3) strengthening of the quarantine and sanitary control to ensure proper deactivation of microorganisms that may be present in samples collected and returned to Earth. These problems could be successfully solved by an adequate selection of model objects. The forms and mechanisms of long-time (several hundred thousand years) sur-vival of microorganisms in such extreme ecological niches as tundra permafrost and Antarctic lakes are the most complete analogue of those of extraterrestrial microorganisms that may be found in return samples. Samples of terrestrial micro-and macroorganisms that survived long exposure (up to 3 years) to the space environment ("Phobos-Grunt" Sample Return Mission) can be considered an alternative model. The following statements based on our previous data deserve high attention: -The high level of heterogeneity of microbial populations that sur-vived in space with respect to the intensity of their hypometabolic (anabiotic) response should be taken into consideration. This assumes the application of revival methods for reactivation of resting cells. -The conditions favorable for cell germination, reactivation, and subsequent division may differ. The selection and application of low-molecular-weight compounds with cytokine activity (cytokinins) show considerable promise. -Microbial populations develop as unique multicellular organisms, which determines the applicability of cultivation methods for detection of microorganisms in the presence of low-molecular-weight compounds with the cu-mulative function and adaptogenic properties. -During the germination of surviving cells, "stress induced by the new environment and changes in the physiological status" is observed, which requires soft conditions and the use of stress protector and antioxidants. -The virulence and pathogenicity of microorganisms develop and manifest only as a result of the long-term co-evolution of microorganisms and host macroorganisms, or bacteriophages and host microor-ganisms. No mutations of an admittedly nonpathogenic microorganism, and in the absence of a potential victim of the disease, can make this microorganism pathogenic. To detect microbial cells by direct methods, we may recommend to take the following aspects into consideration: -characteristic traits of the ultrastructure of surviving (resting) cells; -characteristic profiles of biogenic elements, which distinguish cells from biomorphs; -specific dyes. Deactivation of microorganisms in accordance with the quarantine requirements may be achieved via the use of an original technique of "cell mummification". This technique works well with the methods used to solve the above-stated problems. A mummified cell (micromummy) retains its morpho-logical intactness and characteristic ultrastructure (except for the membrane structure), which allows us to identify this cell as a microorganism (microbial cell).

Connectivity of microbial populations in coral reef environments: microbiomes of sediment, fish and water

NASA Astrophysics Data System (ADS)

Biddle, J.; Leon, Z. R.; McCargar, M.; Drew, J.

2016-12-01

The benthic environments of coral reefs are heavily shaped by physiochemical factors, but also the ecological interactions of the animals and plants in the reef ecosystem. Microbial populations may be shared between the ecosystem of sediments, seagrasses and reef fish, however it is unknown to what degree. We investigated the potential connections between the microbiomes of sediments, seagrass blades and roots (Syringodium isoetifolium), Surgeonfish (A. nigricauda, Acanthurinae sp. unknown, C. striatus) and Parrotfish (C. spinidens) guts in reef areas of Fiji. We contrasted these with sediment samples from the Florida Keys and ocean water microbiomes from the Atlantic, Pacific and Indian Oceans. In general, we see a higher diversity of sediment microbial communities in Fiji compared to the Florida Keys. However, many of the same taxa are shared in these chemically similar environments, whereas the ocean water environments are completely distinct with few overlapping groups. We were able to show connectivity of a core microbiome between seagrass, fish and sediments in Fiji, including identifying a potential environmental reservoir of a surgeonfish symbiont, Epulopiscum. Finally, we show that fish guts have different microbial populations from crop to hindgut, and that microbial populations differ based on food source. The connection of these ecosystems suggest that the total microbiome of these environments may vary as their animal inhabitants shift in a changing ocean.

Invited review: Essential oils as modifiers of rumen microbial fermentation.

PubMed

Calsamiglia, S; Busquet, M; Cardozo, P W; Castillejos, L; Ferret, A

2007-06-01

Microorganisms in the rumen degrade nutrients to produce volatile fatty acids and synthesize microbial protein as an energy and protein supply for the ruminant, respectively. However, this fermentation process has energy (losses of methane) and protein (losses of ammonia N) inefficiencies that may limit production performance and contribute to the release of pollutants to the environment. Antibiotic ionophores have been very successful in reducing these energy and protein losses in the rumen, but the use of antibiotics in animal feeds is facing reduced social acceptance, and their use has been banned in the European Union since January 2006. For this reason, scientists have become interested in evaluating other alternatives to control specific microbial populations to modulate rumen fermentation. Essential oils can interact with microbial cell membranes and inhibit the growth of some gram-positive and gram-negative bacteria. As a result of such inhibition, the addition of some plant extracts to the rumen results in an inhibition of deamination and methanogenesis, resulting in lower ammonia N, methane, and acetate, and in higher propionate and butyrate concentrations. Results have indicated that garlic oil, cinnamaldehyde (the main active component of cinnamon oil), eugenol (the main active component of the clove bud), capsaicin (the active component of hot peppers), and anise oil, among others, may increase propionate production, reduce acetate or methane production, and modify proteolysis, peptidolysis, or deamination in the rumen. However, the effects of some of these essential oils are pH and diet dependent, and their use may be beneficial only under specific conditions and production systems. For example, capsaicin appears to have small effects in high-forage diets, whereas the changes observed in high-concentrate diets (increases in dry matter intake and total VFA, and reduction in the acetateto-propionate ratio and ammonia N concentration) may be beneficial. Because plant extracts may act at different levels in the carbohydrate and protein degradation pathways, their careful selection and combination may provide a useful tool to manipulate rumen microbial fermentation effectively. However, additional research is required to establish the optimal dose in vivo in units of the active component, to consider the potential adaptation of microbial populations to their activities, to examine the presence of residues in the products (milk or meat), and to demonstrate improvements in animal performance.

CRISPR Associated Diversity within a Population of Sulfolobus islandicus

PubMed Central

Held, Nicole L.; Herrera, Alfa; Cadillo-Quiroz, Hinsby; Whitaker, Rachel J.

2010-01-01

Background Predator-prey models for virus-host interactions predict that viruses will cause oscillations of microbial host densities due to an arms race between resistance and virulence. A new form of microbial resistance, CRISPRs (clustered regularly interspaced short palindromic repeats) are a rapidly evolving, sequence-specific immunity mechanism in which a short piece of invading viral DNA is inserted into the host's chromosome, thereby rendering the host resistant to further infection. Few studies have linked this form of resistance to population dynamics in natural microbial populations. Methodology/Principal Findings We examined sequence diversity in 39 strains of the archeaon Sulfolobus islandicus from a single, isolated hot spring from Kamchatka, Russia to determine the effects of CRISPR immunity on microbial population dynamics. First, multiple housekeeping genetic markers identify a large clonal group of identical genotypes coexisting with a diverse set of rare genotypes. Second, the sequence-specific CRISPR spacer arrays split the large group of isolates into two very different groups and reveal extensive diversity and no evidence for dominance of a single clone within the population. Conclusions/Significance The evenness of resistance genotypes found within this population of S. islandicus is indicative of a lack of strain dominance, in contrast to the prediction for a resistant strain in a simple predator-prey interaction. Based on evidence for the independent acquisition of resistant sequences, we hypothesize that CRISPR mediated clonal interference between resistant strains promotes and maintains diversity in this natural population. PMID:20927396

Shape recognition of microbial cells by colloidal cell imprints

NASA Astrophysics Data System (ADS)

Borovička, Josef; Stoyanov, Simeon D.; Paunov, Vesselin N.

2013-08-01

We have engineered a class of colloids which can recognize the shape and size of targeted microbial cells and selectively bind to their surfaces. These imprinted colloid particles, which we called ``colloid antibodies'', were fabricated by partial fragmentation of silica shells obtained by templating the targeted microbial cells. We successfully demonstrated the shape and size recognition between such colloidal imprints and matching microbial cells. High percentage of binding events of colloidal imprints with the size matching target particles was achieved. We demonstrated selective binding of colloidal imprints to target microbial cells in a binary mixture of cells of different shapes and sizes, which also resulted in high binding selectivity. We explored the role of the electrostatic interactions between the target cells and their colloid imprints by pre-coating both of them with polyelectrolytes. Selective binding occurred predominantly in the case of opposite surface charges of the colloid cell imprint and the targeted cells. The mechanism of the recognition is based on the amplification of the surface adhesion in the case of shape and size match due to the increased contact area between the target cell and the colloidal imprint. We also tested the selective binding for colloid imprints of particles of fixed shape and varying sizes. The concept of cell recognition by colloid imprints could be used for development of colloid antibodies for shape-selective binding of microbes. Such colloid antibodies could be additionally functionalized with surface groups to enhance their binding efficiency to cells of specific shape and deliver a drug payload directly to their surface or allow them to be manipulated using external fields. They could benefit the pharmaceutical industry in developing selective antimicrobial therapies and formulations.

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.

Effect of sulfur supplements on cellulolytic rumen micro-organisms and microbial protein synthesis in cattle fed a high fibre diet.

PubMed

McSweeney, C S; Denman, S E

2007-11-01

To examine the effect of sulfur-containing compounds on the growth of anaerobic rumen fungi and the fibrolytic rumen bacteria Ruminococcus albus, Ruminococcus flavefaciens and Fibrobacter succinogenes in pure culture and within the cattle rumen. The effect of two reduced sulfur compounds, 3-mercaptopropionic acid (MPA) or 3-mercapto-1-propanesulfonic acid as the sole S source on growth of pure fibroyltic fungal and bacterial cultures showed that these compounds were capable of sustaining growth. An in vivo trial was then conducted to determine the effect of sulfur supplements (MPA and sodium sulfate) on microbial population dynamics in cattle fed the roughage Dichanthium aristatum. Real-time PCR showed significant increases in fibrolytic bacterial and fungal populations when cattle were supplemented with these compounds. Sulfate supplementation leads to an increase in dry matter intake without a change in whole tract dry matter digestibility. Supplementation of low S-containing diets with either sodium sulfate or MPA stimulates microbial growth with an increase in rumen microbial protein supply to the animal. Through the use of real-time PCR monitoring, a better understanding of the effect of S supplementation on discrete microbial populations within the rumen is provided.

Experience matters: prior exposure to plant toxins enhances diversity of gut microbes in herbivores.

PubMed

Kohl, Kevin D; Dearing, M D

2012-09-01

For decades, ecologists have hypothesised that exposure to plant secondary compounds (PSCs) modifies herbivore-associated microbial community composition. This notion has not been critically evaluated in wild mammalian herbivores on evolutionary timescales. We investigated responses of the microbial communities of two woodrat species (Neotoma bryanti and N. lepida). For each species, we compared experienced populations that independently converged to feed on the same toxic plant (creosote bush, Larrea tridentata) to naïve populations with no exposure to creosote toxins. The addition of dietary PSCs significantly altered gut microbial community structure, and the response was dependent on previous experience. Microbial diversity and relative abundances of several dominant phyla increased in experienced woodrats in response to PSCs; however, opposite effects were observed in naïve woodrats. These differential responses were convergent in experienced populations of both species. We hypothesise that adaptation of the foregut microbiota to creosote PSCs in experienced woodrats drives this differential response. © 2012 Blackwell Publishing Ltd/CNRS.

Microbial consortia at steady supply

PubMed Central

Taillefumier, Thibaud; Posfai, Anna; Meir, Yigal; Wingreen, Ned S

2017-01-01

Metagenomics has revealed hundreds of species in almost all microbiota. In a few well-studied cases, microbial communities have been observed to coordinate their metabolic fluxes. In principle, microbes can divide tasks to reap the benefits of specialization, as in human economies. However, the benefits and stability of an economy of microbial specialists are far from obvious. Here, we physically model the population dynamics of microbes that compete for steadily supplied resources. Importantly, we explicitly model the metabolic fluxes yielding cellular biomass production under the constraint of a limited enzyme budget. We find that population dynamics generally leads to the coexistence of different metabolic types. We establish that these microbial consortia act as cartels, whereby population dynamics pins down resource concentrations at values for which no other strategy can invade. Finally, we propose that at steady supply, cartels of competing strategies automatically yield maximum biomass, thereby achieving a collective optimum. DOI: http://dx.doi.org/10.7554/eLife.22644.001 PMID:28473032

Cancer in light of experimental evolution.

PubMed

Sprouffske, Kathleen; Merlo, Lauren M F; Gerrish, Philip J; Maley, Carlo C; Sniegowski, Paul D

2012-09-11

Cancer initiation, progression, and the emergence of therapeutic resistance are evolutionary phenomena of clonal somatic cell populations. Studies in microbial experimental evolution and the theoretical work inspired by such studies are yielding deep insights into the evolutionary dynamics of clonal populations, yet there has been little explicit consideration of the relevance of this rapidly growing field to cancer biology. Here, we examine how the understanding of mutation, selection, and spatial structure in clonal populations that is emerging from experimental evolution may be applicable to cancer. Along the way, we discuss some significant ways in which cancer differs from the model systems used in experimental evolution. Despite these differences, we argue that enhanced prediction and control of cancer may be possible using ideas developed in the context of experimental evolution, and we point out some prospects for future research at the interface between these traditionally separate areas. Copyright © 2012 Elsevier Ltd. All rights reserved.

Cancer in Light of Experimental Evolution

PubMed Central

Sprouffske, Kathleen; Merlo, Lauren M.F.; Gerrish, Philip J.; Maley, Carlo C.; Sniegowski, Paul D.

2012-01-01

Cancer initiation, progression, and the emergence of therapeutic resistance are evolutionary phenomena of clonal somatic cell populations. Studies in microbial experimental evolution and the theoretical work inspired by such studies are yielding deep insights into the evolutionary dynamics of clonal populations, yet there has been little explicit consideration of the relevance of this rapidly growing field to cancer biology. Here, we examine how the understanding of mutation, selection, and spatial structure in clonal populations that is emerging from experimental evolution may be applicable to cancer. Along the way, we discuss some significant ways in which cancer differs from the model systems used in experimental evolution. Despite these differences, we argue that enhanced prediction and control of cancer may be possible using ideas developed in the context of experimental evolution, and we point out some prospects for future research at the interface between these traditionally separate areas. PMID:22975007

Microbiota of the major South Atlantic reef building coral Mussismilia.

PubMed

Fernando, Samodha C; Wang, Jia; Sparling, Kimberly; Garcia, Gizele D; Francini-Filho, Ronaldo B; de Moura, Rodrigo L; Paranhos, Rodolfo; Thompson, Fabiano L; Thompson, Janelle R

2015-02-01

The Brazilian endemic scleractinian corals, genus Mussismilia, are among the main reef builders of the South Atlantic and are threatened by accelerating rates of disease. To better understand how holobiont microbial populations interact with corals during health and disease and to evaluate whether selective pressures in the holobiont or neutral assembly shape microbial composition, we have examined the microbiota structure of Mussismilia corals according to coral lineage, environment, and disease/health status. Microbiota of three Mussismilia species (Mussismilia harttii, Mussismilia hispida, and Mussismilia braziliensis) was compared using 16S rRNA pyrosequencing and clone library analysis of coral fragments. Analysis of biological triplicates per Mussismilia species and reef site allowed assessment of variability among Mussismilia species and between sites for M. braziliensis. From 173,487 V6 sequences, 6,733 coral- and 1,052 water-associated operational taxonomic units (OTUs) were observed. M. braziliensis microbiota was more similar across reefs than to other Mussismilia species microbiota from the same reef. Highly prevalent OTUs were more significantly structured by coral lineage and were enriched in Alpha- and Gammaproteobacteria. Bacterial OTUs from healthy corals were recovered from a M. braziliensis skeleton sample at twice the frequency of recovery from water or a diseased coral suggesting the skeleton is a significant habitat for microbial populations in the holobiont. Diseased corals were enriched with pathogens and opportunists (Vibrios, Bacteroidetes, Thalassomonas, and SRB). Our study examines for the first time intra- and inter-specific variability of microbiota across the genus Mussismilia. Changes in microbiota may be useful indicators of coral health and thus be a valuable tool for coral reef management and conservation.

Microbial community and treatment ability investigation in AOAO process for the optoelectronic wastewater treatment using PCR-DGGE biotechnology.

PubMed

Chen, Hsi-Jien; Lin, Yi-Zi; Fanjiang, Jen-Mao; Fan, Chihhao

2013-04-01

This study aimed to explore the microbial community variation and treatment ability of a full-scale anoxic-aerobic-anoxic-aerobic (AOAO) process used for optoelectronic wastewater treatment. The sludge samples in the biological treatment units were collected and subsequently subjected to polymerase chain reaction (PCR) amplification and denaturing gradient gel electrophoresis identification and the wastewater components such as BOD5 and NH3-N were evaluated during the processes. The group specific primers selected were targeting at the kingdom Bacteria, the Acidobacterium, the α-proteobacteria, the β-proteobacteria ammonia oxidizers, Actinobacteria and methyllotrophs, and the 16S rDNA clone libraries were established. Ten different clones were obtained using the Bacteria primers and eight different clones were obtained using the β-proteobacteria ammonia oxidizer primers. Over 95 % of BOD5 and 90 % of NH3-N were removed from the system. The microbial community analysis showed that the Janthinobacterium sp. An8 and Nitrosospira sp. were the dominant species throughout the AOAO process. Across the whole clone library, six clones showed closely related to Janthinobacterium sp. and these species seemed to be the dominant species with more than 50 % occupancy of the total population. Nitrosospira sp. was the predominant species within the β-proteobacteria and occupied more than 30 % of the total population in the system. These two strains were the novel species specific to the AOAO process for optoelectronic treatment, and they were found strongly related to the system capability of removing aquatic contaminants by inspecting the wastewater concentration variation across the system.

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

PubMed

Larsen, Peter; Hamada, Yuki; Gilbert, Jack

2012-07-31

Never has there been a greater opportunity for investigating microbial communities. Not only are the profound effects of microbial ecology on every aspect of Earth's geochemical cycles beginning to be understood, but also the analytical and computational tools for investigating microbial Earth are undergoing a rapid revolution. This environmental microbial interactome, the system of interactions between the microbiome and the environment, has shaped the planet's past and will undoubtedly continue to do so in the future. We review recent approaches for modeling microbial community structures and the interactions of microbial populations with their environments. Different modeling approaches consider the environmental microbial interactome from different aspects, and each provides insights to different facets of microbial ecology. We discuss the challenges and opportunities for the future of microbial modeling and describe recent advances in microbial community modeling that are extending current descriptive technologies into a predictive science. Copyright © 2012 Elsevier B.V. All rights reserved.

Identification, Comparison, and Validation of Robust Rumen Microbial Biomarkers for Methane Emissions Using Diverse Bos Taurus Breeds and Basal Diets

PubMed Central

Auffret, Marc D.; Stewart, Robert; Dewhurst, Richard J.; Duthie, Carol-Anne; Rooke, John A.; Wallace, Robert J.; Freeman, Tom C.; Snelling, Timothy J.; Watson, Mick; Roehe, Rainer

2018-01-01

Previous shotgun metagenomic analyses of ruminal digesta identified some microbial information that might be useful as biomarkers to select cattle that emit less methane (CH4), which is a potent greenhouse gas. It is known that methane production (g/kgDMI) and to an extent the microbial community is heritable and therefore biomarkers can offer a method of selecting cattle for low methane emitting phenotypes. In this study a wider range of Bos Taurus cattle, varying in breed and diet, was investigated to determine microbial communities and genetic markers associated with high/low CH4 emissions. Digesta samples were taken from 50 beef cattle, comprising four cattle breeds, receiving two basal diets containing different proportions of concentrate and also including feed additives (nitrate or lipid), that may influence methane emissions. A combination of partial least square analysis and network analysis enabled the identification of the most significant and robust biomarkers of CH4 emissions (VIP > 0.8) across diets and breeds when comparing all potential biomarkers together. Genes associated with the hydrogenotrophic methanogenesis pathway converting carbon dioxide to methane, provided the dominant biomarkers of CH4 emissions and methanogens were the microbial populations most closely correlated with CH4 emissions and identified by metagenomics. Moreover, these genes grouped together as confirmed by network analysis for each independent experiment and when combined. Finally, the genes involved in the methane synthesis pathway explained a higher proportion of variation in CH4 emissions by PLS analysis compared to phylogenetic parameters or functional genes. These results confirmed the reproducibility of the analysis and the advantage to use these genes as robust biomarkers of CH4 emissions. Volatile fatty acid concentrations and ratios were significantly correlated with CH4, but these factors were not identified as robust enough for predictive purposes. Moreover, the methanotrophic Methylomonas genus was found to be negatively correlated with CH4. Finally, this study confirmed the importance of using robust and applicable biomarkers from the microbiome as a proxy of CH4 emissions across diverse production systems and environments. PMID:29375511

Identification, Comparison, and Validation of Robust Rumen Microbial Biomarkers for Methane Emissions Using Diverse Bos Taurus Breeds and Basal Diets.

PubMed

Auffret, Marc D; Stewart, Robert; Dewhurst, Richard J; Duthie, Carol-Anne; Rooke, John A; Wallace, Robert J; Freeman, Tom C; Snelling, Timothy J; Watson, Mick; Roehe, Rainer

2017-01-01

Previous shotgun metagenomic analyses of ruminal digesta identified some microbial information that might be useful as biomarkers to select cattle that emit less methane (CH 4 ), which is a potent greenhouse gas. It is known that methane production (g/kgDMI) and to an extent the microbial community is heritable and therefore biomarkers can offer a method of selecting cattle for low methane emitting phenotypes. In this study a wider range of Bos Taurus cattle, varying in breed and diet, was investigated to determine microbial communities and genetic markers associated with high/low CH 4 emissions. Digesta samples were taken from 50 beef cattle, comprising four cattle breeds, receiving two basal diets containing different proportions of concentrate and also including feed additives (nitrate or lipid), that may influence methane emissions. A combination of partial least square analysis and network analysis enabled the identification of the most significant and robust biomarkers of CH 4 emissions (VIP > 0.8) across diets and breeds when comparing all potential biomarkers together. Genes associated with the hydrogenotrophic methanogenesis pathway converting carbon dioxide to methane, provided the dominant biomarkers of CH 4 emissions and methanogens were the microbial populations most closely correlated with CH 4 emissions and identified by metagenomics. Moreover, these genes grouped together as confirmed by network analysis for each independent experiment and when combined. Finally, the genes involved in the methane synthesis pathway explained a higher proportion of variation in CH 4 emissions by PLS analysis compared to phylogenetic parameters or functional genes. These results confirmed the reproducibility of the analysis and the advantage to use these genes as robust biomarkers of CH 4 emissions. Volatile fatty acid concentrations and ratios were significantly correlated with CH 4 , but these factors were not identified as robust enough for predictive purposes. Moreover, the methanotrophic Methylomonas genus was found to be negatively correlated with CH 4 . Finally, this study confirmed the importance of using robust and applicable biomarkers from the microbiome as a proxy of CH 4 emissions across diverse production systems and environments.

Seasonal hyporheic dynamics control coupled microbiology and geochemistry in Colorado River sediments

DOE PAGES

Danczak, Robert E.; Sawyer, Audrey H.; Williams, Kenneth H.; ...

2016-12-03

Riverbed microbial communities play an oversized role in many watershed ecosystem functions, including the processing of organic carbon, cycling of nitrogen, and alterations to metal mobility. The structure and activity of microbial assemblages depend in part on geochemical conditions set by river-groundwater exchange or hyporheic exchange. In order to assess how seasonal changes in river-groundwater mixing affect these populations in a snowmelt-dominated fluvial system, vertical sediment and pore water profiles were sampled at three time points at one location in the hyporheic zone of the Colorado River and analyzed by using geochemical measurements, 16S rRNA gene sequencing, and ecological modeling.more » Oxic river water penetrated deepest into the subsurface during peak river discharge, while under base flow conditions, anoxic groundwater dominated shallower depths. Over a 70 cm thick interval, riverbed sediments were therefore exposed to seasonally fluctuating redox conditions and hosted microbial populations statistically different from those at both shallower and deeper locations. Additionally, microbial populations within this zone were shown to be the most dynamic across sampling time points, underlining the critical role that hyporheic mixing plays in constraining microbial abundances. Given such mixing effects, we anticipate that future changes in river discharge in mountainous, semiarid western U.S. watersheds may affect microbial community structure and function in riverbed environments, with potential implications for biogeochemical processes in riparian regions.« less

Seasonal hyporheic dynamics control coupled microbiology and geochemistry in Colorado River sediments

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

Danczak, Robert E.; Sawyer, Audrey H.; Williams, Kenneth H.

