Salinity shapes microbial diversity and community structure in surface sediments of the Qinghai-Tibetan Lakes.

PubMed

Yang, Jian; Ma, Li'an; Jiang, Hongchen; Wu, Geng; Dong, Hailiang

2016-04-26

Investigating microbial response to environmental variables is of great importance for understanding of microbial acclimatization and evolution in natural environments. However, little is known about how microbial communities responded to environmental factors (e.g. salinity, geographic distance) in lake surface sediments of the Qinghai-Tibetan Plateau (QTP). In this study, microbial diversity and community structure in the surface sediments of nine lakes on the QTP were investigated by using the Illumina Miseq sequencing technique and the resulting microbial data were statistically analyzed in combination with environmental variables. The results showed total microbial community of the studied lakes was significantly correlated (r = 0.631, P < 0.001) with lake salinity instead of geographic distance. This suggests that lake salinity is more important than geographic distance in shaping the microbial diversity and community structure in the studied samples. In addition, the abundant and rare taxa (OTUs with relative abundance higher than 1% and lower than 0.01% within one sample, respectively) were significantly (P < 0.05) correlated (r = 0.427 and 0.783, respectively) with salinity, suggesting rare taxa might be more sensitive to salinity than their abundant counterparts, thus cautions should be taken in future when evaluating microbial response (abundant vs. rare sub-communities) to environmental conditions.

Utilizing novel diversity estimators to quantify multiple dimensions of microbial biodiversity across domains

PubMed Central

2013-01-01

Background Microbial ecologists often employ methods from classical community ecology to analyze microbial community diversity. However, these methods have limitations because microbial communities differ from macro-organismal communities in key ways. This study sought to quantify microbial diversity using methods that are better suited for data spanning multiple domains of life and dimensions of diversity. Diversity profiles are one novel, promising way to analyze microbial datasets. Diversity profiles encompass many other indices, provide effective numbers of diversity (mathematical generalizations of previous indices that better convey the magnitude of differences in diversity), and can incorporate taxa similarity information. To explore whether these profiles change interpretations of microbial datasets, diversity profiles were calculated for four microbial datasets from different environments spanning all domains of life as well as viruses. Both similarity-based profiles that incorporated phylogenetic relatedness and naïve (not similarity-based) profiles were calculated. Simulated datasets were used to examine the robustness of diversity profiles to varying phylogenetic topology and community composition. Results Diversity profiles provided insights into microbial datasets that were not detectable with classical univariate diversity metrics. For all datasets analyzed, there were key distinctions between calculations that incorporated phylogenetic diversity as a measure of taxa similarity and naïve calculations. The profiles also provided information about the effects of rare species on diversity calculations. Additionally, diversity profiles were used to examine thousands of simulated microbial communities, showing that similarity-based and naïve diversity profiles only agreed approximately 50% of the time in their classification of which sample was most diverse. This is a strong argument for incorporating similarity information and calculating diversity with a range of emphases on rare and abundant species when quantifying microbial community diversity. Conclusions For many datasets, diversity profiles provided a different view of microbial community diversity compared to analyses that did not take into account taxa similarity information, effective diversity, or multiple diversity metrics. These findings are a valuable contribution to data analysis methodology in microbial ecology. PMID:24238386

Identification of microbial species present in a pesticide dissipation process in biobed systems using typical substrates from southeastern Mexico as a biomixture at a laboratory scale.

PubMed

Góngora-Echeverría, Virgilio R; Quintal-Franco, Carlos; Arena-Ortiz, María Leticia; Giácoman-Vallejos, Germán; Ponce-Caballero, Carmen

2018-07-01

Biobed systems are an important option to control point pollution in agricultural areas. Substrates used and microbial diversity present in a biomixture perform an essential function in pesticide dissipation. In this study, the effects of soil (50% of volume/volume [V/V] proportion for all biomixtures) and four soil-based biomixtures (miniaturized biobeds; addition of novel substrates from southeastern Mexico) on dissipation of high concentrations of 2,4-dichlorophenoxyacetic acid (2,4-D), atrazine, carbofuran, diazinon, and glyphosate and on microbial diversity in biomixtures were evaluated. Small residual amounts of all pesticides at 20 (<2%) and 41 (<1%) days were observed; however, the lowest efficiency rates were observed in soil. Glyphosate was the only pesticide that completely dissipated in soil and biomixtures. Archaea, bacteria, and fungi were identified in biobeds, with bacteria being the most diverse microorganisms according to the identified species. The presence of white-rot fungi (normally related to pesticide degradation in biomixtures) was observed. Effects of the pesticide type and of biomixtures on pesticide dissipation were significant (P<0.05); however, only the effect of biomixtures on microbial diversity was significant (P<0.05); microbial diversity and richness had a significant effect on the residual amount of pesticides (P<0.05). Microbial diversity in terms of phyla was directly related to physicochemical parameters such as organic matter, lignin, water-holding capacity, and pH of soil and biomixtures. Copyright © 2018 Elsevier B.V. All rights reserved.

Influence of red mud on soil microbial communities: Application and comprehensive evaluation of the Biolog EcoPlate approach as a tool in soil microbiological studies.

PubMed

Feigl, Viktória; Ujaczki, Éva; Vaszita, Emese; Molnár, Mónika

2017-10-01

Red mud can be applied as soil ameliorant to acidic, sandy and micronutrient deficient soils. There are still knowledge gaps regarding the effects of red mud on the soil microbial community. The Biolog EcoPlate technique is a promising tool for community level physiological profiling. This study presents a detailed evaluation of Biolog EcoPlate data from two case studies. In experiment "A" red mud from Ajka (Hungary) was mixed into acidic sandy soil in soil microcosms at 5-50 w/w%. In experiement "B" red mud soil mixture was mixed into low quality subsoil in a field experiment at 5-50 w/w%. According to average well color development, substrate average well color development and substrate richness 5-20% red mud increased the microbial activity of the acidic sandy soil over the short term, but the effect did not last for 10months. Shannon diversity index showed that red mud at up to 20% did not change microbial diversity over the short term, but the diversity decreased by the 10th month. 30-50% red mud had deteriorating effect on the soil microflora. 5-20% red mud soil mixture in the low quality subsoil had a long lasting enhancing effect on the microbial community based on all Biolog EcoPlate parameters. However, 50% red mud soil mixture caused a decrease in diversity and substrate richness. With the Biolog EcoPlate we were able to monitor the changes of the microbial community in red mud affected soils and to assess the amount of red mud and red mud soil mixture applicable for soil treatment in these cases. Copyright © 2017 Elsevier B.V. All rights reserved.

Spatial heterogeneity of physicochemical properties explains differences in microbial composition in arid soils from Cuatro Cienegas, Mexico.

PubMed

Pajares, Silvia; Escalante, Ana E; Noguez, Ana M; García-Oliva, Felipe; Martínez-Piedragil, Celeste; Cram, Silke S; Eguiarte, Luis Enrique; Souza, Valeria

2016-01-01

Arid ecosystems are characterized by high spatial heterogeneity, and the variation among vegetation patches is a clear example. Soil biotic and abiotic factors associated with these patches have also been well documented as highly heterogeneous in space. Given the low vegetation cover and little precipitation in arid ecosystems, soil microorganisms are the main drivers of nutrient cycling. Nonetheless, little is known about the spatial distribution of microorganisms and the relationship that their diversity holds with nutrients and other physicochemical gradients in arid soils. In this study, we evaluated the spatial variability of soil microbial diversity and chemical parameters (nutrients and ion content) at local scale (meters) occurring in a gypsum-based desert soil, to gain knowledge on what soil abiotic factors control the distribution of microbes in arid ecosystems. We analyzed 32 soil samples within a 64 m(2) plot and: (a) characterized microbial diversity using T-RFLPs of the bacterial 16S rRNA gene, (b) determined soil chemical parameters, and (c) identified relationships between microbial diversity and chemical properties. Overall, we found a strong correlation between microbial composition heterogeneity and spatial variation of cations (Ca(2), K(+)) and anions (HCO[Formula: see text], Cl(-), SO[Formula: see text]) content in this small plot. Our results could be attributable to spatial differences of soil saline content, favoring the patchy emergence of salt and soil microbial communities.

SURVEY OF CULTURABLE AIRBORNE BACTERIA AT FOUR DIVERSE LOCATIONS IN OREGON: URBAN, RURAL, FOREST, AND COASTAL

EPA Science Inventory

To determine the risks of microbial air pollution from microorganisms used for pesticides and bioremediation, or emanating from composting, fermentation tanks, or other agricultural and urban sources, airborne microbial levels must be evaluated. This study surveyed the atmospheri...

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.

Microbial functional diversity plays an important role in the degradation of polyhydroxybutyrate (PHB) in soil.

PubMed

Dey, Samrat; Tribedi, Prosun

2018-03-01

Towards bioremediation of recalcitrant materials like synthetic polymer, soil has been recognized as a traditional site for disposal and subsequent degradation as some microorganisms in soil can degrade the polymer in a non-toxic, cost-effective, and environment friendly way. Microbial functional diversity is a constituent of biodiversity that includes wide range of metabolic activities that can influence numerous aspects of ecosystem functioning like ecosystem stability, nutrient availability, ecosystem dynamics, etc. Thus, in the current study, we assumed that microbial functional diversity could play an important role in polymer degradation in soil. To verify this hypothesis, we isolated soil from five different sites of landfill and examined several microbiological parameters wherein we observed a significant variation in heterotrophic microbial count as well as microbial activities among the soil microcosms tested. Multivariate analysis (principle component analysis) based on the carbon sources utilization pattern revealed that soil microcosms showed different metabolic patterns suggesting the variable distribution of microorganisms among the soil microcosms tested. Since microbial functional diversity depends on both microbial richness and evenness, Shannon diversity index was determined to measure microbial richness and Gini coefficient was determined to measure microbial evenness. The tested soil microcosms exhibited variation in both microbial richness and evenness suggesting the considerable difference in microbial functional diversity among the tested microcosms. We then measured polyhydroxybutyrate (PHB) degradation in soil microcosms after desired period of incubation of PHB in soil wherein we found that soil microcosms having higher functional diversity showed enhanced PHB degradation and soil microcosms having lower functional diversity showed reduced PHB degradation. We also noticed that all the tested soil microcosms showed similar pattern in both microbial functional diversity and PHB degradation suggesting a strong positive correlation ( r  = 0.95) between microbial functional diversity and PHB degradation. Thus, the results demonstrate that microbial functional diversity plays an important role in PHB degradation in soil by exhibiting versatile microbial metabolic potentials that lead to the enhanced degradation of PHB.

Microbial diversity--insights from population genetics.

PubMed

Mes, Ted H M

2008-01-01

Although many environmental microbial populations are large and genetically diverse, both the level of diversity and the extent to which it is ecologically relevant remain enigmatic. Because the effective (or long-term) population size, N(e), is one of the parameters that determines population genetic diversity, tests and simulations that assume selectively neutral mutations may help to identify the processes that have shaped microbial diversity. Using ecologically important genes, tests of selective neutrality suggest that adaptive as well as non-adaptive types of selection act and that departure from neutrality may be widespread or restricted to small groups of genotypes. Population genetic simulations using population sizes between 10(3) and 10(7) suggest extremely high levels of microbial diversity in environments that sustain large populations. However, census and effective population sizes may differ considerably, and because we know nothing of the evolutionary history of environmental microbial populations, we also have no idea what N(e) of environmental populations is. On the one hand, this reflects our ignorance of the microbial world. On the other hand, the tests and simulations illustrate interactions between microbial diversity and microbial population genetics that should inform our thinking in microbial ecology. Because of the different views on microbial diversity across these disciplines, such interactions are crucial if we are to understand the role of genes in microbial communities.

Microbial taxonomy in the post-genomic era: Rebuilding from scratch?

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

Thompson, Cristiane C.; Amaral, Gilda R.; Campeão, Mariana

2014-12-23

Microbial taxonomy should provide adequate descriptions of bacterial, archaeal, and eukaryotic microbial diversity in ecological, clinical, and industrial environments. We re-evaluated the prokaryote species twice. It is time to revisit polyphasic taxonomy, its principles, and its practice, including its underlying pragmatic species concept. We will be able to realize an old dream of our predecessor taxonomists and build a genomic-based microbial taxonomy, using standardized and automated curation of high-quality complete genome sequences as the new gold standard.

Community Structure Comparisons of Hydrothermal Vent Microbial Mats Along the Mariana Arc and Back-arc

NASA Astrophysics Data System (ADS)

Hager, K. W.; Fullerton, H.; Moyer, C. L.

2015-12-01

Hydrothermal vents along the Mariana Arc and back-arc represent a hotspot of microbial diversity that has not yet been fully recognized. The Mariana Arc and back-arc contain hydrothermal vents with varied vent effluent chemistry and temperature, which translates to diverse community composition. We have focused on iron-rich sites where the dominant primary producers are iron oxidizing bacteria. Because microbes from these environments have proven elusive in culturing efforts, we performed culture independent analysis among different microbial communities found at these hydrothermal vents. Terminal-restriction fragment length polymorphism (T-RFLP) and Illumina sequencing of small subunit ribosomal gene amplicons were used to characterize community members and identify samples for shotgun metagenomics. Used in combination, these methods will better elucidate the composition and characteristics of the bacterial communities at these hydrothermal vent systems. The overarching goal of this study is to evaluate and compare taxonomic and metabolic diversity among different communities of microbial mats. We compared communities collected on a fine scale to analyze the bacterial community based on gross mat morphology, geography, and nearby vent effluent chemistry. Taxa richness and evenness are compared with rarefaction curves to visualize diversity. As well as providing a survey of diversity this study also presents a juxtaposition of three methods in which ribosomal small subunit diversity is compared with T-RFLP, next generation amplicon sequencing, and metagenomic shotgun sequencing.

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

PubMed

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

2014-11-15

The study of the microbial ecology of drinking water distribution systems (DWDS) has traditionally been based on culturing organisms from bulk water samples. The development and application of molecular methods has supplied new tools for examining the microbial diversity and activity of environmental samples, yielding new insights into the microbial community and its diversity within these engineered ecosystems. In this review, the currently available methods and emerging approaches for characterising microbial communities, including both planktonic and biofilm ways of life, are critically evaluated. The study of biofilms is considered particularly important as it plays a critical role in the processes and interactions occurring at the pipe wall and bulk water interface. The advantages, limitations and usefulness of methods that can be used to detect and assess microbial abundance, community composition and function are discussed in a DWDS context. This review will assist hydraulic engineers and microbial ecologists in choosing the most appropriate tools to assess drinking water microbiology and related aspects. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Microbial diversity and impact on carbonate geochemistry across a changing geochemical gradient in a karst aquifer

PubMed Central

Gray, Cassie J; Engel, Annette S

2013-01-01

Although microbes are known to influence karst (carbonate) aquifer ecosystem-level processes, comparatively little information is available regarding the diversity of microbial activities that could influence water quality and geological modification. To assess microbial diversity in the context of aquifer geochemistry, we coupled 16S rRNA Sanger sequencing and 454 tag pyrosequencing to in situ microcosm experiments from wells that cross the transition from fresh to saline and sulfidic water in the Edwards Aquifer of central Texas, one of the largest karst aquifers in the United States. The distribution of microbial groups across the transition zone correlated with dissolved oxygen and sulfide concentration, and significant variations in community composition were explained by local carbonate geochemistry, specifically calcium concentration and alkalinity. The waters were supersaturated with respect to prevalent aquifer minerals, calcite and dolomite, but in situ microcosm experiments containing these minerals revealed significant mass loss from dissolution when colonized by microbes. Despite differences in cell density on the experimental surfaces, carbonate loss was greater from freshwater wells than saline, sulfidic wells. However, as cell density increased, which was correlated to and controlled by local geochemistry, dissolution rates decreased. Surface colonization by metabolically active cells promotes dissolution by creating local disequilibria between bulk aquifer fluids and mineral surfaces, but this also controls rates of karst aquifer modification. These results expand our understanding of microbial diversity in karst aquifers and emphasize the importance of evaluating active microbial processes that could affect carbonate weathering in the subsurface. PMID:23151637

Microbial diversity and impact on carbonate geochemistry across a changing geochemical gradient in a karst aquifer.

PubMed

Gray, Cassie J; Engel, Annette S

2013-02-01

Although microbes are known to influence karst (carbonate) aquifer ecosystem-level processes, comparatively little information is available regarding the diversity of microbial activities that could influence water quality and geological modification. To assess microbial diversity in the context of aquifer geochemistry, we coupled 16S rRNA Sanger sequencing and 454 tag pyrosequencing to in situ microcosm experiments from wells that cross the transition from fresh to saline and sulfidic water in the Edwards Aquifer of central Texas, one of the largest karst aquifers in the United States. The distribution of microbial groups across the transition zone correlated with dissolved oxygen and sulfide concentration, and significant variations in community composition were explained by local carbonate geochemistry, specifically calcium concentration and alkalinity. The waters were supersaturated with respect to prevalent aquifer minerals, calcite and dolomite, but in situ microcosm experiments containing these minerals revealed significant mass loss from dissolution when colonized by microbes. Despite differences in cell density on the experimental surfaces, carbonate loss was greater from freshwater wells than saline, sulfidic wells. However, as cell density increased, which was correlated to and controlled by local geochemistry, dissolution rates decreased. Surface colonization by metabolically active cells promotes dissolution by creating local disequilibria between bulk aquifer fluids and mineral surfaces, but this also controls rates of karst aquifer modification. These results expand our understanding of microbial diversity in karst aquifers and emphasize the importance of evaluating active microbial processes that could affect carbonate weathering in the subsurface.

Microbial community structure and diversity in the soil spatial profile of 5-year-old Robinia pseudoacacia 'Idaho,' determined by 454 sequencing of the 16S RNA gene.

PubMed

Chang, Yanping; Bu, Xiangpan; Niu, Weibo; Xiu, Yu; Wang, Huafang

2013-01-01

Relatively little information is available regarding the variability of microbial communities inhabiting deeper soil layers. We investigated the distribution of soil microbial communities down to 1.2 m in 5-year-old Robinia pseudoacacia 'Idaho' soil by 454 sequencing of the 16S RNA gene. The average number of sequences per sample was 12,802. The Shannon and Chao 1 indices revealed various relative microbial abundances and even distribution of microbial diversity for all evaluated sample depths. The predicted diversity in the topsoil exceeded that of the corresponding subsoil. The changes in the relative abundance of the major soil bacterial phyla showed decreasing, increasing, or no consistent trends with respect to sampling depth. Despite their novelty, members of the new candidate phyla OD1 and TM7 were widespread. Environmental variables affecting the bacterial community within the environment appeared to differ from those reported previously, especially the lack of detectable effect from pH. Overall, we found that the overall relative abundance fluctuated with the physical and chemical properties of the soil, root system, and sampling depth. Such information may facilitate forest soil management.

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

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

High Microbial Diversity Promotes Soil Ecosystem Functioning.

PubMed

Maron, Pierre-Alain; Sarr, Amadou; Kaisermann, Aurore; Lévêque, Jean; Mathieu, Olivier; Guigue, Julien; Karimi, Battle; Bernard, Laetitia; Dequiedt, Samuel; Terrat, Sébastien; Chabbi, Abad; Ranjard, Lionel

2018-05-01

In soil, the link between microbial diversity and carbon transformations is challenged by the concept of functional redundancy. Here, we hypothesized that functional redundancy may decrease with increasing carbon source recalcitrance and that coupling of diversity with C cycling may change accordingly. We manipulated microbial diversity to examine how diversity decrease affects the decomposition of easily degradable (i.e., allochthonous plant residues) versus recalcitrant (i.e., autochthonous organic matter) C sources. We found that a decrease in microbial diversity (i) affected the decomposition of both autochthonous and allochthonous carbon sources, thereby reducing global CO 2 emission by up to 40%, and (ii) shaped the source of CO 2 emission toward preferential decomposition of most degradable C sources. Our results also revealed that the significance of the diversity effect increases with nutrient availability. Altogether, these findings show that C cycling in soil may be more vulnerable to microbial diversity changes than expected from previous studies, particularly in ecosystems exposed to nutrient inputs. Thus, concern about the preservation of microbial diversity may be highly relevant in the current global-change context assumed to impact soil biodiversity and the pulse inputs of plant residues and rhizodeposits into the soil. IMPORTANCE With hundreds of thousands of taxa per gram of soil, microbial diversity dominates soil biodiversity. While numerous studies have established that microbial communities respond rapidly to environmental changes, the relationship between microbial diversity and soil functioning remains controversial. Using a well-controlled laboratory approach, we provide empirical evidence that microbial diversity may be of high significance for organic matter decomposition, a major process on which rely many of the ecosystem services provided by the soil ecosystem. These new findings should be taken into account in future studies aimed at understanding and predicting the functional consequences of changes in microbial diversity on soil ecosystem services and carbon storage in soil. Copyright © 2018 American Society for Microbiology.

Plant diversity drives soil microbial biomass carbon in grasslands irrespective of global environmental change factors.

PubMed

Thakur, Madhav Prakash; Milcu, Alexandru; Manning, Pete; Niklaus, Pascal A; Roscher, Christiane; Power, Sally; Reich, Peter B; Scheu, Stefan; Tilman, David; Ai, Fuxun; Guo, Hongyan; Ji, Rong; Pierce, Sarah; Ramirez, Nathaly Guerrero; Richter, Annabell Nicola; Steinauer, Katja; Strecker, Tanja; Vogel, Anja; Eisenhauer, Nico

2015-11-01

Soil microbial biomass is a key determinant of carbon dynamics in the soil. Several studies have shown that soil microbial biomass significantly increases with plant species diversity, but it remains unclear whether plant species diversity can also stabilize soil microbial biomass in a changing environment. This question is particularly relevant as many global environmental change (GEC) factors, such as drought and nutrient enrichment, have been shown to reduce soil microbial biomass. Experiments with orthogonal manipulations of plant diversity and GEC factors can provide insights whether plant diversity can attenuate such detrimental effects on soil microbial biomass. Here, we present the analysis of 12 different studies with 14 unique orthogonal plant diversity × GEC manipulations in grasslands, where plant diversity and at least one GEC factor (elevated CO2 , nutrient enrichment, drought, earthworm presence, or warming) were manipulated. Our results show that higher plant diversity significantly enhances soil microbial biomass with the strongest effects in long-term field experiments. In contrast, GEC factors had inconsistent effects with only drought having a significant negative effect. Importantly, we report consistent non-significant effects for all 14 interactions between plant diversity and GEC factors, which indicates a limited potential of plant diversity to attenuate the effects of GEC factors on soil microbial biomass. We highlight that plant diversity is a major determinant of soil microbial biomass in experimental grasslands that can influence soil carbon dynamics irrespective of GEC. © 2015 John Wiley & Sons Ltd.

Exploring the diversity-stability paradigm using sponge microbial communities.

PubMed

Glasl, Bettina; Smith, Caitlin E; Bourne, David G; Webster, Nicole S

2018-05-30

A key concept in theoretical ecology is the positive correlation between biodiversity and ecosystem stability. When applying this diversity-stability concept to host-associated microbiomes, the following questions emerge: (1) Does microbial diversity influence the stability of microbiomes upon environmental fluctuations? (2) Do hosts that harbor high versus low microbial diversity differ in their stress response? To test the diversity-stability concept in host-associated microbiomes, we exposed six marine sponge species with varying levels of microbial diversity to non-lethal salinity disturbances and followed their microbial composition over time using 16S rRNA gene amplicon sequencing. No signs of sponge stress were evident following salinity amendment and microbiomes exhibited compositional resistance irrespective of their microbial diversity. Compositional stability of the sponge microbiome manifests itself at distinct host taxonomic and host microbial diversity groups, with (1) stable host genotype-specific microbiomes at oligotype-level; (2) stable host species-specific microbiomes at genus-level; and (3) stable and specific microbiomes at phylum-level for hosts with high versus low microbial diversity. The resistance of sponge microbiomes together with the overall stability of sponge holobionts upon salinity fluctuations suggest that the stability-diversity concept does not appear to hold for sponge microbiomes and provides further evidence for the widely recognized environmental tolerance of sponges.

Evaluation of the ruminal bacterial diversity of cattle fed diets containing citrus pulp pellets

USDA-ARS?s Scientific Manuscript database

The rumen microbial ecosystem remains a mystery from a quantitative perspective. Dietary components and changes cause shifts in the ruminal microbial ecology that can play a role in animal health and productivity, but the magnitude of these changes remains unknown. The objective of this study was ...

Cow teat skin, a potential source of diverse microbial populations for cheese production.

PubMed

Verdier-Metz, Isabelle; Gagne, Geneviève; Bornes, Stéphanie; Monsallier, Françoise; Veisseire, Philippe; Delbès-Paus, Céline; Montel, Marie-Christine

2012-01-01

The diversity of the microbial community on cow teat skin was evaluated using a culture-dependent method based on the use of different dairy-specific media, followed by the identification of isolates by 16S rRNA gene sequencing. This was combined with a direct molecular approach by cloning and 16S rRNA gene sequencing. This study highlighted the large diversity of the bacterial community that may be found on teat skin, where 79.8% of clones corresponded to various unidentified species as well as 66 identified species, mainly belonging to those commonly found in raw milk (Enterococcus, Pediococcus, Enterobacter, Pantoea, Aerococcus, and Staphylococcus). Several of them, such as nonstarter lactic acid bacteria (NSLAB), Staphylococcus, and Actinobacteria, may contribute to the development of the sensory characteristics of cheese during ripening. Therefore, teat skin could be an interesting source or vector of biodiversity for milk. Variations of microbial counts and diversity between the farms studied have been observed. Moreover, Staphylococcus auricularis, Staphylococcus devriesei, Staphylococcus arlettae, Streptococcus bovis, Streptococcus equinus, Clavibacter michiganensis, Coprococcus catus, or Arthrobacter gandavensis commensal bacteria of teat skin and teat canal, as well as human skin, are not common in milk, suggesting that there is a breakdown of microbial flow from animal to milk. It would then be interesting to thoroughly study this microbial flow from teat to milk.

[Research on functional diversity of microorganisms on jujube fruit surface in storage].

PubMed

Sha, Yuexia

2009-10-01

Disease during storage caused by microbial infection is a serious problem of jujube fruits. The aim of the study was to characterize the microbial diversity in stored jujube fruits. I used Biolog in experiment. The types of micro-plates were Filamentous Fungi micro-plate and Economicmicro-plate. There was much difference in microbial functional diversity on the surface of stored jujube fruit. The microbial functional diversity of stored 30 days was richer than it of stored 15 days. The diversity, homogeneity and average well color development of jujube used by fruit perservatives were lower than it not used by fruit preservatives. There were six kinds of the characteristic carbon. Our study firstly showed microbial diversity on the surface of stored jujube fruit. Biolog could be applied in the research on microbial functional diversity of fruit surface.

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

PubMed Central

Zeglin, Lydia H.

2015-01-01

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

Long-term no-tillage and organic input management enhanced the diversity and stability of soil microbial community.

PubMed

Wang, Yi; Li, Chunyue; Tu, Cong; Hoyt, Greg D; DeForest, Jared L; Hu, Shuijin

2017-12-31

Intensive tillage and high inputs of chemicals are frequently used in conventional agriculture management, which critically depresses soil properties and causes soil erosion and nonpoint source pollution. Conservation practices, such as no-tillage and organic farming, have potential to enhance soil health. However, the long-term impact of no-tillage and organic practices on soil microbial diversity and community structure has not been fully understood, particularly in humid, warm climate regions such as the southeast USA. We hypothesized that organic inputs will lead to greater microbial diversity and a more stable microbial community, and that the combination of no-tillage and organic inputs will maximize soil microbial diversity. We conducted a long-term experiment in the southern Appalachian mountains of North Carolina, USA to test these hypotheses. The results showed that soil microbial diversity and community structure diverged under different management regimes after long term continuous treatments. Organic input dominated the effect of management practices on soil microbial properties, although no-tillage practice also exerted significant impacts. Both no-tillage and organic inputs significantly promoted soil microbial diversity and community stability. The combination of no-tillage and organic management increased soil microbial diversity over the conventional tillage and led to a microbial community structure more similar to the one in an adjacent grassland. These results indicate that effective management through reducing tillage and increasing organic C inputs can enhance soil microbial diversity and community stability. Copyright © 2017 Elsevier B.V. All rights reserved.

Individuals' diet diversity influences gut microbial diversity in two freshwater fish (threespine stickleback and Eurasian perch)

PubMed Central

Bolnick, Daniel I; Snowberg, Lisa K; Hirsch, Philipp E; Lauber, Christian L; Knight, Rob; Caporaso, J Gregory; Svanbäck, Richard; Post, David

2014-01-01

Vertebrates' diets profoundly influence the composition of symbiotic gut microbial communities. Studies documenting diet-microbiota associations typically focus on univariate or categorical diet variables. However, in nature individuals often consume diverse combinations of foods. If diet components act independently, each providing distinct microbial colonists or nutrients, we expect a positive relationship between diet diversity and microbial diversity. We tested this prediction within each of two fish species (stickleback and perch), in which individuals vary in their propensity to eat littoral or pelagic invertebrates or mixtures of both prey. Unexpectedly, in most cases individuals with more generalised diets had less diverse microbiota than dietary specialists, in both natural and laboratory populations. This negative association between diet diversity and microbial diversity was small but significant, and most apparent after accounting for complex interactions between sex, size and diet. Our results suggest that multiple diet components can interact non-additively to influence gut microbial diversity. PMID:24847735

Microbial examination of anaerobic sludge adaptation to animal slurry.

PubMed

Moset, V; Cerisuelo, A; Ferrer, P; Jimenez, A; Bertolini, E; Cambra-López, M

2014-01-01

The objective of this study was to evaluate changes in the microbial population of anaerobic sludge digesters during the adaptation to pig slurry (PS) using quantitative real-time polymerase chain reaction (qPCR) and qualitative scanning electron microscopy (SEM). Additionally, the relationship between microbial parameters and sludge physicochemical composition and methane yield was examined. Results showed that the addition of PS to an unadapted thermophilic anaerobic digester caused an increase in volatile fatty acids (VFA) concentration, a decrease in removal efficiency and CH4 yield. Additionally, increases in total bacteria and total archaea were observed using qPCR. Scanning electron micrographs provided a general overview of the sludge's cell morphology, morphological diversity and degree of organic matter degradation. A change in microbial morphotypes from homogeneous cell morphologies to a higher morphological diversity, similar to that observed in PS, was observed with the addition of PS by SEM. Therefore, the combination of qPCR and SEM allowed expanding the knowledge about the microbial adaptation to animal slurry in thermophilic anaerobic digesters.

Differential sensitivity of total and active soil microbial communities to drought and forest management.

PubMed

Bastida, Felipe; Torres, Irene F; Andrés-Abellán, Manuela; Baldrian, Petr; López-Mondéjar, Rubén; Větrovský, Tomáš; Richnow, Hans H; Starke, Robert; Ondoño, Sara; García, Carlos; López-Serrano, Francisco R; Jehmlich, Nico

2017-10-01

Climate change will affect semiarid ecosystems through severe droughts that increase the competition for resources in plant and microbial communities. In these habitats, adaptations to climate change may consist of thinning-that reduces competition for resources through a decrease in tree density and the promotion of plant survival. We deciphered the functional and phylogenetic responses of the microbial community to 6 years of drought induced by rainfall exclusion and how forest management affects its resistance to drought, in a semiarid forest ecosystem dominated by Pinus halepensis Mill. A multiOMIC approach was applied to reveal novel, community-based strategies in the face of climate change. The diversity and the composition of the total and active soil microbiome were evaluated by 16S rRNA gene (bacteria) and ITS (fungal) sequencing, and by metaproteomics. The microbial biomass was analyzed by phospholipid fatty acids (PLFAs), and the microbially mediated ecosystem multifunctionality was studied by the integration of soil enzyme activities related to the cycles of C, N, and P. The microbial biomass and ecosystem multifunctionality decreased in drought-plots, as a consequence of the lower soil moisture and poorer plant development, but this decrease was more notable in unthinned plots. The structure and diversity of the total bacterial community was unaffected by drought at phylum and order level, but did so at genus level, and was influenced by seasonality. However, the total fungal community and the active microbial community were more sensitive to drought and were related to ecosystem multifunctionality. Thinning in plots without drought increased the active diversity while the total diversity was not affected. Thinning promoted the resistance of ecosystem multifunctionality to drought through changes in the active microbial community. The integration of total and active microbiome analyses avoids misinterpretations of the links between the soil microbial community and climate change. © 2017 John Wiley & Sons Ltd.

Greatest soil microbial diversity found in micro-habitats

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

Bach, Elizabeth M.; Williams, Ryan J.; Hargreaves, Sarah K.

Microbial interactions occur in habitats much smaller than typically considered in classic ecological studies. This study uses soil aggregates to examine soil microbial community composition and structure of both bacteria and fungi at a microbially relevant scale. Aggregates were isolated from three land management systems in central Iowa, USA to test if aggregate-level microbial responses were sensitive to large-scale shifts in plant community and management practices. Bacteria and fungi exhibited similar patterns of community structure and diversity among soil aggregates, regardless of land management. Microaggregates supported more diverse microbial communities, both taxonomically and functionally. Calculation of a weighted proportional wholemore » soil diversity, which accounted for microbes found in aggregate fractions, resulted in 65% greater bacterial richness and 100% greater fungal richness over independently sampled whole soil. Our results show microaggregates support a previously unrecognized diverse microbial community that likely effects microbial access and metabolism of soil substrates.« less

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

PubMed Central

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

2013-01-01

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

Biological Diversity Comprising Microbial Structures of Antarctic Ice Covered Lakes

NASA Astrophysics Data System (ADS)

Matys, E. D.

2015-12-01

Analysis of microbial membrane lipids is a rapid and non-selective method for evaluating the composition of microbial communities. To fully realise the diagnostic potential of these lipids, we must first understand their structural diversity, biological sources, physiological functions, and pathways of preservation. Particular environmental conditions likely prompt the production of different membrane lipid structures. Antarctica's McMurdo Dry Valleys host numerous ice-covered lakes with sharp chemical gradients that vary in illumination, geochemical structure, and benthic mat morphologies that are structured by nutrient availability and water chemistry. The lipid contents of these benthic mats have not received extensive study nor have the communities yet been thoroughly characterized. Accordingly, a combination of lipid biomarker and nucleic acid sequence data provides the means of assessing species diversity and environmental controls on the composition and diversity of membrane lipid assemblages. We investigated the richness and diversity of benthic microbial communities and accumulated organic matter in Lake Vanda of the McMurdo Dry Valleys. We have identified diverse glycolipids, aminolipids, and phospholipids in addition to many unknown compounds that may be specific to these particular environments. Light levels fluctuate seasonally, favoring low-light-tolerant cyanobacteria and specific lipid assemblages. Adaptations to nutrient limitations are reflected in contrasting intact polar lipid assemblages. For example, under P-limiting conditions, phospholipids are subsidiary to membrane-forming lipids that do not contain P (i.e. ornithine, betaine, and sulfolipids). The bacteriohopanepolyol (BHP) composition is dominated by bacteriohopanetetrol (BHT), a ubiquitous BHP, and 2-methylhopanoids. The relative abundance of 2-methylhopanoids is unprecedented and may reflect the unusual seasonal light regime of this polar environment. By establishing correlations between environmental conditions, microbial community composition and the lipid assemblages of microbial structures in ice-covered lakes of Antarctica's McMurdo Dry Valleys, our data provides important ecological and evolutionary insights into these unusual environments.

Measures of phylogenetic differentiation provide robust and complementary insights into microbial communities.

PubMed

Parks, Donovan H; Beiko, Robert G

2013-01-01

High-throughput sequencing techniques have made large-scale spatial and temporal surveys of microbial communities routine. Gaining insight into microbial diversity requires methods for effectively analyzing and visualizing these extensive data sets. Phylogenetic β-diversity measures address this challenge by allowing the relationship between large numbers of environmental samples to be explored using standard multivariate analysis techniques. Despite the success and widespread use of phylogenetic β-diversity measures, an extensive comparative analysis of these measures has not been performed. Here, we compare 39 measures of phylogenetic β diversity in order to establish the relative similarity of these measures along with key properties and performance characteristics. While many measures are highly correlated, those commonly used within microbial ecology were found to be distinct from those popular within classical ecology, and from the recently recommended Gower and Canberra measures. Many of the measures are surprisingly robust to different rootings of the gene tree, the choice of similarity threshold used to define operational taxonomic units, and the presence of outlying basal lineages. Measures differ considerably in their sensitivity to rare organisms, and the effectiveness of measures can vary substantially under alternative models of differentiation. Consequently, the depth of sequencing required to reveal underlying patterns of relationships between environmental samples depends on the selected measure. Our results demonstrate that using complementary measures of phylogenetic β diversity can further our understanding of how communities are phylogenetically differentiated. Open-source software implementing the phylogenetic β-diversity measures evaluated in this manuscript is available at http://kiwi.cs.dal.ca/Software/ExpressBetaDiversity.

Microbial analysis of in situ biofilm formation in drinking water distribution systems: implications for monitoring and control of drinking water quality.

PubMed

Douterelo, Isabel; Jackson, M; Solomon, C; Boxall, J

2016-04-01

Biofilm formation in drinking water distribution systems (DWDS) is influenced by the source water, the supply infrastructure and the operation of the system. A holistic approach was used to advance knowledge on the development of mixed species biofilms in situ, by using biofilm sampling devices installed in chlorinated networks. Key physico-chemical parameters and conventional microbial indicators for drinking water quality were analysed. Biofilm coverage on pipes was evaluated by scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM). The microbial community structure, bacteria and fungi, of water and biofilms was assessed using pyrosequencing. Conventional wisdom leads to an expectation for less microbial diversity in groundwater supplied systems. However, the analysis of bulk water showed higher microbial diversity in groundwater site samples compared with the surface water site. Conversely, higher diversity and richness were detected in biofilms from the surface water site. The average biofilm coverage was similar among sites. Disinfection residual and other key variables were similar between the two sites, other than nitrates, alkalinity and the hydraulic conditions which were extremely low at the groundwater site. Thus, the unexpected result of an exceptionally low diversity with few dominant genera (Pseudomonas and Basidiobolus) in groundwater biofilm samples, despite the more diverse community in the bulk water, is attributed to the low-flow hydraulic conditions. This finding evidences that the local environmental conditions are shaping biofilm formation, composition and amount, and hence managing these is critical for the best operation of DWDS to safeguard water quality.

Short-term microbial effects of a large-scale mine-tailing storage facility collapse on the local natural environment

PubMed Central

Baldwin, Susan A.; Taylor, Jon; Gurr, David B.; Denesiuk, Daniel R.; Van Hamme, Jonathan D.; Fraser, Lauchlan H.

2018-01-01

We investigated the impacts of the Mount Polley tailings impoundment failure on chemical, physical, and microbial properties of substrates within the affected watershed, comprised of 70 hectares of riparian wetlands and 40 km of stream and lake shore. We established a biomonitoring network in October of 2014, two months following the disturbance, and evaluated riparian and wetland substrates for microbial community composition and function via 16S and full metagenome sequencing. A total of 234 samples were collected from substrates at 3 depths and 1,650,752 sequences were recorded in a geodatabase framework. These data revealed a wealth of information regarding watershed-scale distribution of microbial community members, as well as community composition, structure, and response to disturbance. Substrates associated with the impact zone were distinct chemically as indicated by elevated pH, nitrate, and sulphate. The microbial community exhibited elevated metabolic capacity for selenate and sulfate reduction and an abundance of chemolithoautotrophs in the Thiobacillus thiophilus/T. denitrificans/T. thioparus clade that may contribute to nitrate attenuation within the affected watershed. The most impacted area (a 6 km stream connecting two lakes) exhibited 30% lower microbial diversity relative to the remaining sites. The tailings impoundment failure at Mount Polley Mine has provided a unique opportunity to evaluate functional and compositional diversity soon after a major catastrophic disturbance to assess metabolic potential for ecosystem recovery. PMID:29694379

Mapping and determinism of soil microbial community distribution across an agricultural landscape

PubMed Central

Constancias, Florentin; Terrat, Sébastien; Saby, Nicolas P A; Horrigue, Walid; Villerd, Jean; Guillemin, Jean-Philippe; Biju-Duval, Luc; Nowak, Virginie; Dequiedt, Samuel; Ranjard, Lionel; Chemidlin Prévost-Bouré, Nicolas

2015-01-01

Despite the relevance of landscape, regarding the spatial patterning of microbial communities and the relative influence of environmental parameters versus human activities, few investigations have been conducted at this scale. Here, we used a systematic grid to characterize the distribution of soil microbial communities at 278 sites across a monitored agricultural landscape of 13 km². Molecular microbial biomass was estimated by soil DNA recovery and bacterial diversity by 16S rRNA gene pyrosequencing. Geostatistics provided the first maps of microbial community at this scale and revealed a heterogeneous but spatially structured distribution of microbial biomass and diversity with patches of several hundreds of meters. Variance partitioning revealed that both microbial abundance and bacterial diversity distribution were highly dependent of soil properties and land use (total variance explained ranged between 55% and 78%). Microbial biomass and bacterial richness distributions were mainly explained by soil pH and texture whereas bacterial evenness distribution was mainly related to land management. Bacterial diversity (richness, evenness, and Shannon index) was positively influenced by cropping intensity and especially by soil tillage, resulting in spots of low microbial diversity in soils under forest management. Spatial descriptors also explained a small but significant portion of the microbial distribution suggesting that landscape configuration also shapes microbial biomass and bacterial diversity. PMID:25833770

Biocrust-forming mosses mitigate the impact of aridity on soil microbial communities in drylands: observational evidence from three continents.

PubMed

Delgado-Baquerizo, Manuel; Maestre, Fernando T; Eldridge, David J; Bowker, Matthew A; Jeffries, Thomas C; Singh, Brajesh K

2018-04-02

Recent research indicates that increased aridity linked to climate change will reduce the diversity of soil microbial communities and shift their community composition in drylands, Earth's largest biome. However, we lack both a theoretical framework and solid empirical evidence of how important biotic components from drylands, such as biocrust-forming mosses, will regulate the responses of microbial communities to expected increases in aridity with climate change. Here we report results from a cross-continental (North America, Europe and Australia) survey of 39 locations from arid to humid ecosystems, where we evaluated how biocrust-forming mosses regulate the relationship between aridity and the community composition and diversity of soil bacteria and fungi in dryland ecosystems. Increasing aridity was negatively related to the richness of fungi, and either positively or negatively related to the relative abundance of selected microbial phyla, when biocrust-forming mosses were absent. Conversely, we found an overall lack of relationship between aridity and the relative abundance and richness of microbial communities under biocrust-forming mosses. Our results suggest that biocrust-forming mosses mitigate the impact of aridity on the community composition of globally distributed microbial taxa, and the diversity of fungi. They emphasize the importance of maintaining biocrusts as a sanctuary for soil microbes in drylands. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

Functional Diversity of Microbial Communities in Sludge-Amended Soils

NASA Astrophysics Data System (ADS)

Sun, Y. H.; Yang, Z. H.; Zhao, J. J.; Li, Q.

The BIOLOG method was applied to exploration of functional diversity of soil microbial communities in sludge-amended soils sampled from the Yangtze River Delta. Results indicated that metabolic profile, functional diversity indexes and Kinetic parameters of the soil microbial communities changed following soil amendment with sewage sludge, suggesting that the changes occurred in population of the microbes capable of exploiting carbon substrates and in this capability as well. The kinetic study of the functional diversity revealed that the metabolic profile of the soil microbial communities exhibited non-linear correlation with the incubation time, showing a curse of sigmoid that fits the dynamic model of growth of the soil microbial communities. In all the treatments, except for treatments of coastal fluvo-aquic soil amended with fresh sludge and dried sludge from Hangzhou, kinetic parameters K and r of the functional diversity of the soil microbial communities decreased significantly and parameter S increased. Changes in characteristics of the functional diversity well reflected differences in C utilizing capacity and model of the soil microbial communities in the sludge-amended soils, and changes in functional diversity of the soil microbial communities in a particular eco-environment, like soil amended with sewage sludge.

Study of the Microbial Diversity of a Newly Discovered East Antarctic Freshwater Lake, L27C, and of a Perennially Ice-Covered Lake Untersee

NASA Technical Reports Server (NTRS)

Huang, Jonathan P.; Hoover, Richard B.; Andersen, Dale; Bej, Asim K.

2010-01-01

The microbial communities that reside within freshwater lakes of Schirmacher and Untersee Oases in East Antarctica must cope with extreme conditions that may include cold temperature, annual freeze-thaw cycles, exposure to UV radiation, especially during the austral summer months, low light beneath thick ice-cover, followed by seasonal darkness. The objective of this study was to assess the microbial biodiversity and distribution from samples taken from two freshwater lakes (L27C and Lake Untersee) that were collected during the Tawani 2008 International Antarctic Expedition that conducted research in this region of Antarctica. L27C is a small, previously unreported lake residing 2 km WNW of Maitri Station at Schirmacher Oasis. Biodiversity and distribution of microorganisms within the lake were studied using both culture-independent and culture-dependent methodologies based upon the analysis of eubacterial 16S rRNA gene sequences. Lake Untersee, a perennially ice-covered, ultra-oligotrophic, lake in the Otto-von-Gruber-Gebirge (Gruber Mountains) of central Dronning Maud Land was also sampled and the microbial diversity was analyzed by eubacterial 16S rRNA gene sequences derived from pure cultures. Direct culturing of water samples from each lake on separate R2A growth medium exhibited a variety of microorganisms including: Janthinobacterium, Hymenobacter, Sphingamonas, Subtercola, Deinococcus, Arthrobacter, Flavobacterium, Polaromonas, Rhodoferax and Duganella. The evaluation of samples from L27C through culture-independent methodology identified a rich microbial diversity consisting of six different phyla of bacteria. The culture-independent analysis also displayed the majority of bacteria (56%) belonged to the Class gamma-proteobacteria within the phylum Proteobacteria. Within the Class gamma-proteobacteria, Acinetobacter dominated (48%) the total microbial load. Overall, L27C exhibited 7 different phyla of bacteria and 20 different genera. Statistical analysis (Shannon-Weaver Diversity Index and Simpson Diversity Index) of the biodiversity of L27C displayed a moderately rich and diverse community. Investigations of the biodiversity and distribution of microorganisms in these lakes will help further our understanding of how the physical environment impact the structure and function within these microbially dominated ecosystems.