Riverbed microbial communities play an oversized role in many watershed ecosystem functions, including the processing of organic carbon, cycling of nitrogen, and alterations to metal mobility. The structure and activity of microbial assemblages depend in part on geochemical conditions set by river-groundwater exchange or hyporheic exchange. In order to assess how seasonal changes in river-groundwater mixing affect these populations in a snowmelt-dominated fluvial system, vertical sediment and pore water profiles were sampled at three time points at one location in the hyporheic zone of the Colorado River and analyzed by using geochemical measurements, 16S rRNA gene sequencing, and ecological modeling.more » Oxic river water penetrated deepest into the subsurface during peak river discharge, while under base flow conditions, anoxic groundwater dominated shallower depths. Over a 70 cm thick interval, riverbed sediments were therefore exposed to seasonally fluctuating redox conditions and hosted microbial populations statistically different from those at both shallower and deeper locations. Additionally, microbial populations within this zone were shown to be the most dynamic across sampling time points, underlining the critical role that hyporheic mixing plays in constraining microbial abundances. Given such mixing effects, we anticipate that future changes in river discharge in mountainous, semiarid western U.S. watersheds may affect microbial community structure and function in riverbed environments, with potential implications for biogeochemical processes in riparian regions.« less

Seasonal hyporheic dynamics control coupled microbiology and geochemistry in Colorado River sediments

NASA Astrophysics Data System (ADS)

Danczak, Robert E.; Sawyer, Audrey H.; Williams, Kenneth H.; Stegen, James C.; Hobson, Chad; Wilkins, Michael J.

2016-12-01

Riverbed microbial communities play an oversized role in many watershed ecosystem functions, including the processing of organic carbon, cycling of nitrogen, and alterations to metal mobility. The structure and activity of microbial assemblages depend in part on geochemical conditions set by river-groundwater exchange or hyporheic exchange. To assess how seasonal changes in river-groundwater mixing affect these populations in a snowmelt-dominated fluvial system, vertical sediment and pore water profiles were sampled at three time points at one location in the hyporheic zone of the Colorado River and analyzed by using geochemical measurements, 16S rRNA gene sequencing, and ecological modeling. Oxic river water penetrated deepest into the subsurface during peak river discharge, while under base flow conditions, anoxic groundwater dominated shallower depths. Over a 70 cm thick interval, riverbed sediments were therefore exposed to seasonally fluctuating redox conditions and hosted microbial populations statistically different from those at both shallower and deeper locations. Additionally, microbial populations within this zone were shown to be the most dynamic across sampling time points, underlining the critical role that hyporheic mixing plays in constraining microbial abundances. Given such mixing effects, we anticipate that future changes in river discharge in mountainous, semiarid western U.S. watersheds may affect microbial community structure and function in riverbed environments, with potential implications for biogeochemical processes in riparian regions.

Stochastic Assembly of Bacteria in Microwell Arrays Reveals the Importance of Confinement in Community Development

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

Hansen, Ryan H.; Timm, Andrea C.; Timm, Collin M.

The structure, function and evolving composition of microbial communities is deeply influenced by the physical and chemical architecture of the local microenvironment. The complexity of this parameter space in naturally occurring systems has made a clear understanding of the key drivers of community development elusive. Here, we examine the role of spatial confinement on community development using a microwell platform that allows for assembly and monitoring of unique microbial communities en masse. This platform was designed to contain microwells with varied size features in order to mimic various levels of spatial confinement found in natural systems. Microbial populations assembled inmore » wells with incrementally smaller size features showed increasingly larger variations in inoculum levels. By exploiting this size dependence, large wells were used to assemble homogenous initial populations of Pseudomonas aeruginosa, allowing for reproducible, directed growth trajectories. In contrast, smaller wells were used to assemble a heterogeneous range of initial populations, resulting in a variety of growth and decay trajectories. This allowed for parallel screening of single member communities across different levels of confinement to identify initial conditions in which P. aeruginosa colonies have dramatically higher probabilities of survival. These results demonstrate a unique approach for manipulating the distribution of initial microbial populations assembled into controlled microenvironments to rapidly identify population and environmental parameters conducive or inhibitive to growth. Additionally, multi-member community assembly was characterized to demonstrate the power of this platform for studying the role of member abundance on microbial competition, mutualism and community succession.« less

Stochastic Assembly of Bacteria in Microwell Arrays Reveals the Importance of Confinement in Community Development

DOE PAGES

Hansen, Ryan H.; Timm, Andrea C.; Timm, Collin M.; ...

2016-05-06

The structure, function and evolving composition of microbial communities is deeply influenced by the physical and chemical architecture of the local microenvironment. The complexity of this parameter space in naturally occurring systems has made a clear understanding of the key drivers of community development elusive. Here, we examine the role of spatial confinement on community development using a microwell platform that allows for assembly and monitoring of unique microbial communities en masse. This platform was designed to contain microwells with varied size features in order to mimic various levels of spatial confinement found in natural systems. Microbial populations assembled inmore » wells with incrementally smaller size features showed increasingly larger variations in inoculum levels. By exploiting this size dependence, large wells were used to assemble homogenous initial populations of Pseudomonas aeruginosa, allowing for reproducible, directed growth trajectories. In contrast, smaller wells were used to assemble a heterogeneous range of initial populations, resulting in a variety of growth and decay trajectories. This allowed for parallel screening of single member communities across different levels of confinement to identify initial conditions in which P. aeruginosa colonies have dramatically higher probabilities of survival. These results demonstrate a unique approach for manipulating the distribution of initial microbial populations assembled into controlled microenvironments to rapidly identify population and environmental parameters conducive or inhibitive to growth. Additionally, multi-member community assembly was characterized to demonstrate the power of this platform for studying the role of member abundance on microbial competition, mutualism and community succession.« less

Effects of chitosan-essential oil coatings on safety and quality of fresh blueberries.

PubMed

Sun, Xiuxiu; Narciso, Jan; Wang, Zhe; Ference, Christopher; Bai, Jinhe; Zhou, Kequan

2014-05-01

Chitosan coating plus different essential oils was developed and applied to fresh blueberries in order to find more natural treatments to preserve fresh fruit quality and safety during postharvest storage. Studies were 1st performed in vitro where wild-type Escherichia coli and Penicillium digitatum were grown in suitable media, and then subjected to 6 essential oils. Three compounds, carvacrol (CAR), cinnamaldehyde (CIN), and trans-cinnamaldehyde (ECIN) had high antimicrobial capacity and were selected for an in vivo study for postharvest storage of blueberries. The selected essential oils, 0.5% each, were added into a chitosan solution and coated on fresh blueberries. After storage at 5, 10, and 20 °C for various days, fruit firmness and microbial populations were evaluated. The chitosan coating substantially decreased bacteria and yeasts/molds on the fruit, and all 3 essential oils added to the antimicrobial activities. Further dosage experiments showed that the antimicrobial activity remained even when lowering CAR concentration to 0.1% and ECIN to 0.2%. Chitosan, CAR, and ECIN also maintained fruit firmness. Our results suggest that chitosan coatings containing essential oils are effective in extending the shelf life of fresh blueberries. Blueberries are high-value fruit with strong antioxidant capacity and other health-promoting benefits. However, microbial food safety is an increasing concern, and decay and softening limits their storability. A combination of ≥ 0.1% CAR or ≥ 0.2% ECIN with a chitosan coating effectively reduced softening of fresh berries and decay by inhibiting microbial growth. © 2014 Institute of Food Technologists®

Microbial Populations in Two Swamp Soils of South Carolina

Treesearch

David S. Priester; William R. Harms

1971-01-01

Microbial populations were counted in agar-plated samples of two swamp soils collected in summer and winter. Number of aerobic and anaerobic microorganisms differed significantly among the soils and between seasons. Alluvial soil from the river swamp was high in organic matter, N, K, Ca, and pH and averaged 88 million microorganisms per gram over the growing season....

Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platform (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

ScienceCinema

Tremblay, Julien

2018-01-22

Julien Tremblay from DOE JGI presents "Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platorm" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platform (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

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

Tremblay, Julien

2012-06-01

Julien Tremblay from DOE JGI presents "Evaluation of Multiplexed 16S rRNA Microbial Population Surveys Using Illumina MiSeq Platorm" at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

In situ determination of the effects of lead and copper on cyanobacterial populations in microcosms.

PubMed

Burnat, Mireia; Diestra, Elia; Esteve, Isabel; Solé, Antonio

2009-07-10

Biomass has been studied as biomarker to evaluate the effect of heavy metals on microbial communities. Nevertheless, the most important methodological problem when working with natural and artificial microbial mats is the difficulty to evaluate changes produced on microorganism populations that are found in thicknesses of just a few mm depth. Here, we applied for first time a recently published new method based on confocal laser scanning microscopy and image-program analysis to determine in situ the effect of Pb and Cu stress in cyanobacterial populations. The results showed that both in the microcosm polluted by Cu and by Pb, a drastic reduction in total biomass for cyanobacterial and Microcoleus sp. (the dominant filamentous cyanobacterium in microbial mats) was detected within a week. According to the data presented in this report, this biomass inspection has a main advantage: besides total biomass, diversity, individual biomass of each population and their position can be analysed at microscale level. CLSM-IA could be a good method for analyzing changes in microbial biomass as a response to the addition of heavy metals and also to other kind of pollutants.

Unusual bacterioplankton community structure in ultra-oligotrophic Crater Lake

USGS Publications Warehouse

Urbach, Ena; Vergin, Kevin L.; Morse, Ariel

2001-01-01

The bacterioplankton assemblage in Crater Lake, Oregon (U.S.A.), is different from communities found in other oxygenated lakes, as demonstrated by four small subunit ribosomal ribonucleic acid (SSU rRNA) gene clone libraries and oligonucleotide probe hybridization to RNA from lake water. Populations in the euphotic zone of this deep (589 m), oligotrophic caldera lake are dominated by two phylogenetic clusters of currently uncultivated bacteria: CL120-10, a newly identified cluster in the verrucomicrobiales, and ACK4 actinomycetes, known as a minor constituent of bacterioplankton in other lakes. Deep-water populations at 300 and 500 m are dominated by a different pair of uncultivated taxa: CL500-11, a novel cluster in the green nonsulfur bacteria, and group I marine crenarchaeota. b-Proteobacteria, dominant in most other freshwater environments, are relatively rare in Crater Lake (<=16% of nonchloroplast bacterial rRNA at all depths). Other taxa identified in Crater Lake libraries include a newly identified candidate bacterial division, ABY1, and a newly identified subcluster, CL0-1, within candidate division OP10. Probe analyses confirmed vertical stratification of several microbial groups, similar to patterns observed in open-ocean systems. Additional similarities between Crater Lake and ocean microbial populations include aphotic zone dominance of group I marine crenarchaeota and green nonsulfur bacteria. Comparison of Crater Lake to other lakes studied by rRNA methods suggests that selective factors structuring Crater Lake bacterioplankton populations may include low concentrations of available trace metals and dissolved organic matter, chemistry of infiltrating hydrothermal waters, and irradiation by high levels of ultraviolet light.

The effects of plant extracts on microbial community structure in a rumen-simulating continuous-culture system as revealed by molecular profiling.

PubMed

Ferme, D; Banjac, M; Calsamiglia, S; Busquet, M; Kamel, C; Avgustin, G

2004-01-01

An in vitro study in dual-flow continuous-culture fermentors was conducted with two different concentrations of monensin, cinnamaldehyde or garlic extract added to 1:1 forage-to-concentrate diet in order to determine their effects on selected rumen bacterial populations. Samples were subjected to total DNA extraction, restriction analysis of PCR amplified parts of 16S rRNA genes (ARDRA) and subsequent analysis of the restriction profiles by lab-on-chip technology with the Agilent's Bioanalyser 2100. Eub338-BacPre primer pair was used to select for the bacteria from the genera Bacteroides, Porphyromonas and Prevotella, especially the latter representing the dominant Gram-negative bacterial population in the rumen. Preliminary results of HaeIII restriction analysis show that the effects of monensin, cinnamaldehyde and garlic extract on the BacPre targeted ruminal bacteria are somewhat different in regard to targeted populations and to the nature of the effect. Garlic extract was found to trigger the most intensive changes in the structure of the BacPre targeted population. Comparison of the in silico restriction analysis of BacPre sequences deposited in different DNA databanks and of the results of performed amplified ribosomal DNA restriction analysis showed differences between the predicted and obtained HaeIII restriction profiles, and suggested the presence of novel, still unknown Prevotella populations in studied samples.

Chemical and microbial characteristics of municipal drinking water supply systems in the Canadian Arctic.

PubMed

Daley, Kiley; Truelstrup Hansen, Lisbeth; Jamieson, Rob C; Hayward, Jenny L; Piorkowski, Greg S; Krkosek, Wendy; Gagnon, Graham A; Castleden, Heather; MacNeil, Kristen; Poltarowicz, Joanna; Corriveau, Emmalina; Jackson, Amy; Lywood, Justine; Huang, Yannan

2017-06-13

Drinking water in the vast Arctic Canadian territory of Nunavut is sourced from surface water lakes or rivers and transferred to man-made or natural reservoirs. The raw water is at a minimum treated by chlorination and distributed to customers either by trucks delivering to a water storage tank inside buildings or through a piped distribution system. The objective of this study was to characterize the chemical and microbial drinking water quality from source to tap in three hamlets (Coral Harbour, Pond Inlet and Pangnirtung-each has a population of <2000) on trucked service, and in Iqaluit (population ~6700), which uses a combination of trucked and piped water conveyance. Generally, the source and drinking water was of satisfactory microbial quality, containing Escherichia coli levels of <1 MPN/100 mL with a few exceptions, and selected pathogenic bacteria and parasites were below detection limits using quantitative polymerase chain reaction (qPCR) methods. Tap water in households receiving trucked water contained less than the recommended 0.2 mg/L of free chlorine, while piped drinking water in Iqaluit complied with Health Canada guidelines for residual chlorine (i.e. >0.2 mg/L free chlorine). Some buildings in the four communities contained manganese (Mn), copper (Cu), iron (Fe) and/or lead (Pb) concentrations above Health Canada guideline values for the aesthetic (Mn, Cu and Fe) and health (Pb) objectives. Corrosion of components of the drinking water distribution system (household storage tanks, premise plumbing) could be contributing to Pb, Cu and Fe levels, as the source water in three of the four communities had low alkalinity. The results point to the need for robust disinfection, which may include secondary disinfection or point-of-use disinfection, to prevent microbial risks in drinking water tanks in buildings and ultimately at the tap.

Developing Model Benchtop Systems for Microbial Experimental Evolution

NASA Astrophysics Data System (ADS)

Gentry, D.; Wang, J.; Arismendi, D.; Alvarez, J.; Ouandji, C.; Blaich, J.

2017-12-01

Understanding how microbes impact an ecosystem has improved through advances of molecular and genetic tools, but creating complex systems that emulate natural biology goes beyond current technology. In fact, many chemical, biological, and metabolic pathways of even model organisms are still poorly characterized. Even then, standard laboratory techniques for testing microbial impact on environmental change can have many drawbacks; they are time-consuming, labor intensive, and are at risk of contamination. By having an automated process, many of these problems can be reduced or even eliminated. We are developing a benchtop system that can run for long periods of time without the need for human intervention, involve multiple environmental stressors at once, perform real-time adjustments of stressor exposure based on current state of the population, and minimize contamination risks. Our prototype device allows operators to generate an analogue of real world micro-scale ecosystems that can be used to model the effects of disruptive environmental change on microbial ecosystems. It comprises of electronics, mechatronics, and fluidics based systems to control, measure, and evaluate the before and after state of microbial cultures from exposure to environmental stressors. Currently, it uses four parallel growth chambers to perform tests on liquid cultures. To measure the population state, optical sensors (LED/photodiode) are used. Its primary selection pressure is UV-C radiation, a well-studied stressor known for its cell- and DNA- damaging effects and as a mutagen. Future work will involve improving the current growth chambers, as well as implementing additional sensors and environmental stressors into the system. Full integration of multiple culture testing will allow inter-culture comparisons. Besides the temperature and OD sensors, other types of sensors can be integrated such as conductivity, biomass, pH, and dissolved gasses such as CO2 and O2. Additional environmental stressor systems like temperature (extreme heat or cold), metal toxicity, and other forms of radiation will increase the scale and testing range.

Antimicrobial Resistance Profiles and Diversity in Salmonella from Humans and Cattle, 2004-2011.

PubMed

Afema, J A; Mather, A E; Sischo, W M

2015-11-01

Analysis of long-term anti-microbial resistance (AMR) data is useful to understand source and transmission dynamics of AMR. We analysed 5124 human clinical isolates from Washington State Department of Health, 391 cattle clinical isolates from the Washington Animal Disease Diagnostic Laboratory and 1864 non-clinical isolates from foodborne disease research on dairies in the Pacific Northwest. Isolates were assigned profiles based on phenotypic resistance to 11 anti-microbials belonging to eight classes. Salmonella Typhimurium (ST), Salmonella Newport (SN) and Salmonella Montevideo (SM) were the most common serovars in both humans and cattle. Multinomial logistic regression showed ST and SN from cattle had greater probability of resistance to multiple classes of anti-microbials than ST and SN from humans (P < 0.0001). While these findings could be consistent with the belief that cattle are a source of resistant ST and SN for people, occurrence of profiles unique to cattle and not observed in temporally related human isolates indicates these profiles are circulating in cattle only. We used various measures to assess AMR diversity, conditional on the weighting of rare versus abundant profiles. AMR profile richness was greater in the common serovars from humans, although both source data sets were dominated by relatively few profiles. The greater profile richness in human Salmonella may be due to greater diversity of sources entering the human population compared to cattle or due to continuous evolution in the human environment. Also, AMR diversity was greater in clinical compared to non-clinical cattle Salmonella, and this could be due to anti-microbial selection pressure in diseased cattle that received treatment. The use of bootstrapping techniques showed that although there were shared profiles between humans and cattle, the expected and observed number of profiles was different, suggesting Salmonella and associated resistance from humans and cattle may not be wholly derived from a common population. © 2014 The Authors. Zoonoses and Public Health Published by Blackwell Verlag GmbH.

Developing Model Benchtop Systems for Microbial Experimental Evolution

NASA Technical Reports Server (NTRS)

Wang, Jonathan; Arismendi, Dillon; Alvarez, Jennifer; Ouandji, Cynthia; Blaich, Justin; Gentry, Diana

2017-01-01

Understanding how microbes impact an ecosystem has improved through advances of molecular and genetic tools, but creating complex systems that emulate natural biology goes beyond current technology. In fact, many chemical, biological, and metabolic pathways of even model organisms are still poorly characterized. Even then, standard laboratory techniques for testing microbial impact on environmental change can have many drawbacks; they are time-consuming, labor intensive, and are at risk of contamination. By having an automated process, many of these problems can be reduced or even eliminated. We are developing a benchtop system that can run for long periods of time without the need for human intervention, involve multiple environmental stressors at once, perform real-time adjustments of stressor exposure based on current state of the population, and minimize contamination risks. Our prototype device allows operators to generate an analogue of real world micro-scale ecosystems that can be used to model the effects of disruptive environmental change on microbial ecosystems. It comprises of electronics, mechatronics, and fluidics based systems to control, measure, and evaluate the before and after state of microbial cultures from exposure to environmental stressors. Currently, it uses four parallel growth chambers to perform tests on liquid cultures. To measure the population state, optical sensors (LED/photodiode) are used. Its primary selection pressure is UV-C radiation, a well-studied stressor known for its cell- and DNA-damaging effects and as a mutagen. Future work will involve improving the current growth chambers, as well as implementing additional sensors and environmental stressors into the system. Full integration of multiple culture testing will allow inter-culture comparisons. Besides the temperature and OD sensors, other types of sensors can be integrated such as conductivity, biomass, pH, and dissolved gasses such as CO and O. Additional environmental stressor systems like temperature (extreme heat or cold), metal toxicity, and other forms of radiation will increase the scale and testing range.

Experimental evolution and the dynamics of genomic mutation rate modifiers.

PubMed

Raynes, Y; Sniegowski, P D

2014-11-01

Because genes that affect mutation rates are themselves subject to mutation, mutation rates can be influenced by natural selection and other evolutionary forces. The population genetics of mutation rate modifier alleles has been a subject of theoretical interest for many decades. Here, we review experimental contributions to our understanding of mutation rate modifier dynamics. Numerous evolution experiments have shown that mutator alleles (modifiers that elevate the genomic mutation rate) can readily rise to high frequencies via genetic hitchhiking in non-recombining microbial populations. Whereas these results certainly provide an explanatory framework for observations of sporadically high mutation rates in pathogenic microbes and in cancer lineages, it is nonetheless true that most natural populations have very low mutation rates. This raises the interesting question of how mutator hitchhiking is suppressed or its phenotypic effect reversed in natural populations. Very little experimental work has addressed this question; with this in mind, we identify some promising areas for future experimental investigation.

MICROBIAL CHARACTERIZATION OF DRINKING WATER SYSTEMS RECEIVING GROUNDWATER AND SURFACE WATER AS THE PRIMARY SOURCES OF WATER

EPA Science Inventory

Earlier descriptions of water distribution systems (WDS) microbial communities have relied on culturing techniques. These techniques are known to be highly selective in nature, but more importantly, they tend to grossly underestimate the microbial diversity of most environments. ...

MICROBIAL TRANSFORMATION OF SELECTED ORGANIC CHEMICALS IN NATURAL AQUATIC SYSTEMS

EPA Science Inventory

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

Engineering microbial consortia to enhance biomining and bioremediation.

PubMed

Brune, Karl D; Bayer, Travis S

2012-01-01

In natural environments microorganisms commonly exist as communities of multiple species that are capable of performing more varied and complicated tasks than clonal populations. Synthetic biologists have engineered clonal populations with characteristics such as differentiation, memory, and pattern formation, which are usually associated with more complex multicellular organisms. The prospect of designing microbial communities has alluring possibilities for environmental, biomedical, and energy applications, and is likely to reveal insight into how natural microbial consortia function. Cell signaling and communication pathways between different species are likely to be key processes for designing novel functions in synthetic and natural consortia. Recent efforts to engineer synthetic microbial interactions will be reviewed here, with particular emphasis given to research with significance for industrial applications in the field of biomining and bioremediation of acid mine drainage.

Engineering microbial consortia to enhance biomining and bioremediation

PubMed Central

Brune, Karl D.; Bayer, Travis S.

2012-01-01

In natural environments microorganisms commonly exist as communities of multiple species that are capable of performing more varied and complicated tasks than clonal populations. Synthetic biologists have engineered clonal populations with characteristics such as differentiation, memory, and pattern formation, which are usually associated with more complex multicellular organisms. The prospect of designing microbial communities has alluring possibilities for environmental, biomedical, and energy applications, and is likely to reveal insight into how natural microbial consortia function. Cell signaling and communication pathways between different species are likely to be key processes for designing novel functions in synthetic and natural consortia. Recent efforts to engineer synthetic microbial interactions will be reviewed here, with particular emphasis given to research with significance for industrial applications in the field of biomining and bioremediation of acid mine drainage. PMID:22679443

The effect of microbial starter composition on cassava chips fermentation for the production of fermented cassava flour

NASA Astrophysics Data System (ADS)

Kresnowati, M. T. A. P.; Listianingrum, Zaenudin, Ahmad; Trihatmoko, Kharisrama

2015-12-01

The processing of cassava into fermented cassava flour (fercaf) or the widely known as modified cassava flour (mocaf) presents an alternative solution to improve the competitiveness of local foods and to support national food security. However, the mass production of fercaf is being limited by several problems, among which is the availability of starter cultures. This paper presents the mapping of the effect of microbial starter compositions on the nutritional content of fercaf in order to obtain the suitable nutritional composition. Based on their enzymatic activities, the combination of Lactobacillus plantarum, Bacillus subtilis, and Aspergillus oryzae were tested during the study. In addition, commercial starter was also tested. During the fermentation, the dynamics in microbial population were measured as well as changes in cyanogenic glucoside content. The microbial starter composition was observed to affect the dynamics in microbial populationcynaogenic glucoside content of the produced fercaf. In general, steady state microbial population was reached within 12 hours of fermentation. Cyanogenic glucoside was observed to decrease along the fermentation.

SNP-VISTA: An Interactive SNPs Visualization Tool

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

Shah, Nameeta; Teplitsky, Michael V.; Pennacchio, Len A.

2005-07-05

Recent advances in sequencing technologies promise better diagnostics for many diseases as well as better understanding of evolution of microbial populations. Single Nucleotide Polymorphisms(SNPs) are established genetic markers that aid in the identification of loci affecting quantitative traits and/or disease in a wide variety of eukaryotic species. With today's technological capabilities, it is possible to re-sequence a large set of appropriate candidate genes in individuals with a given disease and then screen for causative mutations.In addition, SNPs have been used extensively in efforts to study the evolution of microbial populations, and the recent application of random shotgun sequencing to environmentalmore » samples makes possible more extensive SNP analysis of co-occurring and co-evolving microbial populations. The program is available at http://genome.lbl.gov/vista/snpvista.« less

Metabolic heterogeneity in clonal microbial populations.

PubMed

Takhaveev, Vakil; Heinemann, Matthias

2018-02-21

In the past decades, numerous instances of phenotypic diversity were observed in clonal microbial populations, particularly, on the gene expression level. Much less is, however, known about phenotypic differences that occur on the level of metabolism. This is likely explained by the fact that experimental tools probing metabolism of single cells are still at an early stage of development. Here, we review recent exciting discoveries that point out different causes for metabolic heterogeneity within clonal microbial populations. These causes range from ecological factors and cell-inherent dynamics in constant environments to molecular noise in gene expression that propagates into metabolism. Furthermore, we provide an overview of current methods to quantify the levels of metabolites and biomass components in single cells. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Distribution of microbial physiologic types in an aquifer contaminated by crude oil

USGS Publications Warehouse

Bekins, B.A.; Godsy, E.M.; Warren, E.

1999-01-01

We conducted a plume-scale study of the microbial ecology in the anaerobic portion of an aquifer contaminated by crude-oil compounds. The data provide insight into the patterns of ecological succession, microbial nutrient demands, and the relative importance of free-living versus attached microbial populations. The most probable number (MPN) method was used to characterize the spatial distribution of six physiologic types: aerobes, denitrifiers, iron-reducers, heterotrophic fermenters, sulfate-reducers, and methanogens. Both free-living and attached numbers were determined over a broad cross-section of the aquifer extending horizontally from the source of the plume at a nonaqueous oil body to 66 m downgradient, and vertically from above the water table to the base of the plume below the water table. Point samples from widely spaced locations were combined with three closely spaced vertical profiles to create a map of physiologic zones for a cross-section of the plume. Although some estimates suggest that less than 1% of the subsurface microbial population can be grown in laboratory cultures, the MPN results presented here provide a comprehensive qualitative picture of the microbial ecology at the plume scale. Areas in the plume that are evolving from iron-reducing to methanogenic conditions are clearly delineated and generally occupy 25-50% of the plume thickness. Lower microbial numbers below the water table compared to the unsaturated zone suggest that nutrient limitations may be important in limiting growth in the saturated zone. Finally, the data indicate that an average of 15% of the total population is suspended.

Climate and edaphic controllers influence rhizosphere community assembly for a wild annual grass

DOE PAGES

Nuccio, Erin E.; Anderson-Furgeson, James; Estera, Katerina Y.; ...

2016-05-09

The interface between roots and soil, known as the rhizosphere, is a dynamic habitat in the soil ecosystem. Unraveling the factors that control rhizosphere community assembly is a key starting point for understanding the diversity of plant-microbial interactions that occur in soil. The goals of this study were to determine how environmental factors shape rhizosphere microbial communities, such as local soil characteristics and the regional climate, and to determine the relative influence of the rhizosphere on microbial community assembly compared to the pressures imposed by the local and regional environment. We identified the bacteria present in the soil immediately adjacentmore » to the roots of wild oat (Avena spp.) in three California grasslands using deep Illumina 16S sequencing. Rhizosphere communities were more similar to each other than to the surrounding soil communities from which they were derived, despite the fact that the grasslands studied were separated by hundreds of kilometers. The rhizosphere was the dominant factor structuring bacterial community composition (38% variance explained), and was comparable in magnitude to the combined local and regional effects (22% and 21%, respectively). Rhizosphere communities were most influenced by factors related to the regional climate (soil moisture and temperature), while background soil communities were more influenced by soil characteristics (pH, CEC, exchangeable cations, clay content). The Avena core microbiome was strongly phylogenetically clustered according to the metrics NRI and NTI, which indicates that selective processes likely shaped these communities. Furthermore, 17% of these taxa were not detectable in the background soil, even with a robust sequencing depth of approximately 70,000 sequences per sample. In conclusion, these results support the hypothesis that roots select less abundant or possibly rare populations in the soil microbial community, which appear to be lineages of bacteria that have made a physiological tradeoff for rhizosphere competence at the expense of their competitiveness in non-rhizosphere soil.« less

Climate and edaphic controllers influence rhizosphere community assembly for a wild annual grass

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

Nuccio, Erin E.; Anderson-Furgeson, James; Estera, Katerina Y.

The interface between roots and soil, known as the rhizosphere, is a dynamic habitat in the soil ecosystem. Unraveling the factors that control rhizosphere community assembly is a key starting point for understanding the diversity of plant-microbial interactions that occur in soil. The goals of this study were to determine how environmental factors shape rhizosphere microbial communities, such as local soil characteristics and the regional climate, and to determine the relative influence of the rhizosphere on microbial community assembly compared to the pressures imposed by the local and regional environment. We identified the bacteria present in the soil immediately adjacentmore » to the roots of wild oat (Avena spp.) in three California grasslands using deep Illumina 16S sequencing. Rhizosphere communities were more similar to each other than to the surrounding soil communities from which they were derived, despite the fact that the grasslands studied were separated by hundreds of kilometers. The rhizosphere was the dominant factor structuring bacterial community composition (38% variance explained), and was comparable in magnitude to the combined local and regional effects (22% and 21%, respectively). Rhizosphere communities were most influenced by factors related to the regional climate (soil moisture and temperature), while background soil communities were more influenced by soil characteristics (pH, CEC, exchangeable cations, clay content). The Avena core microbiome was strongly phylogenetically clustered according to the metrics NRI and NTI, which indicates that selective processes likely shaped these communities. Furthermore, 17% of these taxa were not detectable in the background soil, even with a robust sequencing depth of approximately 70,000 sequences per sample. In conclusion, these results support the hypothesis that roots select less abundant or possibly rare populations in the soil microbial community, which appear to be lineages of bacteria that have made a physiological tradeoff for rhizosphere competence at the expense of their competitiveness in non-rhizosphere soil.« less

Location of Microbial Ecology Evaluation Device in Apollo Command Module

NASA Technical Reports Server (NTRS)

1971-01-01

The location of the Microbial Ecology Evaluation Device (MEED) installed on the open hatch of the Apollo Command Module is illustrated in this photograph. The MEED, equipment of the Microbial Response in Space Environment experiment, will house a selection of microbial systems. The MEED will be deployed during the extravehicular activity on the transearth coast phase of the Aopllo 16 lunar landing mission. The purpose of the experiment will be to measure the effects of certain space environmental parameters on the microbial test systems.

The fifth international conference on microbial enhanced oil recovery and related biotechnology for solving environmental problems: 1995 Conference proceedings

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

Bryant, R.

1995-12-31

This volume contains 41 papers covering the following topics: field trials of microbial enhanced recovery of oil; control and treatment of sour crudes and natural gas with microorganisms; bioremediation of hydrocarbon contamination in soils; microbial plugging processes; microbial waste water treatment; the use of microorganisms as biological indicators of oils; and characterization and behavior of microbial systems. Selected papers are indexed separately for inclusion in the Energy Science and Technology Database.

Development of sequence-specific antimicrobials based on programmable CRISPR-Cas nucleases

PubMed Central

Bikard, David; Euler, Chad; Jiang, Wenyan; Nussenzweig, Philip M.; Goldberg, Gregory W.; Duportet, Xavier; Fischetti, Vincent A.; Marraffini, Luciano A.

2014-01-01

Antibiotics target conserved bacterial cellular pathways or growth functions and therefore cannot selectively kill specific members of a complex microbial population. Here, we develop programmable, sequence-specific antimicrobials using the RNA-guided nuclease Cas91, 2 delivered by a bacteriophage. We show that Cas9 re-programmed to target virulence genes kills virulent, but not avirulent, Staphylococcus aureus. Re-programming the nuclease to target antibiotic resistance genes destroys staphylococcal plasmids that harbor antibiotic resistance genes3, 4 and immunizes avirulent staphylococci to prevent the spread of plasmid-borne resistance genes. We also demonstrate the approach in vivo, showing its efficacy against S. aureus in a mouse skin colonization model. This new technology creates opportunities to manipulate complex bacterial populations in a sequence-specific manner. PMID:25282355

Biogeochemistry of hypersaline microbial mats illustrates the dynamics of modern microbial ecosystems and the early evolution of the biosphere

NASA Technical Reports Server (NTRS)

Des Marais, David J.

2003-01-01

Photosynthetic microbial mats are remarkably complete self-sustaining ecosystems at the millimeter scale, yet they have substantially affected environmental processes on a planetary scale. These mats may be direct descendents of the most ancient biological communities in which even oxygenic photosynthesis might have developed. Photosynthetic mats are excellent natural laboratories to help us to learn how microbial populations associate to control dynamic biogeochemical gradients.

Thousands of Viral Populations Recovered from Peatland Soil Metagenomes Reveal Viral Impacts on Carbon Cycling in Thawing Permafrost

NASA Astrophysics Data System (ADS)

Emerson, J. B.; Brum, J. R.; Roux, S.; Bolduc, B.; Woodcroft, B. J.; Singleton, C. M.; Boyd, J. A.; Hodgkins, S. B.; Wilson, R.; Trubl, G. G.; Jang, H. B.; Crill, P. M.; Chanton, J.; Saleska, S. R.; Rich, V. I.; Tyson, G. W.; Sullivan, M. B.

2016-12-01

Methane and carbon dioxide emissions, which are under significant microbial control, provide positive feedbacks to climate change in thawing permafrost peatlands. Although viruses in marine systems have been shown to impact microbial ecology and biogeochemical cycling through host cell lysis, horizontal gene transfer, and auxiliary metabolic gene expression, viral ecology in permafrost and other soils remains virtually unstudied due to methodological challenges. Here, we identified viral sequences in 208 assembled bulk soil metagenomes derived from a permafrost thaw gradient in Stordalen Mire, northern Sweden, from 2010-2012. 2,048 viral populations were recovered, which genome- and network-based classification revealed to be largely novel, increasing known viral genera globally by 40%. Ecologically, viral communities differed significantly across the thaw gradient and by soil depth. Co-occurring microbial community composition, soil moisture, and pH were predictors of viral community composition, indicative of biological and biogeochemical feedbacks as permafrost thaws. Host prediction—achieved through clustered regularly interspaced short palindromic repeats (CRISPRs), tetranucleotide frequency patterns, and other sequence similarities to binned microbial population genomes—was able to link 38% of the viral populations to a microbial host. 5% of the implicated hosts were archaea, predominantly methanogens and ammonia-oxidizing Nitrososphaera, 45% were Acidobacteria or Verrucomicrobia (mostly predicted heterotrophic complex carbon degraders), and 21% were Proteobacteria, including methane oxidizers. Recovered viral genome fragments also contained auxiliary metabolic genes involved in carbon and nitrogen cycling. Together, these data reveal multiple levels of previously unknown viral contributions to biogeochemical cycling, including to carbon gas emissions, in peatland soils undergoing and contributing to climate change. This work represents a significant step towards understanding viral roles in microbially-mediated biogeochemical cycling in soil.

Tracking microbial colonization patterns associated with micro-environments of rice

NASA Astrophysics Data System (ADS)

Schmidt, Hannes; Eickhorst, Thilo

2015-04-01

The interface between soil and roots (i.e. the rhizosphere) represents a highly dynamic micro-environment for microbial populations. Root-derived compounds are released into the rhizosphere and may attract, stimulate, or inhibit native soil microorganisms. Microbes associated with the rhizosphere, in turn, may have deleterious, neutral, or promoting effects on the plant. Such influences of microbial populations on the plant and vice versa are likely to be greatest in close vicinity to the root surface. It is therefore essential to detect and visualize preferential micro-sites of microbial root colonization to identify potential areas of microbe-plant interaction. We present a single-cell based approach allowing for the localization, quantification, and visualization of native microbial populations in the rhizosphere and on the rhizoplane of soil-grown roots in situ. Catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) in combination with confocal laser scanning microscopy was applied to observe colonization densities and patterns of microbial populations associated with wetland rice. Hybridizations with domain- and phylum-specific oligonucleotide probes showed that the growth stage of the rice plant as well as the distance to the root surface had a strong influence on microbial colonization patterns. Three-dimensional visualizations of root-associated microbes revealed micro-sites of preferential colonization. Highest cell numbers of archaea and bacteria were found at flowering stage of rice plant development. Irregular distribution patterns of microbiota observed at early growth stages shifted towards more uniform colonization with plant age. Accordingly, the highest colonization densities shifted from the tip to more mature regions of rice roots. Methanogenic archaea and methanotrophic bacteria were found to be co-localized at basal regions of lateral roots. Beneficial effects of a close association with root surfaces were indicated by proportionally higher numbers of methane-oxidizing bacteria on the rhizoplane compared to the rhizosphere. Such spatial effects could not be observed for methanogenic archaea. As a consequence, the detection and visualization of microbial colonization patterns on a micro-scale via CARD-FISH represents an instrumental approach in revealing potential sites of interaction between microbes and plants in soil micro-environments.

Dynamics of microbial community composition and function during in-situ bioremediation of a uranium-contaminated aquifer

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

Nostrand, J.D. Van; Wu, L.; Wu, W.M.

2010-08-15

A pilot-scale system was established to examine the feasibility of in situ U(VI) immobilization at a highly contaminated aquifer (U.S. DOE Integrated Field Research Challenge site, Oak Ridge, TN). Ethanol was injected intermittently as an electron donor to stimulate microbial U(VI) reduction, and U(VI) concentrations fell to below the Environmental Protection Agency drinking water standard (0.03 mg liter{sup -1}). Microbial communities from three monitoring wells were examined during active U(VI) reduction and maintenance phases with GeoChip, a high-density, comprehensive functional gene array. The overall microbial community structure exhibited a considerable shift over the remediation phases examined. GeoChip-based analysis revealed thatmore » Fe(III)-reducing bacterial (FeRB), nitrate-reducing bacterial (NRB), and sulfate-reducing bacterial (SRB) functional populations reached their highest levels during the active U(VI) reduction phase (days 137 to 370), in which denitrification and Fe(III) and sulfate reduction occurred sequentially. A gradual decrease in these functional populations occurred when reduction reactions stabilized, suggesting that these functional populations could play an important role in both active U(VI) reduction and maintenance of the stability of reduced U(IV). These results suggest that addition of electron donors stimulated the microbial community to create biogeochemical conditions favorable to U(VI) reduction and prevent the reduced U(IV) from reoxidation and that functional FeRB, SRB, and NRB populations within this system played key roles in this process.« less

Comparison of microbial populations in the small intestine, large intestine and feces of healthy horses using terminal restriction fragment length polymorphism

PubMed Central

2013-01-01

Background The composition of the microbiota of the equine intestinal tract is complex. Determining whether the microbial composition of fecal samples is representative of proximal compartments of the digestive tract could greatly simplify future studies. The objectives of this study were to compare the microbial populations of the duodenum, ileum, cecum, colon and rectum (feces) within and between healthy horses, and to determine whether rectal (fecal) samples are representative of proximal segments of the gastrointestinal tract. Intestinal samples were collected from ten euthanized horses. 16S rRNA gene PCR-based TRFLP was used to investigate microbiota richness in various segments of the gastrointestinal tract, and dice similarity indices were calculated to compare the samples. Results Within horses large variations of microbial populations along the gastrointestinal tract were seen. The microbiota in rectal samples was only partially representative of other intestinal compartments. The highest similarity was obtained when feces were compared to the cecum. Large compartmental variations were also seen when microbial populations were compared between six horses with similar dietary and housing management. Conclusion Rectal samples were not entirely representative of intestinal compartments in the small or large intestine. This should be taken into account when designing studies using fecal sampling to assess other intestinal compartments. Similarity between horses with similar dietary and husbandry management was also limited, suggesting that parts of the intestinal microbiota were unique to each animal in this study. PMID:23497580

Dynamics of Microbial Community Composition and Function during In Situ Bioremediation of a Uranium-Contaminated Aquifer▿‡

PubMed Central

Van Nostrand, Joy D.; Wu, Liyou; Wu, Wei-Min; Huang, Zhijian; Gentry, Terry J.; Deng, Ye; Carley, Jack; Carroll, Sue; He, Zhili; Gu, Baohua; Luo, Jian; Criddle, Craig S.; Watson, David B.; Jardine, Philip M.; Marsh, Terence L.; Tiedje, James M.; Hazen, Terry C.; Zhou, Jizhong

2011-01-01

A pilot-scale system was established to examine the feasibility of in situ U(VI) immobilization at a highly contaminated aquifer (U.S. DOE Integrated Field Research Challenge site, Oak Ridge, TN). Ethanol was injected intermittently as an electron donor to stimulate microbial U(VI) reduction, and U(VI) concentrations fell to below the Environmental Protection Agency drinking water standard (0.03 mg liter−1). Microbial communities from three monitoring wells were examined during active U(VI) reduction and maintenance phases with GeoChip, a high-density, comprehensive functional gene array. The overall microbial community structure exhibited a considerable shift over the remediation phases examined. GeoChip-based analysis revealed that Fe(III)-reducing bacterial (FeRB), nitrate-reducing bacterial (NRB), and sulfate-reducing bacterial (SRB) functional populations reached their highest levels during the active U(VI) reduction phase (days 137 to 370), in which denitrification and Fe(III) and sulfate reduction occurred sequentially. A gradual decrease in these functional populations occurred when reduction reactions stabilized, suggesting that these functional populations could play an important role in both active U(VI) reduction and maintenance of the stability of reduced U(IV). These results suggest that addition of electron donors stimulated the microbial community to create biogeochemical conditions favorable to U(VI) reduction and prevent the reduced U(IV) from reoxidation and that functional FeRB, SRB, and NRB populations within this system played key roles in this process. PMID:21498771

Cellulose digestion in primitive hexapods: Effect of ingested antibiotics on gut microbial populations and gut cellulase levels in the firebrat,Thermobia domestica (Zygentoma, Lepismatidae).

PubMed

Treves, D S; Martin, M M

1994-08-01

Antibiotic feeding studies were conducted on the firebrat,Thermobia domestica (Zygentoma, Lepismatidae) to determine if the insect's gut cellulases were of insect or microbial origin. Firebrats were fed diets containing either nystatin, metronidazole, streptomycin, tetracycline, or an antibiotic cocktail consisting of all four antibiotics, and then their gut microbial populations and gut cellulase levels were monitored and compared with the gut microbial populations and gut cellulase levels in firebrats feeding on antibiotic-free diets. Each antibiotic significantly reduced the firebrat's gut micro-flora. Nystatin reduced the firebrat's viable gut fungi by 89%. Tetracycline and the antibiotic cocktail reduced the firebrat's viable gut bacteria by 81% and 67%, respectively, and metronidazole, streptomycin, tetracycline, and the antibiotic cocktail reduced the firebrat's total gut flora by 35%, 32%, 55%, and 64%, respectively. Although antibiotics significantly reduced the firebrat's viable and total gut flora, gut cellulase levels in firebrats fed antibiotics were not significantly different from those in firebrats on an antibiotic-free diet. Furthermore, microbial populations in the firebrat's gut decreased significantly over time, even in firebrats feeding on the antibiotic-free diet, without corresponding decreases in gut cellulase levels. Based on this evidence, we conclude that the gut cellulases of firebrats are of insect origin. This conclusion implies that symbiont-independent cellulose digestion is a primitive trait in insects and that symbiont-mediated cellulose digestion is a derived condition.

Taxonomical and functional microbial community selection in soybean rhizosphere

PubMed Central

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

2014-01-01

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

Freshly characterization and storability of mini head lettuces at optimal and abusive temperatures.

PubMed

Viacava, Gabriela E; Ponce, Alejandra G; Goyeneche, Rosario; Carrozzi, Liliana; Yommi, Alejandra; Roura, Sara I

2016-01-01

Selection of lettuce varieties less sensitive to quality deterioration and more tolerant to abusive temperatures during handling, transportation, and storage is essential to minimize economical and quality losses that affect both producers and consumers. This work was focused on the quality changes of four baby head lettuces (Lactuca sativa L.), two butter (red and green) and two oak-leaf (red and green) types, during storage at 0 ℃ and 10 ℃ for 10 days. Lettuce quality was determined by measuring bioactive content (ascorbic acid, total phenolics), physicochemical (total chlorophyll, browning potential), and microbiological indices. At harvest, red varieties presented lower browning potential and higher bioactive compounds but no differences were observed in microbial populations. During storage, ascorbic acid underwent first order degradation for all varieties, with a degradation rate at 10 ℃ twice faster than at 0 ℃. At 0 ℃, only the red oak-leaf lettuce exhibited chlorophyll degradation, while at 10 ℃ all varieties presented degradation. No changes were observed in total phenolics and browning potential of butter lettuces during storage at both temperatures. Microbial population counts were significant affected by the storage temperature. Red butter baby lettuce presented slightly better bioactive content and microbiological characteristics and then better storability. © The Author(s) 2015.

Purification, characterization, and prebiotic properties of pectic oligosaccharides from orange peel wastes.

PubMed

Gómez, Belén; Gullón, Beatriz; Remoroza, Connie; Schols, Henk A; Parajó, Juan C; Alonso, José L

2014-10-08

Pectic oligosaccharides (POS) were obtained by hydrothermal treatment of orange peel wastes (OPW) and purified by membrane filtration to yield a refined product containing 90 wt % of the target products. AraOS (DP 3-21), GalOS (DP 5-12), and OGalA (DP 2-12, with variable DM) were identified in POS mixtures, but long-chain products were also present. The prebiotic potential of the concentrate was assessed by in vitro fermentation using human fecal inocula. For comparative purposes, similar experiments were performed using orange pectin and commercial fructo-oligosaccharides (FOS) as substrates for fermentation. The dynamics of selected microbial populations was assessed by fluorescent in situ hybridization (FISH). Gas generation, pH, and short-chain fatty acid (SCFA) production were also measured. Under the tested conditions, all of the considered substrates were utilized by the microbiota, and fermentation resulted in increased numbers of all the bacterial groups, but the final profile of the microbial population depended on the considered carbon source. POS boosted particularly the numbers of bifidobacteria and lactobacilli, so that the ratio between the joint counts of both genera and the total cell number increased from 17% in the inocula to 27% upon fermentation. SCFA generation from POS fermentation was similar to that observed with FOS, but pectin fermentation resulted in reduced butyrate generation.

Limitations in the use of ozone to disinfect maple sap.

PubMed

Labbe, R G; Kinsley, M; Wu, J

2001-01-01

The sap of the maple sugar tree (Acer saccharum) contains 2 to 3% sucrose and is traditionally collected early in the year and concentrated by boiling to produce maple syrup. High levels of microorganisms in the sap occur during holding, leading to a darker syrup with lower economic value. We investigated the use of dissolved ozone as a method to reduce the microbial population in sap. After 40 min of ozone treatment, concentrations of up to 0.30 mg/liter were achieved but were ineffective in reducing the aerobic plate count. Three predominant colonies on nutrient agar were selected for isolation and identification from sap. These included one mucoid and one nonmucoid yeast, both identified as Candida, and Pseudomonas fluorescens. When suspended in buffer, each was readily inactivated by ozone. Addition of 3% sucrose to the buffer markedly reduced the effectiveness of ozone. With the use of an ozone generator with a larger ozone output, saturating ozone concentrations (1 mg/liter) were achieved within 5 min but were accompanied by only a 1-log reduction in aerobic plate count of maple sap. After 40 min of ozone treatment, a less than 3-log reduction occurred. The results indicate that, because of the presence of sucrose, ozone may be of limited use in reducing the microbial population in sap.

Development of microbial genome-probing microarrays using digital multiple displacement amplification of uncultivated microbial single cells.

PubMed

Chang, Ho-Won; Sung, Youlboong; Kim, Kyoung-Ho; Nam, Young-Do; Roh, Seong Woon; Kim, Min-Soo; Jeon, Che Ok; Bae, Jin-Woo

2008-08-15

A crucial problem in the use of previously developed genome-probing microarrays (GPM) has been the inability to use uncultivated bacterial genomes to take advantage of the high sensitivity and specificity of GPM in microbial detection and monitoring. We show here a method, digital multiple displacement amplification (MDA), to amplify and analyze various genomes obtained from single uncultivated bacterial cells. We used 15 genomes from key microbes involved in dichloromethane (DCM)-dechlorinating enrichment as microarray probes to uncover the bacterial population dynamics of samples without PCR amplification. Genomic DNA amplified from single cells originating from uncultured bacteria with 80.3-99.4% similarity to 16S rRNA genes of cultivated bacteria. The digital MDA-GPM method successfully monitored the dynamics of DCM-dechlorinating communities from different phases of enrichment status. Without a priori knowledge of microbial diversity, the digital MDA-GPM method could be designed to monitor most microbial populations in a given environmental sample.

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. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.

Caught in the middle with multiple displacement amplification: the myth of pooling for avoiding multiple displacement amplification bias in a metagenome.

PubMed

Marine, Rachel; McCarren, Coleen; Vorrasane, Vansay; Nasko, Dan; Crowgey, Erin; Polson, Shawn W; Wommack, K Eric

2014-01-30

Shotgun metagenomics has become an important tool for investigating the ecology of microorganisms. Underlying these investigations is the assumption that metagenome sequence data accurately estimates the census of microbial populations. Multiple displacement amplification (MDA) of microbial community DNA is often used in cases where it is difficult to obtain enough DNA for sequencing; however, MDA can result in amplification biases that may impact subsequent estimates of population census from metagenome data. Some have posited that pooling replicate MDA reactions negates these biases and restores the accuracy of population analyses. This assumption has not been empirically tested. Using mock viral communities, we examined the influence of pooling on population-scale analyses. In pooled and single reaction MDA treatments, sequence coverage of viral populations was highly variable and coverage patterns across viral genomes were nearly identical, indicating that initial priming biases were reproducible and that pooling did not alleviate biases. In contrast, control unamplified sequence libraries showed relatively even coverage across phage genomes. MDA should be avoided for metagenomic investigations that require quantitative estimates of microbial taxa and gene functional groups. While MDA is an indispensable technique in applications such as single-cell genomics, amplification biases cannot be overcome by combining replicate MDA reactions. Alternative library preparation techniques should be utilized for quantitative microbial ecology studies utilizing metagenomic sequencing approaches.