Microbial and physical properties as indicators of sandy soil quality under cropland and grassland

NASA Astrophysics Data System (ADS)

Frac, Magdalena; Lipiec, Jerzy; Usowicz, Boguslaw; Oszust, Karolina; Brzezinska, Malgorzata

2017-04-01

Land use is one of the key factor driving changes in soil properties influencing on soil health and quality. Microbial diversity and physical properties are sensitive indicators for assessing soil health and quality. The alterations of microbial diversity and physical properties following land use changes have not been sufficiently elucidated, especially for sandy soils. We investigated microbial diversity indicators including fungal communities composition and physical properties of sandy acid soil under cropland and more than 20-yr-old grassland (after cropland) in Trzebieszów, Podlasie Region, Poland (N 51° 59' 24", E 22° 33' 37"). The study included four depths within 0-60 cm. Microbial genetic diversity was assessed by terminal restriction fragment length polymorphism (t-RFLP) analysis, fungal community composition was evaluated by next generation sequencing (NGS) analysis and functional diversity was determined by Biolog EcoPlate method. Overall microbial activity was assessed by soil enzymes (dehydrogenases, β-glucosidase) and respiration test. At the same places soil texture, organic carbon content, pH, bulk density, water holding capacity were determined. Our results showed that grassland soil was characterized by higher activity of soil enzymes than cropland. The average well color development of soil microorganisms, the microbial functional diversity and the number of carbon source utilization were significantly affected by land use type and were differentiated among soil depths. In grassland compared to cropland soil a significant increase of carboxylic acids and decrease of amino acids utilization was observed. The quantitative and qualitative differences were found in community of ammonia oxidizing archaea in cropland and grassland soil. The results of fungal community composition help to explain the soil health of grassland and cropland based on the appearance of phytopathogenic and antagonistic fungi. In general bulk density and field water capacity were greater and saturated hydraulic conductivity was lower under grassland than cropland soil. The study was funded by HORIZON 2020, European Commission, Programme: H2020-SFS-4-2014: Soil quality and function, project No. 635750, Interactive Soil Quality Assessment in Europe and China for Agricultural Productivity and Environmental Resilience (iSQAPER, 2015-2020).

Decreased plant productivity resulting from plant group removal experiment constrains soil microbial functional diversity.

PubMed

Zhang, Ximei; Johnston, Eric R; Barberán, Albert; Ren, Yi; Lü, Xiaotao; Han, Xingguo

2017-10-01

Anthropogenic environmental changes are accelerating the rate of biodiversity loss on Earth. Plant diversity loss is predicted to reduce soil microbial diversity primarily due to the decreased variety of carbon/energy resources. However, this intuitive hypothesis is supported by sparse empirical evidence, and most underlying mechanisms remain underexplored or obscure altogether. We constructed four diversity gradients (0-3) in a five-year plant functional group removal experiment in a steppe ecosystem in Inner Mongolia, China, and quantified microbial taxonomic and functional diversity with shotgun metagenome sequencing. The treatments had little effect on microbial taxonomic diversity, but were found to decrease functional gene diversity. However, the observed decrease in functional gene diversity was more attributable to a loss in plant productivity, rather than to the loss of any individual plant functional group per se. Reduced productivity limited fresh plant resources supplied to microorganisms, and thus, intensified the pressure of ecological filtering, favoring genes responsible for energy production/conversion, material transport/metabolism and amino acid recycling, and accordingly disfavored many genes with other functions. Furthermore, microbial respiration was correlated with the variation in functional composition but not taxonomic composition. Overall, the amount of carbon/energy resources driving microbial gene diversity was identified to be the critical linkage between above- and belowground communities, contrary to the traditional framework of linking plant clade/taxonomic diversity to microbial taxonomic diversity. © 2017 John Wiley & Sons Ltd.

Addition of Rubber to soil damages the functional diversity of soil.

PubMed

Goswami, Madhurankhi; Bhattacharyya, Purnita; Tribedi, Prosun

2017-07-01

Rubber is a polymer of isoprene, consisting mainly of cis-1,4-polyisoprene units. The unmanageable production and its irresponsible disposal pose severe threats to environmental ecology. Therefore, the current study focuses extensively on the ill-effects of Rubber disposal on soil microbial functional diversity as it reflects the health of ecosystem by acting as a key component in ecosystem productivity. To investigate the effect of Rubber on soil microbial functional diversity, soil samples were collected from landfill sites and three different soil microcosms (Rubber treated, untreated, and sterile soil) were prepared. The soil enzymatic activity was determined by fluorescein diacetate hydrolysis followed by the determination of the microbial metabolic potential and functional diversity by average well color development and Shannon-Weaver index (H), respectively. BiOLOG ECO plates were used for determining the microbial functional diversity of the soil microcosms. Higher heterotrophic microbial count as well as higher soil microbial activity was observed in Rubber untreated soil than Rubber treated soil microcosm. The result indicated that the addition of Rubber to soil reduced soil heterotrophic microbial count and soil microbial activity considerably. Similarly, soil microbial metabolic potential as well as microbial functional diversity of soil had been decreased by the addition of Rubber gloves in it. Variation in soil microbial metabolic spectrum between Rubber treated and untreated microcosm was confirmed by multivariate analysis. Collectively, all the results demonstrated that the addition of Rubber to soil reduced the soil microbial functional diversity considerably. Therefore, it is necessary for the commission of serious steps regarding Rubber disposal and protection of the environment from serious environmental issues.

Biotic and Abiotic Properties Mediating Plant Diversity Effects on Soil Microbial Communities in an Experimental Grassland

PubMed Central

Lange, Markus; Habekost, Maike; Eisenhauer, Nico; Roscher, Christiane; Bessler, Holger; Engels, Christof; Oelmann, Yvonne; Scheu, Stefan; Wilcke, Wolfgang; Schulze, Ernst-Detlef; Gleixner, Gerd

2014-01-01

Plant diversity drives changes in the soil microbial community which may result in alterations in ecosystem functions. However, the governing factors between the composition of soil microbial communities and plant diversity are not well understood. We investigated the impact of plant diversity (plant species richness and functional group richness) and plant functional group identity on soil microbial biomass and soil microbial community structure in experimental grassland ecosystems. Total microbial biomass and community structure were determined by phospholipid fatty acid (PLFA) analysis. The diversity gradient covered 1, 2, 4, 8, 16 and 60 plant species and 1, 2, 3 and 4 plant functional groups (grasses, legumes, small herbs and tall herbs). In May 2007, soil samples were taken from experimental plots and from nearby fields and meadows. Beside soil texture, plant species richness was the main driver of soil microbial biomass. Structural equation modeling revealed that the positive plant diversity effect was mainly mediated by higher leaf area index resulting in higher soil moisture in the top soil layer. The fungal-to-bacterial biomass ratio was positively affected by plant functional group richness and negatively by the presence of legumes. Bacteria were more closely related to abiotic differences caused by plant diversity, while fungi were more affected by plant-derived organic matter inputs. We found diverse plant communities promoted faster transition of soil microbial communities typical for arable land towards grassland communities. Although some mechanisms underlying the plant diversity effect on soil microorganisms could be identified, future studies have to determine plant traits shaping soil microbial community structure. We suspect differences in root traits among different plant communities, such as root turnover rates and chemical composition of root exudates, to structure soil microbial communities. PMID:24816860

Mapping and determinism of soil microbial community distribution across an agricultural landscape.

PubMed

Constancias, Florentin; Terrat, Sébastien; Saby, Nicolas P A; Horrigue, Walid; Villerd, Jean; Guillemin, Jean-Philippe; Biju-Duval, Luc; Nowak, Virginie; Dequiedt, Samuel; Ranjard, Lionel; Chemidlin Prévost-Bouré, Nicolas

2015-06-01

Despite the relevance of landscape, regarding the spatial patterning of microbial communities and the relative influence of environmental parameters versus human activities, few investigations have been conducted at this scale. Here, we used a systematic grid to characterize the distribution of soil microbial communities at 278 sites across a monitored agricultural landscape of 13 km². Molecular microbial biomass was estimated by soil DNA recovery and bacterial diversity by 16S rRNA gene pyrosequencing. Geostatistics provided the first maps of microbial community at this scale and revealed a heterogeneous but spatially structured distribution of microbial biomass and diversity with patches of several hundreds of meters. Variance partitioning revealed that both microbial abundance and bacterial diversity distribution were highly dependent of soil properties and land use (total variance explained ranged between 55% and 78%). Microbial biomass and bacterial richness distributions were mainly explained by soil pH and texture whereas bacterial evenness distribution was mainly related to land management. Bacterial diversity (richness, evenness, and Shannon index) was positively influenced by cropping intensity and especially by soil tillage, resulting in spots of low microbial diversity in soils under forest management. Spatial descriptors also explained a small but significant portion of the microbial distribution suggesting that landscape configuration also shapes microbial biomass and bacterial diversity. © 2015 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Do temperate tree species diversity and identity influence soil microbial community function and composition?

PubMed

Khlifa, Rim; Paquette, Alain; Messier, Christian; Reich, Peter B; Munson, Alison D

2017-10-01

Studies of biodiversity-ecosystem function in treed ecosystems have generally focused on aboveground functions. This study investigates intertrophic links between tree diversity and soil microbial community function and composition. We examined how microbial communities in surface mineral soil responded to experimental gradients of tree species richness (SR), functional diversity (FD), community-weighted mean trait value (CWM), and tree identity. The site was a 4-year-old common garden experiment near Montreal, Canada, consisting of deciduous and evergreen tree species mixtures. Microbial community composition, community-level physiological profiles, and respiration were evaluated using phospholipid fatty acid (PLFA) analysis and the MicroResp ™ system, respectively. The relationship between tree species richness and glucose-induced respiration (GIR), basal respiration (BR), metabolic quotient (qCO 2 ) followed a positive but saturating shape. Microbial communities associated with species mixtures were more active (basal respiration [BR]), with higher biomass (glucose-induced respiration [GIR]), and used a greater number of carbon sources than monocultures. Communities associated with deciduous tree species used a greater number of carbon sources than those associated with evergreen species, suggesting a greater soil carbon storage capacity. There were no differences in microbial composition (PLFA) between monocultures and SR mixtures. The FD and the CWM of several functional traits affected both BR and GIR. In general, the CWM of traits had stronger effects than did FD, suggesting that certain traits of dominant species have more effect on ecosystem processes than does FD. Both the functions of GIR and BR were positively related to aboveground tree community productivity. Both tree diversity (SR) and identity (species and functional identity-leaf habit) affected soil microbial community respiration, biomass, and composition. For the first time, we identified functional traits related to life-history strategy, as well as root traits that influence another trophic level, soil microbial community function, via effects on BR and GIR.

New Arsenate Reductase Gene (arrA) PCR Primers for Diversity Assessment and Quantification in Environmental Samples

PubMed Central

Sorensen, Darwin L.; Dupont, R. Ryan

2016-01-01

ABSTRACT The extent of arsenic contamination in drinking water and its potential threat to human health have resulted in considerable research interest in the microbial species responsible for arsenic reduction. The arsenate reductase gene (arrA), an important component of the microbial arsenate reduction system, has been widely used as a biomarker to study arsenate-reducing microorganisms. A new primer pair was designed and evaluated for quantitative PCR (qPCR) and high-throughput sequencing of the arrA gene, because currently available PCR primers are not suitable for these applications. The primers were evaluated in silico and empirically tested for amplification of arrA genes in clones and for amplification and high-throughput sequencing of arrA genes from soil and groundwater samples. In silico, this primer pair matched (≥90% DNA identity) 86% of arrA gene sequences from GenBank. Empirical evaluation showed successful amplification of arrA gene clones of diverse phylogenetic groups, as well as amplification and high-throughput sequencing of independent soil and groundwater samples without preenrichment, suggesting that these primers are highly specific and can amplify a broad diversity of arrA genes. The arrA gene diversity from soil and groundwater samples from the Cache Valley Basin (CVB) in Utah was greater than anticipated. We observed a significant correlation between arrA gene abundance, quantified through qPCR, and reduced arsenic (AsIII) concentrations in the groundwater samples. Furthermore, we demonstrated that these primers can be useful for studying the diversity of arsenate-reducing microbial communities and the ways in which their relative abundance in groundwater may be associated with different groundwater quality parameters. IMPORTANCE Arsenic is a major drinking water contaminant that threatens the health of millions of people worldwide. The extent of arsenic contamination and its potential threat to human health have resulted in considerable interest in the study of microbial species responsible for the reduction of arsenic, i.e., the conversion of AsV to AsIII. In this study, we developed a new primer pair to evaluate the diversity and abundance of arsenate-reducing microorganisms in soil and groundwater samples from the CVB in Utah. We observed significant arrA gene diversity in the CVB soil and groundwater samples, and arrA gene abundance was significantly correlated with the reduced arsenic (AsIII) concentrations in the groundwater samples. We think that these primers are useful for studying the ecology of arsenate-reducing microorganisms in different environments. PMID:27913413

An improved method to set significance thresholds for β diversity testing in microbial community comparisons.

PubMed

Gülay, Arda; Smets, Barth F

2015-09-01

Exploring the variation in microbial community diversity between locations (β diversity) is a central topic in microbial ecology. Currently, there is no consensus on how to set the significance threshold for β diversity. Here, we describe and quantify the technical components of β diversity, including those associated with the process of subsampling. These components exist for any proposed β diversity measurement procedure. Further, we introduce a strategy to set significance thresholds for β diversity of any group of microbial samples using rarefaction, invoking the notion of a meta-community. The proposed technique was applied to several in silico generated operational taxonomic unit (OTU) libraries and experimental 16S rRNA pyrosequencing libraries. The latter represented microbial communities from different biological rapid sand filters at a full-scale waterworks. We observe that β diversity, after subsampling, is inflated by intra-sample differences; this inflation is avoided in the proposed method. In addition, microbial community evenness (Gini > 0.08) strongly affects all β diversity estimations due to bias associated with rarefaction. Where published methods to test β significance often fail, the proposed meta-community-based estimator is more successful at rejecting insignificant β diversity values. Applying our approach, we reveal the heterogeneous microbial structure of biological rapid sand filters both within and across filters. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

Evaluating variation in human gut microbiota profiles due to DNA extraction method and inter-subject differences.

PubMed

Wagner Mackenzie, Brett; Waite, David W; Taylor, Michael W

2015-01-01

The human gut contains dense and diverse microbial communities which have profound influences on human health. Gaining meaningful insights into these communities requires provision of high quality microbial nucleic acids from human fecal samples, as well as an understanding of the sources of variation and their impacts on the experimental model. We present here a systematic analysis of commonly used microbial DNA extraction methods, and identify significant sources of variation. Five extraction methods (Human Microbiome Project protocol, MoBio PowerSoil DNA Isolation Kit, QIAamp DNA Stool Mini Kit, ZR Fecal DNA MiniPrep, phenol:chloroform-based DNA isolation) were evaluated based on the following criteria: DNA yield, quality and integrity, and microbial community structure based on Illumina amplicon sequencing of the V4 region of bacterial and archaeal 16S rRNA genes. Our results indicate that the largest portion of variation within the model was attributed to differences between subjects (biological variation), with a smaller proportion of variation associated with DNA extraction method (technical variation) and intra-subject variation. A comprehensive understanding of the potential impact of technical variation on the human gut microbiota will help limit preventable bias, enabling more accurate diversity estimates.

Short-term parasite-infection alters already the biomass, activity and functional diversity of soil microbial communities

PubMed Central

Li, Jun-Min; Jin, Ze-Xin; Hagedorn, Frank; Li, Mai-He

2014-01-01

Native parasitic plants may be used to infect and control invasive plants. We established microcosms with invasive Mikania micrantha and native Coix lacryma-jobi growing in mixture on native soils, with M. micrantha being infected by parasitic Cuscuta campestris at four intensity levels for seven weeks to estimate the top-down effects of plant parasitism on the biomass and functional diversity of soil microbial communities. Parasitism significantly decreased root biomass and altered soil microbial communities. Soil microbial biomass decreased, but soil respiration increased at the two higher infection levels, indicating a strong stimulation of soil microbial metabolic activity (+180%). Moreover, a Biolog assay showed that the infection resulted in a significant change in the functional diversity indices of soil microbial communities. Pearson correlation analysis indicated that microbial biomass declined significantly with decreasing root biomass, particularly of the invasive M. micrantha. Also, the functional diversity indices of soil microbial communities were positively correlated with soil microbial biomass. Therefore, the negative effects on the biomass, activity and functional diversity of soil microbial community by the seven week long plant parasitism was very likely caused by decreased root biomass and root exudation of the invasive M. micrantha. PMID:25367357

Short-term parasite-infection alters already the biomass, activity and functional diversity of soil microbial communities

NASA Astrophysics Data System (ADS)

Li, Jun-Min; Jin, Ze-Xin; Hagedorn, Frank; Li, Mai-He

2014-11-01

Native parasitic plants may be used to infect and control invasive plants. We established microcosms with invasive Mikania micrantha and native Coix lacryma-jobi growing in mixture on native soils, with M. micrantha being infected by parasitic Cuscuta campestris at four intensity levels for seven weeks to estimate the top-down effects of plant parasitism on the biomass and functional diversity of soil microbial communities. Parasitism significantly decreased root biomass and altered soil microbial communities. Soil microbial biomass decreased, but soil respiration increased at the two higher infection levels, indicating a strong stimulation of soil microbial metabolic activity (+180%). Moreover, a Biolog assay showed that the infection resulted in a significant change in the functional diversity indices of soil microbial communities. Pearson correlation analysis indicated that microbial biomass declined significantly with decreasing root biomass, particularly of the invasive M. micrantha. Also, the functional diversity indices of soil microbial communities were positively correlated with soil microbial biomass. Therefore, the negative effects on the biomass, activity and functional diversity of soil microbial community by the seven week long plant parasitism was very likely caused by decreased root biomass and root exudation of the invasive M. micrantha.

Structural and functional diversity of soil bacterial and fungal communities following woody plant encroachment in the southern Great Plains

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

Hollister, Emily B; Schadt, Christopher Warren; Palumbo, Anthony Vito

In the southern Great Plains (USA), encroachment of grassland ecosystems by Prosopis glandulosa (honey mesquite) is widespread. Mesquite encroachment alters net primary productivity, enhances stores of C and N in plants and soil, and leads to increased levels of soil microbial biomass and activity. While mesquite's impact on the biogeochemistry of the region is well established, it effects on soil microbial diversity and function are unknown. In this study, soils associated with four plant types (C{sub 3} perennial grasses, C{sub 4} midgrasses, C{sub 4} shortgrasses, and mesquite) from a mesquite-encroached mixed grass prairie were surveyed to in an attempt tomore » characterize the structure, diversity, and functional capacity of their soil microbial communities. rRNA gene cloning and sequencing were used in conjunction with the GeoChip functional gene array to evaluate these potential differences. Mesquite soil supported increased bacterial and fungal diversity and harbored a distinct fungal community relative to other plant types. Despite differences in composition and diversity, few significant differences were detected with respect to the potential functional capacity of the soil microbial communities. These results may suggest that a high level of functional redundancy exists within the bacterial portion of the soil communities; however, given the bias of the GeoChip toward bacterial functional genes, potential functional differences among soil fungi could not be addressed. The results of this study illustrate the linkages shared between above- and belowground communities and demonstrate that soil microbial communities, and in particular soil fungi, may be altered by the process of woody plant encroachment.« less

Plant attributes explain the distribution of soil microbial communities in two contrasting regions of the globe.

PubMed

Delgado-Baquerizo, Manuel; Fry, Ellen L; Eldridge, David J; de Vries, Franciska T; Manning, Peter; Hamonts, Kelly; Kattge, Jens; Boenisch, Gerhard; Singh, Brajesh K; Bardgett, Richard D

2018-04-19

We lack strong empirical evidence for links between plant attributes (plant community attributes and functional traits) and the distribution of soil microbial communities at large spatial scales. Using datasets from two contrasting regions and ecosystem types in Australia and England, we report that aboveground plant community attributes, such as diversity (species richness) and cover, and functional traits can predict a unique portion of the variation in the diversity (number of phylotypes) and community composition of soil bacteria and fungi that cannot be explained by soil abiotic properties and climate. We further identify the relative importance and evaluate the potential direct and indirect effects of climate, soil properties and plant attributes in regulating the diversity and community composition of soil microbial communities. Finally, we deliver a list of examples of common taxa from Australia and England that are strongly related to specific plant traits, such as specific leaf area index, leaf nitrogen and nitrogen fixation. Together, our work provides new evidence that plant attributes, especially plant functional traits, can predict the distribution of soil microbial communities at the regional scale and across two hemispheres. © 2018 The Authors. New Phytologist © 2018 New Phytologist Trust.

Spatial heterogeneity of physicochemical properties explains differences in microbial composition in arid soils from Cuatro Cienegas, Mexico

PubMed Central

Pajares, Silvia; Noguez, Ana M.; García-Oliva, Felipe; Martínez-Piedragil, Celeste; Cram, Silke S.; Eguiarte, Luis Enrique; Souza, Valeria

2016-01-01

Arid ecosystems are characterized by high spatial heterogeneity, and the variation among vegetation patches is a clear example. Soil biotic and abiotic factors associated with these patches have also been well documented as highly heterogeneous in space. Given the low vegetation cover and little precipitation in arid ecosystems, soil microorganisms are the main drivers of nutrient cycling. Nonetheless, little is known about the spatial distribution of microorganisms and the relationship that their diversity holds with nutrients and other physicochemical gradients in arid soils. In this study, we evaluated the spatial variability of soil microbial diversity and chemical parameters (nutrients and ion content) at local scale (meters) occurring in a gypsum-based desert soil, to gain knowledge on what soil abiotic factors control the distribution of microbes in arid ecosystems. We analyzed 32 soil samples within a 64 m2 plot and: (a) characterized microbial diversity using T-RFLPs of the bacterial 16S rRNA gene, (b) determined soil chemical parameters, and (c) identified relationships between microbial diversity and chemical properties. Overall, we found a strong correlation between microbial composition heterogeneity and spatial variation of cations (Ca2, K+) and anions (HCO\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} }{}${}_{3}^{-}$\\end{document}3−, Cl−, SO\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{upgreek} \\usepackage{mathrsfs} \\setlength{\\oddsidemargin}{-69pt} \\begin{document} }{}${}_{4}^{2-}$\\end{document}42−) content in this small plot. Our results could be attributable to spatial differences of soil saline content, favoring the patchy emergence of salt and soil microbial communities. PMID:27652001

[Soil microbial functional diversity of different altitude Pinus koraiensis forests].

PubMed

Han, Dong-xue; Wang, Ning; Wang, Nan-nan; Sun, Xue; Feng, Fu-juan

2015-12-01

In order to comprehensively understand the soil microbial carbon utilization characteristics of Pinus koraiensis forests, we took the topsoil (0-5 cm and 5-10 cm) along the 700-1100 m altitude in Changbai Mountains and analyzed the vertical distributed characteristics and variation of microbial functional diversity along the elevation gradient by Biolog microplate method. The results showed that there were significant differences in functional diversity of microbial communities at different elevations. AWCD increased with the extension of incubation time and AWCD at the same soil depth gradually decreased along with increasing altitude; Shannon, Simpson and McIntosh diversity index also showed the same trend with AWCD and three different diversity indices were significantly different along the elevation gradient; Species diversity and functional diversity showed the same variation. The utilization intensities of six categories carbon sources had differences while amino acids were constantly the most dominant carbon source. Principal component analysis (PCA) identified that soil microbial carbon utilization at different altitudes had obvious spatial differentiation, as reflected in the use of carbohydrates, amino acids and carboxylic acids. In addition, the cluster of the microbial diversity indexes and AWCD values of different altitudes showed that the composition of vegetation had a significant impact on soil microbial composition and functional activity.

Detection of Metabolism Function of Microbial Community of Corpses by Biolog-Eco Method.

PubMed

Jiang, X Y; Wang, J F; Zhu, G H; Ma, M Y; Lai, Y; Zhou, H

2016-06-01

To detect the changes of microbial community functional diversity of corpses with different postmortem interval （PMI） and to evaluate forensic application value for estimating PMI. The cultivation of microbial community from the anal swabs of a Sus scrofa and a human corpse placed in field environment from 0 to 240 h after death was performed using the Biolog-Eco Microplate and the variations of the absorbance values were also monitored. Combined with the technology of forensic pathology and flies succession, the metabolic characteristics and changes of microbial community on the decomposed corpse under natural environment were also observed. The diversity of microbial metabolism function was found to be negatively correlated with the number of maggots in the corpses. The freezing processing had the greatest impact on average well color development value at 0 h and the impact almost disappeared after 48 h. The diversity of microbial metabolism of the samples became relatively unstable after 192 h. The principal component analysis showed that 31 carbon sources could be consolidated for 5 principal components （accumulative contribution ratio >90%）.The carbon source tsquare-analysis showed that N -acetyl- D -glucosamine and L -serine were the dominant carbon sources for estimating the PMI （0=240 h） of the Sus scrofa and human corpse. The Biolog-Eco method can be used to reveal the metabolic differences of the carbon resources utilization of the microbial community on the corpses during 0-240 h after death, which could provide a new basis for estimating the PMI. Copyright© by the Editorial Department of Journal of Forensic Medicine

Response of microbial communities to pesticide residues in soil restored with Azolla imbricata.

PubMed

Lu, Xiao-Ming; Lu, Peng-Zhen

2018-01-01

Under conditions of Azolla imbricata restoration, the high-throughput sequencing technology was employed to determine change trends of microbial community structures in the soil that had undergone long-term application of pesticides. The relationship between the content of pesticide residues in the soil and the microbial community structure was analyzed. The results indicated that the microbial diversity was strongly negatively correlated with the contents of pesticide residues in the soil. At a suitable dosage of 5 kg fresh A. imbricata per square meter of soil area, the soil microbial diversity increased by 12.0%, and the contents of pesticide residues decreased by 26.8-72.1%. Sphingobacterium, Sphingopyxis, Thermincola, Sphingobium, Acaryochloris, Megasphaera, Ralstonia, Pseudobutyrivibrio, Desulfitobacterium, Nostoc, Oscillochloris, and Aciditerrimonas may play major roles in the degradation of pesticide residues. Thauera, Levilinea, Geothrix, Thiobacillus, Thioalkalispira, Desulfobulbus, Polycyclovorans, Fluviicola, Deferrisoma, Erysipelothrix, Desulfovibrio, Cytophaga, Vogesella, Zoogloea, Azovibrio, Halomonas, Paludibacter, Crocinitomix, Haliscomenobacter, Hirschia, Silanimonas, Alkalibacter, Woodsholea, Peredibacter, Leptolinea, Chitinivorax, Candidatus_Lumbricincola, Anaerovorax, Propionivibrio, Parasegetibacter, Byssovorax, Runella, Leptospira, and Nitrosomonas may be indicators to evaluate the contents of pesticide residues.

Effect of preservation method on spider monkey (Ateles geoffroyi) fecal microbiota over 8 weeks.

PubMed

Hale, Vanessa L; Tan, Chia L; Knight, Rob; Amato, Katherine R

2015-06-01

Studies of the gut microbiome have become increasingly common with recent technological advances. Gut microbes play an important role in human and animal health, and gut microbiome analysis holds great potential for evaluating health in wildlife, as microbiota can be assessed from non-invasively collected fecal samples. However, many common fecal preservation protocols (e.g. freezing at -80 °C) are not suitable for field conditions, or have not been tested for long-term (greater than 2 weeks) storage. In this study, we collected fresh fecal samples from captive spider monkeys (Ateles geoffroyi) at the Columbian Park Zoo (Lafayette, IN, USA). The samples were pooled, homogenized, and preserved for up to 8 weeks prior to DNA extraction and sequencing. Preservation methods included: freezing at -20 °C, freezing at -80 °C, immersion in 100% ethanol, application to FTA cards, and immersion in RNAlater. At 0 (fresh), 1, 2, 4, and 8 weeks from fecal collection, DNA was extracted and microbial DNA was amplified and sequenced. DNA concentration, purity, microbial diversity, and microbial composition were compared across all methods and time points. DNA concentration and purity did not correlate with microbial diversity or composition. Microbial composition of frozen and ethanol samples were most similar to fresh samples. FTA card and RNAlater-preserved samples had the least similar microbial composition and abundance compared to fresh samples. Microbial composition and diversity were relatively stable over time within each preservation method. Based on these results, if freezers are not available, we recommend preserving fecal samples in ethanol (for up to 8weeks) prior to microbial extraction and analysis. Copyright © 2015 Elsevier B.V. All rights reserved.

Microbial diversity and structure are drivers of the biological barrier effect against Listeria monocytogenes in soil.

PubMed

Vivant, Anne-Laure; Garmyn, Dominique; Maron, Pierre-Alain; Nowak, Virginie; Piveteau, Pascal

2013-01-01

Understanding the ecology of pathogenic organisms is important in order to monitor their transmission in the environment and the related health hazards. We investigated the relationship between soil microbial diversity and the barrier effect against Listeria monocytogenes invasion. By using a dilution-to-extinction approach, we analysed the consequence of eroding microbial diversity on L. monocytogenes population dynamics under standardised conditions of abiotic parameters and microbial abundance in soil microcosms. We demonstrated that highly diverse soil microbial communities act as a biological barrier against L. monocytogenes invasion and that phylogenetic composition of the community also has to be considered. This suggests that erosion of diversity may have damaging effects regarding circulation of pathogenic microorganisms in the environment.

Comparative evaluation of the indigenous microbial diversity vs. drilling fluid contaminants in the NEEM Greenland ice core.

PubMed

Miteva, Vanya; Burlingame, Caroline; Sowers, Todd; Brenchley, Jean

2014-08-01

Demonstrating that the detected microbial diversity in nonaseptically drilled deep ice cores is truly indigenous is challenging because of potential contamination with exogenous microbial cells. The NEEM Greenland ice core project provided a first-time opportunity to determine the origin and extent of contamination throughout drilling. We performed multiple parallel cultivation and culture-independent analyses of five decontaminated ice core samples from different depths (100-2051 m), the drilling fluid and its components Estisol and Coasol, and the drilling chips collected during drilling. We created a collection of diverse bacterial and fungal isolates (84 from the drilling fluid and its components, 45 from decontaminated ice, and 66 from drilling chips). Their categorization as contaminants or intrinsic glacial ice microorganisms was based on several criteria, including phylogenetic analyses, genomic fingerprinting, phenotypic characteristics, and presence in drilling fluid, chips, and/or ice. Firmicutes and fungi comprised the dominant group of contaminants among isolates and cloned rRNA genes. Conversely, most Proteobacteria and Actinobacteria originating from the ice were identified as intrinsic. This study provides a database of potential contaminants useful for future studies of NEEM cores and can contribute toward developing standardized protocols for contamination detection and ensuring the authenticity of the microbial diversity in deep glacial ice. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Characterisation of culture-independent and -dependent microbial communities in a high-temperature offshore chalk petroleum reservoir.

PubMed

Kaster, Krista M; Bonaunet, Kristin; Berland, Harald; Kjeilen-Eilertsen, Grethe; Brakstad, Odd Gunnar

2009-11-01

Recent studies have indicated that oil reservoirs harbour diverse microbial communities. Culture-dependent and culture-independent methods were used to evaluate the microbial diversity in produced water samples of the Ekofisk oil field, a high temperature, and fractured chalk reservoir in the North Sea. DGGE analyses of 16S rRNA gene fragments were used to assess the microbial diversity of both archaeal and bacterial communities in produced water samples and enrichment cultures from 4 different wells (B-08, X-08, X-18 and X-25). Low diversity communities were found when 16S rDNA libraries of bacterial and archaeal assemblages were generated from total community DNA obtained from produced water samples and enrichment cultures. Sequence analysis of the clones indicated close matches to microbes associated with high-temperature oil reservoirs or other similar environments. Sequences were found to be similar to members of the genera Thermotoga, Caminicella, Thermoanaerobacter, Archaeoglobus, Thermococcus, and Methanobulbus. Enrichment cultures obtained from the produced water samples were dominated by sheathed rods. Sequence analyses of the cultures indicated predominance of the genera Petrotoga, Arcobacter, Archaeoglobus and Thermococcus. The communities of both produced water and enrichment cultures appeared to be dominated by thermophilic fermenters capable of reducing sulphur compounds. These results suggest that the biochemical processes in the Ekofisk chalk reservoir are similar to those observed in high-temperature sandstone reservoirs.

Distinct microbial communities in the active and permafrost layers on the Tibetan Plateau.

PubMed

Chen, Yong-Liang; Deng, Ye; Ding, Jin-Zhi; Hu, Hang-Wei; Xu, Tian-Le; Li, Fei; Yang, Gui-Biao; Yang, Yuan-He

2017-12-01

Permafrost represents an important understudied genetic resource. Soil microorganisms play important roles in regulating biogeochemical cycles and maintaining ecosystem function. However, our knowledge of patterns and drivers of permafrost microbial communities is limited over broad geographic scales. Using high-throughput Illumina sequencing, this study compared soil bacterial, archaeal and fungal communities between the active and permafrost layers on the Tibetan Plateau. Our results indicated that microbial alpha diversity was significantly higher in the active layer than in the permafrost layer with the exception of fungal Shannon-Wiener index and Simpson's diversity index, and microbial community structures were significantly different between the two layers. Our results also revealed that environmental factors such as soil fertility (soil organic carbon, dissolved organic carbon and total nitrogen contents) were the primary drivers of the beta diversity of bacterial, archaeal and fungal communities in the active layer. In contrast, environmental variables such as the mean annual precipitation and total phosphorus played dominant roles in driving the microbial beta diversity in the permafrost layer. Spatial distance was important for predicting the bacterial and archaeal beta diversity in both the active and permafrost layers, but not for fungal communities. Collectively, these results demonstrated different driving factors of microbial beta diversity between the active layer and permafrost layer, implying that the drivers of the microbial beta diversity observed in the active layer cannot be used to predict the biogeographic patterns of the microbial beta diversity in the permafrost layer. © 2017 John Wiley & Sons Ltd.

Microbial eukaryotic diversity and distribution in a river plume and cyclonic eddy-influenced ecosystem in the South China Sea

PubMed Central

Wu, Wenxue; Wang, Lei; Liao, Yu; Huang, Bangqin

2015-01-01

To evaluate microbial eukaryotic diversity and distribution in mesoscale processes, we investigated 18S rDNA diversity in a river plume and cyclonic eddy-influenced ecosystem in the southwestern South China Sea (SCS). Restriction fragment length polymorphism analysis was carried out using multiple primer sets. Relative to a wide range of previous similar studies, we observed a significantly higher proportion of sequences of pigmented taxa. Among the photosynthetic groups, Haptophyta accounted for 27.7% of the sequenced clones, which belonged primarily to Prymnesiophyceae. Unexpectedly, five operational taxonomic units of Cryptophyta were closely related to freshwater species. The Chlorophyta mostly fell within the Prasinophyceae, which was comprised of six clades, including Clade III, which is detected in the SCS for the first time in this study. Among the photosynthetic stramenopiles, Chrysophyceae was the most diverse taxon, which included seven clades. The majority of 18S rDNA sequences affiliated with the Dictyochophyceae, Eustigmatophyceae, and Pelagophyceae were closely related to those of pure cultures. The results of redundancy analysis and the permutation Mantel test based on unweighted UniFrac distances, conducted for spatial analyses of the Haptophyta subclades suggested that the Mekong River plume and cyclonic eddy play important roles in regulating microbial eukaryotic diversity and distribution in the southwestern SCS. PMID:26268071

[Effect of X-ray micro-computed tomography on the metabolic activity and diversity of soil microbial communities in two Chinese soils].

PubMed

Zu, Qianhui; Fang, Huan; Zhou, Hu; Zhang, Jianwei; Peng, Xinhua; Lin, Xiangui; Feng, Youzhi

2016-01-04

X-ray micro-computed tomography (micro-CT) technology, as used in the in situ and nondestructive analysis of soil physical structure, provides the opportunity of associating soil physical and biological assays. Due to the high heterogeneity of the soil matrix, X-ray micro-CT scanning and soil microbial assays should be conducted on the same soil sample. This raises the question whether X-ray micro-CT influences microbial function and diversity of the sample soil to be analyzed. To address this question, we used plate counting, microcalorimetry and pyrosequencing approaches to evaluate the effect of X-ray--at doses typically used in micro-CT--on soil microorganisms in a typical soil of North China Plain, Fluvo-aquic soil and in a typical soil of subtropical China, Ultisol soil, respectively. In both soils radiation decreased the number of viable soil bacteria and disturbed their thermogenic profiles. At DNA level, pyrosequencing revealed that alpha diversities of two soils biota were influenced in opposite ways, while beta diversity was not affected although the relative abundances of some guilds were changed. These findings indicate that the metabolically active aspects of soil biota are not compatible with X-ray micro-CT; while the beta molecular diversity based on pyrosequencing could be compatible.

Fungicides degradation in an organic biomixture: impact on microbial diversity.

PubMed

Coppola, Laura; Comitini, Francesca; Casucci, Cristiano; Milanovic, Vesna; Monaci, Elga; Marinozzi, Maria; Taccari, Manuela; Ciani, Maurizio; Vischetti, Costantino

2011-12-15

Biological systems are being developed all over EU countries to protect water-bodies from pesticide contamination at farm level. A laboratory experiment was carried out to test the efficiency of a mixture of compost and straw in bio-degrading different mixtures of fungicides usually applied in vineyards. At the same time the effects of fungicide applications on microbial community of biomixture were also evaluated. Results showed that the biomixture had a good capability of degrading pesticides. Indeed, at the end of the experiment (112 days), the concentration of most of the pesticides was close to complete degradation. Denaturing gradient gel electrophoresis (DGGE) analysis showed an evident modification of microbial diversity after the addition of fungicides. However, at the end of degradation process, no significant changes in the composition of microbial community were seen. In this specific substrate used in the biomixture, yeast flora and ascomycete filamentous fungi seemed to be involved in the degradation activity. Copyright © 2011 Elsevier B.V. All rights reserved.

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.

Effects of bamboo charcoal on fouling and microbial diversity in a flat-sheet ceramic membrane bioreactor.

PubMed

Zhang, Wenjie; Liu, Xiaoning; Wang, Dunqiu; Jin, Yue

2017-11-01

Membrane fouling is a problem in full-scale membrane bioreactors. In this study, bamboo charcoal (BC) was evaluated for its efficacy in alleviating membrane fouling in flat-sheet membrane bioreactors treating municipal wastewater. The results showed that BC addition markedly improved treatment performance based on COD, NH 4 + -N, total nitrogen, and total phosphorus levels. Adding BC slowed the increase in the trans-membrane pressure rate and resulted in lower levels of soluble microbial products and extracellular polymeric substances detected in the flat-sheet membrane bioreactor. BC has a porous structure, and a large quantity of biomass was detected using scanning electron microscopy. The microbial community analysis results indicated that BC increased the microbial diversity and Aminomonas, Anaerofustis, uncultured Anaerolineaceae, Anaerolinea, and Anaerotruncus were found in higher abundances in the reactor with BC. BC addition is an effective method for reducing membrane fouling, and can be applied to full-scale flat-sheet membrane bioreactors to improve their function. Copyright © 2017 Elsevier Ltd. All rights reserved.

Inorganic species distribution and microbial diversity within high Arctic cryptoendolithic habitats.

PubMed

Omelon, Christopher R; Pollard, Wayne H; Ferris, F Grant

2007-11-01

Cryptoendolithic habitats in the Canadian high Arctic are associated with a variety of microbial community assemblages, including cyanobacteria, algae, and fungi. These habitats were analyzed for the presence of metal ions by sequential extraction and evaluated for relationships between these and the various microorganisms found at each site using multivariate statistical methods. Cyanobacteria-dominated communities exist under higher pH conditions with elevated concentrations of calcium and magnesium, whereas communities dominated by fungi and algae are characterized by lower pH conditions and higher concentrations of iron, aluminum, and silicon in the overlying surfaces. These results suggest that the activity of the dominant microorganisms controls the pH of the surrounding environment, which in turn dictates rates of weathering or the possibility for surface crust formation, both ultimately deciding the structure of microbial diversity for each cryptoendolithic habitat.

The Biogeographic Pattern of Microbial Functional Genes along an Altitudinal Gradient of the Tibetan Pasture

PubMed Central

Qi, Qi; Zhao, Mengxin; Wang, Shiping; Ma, Xingyu; Wang, Yuxuan; Gao, Ying; Lin, Qiaoyan; Li, Xiangzhen; Gu, Baohua; Li, Guoxue; Zhou, Jizhong; Yang, Yunfeng

2017-01-01

As the highest place of the world, the Tibetan plateau is a fragile ecosystem. Given the importance of microbial communities in driving soil nutrient cycling, it is of interest to document the microbial biogeographic pattern here. We adopted a microarray-based tool named GeoChip 4.0 to investigate grassland microbial functional genes along an elevation gradient from 3200 to 3800 m above sea level open to free grazing by local herdsmen and wild animals. Interestingly, microbial functional diversities increase with elevation, so does the relative abundances of genes associated with carbon degradation, nitrogen cycling, methane production, cold shock and oxygen limitation. The range of Shannon diversities (10.27–10.58) showed considerably smaller variation than what was previously observed at ungrazed sites nearby (9.95–10.65), suggesting the important role of livestock grazing on microbial diversities. Closer examination showed that the dissimilarity of microbial community at our study sites increased with elevations, revealing an elevation-decay relationship of microbial functional genes. Both microbial functional diversity and the number of unique genes increased with elevations. Furthermore, we detected a tight linkage of greenhouse gas (CO2) and relative abundances of carbon cycling genes. Our biogeographic study provides insights on microbial functional diversity and soil biogeochemical cycling in Tibetan pastures. PMID:28659870

Deciphering Diversity Indices for a Better Understanding of Microbial Communities.

PubMed

Kim, Bo-Ra; Shin, Jiwon; Guevarra, Robin; Lee, Jun Hyung; Kim, Doo Wan; Seol, Kuk-Hwan; Lee, Ju-Hoon; Kim, Hyeun Bum; Isaacson, Richard

2017-12-28

The past decades have been a golden era during which great tasks were accomplished in the field of microbiology, including food microbiology. In the past, culture-dependent methods have been the primary choice to investigate bacterial diversity. However, using cultureindependent high-throughput sequencing of 16S rRNA genes has greatly facilitated studies exploring the microbial compositions and dynamics associated with health and diseases. These culture-independent DNA-based studies generate large-scale data sets that describe the microbial composition of a certain niche. Consequently, understanding microbial diversity becomes of greater importance when investigating the composition, function, and dynamics of the microbiota associated with health and diseases. Even though there is no general agreement on which diversity index is the best to use, diversity indices have been used to compare the diversity among samples and between treatments with controls. Tools such as the Shannon- Weaver index and Simpson index can be used to describe population diversity in samples. The purpose of this review is to explain the principles of diversity indices, such as Shannon- Weaver and Simpson, to aid general microbiologists in better understanding bacterial communities. In this review, important questions concerning microbial diversity are addressed. Information from this review should facilitate evidence-based strategies to explore microbial communities.

Impacts of environmental factors on the whole microbial communities in the rhizosphere of a metal-tolerant plant: Elsholtzia haichowensis Sun.

PubMed

Deng, Songqiang; Ke, Tan; Li, Longtai; Cai, Shenwen; Zhou, Yuyue; Liu, Yue; Guo, Limin; Chen, Lanzhou; Zhang, Dayi

2018-06-01

Rhizospheric microbes play important roles in plant growth and heavy metals (HMs) transformation, possessing great potential for the successful phytoremediation of environmental pollutants. In the present study, the rhizosphere of Elsholtzia haichowensis Sun was comprehensively studied to uncover the influence of environmental factors (EFs) on the whole microbial communities including bacteria, fungi and archaea, via quantitative polymerase chain reaction (qPCR) and high-throughput sequencing. By analyzing molecular ecological network and multivariate regression trees (MRT), we evaluated the distinct impacts of 37 EFs on soil microbial community. Of them, soil pH, HMs, soil texture and nitrogen were identified as the most influencing factors, and their roles varied across different domains. Soil pH was the main environmental variable on archaeal and bacterial community but not fungi, explaining 25.7%, 46.5% and 40.7% variation of bacterial taxonomic composition, archaeal taxonomic composition and a-diversity, respectively. HMs showed important roles in driving the whole microbial community and explained the major variation in different domains. Nitrogen (NH 4 -N, NO 3 -N, NO 2 -N and TN) explained 47.3% variation of microbial population composition and 15.9% of archaeal taxonomic composition, demonstrating its influence in structuring the rhizospheric microbiome, particularly archaeal and bacterial community. Soil texture accounted for 10.2% variation of population composition, 28.9% of fungal taxonomic composition, 19.2% of fungal a-diversity and 7.8% of archaeal a-diversity. Rhizosphere only showed strong impacts on fungi and bacteria, accounting for 14.7% and 4.9% variation of fungal taxonomic composition and bacterial a-diversity. Spatial distance had stronger influence on bacteria and archaea than fungi, but not as significant as other EFs. For the first time, our study provides a complete insight into key influential EFs on rhizospheric microbes and how their roles vary across microbial domains, giving a hand for understanding the construction of microbial communities in rhizosphere. Copyright © 2017 Elsevier Ltd. All rights reserved.

Toward Understanding, Managing, and Protecting Microbial Ecosystems

PubMed Central

Bodelier, Paul L. E.

2011-01-01

Microbial communities are at the very basis of life on earth, catalyzing biogeochemical reactions driving global nutrient cycles. However, unlike for plants and animals, microbial diversity is not on the biodiversity–conservation agenda. The latter, however, would imply that microbial diversity is not under any threat by anthropogenic disturbance or climate change. This maybe a misconception caused by the rudimentary knowledge we have concerning microbial diversity and its role in ecosystem functioning. This perspective paper identifies major areas with knowledge gaps within the field of environmental microbiology that preclude a comprehension of microbial ecosystems on the level we have for plants and animals. Opportunities and challenges are pointed out to open the microbial black box and to go from descriptive to predictive microbial ecology. PMID:21747797

The complicated substrates enhance the microbial diversity and zinc leaching efficiency in sphalerite bioleaching system.

PubMed

Xiao, Yunhua; Xu, YongDong; Dong, Weiling; Liang, Yili; Fan, Fenliang; Zhang, Xiaoxia; Zhang, Xian; Niu, Jiaojiao; Ma, Liyuan; She, Siyuan; He, Zhili; Liu, Xueduan; Yin, Huaqun

2015-12-01

This study used an artificial enrichment microbial consortium to examine the effects of different substrate conditions on microbial diversity, composition, and function (e.g., zinc leaching efficiency) through adding pyrite (SP group), chalcopyrite (SC group), or both (SPC group) in sphalerite bioleaching systems. 16S rRNA gene sequencing analysis showed that microbial community structures and compositions dramatically changed with additions of pyrite or chalcopyrite during the sphalerite bioleaching process. Shannon diversity index showed a significantly increase in the SP (1.460), SC (1.476), and SPC (1.341) groups compared with control (sphalerite group, 0.624) on day 30, meanwhile, zinc leaching efficiencies were enhanced by about 13.4, 2.9, and 13.2%, respectively. Also, additions of pyrite or chalcopyrite could increase electric potential (ORP) and the concentrations of Fe3+ and H+, which were the main factors shaping microbial community structures by Mantel test analysis. Linear regression analysis showed that ORP, Fe3+ concentration, and pH were significantly correlated to zinc leaching efficiency and microbial diversity. In addition, we found that leaching efficiency showed a positive and significant relationship with microbial diversity. In conclusion, our results showed that the complicated substrates could significantly enhance microbial diversity and activity of function.