Microbial Ecology of a Regional Flow System: Deep, Aerobic, Fractured Rock Aquifers of the US Basin and Range (Invited)

NASA Astrophysics Data System (ADS)

Moser, D. P.; Hamilton-Brehm, S.; Zhang, G.; Fisher, J.; Hughes, K.; Wheatley, A.; Thomas, J.; Zavarin, M.; Roberts, S. K.; Kryder, L.; McRae, R.; Howard, W.; Walker, J.; Federwisch, R.; King, M.; Friese, R.; Grim, S.; Amend, J.; Momper, L.; Sherwood Lollar, B.; Onstott, T. C.

2013-12-01

Recent decades have revealed anaerobic microbial ecosystems across a range of deep, continental settings; however, aerobic, regional aquifers represent a little-studied habitat for deep life. The US' Basin and Range Province is an extensional zone defined by deep, interconnected fracture systems that span multiple hydrologic basins and host regional aquifers. Here we describe a multi-basin microbiological assessment, applied to the Death Valley Regional Flow System (DVRFS). Our group has surveyed more than thirty deep boreholes (~ 1,000 m depth average) and deeply-sourced springs across a ~170 km inferred flow path from recharge areas in volcanic and carbonate rock highlands of the Nevada National Security Site (NNSS) and the Spring Mountains to discharge zones in Oasis, Amargosa, and Death Valleys. DVRFS waters were characterized by temperatures of 30 - 50 oC and the presence of dissolved O2 (4 - 8 mg/L in the recharge areas and ~0.2 - 2 mg/L in the discharge zones). Planktonic microbial populations, as tracked by molecular DNA approaches (e.g. 454 pyrotag), were of low abundance (e.g. ~ 10e3 ~10e6 per mL) and dominated by Proteobacteria and Nitrospirae. Archaea were also present and dominated by novel Thaumarchaeotes. Patterns of microbial diversity and the hypothesis that these patterns may have utility for recognition of hydrologic connectivity were assessed by statistical tools. At the species level, cosmopolitan, system-wide, and flow-path-specific groupings of both bacteria and archaea were detected. Even when in close proximity to aerobic springs and wells, sites sampling deep, hot, anaerobic groundwaters possessed completely distinct microbial populations (e.g. dominance by Firmicutes, ANME, and predicted methanogens). Among methodological refinements developed from this work, the repeated sampling of one deep borehole over a month-long pump test revealed that well-bore-associated contaminants required several days of pumping for complete removal and enabled the identification of the specific depth that produced most of the water. Our results reveal details of microbial community structure for a common, but little-studied microbial ecosystem and support the concept that regional flow systems possess distinct microbial populations, consistent with their geochemical and hydrologic characteristics. These results generally support the concept that microbial populations may have utility as amplifiable tracers for tracking the connectivity of fluids in the subsurface.

Microbial and chemical properties of log ponds along the Oregon Coast.

Treesearch

Iwan Ho; Ching Yan Li

1987-01-01

The microbial and chemical properties of log ponds along the Oregon coast were investigated. The log ponds were highly eutrophic, containing high concentrations of ammonium and nitrate nitrogen, phosphate, and organic compounds. Because of large microbial populations, the biochemical oxygen demand was high and dissolved oxygen was low. Bacterial species in log ponds...

Nonantibiotic interventions to control pathogens and undesired microbial activities in mixed microbial populations residing in the gut of food-producing animals and their excreted wastes

USDA-ARS?s Scientific Manuscript database

The intensification and industrialization of animal agriculture throughout the world has led to considerable increases in animal production efficiencies but has also led to concerns that microbial pathogens, antibiotic residues, and other chemical contaminants could be concentrated in the environmen...

Diversity of anaerobic microbes in spacecraft assembly clean rooms.

PubMed

Probst, Alexander; Vaishampayan, Parag; Osman, Shariff; Moissl-Eichinger, Christine; Andersen, Gary L; Venkateswaran, Kasthuri

2010-05-01

Although the cultivable and noncultivable microbial diversity of spacecraft assembly clean rooms has been previously documented using conventional and state-of-the-art molecular techniques, the occurrence of obligate anaerobes within these clean rooms is still uncertain. Therefore, anaerobic bacterial communities of three clean-room facilities were analyzed during assembly of the Mars Science Laboratory rover. Anaerobic bacteria were cultured on several media, and DNA was extracted from suitable anaerobic enrichments and examined with conventional 16S rRNA gene clone library, as well as high-density phylogenetic 16S rRNA gene microarray (PhyloChip) technologies. The culture-dependent analyses predominantly showed the presence of clostridial and propionibacterial strains. The 16S rRNA gene sequences retrieved from clone libraries revealed distinct microbial populations associated with each clean-room facility, clustered exclusively within gram-positive organisms. PhyloChip analysis detected a greater microbial diversity, spanning many phyla of bacteria, and provided a deeper insight into the microbial community structure of the clean-room facilities. This study presents an integrated approach for assessing the anaerobic microbial population within clean-room facilities, using both molecular and cultivation-based analyses. The results reveal that highly diverse anaerobic bacterial populations persist in the clean rooms even after the imposition of rigorous maintenance programs and will pose a challenge to planetary protection implementation activities.

Development of Novel Random Network Theory-Based Approaches to Identify Network Interactions among Nitrifying Bacteria

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

Shi, Cindy

2015-07-17

The interactions among different microbial populations in a community could play more important roles in determining ecosystem functioning than species numbers and their abundances, but very little is known about such network interactions at a community level. The goal of this project is to develop novel framework approaches and associated software tools to characterize the network interactions in microbial communities based on high throughput, large scale high-throughput metagenomics data and apply these approaches to understand the impacts of environmental changes (e.g., climate change, contamination) on network interactions among different nitrifying populations and associated microbial communities.

Determination of the concentration of potential efflux pump inhibitors, pheophorbide a and pyropheophorbide a, in the feces of animals by fluorescence spectroscopy.

PubMed

Barnes, Charles A; Rasmussen, Sharon L; Petrich, Jacob W; Rasmussen, Mark A

2012-10-24

Efflux pumps are vital bacterial components, and research has demonstrated that some plant compounds such as pheophorbide a (php) possess efflux pump inhibitor (EPI) activity. This study determined the quantity of php present in feces as an indicator of EPI activity. Feces were collected from different species of animals fed a variety of feeds. The chlorophyll metabolites php and pyropheophorbide a (pyp) were determined using fluorescense spectroscopy. The average concentrations [μg/g dry matter (DM) feces] of pyp/php in feces were as follows: guinea pig, 180; goat, 150; rabbit, 150; dairy cow, 120; feedlot cattle, 60; rat, <1; pig, <1; chicken, <1. These data indicate that animals consuming "green" diets will excrete feces with concentrations of php/pyp that exceed levels demonstrated to be inhibitory to bacterial efflux pumps (0.5 μg/mL). The natural presence EPIs in the gastrointestinal tract may modulate the activity of microbial efflux pumps and exert selection pressure upon resident microbial populations.

Microbiological and physicochemical characterization of dry-cured Halal goat meat. Effect of salting time and addition of olive oil and paprika covering.

PubMed

Cherroud, Sanâa; Cachaldora, Aida; Fonseca, Sonia; Laglaoui, Amin; Carballo, Javier; Franco, Inmaculada

2014-10-01

The objective of this work was to define a simple technological process for dry-cured Halal goat meat elaboration. The aims of this study were to analyze physicochemical parameters and to enumerate the microbial population at the end of the different manufacturing processes (two salting times and the addition of olive oil and paprika covering) on 36 units of meat product. A total of 532 strains were isolated from several selective culture media and then identified using classical and molecular methods. In general, salt effect and the addition of olive oil and paprika were significant for all the studied microbial groups as well as on NaCl content and water activity. Molecular analysis proves that staphylococci, especially Staphylococcus xylosus and Staphylococcus equorum, were the most common naturally occurring microbiota. The best manufacturing process would be obtained with a longer salting time and the addition of the olive oil and paprika covering. Copyright © 2014 Elsevier Ltd. All rights reserved.

Molecular mechanisms of CRISPR-mediated microbial immunity.

PubMed

Gasiunas, Giedrius; Sinkunas, Tomas; Siksnys, Virginijus

2014-02-01

Bacteriophages (phages) infect bacteria in order to replicate and burst out of the host, killing the cell, when reproduction is completed. Thus, from a bacterial perspective, phages pose a persistent lethal threat to bacterial populations. Not surprisingly, bacteria evolved multiple defense barriers to interfere with nearly every step of phage life cycles. Phages respond to this selection pressure by counter-evolving their genomes to evade bacterial resistance. The antagonistic interaction between bacteria and rapidly diversifying viruses promotes the evolution and dissemination of bacteriophage-resistance mechanisms in bacteria. Recently, an adaptive microbial immune system, named clustered regularly interspaced short palindromic repeats (CRISPR) and which provides acquired immunity against viruses and plasmids, has been identified. Unlike the restriction–modification anti-phage barrier that subjects to cleavage any foreign DNA lacking a protective methyl-tag in the target site, the CRISPR–Cas systems are invader-specific, adaptive, and heritable. In this review, we focus on the molecular mechanisms of interference/immunity provided by different CRISPR–Cas systems.

Role of soil rhizobacteria in phytoremediation of heavy metal contaminated soils*

PubMed Central

Jing, Yan-de; He, Zhen-li; Yang, Xiao-e

2007-01-01

Heavy metal pollution of soil is a significant environmental problem and has its negative impact on human health and agriculture. Rhizosphere, as an important interface of soil and plant, plays a significant role in phytoremediation of contaminated soil by heavy metals, in which, microbial populations are known to affect heavy metal mobility and availability to the plant through release of chelating agents, acidification, phosphate solubilization and redox changes, and therefore, have potential to enhance phytoremediation processes. Phytoremediation strategies with appropriate heavy metal-adapted rhizobacteria have received more and more attention. This article paper reviews some recent advances in effect and significance of rhizobacteria in phytoremediation of heavy metal contaminated soils. There is also a need to improve our understanding of the mechanisms involved in the transfer and mobilization of heavy metals by rhizobacteria and to conduct research on the selection of microbial isolates from rhizosphere of plants growing on heavy metal contaminated soils for specific restoration programmes. PMID:17323432

Does Dietary Mitigation of Enteric Methane Production Affect Rumen Function and Animal Productivity in Dairy Cows?

PubMed Central

Veneman, Jolien B.; Muetzel, Stefan; Hart, Kenton J.; Faulkner, Catherine L.; Moorby, Jon M.; Perdok, Hink B.; Newbold, Charles J.

2015-01-01

It has been suggested that the rumen microbiome and rumen function might be disrupted if methane production in the rumen is decreased. Furthermore concerns have been voiced that geography and management might influence the underlying microbial population and hence the response of the rumen to mitigation strategies. Here we report the effect of the dietary additives: linseed oil and nitrate on methane emissions, rumen fermentation, and the rumen microbiome in two experiments from New Zealand (Dairy 1) and the UK (Dairy 2). Dairy 1 was a randomized block design with 18 multiparous lactating cows. Dairy 2 was a complete replicated 3 x 3 Latin Square using 6 rumen cannulated, lactating dairy cows. Treatments consisted of a control total mixed ration (TMR), supplementation with linseed oil (4% of feed DM) and supplementation with nitrate (2% of feed DM) in both experiments. Methane emissions were measured in open circuit respiration chambers and rumen samples were analyzed for rumen fermentation parameters and microbial population structure using qPCR and next generation sequencing (NGS). Supplementation with nitrate, but not linseed oil, decreased methane yield (g/kg DMI; P<0.02) and increased hydrogen (P<0.03) emissions in both experiments. Furthermore, the effect of nitrate on gaseous emissions was accompanied by an increased rumen acetate to propionate ratio and consistent changes in the rumen microbial populations including a decreased abundance of the main genus Prevotella and a decrease in archaeal mcrA (log10 copies/ g rumen DM content). These results demonstrate that methane emissions can be significantly decreased with nitrate supplementation with only minor, but consistent, effects on the rumen microbial population and its function, with no evidence that the response to dietary additives differed due to geography and different underlying microbial populations. PMID:26509835

Does Dietary Mitigation of Enteric Methane Production Affect Rumen Function and Animal Productivity in Dairy Cows?

PubMed

Veneman, Jolien B; Muetzel, Stefan; Hart, Kenton J; Faulkner, Catherine L; Moorby, Jon M; Perdok, Hink B; Newbold, Charles J

2015-01-01

It has been suggested that the rumen microbiome and rumen function might be disrupted if methane production in the rumen is decreased. Furthermore concerns have been voiced that geography and management might influence the underlying microbial population and hence the response of the rumen to mitigation strategies. Here we report the effect of the dietary additives: linseed oil and nitrate on methane emissions, rumen fermentation, and the rumen microbiome in two experiments from New Zealand (Dairy 1) and the UK (Dairy 2). Dairy 1 was a randomized block design with 18 multiparous lactating cows. Dairy 2 was a complete replicated 3 x 3 Latin Square using 6 rumen cannulated, lactating dairy cows. Treatments consisted of a control total mixed ration (TMR), supplementation with linseed oil (4% of feed DM) and supplementation with nitrate (2% of feed DM) in both experiments. Methane emissions were measured in open circuit respiration chambers and rumen samples were analyzed for rumen fermentation parameters and microbial population structure using qPCR and next generation sequencing (NGS). Supplementation with nitrate, but not linseed oil, decreased methane yield (g/kg DMI; P<0.02) and increased hydrogen (P<0.03) emissions in both experiments. Furthermore, the effect of nitrate on gaseous emissions was accompanied by an increased rumen acetate to propionate ratio and consistent changes in the rumen microbial populations including a decreased abundance of the main genus Prevotella and a decrease in archaeal mcrA (log10 copies/g rumen DM content). These results demonstrate that methane emissions can be significantly decreased with nitrate supplementation with only minor, but consistent, effects on the rumen microbial population and its function, with no evidence that the response to dietary additives differed due to geography and different underlying microbial populations.

Quantification of Functional Marker Genes for Denitrifying Microbial Populations in the Chandeleur Islands Impacted by the 2010 Gulf of Mexico Oil Spill

NASA Astrophysics Data System (ADS)

Crawford, P.; Flournoy, N.; Taylor, C.; Tatariw, C.; Mortazavi, B.; Sobecky, P.

2017-12-01

Barrier island ecosystems provide protection by reducing storm surges, dissipating wave energy, and economically through services such as fisheries, water catchment, and water quality. As these ecosystems are deteriorating and threatened in this century, services provided to humans are being valued monetarily to communicate their importance. Events such as the 2010 Gulf of Mexico oil spill, act as catalysts to accelerate deterioration and further loss of these vital ecosystem services. The oil spill impacted the Chandeleur Islands, barrier islands in Louisiana waters located forty miles south of Gulfport, MS. Island chain vegetation; i.e., Avicennia germinans and native Spartina alterniflora was heavily damaged as a result of the oil spill. As oil was deposited differentially, it was important to investigate the microbiology of oil-impacted areas as marsh vegetation is directly linked to microbe-driven ecosystem services such as denitrification, a nitrogen (N) cycle pathway. The objectives of this study were: i) characterize the biodiversity of microorganisms; ii) quantify denitrifying microbial populations using functional marker genes; and iii) measure rates of denitrification during a one-year period. Eco-functional marker genes narG, nirS, norB, nosZ, and nrfA were selected to represent denitrification. Three different marsh sites were selected for study based upon estimated amounts of prior oiling. Highest rates of denitrification were in September while the lowest rates were observed in February. The highest nirS abundance was detected for two of the three sites (Site 1 and 2) in September while Site 3 exhibited the highest abundance in November. Similarly, the highest abundances observed for norB and nosZ varied by site and by month. Weathered oil was also detected in some of the marsh sediment cores and chemically typed to Macondo oil. Studies such as this one are designed to characterize the barrier island microbial biodiversity and N cycle processes to better understand long-term effects disturbances such as the 2010 oil spill pose to an ecosystem service that contributes to maintaining marine water quality. This is especially important in light of the fact that weathered oil continues to be observed seven years post spill.

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.

Dispersal-Based Microbial Community Assembly Decreases Biogeochemical Function

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

Graham, Emily B.; Stegen, James C.

Ecological mechanisms influence relationships among microbial communities, which in turn impact biogeochemistry. In particular, microbial communities are assembled by deterministic (e.g., selection) and stochastic (e.g., dispersal) processes, and the relative balance of these two process types is hypothesized to alter the influence of microbial communities over biogeochemical function. We used an ecological simulation model to evaluate this hypothesis, defining biogeochemical function generically to represent any biogeochemical reaction of interest. We assembled receiving communities under different levels of dispersal from a source community that was assembled purely by selection. The dispersal scenarios ranged from no dispersal (i.e., selection-only) to dispersal ratesmore » high enough to overwhelm selection (i.e., homogenizing dispersal). We used an aggregate measure of community fitness to infer a given community’s biogeochemical function relative to other communities. We also used ecological null models to further link the relative influence of deterministic assembly to function. We found that increasing rates of dispersal decrease biogeochemical function by increasing the proportion of maladapted taxa in a local community. Niche breadth was also a key determinant of biogeochemical function, suggesting a tradeoff between the function of generalist and specialist species. Finally, we show that microbial assembly processes exert greater influence over biogeochemical function when there is variation in the relative contributions of dispersal and selection among communities. Taken together, our results highlight the influence of spatial processes on biogeochemical function and indicate the need to account for such effects in models that aim to predict biogeochemical function under future environmental scenarios.« less

Dispersal-Based Microbial Community Assembly Decreases Biogeochemical Function

DOE PAGES

Graham, Emily B.; Stegen, James C.

2017-11-01

Ecological mechanisms influence relationships among microbial communities, which in turn impact biogeochemistry. In particular, microbial communities are assembled by deterministic (e.g., selection) and stochastic (e.g., dispersal) processes, and the relative balance of these two process types is hypothesized to alter the influence of microbial communities over biogeochemical function. We used an ecological simulation model to evaluate this hypothesis, defining biogeochemical function generically to represent any biogeochemical reaction of interest. We assembled receiving communities under different levels of dispersal from a source community that was assembled purely by selection. The dispersal scenarios ranged from no dispersal (i.e., selection-only) to dispersal ratesmore » high enough to overwhelm selection (i.e., homogenizing dispersal). We used an aggregate measure of community fitness to infer a given community’s biogeochemical function relative to other communities. We also used ecological null models to further link the relative influence of deterministic assembly to function. We found that increasing rates of dispersal decrease biogeochemical function by increasing the proportion of maladapted taxa in a local community. Niche breadth was also a key determinant of biogeochemical function, suggesting a tradeoff between the function of generalist and specialist species. Finally, we show that microbial assembly processes exert greater influence over biogeochemical function when there is variation in the relative contributions of dispersal and selection among communities. Taken together, our results highlight the influence of spatial processes on biogeochemical function and indicate the need to account for such effects in models that aim to predict biogeochemical function under future environmental scenarios.« less

Specificity of marine microbial surface interactions.

PubMed Central

Imam, S H; Bard, R F; Tosteson, T R

1984-01-01

The macromolecular surface components involved in intraspecific cell surface interactions of the green microalga Chlorella vulgaris and closely associated bacteria were investigated. The specific surface attachment between this alga and its associated bacteria is mediated by lectin-like macromolecules associated with the surfaces of these cells. The binding activity of these surface polymers was inhibited by specific simple sugars; this suggests the involvement of specific receptor-ligand binding sites on the interactive surfaces. Epifluorescent microscopic evaluation of bacteria-alga interactions in the presence and absence of the macromolecules that mediate these interactions showed that the glycoproteins active in these processes were specific to the microbial sources from which they were obtained. The demonstration and definition of the specificity of these interactions in mixed microbial populations may play an important role in our understanding of the dynamics of marine microbial populations in the sea. PMID:6508293

Effects of dilution on dissolved oxygen depletion and microbial populations in the biochemical oxygen demand determination.

PubMed

Seo, Kyo Seong; Chang, Ho Nam; Park, Joong Kon; Choo, Kwang-Ho

2007-09-01

The biochemical oxygen demand (BOD) value is still a key parameter that can determine the level of organics, particularly the content of biodegradable organics in water. In this work, the effects of sample dilution, which should be done inevitably to get appropriate dissolved oxygen (DO) depletion, on the measurement of 5-day BOD (BOD(5)), was investigated with and without seeding using natural and synthetic water. The dilution effects were also evaluated for water samples taken in different seasons such as summer and winter because water temperature can cause a change in the types of microbial species, thus leading to different oxygen depletion profiles during BOD testing. The predation phenomenon between microbial cells was found to be dependent on the inorganic nutrients and carbon sources, showing a change in cell populations according to cell size after 5-day incubation. The dilution of water samples for BOD determination was linked to changes in the environment for microbial growth such as nutrition. The predation phenomenon between microbial cells was more important with less dilution. BOD(5) increased with the specific amount of inorganic nutrient per microbial mass when the natural water was diluted. When seeding was done for synthetic water samples, the seed volume also affected BOD due to the rate of organic uptake by microbes. BOD(5) increased with the specific bacterial population per organic source supplied at the beginning of BOD measurement. For more accurate BOD measurements, specific guidelines on dilution should be established.

Phylogenetic perspective and the search for life on earth and elsewhere

NASA Technical Reports Server (NTRS)

Pace, Norman R.

1989-01-01

Any search for microbial life on Mars cannot rely upon cultivation of indigenous organisms. Only a minority of even terrestrial organisms that are observed in mixed, naturally-occurring microbial populations can be cultivated in the laboratory. Consequently, methods are being developed for analyzing the phylogenetic affiliations of the constituents of natural microbial populations without the need for their cultivation. This is more than an exercise in taxonomy, for the extent of phylogenetic relatedness between unknown and known organisms is some measure of the extent of their biochemical commonalities. In one approach, total DNA is isolated from natural microbial populations and 16S rRNA genes are shotgun cloned for rapid sequence determinations and phylogenetic analyses. A second approach employs oligodeoxynucleotide hybridization probes that bind to phylogenetic group-specific sequences in 16S rRNA. Since each actively growing cell contains about 104 ribosomes, the binding of the diagnostic probes to single cells can be visualized by radioactivity or fluorescence. The application of these methods and the use of in situ cultivation techniques is illustrated using submarine hydrothermal vent communities. Recommendations are made regarding planning toward future Mars missions.

Cervical precancerous changes and selected cervical microbial infections, Kiambu County, Kenya, 2014: a cross sectional study.

PubMed

Kanyina, Evalyne Wambui; Kamau, Lucy; Muturi, Margaret

2017-09-25

Cervical cancer is the predominant cancer among women in Kenya and second most common in women in developing regions. Population-based cytological screening and early treatment reduces morbidity and mortality associated with the cancer. We determined the occurrence of cervical precancerous changes and cervical microbial infections (Trichomonas vaginalis, Candida albicans, Neisseria gonorrhea and Actinomyces) among women attending Family Health Option Kenya (FHOK) clinic in Thika. This was a hospital based cross sectional study among women attending reproductive health screening clinic from November 2013 to January 2014. Cervical Intraepithelial Neoplasia (CIN) I, II, III, cervical cancer and microbial infection (Actinomyces, Trichomonas vaginalis and Yeast cells) diagnosis was based on Pap smear screening test and High Vaginal Swab wet preparation microscopy. Neisseria gonorrhea was diagnosed through Gram staining. Socio-demographic and reproductive health data was collected using a structured questionnaire administered to the study participants and analyzed using Epi Info version 3.5.1. Of the 244 women screened, 238 (97.5%) presented with cervical inflammation, 80 (32.8%) cervical microbial infections and 12 (4.9%) cervical precancerous changes; 10 (83.3%) with CIN I and 2 (16.7%) CIN II. Of the 80 cervical microbial infections, 62 (77.5%) were yeast cell and 18 (22.5%) T. vaginalis. One thirty four (55%) participants had no history of Pap smear screening of which 84 (62.7%) were 20-40 years. Use of IUCDs (OR: 2.47, 95% CI 1.3-4.6) was associated with cervical inflammation. CIN I was the predominant cervical precancerous change. There is need to scale up cervical screening test to capture all categories of women.

SYNTHETIC BIOLOGY. Emergent genetic oscillations in a synthetic microbial consortium.

PubMed

Chen, Ye; Kim, Jae Kyoung; Hirning, Andrew J; Josić, Krešimir; Bennett, Matthew R

2015-08-28

A challenge of synthetic biology is the creation of cooperative microbial systems that exhibit population-level behaviors. Such systems use cellular signaling mechanisms to regulate gene expression across multiple cell types. We describe the construction of a synthetic microbial consortium consisting of two distinct cell types—an "activator" strain and a "repressor" strain. These strains produced two orthogonal cell-signaling molecules that regulate gene expression within a synthetic circuit spanning both strains. The two strains generated emergent, population-level oscillations only when cultured together. Certain network topologies of the two-strain circuit were better at maintaining robust oscillations than others. The ability to program population-level dynamics through the genetic engineering of multiple cooperative strains points the way toward engineering complex synthetic tissues and organs with multiple cell types. Copyright © 2015, American Association for the Advancement of Science.