Effect of residual H2O2 from advanced oxidation processes on subsequent biological water treatment: A laboratory batch study.

PubMed

Wang, Feifei; van Halem, Doris; Liu, Gang; Lekkerkerker-Teunissen, Karin; van der Hoek, Jan Peter

2017-10-01

H 2 O 2 residuals from advanced oxidation processes (AOPs) may have critical impacts on the microbial ecology and performance of subsequent biological treatment processes, but little is known. The objective of this study was to evaluate how H 2 O 2 residuals influence sand systems with an emphasis on dissolved organic carbon (DOC) removal, microbial activity change and bacterial community evolution. The results from laboratory batch studies showed that 0.25 mg/L H 2 O 2 lowered DOC removal by 10% while higher H 2 O 2 concentrations at 3 and 5 mg/L promoted DOC removal by 8% and 28%. A H 2 O 2 dosage of 0.25 mg/L did not impact microbial activity (as measured by ATP) while high H 2 O 2 dosages, 1, 3 and 5 mg/L, resulted in reduced microbial activity of 23%, 37% and 37% respectively. Therefore, DOC removal was promoted by the increase of H 2 O 2 dosage while microbial activity was reduced. The pyrosequencing results illustrated that bacterial communities were dominated by Proteobacteria. The presence of H 2 O 2 showed clear influence on the diversity and composition of bacterial communities, which became more diverse under 0.25 mg/L H 2 O 2 but conversely less diverse when the dosage increased to 5 mg/L H 2 O 2 . Anaerobic bacteria were found to be most sensitive to H 2 O 2 as their growth in batch reactors was limited by both 0.25 and 5 mg/L H 2 O 2 (17-88% reduction). In conclusion, special attention should be given to effects of AOPs residuals on microbial ecology before introducing AOPs as a pre-treatment to biological (sand) processes. Additionally, the guideline on the maximum allowable H 2 O 2 concentration should be properly evaluated. Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Microbial Diversity and Structure Are Drivers of the Biological Barrier Effect against Listeria monocytogenes in Soil

PubMed Central

Vivant, Anne-Laure; Garmyn, Dominique; Maron, Pierre-Alain; Nowak, Virginie; Piveteau, Pascal

2013-01-01

Understanding the ecology of pathogenic organisms is important in order to monitor their transmission in the environment and the related health hazards. We investigated the relationship between soil microbial diversity and the barrier effect against Listeria monocytogenes invasion. By using a dilution-to-extinction approach, we analysed the consequence of eroding microbial diversity on L. monocytogenes population dynamics under standardised conditions of abiotic parameters and microbial abundance in soil microcosms. We demonstrated that highly diverse soil microbial communities act as a biological barrier against L. monocytogenes invasion and that phylogenetic composition of the community also has to be considered. This suggests that erosion of diversity may have damaging effects regarding circulation of pathogenic microorganisms in the environment. PMID:24116193

Microbial diversity arising from thermodynamic constraints

PubMed Central

Großkopf, Tobias; Soyer, Orkun S

2016-01-01

The microbial world displays an immense taxonomic diversity. This diversity is manifested also in a multitude of metabolic pathways that can utilise different substrates and produce different products. Here, we propose that these observations directly link to thermodynamic constraints that inherently arise from the metabolic basis of microbial growth. We show that thermodynamic constraints can enable coexistence of microbes that utilise the same substrate but produce different end products. We find that this thermodynamics-driven emergence of diversity is most relevant for metabolic conversions with low free energy as seen for example under anaerobic conditions, where population dynamics is governed by thermodynamic effects rather than kinetic factors such as substrate uptake rates. These findings provide a general understanding of the microbial diversity based on the first principles of thermodynamics. As such they provide a thermodynamics-based framework for explaining the observed microbial diversity in different natural and synthetic environments. PMID:27035705

Functional gene diversity of soil microbial communities from five oil-contaminated fields in China.

PubMed

Liang, Yuting; Van Nostrand, Joy D; Deng, Ye; He, Zhili; Wu, Liyou; Zhang, Xu; Li, Guanghe; Zhou, Jizhong

2011-03-01

To compare microbial functional diversity in different oil-contaminated fields and to know the effects of oil contaminant and environmental factors, soil samples were taken from typical oil-contaminated fields located in five geographic regions of China. GeoChip, a high-throughput functional gene array, was used to evaluate the microbial functional genes involved in contaminant degradation and in other major biogeochemical/metabolic processes. Our results indicated that the overall microbial community structures were distinct in each oil-contaminated field, and samples were clustered by geographic locations. The organic contaminant degradation genes were most abundant in all samples and presented a similar pattern under oil contaminant stress among the five fields. In addition, alkane and aromatic hydrocarbon degradation genes such as monooxygenase and dioxygenase were detected in high abundance in the oil-contaminated fields. Canonical correspondence analysis indicated that the microbial functional patterns were highly correlated to the local environmental variables, such as oil contaminant concentration, nitrogen and phosphorus contents, salt and pH. Finally, a total of 59% of microbial community variation from GeoChip data can be explained by oil contamination, geographic location and soil geochemical parameters. This study provided insights into the in situ microbial functional structures in oil-contaminated fields and discerned the linkages between microbial communities and environmental variables, which is important to the application of bioremediation in oil-contaminated sites.

Functional gene diversity of soil microbial communities from five oil-contaminated fields in China

PubMed Central

Liang, Yuting; Van Nostrand, Joy D; Deng, Ye; He, Zhili; Wu, Liyou; Zhang, Xu; Li, Guanghe; Zhou, Jizhong

2011-01-01

To compare microbial functional diversity in different oil-contaminated fields and to know the effects of oil contaminant and environmental factors, soil samples were taken from typical oil-contaminated fields located in five geographic regions of China. GeoChip, a high-throughput functional gene array, was used to evaluate the microbial functional genes involved in contaminant degradation and in other major biogeochemical/metabolic processes. Our results indicated that the overall microbial community structures were distinct in each oil-contaminated field, and samples were clustered by geographic locations. The organic contaminant degradation genes were most abundant in all samples and presented a similar pattern under oil contaminant stress among the five fields. In addition, alkane and aromatic hydrocarbon degradation genes such as monooxygenase and dioxygenase were detected in high abundance in the oil-contaminated fields. Canonical correspondence analysis indicated that the microbial functional patterns were highly correlated to the local environmental variables, such as oil contaminant concentration, nitrogen and phosphorus contents, salt and pH. Finally, a total of 59% of microbial community variation from GeoChip data can be explained by oil contamination, geographic location and soil geochemical parameters. This study provided insights into the in situ microbial functional structures in oil-contaminated fields and discerned the linkages between microbial communities and environmental variables, which is important to the application of bioremediation in oil-contaminated sites. PMID:20861922

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.

Plant diversity predicts beta but not alpha diversity of soil microbes across grasslands worldwide

USGS Publications Warehouse

Prober, Suzanne M.; Leff, Jonathan W.; Bates, Scott T.; Borer, Elizabeth T.; Firn, Jennifer; Harpole, W. Stanley; Lind, Eric M.; Seabloom, Eric W.; Adler, Peter B.; Bakker, Jonathan D.; Cleland, Elsa E.; DeCrappeo, Nicole; DeLorenze, Elizabeth; Hagenah, Nicole; Hautier, Yann; Hofmockel, Kirsten S.; Kirkman, Kevin P.; Knops, Johannes M. H.; La Pierre, Kimberly J.; MacDougall, Andrew S.; McCulley, Rebecca L.; Mitchell, Charles E.; Risch, Anita C.; Schuetz, Martin; Stevens, Carly J.; Williams, Ryan J.; Fierer, Noah

2015-01-01

Aboveground–belowground interactions exert critical controls on the composition and function of terrestrial ecosystems, yet the fundamental relationships between plant diversity and soil microbial diversity remain elusive. Theory predicts predominantly positive associations but tests within single sites have shown variable relationships, and associations between plant and microbial diversity across broad spatial scales remain largely unexplored. We compared the diversity of plant, bacterial, archaeal and fungal communities in one hundred and forty-five 1 m2 plots across 25 temperate grassland sites from four continents. Across sites, the plant alpha diversity patterns were poorly related to those observed for any soil microbial group. However, plant beta diversity (compositional dissimilarity between sites) was significantly correlated with the beta diversity of bacterial and fungal communities, even after controlling for environmental factors. Thus, across a global range of temperate grasslands, plant diversity can predict patterns in the composition of soil microbial communities, but not patterns in alpha diversity.

Soil microbial biomass and function are altered by 12 years of crop rotation

NASA Astrophysics Data System (ADS)

McDaniel, Marshall D.; Grandy, A. Stuart

2016-11-01

Declines in plant diversity will likely reduce soil microbial biomass, alter microbial functions, and threaten the provisioning of soil ecosystem services. We examined whether increasing temporal plant biodiversity in agroecosystems (by rotating crops) can partially reverse these trends and enhance soil microbial biomass and function. We quantified seasonal patterns in soil microbial biomass, respiration rates, extracellular enzyme activity, and catabolic potential three times over one growing season in a 12-year crop rotation study at the W. K. Kellogg Biological Station LTER. Rotation treatments varied from one to five crops in a 3-year rotation cycle, but all soils were sampled under a corn year. We hypothesized that crop diversity would increase microbial biomass, activity, and catabolic evenness (a measure of functional diversity). Inorganic N, the stoichiometry of microbial biomass and dissolved organic C and N varied seasonally, likely reflecting fluctuations in soil resources during the growing season. Soils from biodiverse cropping systems increased microbial biomass C by 28-112 % and N by 18-58 % compared to low-diversity systems. Rotations increased potential C mineralization by as much as 53 %, and potential N mineralization by 72 %, and both were related to substantially higher hydrolase and lower oxidase enzyme activities. The catabolic potential of the soil microbial community showed no, or slightly lower, catabolic evenness in more diverse rotations. However, the catabolic potential indicated that soil microbial communities were functionally distinct, and microbes from monoculture corn preferentially used simple substrates like carboxylic acids, relative to more diverse cropping systems. By isolating plant biodiversity from differences in fertilization and tillage, our study illustrates that crop biodiversity has overarching effects on soil microbial biomass and function that last throughout the growing season. In simplified agricultural systems, relatively small increases in crop diversity can have large impacts on microbial community size and function, with cover crops appearing to facilitate the largest increases.

Disturbance Regimes Predictably Alter Diversity in an Ecologically Complex Bacterial System

PubMed Central

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

2016-01-01

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

Dramatic Increases of Soil Microbial Functional Gene Diversity at the Treeline Ecotone of Changbai Mountain.

PubMed

Shen, Congcong; Shi, Yu; Ni, Yingying; Deng, Ye; Van Nostrand, Joy D; He, Zhili; Zhou, Jizhong; Chu, Haiyan

2016-01-01

The elevational and latitudinal diversity patterns of microbial taxa have attracted great attention in the past decade. Recently, the distribution of functional attributes has been in the spotlight. Here, we report a study profiling soil microbial communities along an elevation gradient (500-2200 m) on Changbai Mountain. Using a comprehensive functional gene microarray (GeoChip 5.0), we found that microbial functional gene richness exhibited a dramatic increase at the treeline ecotone, but the bacterial taxonomic and phylogenetic diversity based on 16S rRNA gene sequencing did not exhibit such a similar trend. However, the β-diversity (compositional dissimilarity among sites) pattern for both bacterial taxa and functional genes was similar, showing significant elevational distance-decay patterns which presented increased dissimilarity with elevation. The bacterial taxonomic diversity/structure was strongly influenced by soil pH, while the functional gene diversity/structure was significantly correlated with soil dissolved organic carbon (DOC). This finding highlights that soil DOC may be a good predictor in determining the elevational distribution of microbial functional genes. The finding of significant shifts in functional gene diversity at the treeline ecotone could also provide valuable information for predicting the responses of microbial functions to climate change.

Remarkable recovery and colonization behaviour of methane oxidizing bacteria in soil after disturbance is controlled by methane source only.

PubMed

Pan, Yao; Abell, Guy C J; Bodelier, Paul L E; Meima-Franke, Marion; Sessitsch, Angela; Bodrossy, Levente

2014-08-01

Little is understood about the relationship between microbial assemblage history, the composition and function of specific functional guilds and the ecosystem functions they provide. To learn more about this relationship we used methane oxidizing bacteria (MOB) as model organisms and performed soil microcosm experiments comprised of identical soil substrates, hosting distinct overall microbial diversities(i.e., full, reduced and zero total microbial and MOB diversities). After inoculation with undisturbed soil, the recovery of MOB activity, MOB diversity and total bacterial diversity were followed over 3 months by methane oxidation potential measurements and analyses targeting pmoA and 16S rRNA genes. Measurement of methane oxidation potential demonstrated different recovery rates across the different treatments. Despite different starting microbial diversities, the recovery and succession of the MOB communities followed a similar pattern across the different treatment microcosms. In this study we found that edaphic parameters were the dominant factor shaping microbial communities over time and that the starting microbial community played only a minor role in shaping MOB microbial community.

MBGD update 2013: the microbial genome database for exploring the diversity of microbial world.

PubMed

Uchiyama, Ikuo; Mihara, Motohiro; Nishide, Hiroyo; Chiba, Hirokazu

2013-01-01

The microbial genome database for comparative analysis (MBGD, available at http://mbgd.genome.ad.jp/) is a platform for microbial genome comparison based on orthology analysis. As its unique feature, MBGD allows users to conduct orthology analysis among any specified set of organisms; this flexibility allows MBGD to adapt to a variety of microbial genomic study. Reflecting the huge diversity of microbial world, the number of microbial genome projects now becomes several thousands. To efficiently explore the diversity of the entire microbial genomic data, MBGD now provides summary pages for pre-calculated ortholog tables among various taxonomic groups. For some closely related taxa, MBGD also provides the conserved synteny information (core genome alignment) pre-calculated using the CoreAligner program. In addition, efficient incremental updating procedure can create extended ortholog table by adding additional genomes to the default ortholog table generated from the representative set of genomes. Combining with the functionalities of the dynamic orthology calculation of any specified set of organisms, MBGD is an efficient and flexible tool for exploring the microbial genome diversity.

[Effects of plateau zokor disturbance and restoration years on soil nutrients and microbial functional diversity in alpine meadow].

PubMed

Hu, Lei; Ade, Lu-ji; Zi, Hong-biao; Wang, Chang-ting

2015-09-01

To explore the dynamic process of restoration succession in degraded alpine meadow that had been disturbed by plateau zokors in the eastern Tibetan Plateau, we examined soil nutrients and microbial functional diversity using conventional laboratory analysis and the Biolog-ECO microplate method. Our study showed that: 1) The zokors disturbance significantly reduced soil organic matter, total nitrogen, available nitrogen and phosphorus contents, but had no significant effects on soil total phosphorus and potassium contents; 2) Soil microbial carbon utilization efficiency, values of Shannon, Pielou and McIntosh indexes increased with alpine meadow restoration years; 3) Principal component analysis (PCA) showed that carbohydrates and amino acids were the main carbon sources for maintaining soil microbial community; 4) Redundancy analysis ( RDA) indicated that soil pH, soil organic matter, total nitrogen, available nitrogen, and total potassium were the main factors influencing the metabolic rate of soil microbial community and microbial functional diversity. In summary, variations in soil microbial functional diversity at different recovery stages reflected the microbial response to aboveground vegetation, soil microbial composition and soil nutrients.

The Biogeographic Pattern of Microbial Functional Genes along an Altitudinal Gradient of the Tibetan Pasture

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

Qi, Qi; Zhao, Mengxin; Wang, Shiping

As the highest place of the world, the Tibetan plateau is a fragile ecosystem. Given the importance of microbial communities in driving soil nutrient cycling, it is of interest to document the microbial biogeographic pattern here. We adopted a microarray-based tool named GeoChip 4.0 to investigate grassland microbial functional genes along an elevation gradient from 3200 to 3800 m above sea level open to free grazing by local herdsmen and wild animals. Interestingly, microbial functional diversities increase with elevation, so does the relative abundances of genes associated with carbon degradation, nitrogen cycling, methane production, cold shock and oxygen limitation. Themore » range of Shannon diversities (10.27–10.58) showed considerably smaller variation than what was previously observed at ungrazed sites nearby (9.95–10.65), suggesting the important role of livestock grazing on microbial diversities. Closer examination showed that the dissimilarity of microbial community at our study sites increased with elevations, revealing an elevation-decay relationship of microbial functional genes. Both microbial functional diversity and the number of unique genes increased with elevations. Furthermore, we detected a tight linkage of greenhouse gas (CO2) and relative abundances of carbon cycling genes. Our biogeographic study provides insights on microbial functional diversity and soil biogeochemical cycling in Tibetan pastures.« less

Environmental Filtering Process Has More Important Roles than Dispersal Limitation in Shaping Large-Scale Prokaryotic Beta Diversity Patterns of Grassland Soils.

PubMed

Cao, Peng; Wang, Jun-Tao; Hu, Hang-Wei; Zheng, Yuan-Ming; Ge, Yuan; Shen, Ju-Pei; He, Ji-Zheng

2016-07-01

Despite the utmost importance of microorganisms in maintaining ecosystem functioning and their ubiquitous distribution, our knowledge of the large-scale pattern of microbial diversity is limited, particularly in grassland soils. In this study, the microbial communities of 99 soil samples spanning over 3000 km across grassland ecosystems in northern China were investigated using high-throughput sequencing to analyze the beta diversity pattern and the underlying ecological processes. The microbial communities were dominated by Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, and Planctomycetes across all the soil samples. Spearman's correlation analysis indicated that climatic factors and soil pH were significantly correlated with the dominant microbial taxa, while soil microbial richness was positively linked to annual precipitation. The environmental divergence-dissimilarity relationship was significantly positive, suggesting the importance of environmental filtering processes in shaping soil microbial communities. Structural equation modeling found that the deterministic process played a more important role than the stochastic process on the pattern of soil microbial beta diversity, which supported the predictions of niche theory. Partial mantel test analysis have showed that the contribution of independent environmental variables has a significant effect on beta diversity, while independent spatial distance has no such relationship, confirming that the deterministic process was dominant in structuring soil microbial communities. Overall, environmental filtering process has more important roles than dispersal limitation in shaping microbial beta diversity patterns in the grassland soils.

Effects of Plant Diversity, Functional Group Composition, and Fertilization on Soil Microbial Properties in Experimental Grassland

PubMed Central

Strecker, Tanja; Barnard, Romain L.; Niklaus, Pascal A.; Scherer-Lorenzen, Michael; Weigelt, Alexandra; Scheu, Stefan; Eisenhauer, Nico

2015-01-01

Background Loss of biodiversity and increased nutrient inputs are two of the most crucial anthropogenic factors driving ecosystem change. Although both received considerable attention in previous studies, information on their interactive effects on ecosystem functioning is scarce. In particular, little is known on how soil biota and their functions are affected by combined changes in plant diversity and fertilization. Methodology/Principal Findings We investigated the effects of plant diversity, functional community composition, and fertilization on the biomass and respiration of soil microbial communities in a long-term biodiversity experiment in semi-natural grassland (Jena Experiment). Plant species richness enhanced microbial basal respiration and microbial biomass, but did not significantly affect microbial specific respiration. In contrast, the presence of legumes and fertilization significantly decreased microbial specific respiration, without altering microbial biomass. The effect of legumes was superimposed by fertilization as indicated by a significant interaction between the presence of legumes and fertilization. Further, changes in microbial stoichiometry (C-to-N ratio) and specific respiration suggest the presence of legumes to reduce N limitation of soil microorganisms and to modify microbial C use efficiency. Conclusions/Significance Our study highlights the role of plant species and functional group diversity as well as interactions between plant community composition and fertilizer application for soil microbial functions. Our results suggest soil microbial stoichiometry to be a powerful indicator of microbial functioning under N limited conditions. Although our results support the notion that plant diversity and fertilizer application independently affect microbial functioning, legume effects on microbial N limitation were superimposed by fertilization, indicating significant interactions between the functional composition of plant communities and nutrient inputs for soil processes. PMID:25938580

Responses of soil ammonia-oxidizing microorganisms to repeated exposure of single-walled and multi-walled carbon nanotubes.

PubMed

Chen, Qinglin; Wang, Hui; Yang, Baoshan; He, Fei; Han, Xuemei; Song, Ziheng

2015-02-01

The impacts of carbon nanotubes (CNTs) including single-walled carbon nanotubes (SWNTs) and multi-walled carbon nanotubes (MWNTs) on soil microbial biomass and microbial community composition (especially on ammonium oxidizing microorganisms) have been evaluated. The first exposure of CNTs lowered the microbial biomass immediately, but the values recovered to the level of the control at the end of the experiment despite the repeated addition of CNTs. The abundance and diversity of ammonium-oxidizing archaea (AOA) were higher than that of ammonium-oxidizing bacteria (AOB) under the exposure of CNTs. The addition of CNTs decreased Shannon-Wiener diversity index of AOB and AOA. Two-way ANOVA analysis showed that CNTs had significant effects on the abundance and diversity of AOB and AOA. Dominant terminal restriction fragments (TRFs) of AOB exhibited a positive relationship with NH4(+), while AOA was on the contrary. It implied that AOB prefer for high-NH4(+) soils whereas AOA is favored in low NH4(+) soils in the CNT-contaminated soil. Copyright © 2014 Elsevier B.V. All rights reserved.

GeoChip-Based Analysis of the Functional Gene Diversity and Metabolic Potential of Microbial Communities in Acid Mine Drainage▿ †

PubMed Central

Xie, Jianping; He, Zhili; Liu, Xinxing; Liu, Xueduan; Van Nostrand, Joy D.; Deng, Ye; Wu, Liyou; Zhou, Jizhong; Qiu, Guanzhou

2011-01-01

Acid mine drainage (AMD) is an extreme environment, usually with low pH and high concentrations of metals. Although the phylogenetic diversity of AMD microbial communities has been examined extensively, little is known about their functional gene diversity and metabolic potential. In this study, a comprehensive functional gene array (GeoChip 2.0) was used to analyze the functional diversity, composition, structure, and metabolic potential of AMD microbial communities from three copper mines in China. GeoChip data indicated that these microbial communities were functionally diverse as measured by the number of genes detected, gene overlapping, unique genes, and various diversity indices. Almost all key functional gene categories targeted by GeoChip 2.0 were detected in the AMD microbial communities, including carbon fixation, carbon degradation, methane generation, nitrogen fixation, nitrification, denitrification, ammonification, nitrogen reduction, sulfur metabolism, metal resistance, and organic contaminant degradation, which suggested that the functional gene diversity was higher than was previously thought. Mantel test results indicated that AMD microbial communities are shaped largely by surrounding environmental factors (e.g., S, Mg, and Cu). Functional genes (e.g., narG and norB) and several key functional processes (e.g., methane generation, ammonification, denitrification, sulfite reduction, and organic contaminant degradation) were significantly (P < 0.10) correlated with environmental variables. This study presents an overview of functional gene diversity and the structure of AMD microbial communities and also provides insights into our understanding of metabolic potential in AMD ecosystems. PMID:21097602

Impact of Organic and Conventional Systems of Coffee Farming on Soil Properties and Culturable Microbial Diversity

PubMed Central

2016-01-01

A study was undertaken with an objective of evaluating the long-term impacts of organic (ORG) and conventional (CON) methods of coffee farming on soil physical, chemical, biological, and microbial diversity. Electrical conductivity and bulk density were found to increase by 34% and 21%, respectively, in CON compared to ORG system, while water holding capacity was found decreased in both the systems. Significant increase in organic carbon was observed in ORG system. Major nutrients, nitrogen and potassium, levels showed inclination in both ORG and CON system, but the trend was much more pronounced in CON system. Phosphorus was found to increase in both ORG and CON system, but its availability was found to be more with CON system. In biological attributes, higher soil respiration and fluorescein diacetate activity were recorded in ORG system compared to CON system. Higher soil urease activity was observed in CON system, while dehydrogenase activity does not show significant differences between ORG and CON systems. ORG system was found to have higher macrofauna (31.4%), microbial population (34%), and microbial diversity indices compared to CON system. From the present study, it is accomplished that coffee soil under long-term ORG system has better soil properties compared to CON system. PMID:27042378

Impact of Organic and Conventional Systems of Coffee Farming on Soil Properties and Culturable Microbial Diversity.

PubMed

Velmourougane, Kulandaivelu

2016-01-01

A study was undertaken with an objective of evaluating the long-term impacts of organic (ORG) and conventional (CON) methods of coffee farming on soil physical, chemical, biological, and microbial diversity. Electrical conductivity and bulk density were found to increase by 34% and 21%, respectively, in CON compared to ORG system, while water holding capacity was found decreased in both the systems. Significant increase in organic carbon was observed in ORG system. Major nutrients, nitrogen and potassium, levels showed inclination in both ORG and CON system, but the trend was much more pronounced in CON system. Phosphorus was found to increase in both ORG and CON system, but its availability was found to be more with CON system. In biological attributes, higher soil respiration and fluorescein diacetate activity were recorded in ORG system compared to CON system. Higher soil urease activity was observed in CON system, while dehydrogenase activity does not show significant differences between ORG and CON systems. ORG system was found to have higher macrofauna (31.4%), microbial population (34%), and microbial diversity indices compared to CON system. From the present study, it is accomplished that coffee soil under long-term ORG system has better soil properties compared to CON system.

It's all relative: ranking the diversity of aquatic bacterial communities.

PubMed

Shaw, Allison K; Halpern, Aaron L; Beeson, Karen; Tran, Bao; Venter, J Craig; Martiny, Jennifer B H

2008-09-01

The study of microbial diversity patterns is hampered by the enormous diversity of microbial communities and the lack of resources to sample them exhaustively. For many questions about richness and evenness, however, one only needs to know the relative order of diversity among samples rather than total diversity. We used 16S libraries from the Global Ocean Survey to investigate the ability of 10 diversity statistics (including rarefaction, non-parametric, parametric, curve extrapolation and diversity indices) to assess the relative diversity of six aquatic bacterial communities. Overall, we found that the statistics yielded remarkably similar rankings of the samples for a given sequence similarity cut-off. This correspondence, despite the different underlying assumptions of the statistics, suggests that diversity statistics are a useful tool for ranking samples of microbial diversity. In addition, sequence similarity cut-off influenced the diversity ranking of the samples, demonstrating that diversity statistics can also be used to detect differences in phylogenetic structure among microbial communities. Finally, a subsampling analysis suggests that further sequencing from these particular clone libraries would not have substantially changed the richness rankings of the samples.

Importance of Soil Temperature for the Growth of Temperate Crops under a Tropical Climate and Functional Role of Soil Microbial Diversity.

PubMed

Sabri, Nurul Syazwani Ahmad; Zakaria, Zuriati; Mohamad, Shaza Eva; Jaafar, A Bakar; Hara, Hirofumi

2018-04-28

A soil cooling system that prepares soil for temperate soil temperatures for the growth of temperate crops under a tropical climate is described herein. Temperate agriculture has been threatened by the negative impact of temperature increases caused by climate change. Soil temperature closely correlates with the growth of temperate crops, and affects plant processes and soil microbial diversity. The present study focuses on the effects of soil temperatures on lettuce growth and soil microbial diversity that maintains the growth of lettuce at low soil temperatures. A model temperate crop, loose leaf lettuce, was grown on eutrophic soil under soil cooling and a number of parameters, such as fresh weight, height, the number of leaves, and root length, were evaluated upon harvest. Under soil cooling, significant differences were observed in the average fresh weight (P<0.05) and positive development of the roots, shoots, and leaves of lettuce. Janthinobacterium (8.142%), Rhodoplanes (1.991%), Arthrospira (1.138%), Flavobacterium (0.857%), Sphingomonas (0.790%), Mycoplana (0.726%), and Pseudomonas (0.688%) were the dominant bacterial genera present in cooled soil. Key soil fungal communities, including Pseudaleuria (18.307%), Phoma (9.968%), Eocronartium (3.527%), Trichosporon (1.791%), and Pyrenochaeta (0.171%), were also recovered from cooled soil. The present results demonstrate that the growth of temperate crops is dependent on soil temperature, which subsequently affects the abundance and diversity of soil microbial communities that maintain the growth of temperate crops at low soil temperatures.

Studying Microbial Mat Functioning Amidst "Unexpected Diversity": Methodological Approaches and Initial Results from Metatranscriptomes of Mats Over Diel cycles, iTags from Long Term Manipulations, and Biogeochemical Cycling in Simplified Microbial Mats Constructed from Cultures

NASA Astrophysics Data System (ADS)

Bebout, B.; Bebout, L. E.; Detweiler, A. M.; Everroad, R. C.; Lee, J.; Pett-Ridge, J.; Weber, P. K.

2014-12-01

Microbial mats are famously amongst the most diverse microbial ecosystems on Earth, inhabiting some of the most inclement environments known, including hypersaline, dry, hot, cold, nutrient poor, and high UV environments. The high microbial diversity of microbial mats makes studies of microbial ecology notably difficult. To address this challenge, we have been using a combination of metagenomics, metatranscriptomics, iTags and culture-based simplified microbial mats to study biogeochemical cycling (H2 production, N2 fixation, and fermentation) in microbial mats collected from Elkhorn Slough, Monterey Bay, California. Metatranscriptomes of microbial mats incubated over a diel cycle have revealed that a number of gene systems activate only during the day in Cyanobacteria, while the remaining appear to be constitutive. The dominant cyanobacterium in the mat (Microcoleus chthonoplastes) expresses several pathways for nitrogen scavenging undocumented in cultured strains, as well as the expression of two starch storage and utilization cycles. Community composition shifts in response to long term manipulations of mats were assessed using iTags. Changes in community diversity were observed as hydrogen fluxes increased in response to a lowering of sulfate concentrations. To produce simplified microbial mats, we have isolated members of 13 of the 15 top taxa from our iTag libraries into culture. Simplified microbial mats and simple co-cultures and consortia constructed from these isolates reproduce many of the natural patterns of biogeochemical cycling in the parent natural microbial mats, but against a background of far lower overall diversity, simplifying studies of changes in gene expression (over the short term), interactions between community members, and community composition changes (over the longer term), in response to environmental forcing.

Metagenomic and functional analyses of the consequences of reduction of bacterial diversity on soil functions and bioremediation in diesel-contaminated microcosms.

PubMed

Jung, Jaejoon; Philippot, Laurent; Park, Woojun

2016-03-14

The relationship between microbial biodiversity and soil function is an important issue in ecology, yet most studies have been performed in pristine ecosystems. Here, we assess the role of microbial diversity in ecological function and remediation strategies in diesel-contaminated soils. Soil microbial diversity was manipulated using a removal by dilution approach and microbial functions were determined using both metagenomic analyses and enzymatic assays. A shift from Proteobacteria- to Actinobacteria-dominant communities was observed when species diversity was reduced. Metagenomic analysis showed that a large proportion of functional gene categories were significantly altered by the reduction in biodiversity. The abundance of genes related to the nitrogen cycle was significantly reduced in the low-diversity community, impairing denitrification. In contrast, the efficiency of diesel biodegradation was increased in the low-diversity community and was further enhanced by addition of red clay as a stimulating agent. Our results suggest that the relationship between microbial diversity and ecological function involves trade-offs among ecological processes, and should not be generalized as a positive, neutral, or negative relationship.

Metagenomic and functional analyses of the consequences of reduction of bacterial diversity on soil functions and bioremediation in diesel-contaminated microcosms

PubMed Central

Jung, Jaejoon; Philippot, Laurent; Park, Woojun

2016-01-01

The relationship between microbial biodiversity and soil function is an important issue in ecology, yet most studies have been performed in pristine ecosystems. Here, we assess the role of microbial diversity in ecological function and remediation strategies in diesel-contaminated soils. Soil microbial diversity was manipulated using a removal by dilution approach and microbial functions were determined using both metagenomic analyses and enzymatic assays. A shift from Proteobacteria- to Actinobacteria-dominant communities was observed when species diversity was reduced. Metagenomic analysis showed that a large proportion of functional gene categories were significantly altered by the reduction in biodiversity. The abundance of genes related to the nitrogen cycle was significantly reduced in the low-diversity community, impairing denitrification. In contrast, the efficiency of diesel biodegradation was increased in the low-diversity community and was further enhanced by addition of red clay as a stimulating agent. Our results suggest that the relationship between microbial diversity and ecological function involves trade-offs among ecological processes, and should not be generalized as a positive, neutral, or negative relationship. PMID:26972977

Possible roles of uncultured archaea in carbon cycling in methane-seep sediments

NASA Astrophysics Data System (ADS)

Yoshinaga, Marcos Y.; Lazar, Cassandre S.; Elvert, Marcus; Lin, Yu-Shih; Zhu, Chun; Heuer, Verena B.; Teske, Andreas; Hinrichs, Kai-Uwe

2015-09-01

Studies on microbial carbon cycling uniformly confirm that anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria represent the dominant and most active fraction of the sedimentary microbial community in methane-seep sediments. However, little is known about other frequently observed and abundant microbial taxa, their role in carbon cycling and association with the anaerobic oxidation of methane (AOM). Here, we provide a comprehensive characterization of stable carbon isotopes (δ13C) from several intact polar lipid (IPL) classes and metabolite pools in a downcore profile at a cold seep within the oxygen minimum zone off Pakistan. We aimed to evaluate microbial carbon metabolism using IPLs in relation to redox conditions, metabolites and 16S rRNA gene libraries. The 13C-depleted signature of carbon pools and microbial metabolites in pore waters (e.g., dissolved inorganic carbon, lactate and acetate) demonstrated high accumulation of AOM-associated biomass and subsequent turnover thereof. ANMEs accounted for a small fraction of the archaeal 16S rRNA gene survey, whereas sequences of other uncultured benthic archaea dominated the clone libraries, particularly the Marine Benthic Group D. On the basis of lipid diversity and carbon isotope information, we suggest that structurally diverse phospho- and glycolipids, including the recently identified unsaturated tetraethers that are particularly abundant in this setting, are likely derived from archaea other than ANMEs. Through the evaluation of δ13C values of individual IPL, our results indicate heterotrophy as a possible metabolic pathway of archaea in these AOM-dominated sediments.

Mississippi River Plume Enriches Microbial Diversity in the Northern Gulf of Mexico

PubMed Central

Mason, Olivia U.; Canter, Erin J.; Gillies, Lauren E.; Paisie, Taylor K.; Roberts, Brian J.

2016-01-01

The Mississippi River (MR) serves as the primary source of freshwater and nutrients to the northern Gulf of Mexico (nGOM). Whether this input of freshwater also enriches microbial diversity as the MR plume migrates and mixes with the nGOM serves as the central question addressed herein. Specifically, in this study physicochemical properties and planktonic microbial community composition and diversity was determined using iTag sequencing of 16S rRNA genes in 23 samples collected along a salinity (and nutrient) gradient from the mouth of the MR, in the MR plume, in the canyon, at the Deepwater Horizon wellhead and out to the loop current. Analysis of these datasets revealed that the MR influenced microbial diversity as far offshore as the Deepwater Horizon wellhead. The MR had the highest microbial diversity, which decreased with increasing salinity. MR bacterioplankton communities were distinct compared to the nGOM, particularly in the surface where Actinobacteria and Proteobacteria dominated, while the deeper MR was also enriched in Thaumarchaeota. Statistical analyses revealed that nutrients input by the MR, along with salinity and depth, were the primary drivers in structuring the microbial communities. These results suggested that the reduced salinity, nutrient enriched MR plume could act as a seed bank for microbial diversity as it mixes with the nGOM. Whether introduced microorganisms are active at higher salinities than freshwater would determine if this seed bank for microbial diversity is ecologically significant. Alternatively, microorganisms that are physiologically restricted to freshwater habitats that are entrained in the plume could be used as tracers for freshwater input to the marine environment. PMID:27458442

Microbial eukaryotic diversity and distribution in a river plume and cyclonic eddy-influenced ecosystem in the South China Sea.

PubMed

Wu, Wenxue; Wang, Lei; Liao, Yu; Huang, Bangqin

2015-10-01

To evaluate microbial eukaryotic diversity and distribution in mesoscale processes, we investigated 18S rDNA diversity in a river plume and cyclonic eddy-influenced ecosystem in the southwestern South China Sea (SCS). Restriction fragment length polymorphism analysis was carried out using multiple primer sets. Relative to a wide range of previous similar studies, we observed a significantly higher proportion of sequences of pigmented taxa. Among the photosynthetic groups, Haptophyta accounted for 27.7% of the sequenced clones, which belonged primarily to Prymnesiophyceae. Unexpectedly, five operational taxonomic units of Cryptophyta were closely related to freshwater species. The Chlorophyta mostly fell within the Prasinophyceae, which was comprised of six clades, including Clade III, which is detected in the SCS for the first time in this study. Among the photosynthetic stramenopiles, Chrysophyceae was the most diverse taxon, which included seven clades. The majority of 18S rDNA sequences affiliated with the Dictyochophyceae, Eustigmatophyceae, and Pelagophyceae were closely related to those of pure cultures. The results of redundancy analysis and the permutation Mantel test based on unweighted UniFrac distances, conducted for spatial analyses of the Haptophyta subclades suggested that the Mekong River plume and cyclonic eddy play important roles in regulating microbial eukaryotic diversity and distribution in the southwestern SCS. © 2015 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Dramatic Increases of Soil Microbial Functional Gene Diversity at the Treeline Ecotone of Changbai Mountain

PubMed Central

Shen, Congcong; Shi, Yu; Ni, Yingying; Deng, Ye; Van Nostrand, Joy D.; He, Zhili; Zhou, Jizhong; Chu, Haiyan

2016-01-01

The elevational and latitudinal diversity patterns of microbial taxa have attracted great attention in the past decade. Recently, the distribution of functional attributes has been in the spotlight. Here, we report a study profiling soil microbial communities along an elevation gradient (500–2200 m) on Changbai Mountain. Using a comprehensive functional gene microarray (GeoChip 5.0), we found that microbial functional gene richness exhibited a dramatic increase at the treeline ecotone, but the bacterial taxonomic and phylogenetic diversity based on 16S rRNA gene sequencing did not exhibit such a similar trend. However, the β-diversity (compositional dissimilarity among sites) pattern for both bacterial taxa and functional genes was similar, showing significant elevational distance-decay patterns which presented increased dissimilarity with elevation. The bacterial taxonomic diversity/structure was strongly influenced by soil pH, while the functional gene diversity/structure was significantly correlated with soil dissolved organic carbon (DOC). This finding highlights that soil DOC may be a good predictor in determining the elevational distribution of microbial functional genes. The finding of significant shifts in functional gene diversity at the treeline ecotone could also provide valuable information for predicting the responses of microbial functions to climate change. PMID:27524983

Microbial diversity of an anoxic zone of a hydroelectric power station reservoir in Brazilian Amazonia.

PubMed

Graças, Diego A; Miranda, Paulo R; Baraúna, Rafael A; McCulloch, John A; Ghilardi, Rubens; Schneider, Maria Paula C; Silva, Artur

2011-11-01

Microbial diversity was evaluated in an anoxic zone of Tucuruí Hydroelectric Power Station reservoir in Brazilian Amazonia using a culture-independent approach by amplifying and sequencing fragments of the 16S rRNA gene using metagenomic DNA as a template. Samples obtained from the photic, aphotic (40 m) and sediment (60 m) layers were used to construct six 16S rDNA libraries containing a total of 1,152 clones. The sediment, aphotic and photic layers presented 64, 33 and 35 unique archaeal operational taxonomic units (OTUs). The estimated richness of these layers was evaluated to be 153, 106 and 79 archaeal OTUs, respectively, using the abundance-based coverage estimator (ACE) and 114, 83 and 77 OTUs using the Chao1 estimator. For bacterial sequences, 114, 69 and 57 OTUs were found in the sediment, aphotic and photic layers, which presented estimated richnesses of 1,414, 522 and 197 OTUs (ACE) and 1,059, 1,014 and 148 OTUs (Chao1), respectively. Phylogenetic analyses of the sequences obtained revealed a high richness of microorganisms which participate in the carbon cycle, namely, methanogenic archaea and methanotrophic proteobacteria. Most sequences obtained belong to non-culturable prokaryotes. The present study offers the first glimpse of the huge microbial diversity of an anoxic area of a man-made lacustrine environment in the tropics.

Climate change and human activities altered the diversity and composition of soil microbial community in alpine grasslands of the Qinghai-Tibetan Plateau.

PubMed

Zhang, Yong; Dong, Shikui; Gao, Qingzhu; Liu, Shiliang; Zhou, Huakun; Ganjurjav, Hasbagan; Wang, Xuexia

2016-08-15

Alpine ecosystems are known to be sensitive to climate change and human disturbances. However, the knowledge about the changes of their underground microbial communities is inadequate. We explored the diversity and structure of soil bacterial and fungal communities using Ilumina MiSeq sequencing in native alpine grasslands (i.e. the alpine meadow, alpine steppe) and cultivated grassland of the Qinghai-Tibetan Plateau (QTP) under three-year treatments of overgrazing, warming and enhanced rainfall. Enhanced rainfall rather than warming significantly reduced soil microbial diversity in native alpine grasslands. Variable warming significantly reduced it in the cultivated grassland. Over 20% and 40% variations of microbial diversity could be explained by soil nutrients and moisture in the alpine meadow and cultivated grassland, separately. Soil microbial communities could be clustered into different groups according to different treatments in the alpine meadow and cultivated grassland. For the alpine steppe, with the lowest soil nutrients and moistures, <10% variations of microbial diversity was explained by soil properties; and the soil microbial communities among different treatments were similar. The soil microbial community in the cultivated grassland was varied from it in native grasslands. Over 50% variations of soil microbial communities among different treatments were explained by soil nutrients and moisture in each grassland type. Our results suggest that climate change and human activities strongly affected soil microbial communities by changing soil nutrients and moistures in alpine grassland ecosystems. Copyright © 2016 Elsevier B.V. All rights reserved.

Microbial communities in low permeability, high pH uranium mine tailings: characterization and potential effects.

PubMed

Bondici, V F; Lawrence, J R; Khan, N H; Hill, J E; Yergeau, E; Wolfaardt, G M; Warner, J; Korber, D R

2013-06-01

To describe the diversity and metabolic potential of microbial communities in uranium mine tailings characterized by high pH, high metal concentration and low permeability. To assess microbial diversity and their potential to influence the geochemistry of uranium mine tailings using aerobic and anaerobic culture-based methods, in conjunction with next generation sequencing and clone library sequencing targeting two universal bacterial markers (the 16S rRNA and cpn60 genes). Growth assays revealed that 69% of the 59 distinct culturable isolates evaluated were multiple-metal resistant, with 15% exhibiting dual-metal hypertolerance. There was a moderately positive correlation coefficient (R = 0·43, P < 0·05) between multiple-metal resistance of the isolates and their enzyme expression profile. Of the isolates tested, 17 reduced amorphous iron, 22 reduced molybdate and seven oxidized arsenite. Based on next generation sequencing, tailings depth was shown to influence bacterial community composition, with the difference in the microbial diversity of the upper (0-20 m) and middle (20-40 m) tailings zones being highly significant (P < 0·01) from the lower zone (40-60 m) and the difference in diversity of the upper and middle tailings zone being significant (P < 0·05). Phylotypes closely related to well-known sulfate-reducing and iron-reducing bacteria were identified with low abundance, yet relatively high diversity. The presence of a population of metabolically-diverse, metal-resistant micro-organisms within the tailings environment, along with their demonstrated capacity for transforming metal elements, suggests that these organisms have the potential to influence the long-term geochemistry of the tailings. This study is the first investigation of the diversity and functional potential of micro-organisms present in low permeability, high pH uranium mine tailings. © 2013 The Society for Applied Microbiology.

Succession of Bacterial Community Structure and Diversity in Soil along a Chronosequence of Reclamation and Re-Vegetation on Coal Mine Spoils in China

PubMed Central

Li, Yuanyuan; Wen, Hongyu; Chen, Longqian; Yin, Tingting

2014-01-01

The growing concern about the effectiveness of reclamation strategies has motivated the evaluation of soil properties following reclamation. Recovery of belowground microbial community is important for reclamation success, however, the response of soil bacterial communities to reclamation has not been well understood. In this study, PCR-based 454 pyrosequencing was applied to compare bacterial communities in undisturbed soils with those in reclaimed soils using chronosequences ranging in time following reclamation from 1 to 20 year. Bacteria from the Proteobacteria, Chloroflexi, Actinobacteria, Acidobacteria, Planctomycetes and Bacteroidetes were abundant in all soils, while the composition of predominant phyla differed greatly across all sites. Long-term reclamation strongly affected microbial community structure and diversity. Initial effects of reclamation resulted in significant declines in bacterial diversity indices in younger reclaimed sites (1, 8-year-old) compared to the undisturbed site. However, bacterial diversity indices tended to be higher in older reclaimed sites (15, 20-year-old) as recovery time increased, and were more similar to predisturbance levels nearly 20 years after reclamation. Bacterial communities are highly responsive to soil physicochemical properties (pH, soil organic matter, Total N and P), in terms of both their diversity and community composition. Our results suggest that the response of soil microorganisms to reclamation is likely governed by soil characteristics and, indirectly, by the effects of vegetation restoration. Mixture sowing of gramineae and leguminosae herbage largely promoted soil geochemical conditions and bacterial diversity that recovered to those of undisturbed soil, representing an adequate solution for soil remediation and sustainable utilization for agriculture. These results confirm the positive impacts of reclamation and vegetation restoration on soil microbial diversity and suggest that the most important phase of microbial community recovery occurs between 15 and 20 years after reclamation. PMID:25502754

The Effect of a Reduction in Microbial Diversity on Greenhouse Gas Production in Alaskan Tundra Soils.

NASA Astrophysics Data System (ADS)

Wagner, R.; Oechel, W. C.; Lipson, D.