Subseafloor Microbial Life in Venting Fluids from the Mid Cayman Rise Hydrothermal System

NASA Astrophysics Data System (ADS)

Huber, J. A.; Reveillaud, J.; Reddington, E.; McDermott, J. M.; Sylva, S. P.; Breier, J. A.; German, C. R.; Seewald, J.

2012-12-01

In hard rock seafloor environments, fluids emanating from hydrothermal vents are one of the best windows into the subseafloor and its resident microbial community. The functional consequences of an extensive population of microbes living in the subseafloor remains unknown, as does our understanding of how these organisms interact with one another and influence the biogeochemistry of the oceans. Here we report the abundance, activity, and diversity of microbes in venting fluids collected from two newly discovered deep-sea hydrothermal vents along the ultra-slow spreading Mid-Cayman Rise (MCR). Fluids for geochemical and microbial analysis were collected from the Von Damm and Piccard vent fields, which are located within 20 km of one another, yet have extremely different thermal, geological, and depth regimes. Geochemical data indicates that both fields are highly enriched in volatiles, in particular hydrogen and methane, important energy sources for and by-products of microbial metabolism. At both sites, total microbial cell counts in the fluids ranged in concentration from 5 x 10 4 to 3 x 10 5 cells ml-1 , with background seawater concentrations of 1-2 x 10 4 cells ml-1 . In addition, distinct cell morphologies and clusters of cells not visible in background seawater were seen, including large filaments and mineral particles colonized by microbial cells. These results indicate local enrichments of microbial communities in the venting fluids, distinct from background populations, and are consistent with previous enumerations of microbial cells in venting fluids. Stable isotope tracing experiments were used to detect utilization of acetate, formate, and dissolve inorganic carbon and generation of methane at 70 °C under anaerobic conditions. At Von Damm, a putatively ultra-mafic hosted site located at ~2200 m with a maximum temperature of 226 °C, stable isotope tracing experiments indicate methanogenesis is occurring in most fluid samples. No activity was detected in Piccard vent fluids, a basalt-hosted black smoker site located at ~4950 m with a maximum temperature of 403 °C. However, hyperthermophilic and thermophilic heterotrophs of the genus Thermococcus were isolated from Piccard vent fluids, but not Von Damm. These obligate anaerobes, growing optimally at 55-90 °C, are ubiquitous at hydrothermal systems and serve as a readily cultivable indicator organism of subseafloor populations. Finally, molecular analysis of vent fluids is on-going and will define the microbial population structure in this novel ecosystem and allow for direct comparisons with other deep-sea and subsurface habitats as part of our continuing efforts to explore the deep microbial biosphere on Earth.

An overview of field-specific designs of microbial EOR

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

Robertson, E.P.; Bala, G.A.; Fox, S.L.

1995-12-31

The selection and design of an MEOR process for application in a specific field involves geological, reservoir, and biological characterization. Microbially mediated oil recovery mechanisms (bigenic gas, biopolymers, and biosurfactants) are defined by the types of microorganisms used. The engineering and biological character of a given reservoir must be understood to correctly select a microbial system to enhance oil recovery. This paper discusses the methods used to evaluate three fields with distinct characteristics and production problems for the applicability of MEOR would not be applicable in two of the three fields considered. The development of a microbial oil recovery processmore » for the third field appeared promising. Development of a bacterial consortium capable of producing the desired metabolites was initiated, and field isolates were characterized.« less

Temporal and Spatial Differences in Microbial Composition during the Manufacture of a Continental-Type Cheese

PubMed Central

O'Sullivan, Daniel J.; O'Sullivan, Orla; McSweeney, Paul L. H.; Sheehan, Jeremiah J.

2015-01-01

We sought to determine if the time, within a production day, that a cheese is manufactured has an influence on the microbial community present within that cheese. To facilitate this, 16S rRNA amplicon sequencing was used to elucidate the microbial community dynamics of brine-salted continental-type cheese in cheeses produced early and late in the production day. Differences in the microbial composition of the core and rind of the cheese were also investigated. Throughout ripening, it was apparent that cheeses produced late in the day had a more diverse microbial population than their early equivalents. Spatial variation between the cheese core and rind was also noted in that cheese rinds were initially found to have a more diverse microbial population but thereafter the opposite was the case. Interestingly, the genera Thermus, Pseudoalteromonas, and Bifidobacterium, not routinely associated with a continental-type cheese produced from pasteurized milk, were detected. The significance, if any, of the presence of these genera will require further attention. Ultimately, the use of high-throughput sequencing has facilitated a novel and detailed analysis of the temporal and spatial distribution of microbes in this complex cheese system and established that the period during a production cycle at which a cheese is manufactured can influence its microbial composition. PMID:25636841

Labial and Vaginal Microbiology: Effects of Extended Panty Liner Use

PubMed Central

Enane, N. A.; Baldwin, S.; Berg, R. W.

1997-01-01

Objective: The goals of this study were 1) to better define the labial microflora and 2) to evaluate whether extended non-menstrual use of panty liners would increase genital carriage of undesirable bacteria and predispose to infection. Methods: Healthy female volunteers (224) were prospectively randomized into panty liner wear groups A (Always® deodorant) and B (Always® non-deodorant) and into a control group C (no panty liner wear) with instructions for non-menstrual ± menstrual use ≥5 h daily for 6 months. Selected aerobic bacteria were semiquantitatively cultured from the inner labial groove, the posterior fornix of the vagina, and the cervix pre-study and post-study. Used panty liners were quantitatively cultured, and vaginal secretions were examined by gas chromatography for fatty acid ratios as a measure of microbial flora shifts. Results: At the pre-study, labial microflora in this study population contained significantly higher frequencies of Staphylococcus, coliforms, other gram-negative rods, and enterococci, and a decreased frequency of Gardnerella vaginalis relative to the vaginal microflora. After 6 months use of panty liners the frequencies (and densities) of the selected microorganisms in these two sites had not changed compared to controls, and fatty acid analyses of vaginal secretions gave no evidence of shifts in the microbial flora. Conclusions: Frequencies of selected genital microflora were different for the labia compared to the vagina. No increased carriage of medically important species was detected for either site after 6 months of daily (average 7.8 h) panty liner use. PMID:18476146

Rumen Bacterial Diversity of 80 to 110-Day-Old Goats Using 16S rRNA Sequencing

PubMed Central

Han, Xufeng; Yang, Yuxin; Yan, Hailong; Wang, Xiaolong; Qu, Lei; Chen, Yulin

2015-01-01

The ability of rumen microorganisms to use fibrous plant matter plays an important role in ruminant animals; however, little information about rumen colonization by microbial populations after weaning has been reported. In this study, high-throughput sequencing was used to investigate the establishment of this microbial population in 80 to 110-day-old goats. Illumina sequencing of goat rumen samples yielded 101,356,610 nucleotides that were assembled into 256,868 reads with an average read length of 394 nucleotides. Taxonomic analysis of metagenomic reads indicated that the predominant phyla were distinct at different growth stages. The phyla Firmicutes and Synergistetes were predominant in samples taken from 80 to 100-day-old goats, but Bacteroidetes and Firmicutes became the most abundant phyla in samples from 110-day-old animals. There was a remarkable variation in the microbial populations with age; Firmicutes and Synergistetes decreased after weaning, but Bacteroidetes and Proteobacteria increased from 80 to 110 day of age. These findings suggested that colonization of the rumen by microorganisms is related to their function in the rumen digestive system. These results give a better understanding of the role of rumen microbes and the establishment of the microbial population, which help to maintain the host’s health and improve animal performance. PMID:25700157

The role of microbial reductive dechlorination of TCE at a phytoremediation site

USGS Publications Warehouse

Godsy, E.M.; Warren, E.; Paganelli, V.V.

2003-01-01

In April 1996, a phytoremediation field demonstration site at the Naval Air Station, Fort Worth, Texas, was developed to remediate shallow oxic ground water (< 3.7 m deep) contaminated with chlorinated ethenes. Microbial populations were sampled in February and June 1998. The populations under the newly planted cottonwood trees had not yet matured to an anaerobic community that could dechlorinate trichloroethene (TCE) to cis-1,2-dichloroethene (DCE); however, the microbial population under a mature (???22-year-old) cottonwood tree about 30 m southwest of the plantings had a mature anaerobic population capable of dechlorinating TCE to DCE, and DCE to vinyl chloride (VC). Oxygen-free sediment incubations with contaminated groundwater also demonstrated that resident microorganisms were capable of the dechlorination of TCE to DCE. This suggests that a sufficient amount of organic material is present for microbial dechlorination in aquifer microniches where dissolved O2 concentrations are low. Phenol, benzoic acid, acetic acid, and a cyclic hydrocarbon, compounds consistent with the degradation of root exudates and complex aromatic compounds, were identified by gas chromatography/mass spectrometry (GC/MS) in sediment samples under the mature cottonwood tree. Elsewhere at the site, transpiration and degradation by the cottonwood trees appears to be responsible for loss of chlorinated ethenes.

Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion.

PubMed

Vanwonterghem, Inka; Jensen, Paul D; Rabaey, Korneel; Tyson, Gene W

2016-09-01

Our understanding of the complex interconnected processes performed by microbial communities is hindered by our inability to culture the vast majority of microorganisms. Metagenomics provides a way to bypass this cultivation bottleneck and recent advances in this field now allow us to recover a growing number of genomes representing previously uncultured populations from increasingly complex environments. In this study, a temporal genome-centric metagenomic analysis was performed of lab-scale anaerobic digesters that host complex microbial communities fulfilling a series of interlinked metabolic processes to enable the conversion of cellulose to methane. In total, 101 population genomes that were moderate to near-complete were recovered based primarily on differential coverage binning. These populations span 19 phyla, represent mostly novel species and expand the genomic coverage of several rare phyla. Classification into functional guilds based on their metabolic potential revealed metabolic networks with a high level of functional redundancy as well as niche specialization, and allowed us to identify potential roles such as hydrolytic specialists for several rare, uncultured populations. Genome-centric analyses of complex microbial communities across diverse environments provide the key to understanding the phylogenetic and metabolic diversity of these interactive communities. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

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

PubMed

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.

Modelling the impact of future socio-economic and climate change scenarios on river microbial water quality.

PubMed

Islam, M M Majedul; Iqbal, Muhammad Shahid; Leemans, Rik; Hofstra, Nynke

2018-03-01

Microbial surface water quality is important, as it is related to health risk when the population is exposed through drinking, recreation or consumption of irrigated vegetables. The microbial surface water quality is expected to change with socio-economic development and climate change. This study explores the combined impacts of future socio-economic and climate change scenarios on microbial water quality using a coupled hydrodynamic and water quality model (MIKE21FM-ECOLab). The model was applied to simulate the baseline (2014-2015) and future (2040s and 2090s) faecal indicator bacteria (FIB: E. coli and enterococci) concentrations in the Betna river in Bangladesh. The scenarios comprise changes in socio-economic variables (e.g. population, urbanization, land use, sanitation and sewage treatment) and climate variables (temperature, precipitation and sea-level rise). Scenarios have been developed building on the most recent Shared Socio-economic Pathways: SSP1 and SSP3 and Representative Concentration Pathways: RCP4.5 and RCP8.5 in a matrix. An uncontrolled future results in a deterioration of the microbial water quality (+75% by the 2090s) due to socio-economic changes, such as higher population growth, and changes in rainfall patterns. However, microbial water quality improves under a sustainable scenario with improved sewage treatment (-98% by the 2090s). Contaminant loads were more influenced by changes in socio-economic factors than by climatic change. To our knowledge, this is the first study that combines climate change and socio-economic development scenarios to simulate the future microbial water quality of a river. This approach can also be used to assess future consequences for health risks. Copyright © 2017 The Authors. Published by Elsevier GmbH.. All rights reserved.

Effect of calcium cyanamide, ammonium bicarbonate and lime mixture, and ammonia water on survival of Ralstonia solanacearum and microbial community

PubMed Central

Liu, Lijuan; Sun, Chengliang; Liu, Xingxing; He, Xiaolin; Liu, Miao; Wu, Hao; Tang, Caixian; Jin, Chongwei; Zhang, Yongsong

2016-01-01

The inorganic nitrogenous amendments calcium cyanamide (CC), ammonia water (AW), and a mixture of ammonium bicarbonate with lime (A+L) are popularly used as fumigants to control soil-borne disease in China. However, it is unclear which of these fumigants is more effective in controlling R. solanacearum. This present study compared the efficiencies of the three nitrogenous amendments listed above at four nitrogen levels in suppressing the survival of R. solanacearum in soil. The CC showed the best ability to suppress R. solanacearum due to its highest capacity to increase soil and NO2− contents and pH. However, AW was more suitable to controlling bacterial wilt caused by R. solanacearum because it had a lower cost and its application rate of 0.25 g N kg−1 soil could effectively suppress the survival of R. solanacearum. Additionally, soil microbial activity and community populations were restored to their initial state four weeks after the application of each fumigant, indicating that the three fumigants had few detrimental impacts on soil microbial activity and community structure with an exception of the suppression of R. solanacearum. The present study provides guidance for the selection of a suitable alkaline nitrogenous amendment and its application rate in controlling bacterial wilt. PMID:26738601

Temperature and solids retention time control microbial population dynamics and volatile fatty acid production in replicated anaerobic digesters

PubMed Central

Vanwonterghem, Inka; Jensen, Paul D.; Rabaey, Korneel; Tyson, Gene W.

2015-01-01

Anaerobic digestion is a widely used technology for waste stabilization and generation of biogas, and has recently emerged as a potentially important process for the production of high value volatile fatty acids (VFAs) and alcohols. Here, three reactors were seeded with inoculum from a stably performing methanogenic digester, and selective operating conditions (37°C and 55°C; 12 day and 4 day solids retention time) were applied to restrict methanogenesis while maintaining hydrolysis and fermentation. Replicated experiments performed at each set of operating conditions led to reproducible VFA production profiles which could be correlated with specific changes in microbial community composition. The mesophilic reactor at short solids retention time showed accumulation of propionate and acetate (42 ± 2% and 15 ± 6% of CODhydrolyzed, respectively), and dominance of Fibrobacter and Bacteroidales. Acetate accumulation (>50% of CODhydrolyzed) was also observed in the thermophilic reactors, which were dominated by Clostridium. Under all tested conditions, there was a shift from acetoclastic to hydrogenotrophic methanogenesis, and a reduction in methane production by >50% of CODhydrolyzed. Our results demonstrate that shortening the SRT and increasing the temperature are effective strategies for driving microbial communities towards controlled production of high levels of specific volatile fatty acids. PMID:25683239

Effect of calcium cyanamide, ammonium bicarbonate and lime mixture, and ammonia water on survival of Ralstonia solanacearum and microbial community.

PubMed

Liu, Lijuan; Sun, Chengliang; Liu, Xingxing; He, Xiaolin; Liu, Miao; Wu, Hao; Tang, Caixian; Jin, Chongwei; Zhang, Yongsong

2016-01-07

The inorganic nitrogenous amendments calcium cyanamide (CC), ammonia water (AW), and a mixture of ammonium bicarbonate with lime (A+L) are popularly used as fumigants to control soil-borne disease in China. However, it is unclear which of these fumigants is more effective in controlling R. solanacearum. This present study compared the efficiencies of the three nitrogenous amendments listed above at four nitrogen levels in suppressing the survival of R. solanacearum in soil. The CC showed the best ability to suppress R. solanacearum due to its highest capacity to increase soil and NO2(-) contents and pH. However, AW was more suitable to controlling bacterial wilt caused by R. solanacearum because it had a lower cost and its application rate of 0.25 g N kg(-1) soil could effectively suppress the survival of R. solanacearum. Additionally, soil microbial activity and community populations were restored to their initial state four weeks after the application of each fumigant, indicating that the three fumigants had few detrimental impacts on soil microbial activity and community structure with an exception of the suppression of R. solanacearum. The present study provides guidance for the selection of a suitable alkaline nitrogenous amendment and its application rate in controlling bacterial wilt.

Master apical file size - smaller or larger: a systematic review of microbial reduction.

PubMed

Aminoshariae, A; Kulild, J

2015-11-01

The purpose of this systematic review was to determine, in patients undergoing root canal treatment, whether apical enlargement of canals affected microbial reduction. A PICO (population, intervention, comparison and outcome) strategy was developed to identify previously published studies dealing with apical size of canal and microbial reduction. The MEDLINE, Embase, Cochrane and PubMed databases were searched. Additionally, the bibliographies of all relevant articles and textbooks were manually searched. Based on inclusion and exclusion criteria, two reviewers independently selected the relevant articles. Due to the variety of methodologies and different techniques used to measure outcome for master apical file enlargement, it was not possible to standardize the research data and to apply a meta-analysis. Seven articles were identified that met the inclusion criteria. Five of the seven articles generally concluded that canal enlargement reduced bioburden in the root canal system. Two articles reported no difference in canals enlarged to size 25 or 40. The results of the systematic review confirmed that more evidence-based research in this area is needed. With the limited information currently available, the best current available clinical evidence suggests that contemporary chemomechanical debridement techniques with canal enlargement techniques do not eliminate bacteria during root canal treatment at any size. © 2014 International Endodontic Journal. Published by John Wiley & Sons Ltd.

Ozonation of oil sands process-affected water accelerates microbial bioremediation.

PubMed

Martin, Jonathan W; Barri, Thaer; Han, Xiumei; Fedorak, Phillip M; El-Din, Mohamed Gamal; Perez, Leonidas; Scott, Angela C; Jiang, Jason Tiange

2010-11-01

Ozonation can degrade toxic naphthenic acids (NAs) in oil sands process-affected water (OSPW), but even after extensive treatment a residual NA fraction remains. Here we hypothesized that mild ozonation would selectively oxidize the most biopersistent NA fraction, thereby accelerating subsequent NA biodegradation and toxicity removal by indigenous microbes. OSPW was ozonated to achieve approximately 50% and 75% NA degradation, and the major ozonation byproducts included oxidized NAs (i.e., hydroxy- or keto-NAs). However, oxidized NAs are already present in untreated OSPW and were shown to be formed during the microbial biodegradation of NAs. Ozonation alone did not affect OSPW toxicity, based on Microtox; however, there was a significant acceleration of toxicity removal in ozonated OSPW following inoculation with native microbes. Furthermore, all residual NAs biodegraded significantly faster in ozonated OSPW. The opposite trend was found for ozonated commercial NAs, which are known to contain no significant biopersistent fraction. Thus, we suggest that ozonation preferentially degraded the most biopersistent OSPW NA fraction, and that ozonation is complementary to the biodegradation capacity of microbial populations in OSPW. The toxicity of ozonated OSPW to higher organisms needs to be assessed, but there is promise that this technique could be applied to accelerate the bioremediation of large volumes of OSPW in Northern Alberta, Canada.

Effect of calcium cyanamide, ammonium bicarbonate and lime mixture, and ammonia water on survival of Ralstonia solanacearum and microbial community

NASA Astrophysics Data System (ADS)

Liu, Lijuan; Sun, Chengliang; Liu, Xingxing; He, Xiaolin; Liu, Miao; Wu, Hao; Tang, Caixian; Jin, Chongwei; Zhang, Yongsong

2016-01-01

The inorganic nitrogenous amendments calcium cyanamide (CC), ammonia water (AW), and a mixture of ammonium bicarbonate with lime (A+L) are popularly used as fumigants to control soil-borne disease in China. However, it is unclear which of these fumigants is more effective in controlling R. solanacearum. This present study compared the efficiencies of the three nitrogenous amendments listed above at four nitrogen levels in suppressing the survival of R. solanacearum in soil. The CC showed the best ability to suppress R. solanacearum due to its highest capacity to increase soil and NO2- contents and pH. However, AW was more suitable to controlling bacterial wilt caused by R. solanacearum because it had a lower cost and its application rate of 0.25 g N kg-1 soil could effectively suppress the survival of R. solanacearum. Additionally, soil microbial activity and community populations were restored to their initial state four weeks after the application of each fumigant, indicating that the three fumigants had few detrimental impacts on soil microbial activity and community structure with an exception of the suppression of R. solanacearum. The present study provides guidance for the selection of a suitable alkaline nitrogenous amendment and its application rate in controlling bacterial wilt.

A methodology for a quantitative interpretation of DGGE with the help of mathematical modelling: application in biohydrogen production.

PubMed

Tapia, Estela; Donoso-Bravo, Andres; Cabrol, Léa; Alves, Madalena; Pereira, Alcina; Rapaport, Alain; Ruiz-Filippi, Gonzalo

2014-01-01

Molecular biology techniques provide valuable insights in the investigation of microbial dynamics and evolution. Denaturing gradient gel electrophoresis (DGGE) analysis is one of the most popular methods which have been used in bioprocess assessment. Most of the anaerobic digestion models consider several microbial populations as state variables. However, the difficulty of measuring individual species concentrations may cause inaccurate model predictions. The integration of microbial data and ecosystem modelling is currently a challenging issue for improved system control. A novel procedure that combines common experimental measurements, DGGE, and image analysis is presented in this study in order to provide a preliminary estimation of the actual concentration of the dominant bacterial ribotypes in a bioreactor, for further use as a variable in mathematical modelling of the bioprocess. This approach was applied during the start-up of a continuous anaerobic bioreactor for hydrogen production. The experimental concentration data were used for determining the kinetic parameters of each species, by using a multi-species chemostat-model. The model was able to reproduce the global trend of substrate and biomass concentrations during the reactor start-up, and predicted in an acceptable way the evolution of each ribotype concentration, depicting properly specific ribotype selection and extinction.

Identification of dominant pathogens in periapical lesions associated with persistent apical periodontitis.

PubMed

Zhang, Shuang; Wang, Qian Qian; Zhang, Cheng Fei; Soo, Irwan

2010-01-01

to identify dominant pathogens in the periapical lesions associated with persistent apical periodontitis. thirty-three root-filled teeth with persistent apical periodontitis referred for surgical treatment were selected. Microbial samples were collected from the periapical lesions during apical surgery. Microbial identification was performed with species-specific primers prepared according to the sequence analysis data using a 16S rRNA technique. among the 33 cases, in 5 cases none of the target species were detected, 6 cases showed the presence of only one species, and 22 cases showed more than two species. Porphyromonas endodontalis (45% of sample) was the most commonly detected dominant microbial species in the study sample, followed by Actinomyces viscosus (42%), Candida albicans (36%) and Porphyromonas gingivalis (27%). Fusobacterium, Actinomyces israelii and Enterococcus faecalis were also detected in 27%, 21% and 15% of the sample, respectively. The most frequently isolated species, P. endodontalis, was in most cases detected together with Actinomyces (14 cases) and P. gingivalis (6 cases). None of the lesions analysed in the present study contained Prevotella intermedia. There was no correlation in relation to the presence of sinus tracts and the bacterial species. a mixed population of pathogens was found in the endodontic lesions associated with persistent apical periodontitis. P. endodontalis, A. viscosus, C. albicans and P. gingivalis were the dominant species identified.

Temperature and solids retention time control microbial population dynamics and volatile fatty acid production in replicated anaerobic digesters

NASA Astrophysics Data System (ADS)

Vanwonterghem, Inka; Jensen, Paul D.; Rabaey, Korneel; Tyson, Gene W.

2015-02-01

Anaerobic digestion is a widely used technology for waste stabilization and generation of biogas, and has recently emerged as a potentially important process for the production of high value volatile fatty acids (VFAs) and alcohols. Here, three reactors were seeded with inoculum from a stably performing methanogenic digester, and selective operating conditions (37°C and 55°C 12 day and 4 day solids retention time) were applied to restrict methanogenesis while maintaining hydrolysis and fermentation. Replicated experiments performed at each set of operating conditions led to reproducible VFA production profiles which could be correlated with specific changes in microbial community composition. The mesophilic reactor at short solids retention time showed accumulation of propionate and acetate (42 +/- 2% and 15 +/- 6% of CODhydrolyzed, respectively), and dominance of Fibrobacter and Bacteroidales. Acetate accumulation (>50% of CODhydrolyzed) was also observed in the thermophilic reactors, which were dominated by Clostridium. Under all tested conditions, there was a shift from acetoclastic to hydrogenotrophic methanogenesis, and a reduction in methane production by >50% of CODhydrolyzed. Our results demonstrate that shortening the SRT and increasing the temperature are effective strategies for driving microbial communities towards controlled production of high levels of specific volatile fatty acids.

Adaptation to reef habitats through selection on the coral animal and its associated microbiome.

PubMed

van Oppen, Madeleine J H; Bongaerts, Pim; Frade, Pedro; Peplow, Lesa M; Boyd, Sarah E; Nim, Hieu T; Bay, Line K

2018-06-13

Spatially adjacent habitats on coral reefs can represent highly distinct environments, often harbouring different coral communities. Yet, certain coral species thrive across divergent environments. It is unknown whether the forces of selection are sufficiently strong to overcome the counteracting effects of the typically high gene flow over short distances, and for local adaptation to occur. We screened the coral genome (using restriction-site-associated sequencing [RAD-seq]), and characterized both the dinoflagellate photosymbiont and tissue-associated prokaryote microbiomes (using metabarcoding) of a reef flat and slope population of the reef-building coral, Pocillopora damicornis, at two locations on Heron Island in the southern Great Barrier Reef. Reef flat and slope populations were separated by <100 m horizontally and ~5 m vertically and the two study locations were separated by ~1 km. For the coral host, genetic divergence between habitats was much greater than between locations, suggesting limited gene flow between the flat and slope populations. Consistent with environmental selection, outlier loci primarily belonged to the conserved, minimal cellular stress response, likely reflecting adaptation to the different temperature and irradiance regimes on the reef flat and slope. Similarly, the prokaryote community differed across both habitat and, to a lesser extent, location, whereas the dinoflagellate photosymbionts differed by habitat but not location. The observed intra-specific diversity associated with divergent habitats supports that environmental adaptation involves multiple members of the coral holobiont. Adaptive alleles or microbial associations present in coral populations from the environmentally-variable reef flat may provide a source of adaptive variation for assisted evolution approaches, through assisted gene flow, artificial cross-breeding or probiotic inoculations, with the aim to increase climate resilience in the slope populations. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Plant Community Richness Mediates Inhibitory Interactions and Resource Competition between Streptomyces and Fusarium Populations in the Rhizosphere.

PubMed

Essarioui, Adil; LeBlanc, Nicholas; Kistler, Harold C; Kinkel, Linda L

2017-07-01

Plant community characteristics impact rhizosphere Streptomyces nutrient competition and antagonistic capacities. However, the effects of Streptomyces on, and their responses to, coexisting microorganisms as a function of plant host or plant species richness have received little attention. In this work, we characterized antagonistic activities and nutrient use among Streptomyces and Fusarium from the rhizosphere of Andropogon gerardii (Ag) and Lespedeza capitata (Lc) plants growing in communities of 1 (monoculture) or 16 (polyculture) plant species. Streptomyces from monoculture were more antagonistic against Fusarium than those from polyculture. In contrast, Fusarium isolates from polyculture had greater inhibitory capacities against Streptomyces than isolates from monoculture. Although Fusarium isolates had on average greater niche widths, the collection of Streptomyces isolates in total used a greater diversity of nutrients for growth. Plant richness, but not plant host, influenced the potential for resource competition between the two taxa. Fusarium isolates had greater niche overlap with Streptomyces in monoculture than polyculture, suggesting greater potential for Fusarium to competitively challenge Streptomyces in monoculture plant communities. In contrast, Streptomyces had greater niche overlap with Fusarium in polyculture than monoculture, suggesting that Fusarium experiences greater resource competition with Streptomyces in polyculture than monoculture. These patterns of competitive and inhibitory phenotypes among Streptomyces and Fusarium populations are consistent with selection for Fusarium-antagonistic Streptomyces populations in the presence of strong Fusarium resource competition in plant monocultures. Similarly, these results suggest selection for Streptomyces-inhibitory Fusarium populations in the presence of strong Streptomyces resource competition in more diverse plant communities. Thus, landscape-scale variation in plant species richness may be critical to mediating the coevolutionary dynamics and selective trajectories for inhibitory and nutrient use phenotypes among Streptomyces and Fusarium populations in soil, with significant implications for microbial community functional characteristics.

Microbial Certification of the MER spacecraft

NASA Technical Reports Server (NTRS)

Schubert, W. W.; Arakelian, T.; Barengoltz, J. B.; Chough, N. G.; Chung, S. Y.; Law, J.; Kirschner, L.; Koukol, R. C.; Newlin, L. E.; Morales, F.

2003-01-01

Spacecraft such as the Mars Exploration Rovers (MER) must meet acceptable microbial population levels prior to launch. Sensitive parts and materials prevent any single sterilization method from being used as a final step on the assembled spacecraft.

Teaching Microbial Growth by Simulation.

ERIC Educational Resources Information Center

Ruiz, A. Fernandez; And Others

1989-01-01

Presented is a simulation program for Apple II computer which assays the effects of a series of variables on bacterial growth and interactions between microbial populations. Results of evaluation of the program with students are summarized. (CW)

A microbial perspective of human developmental biology.

PubMed

Charbonneau, Mark R; Blanton, Laura V; DiGiulio, Daniel B; Relman, David A; Lebrilla, Carlito B; Mills, David A; Gordon, Jeffrey I

2016-07-07

When most people think of human development, they tend to consider only human cells and organs. Yet there is another facet that involves human-associated microbial communities. A microbial perspective of human development provides opportunities to refine our definitions of healthy prenatal and postnatal growth and to develop innovative strategies for disease prevention and treatment. Given the dramatic changes in lifestyles and disease patterns that are occurring with globalization, we issue a call for the establishment of 'human microbial observatories' designed to examine microbial community development in birth cohorts representing populations with diverse anthropological characteristics, including those undergoing rapid change.

Human developmental biology viewed from a microbial perspective

PubMed Central

Charbonneau, Mark R.; Blanton, Laura V.; DiGiulio, Daniel B.; Relman, David A.; Lebrilla, Carlito B.; Mills, David A.; Gordon, Jeffrey I.

2017-01-01

Preface Most people think of human development only in terms of ‘human’ cells and organs. Here, we discuss another facet involving human-associated microbial communities. A microbial perspective of human development provides opportunities to refine our definitions of healthy pre- and postnatal growth and to develop new strategies for disease prevention and treatment. Considering the dramatic changes in lifestyles and disease patterns that are occurring with globalization, we issue a call for human microbial observatory programs designed to examine microbial community development in birth cohorts representing populations with diverse anthropologic characteristics, including those undergoing rapid change. PMID:27383979

Trophic interactions induce spatial self-organization of microbial consortia on rough surfaces.

PubMed

Wang, Gang; Or, Dani

2014-10-24

The spatial context of microbial interactions common in natural systems is largely absent in traditional pure culture-based microbiology. The understanding of how interdependent microbial communities assemble and coexist in limited spatial domains remains sketchy. A mechanistic model of cell-level interactions among multispecies microbial populations grown on hydrated rough surfaces facilitated systematic evaluation of how trophic dependencies shape spatial self-organization of microbial consortia in complex diffusion fields. The emerging patterns were persistent irrespective of initial conditions and resilient to spatial and temporal perturbations. Surprisingly, the hydration conditions conducive for self-assembly are extremely narrow and last only while microbial cells remain motile within thin aqueous films. The resulting self-organized microbial consortia patterns could represent optimal ecological templates for the architecture that underlie sessile microbial colonies on natural surfaces. Understanding microbial spatial self-organization offers new insights into mechanisms that sustain small-scale soil microbial diversity; and may guide the engineering of functional artificial microbial consortia.

Practical Approaches for Detecting Selection in Microbial Genomes.

PubMed

Hedge, Jessica; Wilson, Daniel J

2016-02-01

Microbial genome evolution is shaped by a variety of selective pressures. Understanding how these processes occur can help to address important problems in microbiology by explaining observed differences in phenotypes, including virulence and resistance to antibiotics. Greater access to whole-genome sequencing provides microbiologists with the opportunity to perform large-scale analyses of selection in novel settings, such as within individual hosts. This tutorial aims to guide researchers through the fundamentals underpinning popular methods for measuring selection in pathogens. These methods are transferable to a wide variety of organisms, and the exercises provided are designed for researchers with any level of programming experience.

40 CFR 158.2170 - Experimental use permit data requirements-microbial pesticides.

Code of Federal Regulations, 2013 CFR

2013-07-01

... requirements for genetically modified microbial pesticides may include but are not limited to: genetic... genetic stability and exchange; and selected Tier II environmental expression and toxicology tests. ...

40 CFR 158.2170 - Experimental use permit data requirements-microbial pesticides.

Code of Federal Regulations, 2014 CFR

2014-07-01

... requirements for genetically modified microbial pesticides may include but are not limited to: genetic... genetic stability and exchange; and selected Tier II environmental expression and toxicology tests. ...

40 CFR 158.2170 - Experimental use permit data requirements-microbial pesticides.

Code of Federal Regulations, 2012 CFR

2012-07-01

... requirements for genetically modified microbial pesticides may include but are not limited to: genetic... genetic stability and exchange; and selected Tier II environmental expression and toxicology tests. ...

40 CFR 158.2170 - Experimental use permit data requirements-microbial pesticides.

Code of Federal Regulations, 2011 CFR

2011-07-01

... requirements for genetically modified microbial pesticides may include but are not limited to: genetic... genetic stability and exchange; and selected Tier II environmental expression and toxicology tests. ...

Natural Microbial Assemblages Reflect Distinct Organismal and Functional Partitioning

NASA Astrophysics Data System (ADS)

Wilmes, P.; Andersson, A.; Kalnejais, L. H.; Verberkmoes, N. C.; Lefsrud, M. G.; Wexler, M.; Singer, S. W.; Shah, M.; Bond, P. L.; Thelen, M. P.; Hettich, R. L.; Banfield, J. F.

2007-12-01

The ability to link microbial community structure to function has long been a primary focus of environmental microbiology. With the advent of community genomic and proteomic techniques, along with advances in microscopic imaging techniques, it is now possible to gain insights into the organismal and functional makeup of microbial communities. Biofilms growing within highly acidic solutions inside the Richmond Mine (Iron Mountain, Redding, California) exhibit distinct macro- and microscopic morphologies. They are composed of microorganisms belonging to the three domains of life, including archaea, bacteria and eukarya. The proportion of each organismal type depends on sampling location and developmental stage. For example, mature biofilms floating on top of acid mine drainage (AMD) pools exhibit layers consisting of a densely packed bottom layer of the chemoautolithotroph Leptospirillum group II, a less dense top layer composed mainly of archaea, and fungal filaments spanning across the entire biofilm. The expression of cytochrome 579 (the most highly abundant protein in the biofilm, believed to be central to iron oxidation and encoded by Leptospirillum group II) is localized at the interface of the biofilm with the AMD solution, highlighting that biofilm architecture is reflected at the functional gene expression level. Distinct functional partitioning is also apparent in a biological wastewater treatment system that selects for distinct polyphosphate accumulating organisms. Community genomic data from " Candidatus Accumulibacter phosphatis" dominated activated sludge has enabled high mass-accuracy shotgun proteomics for identification of key metabolic pathways. Comprehensive genome-wide alignment of orthologous proteins suggests distinct partitioning of protein variants involved in both core-metabolism and specific metabolic pathways among the dominant population and closely related species. In addition, strain- resolved proteogenomic analysis of the AMD biofilms also highlights the importance of strain heterogeneity for the maintenance of community structure and function. These findings explain the importance of genetic diversity in facilitating the stable performance of complex microbial processes. Furthermore, although very different in terms of habitat, both microbial communities exhibit distinct functional compartmentalization and demonstrate its role in sustaining microbial community structure.

Genome-Enabled Modeling of Biogeochemical Processes Predicts Metabolic Dependencies that Connect the Relative Fitness of Microbial Functional Guilds

NASA Astrophysics Data System (ADS)

Brodie, E.; King, E.; Molins, S.; Karaoz, U.; Steefel, C. I.; Banfield, J. F.; Beller, H. R.; Anantharaman, K.; Ligocki, T. J.; Trebotich, D.

2015-12-01

Pore-scale processes mediated by microorganisms underlie a range of critical ecosystem services, regulating carbon stability, nutrient flux, and the purification of water. Advances in cultivation-independent approaches now provide us with the ability to reconstruct thousands of genomes from microbial populations from which functional roles may be assigned. With this capability to reveal microbial metabolic potential, the next step is to put these microbes back where they belong to interact with their natural environment, i.e. the pore scale. At this scale, microorganisms communicate, cooperate and compete across their fitness landscapes with communities emerging that feedback on the physical and chemical properties of their environment, ultimately altering the fitness landscape and selecting for new microbial communities with new properties and so on. We have developed a trait-based model of microbial activity that simulates coupled functional guilds that are parameterized with unique combinations of traits that govern fitness under dynamic conditions. Using a reactive transport framework, we simulate the thermodynamics of coupled electron donor-acceptor reactions to predict energy available for cellular maintenance, respiration, biomass development, and enzyme production. From metagenomics, we directly estimate some trait values related to growth and identify the linkage of key traits associated with respiration and fermentation, macromolecule depolymerizing enzymes, and other key functions such as nitrogen fixation. Our simulations were carried out to explore abiotic controls on community emergence such as seasonally fluctuating water table regimes across floodplain organic matter hotspots. Simulations and metagenomic/metatranscriptomic observations highlighted the many dependencies connecting the relative fitness of functional guilds and the importance of chemolithoautotrophic lifestyles. Using an X-Ray microCT-derived soil microaggregate physical model combined with genome-enabled reactive flow and transport we simulated the importance of pore network properties including connectivity in regulating metabolic interdependencies between microbial functional guilds.

Global investigation of composition and interaction networks in gut microbiomes of individuals belonging to diverse geographies and age-groups.

PubMed

Yadav, Deepak; Ghosh, Tarini Shankar; Mande, Sharmila S

2016-01-01

Factors like ethnicity, diet and age of an individual have been hypothesized to play a role in determining the makeup of gut microbiome. In order to investigate the gut microbiome structure as well as the inter-microbial associations present therein, we have performed a comprehensive global comparative profiling of the structure (composition, relative heterogeneity and diversity) and the inter-microbial networks in the gut microbiomes of 399 individuals of eight different nationalities. The study identified certain geography-specific trends with respect to composition, intra-group heterogeneity and diversity of the gut microbiomes. Interestingly, the gut microbial association/mutual-exlusion networks were observed to exhibit several cross-geography trends. It was seen that though the composition of gut microbiomes of the American and European individuals were similar, there were distinct patterns in their microbial interaction networks. Amongst European gut-microbiomes, the co-occurrence network obtained for the Danish population was observed to be most dense. Distinct patterns were also observed within Chinese, Japanese and Indian datasets. While performing an age-wise comparison, it was observed that the microbial interactions increased with the age of individuals. Furthermore, certain bacterial groups were identified to be present only in the older age groups. The trends observed in gut microbial networks could be due to the inherent differences in the diet of individuals belonging to different nationalities. For example, the higher number of microbial associations in the Danish population as compared to the Spanish population, may be attributed to the evenly distributed diet of the later. This is in line with previously reported findings which indicate an increase in functional interdependency of microbes in individuals with higher nutritional status. To summarise, the present study identifies geography and age specific patterns in the composition as well as microbial interactions in gut microbiomes.

Feedbacks Between Soil Structure and Microbial Activities in Soil

NASA Astrophysics Data System (ADS)

Bailey, V. L.; Smith, A. P.; Fansler, S.; Varga, T.; Kemner, K. M.; McCue, L. A.

2017-12-01

Soil structure provides the physical framework for soil microbial habitats. The connectivity and size distribution of soil pores controls the microbial access to nutrient resources for growth and metabolism. Thus, a crucial component of soil research is how a soil's three-dimensional structure and organization influences its biological potential on a multitude of spatial and temporal scales. In an effort to understand microbial processes at scale more consistent with a microbial community, we have used soil aggregates as discrete units of soil microbial habitats. Our research has shown that mean pore diameter (x-ray computed tomography) of soil aggregates varies with the aggregate diameter itself. Analyzing both the bacterial composition (16S) and enzyme activities of individual aggregates showed significant differences in the relative abundances of key members the microbial communities associated with high enzyme activities compared to those with low activities, even though we observed no differences in the size of the biomass, nor in the overall richness or diversity of these communities. We hypothesize that resources and substrates have stimulated key populations in the aggregates identified as highly active, and as such, we conducted further research that explored how such key populations (i.e. fungal or bacterial dominated populations) alter pathways of C accumulation in aggregate size domains and microbial C utilization. Fungi support and stabilize soil structure through both physical and chemical effects of their hyphal networks. In contrast, bacterial-dominated communities are purported to facilitate micro- and fine aggregate stabilization. Here we quantify the direct effects fungal versus bacterial dominated communities on aggregate formation (both the rate of aggregation and the quality, quantity and distribution of SOC contained within aggregates). A quantitative understanding of the different mechanisms through which fungi or bacteria shape aggregate formation could alter how we currently treat our predictions of soil biogeochemistry. Current predictions are largely site- or biome-specific; quantitative mechanisms could underpin "rules" that operate at the pore-scale leading to more robust, mechanistic models.

Construction of PAH-degrading mixed microbial consortia by induced selection in soil.

PubMed

Zafra, German; Absalón, Ángel E; Anducho-Reyes, Miguel Ángel; Fernandez, Francisco J; Cortés-Espinosa, Diana V

2017-04-01

Bioremediation of polycyclic aromatic hydrocarbons (PAHs)-contaminated soils through the biostimulation and bioaugmentation processes can be a strategy for the clean-up of oil spills and environmental accidents. In this work, an induced microbial selection method using PAH-polluted soils was successfully used to construct two microbial consortia exhibiting high degradation levels of low and high molecular weight PAHs. Six fungal and seven bacterial native strains were used to construct mixed consortia with the ability to tolerate high amounts of phenanthrene (Phe), pyrene (Pyr) and benzo(a)pyrene (BaP) and utilize these compounds as a sole carbon source. In addition, we used two engineered PAH-degrading fungal strains producing heterologous ligninolytic enzymes. After a previous selection using microbial antagonism tests, the selection was performed in microcosm systems and monitored using PCR-DGGE, CO 2 evolution and PAH quantitation. The resulting consortia (i.e., C1 and C2) were able to degrade up to 92% of Phe, 64% of Pyr and 65% of BaP out of 1000 mg kg -1 of a mixture of Phe, Pyr and BaP (1:1:1) after a two-week incubation. The results indicate that constructed microbial consortia have high potential for soil bioremediation by bioaugmentation and biostimulation and may be effective for the treatment of sites polluted with PAHs due to their elevated tolerance to aromatic compounds, their capacity to utilize them as energy source. Copyright © 2016 Elsevier Ltd. All rights reserved.

The effect of microbial degradation on the chromatographic profiles of tiki torch fuel, lamp oil, and turpentine.

PubMed

Turner, Dee A; Goodpaster, John V

2011-07-01

Biodegradation can result in selective removal of many of the compounds required for the identification of an ignitable liquid. In this study, the effects of microbial degradation on tiki torch fuel, lamp oil, and turpentine are reported. Samples of soil spiked with 20 μL of the liquids were stored at room temperature for up to 7 days. The ignitable liquids were then recovered using passive headspace concentration onto charcoal strips followed by solvent elution using pentane. Microbial degradation of tiki torch fuel resulted in the loss of the n-alkanes relative to the branched alkanes. Changes in the profile of the lamp oil were minor due to the highly branched nature of its alkanes. Microbial degradation of turpentine resulted in the selective loss of limonene and o-cymene. Overall, significant degradation by microbial action could result in the inability to identify the presence of an ignitable liquid or misclassify the ignitable liquid found. © 2011 American Academy of Forensic Sciences.

Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation.

PubMed

Simmons, Sheri L; Dibartolo, Genevieve; Denef, Vincent J; Goltsman, Daniela S Aliaga; Thelen, Michael P; Banfield, Jillian F

2008-07-22

Deeply sampled community genomic (metagenomic) datasets enable comprehensive analysis of heterogeneity in natural microbial populations. In this study, we used sequence data obtained from the dominant member of a low-diversity natural chemoautotrophic microbial community to determine how coexisting closely related individuals differ from each other in terms of gene sequence and gene content, and to uncover evidence of evolutionary processes that occur over short timescales. DNA sequence obtained from an acid mine drainage biofilm was reconstructed, taking into account the effects of strain variation, to generate a nearly complete genome tiling path for a Leptospirillum group II species closely related to L. ferriphilum (sampling depth approximately 20x). The population is dominated by one sequence type, yet we detected evidence for relatively abundant variants (>99.5% sequence identity to the dominant type) at multiple loci, and a few rare variants. Blocks of other Leptospirillum group II types ( approximately 94% sequence identity) have recombined into one or more variants. Variant blocks of both types are more numerous near the origin of replication. Heterogeneity in genetic potential within the population arises from localized variation in gene content, typically focused in integrated plasmid/phage-like regions. Some laterally transferred gene blocks encode physiologically important genes, including quorum-sensing genes of the LuxIR system. Overall, results suggest inter- and intrapopulation genetic exchange involving distinct parental genome types and implicate gain and loss of phage and plasmid genes in recent evolution of this Leptospirillum group II population. Population genetic analyses of single nucleotide polymorphisms indicate variation between closely related strains is not maintained by positive selection, suggesting that these regions do not represent adaptive differences between strains. Thus, the most likely explanation for the observed patterns of polymorphism is divergence of ancestral strains due to geographic isolation, followed by mixing and subsequent recombination.

Population Genomic Analysis of Strain Variation in Leptospirillum Group II Bacteria Involved in Acid Mine Drainage Formation

PubMed Central

Denef, Vincent J; Goltsman, Daniela S. Aliaga; Thelen, Michael P; Banfield, Jillian F

2008-01-01

Deeply sampled community genomic (metagenomic) datasets enable comprehensive analysis of heterogeneity in natural microbial populations. In this study, we used sequence data obtained from the dominant member of a low-diversity natural chemoautotrophic microbial community to determine how coexisting closely related individuals differ from each other in terms of gene sequence and gene content, and to uncover evidence of evolutionary processes that occur over short timescales. DNA sequence obtained from an acid mine drainage biofilm was reconstructed, taking into account the effects of strain variation, to generate a nearly complete genome tiling path for a Leptospirillum group II species closely related to L. ferriphilum (sampling depth ∼20×). The population is dominated by one sequence type, yet we detected evidence for relatively abundant variants (>99.5% sequence identity to the dominant type) at multiple loci, and a few rare variants. Blocks of other Leptospirillum group II types (∼94% sequence identity) have recombined into one or more variants. Variant blocks of both types are more numerous near the origin of replication. Heterogeneity in genetic potential within the population arises from localized variation in gene content, typically focused in integrated plasmid/phage-like regions. Some laterally transferred gene blocks encode physiologically important genes, including quorum-sensing genes of the LuxIR system. Overall, results suggest inter- and intrapopulation genetic exchange involving distinct parental genome types and implicate gain and loss of phage and plasmid genes in recent evolution of this Leptospirillum group II population. Population genetic analyses of single nucleotide polymorphisms indicate variation between closely related strains is not maintained by positive selection, suggesting that these regions do not represent adaptive differences between strains. Thus, the most likely explanation for the observed patterns of polymorphism is divergence of ancestral strains due to geographic isolation, followed by mixing and subsequent recombination. PMID:18651792

Microbial cleavage of organic C-S bonds

DOEpatents

Kilbane, J.J. II.

1994-10-25

A microbial process is described for selective cleavage of organic C-S bonds which may be used for reducing the sulfur content of sulfur-containing organic carbonaceous materials. Microorganisms of Rhodococcus rhodochrous and Bacillus sphaericus have been found which have the ability of selective cleavage of organic C-S bonds. Particularly preferred microorganisms are Rhodococcus rhodochrous strain ATCC 53968 and Bacillus sphaericus strain ATCC 53969 and their derivatives.

Microbial cleavage of organic C-S bonds

DOEpatents

Kilbane, II, John J.

1994-01-01

A microbial process for selective cleavage of organic C--S bonds which may be used for reducing the sulfur content of sulfur-containing organic carbonaceous materials, Microorganisms of Rhodococcus rhodochrous and Bacillus sphaericus have been found which have the ability of selective cleavage of organic C--S bonds. Particularly preferred microorganisms are Rhodococcus rhodochrous strain ATCC 53968 and Bacillus sphaericus strain ATCC 53969 and their derivatives.

Comparative analysis of fecal microbial communities in cattle and Bactrian camels

PubMed Central

Ming, Liang; Yi, Li; Siriguleng; Hasi, Surong; He, Jing; Hai, Le; Wang, Zhaoxia; Guo, Fucheng; Qiao, Xiangyu; Jirimutu

2017-01-01

Bactrian camels may have a unique gastrointestinal (GI) microbiome because of their distinctive digestive systems, unique eating habits and extreme living conditions. However, understanding of the microbial communities in the Bactrian camel GI tract is still limited. In this study, microbial communities were investigated by comparative analyses of 16S rRNA hypervariable region V4 sequences of fecal bacteria sampled from 94 animals in four population groups: Inner Mongolian cattle (IMG-Cattle), Inner Mongolian domestic Bactrian camels (IMG-DBC), Mongolian domestic Bactrian camels (MG-DBC), and Mongolian wild Bactrian camels (MG-WBC). A total of 2,097,985 high-quality reads were obtained and yielded 471,767,607 bases of sequence. Firmicutes was the predominant phylum in the population groups IMG-Cattle, IMG-DBC and MG-WBC, followed (except in the Inner Mongolian cattle) by Verrucomicrobia. Bacteroidetes were abundant in the IMG-DBC and MG-WBC populations. Hierarchical clustered heatmap analysis revealed that the microbial community composition within the three Bactrian camel groups was relatively similar, and somewhat distinct from that in the cattle. A similar result was determined by principal component analysis, in which the camels grouped together. We also found several species-specific differences in microbial communities at the genus level: for example, Desulfovibrio was abundant in the IMG-DBC and MG-WBC groups; Pseudomonas was abundant in the IMG-Cattle group; and Fibrobacter, Coprobacillus, and Paludibacter were scarce in the MG-WBC group. Such differences may be related to different eating habits and living conditions of the cattle and the various camel populations. PMID:28301489

Selection of bioindicators to detect lead pollution in Ebro delta microbial mats, using high-resolution microscopic techniques.