2017-12-01

Atmospheric methane accounts for 20% of the warming potential of all greenhouse gases, has increased by 150% since pre-industrial times, and has the potential to double again over the next century. Microbially mediated CH4 emissions from natural wetlands represent the highest uncertainty in relative contributions to atmospheric CH4 levels of all CH4 sources, with Arctic wetlands currently experiencing twice the rate of warming as the rest of the planet. Notwithstanding the central role that the soil microbial community plays, and the high uncertainty in CH4 emissions from this ecosystem, surprisingly little research has been done to directly connect the microbial community structure to methane production rates. This is especially disconcerting given that most current CH4 emission models completely neglect microbial characteristics, despite the fact that the soil microbial community is predicted to be heavily impacted by a changing climate. Here, the effect of an artificial reduction in soil microbial α-diversity was investigated with regard to methane production and respiration rates. The microbial community was serially diluted followed by re-inoculation of sterilized Arctic soils in a mesocosm experiment. Methane production and respiration rates were measured, metagenomic sequencing was performed to determine microbial community diversity measures, and the effect of the oxidation state of iron was investigated. Preliminary results indicate that microbial communities with reduced α-diversity have lowered respiration rates in these soils. Analyses are ongoing and are expected to provide critical observations linking the role of soil microbial community diversity and greenhouse gas production in Arctic tundra ecosystems.

Diversity and Function of Microbial Community in Chinese Strong-Flavor Baijiu Ecosystem: A Review

PubMed Central

Zou, Wei; Zhao, Changqing; Luo, Huibo

2018-01-01

Strong flavor baijiu (SFB), also called Luzhou-flavor liquor, is the most popular Chinese baijiu. It is manufactured via solid fermentation, with daqu as the starter. Microbial diversity of the SFB ecosystem and the synergistic effects of the enzymes and compounds produced by them are responsible for the special flavor and mouthfeel of SFB. The present review covers research studies focused on microbial community analysis of the SFB ecosystem, including the culturable microorganisms, their metabolic functions, microbial community diversity and their interactions. The review specifically emphasizes on the most recently conducted culture-independent analysis of SFB microbial community diversity. Furthermore, the possible application of systems biology approaches for elucidating the molecular mechanisms of SFB production were also reviewed and prospected. PMID:29686656

A critical evaluation of ecological indices for the comparative analysis of microbial communities based on molecular datasets.

PubMed

Lucas, Rico; Groeneveld, Jürgen; Harms, Hauke; Johst, Karin; Frank, Karin; Kleinsteuber, Sabine

2017-01-01

In times of global change and intensified resource exploitation, advanced knowledge of ecophysiological processes in natural and engineered systems driven by complex microbial communities is crucial for both safeguarding environmental processes and optimising rational control of biotechnological processes. To gain such knowledge, high-throughput molecular techniques are routinely employed to investigate microbial community composition and dynamics within a wide range of natural or engineered environments. However, for molecular dataset analyses no consensus about a generally applicable alpha diversity concept and no appropriate benchmarking of corresponding statistical indices exist yet. To overcome this, we listed criteria for the appropriateness of an index for such analyses and systematically scrutinised commonly employed ecological indices describing diversity, evenness and richness based on artificial and real molecular datasets. We identified appropriate indices warranting interstudy comparability and intuitive interpretability. The unified diversity concept based on 'effective numbers of types' provides the mathematical framework for describing community composition. Additionally, the Bray-Curtis dissimilarity as a beta-diversity index was found to reflect compositional changes. The employed statistical procedure is presented comprising commented R-scripts and example datasets for user-friendly trial application. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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

PubMed

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

2014-03-01

The relationship between the diversity of mixed-species microbial consortia and their electrogenic potential in the anodes of microbial fuel cells was examined using different diversity measures as predictors. Identical microbial fuel cells were sampled at multiple time-points. Biofilm and suspension communities were analysed by denaturing gradient gel electrophoresis to calculate the number and relative abundance of species. Shannon and Simpson indices and richness were examined for association with power using bivariate and multiple linear regression, with biofilm DNA as an additional variable. In simple bivariate regressions, the correlation of Shannon diversity of the biofilm and power is stronger (r=0.65, p=0.001) than between power and richness (r=0.39, p=0.076), or between power and the Simpson index (r=0.5, p=0.018). Using Shannon diversity and biofilm DNA as predictors of power, a regression model can be constructed (r=0.73, p<0.001). Ecological parameters such as the Shannon index are predictive of the electrogenic potential of microbial communities. Copyright © 2014 Elsevier Ltd. All rights reserved.

Analyses of the Microbial Diversity across the Human Microbiome

PubMed Central

Li, Kelvin; Bihan, Monika; Yooseph, Shibu; Methé, Barbara A.

2012-01-01

Analysis of human body microbial diversity is fundamental to understanding community structure, biology and ecology. The National Institutes of Health Human Microbiome Project (HMP) has provided an unprecedented opportunity to examine microbial diversity within and across body habitats and individuals through pyrosequencing-based profiling of 16 S rRNA gene sequences (16 S) from habits of the oral, skin, distal gut, and vaginal body regions from over 200 healthy individuals enabling the application of statistical techniques. In this study, two approaches were applied to elucidate the nature and extent of human microbiome diversity. First, bootstrap and parametric curve fitting techniques were evaluated to estimate the maximum number of unique taxa, Smax, and taxa discovery rate for habitats across individuals. Next, our results demonstrated that the variation of diversity within low abundant taxa across habitats and individuals was not sufficiently quantified with standard ecological diversity indices. This impact from low abundant taxa motivated us to introduce a novel rank-based diversity measure, the Tail statistic, (“τ”), based on the standard deviation of the rank abundance curve if made symmetric by reflection around the most abundant taxon. Due to τ’s greater sensitivity to low abundant taxa, its application to diversity estimation of taxonomic units using taxonomic dependent and independent methods revealed a greater range of values recovered between individuals versus body habitats, and different patterns of diversity within habitats. The greatest range of τ values within and across individuals was found in stool, which also exhibited the most undiscovered taxa. Oral and skin habitats revealed variable diversity patterns, while vaginal habitats were consistently the least diverse. Collectively, these results demonstrate the importance, and motivate the introduction, of several visualization and analysis methods tuned specifically for next-generation sequence data, further revealing that low abundant taxa serve as an important reservoir of genetic diversity in the human microbiome. PMID:22719823

In vitro evaluation, in vivo quantification, and microbial diversity studies of nutritional strategies for reducing enteric methane production.

PubMed

Abdalla, Adibe Luiz; Louvandini, Helder; Sallam, Sobhy Mohamed Abdallah Hassan; Bueno, Ives Cláudio da Silva; Tsai, Siu Mui; Figueira, Antonio Vargas de Oliveira

2012-06-01

The main objective of the present work was to study nutritive strategies for lessening the CH(4) formation associated to ruminant tropical diets. In vitro gas production technique was used for evaluating the effect of tannin-rich plants, essential oils, and biodiesel co-products on CH(4) formation in three individual studies and a small chamber system to measure CH(4) released by sheep for in vivo studies was developed. Microbial rumen population diversity from in vitro assays was studied using qPCR. In vitro studies with tanniniferous plants, herbal plant essential oils derived from thyme, fennel, ginger, black seed, and Eucalyptus oil (EuO) added to the basal diet and cakes of oleaginous plants (cotton, palm, castor plant, turnip, and lupine), which were included in the basal diet to replace soybean meal, presented significant differences regarding fermentation gas production and CH(4) formation. In vivo assays were performed according to the results of the in vitro assays. Mimosa caesalpineaefolia, when supplemented to a basal diet (Tifton-85 hay Cynodon sp, corn grain, soybean meal, cotton seed meal, and mineral mixture) fed to adult Santa Ines sheep reduced enteric CH(4) emission but the supplementation of the basal diet with EuO did not affect (P > 0.05) methane released. Regarding the microbial studies of rumen population diversity using qPCR with DNA samples collected from the in vitro trials, the results showed shifts in microbial communities of the tannin-rich plants in relation to control plant. This research demonstrated that tannin-rich M. caesepineapholia, essential oil from eucalyptus, and biodiesel co-products either in vitro or in vivo assays showed potential to mitigate CH(4) emission in ruminants. The microbial community study suggested that the reduction in CH(4) production may be attributed to a decrease in fermentable substrate rather than to a direct effect on methanogenesis.

Microbial functional diversity responses to 2 years since biochar application in silt-loam soils on the Loess Plateau.

PubMed

Zhu, Li-Xia; Xiao, Qian; Shen, Yu-Fang; Li, Shi-Qing

2017-10-01

The structure and function of soil microbial communities have been widely used as indicators of soil quality and fertility. The effect of biochar application on carbon sequestration has been studied, but the effect on soil microbial functional diversity has received little attention. We evaluated effects of biochar application on the functional diversities of microbes in a loam soil. The effects of biochar on microbial activities and related processes in the 0-10 and 10-20cm soil layers were determined in a two-year experiment in maize field on the Loess Plateau in China. Low-pyrolysis biochar produced from maize straw was applied into soils at rates of 0 (BC0), 10 (BC10) and 30 (BC30)tha -1 . Chemical analysis indicated that the biochar did not change the pH, significantly increased the amounts of organic carbon and nitrogen, and decreased the amount of mineral nitrogen and the microbial quotient. The biochar significantly decreased average well colour development (AWCD) values in Biolog EcoPlates™ for both layers, particularly for the rate of 10tha -1 . Biochar addition significantly decreased substrate richness (S) except for BC30 in the 0-10cm layer. Effects of biochar on the Shannon-Wiener index (H) and Simpson's dominance (D) were not significant, except for a significant increase in evenness index (E) in BC10 in the 10-20cm layer. A principal component analysis clearly differentiated the treatments, and microbial use of six categories of substrates significantly decreased in both layers after biochar addition, although the use of amines and amides did not differ amongst the three treatments in the deeper layer. Maize above ground dry biomass and height did not differ significantly amongst the treatments, and biochar had no significant effect on nitrogen uptake by maize seedlings. H was positively correlated with AWCD, and negatively with pH. AWCD was positively correlated with mineral N and negatively with pH. Our results indicated that shifts in soil microbial functional diversity affected by biochar were not effective indicators of soil quality in earlier maize growth periods in this region. Copyright © 2017. Published by Elsevier Inc.

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

PubMed

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

2004-02-01

Extension of human habitation into space requires that humans carry with them many of the microorganisms with which they coexist on Earth. The ubiquity of microorganisms in close association with all living things and biogeochemical processes on Earth predicates that they must also play a critical role in maintaining the viability of human life in space. Even though bacterial populations exist as locally adapted ecotypes, the abundance of individuals in microbial species is so large that dispersal is unlikely to be limited by geographical barriers on Earth (i.e., for most environments "everything is everywhere" given enough time). This will not be true for microbial communities in space where local species richness will be relatively low because of sterilization protocols prior to launch and physical barriers between Earth and spacecraft after launch. Although community diversity will be sufficient to sustain ecosystem function at the onset, richness and evenness may decline over time such that biological systems either lose functional potential (e.g., bioreactors may fail to reduce BOD or nitrogen load) or become susceptible to invasion by human-associated microorganisms (pathogens) over time. Research at the John F. Kennedy Space Center has evaluated fundamental properties of microbial diversity and community assembly in prototype bioregenerative systems for NASA Advanced Life Support. Successional trends related to increased niche specialization, including an apparent increase in the proportion of nonculturable types of organisms, have been consistently observed. In addition, the stability of the microbial communities, as defined by their resistance to invasion by human-associated microorganisms, has been correlated to their diversity. Overall, these results reflect the significant challenges ahead for the assembly of stable, functional communities using gnotobiotic approaches, and the need to better define the basic biological principles that define ecosystem processes in the space environment. Copyright 2004 Springer-Verlag

Microbial Community Responses to Glycine Addition in Kansas Prairie Soils

NASA Astrophysics Data System (ADS)

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

2015-12-01

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

Microbial astronauts: assembling microbial communities for advanced life support systems

NASA Technical Reports Server (NTRS)

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

2004-01-01

Extension of human habitation into space requires that humans carry with them many of the microorganisms with which they coexist on Earth. The ubiquity of microorganisms in close association with all living things and biogeochemical processes on Earth predicates that they must also play a critical role in maintaining the viability of human life in space. Even though bacterial populations exist as locally adapted ecotypes, the abundance of individuals in microbial species is so large that dispersal is unlikely to be limited by geographical barriers on Earth (i.e., for most environments "everything is everywhere" given enough time). This will not be true for microbial communities in space where local species richness will be relatively low because of sterilization protocols prior to launch and physical barriers between Earth and spacecraft after launch. Although community diversity will be sufficient to sustain ecosystem function at the onset, richness and evenness may decline over time such that biological systems either lose functional potential (e.g., bioreactors may fail to reduce BOD or nitrogen load) or become susceptible to invasion by human-associated microorganisms (pathogens) over time. Research at the John F. Kennedy Space Center has evaluated fundamental properties of microbial diversity and community assembly in prototype bioregenerative systems for NASA Advanced Life Support. Successional trends related to increased niche specialization, including an apparent increase in the proportion of nonculturable types of organisms, have been consistently observed. In addition, the stability of the microbial communities, as defined by their resistance to invasion by human-associated microorganisms, has been correlated to their diversity. Overall, these results reflect the significant challenges ahead for the assembly of stable, functional communities using gnotobiotic approaches, and the need to better define the basic biological principles that define ecosystem processes in the space environment. Copyright 2004 Springer-Verlag.

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes.

PubMed

Fierer, Noah; Leff, Jonathan W; Adams, Byron J; Nielsen, Uffe N; Bates, Scott Thomas; Lauber, Christian L; Owens, Sarah; Gilbert, Jack A; Wall, Diana H; Caporaso, J Gregory

2012-12-26

For centuries ecologists have studied how the diversity and functional traits of plant and animal communities vary across biomes. In contrast, we have only just begun exploring similar questions for soil microbial communities despite soil microbes being the dominant engines of biogeochemical cycles and a major pool of living biomass in terrestrial ecosystems. We used metagenomic sequencing to compare the composition and functional attributes of 16 soil microbial communities collected from cold deserts, hot deserts, forests, grasslands, and tundra. Those communities found in plant-free cold desert soils typically had the lowest levels of functional diversity (diversity of protein-coding gene categories) and the lowest levels of phylogenetic and taxonomic diversity. Across all soils, functional beta diversity was strongly correlated with taxonomic and phylogenetic beta diversity; the desert microbial communities were clearly distinct from the nondesert communities regardless of the metric used. The desert communities had higher relative abundances of genes associated with osmoregulation and dormancy, but lower relative abundances of genes associated with nutrient cycling and the catabolism of plant-derived organic compounds. Antibiotic resistance genes were consistently threefold less abundant in the desert soils than in the nondesert soils, suggesting that abiotic conditions, not competitive interactions, are more important in shaping the desert microbial communities. As the most comprehensive survey of soil taxonomic, phylogenetic, and functional diversity to date, this study demonstrates that metagenomic approaches can be used to build a predictive understanding of how microbial diversity and function vary across terrestrial biomes.

Microbial biodiversity in glacier-fed streams

PubMed Central

Wilhelm, Linda; Singer, Gabriel A; Fasching, Christina; Battin, Tom J; Besemer, Katharina

2013-01-01

While glaciers become increasingly recognised as a habitat for diverse and active microbial communities, effects of their climate change-induced retreat on the microbial ecology of glacier-fed streams remain elusive. Understanding the effect of climate change on microorganisms in these ecosystems is crucial given that microbial biofilms control numerous stream ecosystem processes with potential implications for downstream biodiversity and biogeochemistry. Here, using a space-for-time substitution approach across 26 Alpine glaciers, we show how microbial community composition and diversity, based on 454-pyrosequencing of the 16S rRNA gene, in biofilms of glacier-fed streams may change as glaciers recede. Variations in streamwater geochemistry correlated with biofilm community composition, even at the phylum level. The most dominant phyla detected in glacial habitats were Proteobacteria, Bacteroidetes, Actinobacteria and Cyanobacteria/chloroplasts. Microorganisms from ice had the lowest α diversity and contributed marginally to biofilm and streamwater community composition. Rather, streamwater apparently collected microorganisms from various glacial and non-glacial sources forming the upstream metacommunity, thereby achieving the highest α diversity. Biofilms in the glacier-fed streams had intermediate α diversity and species sorting by local environmental conditions likely shaped their community composition. α diversity of streamwater and biofilm communities decreased with elevation, possibly reflecting less diverse sources of microorganisms upstream in the catchment. In contrast, β diversity of biofilms decreased with increasing streamwater temperature, suggesting that glacier retreat may contribute to the homogenisation of microbial communities among glacier-fed streams. PMID:23486246

Emergence of microbial diversity due to cross-feeding interactions in a spatial model of gut microbial metabolism.

PubMed

Hoek, Milan J A van; Merks, Roeland M H

2017-05-16

The human gut contains approximately 10 14 bacteria, belonging to hundreds of different species. Together, these microbial species form a complex food web that can break down nutrient sources that our own digestive enzymes cannot handle, including complex polysaccharides, producing short chain fatty acids and additional metabolites, e.g., vitamin K. Microbial diversity is important for colonic health: Changes in the composition of the microbiota have been associated with inflammatory bowel disease, diabetes, obesity and Crohn's disease, and make the microbiota more vulnerable to infestation by harmful species, e.g., Clostridium difficile. To get a grip on the controlling factors of microbial diversity in the gut, we here propose a multi-scale, spatiotemporal dynamic flux-balance analysis model to study the emergence of metabolic diversity in a spatial gut-like, tubular environment. The model features genome-scale metabolic models (GEM) of microbial populations, resource sharing via extracellular metabolites, and spatial population dynamics and evolution. In this model, cross-feeding interactions emerge readily, despite the species' ability to metabolize sugars autonomously. Interestingly, the community requires cross-feeding for producing a realistic set of short-chain fatty acids from an input of glucose, If we let the composition of the microbial subpopulations change during invasion of adjacent space, a complex and stratified microbiota evolves, with subspecies specializing on cross-feeding interactions via a mechanism of compensated trait loss. The microbial diversity and stratification collapse if the flux through the gut is enhanced to mimic diarrhea. In conclusion, this in silico model is a helpful tool in systems biology to predict and explain the controlling factors of microbial diversity in the gut. It can be extended to include, e.g., complex nutrient sources, and host-microbiota interactions via the intestinal wall.

Diversity and Phylogenetic Structure of Two Complex Marine Microbial Communities

DTIC Science & Technology

2004-09-01

Science 190 and Engineering DOCTORAL DISSERTATION Diversity and Phylogenetic Structure of Two Complex Marine Microbial Communities by Vanja Klepac-Ceraj...Two Complex Marine Microbial Communities by Vanja Klepac-Ceraj Massachusetts Institute of Technology Cambridge, Massachusetts 02139 and Woods Hole...Phylogenetic Structure of Two Complex Marine Microbial Communities. Ph.D. Thesis. MIT/WHOI, 2004-11. Approved for publication; distribution unlimited

Fifty important research questions in microbial ecology.

PubMed

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

2017-05-01

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

A snapshot on prokaryotic diversity of the Solimões River basin (Amazon, Brazil).

PubMed

Toyama, D; Santos-Júnior, C D; Kishi, L T; Oliveira, T C S; Garcia, J W; Sarmento, H; Miranda, F P; Henrique-Silva, F

2017-05-18

The Amazon region has the largest hydrographic basin on the planet and 
is well known for its huge biodiversity of plants and animals. However, 
there is a lack of studies on aquatic microbial biodiversity in the 
Solimões River, one of its main water courses. To investigate the 
microbial biodiversity of this region, we performed 16S rRNA gene clone 
libraries from Solimões River and adjacent rivers and lakes. Our question was which microorganisms inhabit the different types of aquatic 
environments in this part of the basin, and how diversity varies among 
these environments (rivers and lakes). The microbial 
diversity generating 13 clone libraries of the bacterial 16S rRNA gene 
and 5 libraries of the archaeal 16S rRNA gene was assessed. Diversity measured by several alpha diversity indices (ACE, Chao, Shannon and Simpson) revealed significant differences in diversity indices between lake and river samples. The site with higher microbial diversity was in the Solimões River (4S), downstream the confluence with Purus River. The most common bacterial taxon was the cosmopolitan Polynucleobacter genus, widely observed in all samples. The phylum Thaumarchaeota was the prevailing archaeal taxon. Our results provide the first insight into the microbial diversity of the world's largest river basin.

Robust estimation of microbial diversity in theory and in practice

PubMed Central

Haegeman, Bart; Hamelin, Jérôme; Moriarty, John; Neal, Peter; Dushoff, Jonathan; Weitz, Joshua S

2013-01-01

Quantifying diversity is of central importance for the study of structure, function and evolution of microbial communities. The estimation of microbial diversity has received renewed attention with the advent of large-scale metagenomic studies. Here, we consider what the diversity observed in a sample tells us about the diversity of the community being sampled. First, we argue that one cannot reliably estimate the absolute and relative number of microbial species present in a community without making unsupported assumptions about species abundance distributions. The reason for this is that sample data do not contain information about the number of rare species in the tail of species abundance distributions. We illustrate the difficulty in comparing species richness estimates by applying Chao's estimator of species richness to a set of in silico communities: they are ranked incorrectly in the presence of large numbers of rare species. Next, we extend our analysis to a general family of diversity metrics (‘Hill diversities'), and construct lower and upper estimates of diversity values consistent with the sample data. The theory generalizes Chao's estimator, which we retrieve as the lower estimate of species richness. We show that Shannon and Simpson diversity can be robustly estimated for the in silico communities. We analyze nine metagenomic data sets from a wide range of environments, and show that our findings are relevant for empirically-sampled communities. Hence, we recommend the use of Shannon and Simpson diversity rather than species richness in efforts to quantify and compare microbial diversity. PMID:23407313

Microbial diversity and metabolite composition of Belgian red-brown acidic ales.

PubMed

Snauwaert, Isabel; Roels, Sanne P; Van Nieuwerburg, Filip; Van Landschoot, Anita; De Vuyst, Luc; Vandamme, Peter

2016-03-16

Belgian red-brown acidic ales are sour and alcoholic fermented beers, which are produced by mixed-culture fermentation and blending. The brews are aged in oak barrels for about two years, after which mature beer is blended with young, non-aged beer to obtain the end-products. The present study evaluated the microbial community diversity of Belgian red-brown acidic ales at the end of the maturation phase of three subsequent brews of three different breweries. The microbial diversity was compared with the metabolite composition of the brews at the end of the maturation phase. Therefore, mature brew samples were subjected to 454 pyrosequencing of the 16S rRNA gene (bacteria) and the internal transcribed spacer region (yeasts) and a broad range of metabolites was quantified. The most important microbial species present in the Belgian red-brown acidic ales investigated were Pediococcus damnosus, Dekkera bruxellensis, and Acetobacter pasteurianus. In addition, this culture-independent analysis revealed operational taxonomic units that were assigned to an unclassified fungal community member, Candida, and Lactobacillus. The main metabolites present in the brew samples were L-lactic acid, D-lactic acid, and ethanol, whereas acetic acid was produced in lower quantities. The most prevailing aroma compounds were ethyl acetate, isoamyl acetate, ethyl hexanoate, and ethyl octanoate, which might be of impact on the aroma of the end-products. Copyright © 2016 Elsevier B.V. All rights reserved.

Comparison of the Microbial Diversity and Abundance Between the Freshwater Land-Locked Lakes of Schirmacher Oasis and the Perennially Ice-Covered Lake Untersee in East Antarctica

NASA Technical Reports Server (NTRS)

Huang, Jonathan; Hoover, Richard B.; Swain, Ashit; Murdock, Chris; Bej, Asim K.

2010-01-01

Extreme conditions such as low temperature, dryness, and constant UV-radiation in terrestrial Antarctica are limiting factors of the survival of microbial populations. The objective of this study was to investigate the microbial diversity and enumeration between the open water lakes of Schirmacher Oasis and the permanently ice-covered Lake Untersee. The lakes in Schirmacher Oasis possessed abundant and diverse group of microorganisms compared to the Lake Untersee. Furthermore, the microbial diversity between two lakes in Schirmacher Oasis (Lake L27C and L47) was compared by culture-based molecular approach. It was determined that L27Chad a richer microbial diversity representing 5 different phyla and 7 different genera. In contrast L47 consisted of 4 different phyla and 6 different genera. The difference in microbial community could be due to the wide range of pH between L27C (pH 9.1) and L47 (pH 5.7). Most of the microbes isolated from these lakes consisted of adaptive biological pigmentation. Characterization of the microbial community found in the freshwater lakes of East Antarctica is important because it gives a further glimpse into the adaptation and survival strategies found in extreme conditions.

Differential responses of soil microbial biomass, diversity, and compositions to altitudinal gradients depend on plant and soil characteristics.

PubMed

Ren, Chengjie; Zhang, Wei; Zhong, ZeKun; Han, Xinhui; Yang, Gaihe; Feng, Yongzhong; Ren, Guangxin

2018-01-01

Alt'itudinal gradients strongly affect plant biodiversity, but the effects on microbial patterns remain unclear, especially in the large scale. We therefore designed an altitudinal gradient experiment that covered three climate zones to monitor soil microbial community dynamics and to compare those with plant and soil characteristics. Illumina sequencing of the 16S rRNA gene and ITS gene was used to analyze soil microbial (bacterial and fungal) diversity and composition, and fumigation-extraction was used to determine microbial biomass; the plant community metrics (i.e., percent cover, Shannon-Wiener, grass biomass, and carbon/nitrogen in leaf and biomass) and soil properties (i.e., soil moisture, soil temperature, bulk density, organic carbon, total nitrogen, and available nitrogen) were determined. The results showed that carbon/nitrogen in microbial biomass was higher at medium altitude and was positively related to carbon and nitrogen in both soil and grass biomass along the altitudinal gradients. Soil bacterial alpha diversity was significantly higher at medium altitude but fungal alpha diversity did not affected by altitudinal gradients; the effect of altitudinal gradients on bacterial beta diversity was larger than that on fungal beta diversity, although both groups were significantly affected by altitudinal gradients. Moreover, Alpha-proteobacteria, Beta-proteobacteria, and Gemmatimonadetes were significantly more abundant in higher altitude than in lower altitude, both Acidobacteria and Actinobacteria significantly declined with increasing altitude; other bacterial taxa such as Chloroflexi, Nitrospirae, Gamma-proteobacteria, and Delta-proteobacteria were significantly higher at medium altitudes. For fungal taxa, Basidiomycota and Ascomycota were the dominant phyla and responded insignificantly to the altitudinal gradients. The responses of microbial alpha diversity were mostly associated with plant Shannon index, organic carbon, and total nitrogen, whereas microbial beta diversity and composition mainly depended on soil moisture and temperature. Overall, these results suggest that soil bacteria rather than fungi can reflect changes in plant and soil characteristics along altitudinal gradients. Copyright © 2017 Elsevier B.V. All rights reserved.

Effect of Kampo medicine "Dai-kenchu-to" on microbiome in the intestine of the rats with fast stress.

PubMed

Yoshikawa, Kozo; Shimada, Mitsuo; Kuwahara, Tomomi; Hirakawa, Hideki; Kurita, Nobuhiro; Sato, Hirohiko; Utsunomiya, Tohru; Iwata, Takashi; Miyatani, Tomohiko; Higashijima, Jun; Kashihara, Hideya; Takasu, Chie; Matsumoto, Noriko; Nakayama-Imaohji, Haruyuki

2013-01-01

Diversity of gut microbiome has been recently reported to be lost in inflammatory bowel disease. We have previously reported that the Dai-kenchu-to (DKT) prevented the bacterial translocation through suppression of cytokine and apoptosis in rat's fast stress model. The aim of this study was to evaluate the effect of DKT on maintenance of microbial diversity in rat's intestine with inflammation. Wister rats were received the fast stress for 5 days. In DKT group, rats were administered with DKT (300 mg/kg/day) during the fast stress (DKT-group). The gut microbiomes were analyzed at before- and after- fast stress, and the effect of DKT for on microbial diversities of the gut were evaluated by the PCR-clone library method targeting the 16 S ribosomal RNA gene. In Control-group, Erysipelotrichaceae increased to 86% in after fast stress, OTU of before-fast stress was 111 and after fast stress was only 9 (changing rate: 58%). The diversity of microbiome was severely decreased. On the other hand, in DKT-group, diversity of microbiome was kept after fast stress (Lachnospiraceae: Ruminococcaceae: Coriobacteriales 54%, 22%, 5%), Operational taxonomic units of before fast stress was 52 and after fast stress was 55 (changing rate: 6%). Family Lachnospiraceae which includes butyrate-producing Clostridia (Clostridium IV and XIVa). DKT prevented the reduction of diversity of microbiome in rat's fast stress model. Our data suggested the new anti-inflammatory mechanism of DKT through gut microbiome.

Microbial Signatures of Cadaver Gravesoil During Decomposition.

PubMed

Finley, Sheree J; Pechal, Jennifer L; Benbow, M Eric; Robertson, B K; Javan, Gulnaz T

2016-04-01

Genomic studies have estimated there are approximately 10(3)-10(6) bacterial species per gram of soil. The microbial species found in soil associated with decomposing human remains (gravesoil) have been investigated and recognized as potential molecular determinants for estimates of time since death. The nascent era of high-throughput amplicon sequencing of the conserved 16S ribosomal RNA (rRNA) gene region of gravesoil microbes is allowing research to expand beyond more subjective empirical methods used in forensic microbiology. The goal of the present study was to evaluate microbial communities and identify taxonomic signatures associated with the gravesoil human cadavers. Using 16S rRNA gene amplicon-based sequencing, soil microbial communities were surveyed from 18 cadavers placed on the surface or buried that were allowed to decompose over a range of decomposition time periods (3-303 days). Surface soil microbial communities showed a decreasing trend in taxon richness, diversity, and evenness over decomposition, while buried cadaver-soil microbial communities demonstrated increasing taxon richness, consistent diversity, and decreasing evenness. The results show that ubiquitous Proteobacteria was confirmed as the most abundant phylum in all gravesoil samples. Surface cadaver-soil communities demonstrated a decrease in Acidobacteria and an increase in Firmicutes relative abundance over decomposition, while buried soil communities were consistent in their community composition throughout decomposition. Better understanding of microbial community structure and its shifts over time may be important for advancing general knowledge of decomposition soil ecology and its potential use during forensic investigations.

Genetic profiling of the oral microbiota associated with severe early-childhood caries.

PubMed

Li, Y; Ge, Y; Saxena, D; Caufield, P W

2007-01-01

The determination of the composition of the microbial community in the oral cavity is usually based on cultivation methods; however, nearly half of the bacteria in the saliva and the dental plaque are not cultivable. In this study, we evaluated the difference in oral microbial diversity between children with severe early-childhood caries (S-ECC) and caries-free (CF) controls by means of a cultivation-independent approach called denaturing gradient gel electrophoresis (DGGE). Pooled dental plaque samples were collected from 20 children aged 2 to 8 years. Total microbial genomic DNA was isolated from those subjects, and a portion of the 16S rRNA gene locus was PCR amplified by using universal primers. We observed that the mean species richness of the bacterial population was greater in the CF children (n = 12) (42 +/- 3.7) than in the S-ECC children (n = 8) (35 +/- 4.3); the difference was statistically significant (P = 0.005). The overall diversity of plaque samples as measured by the Shannon index was 3.5 for the S-ECC group and 3.7 for the CF group (P = 0.004). Differences in DGGE profiles were distinguished on the basis of a cluster analysis. Sequence analysis of excised DGGE bands consisted of 2.7 phylotypes, on average. After adjusting for the number of observed bands, we estimated that the S-ECC group exhibited 94.5 total phylotypes and that the CF group exhibited 113.4. These results suggest that the microbial diversity and complexity of the microbial biota in dental plaque are significantly less in S-ECC children than in CF children.

Bacterial, fungal, and plant communities exhibit no biomass or compositional response to two years of simulated nitrogen deposition in a semiarid grassland: Bacterial, fungal, and plant communities

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

McHugh, Theresa A.; Morrissey, Ember M.; Mueller, Rebecca C.

Nitrogen (N) deposition affects myriad aspects of terrestrial ecosystem structure and function, and microbial communities may be particularly sensitive to anthropogenic N inputs. However, our understanding of N deposition effects on microbial communities is far from complete, especially for drylands where data are comparatively rare. To address the need for an improved understanding of dryland biological responses to N deposition, we conducted a two-year fertilization experiment in a semiarid grassland on the Colorado Plateau in the southwestern United States. We evaluated effects of varied levels of N inputs on archaeal, bacterial, fungal and chlorophyte community composition within three microhabitats: biologicalmore » soil crusts (biocrusts), soil below biocrusts, and the plant rhizosphere. Surprisingly, N addition did not affect the community composition or diversity of any of these microbial groups; however, microbial community composition varied significantly among sampling microhabitats. Further, while plant richness, diversity, and cover showed no response to N addition, there were strong linkages between plant properties and microbial community structure. Overall, these findings highlight the potential for some dryland communities to have limited biotic ability to retain augmented N inputs, possibly leading to large N losses to the atmosphere and to aquatic systems.« less

Bacterial, fungal, and plant communities exhibit no biomass or compositional response to two years of simulated nitrogen deposition in a semiarid grassland: Bacterial, fungal, and plant communities

DOE PAGES

McHugh, Theresa A.; Morrissey, Ember M.; Mueller, Rebecca C.; ...

2017-03-13

Nitrogen (N) deposition affects myriad aspects of terrestrial ecosystem structure and function, and microbial communities may be particularly sensitive to anthropogenic N inputs. However, our understanding of N deposition effects on microbial communities is far from complete, especially for drylands where data are comparatively rare. To address the need for an improved understanding of dryland biological responses to N deposition, we conducted a two-year fertilization experiment in a semiarid grassland on the Colorado Plateau in the southwestern United States. We evaluated effects of varied levels of N inputs on archaeal, bacterial, fungal and chlorophyte community composition within three microhabitats: biologicalmore » soil crusts (biocrusts), soil below biocrusts, and the plant rhizosphere. Surprisingly, N addition did not affect the community composition or diversity of any of these microbial groups; however, microbial community composition varied significantly among sampling microhabitats. Further, while plant richness, diversity, and cover showed no response to N addition, there were strong linkages between plant properties and microbial community structure. Overall, these findings highlight the potential for some dryland communities to have limited biotic ability to retain augmented N inputs, possibly leading to large N losses to the atmosphere and to aquatic systems.« less

Bacterial, fungal, and plant communities exhibit no biomass or compositional response to two years of simulated nitrogen deposition in a semiarid grassland

USGS Publications Warehouse

McHugh, Theresa A.; Morrissey, Ember M.; Mueller, Rebecca C.; Gallegos-Graves, La Verne; Kuske, Cheryl R.; Reed, Sasha C.

2017-01-01

Nitrogen (N) deposition affects myriad aspects of terrestrial ecosystem structure and function, and microbial communities may be particularly sensitive to anthropogenic N inputs. However, our understanding of N deposition effects on microbial communities is far from complete, especially for drylands where data are comparatively rare. To address the need for an improved understanding of dryland biological responses to N deposition, we conducted a two-year fertilization experiment in a semiarid grassland on the Colorado Plateau in the southwestern United States. We evaluated effects of varied levels of N inputs on archaeal, bacterial, fungal and chlorophyte community composition within three microhabitats: biological soil crusts (biocrusts), soil below biocrusts, and the plant rhizosphere. Surprisingly, N addition did not affect the community composition or diversity of any of these microbial groups; however, microbial community composition varied significantly among sampling microhabitats. Further, while plant richness, diversity, and cover showed no response to N addition, there were strong linkages between plant properties and microbial community structure. Overall, these findings highlight the potential for some dryland communities to have limited biotic ability to retain augmented N inputs, possibly leading to large N losses to the atmosphere and to aquatic systems.

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

Microbial diversity and community structure across environmental gradients in an seawater intruded shallow confined aquifer

NASA Astrophysics Data System (ADS)

Zhang, X.; Hu, B.

2017-12-01

Seawater intrusion has been an important topic in coastal hydrogeology and making previously freshwater ecosystems saline. Plant and animal responses to variation in the freshwater-saline interface have been well studied in the coastal zone. However, little is known about the biogeography or stability of microbial community response to seawater intrusion. The objective of this study is to characterize and compare bacterial and archaea community diversity and composition in 15 groundwater samples with varied salinity using high-throughput-sequencing of 16S ribosomal RNA genes. The dominant taxonomic group identified in all samples are proteobacteria for bacteria and crenarchaeota for archaea. The other main bacterial groups are varied in samples with different salinities including bacteroidetes, firmicutes and several unidentified taxonomys. A combination of environmental factors seems to influence the microbial community composition where organic carbon is a primary factor shaping microbial communities. Correlation analysis between the relative abundance of bacterial taxa and geochemical parameters uggested that rare taxa may contribute to biogeochemical processes taking place at the mixing zone of freshewater and saltwater. Our results help to understand how the physical and chemical factors shape the microbial community composition and set a baseline for upcoming studies to evaluate the response of this ecosystem to future changes and the efficacy of new remediation efforts.

Potential impact of Andrassy bentonite microbial diversity in the long-term performance of a deep nuclear waste repository

NASA Astrophysics Data System (ADS)

Tadza, M. Y. Mohd; Tadza, M. A. Mohd; Bag, R.; Harith, N. S. H.

2018-01-01

Copper and steel canning and bentonite buffer are normally forseen as the primary containment component of a deep nuclear waste repository. Distribution of microbes in subsurface environments have been found to be extensive and directly or indirectly may exert influence on waste canister corrosion and the mobility of radionuclides. The understanding of clays and microbial interaction with radionuclides will be useful in predicting the microbial impacts on the performance of the waste repositories. The present work characterizes the culture-dependent microbial diversity of Andrassy bentonite recovered from Tawau clay deposits. The evaluation of microbial populations shows the presence of a number of cultivable microbes (e.g. Staphylococcus, Micrococcus, Achromobacter, Bacillus, Paecilomyces, Trichoderma, and Fusarium). Additionally, a pigmented yeast strain Rhodotorula mucilaginosa was also recovered from the formation. Both Bacillus and Rhodotorula mucilaginosa have high tolerance towards U radiation and toxicity. The presence of Rhodotorula mucilaginosa in Andrassy bentonite might be able to change the speciation of radionuclides (e.g. uranium) in a future deep repository. However, concern over the presence of Fe (III) reduction microbes such as Bacillus also found in the formation could lead to corrosion of copper steel canister and affect the overall performance of the containment system.

Small-scale spatial variability of soil microbial community composition and functional diversity in a mixed forest

NASA Astrophysics Data System (ADS)

Wang, Qiufeng; Tian, Jing; Yu, Guirui

2014-05-01

Patterns in the spatial distribution of organisms provide important information about mechanisms that regulate the diversity and complexity of soil ecosystems. Therefore, information on spatial distribution of microbial community composition and functional diversity is urgently necessary. The spatial variability on a 26×36 m plot and vertical distribution (0-10 cm and 10-20 cm) of soil microbial community composition and functional diversity were studied in a natural broad-leaved Korean pine (Pinus koraiensis) mixed forest soil in Changbai Mountain. The phospholipid fatty acid (PLFA) pattern was used to characterize the soil microbial community composition and was compared with the community substrate utilization pattern using Biolog. Bacterial biomass dominated and showed higher variability than fungal biomass at all scales examined. The microbial biomass decreased with soil depths increased and showed less variability in lower 10-20 cm soil layer. The Shannon-Weaver index value for microbial functional diversity showed higher variability in upper 0-10 cm than lower 10-20 cm soil layer. Carbohydrates, carboxylic acids, polymers and amino acids are the main carbon sources possessing higher utilization efficiency or utilization intensity. At the same time, the four carbon source types contributed to the differentiation of soil microbial communities. This study suggests the higher diversity and complexity for this mix forest ecosystem. To determine the driving factors that affect this spatial variability of microorganism is the next step for our study.

Nutrient enrichment induces dormancy and decreases diversity of active bacteria in salt marsh sediments

PubMed Central

Kearns, Patrick J.; Angell, John H.; Howard, Evan M.; Deegan, Linda A.; Stanley, Rachel H. R.; Bowen, Jennifer L.

2016-01-01

Microorganisms control key biogeochemical pathways, thus changes in microbial diversity, community structure and activity can affect ecosystem response to environmental drivers. Understanding factors that control the proportion of active microbes in the environment and how they vary when perturbed is critical to anticipating ecosystem response to global change. Increasing supplies of anthropogenic nitrogen to ecosystems globally makes it imperative that we understand how nutrient supply alters active microbial communities. Here we show that nitrogen additions to salt marshes cause a shift in the active microbial community despite no change in the total community. The active community shift causes the proportion of dormant microbial taxa to double, from 45 to 90%, and induces diversity loss in the active portion of the community. Our results suggest that perturbations to salt marshes can drastically alter active microbial communities, however these communities may remain resilient by protecting total diversity through increased dormancy. PMID:27666199

Nutrient enrichment induces dormancy and decreases diversity of active bacteria in salt marsh sediments.

PubMed

Kearns, Patrick J; Angell, John H; Howard, Evan M; Deegan, Linda A; Stanley, Rachel H R; Bowen, Jennifer L

2016-09-26

Microorganisms control key biogeochemical pathways, thus changes in microbial diversity, community structure and activity can affect ecosystem response to environmental drivers. Understanding factors that control the proportion of active microbes in the environment and how they vary when perturbed is critical to anticipating ecosystem response to global change. Increasing supplies of anthropogenic nitrogen to ecosystems globally makes it imperative that we understand how nutrient supply alters active microbial communities. Here we show that nitrogen additions to salt marshes cause a shift in the active microbial community despite no change in the total community. The active community shift causes the proportion of dormant microbial taxa to double, from 45 to 90%, and induces diversity loss in the active portion of the community. Our results suggest that perturbations to salt marshes can drastically alter active microbial communities, however these communities may remain resilient by protecting total diversity through increased dormancy.

A communal catalogue reveals Earth's multiscale microbial diversity.

PubMed

Thompson, Luke R; Sanders, Jon G; McDonald, Daniel; Amir, Amnon; Ladau, Joshua; Locey, Kenneth J; Prill, Robert J; Tripathi, Anupriya; Gibbons, Sean M; Ackermann, Gail; Navas-Molina, Jose A; Janssen, Stefan; Kopylova, Evguenia; Vázquez-Baeza, Yoshiki; González, Antonio; Morton, James T; Mirarab, Siavash; Zech Xu, Zhenjiang; Jiang, Lingjing; Haroon, Mohamed F; Kanbar, Jad; Zhu, Qiyun; Jin Song, Se; Kosciolek, Tomasz; Bokulich, Nicholas A; Lefler, Joshua; Brislawn, Colin J; Humphrey, Gregory; Owens, Sarah M; Hampton-Marcell, Jarrad; Berg-Lyons, Donna; McKenzie, Valerie; Fierer, Noah; Fuhrman, Jed A; Clauset, Aaron; Stevens, Rick L; Shade, Ashley; Pollard, Katherine S; Goodwin, Kelly D; Jansson, Janet K; Gilbert, Jack A; Knight, Rob

2017-11-23

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.

Microbial biofilms on facial prostheses.

PubMed

Ariani, Nina; Vissink, Arjan; van Oort, Robert P; Kusdhany, Lindawati; Djais, Ariadna; Rahardjo, Tri Budi W; van der Mei, Henny C; Krom, Bastiaan P

2012-01-01

The composition of microbial biofilms on silicone rubber facial prostheses was investigated and compared with the microbial flora on healthy and prosthesis-covered skin. Scanning electron microscopy showed the presence of mixed bacterial and yeast biofilms on and deterioration of the surface of the prostheses. Microbial culturing confirmed the presence of yeasts and bacteria. Microbial colonization was significantly increased on prosthesis-covered skin compared to healthy skin. Candida spp. were exclusively isolated from prosthesis-covered skin and from prostheses. Biofilms from prostheses showed the least diverse band-profile in denaturing gradient gel electrophoresis (DGGE) whereas prosthesis-covered skin showed the most diverse band-profile. Bacterial diversity exceeded yeast diversity in all samples. It is concluded that occlusion of the skin by prostheses creates a favorable niche for opportunistic pathogens such as Candida spp. and Staphylococcus aureus. Biofilms on healthy skin, skin underneath the prosthesis and on the prosthesis had a comparable composition, but the numbers present differed according to the microorganism.

Nutrient enrichment induces dormancy and decreases diversity of active bacteria in salt marsh sediments

NASA Astrophysics Data System (ADS)

Kearns, Patrick J.; Angell, John H.; Howard, Evan M.; Deegan, Linda A.; Stanley, Rachel H. R.; Bowen, Jennifer L.

2016-09-01

Microorganisms control key biogeochemical pathways, thus changes in microbial diversity, community structure and activity can affect ecosystem response to environmental drivers. Understanding factors that control the proportion of active microbes in the environment and how they vary when perturbed is critical to anticipating ecosystem response to global change. Increasing supplies of anthropogenic nitrogen to ecosystems globally makes it imperative that we understand how nutrient supply alters active microbial communities. Here we show that nitrogen additions to salt marshes cause a shift in the active microbial community despite no change in the total community. The active community shift causes the proportion of dormant microbial taxa to double, from 45 to 90%, and induces diversity loss in the active portion of the community. Our results suggest that perturbations to salt marshes can drastically alter active microbial communities, however these communities may remain resilient by protecting total diversity through increased dormancy.

Soil microbial structure and function post-volcanic eruption on Kasatochi Island and regional controls on microbial heterogeneity

NASA Astrophysics Data System (ADS)

Zeglin, L. H.; Rainey, F.; Wang, B.; Waythomas, C.; Talbot, S. L.

2013-12-01

Microorganisms are abundant and diverse in soil and their integrated activity drives nutrient cycling on the ecosystem scale. Organic matter (OM) inputs from plant production support microbial heterotrophic life, and soil geochemistry constrains microbial activity and diversity. As vegetation and soil develops over time, these factors change, modifying the controls on microbial heterogeneity. Following a volcanic eruption, ash deposition creates new surfaces where both organismal growth and weathering processes are effectively reset. The trajectory of microbial community development following this disturbance depends on both organic matter accumulation and geochemical constraints. Also, dispersal of microbial cells to the sterile ash surface may determine microbial community succession. The Aleutian Islands (Alaska, USA) are a dynamic volcanic region, with active and dormant volcanoes distributed across the volcanic arc. One of these volcanoes, Kasatochi, erupted violently in August 2008, burying a small lush island in pryoclastic flows and fine ash. Since, plants and birds are beginning to re-establish on developing surfaces, including legacy soils exposed by rapid erosion of pyroclastic deposits, suggesting that recovery of microbial life is also proceeding. However, soil microbial diversity and function has not been examined on Kasatochi Island or across the greater Aleutian region. The project goal is to address these questions: How is soil microbial community structure and function developing following the Kasatochi eruption? What is the relative importance of dispersal, soil OM and geochemistry to microbial community heterogeneity across the Aleutians? Surface mineral soil (20-cm depth) samples were collected from Kasatochi Island in summer 2013, five years after the 2008 eruption, and from eight additional Aleutian islands. On Kasatochi, pryoclastic deposits, exposed legacy soils supporting regrowth of remnant dune wild-rye (Leymus mollis) and mesic meadow plant communities, and soils impacted by recovering seabird rookeries were sampled. On the other islands, soils supporting both Leymus and mesic meadow communities (representative of dominant vegetation types on Kasatochi pre-eruption) were sampled. For each soil category and island combination, three transects of soil cores at 10-cm, 50-cm, 1-m, 5-m and 10-m distance were collected; with distances between sites and islands included (up to >700 km), the range of geographic distance examined covers over 7 orders of magnitude. For all samples, data on fundamental geochemical and OM factors, bacterial and fungal biomass, activity and diversity (via QPCR, extracellular enzyme potential assays and T-RFLP) are being collected. Covariance analysis is being used to evaluate the scale of maximum spatial heterogeneity in microbial structure and function, and ordination and matrix correlation analyses are being used to identify the key environmental covariates with heterogeneity. We hypothesize that heterogeneity at small (cm) scales will reflect predominant geochemical controls, at medium (m) scales will reflect predominant OM (vegetation) controls and at large (km) scales will reflect dispersal-related controls on microbial community structure and function.

PHYLOGENETIC AND FUNCTIONAL DIVERSITY OF SEAGULL AND CANADIAN GEESE FECAL MICROBIAL COMMUNITIES

EPA Science Inventory

In spite of increasing public health concerns on the risks associated with swimming in waters contaminated with waterfowl feces, there is little information on the gut microbial communities of aquatic birds. To address the molecular microbial diversity of waterfowl, 16S rDNA and ...

Chemical and microbial changes during autothermal thermophilic aerobic digestion (ATAD) of sewage sludge.

PubMed

Liu, Shugen; Song, Fanyong; Zhu, Nanwen; Yuan, Haiping; Cheng, Jiehong

2010-12-01

Autothermal thermophilic aerobic digestion (ATAD) is a promising process for sewage sludge stabilization. Batch experiments were conducted on sewage sludge collected from a municipal wastewater treatment plant in Shanghai, China, to evaluate the effectiveness of the ATAD system by determining changes in volatile suspended solids (VSSs) and to study its microbial diversity by denaturing gradient gel electrophoresis of 16S rRNA gene sequences amplified by PCR. The digestion system achieved rapid degradation of the organic substrate at 55 degrees C. The VSS was removed by up to 45.3% and 50.4% at 216 h and 264 h, respectively, while NH(4)(+)-N, chemical oxidation demand and total organic carbon of supernatant as well as total nitrogen did not exhibit obvious declines after 168 h. The microbial diversity changed during the thermophilic process as thermophiles belonging to the Hydrogenophilaceae, Thermotogaceae, Clostridiaceae and the genus Ureibacillus replaced less temperature-tolerant microorganisms such as Sphingobacteriaceae and the genus Trichococcus. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Phylogenetic analysis of the fecal microbial community in herbivorous land and marine iguanas of the Galápagos Islands using 16S rRNA-based pyrosequencing.

PubMed

Hong, Pei-Ying; Wheeler, Emily; Cann, Isaac K O; Mackie, Roderick I

2011-09-01

Herbivorous reptiles depend on complex gut microbial communities to effectively degrade dietary polysaccharides. The composition of these fermentative communities may vary based on dietary differences. To explore the role of diet in shaping gut microbial communities, we evaluated the fecal samples from two related host species--the algae-consuming marine iguana (Amblyrhynchus cristatus) and land iguanas (LI) (genus Conolophus) that consume terrestrial vegetation. Marine and LI fecal samples were collected from different islands in the Galápagos archipelago. High-throughput 16S rRNA-based pyrosequencing was used to provide a comparative analysis of fecal microbial diversity. At the phylum level, the fecal microbial community in iguanas was predominated by Firmicutes (69.5±7.9%) and Bacteroidetes (6.2±2.8%), as well as unclassified Bacteria (20.6±8.6%), suggesting that a large portion of iguana fecal microbiota is novel and could be involved in currently unknown functions. Host species differed in the abundance of specific bacterial groups. Bacteroides spp., Lachnospiraceae and Clostridiaceae were significantly more abundant in the marine iguanas (MI) (P-value>1E-9). In contrast, Ruminococcaceae were present at >5-fold higher abundance in the LI than MI (P-value>6E-14). Archaea were only detected in the LI. The number of operational taxonomic units (OTUs) in the LI (356-896 OTUs) was >2-fold higher than in the MI (112-567 OTUs), and this increase in OTU diversity could be related to the complexity of the resident bacterial population and their gene repertoire required to breakdown the recalcitrant polysaccharides prevalent in terrestrial plants. Our findings suggest that dietary differences contribute to gut microbial community differentiation in herbivorous lizards. Most importantly, this study provides a better understanding of the microbial diversity in the iguana gut; therefore facilitating future efforts to discover novel bacterial-associated enzymes that can effectively breakdown a wide variety of complex polysaccharides.

Impact of Transgenic Brassica napus Harboring the Antifungal Synthetic Chitinase (NiC) Gene on Rhizosphere Microbial Diversity and Enzyme Activities

PubMed Central

Khan, Mohammad S.; Sadat, Syed U.; Jan, Asad; Munir, Iqbal

2017-01-01

Transgenic Brassica napus harboring the synthetic chitinase (NiC) gene exhibits broad-spectrum antifungal resistance. As the rhizosphere microorganisms play an important role in element cycling and nutrient transformation, therefore, biosafety assessment of NiC containing transgenic plants on soil ecosystem is a regulatory requirement. The current study is designed to evaluate the impact of NiC gene on the rhizosphere enzyme activities and microbial community structure. The transgenic lines with the synthetic chitinase gene (NiC) showed resistance to Alternaria brassicicola, a common disease causing fungal pathogen. The rhizosphere enzyme analysis showed no significant difference in the activities of fivesoil enzymes: alkalyine phosphomonoestarase, arylsulphatase, β-glucosidase, urease and sucrase between the transgenic and non-transgenic lines of B. napus varieties, Durr-e-NIFA (DN) and Abasyne-95 (AB-95). However, varietal differences were observed based on the analysis of molecular variance. Some individual enzymes were significantly different in the transgenic lines from those of non-transgenic but the results were not reproducible in the second trail and thus were considered as environmental effect. Genotypic diversity of soil microbes through 16S–23S rRNA intergenic spacer region amplification was conducted to evaluate the potential impact of the transgene. No significant diversity (4% for bacteria and 12% for fungal) between soil microbes of NiC B. napus and the non-transgenic lines was found. However, significant varietal differences were observed between DN and AB-95 with 79% for bacterial and 54% for fungal diversity. We conclude that the NiC B. napus lines may not affect the microbial enzyme activities and community structure of the rhizosphere soil. Varietal differences might be responsible for minor changes in the tested parameters. PMID:28791039

Captivity results in disparate loss of gut microbial diversity in closely related hosts

PubMed Central

Kohl, Kevin D.; Skopec, Michele M.; Dearing, M. Denise

2014-01-01

The gastrointestinal tracts of animals contain diverse communities of microbes that provide a number of services to their hosts. There is recent concern that these communities may be lost as animals enter captive breeding programmes, due to changes in diet and/or exposure to environmental sources. However, empirical evidence documenting the effects of captivity and captive birth on gut communities is lacking. We conducted three studies to advance our knowledge in this area. First, we compared changes in microbial diversity of the gut communities of two species of woodrats (Neotoma albigula, a dietary generalist, and Neotoma stephensi, which specializes on juniper) before and after 6–9 months in captivity. Second, we investigated whether reintroduction of the natural diet of N. stephensi could restore microbial diversity. Third, we compared the microbial communities between offspring born in captivity and their mothers. We found that the dietary specialist, N. stephensi, lost a greater proportion of its native gut microbiota and overall diversity in response to captivity compared with N. albigula. Addition of the natural diet increased the proportion of the original microbiota but did not restore overall diversity in N. stephensi. Offspring of N. albigula more closely resembled their mothers compared with offspring–mother pairs of N. stephensi. This research suggests that the microbiota of dietary specialists may be more susceptible to captivity. Furthermore, this work highlights the need for further studies investigating the mechanisms underlying how loss of microbial diversity may vary between hosts and what an acceptable level of diversity loss may be to a host. This knowledge will aid conservation biologists in designing captive breeding programmes effective at maintaining microbial diversity. Sequence Accession Numbers: NCBI's Sequence Read Archive (SRA) – SRP033616 PMID:27293630

Microorganism-regulated mechanisms of temperature effects on the performance of anaerobic digestion.

PubMed

Lin, Qiang; He, Guihua; Rui, Junpeng; Fang, Xiaoyu; Tao, Yong; Li, Jiabao; Li, Xiangzhen

2016-06-03

Temperature is an important factor determining the performance and stability of the anaerobic digestion process. However, the microorganism-regulated mechanisms of temperature effects on the performance of anaerobic digestion systems remain further elusive. To address this issue, we investigated the changes in composition, diversity and activities of microbial communities under temperature gradient from 25 to 55 °C using 16S rRNA gene amplicon sequencing approach based on genomic DNA (refer to as "16S rDNA") and total RNA (refer to as "16S rRNA"). Microbial community structure and activities changed dramatically along the temperature gradient, which corresponded to the variations in digestion performance (e.g., daily CH4 production, total biogas production and volatile fatty acids concentration). The ratios of 16S rRNA to 16S rDNA of microbial taxa, as an indicator of the potentially relative activities in situ, and whole activities of microbial community assessed by the similarity between microbial community based on 16S rDNA and rRNA, varied strongly along the temperature gradient, reflecting different metabolic activities. The daily CH4 production increased with temperature from 25 to 50 °C and declined at 55 °C. Among all the examined microbial properties, the whole activities of microbial community and alpha-diversity indices of both microbial communities and potentially relative activities showed highest correlations to the performance. The whole activities of microbial community and alpha-diversity indices of both microbial communities and potentially relative activities were sensitive indicators for the performance of anaerobic digestion systems under temperature gradient, while beta-diversity could predict functional differences. Microorganism-regulated mechanisms of temperature effects on anaerobic digestion performance were likely realized through increasing alpha-diversity of both microbial communities and potentially relative activities to supply more functional pathways and activities for metabolic network, and increasing the whole activities of microbial community, especially methanogenesis, to improve the strength and efficiency in anaerobic digestion process.

The impact of failure: unsuccessful bacterial invasions steer the soil microbial community away from the invader's niche.

PubMed

Mallon, C A; Le Roux, X; van Doorn, G S; Dini-Andreote, F; Poly, F; Salles, J F

2018-03-01

Although many environments like soils are constantly subjected to invasion by alien microbes, invaders usually fail to succeed, succumbing to the robust diversity often found in nature. So far, only successful invasions have been explored, and it remains unknown to what extent an unsuccessful invasion can impact resident communities. Here we hypothesized that unsuccessful invasions can cause impacts to soil functioning by decreasing the diversity and niche breadth of resident bacterial communities, which could cause shifts to community composition and niche structure-an effect that is likely exacerbated when diversity is compromised. To examine this question, diversity gradients of soil microbial communities were subjected to invasion by the frequent, yet oft-unsuccessful soil invader, Escherichia coli, and evaluated for changes to diversity, bacterial community composition, niche breadth, and niche structure. Contrary to expectations, diversity and niche breadth increased across treatments upon invasion. Community composition and niche structure were also altered, with shifts of niche structure revealing an escape by the resident community away from the invader's resources. Importantly, the extent of the escape varied in response to the community's diversity, where less diverse communities experienced larger shifts. Thus, although transient and unsuccessful, the invader competed for resources with resident species and caused tangible impacts that modified both the diversity and functioning of resident communities, which can likely generate a legacy effect that influences future invasion attempts.

Impact of Chemical and Biological Fungicides Applied to Grapevine on Grape Biofilm, Must, and Wine Microbial Diversity

PubMed Central

Escribano-Viana, Rocío; López-Alfaro, Isabel; López, Rosa; Santamaría, Pilar; Gutiérrez, Ana R.; González-Arenzana, Lucía

2018-01-01

This study was aimed to measure the impact of the application of a bio-fungicide against Botrytis cinerea on the microbiota involved in the alcoholic fermentation (AF) of Tempranillo Rioja wines. For this purpose, a bio-fungicide composed of the biological control bacterium Bacillus subtilis QST713 was applied to the vineyard. The microbial diversity was analyzed from grape biofilm to wine. Impact on microbial diversity was measured employing indexes assessed with the software PAST 3.10 P.D. Results were compared to non-treated samples and to samples treated with a chemical fungicide mainly composed by fenhexamid. Overall, the impact of the biological-fungicide (bio-fungicide) on the microbial diversity assessed for grape biofilm and for musts was not remarkable. Neither of the tested fungicides enhanced the growth of any species or acted against the development of any microbial groups. The bio-fungicide had no significant impact on the wine microbiota whereas the chemical fungicide caused a reduction of microbial community richness and diversity. Although environmental threats might generate a detriment of the microbial species richness, in this study the tested bio-fungicide did not modify the structure of the microbial community. Indeed, some of the Bacillus applied at the grape surface, were detected at the end of the AF showing its resilience to the harsh environment of the winemaking; in contrast, its impact on wine quality during aging is yet unknown. PMID:29467723

Impact of Chemical and Biological Fungicides Applied to Grapevine on Grape Biofilm, Must, and Wine Microbial Diversity.

PubMed

Escribano-Viana, Rocío; López-Alfaro, Isabel; López, Rosa; Santamaría, Pilar; Gutiérrez, Ana R; González-Arenzana, Lucía

2018-01-01

This study was aimed to measure the impact of the application of a bio-fungicide against Botrytis cinerea on the microbiota involved in the alcoholic fermentation (AF) of Tempranillo Rioja wines. For this purpose, a bio-fungicide composed of the biological control bacterium Bacillus subtilis QST713 was applied to the vineyard. The microbial diversity was analyzed from grape biofilm to wine. Impact on microbial diversity was measured employing indexes assessed with the software PAST 3.10 P.D. Results were compared to non-treated samples and to samples treated with a chemical fungicide mainly composed by fenhexamid. Overall, the impact of the biological-fungicide (bio-fungicide) on the microbial diversity assessed for grape biofilm and for musts was not remarkable. Neither of the tested fungicides enhanced the growth of any species or acted against the development of any microbial groups. The bio-fungicide had no significant impact on the wine microbiota whereas the chemical fungicide caused a reduction of microbial community richness and diversity. Although environmental threats might generate a detriment of the microbial species richness, in this study the tested bio-fungicide did not modify the structure of the microbial community. Indeed, some of the Bacillus applied at the grape surface, were detected at the end of the AF showing its resilience to the harsh environment of the winemaking; in contrast, its impact on wine quality during aging is yet unknown.

Application of Sequence-based Methods in Human MicrobialEcology

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

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

2005-08-29

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

Environmental Microbial Community Proteomics: Status, Challenges and Perspectives.

PubMed

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

2016-08-05

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

Microbial community characterization of ozone-biofiltration systems in drinking water and potable reuse applications.

PubMed

Gerrity, Daniel; Arnold, Mayara; Dickenson, Eric; Moser, Duane; Sackett, Joshua D; Wert, Eric C

2018-05-15

Microbial community structure in the ozone-biofiltration systems of two drinking water and two wastewater treatment facilities was characterized using 16S rRNA gene sequencing. Collectively, these datasets enabled comparisons by facility, water type (drinking water, wastewater), pre-oxidation (ozonation, chlorination), media type (anthracite, activated carbon), media depth, and backwash dynamics. Proteobacteria was the most abundant phylum in drinking water filters, whereas Bacteroidetes, Chloroflexi, Firmicutes, and Planctomycetes were differentially abundant in wastewater filters. A positive correlation was observed between media depth and relative abundance of Cyanobacteria in drinking water filters, but there was only a slight increase in one alpha diversity metric with depth in the wastewater filters. Media type had a significant effect on beta but not alpha diversity in drinking water and wastewater filters. Pre-ozonation caused a significant decrease in alpha diversity in the wastewater filters, but the effect on beta diversity was not statistically significant. An evaluation of backwash dynamics resulted in two notable observations: (1) endosymbionts such as Neochlamydia and Legionella increased in relative abundance following backwashing and (2) nitrogen-fixing Bradyrhizobium dominated the microbial community in wastewater filters operated with infrequent backwashing. Bradyrhizobium is known to generate extracellular polymeric substances (EPS), which may adversely impact biofilter performance and effluent water quality. These findings have important implications for public health and the operation and resiliency of biofiltration systems. Copyright © 2018 Elsevier Ltd. All rights reserved.

Distribution and Diversity of Bacteria and Fungi Colonization in Stone Monuments Analyzed by High-Throughput Sequencing.

PubMed

Li, Qiang; Zhang, Bingjian; He, Zhang; Yang, Xiaoru

The historical and cultural heritage of Qingxing palace and Lingyin and Kaihua temple, located in Hangzhou of China, include a large number of exquisite Buddhist statues and ancient stone sculptures which date back to the Northern Song (960-1219 A.D.) and Qing dynasties (1636-1912 A.D.) and are considered to be some of the best examples of ancient stone sculpting techniques. They were added to the World Heritage List in 2011 because of their unique craftsmanship and importance to the study of ancient Chinese Buddhist culture. However, biodeterioration of the surface of the ancient Buddhist statues and white marble pillars not only severely impairs their aesthetic value but also alters their material structure and thermo-hygric properties. In this study, high-throughput sequencing was utilized to identify the microbial communities colonizing the stone monuments. The diversity and distribution of the microbial communities in six samples collected from three different environmental conditions with signs of deterioration were analyzed by means of bioinformatics software and diversity indices. In addition, the impact of environmental factors, including temperature, light intensity, air humidity, and the concentration of NO2 and SO2, on the microbial communities' diversity and distribution was evaluated. The results indicate that the presence of predominantly phototrophic microorganisms was correlated with light and humidity, while nitrifying bacteria and Thiobacillus were associated with NO2 and SO2 from air pollution.

Microbial community composition but not diversity changes along succession in arctic sand dunes.

PubMed

Poosakkannu, Anbu; Nissinen, Riitta; Männistö, Minna; Kytöviita, Minna-Maarit

2017-02-01

The generality of increasing diversity of fungi and bacteria across arctic sand dune succession was tested. Microbial communities were examined by high-throughput sequencing of 16S rRNA genes (bacteria) and internal transcribed spacer (ITS) regions (fungi). We studied four microbial compartments (inside leaf, inside root, rhizosphere and bulk soil) and characterized microbes associated with a single plant species (Deschampsia flexuosa) across two sand dune successional stages (early and late). Bacterial richness increased across succession in bulk soil and leaf endosphere. In contrast, soil fungal richness remained constant while root endosphere fungal richness increased across succession. There was, however, no significant difference in Shannon diversity indices between early and late successional stage in any compartment. There was a significant difference in the composition of microbial communities between early and late successional stage in all compartments, although the major microbial OTUs were shared between early and late successional stage. Co-occurrence network analysis revealed successional stage-specific microbial groups. There were more co-occurring modules in early successional stage than in late stage. Altogether, these results emphasize that succession strongly affects distribution of microbial species, but not microbial diversity in arctic sand dune ecosystem and that fungi and bacteria may not follow the same successional trajectories. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Microbial eukaryotic distributions and diversity patterns in a deep-sea methane seep ecosystem.

PubMed

Pasulka, Alexis L; Levin, Lisa A; Steele, Josh A; Case, David H; Landry, Michael R; Orphan, Victoria J

2016-09-01

Although chemosynthetic ecosystems are known to support diverse assemblages of microorganisms, the ecological and environmental factors that structure microbial eukaryotes (heterotrophic protists and fungi) are poorly characterized. In this study, we examined the geographic, geochemical and ecological factors that influence microbial eukaryotic composition and distribution patterns within Hydrate Ridge, a methane seep ecosystem off the coast of Oregon using a combination of high-throughput 18S rRNA tag sequencing, terminal restriction fragment length polymorphism fingerprinting, and cloning and sequencing of full-length 18S rRNA genes. Microbial eukaryotic composition and diversity varied as a function of substrate (carbonate versus sediment), activity (low activity versus active seep sites), sulfide concentration, and region (North versus South Hydrate Ridge). Sulfide concentration was correlated with changes in microbial eukaryotic composition and richness. This work also revealed the influence of oxygen content in the overlying water column and water depth on microbial eukaryotic composition and diversity, and identified distinct patterns from those previously observed for bacteria, archaea and macrofauna in methane seep ecosystems. Characterizing the structure of microbial eukaryotic communities in response to environmental variability is a key step towards understanding if and how microbial eukaryotes influence seep ecosystem structure and function. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Plant diversity does not buffer drought effects on early-stage litter mass loss rates and microbial properties.

PubMed

Vogel, Anja; Eisenhauer, Nico; Weigelt, Alexandra; Scherer-Lorenzen, Michael

2013-09-01

Human activities are decreasing biodiversity and changing the climate worldwide. Both global change drivers have been shown to affect ecosystem functioning, but they may also act in concert in a non-additive way. We studied early-stage litter mass loss rates and soil microbial properties (basal respiration and microbial biomass) during the summer season in response to plant species richness and summer drought in a large grassland biodiversity experiment, the Jena Experiment, Germany. In line with our expectations, decreasing plant diversity and summer drought decreased litter mass loss rates and soil microbial properties. In contrast to our hypotheses, however, this was only true for mass loss of standard litter (wheat straw) used in all plots, and not for plant community-specific litter mass loss. We found no interactive effects between global change drivers, that is, drought reduced litter mass loss rates and soil microbial properties irrespective of plant diversity. High mass loss rates of plant community-specific litter and low responsiveness to drought relative to the standard litter indicate that soil microbial communities were adapted to decomposing community-specific plant litter material including lower susceptibility to dry conditions during summer months. Moreover, higher microbial enzymatic diversity at high plant diversity may have caused elevated mass loss of standard litter. Our results indicate that plant diversity loss and summer drought independently impede soil processes. However, soil decomposer communities may be highly adapted to decomposing plant community-specific litter material, even in situations of environmental stress. Results of standard litter mass loss moreover suggest that decomposer communities under diverse plant communities are able to cope with a greater variety of plant inputs possibly making them less responsive to biotic changes. © 2013 John Wiley & Sons Ltd.

Community Structure of Lithotrophically-Driven Hydrothermal Microbial Mats from the Mariana Arc and Back-Arc

PubMed Central

Hager, Kevin W.; Fullerton, Heather; Butterfield, David A.; Moyer, Craig L.

2017-01-01

The Mariana region exhibits a rich array of hydrothermal venting conditions in a complex geological setting, which provides a natural laboratory to study the influence of local environmental conditions on microbial community structure as well as large-scale patterns in microbial biogeography. We used high-throughput amplicon sequencing of the bacterial small subunit (SSU) rRNA gene from 22 microbial mats collected from four hydrothermally active locations along the Mariana Arc and back-arc to explore the structure of lithotrophically-based microbial mat communities. The vent effluent was classified as iron- or sulfur-rich corresponding with two distinct community types, dominated by either Zetaproteobacteria or Epsilonproteobacteria, respectively. The Zetaproteobacterial-based communities had the highest richness and diversity, which supports the hypothesis that Zetaproteobacteria function as ecosystem engineers creating a physical habitat within a chemical environment promoting enhanced microbial diversity. Gammaproteobacteria were also high in abundance within the iron-dominated mats and some likely contribute to primary production. In addition, we also compare sampling scale, showing that bulk sampling of microbial mats yields higher diversity than micro-scale sampling. We present a comprehensive analysis and offer new insights into the community structure and diversity of lithotrophically-driven microbial mats from a hydrothermal region associated with high microbial biodiversity. Our study indicates an important functional role of for the Zetaproteobacteria altering the mat habitat and enhancing community interactions and complexity. PMID:28970817

A comparative analysis of microbial profile of Guinea fowl and chicken using metagenomic approach

PubMed Central

Bhogoju, Sarayu; Wang, Xiaofei; Darris, Carl; Kilonzo-Nthenge, Agnes

2018-01-01

Probiotics are live microbial feed supplements that promote growth and health to the host by minimizing non-essential and pathogenic microorganisms in the host’s gastrointestinal tract (GIT). The campaign to minimize excessive use of antibiotics in poultry production has necessitated development of probiotics with broad application in multiple poultry species. Design of such probiotics requires understanding of the diversity or similarity in microbial profiles among avian species of economic importance. Therefore, the objective of this research was to establish and compare the microbial profiles of the GIT of Guinea fowl and chicken and to establish the microbial diversity or similarity between the two avian species. A metagenomic approach consisting of the amplification and sequence analysis of the hypervariable regions V1-V9 of the 16S rRNA gene was used to identify the GIT microbes. Collectively, we detected more than 150 microbial families. The total number of microbial species detected in the chicken GIT was higher than that found in the Guinea Fowl GIT. Our studies also revealed phylogenetic diversity among the microbial species found in chicken and guinea fowl. The phylum Firmicutes was most abundant in both avian species whereas Phylum Actinobacteria was most abundant in chickens than Guinea fowls. The diversity of the microbial profiles found in broiler chickens and Guinea fowls suggest that the design of effective avian probiotics would require species specificity. PMID:29494648

Microbial responses to southward and northward Cambisol soil transplant

DOE PAGES

Wang, Mengmeng; Liu, Shanshan; Wang, Feng; ...

2015-10-26

We report that soil transplant serves as a proxy to simulate climate changes. Recently, we have shown that southward transplant of black soil and northward transplant of red soil altered soil microbial communities and biogeochemical variables. However, fundamental differences in soil types have prevented direct comparison between southward and northward transplants. To tackle it, herein we report an analysis of microbial communities of Cambisol soil in an agriculture field after 4 years of adaptation to southward and northward soil transplants over large transects. Analysis of bare fallow soils revealed concurrent increase in microbial functional diversity and coarse-scale taxonomic diversity atmore » both transplanted sites, as detected by GeoChip 3.0 and DGGE, respectively. Furthermore, a correlation between microbial functional diversity and taxonomic diversity was detected, which was masked in maize cropped soils. Mean annual temperature, soil moisture, and nitrate (NO 3¯-N) showed strong correlations with microbial communities. In addition, abundances of ammonium-oxidizing genes (amoA) and denitrification genes were correlated with nitrification capacity and NO 3¯-N contents, suggesting that microbial responses to soil transplant could alter microbe-mediated biogeochemical cycle at the ecosystem level.« less

Effects of spaceflight and simulated microgravity on microbial growth and secondary metabolism.

PubMed

Huang, Bing; Li, Dian-Geng; Huang, Ying; Liu, Chang-Ting

2018-05-14

Spaceflight and ground-based microgravity analog experiments have suggested that microgravity can affect microbial growth and metabolism. Although the effects of microgravity and its analogs on microorganisms have been studied for more than 50 years, plausible conflicting and diverse results have frequently been reported in different experiments, especially regarding microbial growth and secondary metabolism. Until now, only the responses of a few typical microbes to microgravity have been investigated; systematic studies of the genetic and phenotypic responses of these microorganisms to microgravity in space are still insufficient due to technological and logistical hurdles. The use of different test strains and secondary metabolites in these studies appears to have caused diverse and conflicting results. Moreover, subtle changes in the extracellular microenvironments around microbial cells play a key role in the diverse responses of microbial growth and secondary metabolisms. Therefore, "indirect" effects represent a reasonable pathway to explain the occurrence of these phenomena in microorganisms. This review summarizes current knowledge on the changes in microbial growth and secondary metabolism in response to spaceflight and its analogs and discusses the diverse and conflicting results. In addition, recommendations are given for future studies on the effects of microgravity in space on microbial growth and secondary metabolism.

Investigation of Microbial Diversity in Geothermal Hot Springs in Unkeshwar, India, Based on 16S rRNA Amplicon Metagenome Sequencing

PubMed Central

Mehetre, Gajanan T.; Paranjpe, Aditi; Dastager, Syed G.

2016-01-01

Microbial diversity in geothermal waters of the Unkeshwar hot springs in Maharashtra, India, was studied using 16S rRNA amplicon metagenomic sequencing. Taxonomic analysis revealed the presence of Bacteroidetes, Proteobacteria, Cyanobacteria, Actinobacteria, Archeae, and OD1 phyla. Metabolic function prediction analysis indicated a battery of biological information systems indicating rich and novel microbial diversity, with potential biotechnological applications in this niche. PMID:26950332

Microbial community structure and soil pH correspond to methane production in Arctic Alaska soils.

PubMed

Wagner, Robert; Zona, Donatella; Oechel, Walter; Lipson, David

2017-08-01

While there is no doubt that biogenic methane production in the Arctic is an important aspect of global methane emissions, the relative roles of microbial community characteristics and soil environmental conditions in controlling Arctic methane emissions remains uncertain. Here, relevant methane-cycling microbial groups were investigated at two remote Arctic sites with respect to soil potential methane production (PMP). Percent abundances of methanogens and iron-reducing bacteria correlated with increased PMP, while methanotrophs correlated with decreased PMP. Interestingly, α-diversity of the methanogens was positively correlated with PMP, while β-diversity was unrelated to PMP. The β-diversity of the entire microbial community, however, was related to PMP. Shannon diversity was a better correlate of PMP than Simpson diversity across analyses, while rarefied species richness was a weak correlate of PMP. These results demonstrate the following: first, soil pH and microbial community structure both probably control methane production in Arctic soils. Second, there may be high functional redundancy in the methanogens with regard to methane production. Third, iron-reducing bacteria co-occur with methanogens in Arctic soils, and iron-reduction-mediated effects on methanogenesis may be controlled by α- and β-diversity. And finally, species evenness and rare species abundances may be driving relationships between microbial groups, influencing Arctic methane production. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Microbial diversity and their roles in the vinegar fermentation process.

PubMed

Li, Sha; Li, Pan; Feng, Feng; Luo, Li-Xin

2015-06-01

Vinegar is one of the oldest acetic acid-diluted solution products in the world. It is produced from any fermentable sugary substrate by various fermentation methods. The final vinegar products possess unique functions, which are endowed with many kinds of compounds formed in the fermentation process. The quality of vinegar is determined by many factors, especially by the raw materials and microbial diversity involved in vinegar fermentation. Given that metabolic products from the fermenting strains are directly related to the quality of the final products of vinegar, the microbial diversity and features of the dominant strains involved in different fermentation stages should be analyzed to improve the strains and stabilize fermentation. Moreover, although numerous microbiological studies have been conducted to examine the process of vinegar fermentation, knowledge about microbial diversity and their roles involved in fermentation is still fragmentary and not systematic enough. Therefore, in this review, the dominant microorganism species involved in the stages of alcoholic fermentation and acetic acid fermentation of dissimilar vinegars were summarized. We also summarized various physicochemical properties and crucial compounds in disparate types of vinegar. Furthermore, the merits and drawbacks of vital fermentation methods were generalized. Finally, we described in detail the relationships among microbial diversity, raw materials, fermentation methods, physicochemical properties, compounds, functionality, and final quality of vinegar. The integration of this information can provide us a detailed map about the microbial diversity and function involved in vinegar fermentation.

Diet simplification selects for high gut microbial diversity and strong fermenting ability in high-altitude pikas.

PubMed

Li, Huan; Qu, Jiapeng; Li, Tongtong; Wirth, Stephan; Zhang, Yanming; Zhao, Xinquan; Li, Xiangzhen

2018-06-03

The gut microbiota in mammals plays a key role in host metabolism and adaptation. However, relatively little is known regarding to how the animals adapts to extreme environments through regulating gut microbial diversity and function. Here, we investigated the diet, gut microbiota, short-chain fatty acid (SCFA) profiles, and cellulolytic activity from two common pika (Ochotona spp.) species in China, including Plateau pika (Ochotona curzoniae) from the Qinghai-Tibet Plateau and Daurian pika (Ochotona daurica) from the Inner Mongolia Grassland. Despite a partial diet overlap, Plateau pikas harbored lower diet diversity than Daurian pikas. Some bacteria (e.g., Prevotella and Ruminococcus) associated with fiber degradation were enriched in Plateau pikas. They harbored higher gut microbial diversity, total SCFA concentration, and cellulolytic activity than Daurian pikas. Interestingly, cellulolytic activity was positively correlated with the gut microbial diversity and SCFAs. Gut microbial communities and SCFA profiles were segregated structurally between host species. PICRUSt metagenome predictions demonstrated that microbial genes involved in carbohydrate metabolism and energy metabolism were overrepresented in the gut microbiota of Plateau pikas. Our results demonstrate that Plateau pikas harbor a stronger fermenting ability for the plant-based diet than Daurian pikas via gut microbial fermentation. The enhanced ability for utilization of plant-based diets in Plateau pikas may be partly a kind of microbiota adaptation for more energy requirements in cold and hypoxic high-altitude environments.

Soil Microbiome Is More Heterogeneous in Organic Than in Conventional Farming System

PubMed Central

Lupatini, Manoeli; Korthals, Gerard W.; de Hollander, Mattias; Janssens, Thierry K. S.; Kuramae, Eiko E.

2017-01-01

Organic farming system and sustainable management of soil pathogens aim at reducing the use of agricultural chemicals in order to improve ecosystem health. Despite the essential role of microbial communities in agro-ecosystems, we still have limited understanding of the complex response of microbial diversity and composition to organic and conventional farming systems and to alternative methods for controlling plant pathogens. In this study we assessed the microbial community structure, diversity and richness using 16S rRNA gene next generation sequences and report that conventional and organic farming systems had major influence on soil microbial diversity and community composition while the effects of the soil health treatments (sustainable alternatives for chemical control) in both farming systems were of smaller magnitude. Organically managed system increased taxonomic and phylogenetic richness, diversity and heterogeneity of the soil microbiota when compared with conventional farming system. The composition of microbial communities, but not the diversity nor heterogeneity, were altered by soil health treatments. Soil health treatments exhibited an overrepresentation of specific microbial taxa which are known to be involved in soil suppressiveness to pathogens (plant-parasitic nematodes and soil-borne fungi). Our results provide a comprehensive survey on the response of microbial communities to different agricultural systems and to soil treatments for controlling plant pathogens and give novel insights to improve the sustainability of agro-ecosystems by means of beneficial microorganisms. PMID:28101080

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.

Integrating microbial diversity in soil carbon dynamic models parameters

NASA Astrophysics Data System (ADS)

Louis, Benjamin; Menasseri-Aubry, Safya; Leterme, Philippe; Maron, Pierre-Alain; Viaud, Valérie

2015-04-01

Faced with the numerous concerns about soil carbon dynamic, a large quantity of carbon dynamic models has been developed during the last century. These models are mainly in the form of deterministic compartment models with carbon fluxes between compartments represented by ordinary differential equations. Nowadays, lots of them consider the microbial biomass as a compartment of the soil organic matter (carbon quantity). But the amount of microbial carbon is rarely used in the differential equations of the models as a limiting factor. Additionally, microbial diversity and community composition are mostly missing, although last advances in soil microbial analytical methods during the two past decades have shown that these characteristics play also a significant role in soil carbon dynamic. As soil microorganisms are essential drivers of soil carbon dynamic, the question about explicitly integrating their role have become a key issue in soil carbon dynamic models development. Some interesting attempts can be found and are dominated by the incorporation of several compartments of different groups of microbial biomass in terms of functional traits and/or biogeochemical compositions to integrate microbial diversity. However, these models are basically heuristic models in the sense that they are used to test hypotheses through simulations. They have rarely been confronted to real data and thus cannot be used to predict realistic situations. The objective of this work was to empirically integrate microbial diversity in a simple model of carbon dynamic through statistical modelling of the model parameters. This work is based on available experimental results coming from a French National Research Agency program called DIMIMOS. Briefly, 13C-labelled wheat residue has been incorporated into soils with different pedological characteristics and land use history. Then, the soils have been incubated during 104 days and labelled and non-labelled CO2 fluxes have been measured at ten sampling time in order to follow the dynamic of residue and soil organic matter mineralization. Diversity, structure and composition of microbial communities have been characterized before incubation time. The dynamic of carbon fluxes through CO2 emissions has been modelled through a simple model. Using statistical tools, relations between parameters of the model and microbial diversity indexes and/or pedological characteristics have been developed and integrated to the model. First results show that global diversity has an impact on the models parameters. Moreover, larger fungi diversity seems to lead to larger parameters representing decomposition rates and/or carbon use efficiencies than bacterial diversity. Classically, pedological factors such as soil pH and texture must also be taken into account.

GeoChip-based analysis of microbial functional gene diversity in a landfill leachate-contaminated aquifer

USGS Publications Warehouse

Lu, Zhenmei; He, Zhili; Parisi, Victoria A.; Kang, Sanghoon; Deng, Ye; Van Nostrand, Joy D.; Masoner, Jason R.; Cozzarelli, Isabelle M.; Suflita, Joseph M.; Zhou, Jizhong

2012-01-01

The functional gene diversity and structure of microbial communities in a shallow landfill leachate-contaminated aquifer were assessed using a comprehensive functional gene array (GeoChip 3.0). Water samples were obtained from eight wells at the same aquifer depth immediately below a municipal landfill or along the predominant downgradient groundwater flowpath. Functional gene richness and diversity immediately below the landfill and the closest well were considerably lower than those in downgradient wells. Mantel tests and canonical correspondence analysis (CCA) suggested that various geochemical parameters had a significant impact on the subsurface microbial community structure. That is, leachate from the unlined landfill impacted the diversity, composition, structure, and functional potential of groundwater microbial communities as a function of groundwater pH, and concentrations of sulfate, ammonia, and dissolved organic carbon (DOC). Historical geochemical records indicate that all sampled wells chronically received leachate, and the increase in microbial diversity as a function of distance from the landfill is consistent with mitigation of the impact of leachate on the groundwater system by natural attenuation mechanisms.

Effects of plant diversity on microbial nitrogen and phosphorus dynamics in soil

NASA Astrophysics Data System (ADS)

Prommer, Judith; Braun, Judith; Daly, Amanda; Gorka, Stefan; Hu, Yuntao; Kaiser, Christina; Martin, Victoria; Meyerhofer, Werner; Walker, Tom W. N.; Wanek, Wolfgang; Wasner, Daniel; Wiesenbauer, Julia; Zezula, David; Zheng, Qing; Richter, Andreas

2017-04-01

There is a general consensus that plant diversity affects many ecosystem functions. One example of such an effect is the enhanced aboveground and belowground plant biomass production with increasing species richness, with implications for carbon and nutrient distribution in soil. The Jena Experiment (http://www.the-jena-experiment.de/), a grassland biodiversity experiment established in 2002 in Germany, comprises different levels of plant species richness and different numbers of plant functional groups. It provides the opportunity to examine how changes in biodiversity impact on microbially-mediated nutrient cycling processes. We here report on plant diversity and plant functional composition effects on growth and nitrogen and phosphorus transformation rates, including nitrogen use efficiency, of microbial communities. Microbial growth rates and microbial biomass were positively affected by increasing plant species richness. Amino acid and ammonium concentrations in soil were also positively affected by plant species richness, while phosphate concentrations in contrast were negatively affected. The cycling of organic N in soils (estimated as gross protein depolymerization rates) increased about threefold with plant diversity, while gross N and P mineralization were not significantly affected by either species or functional richness. Microbial nitrogen use efficiency did not respond to different levels of plant diversity but was very high (0.96 and 0.98) across all levels of plant species richness, demonstrating a low N availability for microbes. Taken together this indicates that soil microbial communities were able to meet the well-documented increase in plant N content with species richness, and also the higher N demand of the microbial community by increasing the recycling of organic N such as proteins. In fact, the microbial community even overcompensated the increased plant and microbial N demand, as evidenced by increased levels of free amino acids and ammonium in the soil solution at higher species richness. A possible explanation for increased organic nitrogen transformation rates is the increased microbial biomass, which has previously been related to higher quantity and variety of plant derived compounds that are available to the microbial communities at higher plant diversity. Given that this explanation is right, it is interesting to note that the additional (plant-derived) microbial biomass at higher species richness, did not translate in higher soil P mineralization rates or phosphate availability.

Endophyte Microbiome Diversity in Micropropagated Atriplex canescens and Atriplex torreyi var griffithsii

PubMed Central

Lucero, Mary E.; Unc, Adrian; Cooke, Peter; Dowd, Scot; Sun, Shulei

2011-01-01

Microbial diversity associated with micropropagated Atriplex species was assessed using microscopy, isolate culturing, and sequencing. Light, electron, and confocal microscopy revealed microbial cells in aseptically regenerated leaves and roots. Clone libraries and tag-encoded FLX amplicon pyrosequencing (TEFAP) analysis amplified sequences from callus homologous to diverse fungal and bacterial taxa. Culturing isolated some seed borne endophyte taxa which could be readily propagated apart from the host. Microbial cells were observed within biofilm-like residues associated with plant cell surfaces and intercellular spaces. Various universal primers amplified both plant and microbial sequences, with different primers revealing different patterns of fungal diversity. Bacterial and fungal TEFAP followed by alignment with sequences from curated databases revealed 7 bacterial and 17 ascomycete taxa in A. canescens, and 5 bacterial taxa in A. torreyi. Additional diversity was observed among isolates and clone libraries. Micropropagated Atriplex retains a complex, intimately associated microbiome which includes diverse strains well poised to interact in manners that influence host physiology. Microbiome analysis was facilitated by high throughput sequencing methods, but primer biases continue to limit recovery of diverse sequences from even moderately complex communities. PMID:21437280

Effects of mannan oligosaccharide and virginiamycin on the cecal microbial community and intestinal morphology of chickens raised under suboptimal conditions.

PubMed

Pourabedin, Mohsen; Xu, Zhengxin; Baurhoo, Bushansingh; Chevaux, Eric; Zhao, Xin

2014-05-01

There is an increasing movement against use of antibiotic growth promoters in animal feed. Prebiotic supplementation is a potential alternative to enhance the host's natural defense through modulation of gut microbiota. In the present study, the effect of mannan oligosaccharide (MOS) and virginiamycin (VIRG) on cecal microbial ecology and intestinal morphology of broiler chickens raised under suboptimal conditions was evaluated. MOS and VIRG induced different bacterial community structures, as revealed by denaturing gradient gel electrophoresis of 16S rDNA. The antibiotic treatment reduced cecal microbial diversity while the community equitability increased. A higher bacterial diversity was observed in the cecum of MOS-supplemented birds. Quantitative polymerase chain reaction results indicated that MOS changed the cecal microbiota in favor of the Firmicutes population but not the Bacteroidetes population. No difference was observed in total bacterial counts among treatments. MOS promoted the growth of Lactobacillus spp. and Bifidobacterium spp. in the cecum and increased villus height and goblet cell numbers in the ileum and jejunum. These results provide a deeper insight into the microbial ecological changes after supplementation of MOS prebiotic in poultry diets.

A communal catalogue reveals Earth’s multiscale microbial diversity

DOE PAGES

Thompson, Luke R.; Sanders, Jon G.; McDonald, Daniel; ...

2017-11-01

Our growing awareness of the importance and diversity of the microbial world contrasts starkly with our limited understanding of its fundamental structure. Despite remarkable advances in DNA sequence generation, a lack of standardized protocols and common analytical framework impede useful comparison between studies, hindering development of global inferences about microbial life on Earth. Here, we show that with coordinated protocols, exact microbial 16S rRNA gene sequences can be followed across scores of individual studies, revealing patterns of diversity, community structure, and life history strategy at a planetary scale. Using 27,751 crowdsourced environmental samples comprising more than 2.2 billion reads, wemore » find sharp divides between host-associated and free-living communities. We show that the distribution of taxonomic and sequence diversity follows consistent trends across samples types and along gradients of environmental parameters, highlighting some of the global evolutionary patterns and ecological principles that underpin Earth’s microbiome. Here, this dataset provides the most complete environmental survey of our microbial world to date, and serves as a growing reference to provide immediate global context to future microbial surveys.« less

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

Wang, Mengmeng; Liu, Shanshan; Wang, Feng

We report that soil transplant serves as a proxy to simulate climate changes. Recently, we have shown that southward transplant of black soil and northward transplant of red soil altered soil microbial communities and biogeochemical variables. However, fundamental differences in soil types have prevented direct comparison between southward and northward transplants. To tackle it, herein we report an analysis of microbial communities of Cambisol soil in an agriculture field after 4 years of adaptation to southward and northward soil transplants over large transects. Analysis of bare fallow soils revealed concurrent increase in microbial functional diversity and coarse-scale taxonomic diversity atmore » both transplanted sites, as detected by GeoChip 3.0 and DGGE, respectively. Furthermore, a correlation between microbial functional diversity and taxonomic diversity was detected, which was masked in maize cropped soils. Mean annual temperature, soil moisture, and nitrate (NO 3¯-N) showed strong correlations with microbial communities. In addition, abundances of ammonium-oxidizing genes (amoA) and denitrification genes were correlated with nitrification capacity and NO 3¯-N contents, suggesting that microbial responses to soil transplant could alter microbe-mediated biogeochemical cycle at the ecosystem level.« less

A communal catalogue reveals Earth’s multiscale microbial diversity

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

Thompson, Luke R.; Sanders, Jon G.; McDonald, Daniel

Our growing awareness of the importance and diversity of the microbial world contrasts starkly with our limited understanding of its fundamental structure. Despite remarkable advances in DNA sequence generation, a lack of standardized protocols and common analytical framework impede useful comparison between studies, hindering development of global inferences about microbial life on Earth. Here, we show that with coordinated protocols, exact microbial 16S rRNA gene sequences can be followed across scores of individual studies, revealing patterns of diversity, community structure, and life history strategy at a planetary scale. Using 27,751 crowdsourced environmental samples comprising more than 2.2 billion reads, wemore » find sharp divides between host-associated and free-living communities. We show that the distribution of taxonomic and sequence diversity follows consistent trends across samples types and along gradients of environmental parameters, highlighting some of the global evolutionary patterns and ecological principles that underpin Earth’s microbiome. Here, this dataset provides the most complete environmental survey of our microbial world to date, and serves as a growing reference to provide immediate global context to future microbial surveys.« less

Central role of the cell in microbial ecology.

PubMed

Zengler, Karsten

2009-12-01

Over the last few decades, advances in cultivation-independent methods have significantly contributed to our understanding of microbial diversity and community composition in the environment. At the same time, cultivation-dependent methods have thrived, and the growing number of organisms obtained thereby have allowed for detailed studies of their physiology and genetics. Still, most microorganisms are recalcitrant to cultivation. This review not only conveys current knowledge about different isolation and cultivation strategies but also discusses what implications can be drawn from pure culture work for studies in microbial ecology. Specifically, in the light of single-cell individuality and genome heterogeneity, it becomes important to evaluate population-wide measurements carefully. An overview of various approaches in microbial ecology is given, and the cell as a central unit for understanding processes on a community level is discussed.