PubMed

Maldonado, J; Solé, A; Puyen, Z M; Esteve, I

2011-07-01

Lead (Pb) is a metal that is non-essential to any metabolic process and, moreover, highly deleterious to life. In microbial mats - benthic stratified ecosystems - located in coastal areas, phototrophic microorganisms (algae and oxygenic phototrophic bacteria) are the primary producers and they are exposed to pollution by metals. In this paper we describe the search for bioindicators among phototrophic populations of Ebro delta microbial mats, using high-resolution microscopic techniques that we have optimized in previous studies. Confocal laser scanning microscopy coupled to a spectrofluorometric detector (CLSM-λscan) to determine in vivo sensitivity of different cyanobacteria to lead, and scanning electron microscopy (SEM) and transmission electron microscopy (TEM), both coupled to energy dispersive X-ray microanalysis (EDX), to determine the extra- and intracellular sequestration of this metal in cells, were the techniques used for this purpose. Oscillatoria sp. PCC 7515, Chroococcus sp. PCC 9106 and Spirulina sp. PCC 6313 tested in this paper could be considered bioindicators for lead pollution, because all of these microorganisms are indigenous, have high tolerance to high concentrations of lead and are able to accumulate this metal externally in extracellular polymeric substances (EPS) and intracellularly in polyphosphate (PP) inclusions. Experiments made with microcosms demonstrated that Phormidium-like and Lyngbya-like organisms selected themselves at the highest concentrations of lead assayed. In the present study it is shown that all cyanobacteria studied (both in culture and in microcosms) present PP inclusions in their cytoplasm and that these increase in number in lead polluted cultures and microcosms. We believe that the application of these microscopic techniques open up broad prospects for future studies of metal ecotoxicity. Copyright © 2011 Elsevier B.V. All rights reserved.

Variation in microbial activity in histosols and its relationship to soil moisture.

PubMed

Tate, R L; Terry, R E

1980-08-01

Microbial biomass, dehydrogenase activity, carbon metabolism, and aerobic bacterial populations were examined in cropped and fallow Pahokee muck (a lithic medisaprist) of the Florida Everglades. Dehydrogenase activity was two- to sevenfold greater in soil cropped to St. Augustinegrass (Stenotaphrum secundatum (Walt) Kuntz) compared with uncropped soil, whereas biomass ranged from equivalence in the two soils to a threefold stimulation in the cropped soil. Biomass in soil cropped to sugarcane (Saccharum spp. L) approximated that from the grass field, whereas dehydrogenase activities of the cane soil were nearly equivalent to those of the fallow soil. Microbial biomass, dehydrogenase activity, aerobic bacterial populations, and salicylate oxidation rates all correlated with soil moisture levels. These data indicate that within the moisture ranges detected in the surface soils, increased moisture stimulated microbial activity, whereas within the soil profile where moisture ranges reached saturation, increased moisture inhibited aerobic activities and stimulated anaerobic processes.

Variation in Microbial Activity in Histosols and Its Relationship to Soil Moisture †

PubMed Central

Tate, Robert L.; Terry, Richard E.

1980-01-01

Microbial biomass, dehydrogenase activity, carbon metabolism, and aerobic bacterial populations were examined in cropped and fallow Pahokee muck (a lithic medisaprist) of the Florida Everglades. Dehydrogenase activity was two- to sevenfold greater in soil cropped to St. Augustinegrass (Stenotaphrum secundatum (Walt) Kuntz) compared with uncropped soil, whereas biomass ranged from equivalence in the two soils to a threefold stimulation in the cropped soil. Biomass in soil cropped to sugarcane (Saccharum spp. L) approximated that from the grass field, whereas dehydrogenase activities of the cane soil were nearly equivalent to those of the fallow soil. Microbial biomass, dehydrogenase activity, aerobic bacterial populations, and salicylate oxidation rates all correlated with soil moisture levels. These data indicate that within the moisture ranges detected in the surface soils, increased moisture stimulated microbial activity, whereas within the soil profile where moisture ranges reached saturation, increased moisture inhibited aerobic activities and stimulated anaerobic processes. PMID:16345610

Genomic investigations of evolutionary dynamics and epistasis in microbial evolution experiments.

PubMed

Jerison, Elizabeth R; Desai, Michael M

2015-12-01

Microbial evolution experiments enable us to watch adaptation in real time, and to quantify the repeatability and predictability of evolution by comparing identical replicate populations. Further, we can resurrect ancestral types to examine changes over evolutionary time. Until recently, experimental evolution has been limited to measuring phenotypic changes, or to tracking a few genetic markers over time. However, recent advances in sequencing technology now make it possible to extensively sequence clones or whole-population samples from microbial evolution experiments. Here, we review recent work exploiting these techniques to understand the genomic basis of evolutionary change in experimental systems. We first focus on studies that analyze the dynamics of genome evolution in microbial systems. We then survey work that uses observations of sequence evolution to infer aspects of the underlying fitness landscape, concentrating on the epistatic interactions between mutations and the constraints these interactions impose on adaptation. Copyright © 2015 Elsevier Ltd. All rights reserved.

Trichoderma harzianum MTCC 5179 impacts the population and functional dynamics of microbial community in the rhizosphere of black pepper (Piper nigrum L.).

PubMed

Umadevi, Palaniyandi; Anandaraj, Muthuswamy; Srivastav, Vivek; Benjamin, Sailas

2017-11-29

Employing Illumina Hiseq whole genome metagenome sequencing approach, we studied the impact of Trichoderma harzianum on altering the microbial community and its functional dynamics in the rhizhosphere soil of black pepper (Piper nigrum L.). The metagenomic datasets from the rhizosphere with (treatment) and without (control) T. harzianum inoculation were annotated using dual approach, i.e., stand alone and MG-RAST. The probiotic application of T. harzianum in the rhizhosphere soil of black pepper impacted the population dynamics of rhizosphere bacteria, archae, eukaryote as reflected through the selective recruitment of bacteria [Acidobacteriaceae bacterium (p=1.24e-12), Candidatus koribacter versatilis (p=2.66e-10)] and fungi [(Fusarium oxysporum (p=0.013), Talaromyces stipitatus (p=0.219) and Pestalotiopsis fici (p=0.443)] in terms of abundance in population and bacterial chemotaxis (p=0.012), iron metabolism (p=2.97e-5) with the reduction in abundance for pathogenicity islands (p=7.30e-3), phages and prophages (p=7.30e-3) with regard to functional abundance. Interestingly, it was found that the enriched functional metagenomic signatures on phytoremediation such as benzoate transport and degradation (p=2.34e-4), and degradation of heterocyclic aromatic compounds (p=3.59e-13) in the treatment influenced the rhizosphere micro ecosystem favoring growth and health of pepper plant. The population dynamics and functional richness of rhizosphere ecosystem in black pepper influenced by the treatment with T. harzianum provides the ecological importance of T. harzianum in the cultivation of black pepper. Copyright © 2017 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Effects of Momordica charantia Saponins on In vitro Ruminal Fermentation and Microbial Population

PubMed Central

Kang, Jinhe; Zeng, Bo; Tang, Shaoxun; Wang, Min; Han, Xuefeng; Zhou, Chuanshe; Yan, Qiongxian; He, Zhixiong; Liu, Jinfu; Tan, Zhiliang

2016-01-01

This study was conducted to investigate the effects of Momordica charantia saponin (MCS) on ruminal fermentation of maize stover and abundance of selected microbial populations in vitro. Five levels of MCS supplements (0, 0.01, 0.06, 0.30, 0.60 mg/mL) were tested. The pH, NH3-N, and volatile fatty acid were measured at 6, 24, 48 h of in vitro mixed incubation fluids, whilst the selected microbial populations were determined at 6 and 24 h. The high dose of MCS increased the initial fractional rate of degradation at t-value = 0 (FRD0) and the fractional rate of gas production (k), but decreased the theoretical maximum of gas production (VF) and the half-life (t0.5) compared with the control. The NH3-N concentration reached the lowest concentration with 0.01 mg MCS/mL at 6 h. The MSC inclusion increased (p<0.001) the molar proportion of butyrate, isovalerate at 24 h and 48 h, and the molar proportion of acetate at 24 h, but then decreased (p<0.05) them at 48 h. The molar proportion of valerate was increased (p<0.05) at 24 h. The acetate to propionate ratio (A/P; linear, p<0.01) was increased at 24 h, but reached the least value at the level of 0.30 mg/mL MCS. The MCS inclusion decreased (p<0.05) the molar proportion of propionate at 24 h and then increased it at 48 h. The concentration of total volatile fatty acid was decreased (p<0.001) at 24 h, but reached the greatest concentration at the level of 0.01 mg/mL and the least concentration at the level of 0.60 mg/mL. The relative abundance of Ruminococcus albus was increased at 6 h and 24 h, and the relative abundance of Fibrobacter succinogenes was the lowest (p<0.05) at 0.60 mg/mL at 6 h and 24 h. The relative abundance of Butyrivibrio fibrisolvens and fungus reached the greatest value (p<0.05) at low doses of MCS inclusion and the least value (p<0.05) at 0.60 mg/mL at 24 h. The present results demonstrates that a high level of MCS quickly inhibits in vitro fermentation of maize stover, while MCS at low doses has the ability to modulate the ruminal fermentation pattern by regulating the number of functional rumen microbes including cellulolytic bacteria and fungi populations, and may have potential as a feed additive applied in the diets of ruminants. PMID:26949950

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

Konopka, Allan

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

The effect of D123 wheat as a companion crop on soil enzyme activities, microbial biomass and microbial communities in the rhizosphere of watermelon.

PubMed

Xu, Weihui; Wang, Zhigang; Wu, Fengzhi

2015-01-01

The growth of watermelon is often threatened by Fusarium oxysporum f. sp. niveum (Fon) in successively monocultured soil, which results in economic loss. The objective of this study was to investigate the effect of D123 wheat as a companion crop on soil enzyme activities, microbial biomass and microbial communities in the rhizosphere of watermelon and to explore the relationship between the effect and the incidence of wilt caused by Fon. The results showed that the activities of soil polyphenol oxidase, urease and invertase were increased, the microbial biomass nitrogen (MBN) and microbial biomass phosphorus (MBP) were significantly increased, and the ratio of MBC/MBN was decreased (P < 0.05). Real-time PCR analysis showed that the Fon population declined significantly in the watermelon/wheat companion system compared with the monoculture system (P < 0.05). The analysis of microbial communities showed that the relative abundance of microbial communities was changed in the rhizosphere of watermelon. Compared with the monoculture system, the relative abundances of Alphaproteobacteria, Actinobacteria, Gemmatimonadetes and Sordariomycetes were increased, and the relative abundances of Gammaproteobacteria, Sphingobacteria, Cytophagia, Pezizomycetes, and Eurotiomycetes were decreased in the rhizosphere of watermelon in the watermelon/wheat companion system; importantly, the incidence of Fusarium wilt was also decreased in the watermelon/wheat companion system. In conclusion, this study indicated that D123 wheat as a companion crop increased soil enzyme activities and microbial biomass, decreased the Fon population, and changed the relative abundance of microbial communities in the rhizosphere of watermelon, which may be related to the reduction of Fusarium wilt in the watermelon/wheat companion system.

Phylogenetic and Evolutionary Patterns in Microbial Carotenoid Biosynthesis Are Revealed by Comparative Genomics

PubMed Central

Klassen, Jonathan L.

2010-01-01

Background Carotenoids are multifunctional, taxonomically widespread and biotechnologically important pigments. Their biosynthesis serves as a model system for understanding the evolution of secondary metabolism. Microbial carotenoid diversity and evolution has hitherto been analyzed primarily from structural and biosynthetic perspectives, with the few phylogenetic analyses of microbial carotenoid biosynthetic proteins using either used limited datasets or lacking methodological rigor. Given the recent accumulation of microbial genome sequences, a reappraisal of microbial carotenoid biosynthetic diversity and evolution from the perspective of comparative genomics is warranted to validate and complement models of microbial carotenoid diversity and evolution based upon structural and biosynthetic data. Methodology/Principal Findings Comparative genomics were used to identify and analyze in silico microbial carotenoid biosynthetic pathways. Four major phylogenetic lineages of carotenoid biosynthesis are suggested composed of: (i) Proteobacteria; (ii) Firmicutes; (iii) Chlorobi, Cyanobacteria and photosynthetic eukaryotes; and (iv) Archaea, Bacteroidetes and two separate sub-lineages of Actinobacteria. Using this phylogenetic framework, specific evolutionary mechanisms are proposed for carotenoid desaturase CrtI-family enzymes and carotenoid cyclases. Several phylogenetic lineage-specific evolutionary mechanisms are also suggested, including: (i) horizontal gene transfer; (ii) gene acquisition followed by differential gene loss; (iii) co-evolution with other biochemical structures such as proteorhodopsins; and (iv) positive selection. Conclusions/Significance Comparative genomics analyses of microbial carotenoid biosynthetic proteins indicate a much greater taxonomic diversity then that identified based on structural and biosynthetic data, and divides microbial carotenoid biosynthesis into several, well-supported phylogenetic lineages not evident previously. This phylogenetic framework is applicable to understanding the evolution of specific carotenoid biosynthetic proteins or the unique characteristics of carotenoid biosynthetic evolution in a specific phylogenetic lineage. Together, these analyses suggest a “bramble” model for microbial carotenoid biosynthesis whereby later biosynthetic steps exhibit greater evolutionary plasticity and reticulation compared to those closer to the biosynthetic “root”. Structural diversification may be constrained (“trimmed”) where selection is strong, but less so where selection is weaker. These analyses also highlight likely productive avenues for future research and bioprospecting by identifying both gaps in current knowledge and taxa which may particularly facilitate carotenoid diversification. PMID:20582313

Mapping the ecological networks of microbial communities.

PubMed

Xiao, Yandong; Angulo, Marco Tulio; Friedman, Jonathan; Waldor, Matthew K; Weiss, Scott T; Liu, Yang-Yu

2017-12-11

Mapping the ecological networks of microbial communities is a necessary step toward understanding their assembly rules and predicting their temporal behavior. However, existing methods require assuming a particular population dynamics model, which is not known a priori. Moreover, those methods require fitting longitudinal abundance data, which are often not informative enough for reliable inference. To overcome these limitations, here we develop a new method based on steady-state abundance data. Our method can infer the network topology and inter-taxa interaction types without assuming any particular population dynamics model. Additionally, when the population dynamics is assumed to follow the classic Generalized Lotka-Volterra model, our method can infer the inter-taxa interaction strengths and intrinsic growth rates. We systematically validate our method using simulated data, and then apply it to four experimental data sets. Our method represents a key step towards reliable modeling of complex, real-world microbial communities, such as the human gut microbiota.

A Microbial Assessment Scheme to measure microbial performance of Food Safety Management Systems.

PubMed

Jacxsens, L; Kussaga, J; Luning, P A; Van der Spiegel, M; Devlieghere, F; Uyttendaele, M

2009-08-31

A Food Safety Management System (FSMS) implemented in a food processing industry is based on Good Hygienic Practices (GHP), Hazard Analysis Critical Control Point (HACCP) principles and should address both food safety control and assurance activities in order to guarantee food safety. One of the most emerging challenges is to assess the performance of a present FSMS. The objective of this work is to explain the development of a Microbial Assessment Scheme (MAS) as a tool for a systematic analysis of microbial counts in order to assess the current microbial performance of an implemented FSMS. It is assumed that low numbers of microorganisms and small variations in microbial counts indicate an effective FSMS. The MAS is a procedure that defines the identification of critical sampling locations, the selection of microbiological parameters, the assessment of sampling frequency, the selection of sampling method and method of analysis, and finally data processing and interpretation. Based on the MAS assessment, microbial safety level profiles can be derived, indicating which microorganisms and to what extent they contribute to food safety for a specific food processing company. The MAS concept is illustrated with a case study in the pork processing industry, where ready-to-eat meat products are produced (cured, cooked ham and cured, dried bacon).

Application and microbial preparation of D-valine.

PubMed

Chen, Ming; Shi, Chao; Zhao, Jing; Gao, Ziqing; Zhang, Chunzhi

2016-10-01

D-Valine is an important organic chiral source and has extensive industrial application, which is used as intermediate for the synthesis of agricultural pesticides, semi-synthetic veterinary antibiotics and pharmaceutical drugs. Its derivatives have shown great activity in clinical use, such as penicillamine for the treatment of immune-deficiency diseases, and actinomycin D for antitumor therapy. Fluvalinate, a pyrethroid pesticide made from D-valine, is a broad-spectrum insecticide with low mammalian toxicity. Valnemulin, a semi-synthetic pleuromutilin derivative synthesized from D-valine, is an antibiotic for animals. Moreover, D-valine is also used in cell culture for selectively inhibiting fibroblasts proliferation. Due to its widespread application, D-valine is gaining more and more attention and some approaches for D-valine preparation have been investigated. In comparison with other approaches, microbial preparation of D-valine is more competitive and promising because of its high stereo selectivity, mild reaction conditions and environmental friendly process. So far, microbial preparation of D-valine can be mainly classified into three categories: microbial asymmetric degradation of DL-valine, microbial stereoselective hydrolysis of N-acyl-DL-valine by D-aminoacylase, and microbial specific hydrolysis of DL-5-isopropylhydantoin by D-hydantoinase coupled with D-carbamoylase. In this paper, the industrial application of D-valine and its microbial preparation are reviewed.

Analysis of rumen microbial populations in lactating dairy cattle fed diets varying in carbohydrate profiles and Saccharomyces cerevisiae fermentation product.

PubMed

Mullins, C R; Mamedova, L K; Carpenter, A J; Ying, Y; Allen, M S; Yoon, I; Bradford, B J

2013-09-01

The rumen microbial ecosystem is a critical factor that links diets to bovine physiology and productivity; however, information about dietary effects on microbial populations has generally been limited to small numbers of samples and qualitative assessment. To assess whether consistent shifts in microbial populations occur in response to common dietary manipulations in dairy cattle, samples of rumen contents were collected from 2 studies for analysis by quantitative real-time PCR (qPCR). In one study, lactating Holstein cows (n=8) were fed diets in which a nonforage fiber source replaced an increasing proportion of forages and concentrates in a 4×4 Latin square design, and samples of ruminal digesta were collected at 9-h intervals over 3 d at the end of each period. In the second study, lactating Holstein cows (n=15) were fed diets with or without the inclusion of a Saccharomyces cerevisiae fermentation product (SCFP) in a crossover design. In this study, rumen liquid and solid samples were collected during total rumen evacuations before and after feeding in a 42-h period. In total, 146 samples of ruminal digesta were used for microbial DNA isolation and analysis by qPCR. Validated primer sets were used to quantify total bacterial and anaerobic fungal populations as well as 12 well-studied bacterial taxa. The relative abundance of the target populations was similar to those previously reported. No significant treatment effects were observed for any target population. A significant interaction of treatment and dry matter intake was observed, however, for the abundance of Eubacterium ruminantium. Increasing dry matter intake was associated with a quadratic decrease in E. ruminantium populations in control animals but with a quadratic increase in E.ruminantium populations in cows fed SCFP. Analysis of sample time effects revealed that Fibrobacter succinogenes and fungal populations were more abundant postfeeding, whereas Ruminococcus albus tended to be more abundant prefeeding. Seven of the target taxa were more abundant in either the liquid or solid fractions of ruminal digesta. By accounting for the total mass of liquid and solid fractions in the rumen and the relative abundance of total bacteria in each fraction, it was estimated that 92% of total bacteria were found in the solid digesta fraction. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Regime Shift and Microbial Dynamics in a Sequencing Batch Reactor for Nitrification and Anammox Treatment of Urine ▿†

PubMed Central

Bürgmann, Helmut; Jenni, Sarina; Vazquez, Francisco; Udert, Kai M.

2011-01-01

The microbial population and physicochemical process parameters of a sequencing batch reactor for nitrogen removal from urine were monitored over a 1.5-year period. Microbial community fingerprinting (automated ribosomal intergenic spacer analysis), 16S rRNA gene sequencing, and quantitative PCR on nitrogen cycle functional groups were used to characterize the microbial population. The reactor combined nitrification (ammonium oxidation)/anammox with organoheterotrophic denitrification. The nitrogen elimination rate initially increased by 400%, followed by an extended period of performance degradation. This phase was characterized by accumulation of nitrite and nitrous oxide, reduced anammox activity, and a different but stable microbial community. Outwashing of anammox bacteria or their inhibition by oxygen or nitrite was insufficient to explain reactor behavior. Multiple lines of evidence, e.g., regime-shift analysis of chemical and physical parameters and cluster and ordination analysis of the microbial community, indicated that the system had experienced a rapid transition to a new stable state that led to the observed inferior process rates. The events in the reactor can thus be interpreted to be an ecological regime shift. Constrained ordination indicated that the pH set point controlling cycle duration, temperature, airflow rate, and the release of nitric and nitrous oxides controlled the primarily heterotrophic microbial community. We show that by combining chemical and physical measurements, microbial community analysis and ecological theory allowed extraction of useful information about the causes and dynamics of the observed process instability. PMID:21724875

Changes in microbial structure and functional communities at different soil depths during 13C labelled root litter degradation

NASA Astrophysics Data System (ADS)

Sanaullah, Muhammad; Baumann, Karen; Chabbi, Abad; Dignac, Marie-France; Maron, Pierre-Alain; Kuzyakov, Yakov; Rumpel, Cornelia

2014-05-01

Soil organic matter turnover depends on substrate quality and microbial activity in soil but little is known about how addition of freshly added organic material modifies the diversity of soil microbial communities with in a soil profile. We took advantage of a decomposition experiment, which was carried out at different soil depths under field conditions and sampled litterbags with 13C-labelled wheat roots, incubated in subsoil horizons at 30, 60 and 90 cm depth for up to 36 months. The effect of root litter addition on microbial community structure, diversity and activity was studied by determining total microbial biomass, PLFA signatures, molecular tools (DNA genotyping and pyrosequencing of 16S and 18S rDNAs) and extracellular enzyme activities. Automated ribosomal intergenic spacer analysis (ARISA) was also carried out to determine the differences in microbial community structure. We found that with the addition of root litter, total microbial biomass as well as microbial community composition and structure changed at different soil depths and change was significantly higher at top 30cm soil layer. Moreover, in the topsoil, population of both gram-positive and gram-negative bacteria increased with root litter addition over time, while subsoil horizons were relatively dominated by fungal community. Extra-cellular enzyme activities confirmed relatively higher fungal community at subsoil horizons compared with surface soil layer with bacteria dominant microbial population. Bacterial-ARISA profiling illustrated that the addition of root litter enhanced the abundance of Actinobacteria and Proteobacteria, at all three soil depths. These bacteria correspond to copiotrophic attributes, which can preferentially consume of labile soil organic C pools. While disappearance of oligotrophic Acidobacteria confirmed the shifting of microbial communities due to the addition of readily available substrate. We concluded that root litter mixing altered microbial community development which was soil horizon specific and its effects on soil microbial activity may impact on nutrient cycling.

Granule Formation Mechanisms within an Aerobic Wastewater System for Phosphorus Removal▿ †

PubMed Central

Barr, Jeremy J.; Cook, Andrew E.; Bond, Phillip L.

2010-01-01

Granular sludge is a novel alternative for the treatment of wastewater and offers numerous operational and economic advantages over conventional floccular-sludge systems. The majority of research on granular sludge has focused on optimization of engineering aspects relating to reactor operation with little emphasis on the fundamental microbiology. In this study, we hypothesize two novel mechanisms for granule formation as observed in three laboratory scale sequencing batch reactors operating for biological phosphorus removal and treating two different types of wastewater. During the initial stages of granulation, two distinct granule types (white and yellow) were distinguished within the mixed microbial population. White granules appeared as compact, smooth, dense aggregates dominated by 97.5% “Candidatus Accumulibacter phosphatis,” and yellow granules appeared as loose, rough, irregular aggregates with a mixed microbial population of 12.3% “Candidatus Accumulibacter phosphatis” and 57.9% “Candidatus Competibacter phosphatis,” among other bacteria. Microscopy showed white granules as homogeneous microbial aggregates and yellow granules as segregated, microcolony-like aggregates, with phylogenetic analysis suggesting that the granule types are likely not a result of strain-associated differences. The microbial community composition and arrangement suggest different formation mechanisms occur for each granule type. White granules are hypothesized to form by outgrowth from a single microcolony into a granule dominated by one bacterial type, while yellow granules are hypothesized to form via multiple microcolony aggregation into a microcolony-segregated granule with a mixed microbial population. Further understanding and application of these mechanisms and the associated microbial ecology may provide conceptual information benefiting start-up procedures for full-scale granular-sludge reactors. PMID:20851963

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

PubMed

Kim, Hyeun Bum; Isaacson, Richard E

2015-06-12

The importance of the gut microbiota of animals is widely acknowledged because of its pivotal roles in the health and well being of animals. The genetic diversity of the gut microbiota contributes to the overall development and metabolic needs of the animal, and provides the host with many beneficial functions including production of volatile fatty acids, re-cycling of bile salts, production of vitamin K, cellulose digestion, and development of immune system. Thus the intestinal microbiota of animals has been the subject of study for many decades. Although most of the older studies have used culture dependent methods, the recent advent of high throughput sequencing of 16S rRNA genes has facilitated in depth studies exploring microbial populations and their dynamics in the animal gut. These culture independent DNA based studies generate large amounts of data and as a result contribute to a more detailed understanding of the microbiota dynamics in the gut and the ecology of the microbial populations. Of equal importance, is being able to identify and quantify microbes that are difficult to grow or that have not been grown in the laboratory. Interpreting the data obtained from this type of study requires using basic principles of microbial diversity to understand importance of the composition of microbial populations. In this review, we summarize the literature on culture independent studies of the pig gut microbiota with an emphasis on its succession and alterations caused by diverse factors. Copyright © 2015 Elsevier B.V. All rights reserved.