State-of-the-art molecular approaches to elucidate the genetic inventory of spacecraft surfaces and associated environments

NASA Astrophysics Data System (ADS)

Venkateswaran, Kasthuri; La Duc, Myron; James; Osman, Shariff; Andersen, Gary; Huber, Julie; Sogin, Mitchell

The scientific literature teems with reports of microbial diversity from seemingly every niche imaginable, from deep within Antarctic ice to ocean-floor hydrothermal systems. The fields of applied microbiology and molecular biology have made enormous technological advancements over the past two decades, from the development of PCR-amplification of DNA to the forensic detection of what many consider to be "miniscule" amounts of blood and other such biomatter. Despite advances in the specificity and sensitivity of molecular biological technologies, the abilities to efficiently sample and extract nucleic acids from low-biomass matrices, and accurately describe the true microbial diversity housed in such samples, remain significant challenges. To minimize the likelihood of forward contamination of Mars, Europa, or any other extraterrestrial environment, significant effort is invested to ensure that environments in which spacecraft are assembled are maintained appropriately and kept as free of microbial contamination as possible. To this end, routine analyses, largely based on spore-counts and cultivation-based approaches, are carried out to validate the cleanliness of such surfaces. However, only by applying the most efficient and accurate molecular means of analysis can conclusions be drawn on the actual bioburden and microbial diversity associated with these environments. For any measure of sample-derived bioburden, a large portion is inevitably lost in sampling. Furthermore, a 90 Since the surface area of a spacecraft is fixed, it is not possible to simply increase sample size to improve yield. It is therefore critical to assure that current methods of purification of biomolecules sampled from this limited resource are 1) optimal for achieving total yield of biota present and 2) conserving of the true microbial diversity of the sampled environment. This project focuses on the development of capabilities to effectively and efficiently generate a genetic inventory of microbes present about the surfaces of spacecraft and associated clean-room facilities. This entails the evaluation and optimization of molecular-based strategies designed to assess microbial burden and diversity arising from samples of low biomass. Such strategies include conventional clone library analysis, DNA microarray screening, and V6-Tag Sequencing. The capabilities resulting from this work will enable NASA to establish genetic inventories of spacecraft, as recommended by the National Research Council, to better understand the risk of forward contamination.

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

PubMed

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

2014-01-01

The discovery and characterization of protist communities from diverse environments are crucial for understanding the overall evolutionary history of life on earth. However, major questions about the diversity, ecology, and evolutionary history of protists remain unanswered, notably because data obtained from natural protist communities, especially of heterotrophic species, remain limited. In this review, we discuss the challenges associated with "field protistology", defined here as the exploration, characterization, and interpretation of microbial eukaryotic diversity within the context of natural environments or field experiments, and provide suggestions to help fill this important gap in knowledge. We also argue that increased efforts in field studies that combine molecular and microscopical methods offer the most promising path toward (1) the discovery of new lineages that expand the tree of eukaryotes; (2) the recognition of novel evolutionary patterns and processes; (3) the untangling of ecological interactions and functions, and their roles in larger ecosystem processes; and (4) the evaluation of protist adaptations to a changing climate. © 2013 The Author(s) Journal of Eukaryotic Microbiology © 2013 International Society of Protistologists.

The effect of thermal stratification on microbial community diversity and structure in a temperate reservoir

NASA Astrophysics Data System (ADS)

Qu, Jiangqi; Jia, Chengxia; Zhao, Meng; Li, Wentong; Liu, Pan; Yang, Mu; Zhang, Qingjing

2018-02-01

Miyun reservoir is a typical temperate deep reservoir located in the northeast of Beijing, China. In order to explore the effect of thermal stratification on microbial community diversity, structure and its influencing environmental factors, stratified sampling at three sites was conducted during the summer period. Field observations indicate that the water temperature and dissolved oxygen concentrations dropped to 11.9 °C and 1.57 mg/L, respectively, leading to the development of anoxia in the hypolimnetic layer. The Illumina Miseq sequencing results showed that microbial communities from different thermal stratification showed obvious differences, the highest microbial diversity and richness in the hypolimnion samples. RDA ordination analysis suggested that the microbial communities in the epilimnion and metalimnion were mainly affected by water temperature, pH and dissolved oxygen, while total nitrogen was the key environmental factor which shaped the microbial structure in hypolimnion.

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

PubMed Central

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

2014-01-01

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

Plant traits determine the phylogenetic structure of arbuscular mycorrhizal fungal communities.

PubMed

López-García, Álvaro; Varela-Cervero, Sara; Vasar, Martti; Öpik, Maarja; Barea, José M; Azcón-Aguilar, Concepción

2017-12-01

Functional diversity in ecosystems has traditionally been studied using aboveground plant traits. Despite the known effect of plant traits on the microbial community composition, their effects on the microbial functional diversity are only starting to be assessed. In this study, the phylogenetic structure of arbuscular mycorrhizal (AM) fungal communities associated with plant species differing in life cycle and growth form, that is, plant life forms, was determined to unravel the effect of plant traits on the functional diversity of this fungal group. The results of the 454 pyrosequencing showed that the AM fungal community composition differed across plant life forms and this effect was dependent on the soil collection date. Plants with ruderal characteristics tended to associate with phylogenetically clustered AM fungal communities. By contrast, plants with resource-conservative traits associated with phylogenetically overdispersed AM fungal communities. Additionally, the soil collected in different seasons yielded AM fungal communities with different phylogenetic dispersion. In summary, we found that the phylogenetic structure, and hence the functional diversity, of AM fungal communities is dependent on plant traits. This finding adds value to the use of plant traits for the evaluation of belowground ecosystem diversity, functions and processes. © 2017 John Wiley & Sons Ltd.

A highly diverse, desert-like microbial biocenosis on solar panels in a Mediterranean city.

PubMed

Dorado-Morales, Pedro; Vilanova, Cristina; Peretó, Juli; Codoñer, Francisco M; Ramón, Daniel; Porcar, Manuel

2016-07-05

Microorganisms colonize a wide range of natural and artificial environments although there are hardly any data on the microbial ecology of one the most widespread man-made extreme structures: solar panels. Here we show that solar panels in a Mediterranean city (Valencia, Spain) harbor a highly diverse microbial community with more than 500 different species per panel, most of which belong to drought-, heat- and radiation-adapted bacterial genera, and sun-irradiation adapted epiphytic fungi. The taxonomic and functional profiles of this microbial community and the characterization of selected culturable bacteria reveal the existence of a diverse mesophilic microbial community on the panels' surface. This biocenosis proved to be more similar to the ones inhabiting deserts than to any human or urban microbial ecosystem. This unique microbial community shows different day/night proteomic profiles; it is dominated by reddish pigment- and sphingolipid-producers, and is adapted to withstand circadian cycles of high temperatures, desiccation and solar radiation.

A highly diverse, desert-like microbial biocenosis on solar panels in a Mediterranean city

PubMed Central

Dorado-Morales, Pedro; Vilanova, Cristina; Peretó, Juli; Codoñer, Francisco M.; Ramón, Daniel; Porcar, Manuel

2016-01-01

Microorganisms colonize a wide range of natural and artificial environments although there are hardly any data on the microbial ecology of one the most widespread man-made extreme structures: solar panels. Here we show that solar panels in a Mediterranean city (Valencia, Spain) harbor a highly diverse microbial community with more than 500 different species per panel, most of which belong to drought-, heat- and radiation-adapted bacterial genera, and sun-irradiation adapted epiphytic fungi. The taxonomic and functional profiles of this microbial community and the characterization of selected culturable bacteria reveal the existence of a diverse mesophilic microbial community on the panels’ surface. This biocenosis proved to be more similar to the ones inhabiting deserts than to any human or urban microbial ecosystem. This unique microbial community shows different day/night proteomic profiles; it is dominated by reddish pigment- and sphingolipid-producers, and is adapted to withstand circadian cycles of high temperatures, desiccation and solar radiation. PMID:27378552

Investigation of Microbial Diversity in Geothermal Hot Springs in Unkeshwar, India, Based on 16S rRNA Amplicon Metagenome Sequencing.

PubMed

Mehetre, Gajanan T; Paranjpe, Aditi; Dastager, Syed G; Dharne, Mahesh S

2016-02-25

Microbial diversity in geothermal waters of the Unkeshwar hot springs in Maharashtra, India, was studied using 16S rRNA amplicon metagenomic sequencing. Taxonomic analysis revealed the presence of Bacteroidetes, Proteobacteria, Cyanobacteria, Actinobacteria, Archeae, and OD1 phyla. Metabolic function prediction analysis indicated a battery of biological information systems indicating rich and novel microbial diversity, with potential biotechnological applications in this niche. Copyright © 2016 Mehetre et al.

Sniffing on microbes: diverse roles of microbial volatile organic compounds in plant health.

PubMed

Bitas, Vasileios; Kim, Hye-Seon; Bennett, Joan W; Kang, Seogchan

2013-08-01

Secreted proteins and metabolites play diverse and critical roles in organismal and organism-environment interactions. Volatile organic compounds (VOC) can travel far from the point of production through the atmosphere, porous soils, and liquid, making them ideal info-chemicals for mediating both short- and long-distance intercellular and organismal interactions. Critical ecological roles for animal- and plant-derived VOC in directing animal behaviors and for VOC as a language for plant-to-plant communication and regulators of various physiological processes have been well documented. Similarly, microbial VOC appear to be involved in antagonism, mutualism, intra- and interspecies regulation of cellular and developmental processes, and modification of their surrounding environments. However, the available knowledge of how microbial VOC affect other organisms is very limited. Evidence supporting diverse roles of microbial VOC with the focus on their impact on plant health is reviewed here. Given the vast diversity of microbes in nature and the critical importance of microbial communities associated with plants for their ecology and fitness, systematic exploration of microbial VOC and characterization of their biological functions and ecological roles will likely uncover novel mechanisms for controlling diverse biological processes critical to plant health and will also offer tangible practical benefits in addressing agricultural and environmental problems.

[Effect of long-term fertilization on microbial community functional diversity in black soil].

PubMed

Liu, Jing-xin; Chi, Feng-qin; Xu, Xiu-hong; Kuang, En-jun; Zhang, Jiu-ming; Su, Qing-rui; Zhou, Bao-ku

2015-10-01

In order to study the effects of long-term different fertilization on microbial community functional diversity in arable black. soil, we examined microbial metabolic activities in two soil la- yers (0-20 cm, 20-40 cm) under four treatments (CK, NPK, M, MNPK) from a 35-year continuous fertilization field at the Ministry of Agriculture Key Field Observation Station of Harbin Black Soil Ecology Environment using Biolog-ECO method. The results showed that: in the 0-20 cm soil layer, combined application of organic and inorganic fertilizer(MNPK) increased the rate of soil microbial carbon source utilization and community metabolism richness, diversity and dominance; In the 20-40 cm layer, these indices of the MNPK treatment was lower than that of the NPK treat- ment; while NPK treatment decreased soil microbial community metabolism evenness in both layers. Six groups of carbon sources used by soil microbes of all the treatments were different between the two soil layers, and the difference was significant among all treatments in each soil layer (P < 0.05) , while the variations among treatments were different in the two soil layers. Canonical correspondence analysis (CCA) showed that soil microbial community metabolic function of all the treatments was different between the two soil layers, and there was difference among all treatments in each soil layer, while the influences of soil nutrients on soil microbial community metabolic function of all treatments were similar in each soil layer. It was concluded that long-term different fertilization affected soil microbial community functional diversity in both tillage soil layer and down soil layers, and chemical fertilization alone had a larger influence on the microbial community functional diversity in the 20-40 cm layer.

Microbial diversity: a bonanza of phyla.

PubMed

Eme, Laura; Doolittle, W Ford

2015-03-16

Metagenomics and single-cell genomics are now the gold standard for exploring microbial diversity. A new study focusing on enigmatic ultra-small archaea greatly expands known genetic diversity within Archaea, and reports the first complete archaeal genomes reconstructed from metagenomic data only. Copyright © 2015 Elsevier Ltd. All rights reserved.

Microbial stowaways: Addressing oil spill impacts and the artificial reef effect on deep-sea microbiomes

NASA Astrophysics Data System (ADS)

Hamdan, L. J.; Salerno, J. L.; Blackwell, C. A.; Little, B.; McGown, C.; Fitzgerald, L. A.; Damour, M.

2016-02-01

Shipwrecks enhance macro-biological diversity in the deep ocean, but, to date, studies have not explored the reef effect on deep-sea microbiological diversity. This is an important concept to address in a restoration framework, as microbial biogeochemical function impacts recruitment and adhesion of higher trophic levels on artificial reefs. In addition, microbial biofilms influence the preservation of shipwrecks through biologically mediated corrosion. Oil and gas-related activities have potential to disrupt the base of the reef trophic web; therefore, bacterial diversity and gene function at six shipwrecks (3 steel-hulled; 3 wood-hulled) in the northern Gulf of Mexico was investigated as part of the GOM-SCHEMA (Shipwreck Corrosion, Hydrocarbon Exposure, Microbiology, and Archaeology) project. Sites were selected based on proximity to the Deepwater Horizon spill's subsurface plume, depth, hull type, and existing archaeological data. Classification of taxa in sediments adjacent to and at distance from wrecks, in water, and on experimental steel coupons was used to evaluate how the presence of shipwrecks and spill contaminants in the deep biosphere influenced diversity. At all sites, and in all sample types, Proteobacteria were most abundant. Biodiversity was highest in surface sediments and in coupon biofilms adjacent to two steel-hulled wrecks in the study (Halo and Anona) and decreased with sediment depth and distance from the wrecks. Sequences associated with the iron oxidizing Mariprofundus genus were elevated at steel-hulled sites, indicating wreck-specific environmental selection. Despite evidence of the reef effect on microbiomes, bacterial composition was structured primarily by proximity to the spill and secondarily by hull material at all sites. This study provides the first evidence of an artificial reef effect on deep-sea microbial communities and suggests that biodiversity and function of primary colonizers of shipwrecks may be impacted by the spill.

Microbial activity promotes carbon storage in temperate soils

NASA Astrophysics Data System (ADS)

Lange, Markus; Eisenhauer, Nico; Sierra, Carlos; Gleixner, Gerd

2014-05-01

Soils are one of the most important carbon sink and sources. Soils contain up to 3/4 of all terrestrial carbon. Beside physical aspects of soil properties (e.g. soil moisture and texture) plants play an important role in carbon sequestration. The positive effect of plant diversity on carbon storage is already known, though the underlying mechanisms remain still unclear. In the frame of the Jena Experiment, a long term biodiversity experiment, we are able to identify these processes. Nine years after an land use change from an arable field to managed grassland the mean soil carbon concentrations increased towards the concentrations of permanent meadows. The increase was positively linked to a plant diversity gradient. High diverse plant communities produce more biomass, which in turn results in higher amounts of litter inputs. The plant litter is transferred to the soil organic matter by the soil microbial community. However, higher plant diversity also causes changes in micro-climatic condition. For instance, more diverse plant communities have a more dense vegetation structure, which reduced the evaporation of soils surface and thus, increases soil moisture in the top layer. Higher inputs and higher soil moisture lead to an enlarged respiration of the soil microbial community. Most interestingly, the carbon storage in the Jena Experiment was much more related to microbial respiration than to plant root inputs. Moreover, using radiocarbon, we found a significant younger carbon age in soils of more diverse plant communities than in soils of lower diversity, indicating that more fresh carbon is integrated into the carbon pool. Putting these findings together, we could show, that the positive link between plant diversity and carbon storage is due to a higher microbial decomposition of plant litter, pointing out that carbon storage in soils is a function of the microbial community.

Microbial functional diversity covaries with permafrost thaw-induced environmental heterogeneity in tundra soil.

PubMed

Yuan, Mengting M; Zhang, Jin; Xue, Kai; Wu, Liyou; Deng, Ye; Deng, Jie; Hale, Lauren; Zhou, Xishu; He, Zhili; Yang, Yunfeng; Van Nostrand, Joy D; Schuur, Edward A G; Konstantinidis, Konstantinos T; Penton, Christopher R; Cole, James R; Tiedje, James M; Luo, Yiqi; Zhou, Jizhong

2018-01-01

Permafrost soil in high latitude tundra is one of the largest terrestrial carbon (C) stocks and is highly sensitive to climate warming. Understanding microbial responses to warming-induced environmental changes is critical to evaluating their influences on soil biogeochemical cycles. In this study, a functional gene array (i.e., geochip 4.2) was used to analyze the functional capacities of soil microbial communities collected from a naturally degrading permafrost region in Central Alaska. Varied thaw history was reported to be the main driver of soil and plant differences across a gradient of minimally, moderately, and extensively thawed sites. Compared with the minimally thawed site, the number of detected functional gene probes across the 15-65 cm depth profile at the moderately and extensively thawed sites decreased by 25% and 5%, while the community functional gene β-diversity increased by 34% and 45%, respectively, revealing decreased functional gene richness but increased community heterogeneity along the thaw progression. Particularly, the moderately thawed site contained microbial communities with the highest abundances of many genes involved in prokaryotic C degradation, ammonification, and nitrification processes, but lower abundances of fungal C decomposition and anaerobic-related genes. Significant correlations were observed between functional gene abundance and vascular plant primary productivity, suggesting that plant growth and species composition could be co-evolving traits together with microbial community composition. Altogether, this study reveals the complex responses of microbial functional potentials to thaw-related soil and plant changes and provides information on potential microbially mediated biogeochemical cycles in tundra ecosystems. © 2017 John Wiley & Sons Ltd.

Co-culturing of Fungal Strains Against Botrytis cinerea as a Model for the Induction of Chemical Diversity and Therapeutic Agents.

PubMed

Serrano, Rachel; González-Menéndez, Víctor; Rodríguez, Lorena; Martín, Jesús; Tormo, José R; Genilloud, Olga

2017-01-01

New fungal SMs (SMs) have been successfully described to be produced by means of in vitro -simulated microbial community interactions. Co-culturing of fungi has proved to be an efficient way to induce cell-cell interactions that can promote the activation of cryptic pathways, frequently silent when the strains are grown in laboratory conditions. Filamentous fungi represent one of the most diverse microbial groups known to produce bioactive natural products. Triggering the production of novel antifungal compounds in fungi could respond to the current needs to fight health compromising pathogens and provide new therapeutic solutions. In this study, we have selected the fungus Botrytis cinerea as a model to establish microbial interactions with a large set of fungal strains related to ecosystems where they can coexist with this phytopathogen, and to generate a collection of extracts, obtained from their antagonic microbial interactions and potentially containing new bioactive compounds. The antifungal specificity of the extracts containing compounds induced after B. cinerea interaction was determined against two human fungal pathogens ( Candida albicans and Aspergillus fumigatus ) and three phytopathogens ( Colletotrichum acutatum , Fusarium proliferatum , and Magnaporthe grisea ). In addition, their cytotoxicity was also evaluated against the human hepatocellular carcinoma cell line (HepG2). We have identified by LC-MS the production of a wide variety of known compounds induced from these fungal interactions, as well as novel molecules that support the potential of this approach to generate new chemical diversity and possible new therapeutic agents.

Wind and sunlight shape microbial diversity in surface waters of the North Pacific Subtropical Gyre

PubMed Central

Bryant, Jessica A; Aylward, Frank O; Eppley, John M; Karl, David M; Church, Matthew J; DeLong, Edward F

2016-01-01

Few microbial time-series studies have been conducted in open ocean habitats having low seasonal variability such as the North Pacific Subtropical Gyre (NPSG), where surface waters experience comparatively mild seasonal variation. To better describe microbial seasonal variability in this habitat, we analyzed rRNA amplicon and shotgun metagenomic data over two years at the Hawaii Ocean Time-series Station ALOHA. We postulated that this relatively stable habitat might reveal different environmental factors that influence planktonic microbial community diversity than those previously observed in more seasonally dynamic habitats. Unexpectedly, the data showed that microbial diversity at 25 m was positively correlated with average wind speed 3 to 10 days prior to sampling. In addition, microbial community composition at 25 m exhibited significant correlations with solar irradiance. Many bacterial groups whose relative abundances varied with solar radiation corresponded to taxa known to exhibit strong seasonality in other oceanic regions. Network co-correlation analysis of 25 m communities showed seasonal transitions in composition, and distinct successional cohorts of co-occurring phylogenetic groups. Similar network analyses of metagenomic data also indicated distinct seasonality in genes originating from cyanophage, and several bacterial clades including SAR116 and SAR324. At 500 m, microbial community diversity and composition did not vary significantly with any measured environmental parameters. The minimal seasonal variability in the NPSG facilitated detection of more subtle environmental influences, such as episodic wind variation, on surface water microbial diversity. Community composition in NPSG surface waters varied in response to solar irradiance, but less dramatically than reported in other ocean provinces. PMID:26645474

Wind and sunlight shape microbial diversity in surface waters of the North Pacific Subtropical Gyre.

PubMed

Bryant, Jessica A; Aylward, Frank O; Eppley, John M; Karl, David M; Church, Matthew J; DeLong, Edward F

2016-06-01

Few microbial time-series studies have been conducted in open ocean habitats having low seasonal variability such as the North Pacific Subtropical Gyre (NPSG), where surface waters experience comparatively mild seasonal variation. To better describe microbial seasonal variability in this habitat, we analyzed rRNA amplicon and shotgun metagenomic data over two years at the Hawaii Ocean Time-series Station ALOHA. We postulated that this relatively stable habitat might reveal different environmental factors that influence planktonic microbial community diversity than those previously observed in more seasonally dynamic habitats. Unexpectedly, the data showed that microbial diversity at 25 m was positively correlated with average wind speed 3 to 10 days prior to sampling. In addition, microbial community composition at 25 m exhibited significant correlations with solar irradiance. Many bacterial groups whose relative abundances varied with solar radiation corresponded to taxa known to exhibit strong seasonality in other oceanic regions. Network co-correlation analysis of 25 m communities showed seasonal transitions in composition, and distinct successional cohorts of co-occurring phylogenetic groups. Similar network analyses of metagenomic data also indicated distinct seasonality in genes originating from cyanophage, and several bacterial clades including SAR116 and SAR324. At 500 m, microbial community diversity and composition did not vary significantly with any measured environmental parameters. The minimal seasonal variability in the NPSG facilitated detection of more subtle environmental influences, such as episodic wind variation, on surface water microbial diversity. Community composition in NPSG surface waters varied in response to solar irradiance, but less dramatically than reported in other ocean provinces.

The Microbiome in Posttraumatic Stress Disorder and Trauma-Exposed Controls: An Exploratory Study.

PubMed

Hemmings, Sian M J; Malan-Müller, Stefanie; van den Heuvel, Leigh L; Demmitt, Brittany A; Stanislawski, Maggie A; Smith, David G; Bohr, Adam D; Stamper, Christopher E; Hyde, Embriette R; Morton, James T; Marotz, Clarisse A; Siebler, Philip H; Braspenning, Maarten; Van Criekinge, Wim; Hoisington, Andrew J; Brenner, Lisa A; Postolache, Teodor T; McQueen, Matthew B; Krauter, Kenneth S; Knight, Rob; Seedat, Soraya; Lowry, Christopher A

2017-10-01

Inadequate immunoregulation and elevated inflammation may be risk factors for posttraumatic stress disorder (PTSD), and microbial inputs are important determinants of immunoregulation; however, the association between the gut microbiota and PTSD is unknown. This study investigated the gut microbiome in a South African sample of PTSD-affected individuals and trauma-exposed (TE) controls to identify potential differences in microbial diversity or microbial community structure. The Clinician-Administered PTSD Scale for DSM-5 was used to diagnose PTSD according to Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition criteria. Microbial DNA was extracted from stool samples obtained from 18 individuals with PTSD and 12 TE control participants. Bacterial 16S ribosomal RNA gene V3/V4 amplicons were generated and sequenced. Microbial community structure, α-diversity, and β-diversity were analyzed; random forest analysis was used to identify associations between bacterial taxa and PTSD. There were no differences between PTSD and TE control groups in α- or β-diversity measures (e.g., α-diversity: Shannon index, t = 0.386, p = .70; β-diversity, on the basis of analysis of similarities: Bray-Curtis test statistic = -0.033, p = .70); however, random forest analysis highlighted three phyla as important to distinguish PTSD status: Actinobacteria, Lentisphaerae, and Verrucomicrobia. Decreased total abundance of these taxa was associated with higher Clinician-Administered PTSD Scale scores (r = -0.387, p = .035). In this exploratory study, measures of overall microbial diversity were similar among individuals with PTSD and TE controls; however, decreased total abundance of Actinobacteria, Lentisphaerae, and Verrucomicrobia was associated with PTSD status.

Deep Diversity: Novel Approach to Overcoming the PCR Bias Encountered During Environmental Analysis of Microbial Populations for Alpha-Diversity

NASA Technical Reports Server (NTRS)

Ramirez, Gustavo A; Vaishampayan, Parag A.

2011-01-01

Alpha-diversity studies are of crucial importance to environmental microbiologists. The polymerase chain reaction (PCR) method has been paramount for studies interrogating microbial environmental samples for taxon richness. Phylogenetic studies using this technique are based on the amplification and comparison of the 16S rRNA coding regions. PCR, due disproportionate distribution of microbial species in the environment, increasingly favors the amplification of the most predominant phylotypes with every subsequent reaction cycle. The genetic and chemical complexity of environmental samples are intrinsic factors that exacerbate an inherit bias in PCR-based quantitative and qualitative studies of microbial communities. We report that treatment of a genetically complex total genomic environmental DNA extract with Propidium Monoazide (PMA), a DNA intercalating molecule capable of forming a covalent cross-linkage to organic moieties upon light exposure, disproportionally inactivates predominant phylotypes and results in the exponential amplification of previously shadowed microbial ?-diversity quantified as a 19.5% increase in OUTs reported via phylogenetic screening using PhyloChip.

A Survey of Environmental Microbial Flora During Closed Chamber Studies

NASA Technical Reports Server (NTRS)

Ott, C. Mark; Groves, Theron O.; Bell-Robinson, Denetia; Pierson, Duane L.; Paloski, W. H. (Technical Monitor)

1999-01-01

Services, Inc. and NASA Johnson Space Center, Houston, TX As NASA prepares for long-term missions aboard the International Space Station and the eventual exploration of Mars, closed-environment chambers on Earth have become important test beds for systems evaluations. During 2 separate studies of a selfcontained ecosystem containing 4 crewmembers, microbial surveys of samples from 13 surface and 3 air sites were performed. Microbial concentration of samples from surface sites with frequent water contact (e.g., urinal, sink) did not indicate significantly higher levels of contamination than drier areas, though surface cleaning by the crew may have influenced this conclusion. Changes in bacterial diversity on surface sites implied that the number of transient species was high, suggesting movement by crew activities, aerosols, or both. A non-linear relationship between bacterial diversity and enumeration from surface samples indicated that a rapid increase occurred in the number of species as cell concentration increased to 5 CFU/sq cm. Above this concentration, the number of different bacterial species varied between 11 and 16. Airborne bacteria and fungi averaged only 160 and 1 CFU/m3, respectively. Microbial contamination of the potable water system primarily consisted of 3 species of Gram negative bacteria; however, after 60 days during one study, several species of Bacillus became the dominant flora. This study suggests that under these conditions, microbial contamination in the air and water was suppressed by the life-support systems, though contamination was possible. Conversely, the crew and their activities controlled microbial levels on surfaces. Understanding the factors that affect microbial control will improve the design of microbial testing both during space flight and in analogous Earth-based environments.

Microbial Fingerprints of Community Structure Correlate with Changes in Ecosystem Function Induced by Perturbing the Redox Environment

NASA Astrophysics Data System (ADS)

Mills, A. L.; Ford, R. M.; Vallino, J. J.; Herman, J. S.; Hornberger, G. M.

2001-12-01

Restoration of high-quality groundwater has been an elusive engineering goal. Consequently, natural microbially-mediated reactions are increasingly relied upon to degrade organic contaminants, including hydrocarbons and many synthetic compounds. Of concern is how the introduction of an organic chemical contaminant affects the indigenous microbial communities, the geochemistry of the aquifer, and the function of the ecosystem. The presence of functional redundancy in microbial communities suggests that recovery of the community after a disturbance such as a contamination event could easily result in a community that is similar in function to that which existed prior to the contamination, but which is compositionally quite different. To investigate the relationship between community structure and function we observed the response of a diverse microbial community obtained from raw sewage to a dynamic redox environment using an aerobic/anaerobic/aerobic cycle. To evaluate changes in community function CO2, pH, ammonium and nitrate levels were monitored. A phylogenetically-based DNA technique (tRFLP) was used to assess changes in microbial community structure. Principal component analysis of the tRFLP data revealed significant changes in the composition of the microbial community that correlated well with changes in community function. Results from our experiments will be discussed in the context of a metabolic model based the biogeochemistry of the system. The governing philosophy of this thermodynamically constrained metabolic model is that living systems synthesize and allocate cellular machinery in such a way as to "optimally" utilize available resources in the environment. The robustness of this optimization-based approach provides a powerful tool for studying relationships between microbial diversity and ecosystem function.

Diversity and community structure of marine microbes around the Benham Rise underwater plateau, northeastern Philippines.

PubMed

Gajigan, Andrian P; Yñiguez, Aletta T; Villanoy, Cesar L; San Diego-McGlone, Maria Lourdes; Jacinto, Gil S; Conaco, Cecilia

2018-01-01

Microbes are central to the structuring and functioning of marine ecosystems. Given the remarkable diversity of the ocean microbiome, uncovering marine microbial taxa remains a fundamental challenge in microbial ecology. However, there has been little effort, thus far, to describe the diversity of marine microorganisms in the region of high marine biodiversity around the Philippines. Here, we present data on the taxonomic diversity of bacteria and archaea in Benham Rise, Philippines, Western Pacific Ocean, using 16S V4 rRNA gene sequencing. The major bacterial and archaeal phyla identified in the Benham Rise are Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes, Marinimicrobia, Thaumarchaeota and, Euryarchaeota. The upper mesopelagic layer exhibited greater microbial diversity and richness compared to surface waters. Vertical zonation of the microbial community is evident and may be attributed to physical stratification of the water column acting as a dispersal barrier. Canonical Correspondence Analysis (CCA) recapitulated previously known associations of taxa and physicochemical parameters in the environment, such as the association of oligotrophic clades with low nutrient surface water and deep water clades that have the capacity to oxidize ammonia or nitrite at the upper mesopelagic layer. These findings provide foundational information on the diversity of marine microbes in Philippine waters. Further studies are warranted to gain a more comprehensive picture of microbial diversity within the region.

Diversity and community structure of marine microbes around the Benham Rise underwater plateau, northeastern Philippines

PubMed Central

Gajigan, Andrian P.; Yñiguez, Aletta T.; Villanoy, Cesar L.; San Diego-McGlone, Maria Lourdes; Jacinto, Gil S.

2018-01-01

Microbes are central to the structuring and functioning of marine ecosystems. Given the remarkable diversity of the ocean microbiome, uncovering marine microbial taxa remains a fundamental challenge in microbial ecology. However, there has been little effort, thus far, to describe the diversity of marine microorganisms in the region of high marine biodiversity around the Philippines. Here, we present data on the taxonomic diversity of bacteria and archaea in Benham Rise, Philippines, Western Pacific Ocean, using 16S V4 rRNA gene sequencing. The major bacterial and archaeal phyla identified in the Benham Rise are Proteobacteria, Cyanobacteria, Actinobacteria, Bacteroidetes, Marinimicrobia, Thaumarchaeota and, Euryarchaeota. The upper mesopelagic layer exhibited greater microbial diversity and richness compared to surface waters. Vertical zonation of the microbial community is evident and may be attributed to physical stratification of the water column acting as a dispersal barrier. Canonical Correspondence Analysis (CCA) recapitulated previously known associations of taxa and physicochemical parameters in the environment, such as the association of oligotrophic clades with low nutrient surface water and deep water clades that have the capacity to oxidize ammonia or nitrite at the upper mesopelagic layer. These findings provide foundational information on the diversity of marine microbes in Philippine waters. Further studies are warranted to gain a more comprehensive picture of microbial diversity within the region. PMID:29785352

Capturing the genetic makeup of the active microbiome in situ.

PubMed

Singer, Esther; Wagner, Michael; Woyke, Tanja

2017-09-01

More than any other technology, nucleic acid sequencing has enabled microbial ecology studies to be complemented with the data volumes necessary to capture the extent of microbial diversity and dynamics in a wide range of environments. In order to truly understand and predict environmental processes, however, the distinction between active, inactive and dead microbial cells is critical. Also, experimental designs need to be sensitive toward varying population complexity and activity, and temporal as well as spatial scales of process rates. There are a number of approaches, including single-cell techniques, which were designed to study in situ microbial activity and that have been successively coupled to nucleic acid sequencing. The exciting new discoveries regarding in situ microbial activity provide evidence that future microbial ecology studies will indispensably rely on techniques that specifically capture members of the microbiome active in the environment. Herein, we review those currently used activity-based approaches that can be directly linked to shotgun nucleic acid sequencing, evaluate their relevance to ecology studies, and discuss future directions.

Capturing the genetic makeup of the active microbiome in situ

PubMed Central

Singer, Esther; Wagner, Michael; Woyke, Tanja

2017-01-01

More than any other technology, nucleic acid sequencing has enabled microbial ecology studies to be complemented with the data volumes necessary to capture the extent of microbial diversity and dynamics in a wide range of environments. In order to truly understand and predict environmental processes, however, the distinction between active, inactive and dead microbial cells is critical. Also, experimental designs need to be sensitive toward varying population complexity and activity, and temporal as well as spatial scales of process rates. There are a number of approaches, including single-cell techniques, which were designed to study in situ microbial activity and that have been successively coupled to nucleic acid sequencing. The exciting new discoveries regarding in situ microbial activity provide evidence that future microbial ecology studies will indispensably rely on techniques that specifically capture members of the microbiome active in the environment. Herein, we review those currently used activity-based approaches that can be directly linked to shotgun nucleic acid sequencing, evaluate their relevance to ecology studies, and discuss future directions. PMID:28574490

Evaluating the Impact of DNA Extraction Method on the Representation of Human Oral Bacterial and Fungal Communities

PubMed Central

Biswas, Kristi; Taylor, Michael W.; Gear, Kim

2017-01-01

The application of high-throughput, next-generation sequencing technologies has greatly improved our understanding of the human oral microbiome. While deciphering this diverse microbial community using such approaches is more accurate than traditional culture-based methods, experimental bias introduced during critical steps such as DNA extraction may compromise the results obtained. Here, we systematically evaluate four commonly used microbial DNA extraction methods (MoBio PowerSoil® DNA Isolation Kit, QIAamp® DNA Mini Kit, Zymo Bacterial/Fungal DNA Mini PrepTM, phenol:chloroform-based DNA isolation) based on the following criteria: DNA quality and yield, and microbial community structure based on Illumina amplicon sequencing of the V3–V4 region of the 16S rRNA gene of bacteria and the internal transcribed spacer (ITS) 1 region of fungi. Our results indicate that DNA quality and yield varied significantly with DNA extraction method. Representation of bacterial genera in plaque and saliva samples did not significantly differ across DNA extraction methods and DNA extraction method showed no effect on the recovery of fungal genera from plaque. By contrast, fungal diversity from saliva was affected by DNA extraction method, suggesting that not all protocols are suitable to study the salivary mycobiome. PMID:28099455

Temporal dynamics of soil microbial communities under different moisture regimes: high-throughput sequencing and bioinformatics analysis

NASA Astrophysics Data System (ADS)

Semenov, Mikhail; Zhuravleva, Anna; Semenov, Vyacheslav; Yevdokimov, Ilya; Larionova, Alla

2017-04-01

Recent climate scenarios predict not only continued global warming but also an increased frequency and intensity of extreme climatic events such as strong changes in temperature and precipitation regimes. Microorganisms are well known to be more sensitive to changes in environmental conditions than to other soil chemical and physical parameters. In this study, we determined the shifts in soil microbial community structure as well as indicative taxa in soils under three moisture regimes using high-throughput Illumina sequencing and range of bioinformatics approaches for the assessment of sequence data. Incubation experiments were performed in soil-filled (Greyic Phaeozems Albic) rhizoboxes with maize and without plants. Three contrasting moisture regimes were being simulated: 1) optimal wetting (OW), a watering 2-3 times per week to maintain soil moisture of 20-25% by weight; 2) periodic wetting (PW), with alternating periods of wetting and drought; and 3) constant insufficient wetting (IW), while soil moisture of 12% by weight was permanently maintained. Sampled fresh soils were homogenized, and the total DNA of three replicates was extracted using the FastDNA® SPIN kit for Soil. DNA replicates were combined in a pooled sample and the DNA was used for PCR with specific primers for the 16S V3 and V4 regions. In order to compare variability between different samples and replicates within a single sample, some DNA replicates treated separately. The products were purified and submitted to Illumina MiSeq sequencing. Sequence data were evaluated by alpha-diversity (Chao1 and Shannon H' diversity indexes), beta-diversity (UniFrac and Bray-Curtis dissimilarity), heatmap, tagcloud, and plot-bar analyses using the MiSeq Reporter Metagenomics Workflow and R packages (phyloseq, vegan, tagcloud). Shannon index varied in a rather narrow range (4.4-4.9) with the lowest values for microbial communities under PW treatment. Chao1 index varied from 385 to 480, being a more flexible indicator than Shannon index. Chao1 had similar values for OW and IW communities, but alpha-diversity of microbial communities has sharply decreased under PW treatment. There was no visible difference in beta-diversity depending on sampling date and wetting regime, however, it could be possible to distinguish microbial communities in soils with maize and without plants. The presence of maize was acting as scattering agent, making microbial communities more distinguished. In all studied samples, the most dominant phyla were Proteobacteria, Firmicutes, Verrucomicrobia, Actinobacteria, and Acidobacteria. Chthoniobacter, Bacillus, Alicyclobacillus, Rhodoplanes, Cohnella, Kaistobacter, and Solibacter were the most abundant genera. Moreover, these genera were found as the most reactive and variable taxa in microbial community. Thus, DNA high-throughput sequencing revealed no dramatic shifts in bacterial community structure in soils under different moisture regimes. However, this technique allowed us to determine the effect of wetting regime and the presence of plants on soil microbial community which were adaptable to insufficient wetting, but lost diversity under periodic wetting. Furthermore, we detected the indicative taxa which dominate in microbial communities and at the same time strongly react to environmental changes.

Soil bacterial and fungal diversity differently correlated with soil biochemistry in alpine grassland ecosystems in response to environmental changes.

PubMed

Zhang, Yong; Dong, Shikui; Gao, Qingzhu; Liu, Shiliang; Ganjurjav, Hasbagan; Wang, Xuexia; Su, Xukun; Wu, Xiaoyu

2017-03-06

To understand effects of soil microbes on soil biochemistry in alpine grassland ecosystems under environmental changes, we explored relationships between soil microbial diversity and soil total nitrogen, organic carbon, available nitrogen and phosphorus, soil microbial biomass and soil enzyme activities in alpine meadow, alpine steppe and cultivated grassland on the Qinghai-Tibetan plateau under three-year warming, enhanced precipitation and yak overgrazing. Soil total nitrogen, organic carbon and NH 4 -N were little affected by overgrazing, warming or enhanced precipitation in three types of alpine grasslands. Soil microbial biomass carbon and phosphorus along with the sucrase and phosphatase activities were generally stable under different treatments. Soil NO 3 -N, available phosphorus, urease activity and microbial biomass nitrogen were increased by overgrazing in the cultivated grassland. Soil bacterial diversity was positively correlated with, while soil fungal diversity negatively with soil microbial biomass and enzyme activities. Soil bacterial diversity was negatively correlated with, while soil fungal diversity positively with soil available nutrients. Our findings indicated soil bacteria and fungi played different roles in affecting soil nutrients and microbiological activities that might provide an important implication to understand why soil biochemistry was generally stable under environmental changes in alpine grassland ecosystems.

Soil bacterial and fungal diversity differently correlated with soil biochemistry in alpine grassland ecosystems in response to environmental changes

NASA Astrophysics Data System (ADS)

Zhang, Yong; Dong, Shikui; Gao, Qingzhu; Liu, Shiliang; Ganjurjav, Hasbagan; Wang, Xuexia; Su, Xukun; Wu, Xiaoyu

2017-03-01

To understand effects of soil microbes on soil biochemistry in alpine grassland ecosystems under environmental changes, we explored relationships between soil microbial diversity and soil total nitrogen, organic carbon, available nitrogen and phosphorus, soil microbial biomass and soil enzyme activities in alpine meadow, alpine steppe and cultivated grassland on the Qinghai-Tibetan plateau under three-year warming, enhanced precipitation and yak overgrazing. Soil total nitrogen, organic carbon and NH4-N were little affected by overgrazing, warming or enhanced precipitation in three types of alpine grasslands. Soil microbial biomass carbon and phosphorus along with the sucrase and phosphatase activities were generally stable under different treatments. Soil NO3-N, available phosphorus, urease activity and microbial biomass nitrogen were increased by overgrazing in the cultivated grassland. Soil bacterial diversity was positively correlated with, while soil fungal diversity negatively with soil microbial biomass and enzyme activities. Soil bacterial diversity was negatively correlated with, while soil fungal diversity positively with soil available nutrients. Our findings indicated soil bacteria and fungi played different roles in affecting soil nutrients and microbiological activities that might provide an important implication to understand why soil biochemistry was generally stable under environmental changes in alpine grassland ecosystems.

Comparison of Bacterial Diversity in Azorean and Hawai’ian Lava Cave Microbial Mats

PubMed Central

MARSHALL HATHAWAY, JENNIFER J.; GARCIA, MATTHEW G.; BALASCH, MONICA MOYA; SPILDE, MICHAEL N.; STONE, FRED D.; DAPKEVICIUS, MARIA DE LURDES N. E.; AMORIM, ISABEL R.; GABRIEL, ROSALINA; BORGES, PAULO A. V.; NORTHUP, DIANA E.

2015-01-01

Worldwide, lava caves host colorful microbial mats. However, little is known about the diversity of these microorganisms, or what role they may play in the subsurface ecosystem. White and yellow microbial mats were collected from four lava caves each on the Azorean island of Terceira and the Big Island of Hawai’i, to compare the bacterial diversity found in lava caves from two widely separated archipelagos in two different oceans at different latitudes. Scanning electron microscopy of mat samples showed striking similarities between Terceira and Hawai’ian microbial morphologies. 16S rRNA gene clone libraries were constructed to determine the diversity within these lava caves. Fifteen bacterial phyla were found across the samples, with more Actinobacteria clones in Hawai’ian communities and greater numbers of Acidobacteria clones in Terceira communities. Bacterial diversity in the subsurface was correlated with a set of factors. Geographical location was the major contributor to differences in community composition (at the OTU level), together with differences in the amounts of organic carbon, nitrogen and copper available in the lava rock that forms the cave. These results reveal, for the first time, the similarity among the extensive bacterial diversity found in lava caves in two geographically separate locations and contribute to the current debate on the nature of microbial biogeography. PMID:26924866

Soil bacterial and fungal diversity differently correlated with soil biochemistry in alpine grassland ecosystems in response to environmental changes

PubMed Central

Zhang, Yong; Dong, Shikui; Gao, Qingzhu; Liu, Shiliang; Ganjurjav, Hasbagan; Wang, Xuexia; Su, Xukun; Wu, Xiaoyu

2017-01-01

To understand effects of soil microbes on soil biochemistry in alpine grassland ecosystems under environmental changes, we explored relationships between soil microbial diversity and soil total nitrogen, organic carbon, available nitrogen and phosphorus, soil microbial biomass and soil enzyme activities in alpine meadow, alpine steppe and cultivated grassland on the Qinghai-Tibetan plateau under three-year warming, enhanced precipitation and yak overgrazing. Soil total nitrogen, organic carbon and NH4-N were little affected by overgrazing, warming or enhanced precipitation in three types of alpine grasslands. Soil microbial biomass carbon and phosphorus along with the sucrase and phosphatase activities were generally stable under different treatments. Soil NO3-N, available phosphorus, urease activity and microbial biomass nitrogen were increased by overgrazing in the cultivated grassland. Soil bacterial diversity was positively correlated with, while soil fungal diversity negatively with soil microbial biomass and enzyme activities. Soil bacterial diversity was negatively correlated with, while soil fungal diversity positively with soil available nutrients. Our findings indicated soil bacteria and fungi played different roles in affecting soil nutrients and microbiological activities that might provide an important implication to understand why soil biochemistry was generally stable under environmental changes in alpine grassland ecosystems. PMID:28262753

Mineralogical Control on Microbial Diversity in a Weathered Granite?

NASA Astrophysics Data System (ADS)

Gleeson, D.; Clipson, N.; McDermott, F.

2003-12-01

Mineral transformation reactions and the behaviour of metals in rock and soils are affected not only by physicochemical parameters but also by biological factors, particularly by microbial activity. Microbes inhabit a wide range of niches in surface and subsurface environments, with mineral-microbe interactions being generally poorly understood. The focus of this study is to elucidate the role of microbial activity in the weathering of common silicate minerals in granitic rocks. A site in the Wicklow Mountains (Ireland) has been identified that consists of an outcrop surface of Caledonian (ca. 400 million years old) pegmatitic granite from which large intact crystals of variably weathered muscovite, plagioclase, K-feldspar and quartz were sampled, together with whole-rock granite. Culture-based microbial approaches have been widely used to profile microbial communities, particularly from copiotrophic environments, but it is now well established that for oligotrophic environments such as those that would be expected on weathering faces, perhaps less than 1% of microbial diversity can be profiled by cultural means. A number of culture-independent molecular based approaches have been developed to profile microbial diversity and community structure. These rely on successfully isolating environmental DNA from a given environment, followed by the use of the polymerase chain reaction (PCR) to amplify the typically small quantities of extracted DNA. Amplified DNA can then be analysed using cloning based approaches as well as community fingerprinting systems such as denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (TRFLP) and ribosomal intergenic spacer analysis (RISA). Community DNA was extracted and the intergenic spacer region (ITS) between small (16S) and large (23S) bacterial subunit rRNA genes was amplified. RISA fragments were then electrophoresed on a non-denaturing polyacrylamide gel. Banding patterns suggest that the bacterial population in whole rock, which contained approximately 30 separated bands (indicative of the number of bacterial ribotypes), is greater than muscovite (20), K-feldspar (15), and plagioclase feldspar (12) with quartz exhibiting the lowest number (6). These bands were excised from the gel for sequencing, allowing identification of the major populations. An automated approach was also used to assess similarity of bacterial communities present on each sample type, and this allowed for a statistical evaluation of bacterial diversity. Petrographic studies were carried out to assess mineral alteration effects. Scanning electron microscopy (SEM) was used to visualise in-situ bacterial cells.

Assessment of the impact of textile effluents on microbial diversity in Tirupur district, Tamil Nadu

NASA Astrophysics Data System (ADS)

Prabha, Shashi; Gogoi, Anindita; Mazumder, Payal; Ramanathan, AL.; Kumar, Manish

2017-09-01

The expedited advent of urbanization and industrialization for economic growth has adversely affected the biological diversity, which is one of the major concerns of the developing countries. Microbes play a crucial role in decontaminating polluted sites and degrades pollution load of textile effluent. The present study was based on identification of microbial diversity along the Noyaal river of Tirupur area. River water samples from industrial and non-industrial sites and effluent samples of before and after treatment were tested and it was found that microbial diversity was higher in the river water at the industrial site (Kasipalayam) as compared to the non-industrial site (Perur). Similarly, the microbial populations were found to be high in the untreated effluent as compared to the treated one by conventional treatment systems. Similar trends were observed for MBR treatment systems as well. Pseudomonas sp ., Achromobacter sp. (bacterial species) and Aspergillus fumigates (fungal species), found exclusively at the industrial site have been reported to possess decolorization potential of dye effluent, thus can be used for treatment of dye effluent. The comparison of different microbial communities from different dye wastewater sources and textile effluents was done, which showed that the microbes degrade dyestuffs, reduce toxicity of wastewaters, etc. From the study, it can be concluded that the microbial community helps to check on the pollutants and minimize their affect. Therefore, there is a need to understand the systematic variation in microbial diversity with the accumulation of pollution load through monitoring.

GeoChip-based analysis of the microbial community functional structures in simultaneous desulfurization and denitrification process.

PubMed

Yu, Hao; Chen, Chuan; Ma, Jincai; Liu, Wenzong; Zhou, Jizhong; Lee, Duu-Jong; Ren, Nanqi; Wang, Aijie

2014-07-01

The elemental sulfur (S°) recovery was evaluated in the presence of nitrate in two development models of simultaneous desulfurization and denitrification (SDD) process. At the loading rates of 0.9 kg S/(m³·day) for sulfide and 0.4 kg N/(m³·day) for nitrate, S° conversion rate was 91.1% in denitrifying sulfide removal (DSR) model which was higher than in integrated simultaneous desulfurization and denitrification (ISDD) model (25.6%). A comprehensive analysis of functional diversity, structure and metabolic potential of microbial communities was examined in two models by using functional gene array (GeoChip 2.0). GeoChip data indicated that diversity indices, community structure, and abundance of functional genes were distinct between two models. Diversity indices (Simpson's diversity index (1/D) and Shannon-Weaver index (H')) of all detected genes showed that with elevated influent loading rate, the functional diversity decreased in ISDD model but increased in DSR model. In contrast to ISDD model, the overall abundance of dsr genes was lower in DSR model, while some functional genes targeting from nitrate-reducing sulfide-oxidizing bacteria (NR-SOB), such as Thiobacillus denitrificans, Sulfurimonas denitrificans, and Paracoccus pantotrophus were more abundant in DSR model which were highly associated with the change of S(0) conversion rate obtained in two models. The results obtained in this study provide additional insights into the microbial metabolic mechanisms involved in ISDD and DSR models, which in turn will improve the overall performance of SDD process. Copyright © 2014. Published by Elsevier B.V.

Remote Sensing of a Manipulated Prairie Grassland Experiment to Predict Belowground Processes

NASA Astrophysics Data System (ADS)

Cavender-Bares, J.; Schweiger, A. K.; Hobbie, S. E.; Madritch, M. D.; Wang, Z.; Couture, J. J.; Gamon, J. A.; Townsend, P. A.

2017-12-01

Given the importance of plant biodiversity for providing the ecosystem functions and services on which humans depend, rapid and remote methods of monitoring plant biodiversity across large spatial extents and biological scales are increasingly critical. In North American prairie systems, the ecosystem benefits of diversity are a subject of ongoing investigation and relevance to policy. However, detecting belowground components of ecosystem biodiversity, composition and associated functions are not possible directly through remote sensing. Nevertheless, belowground components of diversity may be linked to aboveground components allowing indirect inferences. Here we test a series of hypotheses about how aboveground functional and chemical diversity and composition of plant communities drive belowground functions, including N mineralization, enzyme activity and microbial biomass, as well as microbial diversity and composition. We hypothesize that the quantity and chemical composition of aboveground inputs to soil drive belowground processes, including decomposition and microbial enzyme activity. We use plant spectra (400 nm to 2500 nm) measured at the leaf and airborne level to determine chemical and functional composition of leaves and canopies in a long-term grassland experiment where diversity is manipulated at the Cedar Creek Ecosystem Science Reserve. We then assess the extent to which belowground chemistry, microbial diversity and composition are predicted from aboveground plant diversity, biomass and chemical composition. We find strong associations between aboveground inputs and belowground enzyme activity and microbial biomass but only weak linkages between aboveground diversity and belowground diversity. We discuss the potential for such approaches and the caveats related to the spatial scale of measurements and spatial resolution of airborne detection.

From lithotroph- to organotroph-dominant: directional shift of microbial community in sulphidic tailings during phytostabilization

PubMed Central

Li, Xiaofang; Bond, Philip L.; Van Nostrand, Joy D.; Zhou, Jizhong; Huang, Longbin

2015-01-01

Engineering microbial diversity to enhance soil functions may improve the success of direct revegetation in sulphidic mine tailings. Therefore, it is essential to explore how remediation and initial plant establishment can alter microbial communities, and, which edaphic factors control these changes under field conditions. A long-term revegetation trial was established at a Pb-Zn-Cu tailings impoundment in northwest Queensland. The control and amended and/or revegetated treatments were sampled from the 3-year-old trial. In total, 24 samples were examined using pyrosequencing of 16S rRNA genes and various chemical properties. The results showed that the microbial diversity was positively controlled by soil soluble Si and negatively controlled by soluble S, total Fe and total As, implying that pyrite weathering posed a substantial stress on microbial development in the tailings. All treatments were dominated by typical extremophiles and lithotrophs, typically Truepera, Thiobacillus, Rubrobacter; significant increases in microbial diversity, biomass and frequency of organotrophic genera (typically Nocardioides and Altererythrobacter) were detected in the revegetated and amended treatment. We concluded that appropriate phytostabilization options have the potential to drive the microbial diversity and community structure in the tailings toward those of natural soils, however, inherent environmental stressors may limit such changes. PMID:26268667

Soil microbial diversity, site conditions, shelter forest land, saline water drip-irrigation, drift desert.

PubMed

Jin, Zhengzhong; Lei, Jiaqiang; Li, Shengyu; Xu, Xinwen

2013-10-01

Soil microbes in forest land are crucial to soil development in extreme areas. In this study, methods of conventional culture, PLFA and PCR-DGGE were utilized to analyze soil microbial quantity, fatty acids and microbial DNA segments of soils subjected to different site conditions in the Tarim Desert Highway forest land. The main results were as follows: the soil microbial amount, diversity indexes of fatty acid and DNA segment differed significantly among sites with different conditions (F < F0.05 ). Specifically, the values were higher in the middle and base of dunes than the top part of dunes and hardened flat sand, but all values for dunes were higher than for drift sand. Bacteria was dominant in the soil microbial community (>84%), followed by actinomycetes and then fungi (<0.05%). Vertical differences in the soil microbial diversity were insignificant at 0-35 cm. Correlation analysis indicated that the forest trees grew better as the soil microbial diversity index increased. Therefore, construction of the Tarim Desert Highway shelter-forest promoted soil biological development; however, for enhancing sand control efficiency and promoting sand development, we should consider the effects of site condition in the construction and regeneration of shelter-forest ecological projects. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Soil microbial diversity and activity linked to crop yield and quality in a dryland organic wheat production system

USDA-ARS?s Scientific Manuscript database

One of the primary goals of organic agriculture is increasing soil quality through the enhancement of soil biological diversity and activity. Greater soil microbial activity and diversity increase soil organic matter turnover and contribute to soil fertility, one of the main challenges associated wi...

Thermal processing of food reduces gut microbiota diversity of the host and triggers adaptation of the microbiota: evidence from two vertebrates.

PubMed

Zhang, Zhimin; Li, Dapeng

2018-05-31

Adoption of thermal processing of the diet drives human evolution and gut microbiota diversity changes in a dietary habit-dependent manner. However, whether thermal processing of food triggers gut microbial variation remains unknown. Herein, we compared the microbiota of non-thermally processed and thermally processed food (NF and TF) and investigated gut microbiota associated with NF and TF in catfish Silurus meridionalis and C57BL/6 mice to assess effects of thermal processing of food on gut microbiota and to further identify the differences in host responses. We found no differences in overall microbial composition and structure in the pairwise NF and TF, but identified differential microbial communities between food and gut. Both fish and mice fed TF had significantly lower gut microbial diversity than those fed NF. Moreover, thermal processing of food triggered the changes in their microbial communities. Comparative host studies further indicated host species determined gut microbial assemblies, even if fed with the same food. Fusobacteria was the most abundant phylum in the fish, and Bacteroidetes and Firmicutes dominated in the mice. Besides the consistent reduction of Bacteroidetes and the balanced Protebacteria, the response of other dominated gut microbiota in the fish and mice to TF was taxonomically opposite at the phylum level, and those further found at the genus level. Our results reveal that thermal processing of food strongly contributes to the reduction of gut microbial diversity and differentially drives microbial alterations in a host-dependent manner, suggesting specific adaptations of host-gut microbiota in vertebrates responding to thermal processing of food. These findings open a window of opportunity to understand the decline in gut microbial diversity and the community variation in human evolution and provide new insights into the host-specific microbial assemblages associated with the use of processing techniques in food preparation in humans and domesticated animals.

Available nitrogen is the key factor influencing soil microbial functional gene diversity in tropical rainforest.

PubMed

Cong, Jing; Liu, Xueduan; Lu, Hui; Xu, Han; Li, Yide; Deng, Ye; Li, Diqiang; Zhang, Yuguang

2015-08-20

Tropical rainforests cover over 50% of all known plant and animal species and provide a variety of key resources and ecosystem services to humans, largely mediated by metabolic activities of soil microbial communities. A deep analysis of soil microbial communities and their roles in ecological processes would improve our understanding on biogeochemical elemental cycles. However, soil microbial functional gene diversity in tropical rainforests and causative factors remain unclear. GeoChip, contained almost all of the key functional genes related to biogeochemical cycles, could be used as a specific and sensitive tool for studying microbial gene diversity and metabolic potential. In this study, soil microbial functional gene diversity in tropical rainforest was analyzed by using GeoChip technology. Gene categories detected in the tropical rainforest soils were related to different biogeochemical processes, such as carbon (C), nitrogen (N) and phosphorus (P) cycling. The relative abundance of genes related to C and P cycling detected mostly derived from the cultured bacteria. C degradation gene categories for substrates ranging from labile C to recalcitrant C were all detected, and gene abundances involved in many recalcitrant C degradation gene categories were significantly (P < 0.05) different among three sampling sites. The relative abundance of genes related to N cycling detected was significantly (P < 0.05) different, mostly derived from the uncultured bacteria. The gene categories related to ammonification had a high relative abundance. Both canonical correspondence analysis and multivariate regression tree analysis showed that soil available N was the most correlated with soil microbial functional gene structure. Overall high microbial functional gene diversity and different soil microbial metabolic potential for different biogeochemical processes were considered to exist in tropical rainforest. Soil available N could be the key factor in shaping the soil microbial functional gene structure and metabolic potential.

Strains, functions, and dynamics in the expanded Human Microbiome Project

PubMed Central

Lloyd-Price, Jason; Mahurkar, Anup; Rahnavard, Gholamali; Crabtree, Jonathan; Orvis, Joshua; Hall, A. Brantley; Brady, Arthur; Creasy, Heather H.; McCracken, Carrie; Giglio, Michelle G.; McDonald, Daniel; Franzosa, Eric A.; Knight, Rob; White, Owen; Huttenhower, Curtis

2018-01-01

Summary The characterization of baseline microbial and functional diversity in the human microbiome has enabled studies of microbiome-related disease, microbial population diversity, biogeography, and molecular function. The NIH Human Microbiome Project (HMP) has provided one of the broadest such characterizations to date. Here, we introduce an expanded second phase of the study, abbreviated HMP1-II, comprising 1,631 new metagenomic samples (2,355 total) targeting diverse body sites with multiple time points in 265 individuals. We applied updated profiling and assembly methods to these data to provide new characterizations of microbiome personalization. Strain identification revealed distinct subspecies clades specific to body sites; it also quantified species with phylogenetic diversity under-represented in isolate genomes. Body-wide functional profiling classified pathways into universal, human-enriched, and body site-enriched subsets. Finally, temporal analysis decomposed microbial variation into rapidly variable, moderately variable, and stable subsets. This study furthers our knowledge of baseline human microbial diversity, thus enabling an understanding of personalized microbiome function and dynamics. PMID:28953883

Diversity and Distribution of Prokaryotes within a Shallow-Water Pockmark Field.

PubMed

Giovannelli, Donato; d'Errico, Giuseppe; Fiorentino, Federica; Fattorini, Daniele; Regoli, Francesco; Angeletti, Lorenzo; Bakran-Petricioli, Tatjana; Vetriani, Costantino; Yücel, Mustafa; Taviani, Marco; Manini, Elena

2016-01-01

Pockmarks are crater-like depression on the seafloor associated with hydrocarbon ascent through muddy sediments in continental shelves around the world. In this study, we examine the diversity and distribution of benthic microbial communities at shallow-water pockmarks adjacent to the Middle Adriatic Ridge. We integrate microbial diversity data with characterization of local hydrocarbons concentrations and sediment geochemistry. Our results suggest these pockmarks are enriched in sedimentary hydrocarbons, and host a microbial community dominated by Bacteria, even in deeper sediment layers. Pockmark sediments showed higher prokaryotic abundance and biomass than surrounding sediments, potentially due to the increased availability of organic matter and higher concentrations of hydrocarbons linked to pockmark activity. Prokaryotic diversity analyses showed that the microbial communities of these shallow-water pockmarks are unique, and comprised phylotypes associated with the cycling of sulfur and nitrate compounds, as well as numerous know hydrocarbon degraders. Altogether, this study suggests that shallow-water pockmark habitats enhance the diversity of the benthic prokaryotic biosphere by providing specialized environmental niches.

Nodeomics: Pathogen Detection in Vertebrate Lymph Nodes Using Meta-Transcriptomics

USGS Publications Warehouse

Wittekindt, Nicola E.; Padhi, Abinash; Schuster, Stephan C.; Qi, Ji; Zhao, Fangqing; Tomsho, Lynn P.; Kasson, Lindsay R.; Packard, Michael; Cross, Paul C.; Poss, Mary

2010-01-01

The ongoing emergence of human infections originating from wildlife highlights the need for better knowledge of the microbial community in wildlife species where traditional diagnostic approaches are limited. Here we evaluate the microbial biota in healthy mule deer (Odocoileus hemionus) by analyses of lymph node meta-transcriptomes. cDNA libraries from five individuals and two pools of samples were prepared from retropharyngeal lymph node RNA enriched for polyadenylated RNA and sequenced using Roche-454 Life Sciences technology. Protein-coding and 16S ribosomal RNA (rRNA) sequences were taxonomically profiled using protein and rRNA specific databases. Representatives of all bacterial phyla were detected in the seven libraries based on protein-coding transcripts indicating that viable microbiota were present in lymph nodes. Residents of skin and rumen, and those ubiquitous in mule deer habitat dominated classifiable bacterial species. Based on detection of both rRNA and protein-coding transcripts, we identified two new proteobacterial species; a Helicobacter closely related to Helicobacter cetorum in the Helicobacter pylori/Helicobacter acinonychis complex and an Acinetobacter related to Acinetobacter schindleri. Among viruses, a novel gamma retrovirus and other members of the Poxviridae and Retroviridae were identified. We additionally evaluated bacterial diversity by amplicon sequencing the hypervariable V6 region of 16S rRNA and demonstrate that overall taxonomic diversity is higher with the meta-transcriptomic approach. These data provide the most complete picture to date of the microbial diversity within a wildlife host. Our research advances the use of meta-transcriptomics to study microbiota in wildlife tissues, which will facilitate detection of novel organisms with pathogenic potential to human and animals.

[Effects of outbreak and extinction of algal blooms on the microbial community structure in sediments of Chaohu Lake].

PubMed

Diao, Xiao-jun; Li, Yi-wei; Wang, Shu-guang

2015-01-01

Although impacts of algal bloom on the physicochemical and biological properties of water and sediment in many lakes have been largely studied, less attention is paid to the impact of outbreak and extinction of algal blooms on the microbial community structure in sediment. In this study, outbreak and extinction of algal blooms and their effects on the microbial community structure in sediment of Chaohu Lake were studied by PCR-DGGE method. The results showed that algal blooms formed between May 15 and June 20, sustained from June 20 to September 5, and then went into extinction. In the region without algal blooms, PCR-DGGE analysis showed that microbial species, Shannon-Wiener diversity index and Simpson dominance index changed slightly over time; moreover, the microbial community structure had high similarity during the whole study. Temperature may be the main factor affecting the fluctuation of the microbial community structure in this region. In the region with algal blooms, however, microbial species and Shannon-Wiener diversity index were higher during the formation and extinction of algal blooms and lower in the sustaining blooms stage than those in the region without algal blooms. But the Simpson dominance index showed the opposite trend over time. In addition, the microbial community structure had low similarity during the whole study. The results suggested that outbreak and extinction of algal blooms produced different effects on the microbial community structure and the dominant microbial species, which may be related to the variation of water properties caused by temperature and algal blooms. This study showed that outbreak and extinction of algal blooms caused different effects on microbes in lake sediment, and this is significantly important to deeply evaluate the effects of algal bloom on the aquatic ecosystem of the lake and effectively control algal blooms using sediment microbes.

Metagenomic assessment of the microbial diversity in ground pork products from markets in the North Central Region of South Korea.

PubMed

Koo, Ok-Kyung; Baker, Christopher A; Kim, Hyun-Jung; Park, Si Hong; Ricke, Steven C

2016-09-01

The purpose of this study was to characterize the microbial community in ground pork using molecular approaches. Forty six ground pork products were purchased from local stores in the north central area of South Korea. Aerobic plate counts varied 4.23 ± 5.14 × 10(5) CFU/g with the range between 5.00 × 10(3) and 1.85 × 10(6) CFU/g for ground pork samples. Four ground meat samples were further processed for metagenomic analysis. Pseudomonas species was the most relative abundant with a wide range occurring (1.72 to 77.7%) as part of the microbial genera in ground pork. Bacteria such as Carnobacterium, Yersinia, Photobacterium were also identified in ground pork. Despite the prominence of certain genera across all samples there was still extensive microbial diversity among ground pork products that originated from different slaughter houses and were processed in different markets. Such diversity indicates that designing interventions to extend shelf life may be hampered by the extensive variability in the microbial consortia associated with pork products. However, this diversity may be useful for developing microbial traceability signatures unique to a slaughter house or a particular market.

Elevated carbon dioxide accelerates the spatial turnover of soil microbial communities

DOE PAGES

Deng, Ye; He, Zhili; Xiong, Jinbo; ...

2015-10-23

Although elevated CO 2 (eCO 2) significantly affects the -diversity, composition, function, interaction and dynamics of soil microbial communities at the local scale, little is known about eCO 2 impacts on the geographic distribution of micro-organisms regionally or globally. Here, we examined the -diversity of 110 soil microbial communities across six free air CO 2 enrichment (FACE) experimental sites using a high-throughput functional gene array. The -diversity of soil microbial communities was significantly (P<0.05) correlated with geographic distance under both CO 2 conditions, but declined significantly (P<0.05) faster at eCO 2 with a slope of -0.0250 than at ambient COmore » 2 (aCO 2) with a slope of -0.0231 although it varied within each individual site, indicating that the spatial turnover rate of soil microbial communities was accelerated under eCO 2 at a larger geographic scale (e.g. regionally). Both distance and soil properties significantly (P<0.05) contributed to the observed microbial -diversity. Furthermore, this study provides new hypotheses for further understanding their assembly mechanisms that may be especially important as global CO 2 continues to increase.« less

Elevated carbon dioxide accelerates the spatial turnover of soil microbial communities

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

Deng, Ye; He, Zhili; Xiong, Jinbo

Although elevated CO 2 (eCO 2) significantly affects the -diversity, composition, function, interaction and dynamics of soil microbial communities at the local scale, little is known about eCO 2 impacts on the geographic distribution of micro-organisms regionally or globally. Here, we examined the -diversity of 110 soil microbial communities across six free air CO 2 enrichment (FACE) experimental sites using a high-throughput functional gene array. The -diversity of soil microbial communities was significantly (P<0.05) correlated with geographic distance under both CO 2 conditions, but declined significantly (P<0.05) faster at eCO 2 with a slope of -0.0250 than at ambient COmore » 2 (aCO 2) with a slope of -0.0231 although it varied within each individual site, indicating that the spatial turnover rate of soil microbial communities was accelerated under eCO 2 at a larger geographic scale (e.g. regionally). Both distance and soil properties significantly (P<0.05) contributed to the observed microbial -diversity. Furthermore, this study provides new hypotheses for further understanding their assembly mechanisms that may be especially important as global CO 2 continues to increase.« less

Can the composition of the intestinal microbiota predict the development of urinary tract infections?

PubMed

den Heijer, Casper Dj; Geerlings, Suzanne E; Prins, Jan M; Beerepoot, Mariëlle Aj; Stobberingh, Ellen E; Penders, John

2016-10-01

To evaluate whether intestinal microbiota predicts the development of new-onset urinary tract infections (UTIs) in postmenopausal women with prior recurrent UTIs (rUTIs). Fecal samples (n = 40) originated from women with rUTI who received 12 months' prophylaxis of either trimethoprim-sulfamethoxazole (TMP-SMX) or lactobacilli. Microbial composition was assessed by 16S rRNA pyrosequencing. At baseline, fecal microbiota of women with zero and more than or equal to four UTIs during follow-up showed no significant differences. Only TMP-SMX prophylaxis resulted in reduced microbial diversity. Microbial structure of two samples from the same woman showed limited relatedness. In postmenopausal women with rUTI, the intestinal microbiota was not predictive for new-onset UTIs. Only TMP-SMX, and not lactobacilli, prophylaxis had effects on the microbial composition. Data in ENA:PRJEB13868.

Preparing for the crewed Mars journey: microbiota dynamics in the confined Mars500 habitat during simulated Mars flight and landing.

PubMed

Schwendner, Petra; Mahnert, Alexander; Koskinen, Kaisa; Moissl-Eichinger, Christine; Barczyk, Simon; Wirth, Reinhard; Berg, Gabriele; Rettberg, Petra

2017-10-04

The Mars500 project was conceived as the first full duration simulation of a crewed return flight to Mars. For 520 days, six crew members lived confined in a specifically designed spacecraft mock-up. The herein described "MIcrobial ecology of Confined Habitats and humAn health" (MICHA) experiment was implemented to acquire comprehensive microbiota data from this unique, confined manned habitat, to retrieve important information on the occurring microbiota dynamics, the microbial load and diversity in the air and on various surfaces. In total, 360 samples from 20 (9 air, 11 surface) locations were taken at 18 time-points and processed by extensive cultivation, PhyloChip and next generation sequencing (NGS) of 16S rRNA gene amplicons. Cultivation assays revealed a Staphylococcus and Bacillus-dominated microbial community on various surfaces, with an average microbial load that did not exceed the allowed limits for ISS in-flight requirements indicating adequate maintenance of the facility. Areas with high human activity were identified as hotspots for microbial accumulation. Despite substantial fluctuation with respect to microbial diversity and abundance throughout the experiment, the location within the facility and the confinement duration were identified as factors significantly shaping the microbial diversity and composition, with the crew representing the main source for microbial dispersal. Opportunistic pathogens, stress-tolerant or potentially mobile element-bearing microorganisms were predicted to be prevalent throughout the confinement, while the overall microbial diversity dropped significantly over time. Our findings clearly indicate that under confined conditions, the community structure remains a highly dynamic system which adapts to the prevailing habitat and micro-conditions. Since a sterile environment is not achievable, these dynamics need to be monitored to avoid spreading of highly resistant or potentially pathogenic microorganisms and a potentially harmful decrease of microbial diversity. If necessary, countermeasures are required, to maintain a healthy, diverse balance of beneficial, neutral and opportunistic pathogenic microorganisms. Our results serve as an important data collection for (i) future risk estimations of crewed space flight, (ii) an optimized design and planning of a spacecraft mission and (iii) for the selection of appropriate microbial monitoring approaches and potential countermeasures, to ensure a microbiologically safe space-flight environment.

Heavy metal pollution decreases microbial abundance, diversity and activity within particle-size fractions of a paddy soil.

PubMed

Chen, Junhui; He, Feng; Zhang, Xuhui; Sun, Xuan; Zheng, Jufeng; Zheng, Jinwei

2014-01-01

Chemical and microbial characterisations of particle-size fractions (PSFs) from a rice paddy soil subjected to long-term heavy metal pollution (P) and nonpolluted (NP) soil were performed to investigate whether the distribution of heavy metals (Cd, Cu, Pb and Zn) regulates microbial community activity, abundance and diversity at the microenvironment scale. The soils were physically fractionated into coarse sand, fine sand, silt and clay fractions. Long-term heavy metal pollution notably decreased soil basal respiration (a measurement of the total activity of the soil microbial community) and microbial biomass carbon (MBC) across the fractions by 3-45% and 21-53%, respectively. The coarse sand fraction was more affected by pollution than the clay fraction and displayed a significantly lower MBC content and respiration and dehydrogenase activity compared with the nonpolluted soils. The abundances and diversities of bacteria were less affected within the PSFs under pollution. However, significant decreases in the abundances and diversities of fungi were noted, which may have strongly contributed to the decrease in MBC. Sequencing of denaturing gradient gel electrophoresis bands revealed that the groups Acidobacteria, Ascomycota and Chytridiomycota were clearly inhibited under pollution. Our findings suggest that long-term heavy metal pollution decreased the microbial biomass, activity and diversity in PSFs, particularly in the large-size fractions. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

A survey of microbial community diversity in marine sediments impacted by petroleum hydrocarbons from the Gulf of Mexico and Atlantic shorelines, Texas to Florida

USGS Publications Warehouse

Lisle, John T.; Stellick, Sarah H.

2011-01-01

Microbial community genomic DNA was extracted from sediment samples collected along the Gulf of Mexico and Atlantic coasts from Texas to Florida. Sample sites were identified as being ecologically sensitive and (or) as having high potential of being impacted by Macondo-1 (M-1) well oil from the Deepwater Horizon blowout. The diversity within the microbial communities associated with the collected sediments provides a baseline dataset to which microbial community-diversity data from impacted sites could be compared. To determine the microbial community diversity in the samples, genetic fingerprints were generated and compared. Specific sequences within the community genomic DNA were first amplified using the polymerase chain reaction (PCR) with a primer set that provides possible resolution to the species level. A second nested PCR was performed on the primary PCR products using a primer set on which a GC-clamp was attached to one of the primers. The nested PCR products were separated using denaturing-gradient gel electrophoresis (DGGE) that resolves the nested PCR products based on sequence dissimilarities (or similarities), forming a genomic fingerprint of the microbial diversity within the respective samples. Samples with similar fingerprints were grouped and compared to oil-fingerprint data from the same sites (Rosenbauer and others, 2011). The microbial community fingerprints were generally grouped into sites that had been shown to contain background concentrations of non-Deepwater Horizon oil. However, these groupings also included sites where no oil signature was detected. This report represents some of the first information on naturally occurring microbial communities in sediment from shorelines along the Gulf of Mexico and Atlantic coasts from Texas to Florida.

On the Use of Diversity Measures in Longitudinal Sequencing Studies of Microbial Communities.

PubMed

Wagner, Brandie D; Grunwald, Gary K; Zerbe, Gary O; Mikulich-Gilbertson, Susan K; Robertson, Charles E; Zemanick, Edith T; Harris, J Kirk

2018-01-01

Identification of the majority of organisms present in human-associated microbial communities is feasible with the advent of high throughput sequencing technology. As substantial variability in microbiota communities is seen across subjects, the use of longitudinal study designs is important to better understand variation of the microbiome within individual subjects. Complex study designs with longitudinal sample collection require analytic approaches to account for this additional source of variability. A common approach to assessing community changes is to evaluate the change in alpha diversity (the variety and abundance of organisms in a community) over time. However, there are several commonly used alpha diversity measures and the use of different measures can result in different estimates of magnitude of change and different inferences. It has recently been proposed that diversity profile curves are useful for clarifying these differences, and may provide a more complete picture of the community structure. However, it is unclear how to utilize these curves when interest is in evaluating changes in community structure over time. We propose the use of a bi-exponential function in a longitudinal model that accounts for repeated measures on each subject to compare diversity profiles over time. Furthermore, it is possible that no change in alpha diversity (single community/sample) may be observed despite the presence of a highly divergent community composition. Thus, it is also important to use a beta diversity measure (similarity between multiple communities/samples) that captures changes in community composition. Ecological methods developed to evaluate temporal turnover have currently only been applied to investigate changes of a single community over time. We illustrate the extension of this approach to multiple communities of interest (i.e., subjects) by modeling the beta diversity measure over time. With this approach, a rate of change in community composition is estimated. There is a need for the extension and development of analytic methods for longitudinal microbiota studies. In this paper, we discuss different approaches to model alpha and beta diversity indices in longitudinal microbiota studies and provide both a review of current approaches and a proposal for new methods.

On the Use of Diversity Measures in Longitudinal Sequencing Studies of Microbial Communities

PubMed Central

Wagner, Brandie D.; Grunwald, Gary K.; Zerbe, Gary O.; Mikulich-Gilbertson, Susan K.; Robertson, Charles E.; Zemanick, Edith T.; Harris, J. Kirk

2018-01-01

Identification of the majority of organisms present in human-associated microbial communities is feasible with the advent of high throughput sequencing technology. As substantial variability in microbiota communities is seen across subjects, the use of longitudinal study designs is important to better understand variation of the microbiome within individual subjects. Complex study designs with longitudinal sample collection require analytic approaches to account for this additional source of variability. A common approach to assessing community changes is to evaluate the change in alpha diversity (the variety and abundance of organisms in a community) over time. However, there are several commonly used alpha diversity measures and the use of different measures can result in different estimates of magnitude of change and different inferences. It has recently been proposed that diversity profile curves are useful for clarifying these differences, and may provide a more complete picture of the community structure. However, it is unclear how to utilize these curves when interest is in evaluating changes in community structure over time. We propose the use of a bi-exponential function in a longitudinal model that accounts for repeated measures on each subject to compare diversity profiles over time. Furthermore, it is possible that no change in alpha diversity (single community/sample) may be observed despite the presence of a highly divergent community composition. Thus, it is also important to use a beta diversity measure (similarity between multiple communities/samples) that captures changes in community composition. Ecological methods developed to evaluate temporal turnover have currently only been applied to investigate changes of a single community over time. We illustrate the extension of this approach to multiple communities of interest (i.e., subjects) by modeling the beta diversity measure over time. With this approach, a rate of change in community composition is estimated. There is a need for the extension and development of analytic methods for longitudinal microbiota studies. In this paper, we discuss different approaches to model alpha and beta diversity indices in longitudinal microbiota studies and provide both a review of current approaches and a proposal for new methods. PMID:29872428

Evaluation of Microbial Diversity in Wetland through Polymerase Chain Reaction (PCR) and Restriction Fragment Length Polymorphism (RFLP)

DTIC Science & Technology

2006-06-01

51 Appendix C. Promega Restriction Digest Protocol ....................................................53...Rsa1 Restriction Digest Results............................................................................180 9. DNA Base Pair Comparison...particular restriction endonuclease, the length of the fragments produced will differ when the DNA is digested with a restriction enzyme (Edwards

Genomic and metagenomic analysis of antibiotic resistance in dairy animals

USDA-ARS?s Scientific Manuscript database

The extent to which carriage of antibiotic resistant bacteria in food animals is responsible for the burden of antibiotic resistance in human infections is currently not well known. Thus, there is a need to further evaluate the genomic diversity of multidrug resistant (MDR) bacteria and the microbi...

Performance of Anaerobic Biotrickling Filter and Its Microbial Diversity for the Removal of Stripped Disinfection By-products

EPA Science Inventory

The objective of this research was to evaluate the biodegradation of chloroform by using biotrickling filter (BTF) and determining the dominant bacteria responsible for the degradation. The research was conducted in three phases under anaerobic condition, namely, in the presence ...

Exometabolite niche partitioning among sympatric soil bacteria

DOE PAGES

Baran, Richard; Brodie, Eoin L.; Mayberry-Lewis, Jazmine; ...

2015-09-22

Soils are arguably the most microbially diverse ecosystems. Physicochemical properties have been associated with the maintenance of this diversity. Yet, the role of microbial substrate specialization is largely unexplored since substrate utilization studies have focused on simple substrates, not the complex mixtures representative of the soil environment. Here we examine the exometabolite composition of desert biological soil crusts (biocrusts) and the substrate preferences of seven biocrust isolates. The biocrust's main primary producer releases a diverse array of metabolites, and isolates of physically associated taxa use unique subsets of the complex metabolite pool. Individual isolates use only 13-26% of available metabolites,more » with only 2 out of 470 used by all and 40% not used by any. An extension of this approach to a mesophilic soil environment also reveals high levels of microbial substrate specialization. In conclusion, these results suggest that exometabolite niche partitioning may be an important factor in the maintenance of microbial diversity.« less

Exometabolite niche partitioning among sympatric soil bacteria

PubMed Central

Baran, Richard; Brodie, Eoin L.; Mayberry-Lewis, Jazmine; Hummel, Eric; Da Rocha, Ulisses Nunes; Chakraborty, Romy; Bowen, Benjamin P.; Karaoz, Ulas; Cadillo-Quiroz, Hinsby; Garcia-Pichel, Ferran; Northen, Trent R.

2015-01-01

Soils are arguably the most microbially diverse ecosystems. Physicochemical properties have been associated with the maintenance of this diversity. Yet, the role of microbial substrate specialization is largely unexplored since substrate utilization studies have focused on simple substrates, not the complex mixtures representative of the soil environment. Here we examine the exometabolite composition of desert biological soil crusts (biocrusts) and the substrate preferences of seven biocrust isolates. The biocrust's main primary producer releases a diverse array of metabolites, and isolates of physically associated taxa use unique subsets of the complex metabolite pool. Individual isolates use only 13−26% of available metabolites, with only 2 out of 470 used by all and 40% not used by any. An extension of this approach to a mesophilic soil environment also reveals high levels of microbial substrate specialization. These results suggest that exometabolite niche partitioning may be an important factor in the maintenance of microbial diversity. PMID:26392107

Culture-independent phylogenetic analysis of the microbial community in industrial sugarcane bagasse feedstock piles.

PubMed

Rattanachomsri, Ukrit; Kanokratana, Pattanop; Eurwilaichitr, Lily; Igarashi, Yasuo; Champreda, Verawat

2011-01-01

Sugarcane bagasse is an important lignocellulosic by-product with potential for conversion to biofuels and chemicals in biorefinery. As a step towards an understanding of microbial diversity and the processes existing in bagasse collection sites, the microbial community in industrial bagasse feedstock piles was investigated. Molecular biodiversity analysis of 16S rDNA sequences revealed the presence of a complex bacterial community. A diverse group of mainly aerobic and facultative anaerobic bacteria was identified reflecting the aerobic and high temperature microenvironmental conditions under the pile surface. The major bacterial taxa present were identified as Firmicutes, Alpha- and Gammaproteobacteria, Acidobacteria, Bacteroidetes, and Actinobacteria. Analysis of the eukaryotic microbial assemblage based on an internal transcribed spacer revealed the predominance of diverse cellulolytic and hemicellulolytic ascomycota. A microbial interaction model is proposed, focusing on lignocellulose degradation and methane metabolism. The insights into the microbial community in this study provide a basis for efficient utilization of bagasse in lignocellulosic biomass-based industries.

Stochastic Community Assembly: Does It Matter in Microbial Ecology?

PubMed

Zhou, Jizhong; Ning, Daliang

2017-12-01

Understanding the mechanisms controlling community diversity, functions, succession, and biogeography is a central, but poorly understood, topic in ecology, particularly in microbial ecology. Although stochastic processes are believed to play nonnegligible roles in shaping community structure, their importance relative to deterministic processes is hotly debated. The importance of ecological stochasticity in shaping microbial community structure is far less appreciated. Some of the main reasons for such heavy debates are the difficulty in defining stochasticity and the diverse methods used for delineating stochasticity. Here, we provide a critical review and synthesis of data from the most recent studies on stochastic community assembly in microbial ecology. We then describe both stochastic and deterministic components embedded in various ecological processes, including selection, dispersal, diversification, and drift. We also describe different approaches for inferring stochasticity from observational diversity patterns and highlight experimental approaches for delineating ecological stochasticity in microbial communities. In addition, we highlight research challenges, gaps, and future directions for microbial community assembly research. Copyright © 2017 American Society for Microbiology.

Silver nanoparticles uptake by salt marsh plants - Implications for phytoremediation processes and effects in microbial community dynamics.

PubMed

Fernandes, Joana P; Mucha, Ana P; Francisco, Telmo; Gomes, Carlos Rocha; Almeida, C Marisa R

2017-06-15

This study investigated the uptake of silver nanoparticles (AgNPs) by a salt marsh plant, Phragmites australis, as well as AgNPs effects on rhizospheric microbial community, evaluating the implications for phytoremediation processes. Experiments were carried out with elutriate solution doped with Ag, either in ionic form or in NP form. Metal uptake was evaluated in plant tissues, elutriate solutions and sediments (by AAS) and microbial community was characterized in terms of bacterial community structure (evaluated by ARISA). Results showed Ag accumulation but only in plant belowground tissues and only in the absence of rhizosediment, the presence of sediment reducing Ag availability. But in plant roots Ag accumulation was higher when Ag was in NP form. Multivariate analysis of ARISA profiles showed significant effect of the absence/presence of Ag either in ionic or NP form on microbial community structure, although without significant differences among bacterial richness and diversity. Overall, P. australis can be useful for phytoremediation of medium contaminated with Ag, including with AgNPs. However, the presence of Ag in either forms affected the microbial community structure, which may cause disturbances in ecosystems function and compromise phytoremediation processes. Such considerations need to be address regarding environmental management strategies applied to the very important estuarine areas. The form in which the metal was added affected metal uptake by Phragmites australis and rhizosediment microbial community structure, which can affect phytoremediation. Copyright © 2017 Elsevier Ltd. All rights reserved.

The role of macrobiota in structuring microbial communities along rocky shores

DOE PAGES

Pfister, Catherine A.; Gilbert, Jack A.; Gibbons, Sean M.

2014-10-16

Rocky shore microbial diversity presents an excellent system to test for microbial habitat specificity or generality, enabling us to decipher how common macrobiota shape microbial community structure. At two coastal locations in the northeast Pacific Ocean, we show that microbial composition was significantly different between inert surfaces, the biogenic surfaces that included rocky shore animals and an alga, and the water column plankton. While all sampled entities had a core of common OTUs, rare OTUs drove differences among biotic and abiotic substrates. For the mussel Mytilus californianus, the shell surface harbored greater alpha diversity compared to internal tissues of themore » gill and siphon. Strikingly, a 7-year experimental removal of this mussel from tidepools did not significantly alter the microbial community structure of microbes associated with inert surfaces when compared with unmanipulated tidepools. However, bacterial taxa associated with nitrate reduction had greater relative abundance with mussels present, suggesting an impact of increased animal-derived nitrogen on a subset of microbial metabolism. Because the presence of mussels did not affect the structure and diversity of the microbial community on adjacent inert substrates, microbes in this rocky shore environment may be predominantly affected through direct physical association with macrobiota.« less

The role of macrobiota in structuring microbial communities along rocky shores

PubMed Central

Gilbert, Jack A.; Gibbons, Sean M.

2014-01-01

Rocky shore microbial diversity presents an excellent system to test for microbial habitat specificity or generality, enabling us to decipher how common macrobiota shape microbial community structure. At two coastal locations in the northeast Pacific Ocean, we show that microbial composition was significantly different between inert surfaces, the biogenic surfaces that included rocky shore animals and an alga, and the water column plankton. While all sampled entities had a core of common OTUs, rare OTUs drove differences among biotic and abiotic substrates. For the mussel Mytilus californianus, the shell surface harbored greater alpha diversity compared to internal tissues of the gill and siphon. Strikingly, a 7-year experimental removal of this mussel from tidepools did not significantly alter the microbial community structure of microbes associated with inert surfaces when compared with unmanipulated tidepools. However, bacterial taxa associated with nitrate reduction had greater relative abundance with mussels present, suggesting an impact of increased animal-derived nitrogen on a subset of microbial metabolism. Because the presence of mussels did not affect the structure and diversity of the microbial community on adjacent inert substrates, microbes in this rocky shore environment may be predominantly affected through direct physical association with macrobiota. PMID:25337459

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

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

Ecologists studying microbial life in the environment have recognized the enormous complexity of microbial diversity for more than a decade (Whitman et al. 1998). The development of a variety of culture-independent methods, many of them coupled with high-throughput DNA sequencing, has allowed this diversity to be explored in ever greater detail (Handelsman 2004; Harris et al. 2004; Hugenholtz et al. 1998; Moreira and Lopez-Garcia 2002; Rappe and Giovannoni 2003). Despite the widespread application of these new techniques to the characterization of uncultivated microbes and microbial communities in the environment, their application to human health and disease has lagged behind. Becausemore » these techniques now allow not only cataloging of microbial diversity, but also insight into microbial functions, it is time for clinical microbiologists to apply these tools to the microbial communities that abound on and within us, in what has been aptly called ''the second Human Genome Project'' (Relman and Falkow 2001). In this review we will discuss the sequence-based methods for microbial analysis that are currently available and their application to identify novel human pathogens, improve diagnosis and treatment of known infectious diseases, and finally to advance understanding of our relationship with microbial communities that normally reside in and on the human body.« less

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

USGS Publications Warehouse

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

2011-01-01

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

An Exercise to Demonstrate Soil Microbial Diversity in Introductory Environmental Science Classrooms

ERIC Educational Resources Information Center

Yarwood, Stephanie A.; Sulzman, Elizabeth W.

2008-01-01

High diversity of microorganisms in the soil matrix has been the focus of extensive research in the fields of soil biology and microbial ecology, and is a key concept that students in the environmental or biological sciences should understand. Two activities to demonstrate diversity and highlight the challenges faced in studying soil microbial…

"Bugs on Bugs": An Inquiry-Based, Collaborative Activity to Learn Arthropod & Microbial Biodiversity

ERIC Educational Resources Information Center

Lampert, Evan C.; Morgan, Jeanelle M.

2015-01-01

Diverse communities of arthropods and microbes provide humans with essential ecosystem goods and services. Arthropods are the most diverse and abundant macroscopic animals on the planet, and many remain to be discovered. Much less is known about microbial diversity, despite their importance as free-living species and as symbionts. We created…

Indoor-Air Microbiome in an Urban Subway Network: Diversity and Dynamics

PubMed Central

Leung, Marcus H. Y.; Wilkins, David; Li, Ellen K. T.; Kong, Fred K. F.

2014-01-01

Subway systems are indispensable for urban societies, but microbiological characteristics of subway aerosols are relatively unknown. Previous studies investigating microbial compositions in subways employed methodologies that underestimated the diversity of microbial exposure for commuters, with little focus on factors governing subway air microbiology, which may have public health implications. Here, a culture-independent approach unraveling the bacterial diversity within the urban subway network in Hong Kong is presented. Aerosol samples from multiple subway lines and outdoor locations were collected. Targeting the 16S rRNA gene V4 region, extensive taxonomic diversity was found, with the most common bacterial genera in the subway environment among those associated with skin. Overall, subway lines harbored different phylogenetic communities based on α- and β-diversity comparisons, and closer inspection suggests that each community within a line is dependent on architectural characteristics, nearby outdoor microbiomes, and connectedness with other lines. Microbial diversities and assemblages also varied depending on the day sampled, as well as the time of day, and changes in microbial communities between peak and nonpeak commuting hours were attributed largely to increases in skin-associated genera in peak samples. Microbial diversities within the subway were influenced by temperature and relative humidity, while carbon dioxide levels showed a positive correlation with abundances of commuter-associated genera. This Hong Kong data set and communities from previous studies conducted in the United States formed distinct community clusters, indicating that additional work is required to unravel the mechanisms that shape subway microbiomes around the globe. PMID:25172855

Evaluation of the Microbial Diversity in Amyotrophic Lateral Sclerosis Using High-Throughput Sequencing.

PubMed

Fang, Xin; Wang, Xin; Yang, Shaoguo; Meng, Fanjing; Wang, Xiaolei; Wei, Hua; Chen, Tingtao

2016-01-01

More and more evidences indicate that diseases of the central nervous system have been seriously affected by fecal microbes. However, little work is done to explore interaction between amyotrophic lateral sclerosis (ALS) and fecal microbes. In the present study, high-throughput sequencing method was used to compare the intestinal microbial diversity of healthy people and ALS patients. The principal coordinate analysis, Venn and unweighted pair-group method using arithmetic averages (UPGMA) showed an obvious microbial changes between healthy people (group H) and ALS patients (group A), and the average ratios of Bacteroides , Faecalibacterium , Anaerostipes , Prevotella , Escherichia , and Lachnospira at genus level between ALS patients and healthy people were 0.78, 2.18, 3.41, 0.35, 0.79, and 13.07. Furthermore, the decreased Firmicutes/Bacteroidetes ratio at phylum level using LEfSE (LDA > 4.0), together with the significant increased genus Dorea (harmful microorganisms) and significant reduced genus Oscillibacter , Anaerostipes , Lachnospiraceae (beneficial microorganisms) in ALS patients, indicated that the imbalance in intestinal microflora constitution had a strong association with the pathogenesis of ALS.

Microbial community diversity patterns are related to physical and chemical differences among temperate lakes near Beaver Island, MI

PubMed Central

Hengy, Miranda H.; Horton, Dean J.; Uzarski, Donald G.