Identification of microbes from the surfaces of food-processing lines based on the flow cytometric evaluation of cellular metabolic activity combined with cell sorting.

PubMed

Juzwa, W; Duber, A; Myszka, K; Białas, W; Czaczyk, K

2016-09-01

In this study the design of a flow cytometry-based procedure to facilitate the detection of adherent bacteria from food-processing surfaces was evaluated. The measurement of the cellular redox potential (CRP) of microbial cells was combined with cell sorting for the identification of microorganisms. The procedure enhanced live/dead cell discrimination owing to the measurement of the cell physiology. The microbial contamination of the surface of a stainless steel conveyor used to process button mushrooms was evaluated in three independent experiments. The flow cytometry procedure provided a step towards monitoring of contamination and enabled the assessment of microbial food safety hazards by the discrimination of active, mid-active and non-active bacterial sub-populations based on determination of their cellular vitality and subsequently single cell sorting to isolate microbial strains from discriminated sub-populations. There was a significant correlation (r = 0.97; p < 0.05) between the bacterial cell count estimated by the pour plate method and flow cytometry, despite there being differences in the absolute number of cells detected. The combined approach of flow cytometric CRP measurement and cell sorting allowed an in situ analysis of microbial cell vitality and the identification of species from defined sub-populations, although the identified microbes were limited to culturable cells.

Diversity of Anaerobic Microbes in Spacecraft Assembly Clean Rooms ▿ †

PubMed Central

Probst, Alexander; Vaishampayan, Parag; Osman, Shariff; Moissl-Eichinger, Christine; Andersen, Gary L.; Venkateswaran, Kasthuri

2010-01-01

Although the cultivable and noncultivable microbial diversity of spacecraft assembly clean rooms has been previously documented using conventional and state-of-the-art molecular techniques, the occurrence of obligate anaerobes within these clean rooms is still uncertain. Therefore, anaerobic bacterial communities of three clean-room facilities were analyzed during assembly of the Mars Science Laboratory rover. Anaerobic bacteria were cultured on several media, and DNA was extracted from suitable anaerobic enrichments and examined with conventional 16S rRNA gene clone library, as well as high-density phylogenetic 16S rRNA gene microarray (PhyloChip) technologies. The culture-dependent analyses predominantly showed the presence of clostridial and propionibacterial strains. The 16S rRNA gene sequences retrieved from clone libraries revealed distinct microbial populations associated with each clean-room facility, clustered exclusively within gram-positive organisms. PhyloChip analysis detected a greater microbial diversity, spanning many phyla of bacteria, and provided a deeper insight into the microbial community structure of the clean-room facilities. This study presents an integrated approach for assessing the anaerobic microbial population within clean-room facilities, using both molecular and cultivation-based analyses. The results reveal that highly diverse anaerobic bacterial populations persist in the clean rooms even after the imposition of rigorous maintenance programs and will pose a challenge to planetary protection implementation activities. PMID:20228115

Microbial Genetic Memory to Study Heterogeneous Soil Processes

NASA Astrophysics Data System (ADS)

Fulk, E. M.; Silberg, J. J.; Masiello, C. A.

2017-12-01

Microbes can be engineered to sense environmental conditions and produce a detectable output. These microbial biosensors have traditionally used visual outputs that are difficult to detect in soil. However, recently developed gas-producing biosensors can be used to noninvasively monitor complex soil processes such as horizontal gene transfer or cell-cell signaling. While these biosensors report on the fraction of a microbial population exposed to a process or chemical signal at the time of measurement, they do not record a "memory" of past exposure. Synthetic biologists have recently developed a suite of genetically encoded memory circuits capable of reporting on historical exposure to the signal rather than just the current state. We will provide an overview of the microbial memory systems that may prove useful to studying microbial decision-making in response to environmental conditions. Simple memory circuits can give a yes/no report of any past exposure to the signal (for example anaerobic conditions, osmotic stress, or high nitrate concentrations). More complicated systems can report on the order of exposure of a population to multiple signals or the experiences of spatially distinct populations, such as those in root vs. bulk soil. We will report on proof-of-concept experiments showing the function of a simple permanent memory system in soil-cultured microbes, and we will highlight additional applications. Finally, we will discuss challenges still to be addressed in applying these memory circuits for biogeochemical studies.

Evaluation of methods for the extraction of DNA from drinking water distribution system biofilms.

PubMed

Hwang, Chiachi; Ling, Fangqiong; Andersen, Gary L; LeChevallier, Mark W; Liu, Wen-Tso

2012-01-01

While drinking water biofilms have been characterized in various drinking water distribution systems (DWDS), little is known about the impact of different DNA extraction methods on the subsequent analysis of microbial communities in drinking water biofilms. Since different DNA extraction methods have been shown to affect the outcome of microbial community analysis in other environments, it is necessary to select a DNA extraction method prior to the application of molecular tools to characterize the complex microbial ecology of the DWDS. This study compared the quantity and quality of DNA yields from selected DWDS bacteria with different cell wall properties using five widely used DNA extraction methods. These were further selected and evaluated for their efficiency and reproducibility of DNA extraction from DWDS samples. Terminal restriction fragment length analysis and the 454 pyrosequencing technique were used to interpret the differences in microbial community structure and composition, respectively, from extracted DNA. Such assessments serve as a concrete step towards the determination of an optimal DNA extraction method for drinking water biofilms, which can then provide a reliable comparison of the meta-analysis results obtained in different laboratories.

Microbial translocation and microbiome dsybiosis in HIV-associated immune activation

PubMed Central

Zevin, Alexander S.; McKinnon, Lyle; Burgener, Adam; Klatt, Nichole R.

2016-01-01

Purpose of Review To describe the mechanisms and consequences of both microbial translocation and microbial dysbiosis in HIV infection. Recent Findings Microbes in HIV are likely playing a large role in contributing to HIV pathogenesis, morbidities and mortality. Two major disruptions to microbial systems in HIV infection include microbial translocation and microbiome dysbiosis. Microbial translocation occurs when the bacteria (or bacterial products) that should be in the lumen of the intestine translocate across the tight epithelial barrier into systemic circulation, where they contribute to inflammation and pathogenesis. This is associated with poorer health outcomes in HIV infected individuals. In addition, microbial populations in the GI tract are also altered after HIV infection, resulting in microbiome dysbiosis, which further exacerbates microbial translocation, epithelial barrier disruption, inflammation, and mucosal immune functioning. Summary Altered microbial regulation in HIV infection can lead to poor health outcomes, and understanding the mechanisms underlying microbial dysbiosis and translocation may result in novel pathways for therapeutic interventions. PMID:26679414

Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning.

PubMed

He, Zhili; Zhang, Ping; Wu, Linwei; Rocha, Andrea M; Tu, Qichao; Shi, Zhou; Wu, Bo; Qin, Yujia; Wang, Jianjun; Yan, Qingyun; Curtis, Daniel; Ning, Daliang; Van Nostrand, Joy D; Wu, Liyou; Yang, Yunfeng; Elias, Dwayne A; Watson, David B; Adams, Michael W W; Fields, Matthew W; Alm, Eric J; Hazen, Terry C; Adams, Paul D; Arkin, Adam P; Zhou, Jizhong

2018-02-20

Contamination from anthropogenic activities has significantly impacted Earth's biosphere. However, knowledge about how environmental contamination affects the biodiversity of groundwater microbiomes and ecosystem functioning remains very limited. Here, we used a comprehensive functional gene array to analyze groundwater microbiomes from 69 wells at the Oak Ridge Field Research Center (Oak Ridge, TN), representing a wide pH range and uranium, nitrate, and other contaminants. We hypothesized that the functional diversity of groundwater microbiomes would decrease as environmental contamination (e.g., uranium or nitrate) increased or at low or high pH, while some specific populations capable of utilizing or resistant to those contaminants would increase, and thus, such key microbial functional genes and/or populations could be used to predict groundwater contamination and ecosystem functioning. Our results indicated that functional richness/diversity decreased as uranium (but not nitrate) increased in groundwater. In addition, about 5.9% of specific key functional populations targeted by a comprehensive functional gene array (GeoChip 5) increased significantly ( P < 0.05) as uranium or nitrate increased, and their changes could be used to successfully predict uranium and nitrate contamination and ecosystem functioning. This study indicates great potential for using microbial functional genes to predict environmental contamination and ecosystem functioning. IMPORTANCE Disentangling the relationships between biodiversity and ecosystem functioning is an important but poorly understood topic in ecology. Predicting ecosystem functioning on the basis of biodiversity is even more difficult, particularly with microbial biomarkers. As an exploratory effort, this study used key microbial functional genes as biomarkers to provide predictive understanding of environmental contamination and ecosystem functioning. The results indicated that the overall functional gene richness/diversity decreased as uranium increased in groundwater, while specific key microbial guilds increased significantly as uranium or nitrate increased. These key microbial functional genes could be used to successfully predict environmental contamination and ecosystem functioning. This study represents a significant advance in using functional gene markers to predict the spatial distribution of environmental contaminants and ecosystem functioning toward predictive microbial ecology, which is an ultimate goal of microbial ecology. Copyright © 2018 He et al.

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.

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

PubMed

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

2013-09-01

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

Biogeochemical Processes in Microbial Ecosystems

NASA Technical Reports Server (NTRS)

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

2001-01-01

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

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

Geoelectrical Evidence of Microbial Degradation of Diesel Contaminated Sediments

NASA Astrophysics Data System (ADS)

Werkema, D. D.; Atekwana, E. A.; Rossbach, S.; Sauck, W. A.

2003-12-01

The alteration of physical properties by microbial activity in petroleum contaminated sediments was investigated using geophysical techniques in laboratory column experiments. Microbial population growth was determined by the Most Probable Number technique (MPN), community dynamics were determined by the rDNA intergenic spacer analysis (RISA), microbial mineralization of diesel fuel was assessed using dissolved inorganic carbon (DIC), enhanced mineral dissolution was determined by dissolved calcium, and the vertical geoelectrical profile was measured using DC resistivity (converted to conductivity). The columns simulated a saturation profile and contained sanitized, uniform sand with the following experimental treatments: diesel + microbes, diesel, microbes, and no treatment. After 16 months, two important conclusions were drawn. First, the relative increase in magnitude of the parameters measured was highest in the diesel + microbe column (showing at least 110% increase), lower in the diesel column and lowest (actually showing a decrease) in the column with no treatment. Further, the diesel + microbe column showed the greatest increase in oil degrading microbial populations (135%) compared to the column with no treatment, which showed no changes. Secondly, the depth at which the conductivity reached the maximum occurred within and slightly above the diesel layer (which represents a depth that was originally water wet). It was further observed that the relative change in bulk conductivity below the saturated zone is of a lower magnitude than above (<10%). These results suggest the diesel layer, and the zone slightly above, were the most biologically active. Additionally, the diesel + microbe column showed RISA fragments attributed to microbial succession typically observed in organic contaminant plumes. A simple Archie's Law analysis was used to estimate the pore water conductivities necessary to reproduce the bulk conductivity measured. This analysis shows that relative to the column with only microbes (selected as the control to be most representative of field conditions), the diesel column revealed a 2.3 fold increase and the diesel + microbe column showed a 3 fold increase in pore water conductivity. This increase was located within the diesel layer above the water saturated zone. Within the saturated zone, the no treatment column showed a 0.81 fold increase, the diesel column a 1.28, and the diesel + microbe column 1.45. We conclude from this study that microbial activity and the resultant biogeochemical changes played an important role in modifying the geoelectrical properties of aquifers and sediments rich in organic carbon and mineralized by bacteria by increasing the bulk conductivity. This conductive zone occurred within and immediately above the free-phase petroleum layer. In natural environments with high concentrations of organic compounds available as electron donors, geophysical techniques may potentially be used as indicators of microbial activity. Notice: This is an abstract of a proposed presentation and does not necessarily reflect the United States Environmental Protection Agency (EPA) policy. The actual presentation has not been peer reviewed by EPA. Mention of trade names or commercial products does not constitute endorsement or recommendation for use.

Microbial diversity in European and South American spacecraft assembly clean rooms

NASA Astrophysics Data System (ADS)

Moissl-Eichinger, Christine; Stieglmeier, Michaela; Schwendner, Petra

Spacecraft assembly clean rooms are unique environments for microbes: Due to low nutri-ent levels, desiccated, clean conditions, constant control of humidity and temperature, these environments are quite inhospitable to microbial life and even considered "extreme". Many procedures keep the contamination as low as possible, but these conditions are also highly se-lective for indigenous microbial communities. For space missions under planetary protection requirements, it is crucial to control the contaminating bioburden as much as possible; but for the development of novel cleaning/sterilization methods it is also important to identify and characterize (understand) the present microbial community of spacecraft clean rooms. In prepa-ration for the recently approved ESA ExoMars mission, two European and one South American spacecraft assembly clean rooms were analyzed with respect to their microbial diversity, using standard procedures, new cultivation approaches and molecular methods, that should shed light onto the presence of planetary protection relevant microorganisms. For this study, the Her-schel Space Observatory (launched in May 2009) and its housing clean rooms in Friedrichshafen (Germany), at ESTEC (The Netherlands) and CSG, Kourou (French Guyana) were sampled during assembly, test and launch operations. Although Herschel does not demand planetary protection requirements, all clean rooms were in a fully operating state during sampling. This gave us the opportunity to sample the microbial diversity under strict particulate and molecular contamination-control. Samples were collected from spacecraft and selected clean room surface areas and were subjected to cultivation assays (32 different media), molecular studies (based on 16S rRNA gene sequence analysis) and quantitative PCR. The results from different strategies will be compared and critically discussed, showing the advantages and limits of the selected methodologies. This talk will sum up the lessons learned from this microbial diversity project.

Some Mixotrophic Flagellate Species Selectively Graze on Archaea

PubMed Central

Ballen-Segura, Miguel; Catalan, Jordi

2016-01-01

ABSTRACT Many phototrophic flagellates ingest prokaryotes. This mixotrophic trait becomes a critical aspect of the microbial loop in planktonic food webs because of the typical high abundance of these flagellates. Our knowledge of their selective feeding upon different groups of prokaryotes, particularly under field conditions, is still quite limited. In this study, we investigated the feeding behavior of three species (Rhodomonas sp., Cryptomonas ovata, and Dinobryon cylindricum) via their food vacuole content in field populations of a high mountain lake. We used the catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) protocol with probes specific for the domain Archaea and three groups of Eubacteria: Betaproteobacteria, Actinobacteria, and Cytophaga-Flavobacteria of Bacteroidetes. Our results provide field evidence that contrasting selective feeding exists between coexisting mixotrophic flagellates under the same environmental conditions and that some prokaryotic groups may be preferentially impacted by phagotrophic pressure in aquatic microbial food webs. In our study, Archaea were the preferred prey, chiefly in the case of Rhodomonas sp., which rarely fed on any other prokaryotic group. In general, prey selection did not relate to prey size among the grazed groups. However, Actinobacteria, which were clearly avoided, mostly showed a size of <0.5 μm, markedly smaller than cells from the other groups. IMPORTANCE That mixotrophic flagellates are not randomly feeding in the main prokaryotic groups under field conditions is a pioneer finding in species-specific behavior that paves the way for future studies according to this new paradigm. The particular case that Archaea were preferentially affected in the situation studied shows that phagotrophic pressure cannot be disregarded when considering the distribution of this group in freshwater oligotrophic systems. PMID:27815273

Temporal and spatial differences in microbial composition during the manufacture of a continental-type cheese.

PubMed

O'Sullivan, Daniel J; Cotter, Paul D; O'Sullivan, Orla; Giblin, Linda; McSweeney, Paul L H; Sheehan, Jeremiah J

2015-04-01

We sought to determine if the time, within a production day, that a cheese is manufactured has an influence on the microbial community present within that cheese. To facilitate this, 16S rRNA amplicon sequencing was used to elucidate the microbial community dynamics of brine-salted continental-type cheese in cheeses produced early and late in the production day. Differences in the microbial composition of the core and rind of the cheese were also investigated. Throughout ripening, it was apparent that cheeses produced late in the day had a more diverse microbial population than their early equivalents. Spatial variation between the cheese core and rind was also noted in that cheese rinds were initially found to have a more diverse microbial population but thereafter the opposite was the case. Interestingly, the genera Thermus, Pseudoalteromonas, and Bifidobacterium, not routinely associated with a continental-type cheese produced from pasteurized milk, were detected. The significance, if any, of the presence of these genera will require further attention. Ultimately, the use of high-throughput sequencing has facilitated a novel and detailed analysis of the temporal and spatial distribution of microbes in this complex cheese system and established that the period during a production cycle at which a cheese is manufactured can influence its microbial composition. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Microbial diversity and metabolic networks in acid mine drainage habitats

PubMed Central

Méndez-García, Celia; Peláez, Ana I.; Mesa, Victoria; Sánchez, Jesús; Golyshina, Olga V.; Ferrer, Manuel

2015-01-01

Acid mine drainage (AMD) emplacements are low-complexity natural systems. Low-pH conditions appear to be the main factor underlying the limited diversity of the microbial populations thriving in these environments, although temperature, ionic composition, total organic carbon, and dissolved oxygen are also considered to significantly influence their microbial life. This natural reduction in diversity driven by extreme conditions was reflected in several studies on the microbial populations inhabiting the various micro-environments present in such ecosystems. Early studies based on the physiology of the autochthonous microbiota and the growing success of omics-based methodologies have enabled a better understanding of microbial ecology and function in low-pH mine outflows; however, complementary omics-derived data should be included to completely describe their microbial ecology. Furthermore, recent updates on the distribution of eukaryotes and archaea recovered through sterile filtering (herein referred to as filterable fraction) in these environments demand their inclusion in the microbial characterization of AMD systems. In this review, we present a complete overview of the bacterial, archaeal (including filterable fraction), and eukaryotic diversity in these ecosystems, and include a thorough depiction of the metabolism and element cycling in AMD habitats. We also review different metabolic network structures at the organismal level, which is necessary to disentangle the role of each member of the AMD communities described thus far. PMID:26074887

Composition and dynamics of biostimulated indigenous oil-degrading microbial consortia from the Irish, North and Mediterranean Seas: a mesocosm study.

PubMed

Gertler, Christoph; Näther, Daniela J; Cappello, Simone; Gerdts, Gunnar; Quilliam, Richard S; Yakimov, Michail M; Golyshin, Peter N

2012-09-01

Diversity of indigenous microbial consortia and natural occurrence of obligate hydrocarbon-degrading bacteria (OHCB) are of central importance for efficient bioremediation techniques. To investigate the microbial population dynamics and composition of oil-degrading consortia, we have established a series of identical oil-degrading mesocosms at three different locations, Bangor (Menai Straits, Irish Sea), Helgoland (North Sea) and Messina (Messina Straits, Mediterranean Sea). Changes in microbial community composition in response to oil spiking, nutrient amendment and filtration were assessed by ARISA and DGGE fingerprinting and 16Sr RNA gene library analysis. Bacterial and protozoan cell numbers were quantified by fluorescence microscopy. Very similar microbial population sizes and dynamics, together with key oil-degrading microorganisms, for example, Alcanivorax borkumensis, were observed at all three sites; however, the composition of microbial communities was largely site specific and included variability in relative abundance of OHCB. Reduction in protozoan grazing had little effect on prokaryotic cell numbers but did lead to a decrease in the percentage of A. borkumensis 16S rRNA genes detected in clone libraries. These results underline the complexity of marine oil-degrading microbial communities and cast further doubt on the feasibility of bioaugmentation practices for use in a broad range of geographical locations. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Microbial biogeography: putting microorganisms on the map.

PubMed

Martiny, Jennifer B Hughes; Bohannan, Brendan J M; Brown, James H; Colwell, Robert K; Fuhrman, Jed A; Green, Jessica L; Horner-Devine, M Claire; Kane, Matthew; Krumins, Jennifer Adams; Kuske, Cheryl R; Morin, Peter J; Naeem, Shahid; Ovreås, Lise; Reysenbach, Anna-Louise; Smith, Val H; Staley, James T

2006-02-01

We review the biogeography of microorganisms in light of the biogeography of macroorganisms. A large body of research supports the idea that free-living microbial taxa exhibit biogeographic patterns. Current evidence confirms that, as proposed by the Baas-Becking hypothesis, 'the environment selects' and is, in part, responsible for spatial variation in microbial diversity. However, recent studies also dispute the idea that 'everything is everywhere'. We also consider how the processes that generate and maintain biogeographic patterns in macroorganisms could operate in the microbial world.

Environmental Biotechnology: Moving from the Flask to the Field

DTIC Science & Technology

1991-09-30

biosorption , Biosorption of metal ions is a phenome- non exhibited by both alive and dead microbial cells. The detailed investigation of the mechanism of... biosorption has revealed that biosorption is a physical-chemical process whereby selected areas of the microbial cell exhibit high selectivity and...dead cells than by the same cells alive. The use of proper chemical solutions (eluants) is capable of reversing the equilibrium of biosorption

Microbial abundance on the eggs of a passerine bird and related fitness consequences between urban and rural habitats

PubMed Central

Lee, Sang-im; Lee, Hyunna; Jablonski, Piotr G.; Choe, Jae Chun

2017-01-01

Urban environments present novel and challenging habitats to wildlife. In addition to well-known difference in abiotic factors between rural and urban environments, the biotic environment, including microbial fauna, may also differ significantly. In this study, we aimed to compare the change in microbial abundance on eggshells during incubation between urban and rural populations of a passerine bird, the Eurasian Magpie (Pica pica), and examine the consequences of any differences in microbial abundances in terms of hatching success and nestling survival. Using real-time PCR, we quantified the abundances of total bacteria, Escherichia coli/Shigella spp., surfactin-producing Bacillus spp. and Candida albicans on the eggshells of magpies. We found that urban magpie eggs harboured greater abundances of E. coli/Shigella spp. and C. albicans before incubation than rural magpie eggs. During incubation, there was an increase in the total bacterial load, but a decrease in C. albicans on urban eggs relative to rural eggs. Rural eggs showed a greater increase in E. coli/Shigella spp. relative to their urban counterpart. Hatching success of the brood was generally lower in urban than rural population. Nestling survival was differentially related with the eggshell microbial abundance between urban and rural populations, which was speculated to be the result of the difference in the strength of the interaction among the microbes. This is the first demonstration that avian clutches in urban and rural populations differ in eggshell microbial abundance, which can be further related to the difference in hatching success and nestling survival in these two types of environments. We suggest that future studies on the eggshell microbes should investigate the interaction among the microbes, because the incubation and/or environmental factors such as urbanization or climate condition can influence the dynamic interactions among the microbes on the eggshells which can further determine the breeding success of the parents. PMID:28953940

Microbial abundance on the eggs of a passerine bird and related fitness consequences between urban and rural habitats.

PubMed

Lee, Sang-Im; Lee, Hyunna; Jablonski, Piotr G; Choe, Jae Chun; Husby, Magne

2017-01-01

Urban environments present novel and challenging habitats to wildlife. In addition to well-known difference in abiotic factors between rural and urban environments, the biotic environment, including microbial fauna, may also differ significantly. In this study, we aimed to compare the change in microbial abundance on eggshells during incubation between urban and rural populations of a passerine bird, the Eurasian Magpie (Pica pica), and examine the consequences of any differences in microbial abundances in terms of hatching success and nestling survival. Using real-time PCR, we quantified the abundances of total bacteria, Escherichia coli/Shigella spp., surfactin-producing Bacillus spp. and Candida albicans on the eggshells of magpies. We found that urban magpie eggs harboured greater abundances of E. coli/Shigella spp. and C. albicans before incubation than rural magpie eggs. During incubation, there was an increase in the total bacterial load, but a decrease in C. albicans on urban eggs relative to rural eggs. Rural eggs showed a greater increase in E. coli/Shigella spp. relative to their urban counterpart. Hatching success of the brood was generally lower in urban than rural population. Nestling survival was differentially related with the eggshell microbial abundance between urban and rural populations, which was speculated to be the result of the difference in the strength of the interaction among the microbes. This is the first demonstration that avian clutches in urban and rural populations differ in eggshell microbial abundance, which can be further related to the difference in hatching success and nestling survival in these two types of environments. We suggest that future studies on the eggshell microbes should investigate the interaction among the microbes, because the incubation and/or environmental factors such as urbanization or climate condition can influence the dynamic interactions among the microbes on the eggshells which can further determine the breeding success of the parents.