2017-01-01

Lakes are dynamic and complex ecosystems that can be influenced by physical, chemical, and biological processes. Additionally, individual lakes are often chemically and physically distinct, even within the same geographic region. Here we show that differences in physicochemical conditions among freshwater lakes located on (and around) the same island, as well as within the water column of each lake, are significantly related to aquatic microbial community diversity. Water samples were collected over time from the surface and bottom-water within four freshwater lakes located around Beaver Island, MI within the Laurentian Great Lakes region. Three of the sampled lakes experienced seasonal lake mixing events, impacting either O2, pH, temperature, or a combination of the three. Microbial community alpha and beta diversity were assessed and individual microbial taxa were identified via high-throughput sequencing of the 16S rRNA gene. Results demonstrated that physical and chemical variability (temperature, dissolved oxygen, and pH) were significantly related to divergence in the beta diversity of surface and bottom-water microbial communities. Despite its correlation to microbial community structure in unconstrained analyses, constrained analyses demonstrated that dissolved organic carbon (DOC) concentration was not strongly related to microbial community structure among or within lakes. Additionally, several taxa were correlated (either positively or negatively) to environmental variables, which could be related to aerobic and anaerobic metabolisms. This study highlights the measurable relationships between environmental conditions and microbial communities within freshwater temperate lakes around the same island. PMID:29062609

Exploring Biogeochemistry and Microbial Diversity of Extant Microbialites in Mexico and Cuba

PubMed Central

Valdespino-Castillo, Patricia M.; Hu, Ping; Merino-Ibarra, Martín; López-Gómez, Luz M.; Cerqueda-García, Daniel; González-De Zayas, Roberto; Pi-Puig, Teresa; Lestayo, Julio A.; Holman, Hoi-Ying; Falcón, Luisa I.

2018-01-01

Microbialites are modern analogs of ancient microbial consortia that date as far back as the Archaean Eon. Microbialites have contributed to the geochemical history of our planet through their diverse metabolic capacities that mediate mineral precipitation. These mineral-forming microbial assemblages accumulate major ions, trace elements and biomass from their ambient aquatic environments; their role in the resulting chemical structure of these lithifications needs clarification. We studied the biogeochemistry and microbial structure of microbialites collected from diverse locations in Mexico and in a previously undescribed microbialite in Cuba. We examined their structure, chemistry and mineralogy at different scales using an array of nested methods including 16S rRNA gene high-throughput sequencing, elemental analysis, X-Ray fluorescence (XRF), X-Ray diffraction (XRD), Scanning Electron Microscopy-Energy Dispersive Spectroscopy (SEM-EDS), Fourier Transformed Infrared (FTIR) spectroscopy and Synchrotron Radiation-based Fourier Transformed Infrared (SR-FTIR) spectromicroscopy. The resulting data revealed high biological and chemical diversity among microbialites and specific microbe to chemical correlations. Regardless of the sampling site, Proteobacteria had the most significant correlations with biogeochemical parameters such as organic carbon (Corg), nitrogen and Corg:Ca ratio. Biogeochemically relevant bacterial groups (dominant phototrophs and heterotrophs) showed significant correlations with major ion composition, mineral type and transition element content, such as cadmium, cobalt, chromium, copper and nickel. Microbial-chemical relationships were discussed in reference to microbialite formation, microbial metabolic capacities and the role of transition elements as enzyme cofactors. This paper provides an analytical baseline to drive our understanding of the links between microbial diversity with the chemistry of their lithified precipitations. PMID:29666607

Exploring Biogeochemistry and Microbial Diversity of Extant Microbialites in Mexico and Cuba.

PubMed

Valdespino-Castillo, Patricia M; Hu, Ping; Merino-Ibarra, Martín; López-Gómez, Luz M; Cerqueda-García, Daniel; González-De Zayas, Roberto; Pi-Puig, Teresa; Lestayo, Julio A; Holman, Hoi-Ying; Falcón, Luisa I

2018-01-01

Microbialites are modern analogs of ancient microbial consortia that date as far back as the Archaean Eon. Microbialites have contributed to the geochemical history of our planet through their diverse metabolic capacities that mediate mineral precipitation. These mineral-forming microbial assemblages accumulate major ions, trace elements and biomass from their ambient aquatic environments; their role in the resulting chemical structure of these lithifications needs clarification. We studied the biogeochemistry and microbial structure of microbialites collected from diverse locations in Mexico and in a previously undescribed microbialite in Cuba. We examined their structure, chemistry and mineralogy at different scales using an array of nested methods including 16S rRNA gene high-throughput sequencing, elemental analysis, X-Ray fluorescence (XRF), X-Ray diffraction (XRD), Scanning Electron Microscopy-Energy Dispersive Spectroscopy (SEM-EDS), Fourier Transformed Infrared (FTIR) spectroscopy and Synchrotron Radiation-based Fourier Transformed Infrared (SR-FTIR) spectromicroscopy. The resulting data revealed high biological and chemical diversity among microbialites and specific microbe to chemical correlations. Regardless of the sampling site, Proteobacteria had the most significant correlations with biogeochemical parameters such as organic carbon (C org ), nitrogen and C org :Ca ratio. Biogeochemically relevant bacterial groups (dominant phototrophs and heterotrophs) showed significant correlations with major ion composition, mineral type and transition element content, such as cadmium, cobalt, chromium, copper and nickel. Microbial-chemical relationships were discussed in reference to microbialite formation, microbial metabolic capacities and the role of transition elements as enzyme cofactors. This paper provides an analytical baseline to drive our understanding of the links between microbial diversity with the chemistry of their lithified precipitations.

Long-Term Effects of Irrigation with Waste Water on Soil AM Fungi Diversity and Microbial Activities: The Implications for Agro-Ecosystem Resilience

PubMed Central

del Mar Alguacil, Maria; Torrecillas, Emma; Torres, Pilar; García-Orenes, Fuensanta; Roldán, Antonio

2012-01-01

The effects of irrigation with treated urban wastewater (WW) on the arbuscular mycorrhizal fungi (AMF) diversity and soil microbial activities were assayed on a long-term basis in a semiarid orange-tree orchard. After 43 years, the soil irrigated with fresh water (FW) had higher AMF diversity than soils irrigated with WW. Microbial activities were significantly higher in the soils irrigated with WW than in those irrigated with FW. Therefore, as no negative effects were observed on crop vitality and productivity, it seems that the ecosystem resilience gave rise to the selection of AMF species better able to thrive in soils with higher microbial activity and, thus, to higher soil fertility. PMID:23094075

Performance assessment and microbial diversity of two pilot scale multi-stage sub-surface flow constructed wetland systems.

PubMed

Babatunde, A O; Miranda-CasoLuengo, Raul; Imtiaz, Mehreen; Zhao, Y Q; Meijer, Wim G

2016-08-01

This study assessed the performance and diversity of microbial communities in multi-stage sub-surface flow constructed wetland systems (CWs). Our aim was to assess the impact of configuration on treatment performance and microbial diversity in the systems. Results indicate that at loading rates up to 100gBOD5/(m(2)·day), similar treatment performances can be achieved using either a 3 or 4 stage configuration. In the case of phosphorus (P), the impact of configuration was less obvious and a minimum of 80% P removal can be expected for loadings up to 10gP/(m(2)·day) based on the performance results obtained within the first 16months of operation. Microbial analysis showed an increased bacterial diversity in stage four compared to the first stage. These results indicate that the design and configuration of multi-stage constructed wetland systems may have an impact on the treatment performance and the composition of the microbial community in the systems, and such knowledge can be used to improve their design and performance. Copyright © 2016. Published by Elsevier B.V.

Mechanisms for increased soil C storage with increasing temporal and spatial plant diversity in Agroecosystems

NASA Astrophysics Data System (ADS)

Tiemann, L. K.; Grandy, S.; Marin-Spiotta, E.; Atkinson, E. E.

2012-12-01

Generally, there are positive relationships between plant species diversity and net primary production and other key ecosystem functions. However, the effects of aboveground diversity on soil microbial communities and ecosystem processes they mediate, such as soil C sequestration, remain unclear. In this study, we used an 11-y cropping diversity study where increases in diversity have increased crop yields. At the experimental site, temporal diversity is altered using combinations of annual crop rotations, while spatial diversity is altered using cover crop species. We used five treatments ranging in diversity from one to five species consisting of continuous corn with no cover crop or one cover crop and corn-soy-wheat rotations with no cover, one cover or two cover crop species. We collected soils from four replicate plots of each treatment and measured the distribution of mega- (>2 mm), macro- (0.25-2 mm), and micro- (0.053-0.25 mm) aggregates. Within each aggregate size class, we also measured total soil C and N, permanganate oxidizable C (POXC), extracellular enzyme activities (EEA), and microbial community structure with phospholipid fatty acid (PLFA) analysis. We use these data to address the impacts of both rotational and cover crop diversity on soil physical structure, associated microbial community structure and activity and soil C storage. As spatial diversity increased, we found concurrent increases in mega-aggregate abundance as well as increasing soil C in the mega- and micro-aggregates but not macro-aggregates. The proportion of total soil C in each aggregate size class that is relatively labile (POXC) was highest in the micro-aggregates, as was enzyme activity associated with labile C acquisition across all levels of diversity. Enzyme activity associated with more recalcitrant forms of soil C was highest in the mega-aggregate class, also across all diversity levels; however, the ratio of labile to recalcitrant EEA increased with increasing diversity in the mega- and micro-aggregates. In addition, soil N increased with diversity such that microbial C:N EEA simultaneously decreased in mega-aggregates. We also found that cropping diversity has created distinctive soil microbial communities, highlighted by variation in the abundance of gram positive bacteria and Actinomycetes. Further research will help us determine how these changes in community structure with increasing diversity are related to concomitant changes in aggregation and enzyme activities. We suggest that the additional organic matter inputs from cover crops in the high diversity treatments have increased aggregation processes and C pools. While microbial activity has also increased in association with this increased C availability, the activity of recalcitrant and N-acquiring enzymes has declined, suggesting an overall decrease in SOM mineralization with possible increased SOM stabilization. The addition of crop species in rotation (temporal diversity) had minimal influence on any of the measured parameters. We thus conclude that spatial diversity is a more important driver of soil structure and microbial activity, likely due to the high quality organic matter inputs derived from the leguminous cover crops; however, spatial diversity alone did not lead to the same level of C storage potential as mixtures of temporal and spatial diversity.

Are biological effects of desert shrubs more important than physical effects on soil microorganisms?

PubMed

Berg, Naama; Steinberger, Yosef

2010-01-01

Vegetation cover plays a major role in providing organic matter and in acting as a physical barrier, with both together contributing to the formation of "fertile islands," which play an active role in prolonging biological activity in desert ecosystems. By undertaking this study, a longterm research, we designed an experiment to separate the two components-the physical and biotic parts of the perennial plants-and to identify the factor that contributes the most to the ecosystem. The study site was located in the northern Negev Desert, Israel, where 50 Hammada scoparia shrubs and 50 artificial plants were randomly marked. Soil samples were collected monthly over 3 years of research at three locations: under the canopy of H. scoparia shrubs, in the vicinity of the artificial plants, and between the shrubs (control). The contribution to microbial activity was measured by evaluation of the microbial community functions in soil. The functional aspects of the microbial community that were measured were CO2 evolution, microbial biomass, microbial functional diversity, and the physiological profile of the community. The results of this study are presented in two ways: (1) according to the three locations/treatments; and (2) according to the phenological situation of the vegetation (annual and perennial plants) in the research field: the growing phase, the drying process, and the absence of annual plants. The only parameters that were found to affect microbial activity were the contribution of the organic matter of perennial shrubs and the growth of vegetation (annual and perennial) during the growing seasons. The physical component was found to have no effect on soil microbial functional diversity, which elucidates the important contribution of the desert shrub in enhancing biological multiplicity and activity.

Microbial community functional structure in response to antibiotics in pharmaceutical wastewater treatment systems.

PubMed

Zhang, Yu; Xie, Jianping; Liu, Miaomiao; Tian, Zhe; He, Zhili; van Nostrand, Joy D; Ren, Liren; Zhou, Jizhong; Yang, Min

2013-10-15

It is widely demonstrated that antibiotics in the environment affect microbial community structure. However, direct evidence regarding the impacts of antibiotics on microbial functional structures in wastewater treatment systems is limited. Herein, a high-throughput functional gene array (GeoChip 3.0) in combination with quantitative PCR and clone libraries were used to evaluate the microbial functional structures in two biological wastewater treatment systems, which treat antibiotic production wastewater mainly containing oxytetracycline. Despite the bacteriostatic effects of antibiotics, the GeoChip detected almost all key functional gene categories, including carbon cycling, nitrogen cycling, etc., suggesting that these microbial communities were functionally diverse. Totally 749 carbon-degrading genes belonging to 40 groups (24 from bacteria and 16 from fungi) were detected. The abundance of several fungal carbon-degrading genes (e.g., glyoxal oxidase (glx), lignin peroxidase or ligninase (lip), manganese peroxidase (mnp), endochitinase, exoglucanase_genes) was significantly correlated with antibiotic concentrations (Mantel test; P < 0.05), showing that the fungal functional genes have been enhanced by the presence of antibiotics. However, from the fact that the majority of carbon-degrading genes were derived from bacteria and diverse antibiotic resistance genes were detected in bacteria, it was assumed that many bacteria could survive in the environment by acquiring antibiotic resistance and may have maintained the position as a main player in nutrient removal. Variance partitioning analysis showed that antibiotics could explain 24.4% of variations in microbial functional structure of the treatment systems. This study provides insights into the impacts of antibiotics on microbial functional structure of a unique system receiving antibiotic production wastewater, and reveals the potential importance of the cooperation between fungi and bacteria with antibiotic resistance in maintaining the stability and performance of the systems. Copyright © 2013 Elsevier Ltd. All rights reserved.

Genome Informed Trait-Based Models

NASA Astrophysics Data System (ADS)

Karaoz, U.; Cheng, Y.; Bouskill, N.; Tang, J.; Beller, H. R.; Brodie, E.; Riley, W. J.

2013-12-01

Trait-based approaches are powerful tools for representing microbial communities across both spatial and temporal scales within ecosystem models. Trait-based models (TBMs) represent the diversity of microbial taxa as stochastic assemblages with a distribution of traits constrained by trade-offs between these traits. Such representation with its built-in stochasticity allows the elucidation of the interactions between the microbes and their environment by reducing the complexity of microbial community diversity into a limited number of functional ';guilds' and letting them emerge across spatio-temporal scales. From the biogeochemical/ecosystem modeling perspective, the emergent properties of the microbial community could be directly translated into predictions of biogeochemical reaction rates and microbial biomass. The accuracy of TBMs depends on the identification of key traits of the microbial community members and on the parameterization of these traits. Current approaches to inform TBM parameterization are empirical (i.e., based on literature surveys). Advances in omic technologies (such as genomics, metagenomics, metatranscriptomics, and metaproteomics) pave the way to better-initialize models that can be constrained in a generic or site-specific fashion. Here we describe the coupling of metagenomic data to the development of a TBM representing the dynamics of metabolic guilds from an organic carbon stimulated groundwater microbial community. Illumina paired-end metagenomic data were collected from the community as it transitioned successively through electron-accepting conditions (nitrate-, sulfate-, and Fe(III)-reducing), and used to inform estimates of growth rates and the distribution of metabolic pathways (i.e., aerobic and anaerobic oxidation, fermentation) across a spatially resolved TBM. We use this model to evaluate the emergence of different metabolisms and predict rates of biogeochemical processes over time. We compare our results to observational outputs.

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.

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

Microbial Dark Matter Investigations: How Microbial Studies Transform Biological Knowledge and Empirically Sketch a Logic of Scientific Discovery

PubMed Central

Bernard, Guillaume; Pathmanathan, Jananan S; Lannes, Romain; Lopez, Philippe; Bapteste, Eric

2018-01-01

Abstract Microbes are the oldest and most widespread, phylogenetically and metabolically diverse life forms on Earth. However, they have been discovered only 334 years ago, and their diversity started to become seriously investigated even later. For these reasons, microbial studies that unveil novel microbial lineages and processes affecting or involving microbes deeply (and repeatedly) transform knowledge in biology. Considering the quantitative prevalence of taxonomically and functionally unassigned sequences in environmental genomics data sets, and that of uncultured microbes on the planet, we propose that unraveling the microbial dark matter should be identified as a central priority for biologists. Based on former empirical findings of microbial studies, we sketch a logic of discovery with the potential to further highlight the microbial unknowns. PMID:29420719

Multitrophic microbial interactions for eco- and agro-biotechnological processes: theory and practice.

PubMed

Saleem, Muhammad; Moe, Luke A

2014-10-01

Multitrophic level microbial loop interactions mediated by protist predators, bacteria, and viruses drive eco- and agro-biotechnological processes such as bioremediation, wastewater treatment, plant growth promotion, and ecosystem functioning. To what extent these microbial interactions are context-dependent in performing biotechnological and ecosystem processes remains largely unstudied. Theory-driven research may advance the understanding of eco-evolutionary processes underlying the patterns and functioning of microbial interactions for successful development of microbe-based biotechnologies for real world applications. This could also be a great avenue to test the validity or limitations of ecology theory for managing diverse microbial resources in an era of altering microbial niches, multitrophic interactions, and microbial diversity loss caused by climate and land use changes. Copyright © 2014 Elsevier Ltd. All rights reserved.

Phylogenetic analysis of the fecal microbial community in herbivorous land and marine iguanas of the Galápagos Islands using 16S rRNA-based pyrosequencing

PubMed Central

Hong, Pei-Ying; Wheeler, Emily; Cann, Isaac K O; Mackie, Roderick I

2011-01-01

Herbivorous reptiles depend on complex gut microbial communities to effectively degrade dietary polysaccharides. The composition of these fermentative communities may vary based on dietary differences. To explore the role of diet in shaping gut microbial communities, we evaluated the fecal samples from two related host species—the algae-consuming marine iguana (Amblyrhynchus cristatus) and land iguanas (LI) (genus Conolophus) that consume terrestrial vegetation. Marine and LI fecal samples were collected from different islands in the Galápagos archipelago. High-throughput 16S rRNA-based pyrosequencing was used to provide a comparative analysis of fecal microbial diversity. At the phylum level, the fecal microbial community in iguanas was predominated by Firmicutes (69.5±7.9%) and Bacteroidetes (6.2±2.8%), as well as unclassified Bacteria (20.6±8.6%), suggesting that a large portion of iguana fecal microbiota is novel and could be involved in currently unknown functions. Host species differed in the abundance of specific bacterial groups. Bacteroides spp., Lachnospiraceae and Clostridiaceae were significantly more abundant in the marine iguanas (MI) (P-value>1E−9). In contrast, Ruminococcaceae were present at >5-fold higher abundance in the LI than MI (P-value>6E−14). Archaea were only detected in the LI. The number of operational taxonomic units (OTUs) in the LI (356–896 OTUs) was >2-fold higher than in the MI (112–567 OTUs), and this increase in OTU diversity could be related to the complexity of the resident bacterial population and their gene repertoire required to breakdown the recalcitrant polysaccharides prevalent in terrestrial plants. Our findings suggest that dietary differences contribute to gut microbial community differentiation in herbivorous lizards. Most importantly, this study provides a better understanding of the microbial diversity in the iguana gut; therefore facilitating future efforts to discover novel bacterial-associated enzymes that can effectively breakdown a wide variety of complex polysaccharides. PMID:21451584

Humboldt's spa: microbial diversity is controlled by temperature in geothermal environments

PubMed Central

Sharp, Christine E; Brady, Allyson L; Sharp, Glen H; Grasby, Stephen E; Stott, Matthew B; Dunfield, Peter F

2014-01-01

Over 200 years ago Alexander von Humboldt (1808) observed that plant and animal diversity peaks at tropical latitudes and decreases toward the poles, a trend he attributed to more favorable temperatures in the tropics. Studies to date suggest that this temperature–diversity gradient is weak or nonexistent for Bacteria and Archaea. To test the impacts of temperature as well as pH on bacterial and archaeal diversity, we performed pyrotag sequencing of 16S rRNA genes retrieved from 165 soil, sediment and biomat samples of 36 geothermal areas in Canada and New Zealand, covering a temperature range of 7.5–99 °C and a pH range of 1.8–9.0. This represents the widest ranges of temperature and pH yet examined in a single microbial diversity study. Species richness and diversity indices were strongly correlated to temperature, with R2 values up to 0.62 for neutral–alkaline springs. The distributions were unimodal, with peak diversity at 24 °C and decreasing diversity at higher and lower temperature extremes. There was also a significant pH effect on diversity; however, in contrast to previous studies of soil microbial diversity, pH explained less of the variability (13–20%) than temperature in the geothermal samples. No correlation was observed between diversity values and latitude from the equator, and we therefore infer a direct temperature effect in our data set. These results demonstrate that temperature exerts a strong control on microbial diversity when considered over most of the temperature range within which life is possible. PMID:24430481

Humboldt's spa: microbial diversity is controlled by temperature in geothermal environments.

PubMed

Sharp, Christine E; Brady, Allyson L; Sharp, Glen H; Grasby, Stephen E; Stott, Matthew B; Dunfield, Peter F

2014-06-01

Over 200 years ago Alexander von Humboldt (1808) observed that plant and animal diversity peaks at tropical latitudes and decreases toward the poles, a trend he attributed to more favorable temperatures in the tropics. Studies to date suggest that this temperature-diversity gradient is weak or nonexistent for Bacteria and Archaea. To test the impacts of temperature as well as pH on bacterial and archaeal diversity, we performed pyrotag sequencing of 16S rRNA genes retrieved from 165 soil, sediment and biomat samples of 36 geothermal areas in Canada and New Zealand, covering a temperature range of 7.5-99 °C and a pH range of 1.8-9.0. This represents the widest ranges of temperature and pH yet examined in a single microbial diversity study. Species richness and diversity indices were strongly correlated to temperature, with R(2) values up to 0.62 for neutral-alkaline springs. The distributions were unimodal, with peak diversity at 24 °C and decreasing diversity at higher and lower temperature extremes. There was also a significant pH effect on diversity; however, in contrast to previous studies of soil microbial diversity, pH explained less of the variability (13-20%) than temperature in the geothermal samples. No correlation was observed between diversity values and latitude from the equator, and we therefore infer a direct temperature effect in our data set. These results demonstrate that temperature exerts a strong control on microbial diversity when considered over most of the temperature range within which life is possible.

Back to the future of soil metagenomics

DOE PAGES

Nesme, Joseph; Achouak, Wafa; Agathos, Spiros N.; ...

2016-02-10

Here, direct extraction and characterization of microbial community DNA through PCR amplicon surveys and metagenomics has revolutionized the study of environmental microbiology and microbial ecology. In particular, metagenomic analysis of nucleic acids provides direct access to the genomes of the “uncultivated majority.” Accelerated by advances in sequencing technology, microbiologists have discovered more novel phyla, classes, genera, and genes from microorganisms in the first decade and a half of the twenty-first century than since these “many very little living animalcules” were first discovered by van Leeuwenhoek (Table 1). The unsurpassed diversity of soils promises continued exploration of a range of industrial,more » agricultural, and environmental functions. The ability to explore soil microbial communities with increasing capacity offers the highest promise for answering many outstanding who, what, where, when, why, and with whom questions such as: Which microorganisms are linked to which soil habitats? How do microbial abundances change with changing edaphic conditions? How do microbial assemblages interact and influence one another synergistically or antagonistically? What is the full extent of soil microbial diversity, both functionally and phylogenetically? What are the dynamics of microbial communities in space and time? How sensitive are microbial communities to a changing climate? What is the role of horizontal gene transfer in the stability of microbial communities? Do highly diverse microbial communities confer resistance and resilience in soils?« less

Back to the future of soil metagenomics

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

Nesme, Joseph; Achouak, Wafa; Agathos, Spiros N.

Here, direct extraction and characterization of microbial community DNA through PCR amplicon surveys and metagenomics has revolutionized the study of environmental microbiology and microbial ecology. In particular, metagenomic analysis of nucleic acids provides direct access to the genomes of the “uncultivated majority.” Accelerated by advances in sequencing technology, microbiologists have discovered more novel phyla, classes, genera, and genes from microorganisms in the first decade and a half of the twenty-first century than since these “many very little living animalcules” were first discovered by van Leeuwenhoek (Table 1). The unsurpassed diversity of soils promises continued exploration of a range of industrial,more » agricultural, and environmental functions. The ability to explore soil microbial communities with increasing capacity offers the highest promise for answering many outstanding who, what, where, when, why, and with whom questions such as: Which microorganisms are linked to which soil habitats? How do microbial abundances change with changing edaphic conditions? How do microbial assemblages interact and influence one another synergistically or antagonistically? What is the full extent of soil microbial diversity, both functionally and phylogenetically? What are the dynamics of microbial communities in space and time? How sensitive are microbial communities to a changing climate? What is the role of horizontal gene transfer in the stability of microbial communities? Do highly diverse microbial communities confer resistance and resilience in soils?« less

Co-culturing of Fungal Strains Against Botrytis cinerea as a Model for the Induction of Chemical Diversity and Therapeutic Agents

PubMed Central

Serrano, Rachel; González-Menéndez, Víctor; Rodríguez, Lorena; Martín, Jesús; Tormo, José R.; Genilloud, Olga

2017-01-01

New fungal SMs (SMs) have been successfully described to be produced by means of in vitro-simulated microbial community interactions. Co-culturing of fungi has proved to be an efficient way to induce cell–cell interactions that can promote the activation of cryptic pathways, frequently silent when the strains are grown in laboratory conditions. Filamentous fungi represent one of the most diverse microbial groups known to produce bioactive natural products. Triggering the production of novel antifungal compounds in fungi could respond to the current needs to fight health compromising pathogens and provide new therapeutic solutions. In this study, we have selected the fungus Botrytis cinerea as a model to establish microbial interactions with a large set of fungal strains related to ecosystems where they can coexist with this phytopathogen, and to generate a collection of extracts, obtained from their antagonic microbial interactions and potentially containing new bioactive compounds. The antifungal specificity of the extracts containing compounds induced after B. cinerea interaction was determined against two human fungal pathogens (Candida albicans and Aspergillus fumigatus) and three phytopathogens (Colletotrichum acutatum, Fusarium proliferatum, and Magnaporthe grisea). In addition, their cytotoxicity was also evaluated against the human hepatocellular carcinoma cell line (HepG2). We have identified by LC-MS the production of a wide variety of known compounds induced from these fungal interactions, as well as novel molecules that support the potential of this approach to generate new chemical diversity and possible new therapeutic agents. PMID:28469610

Planktonic microbial community responses to added copper.

PubMed

Le Jeune, Anne-Hélène; Charpin, Marie; Sargos, Denis; Lenain, Jean-François; Deluchat, Véronique; Ngayila, Nadine; Baudu, Michel; Amblard, Christian

2007-07-20

It is generally agreed that autotrophic organisms and especially phytoplanktonic species can be harmed by copper through its effect on photosystem. However, the impact of copper on other components of the pelagic food web, such as the microbial loop (autotrophic and heterotrophic picoplankton, pigmented and non-pigmented flagellates and ciliates) has received little attention. Indoor experiments were conducted to evaluate the direct and indirect effects of copper, supplied in the range of concentrations used to control cyanobacteria growth in ponds, on non-targeted organisms of natural microbial loop communities sampled in spring and summer. Two copper concentrations were tested (80microgL(-1) and 160microgL(-1) final concentrations), set, respectively, below and above the ligand binding capacity of the water samples. Both caused a significant decrease in the biomass and diversity of pigmented organisms (picophytoplankton and pigmented flagellates). Conversely, the heterotrophic bacterioplankton and the heterotrophic flagellates did not seem to be directly affected by either copper treatment in terms of biomass or diversity, according to the descriptor chosen. The ciliate biomass was significantly reduced with increasing copper concentrations, but differences in sensitivity appeared between spring and summer communities. Potential mixotrophic and nanoplanktorivorous ciliates appeared to be more sensitive to copper treatments than bacterivorous ciliates, suggesting a stronger direct and (or) indirect effect of copper on the former. Copper sulphate treatments had a significant restructuring effect on the microbial loop communities, resulting in a dominance of heterotrophic bacterioplankton among microbial microorganisms 27 days after the beginning of the treatment. The spring microbial communities exhibited a greater sensitivity than the summer communities with respect to their initial compositions.

Evaluation of microbial diversity in the pilot-scale beer brewing process by culture-dependent and culture-independent method.

PubMed

Takahashi, M; Kita, Y; Kusaka, K; Mizuno, A; Goto-Yamamoto, N

2015-02-01

In the brewing industry, microbial management is very important for stabilizing the quality of the product. We investigated the detailed microbial community of beer during fermentation and maturation, to manage beer microbiology in more detail. We brewed a beer (all-malt) and two beerlike beverages (half- and low-malt) in pilot-scale fermentation and investigated the microbial community of them using a next-generation sequencer (454 GS FLX titanium), quantitative PCR, flow cytometry and a culture-dependent method. From 28 to 88 genera of bacteria and from 9 to 38 genera of eukaryotic micro-organisms were detected in each sample. Almost all micro-organisms died out during the boiling process. However, bacteria belonging to the genera Acidovorax, Bacillus, Brevundimonas, Caulobacter, Chryseobacterium, Methylobacterium, Paenibacillus, Polaromonas, Pseudomonas, Ralstonia, Sphingomonas, Stenotrophomonas, Tepidimonas and Tissierella were detected at the early and middle stage of fermentation, even though their cell densities were low (below approx. 10(3) cells ml(-1) ) and they were not almost detected at the end of fermentation. We revealed that the microbial community of beer during fermentation and maturation is very diverse and several bacteria possibly survive during fermentation. In this study, we revealed the detailed microbial communities of beer using next-generation sequencing. Some of the micro-organisms detected in this study were found in beer brewing process for the first time. Additionally, the possibility of growth of several bacteria at the early and middle stage of fermentation was suggested. © 2014 The Society for Applied Microbiology.

Microbial functional diversity and enzymatic activity of soil degraded by sulphur mining reclaimed with various waste

NASA Astrophysics Data System (ADS)

Joniec, Jolanta; Frąc, Magdalena

2017-10-01

The aim of the study was to evaluate microbial functional diversity based on community level physiological profiling and β-glucosidase activity changes in soil degraded by sulphur mining and subjected to reclamation with various waste. The experiment was set up in the area of the former `Jeziórko' Sulphur Mine (Poland), on a soilless substrate with a particle size distribution of slightly loamy sand. The experimental variants included the application of post-flotation lime, sewage sludge and mineral wool. The analyses of soil samples included the assessment of the following microbiological indices: β-glucosidase activity and functional diversity average well color development and richness). The results indicate that sewage sludge did not exert a significant impact on the functional diversity of microorganisms present in the reclaimed soil. In turn, the application of other types of waste contributed to a significant increase in the parameters of total metabolic activity and functional diversity of the reclaimed soil. However, the temporal analysis of the metabolic profile of soil microorganisms demonstrated that a single application of waste did not yield a durable, stable metabolic profile in the reclaimed soil. Still, there was an increase in β-glucosidase activity, especially in objects treated with sewage sludge.

[Characterization of microbial community in produced water from a petroleum reservoir subjected to alkali-surfactant-polymer ASP flooding].

PubMed

Hao, Qin Qin; Shi, Rong Jiu; Hao, Jin Sheng; Zhao, Jin Yi; Li, Guo Qiao; Zhao, Feng; Han, Si Qin; Zhang, Ying

2017-10-01

Injection of alkali, surfactant and polymer (ASP) into oil reservoir can substantially increase oil recovery compared with water-flooding strategy. However, the effects of these agents on the microbial diversity and community structure, which is important for water management and corrosion control in oil industry, are hitherto poorly understood. Here, we disclosed the microbial diversity and community structure in the produced water collected from four producing wells of an ASP-flooded oilfield at Daqing, China, using high-throughput sequencing technique. Results showed that the average pH in produced water was as high as 9.65. The microbial diversity varied from well to well, and the Shannon diversity index was between 2.00 to 3.56. The Proteobacteria (85.5%-98.3%), γ-proteobacteria (83.7%-97.8%), and alkaliphilic Nitrincola (51.8%-82.5%) were the most dominant phylogenetic taxa at the phylum, class, and genus levels, respectively. A total of 12 potentially sulfide-producing genera were detected, and the most abundant taxon was Sulfurospirillum (0.4%-7.4%). The microbial community of ASP-flooded petroleum reservoir was distinct, showing an alkaliphilic or alkalitolerant potential; a reduced diversity and more simple structure were observed compared with those of the water-flooded petroleum reservoirs that were previously reported.

Diversity and composition of sediment bacteria in subtropical coastal wetlands of North Stradbroke Island, Queensland, Australia

NASA Astrophysics Data System (ADS)

Chuvochina, Maria; Sampayo, Eugenia; Welti, Nina; Hayes, Matthew; Lu, Yang; Lovelock, Catherine; Lockington, David

2013-04-01

Coastal wetlands provide a wide variety of important ecosystem services but continue to suffer disturbance, degradation and deforestation. Sediment bacteria are responsible for major nutrient transformation and recycling in these ecosystems. Insight into microbial community composition and the factors that determine them may improve our understanding of biogeochemical processes, food web dynamics, biodegradation processes and, thus, help to develop the management strategies for preserving the ecosystem health and services. Characterizing shifts in community taxa along environmental gradients has been shown to provide a useful tool for determining the major drivers affecting community structure and function. North Stradbroke Island (NSI) in Southern Queensland presents considerable habitat diversity including variety of groundwater dependent ecosystems such as lakes, swamps, sedge-like salt marshes and mangroves. Ecological responses of continuous groundwater extraction for municipal purposes and sand mining operations on NSI are still need to be assessed in order to protect its unique environment. Changes in coastal hydrology due to either climate change or human activity may directly affect microbial populations and, thus, biogeochemical cycles of nutrients. These may result in altering/losing some ecosystem services provided by coastal wetlands. In this study we examine microbial diversity and determine environmental controls on bacterial community structure along a natural transition from freshwater forested wetland (melaleuca woodland), sedge-like salt marsh and into mangroves located at NSI. The study area is characterized by significant groundwater flow, nutrient limitation and sharp transition from one ecosystem type to another. Sediment cores (0-5 cm and 20-25 cm depth) were collected from three representative sites of each zone (mangroves - salt marsh - freshwater wetland) along the salinity gradient in August 2012. Subsamples were set aside for use in chemical analyses, microbiological analysis and for porewater extraction. Microbial community structure and diversity are assessed using denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene fragments and barcoded pyrosequencing. To evaluate the relationships between microbial communities and environmental variables we use bioinformatical and statistical tools. Physico-chemical parameters included measurements of sediment pH, temperature, salinity and nutrients composition. Background information regarding hydrology and vegetation is incorporated in the study. Sediment bacteria play a vital role in wetland ecological function, and they are very sensitive to environmental changes. Considering coastal wetlands of NSI as a model area, our study may contribute to the knowledge of factors shaping microbial diversity in tropical wetlands, help to gain insight into the microbe-nutrient-plant relationships, and also serve as background for conservation plans to safeguard these ecosystems.

Functional gene array-based analysis of microbial community structure in groundwaters with a gradient of contaminant levels

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

Waldron, P.J.; Wu, L.; Van Nostrand, J.D.

2009-06-15

To understand how contaminants affect microbial community diversity, heterogeneity, and functional structure, six groundwater monitoring wells from the Field Research Center of the U.S. Department of Energy Environmental Remediation Science Program (ERSP; Oak Ridge, TN), with a wide range of pH, nitrate, and heavy metal contamination were investigated. DNA from the groundwater community was analyzed with a functional gene array containing 2006 probes to detect genes involved in metal resistance, sulfate reduction, organic contaminant degradation, and carbon and nitrogen cycling. Microbial diversity decreased in relation to the contamination levels of the wells. Highly contaminated wells had lower gene diversity butmore » greater signal intensity than the pristine well. The microbial composition was heterogeneous, with 17-70% overlap between different wells. Metal-resistant and metal-reducing microorganisms were detected in both contaminated and pristine wells, suggesting the potential for successful bioremediation of metal-contaminated groundwaters. In addition, results of Mantel tests and canonical correspondence analysis indicate that nitrate, sulfate, pH, uranium, and technetium have a significant (p < 0.05) effect on microbial community structure. This study provides an overall picture of microbial community structure in contaminated environments with functional gene arrays by showing that diversity and heterogeneity can vary greatly in relation to contamination.« less

Impact of diverse soil microbial communities on crop residues decomposition

NASA Astrophysics Data System (ADS)

Mrad, Fida; Bennegadi-Laurent, Nadia; Ailhas, Jérôme; Leblanc, Nathalie; Trinsoutrot-Gattin, Isabelle; Laval, Karine; Gattin, Richard

2017-04-01

Soils provide many basic ecosystem services for our society and most of these services are carried out by the soil communities, thus influencing soils quality. Soil organic matter (SOM) can be considered as one of the most important soil quality indices for it plays a determinant role in many physical, chemical and biological processes, such as soil structure and erosion resistance, cation exchange capacity, nutrient cycling and biological activity (Andrews et al., 2004). Since a long time, exogenous organic inputs are largely used for improving agricultural soils, affecting highly soil fertility and productivity. The use of organic amendments such as crop residues influences the soil microbial populations' diversity and abundance. In the meantime, soil microbial communities play a major role in the organic matter degradation, and the effect of different microbial communities on the decomposition of crop residues is not well documented. In this context, studying the impact of crop residues on soil microbial ecology and the processes controlling the fate of plant residues in different management practices is essential for understanding the long-term environmental and agronomic effects on soil and organic matters. Our purpose in the present work was to investigate the decomposition by two contrasting microbial communities of three crop residues, and compare the effect of different residues amendments on the abundance and function of each soil microbial communities. Among the main crops which produce large amounts of residues, we focused on three different plants: wheat (Triticum aestivum L.), rape (Brassica napus) and sunflower (Helianthus annuus). The residues degradation in two soils of different management practices and the microbial activity were evaluated by: microbial abundance (microbial carbon, culturable bacteria, total DNA, qPCR), in combination with functional indicators (enzymatic assays and Biolog substrate utilization), kinetics of C and N mineralization, and chemical measures. Physicochemical composition of crop residues was assessed by Fourier transform infrared spectroscopy FTIR technique at 0 and 83 days. The experiment was conducted in microcosms over 83 days for the biological measurements and 175 days for the C mineralization. The first results showed variations in the C & N rates, and the microbial abundances and functions over time, with a peak at 5 days and a decrease at 83 days for most of the measurements. The soil microbial communities' composition (different management practices) highly impacted the crop residues decomposition. The biochemical composition of crop residues influenced less the microbial communities of each soil. Further studies on the valorization of these residues into agro materials will be carried out. References: Andrews SS., Karlen DL., and Cambardella CA. (2004) The soil management assessment framework: a quantitative soil quality evaluation method. Soil Science Society of America, 68: 1945-1962

Contributions of understory and/or overstory vegetations to soil microbial PLFA and nematode diversities in Eucalyptus monocultures.

PubMed

Zhao, Jie; Wan, Songze; Zhang, Chenlu; Liu, Zhanfeng; Zhou, Lixia; Fu, Shenglei

2014-01-01

Ecological interactions between aboveground and belowground biodiversity have received many attentions in the recent decades. Although soil biodiversity declined with the decrease of plant diversity, many previous studies found plant species identities were more important than plant diversity in controlling soil biodiversity. This study focused on the responses of soil biodiversity to the altering of plant functional groups, namely overstory and understory vegetations, rather than plant diversity gradient. We conducted an experiment by removing overstory and/or understory vegetation to compare their effects on soil microbial phospholipid fatty acid (PLFA) and nematode diversities in eucalyptus monocultures. Our results indicated that both overstory and understory vegetations could affect soil microbial PLFA and nematode diversities, which manifested as the decrease in Shannon-Wiener diversity index (H') and Pielou evenness index (J) and the increase in Simpson dominance index (λ) after vegetation removal. Soil microclimate change explained part of variance of soil biodiversity indices. Both overstory and understory vegetations positively correlated with soil microbial PLFA and nematode diversities. In addition, the alteration of soil biodiversity might be due to a mixing effect of bottom-up control and soil microclimate change after vegetation removal in the studied plantations. Given the studied ecosystem is common in humid subtropical and tropical region of the world, our findings might have great potential to extrapolate to large scales and could be conducive to ecosystem management and service.

Antimicrobial compounds from seaweeds-associated bacteria and fungi.

PubMed

Singh, Ravindra Pal; Kumari, Puja; Reddy, C R K

2015-02-01

In recent decade, seaweeds-associated microbial communities have been significantly evaluated for functional and chemical analyses. Such analyses let to conclude that seaweeds-associated microbial communities are highly diverse and rich sources of bioactive compounds of exceptional molecular structure. Extracting bioactive compounds from seaweed-associated microbial communities have been recently increased due to their broad-spectrum antimicrobial activities including antibacterial, antifungal, antiviral, anti-settlement, antiprotozoan, antiparasitic, and antitumor. These allelochemicals not only provide protection to host from other surrounding pelagic microorganisms, but also ensure their association with the host. Antimicrobial compounds from marine sources are promising and priority targets of biotechnological and pharmaceutical applications. This review describes the bioactive metabolites reported from seaweed-associated bacterial and fungal communities and illustrates their bioactivities. Biotechnological application of metagenomic approach for identifying novel bioactive metabolites is also dealt, in view of their future development as a strong tool to discover novel drug targets from seaweed-associated microbial communities.

Construction and screening of marine metagenomic libraries.

PubMed

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

2010-01-01

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

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...

MOLECULAR DIVERSITY OF DRINKING WATER MICROBIAL COMMUNITIES: A PHYLOGENETIC APPROACH

EPA Science Inventory

The microbiological quality of drinking water is assessed using culture-based methods that are highly selective and that tend to underestimate the densities and diversity of microbial populations inhabiting distribution systems. In order to better understand the effect of differe...

Patterns of Nitrogen Fixation and Related Genetic Diversity (nifH) in Microbial Mats and Stromatolites from Different Environments

NASA Astrophysics Data System (ADS)

Beltrán, Y. Y.; Centeno, C.; Falcón, L. I.

2010-04-01

We want to estimate the patterns of nitrogen fixation and the related genetic diversity (nifH) of microbial mats and microbialites on dial and temporal scales along a physicochemical and geographical gradient.

Metagenomics uncovers gaps in amplicon-based detection of microbial diversity

DOE PAGES

Eloe-Fadrosh, Emiley A.; Ivanova, Natalia N.; Woyke, Tanja; ...

2016-02-01

Our view of microbial diversity has expanded greatly over the past 40 years, primarily through the wide application of PCR-based surveys of the small-subunit ribosomal RNA (SSU rRNA) gene. Yet significant gaps in knowledge remain due to well-recognized limitations of this method. Here in this paper, we systematically survey primer fidelity in SSU rRNA gene sequences recovered from over 6,000 assembled metagenomes sampled globally. Our findings show that approximately 10% of environmental microbial sequences might be missed from classical PCR-based SSU rRNA gene surveys, mostly members of the Candidate Phyla Radiation (CPR) and as yet uncharacterized Archaea. In conclusion, thesemore » results underscore the extent of uncharacterized microbial diversity and provide fruitful avenues for describing additional phylogenetic lineages.« less

Capturing the genetic makeup of the active microbiome in situ

DOE PAGES

Singer, Esther; Wagner, Michael; Woyke, Tanja

2017-06-02

More than any other technology, nucleic acid sequencing has enabled microbial ecology studies to be complemented with the data volumes necessary to capture the extent of microbial diversity and dynamics in a wide range of environments. In order to truly understand and predict environmental processes, however, the distinction between active, inactive and dead microbial cells is critical. Also, experimental designs need to be sensitive toward varying population complexity and activity, and temporal as well as spatial scales of process rates. There are a number of approaches, including single-cell techniques, which were designed to study in situ microbial activity and thatmore » have been successively coupled to nucleic acid sequencing. The exciting new discoveries regarding in situ microbial activity provide evidence that future microbial ecology studies will indispensably rely on techniques that specifically capture members of the microbiome active in the environment. Herein, we review those currently used activity-based approaches that can be directly linked to shotgun nucleic acid sequencing, evaluate their relevance to ecology studies, and discuss future directions.« less

Capturing the genetic makeup of the active microbiome in situ

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

Singer, Esther; Wagner, Michael; Woyke, Tanja

More than any other technology, nucleic acid sequencing has enabled microbial ecology studies to be complemented with the data volumes necessary to capture the extent of microbial diversity and dynamics in a wide range of environments. In order to truly understand and predict environmental processes, however, the distinction between active, inactive and dead microbial cells is critical. Also, experimental designs need to be sensitive toward varying population complexity and activity, and temporal as well as spatial scales of process rates. There are a number of approaches, including single-cell techniques, which were designed to study in situ microbial activity and thatmore » have been successively coupled to nucleic acid sequencing. The exciting new discoveries regarding in situ microbial activity provide evidence that future microbial ecology studies will indispensably rely on techniques that specifically capture members of the microbiome active in the environment. Herein, we review those currently used activity-based approaches that can be directly linked to shotgun nucleic acid sequencing, evaluate their relevance to ecology studies, and discuss future directions.« less

Natural revegetation of a semiarid habitat alters taxonomic and functional diversity of soil microbial communities.

PubMed

Guo, Yanqing; Chen, Xiaotian; Wu, Yuanyuan; Zhang, Lu; Cheng, Jimin; Wei, Gehong; Lin, Yanbing

2018-04-18

Revegetation of degraded lands has a profound impact on the maintenance and stability of ecosystem processes. However, the impacts of this land use change on functional diversity of soil microbial communities are poorly understood. Here, using 16S rRNA gene amplicon and shotgun metagenomic sequencing, we compared the taxonomic and functional communities of soil microbiome, and analyzed the effects of plant diversity and soil chemical properties, in a chronosequence of restored ex-farmland that had been naturally revegetated to grassland over periods of 5, 15 and 30years with adjacent farmland, on the Loess Plateau, China. We found that microbial taxonomic diversity was positively correlated with plant diversity and was higher in the revegetated sites. Functional diversity increased significantly in the oldest grassland. Actinobacteria, commonly considered a copiotrophic phylum, was more abundant in the revegetated sites, while Acidobacteria, an oligotrophic phylum, was more abundant in farmland. Furthermore, the structure of taxonomic and functional communities was significantly different between revegetated sites and farmland, and organic matter was the best environmental predictor in determining these microbial communities. Compared with the farmland, revegetation increased the proportion of genes associated with energy metabolism, carbohydrate metabolism and xenobiotics biodegradation and metabolism. Notably, the higher proportion of carbohydrate degradation gene subfamilies in the revegetated sites indicated higher levels of soil nutrient cycling. These results elucidate the significant shifts in belowground microbial taxonomic and functional diversity following vegetation restoration and have implications for ecological restoration programs in arid and semi-arid ecosystems. Copyright © 2018. Published by Elsevier B.V.

Indoor-air microbiome in an urban subway network: diversity and dynamics.

PubMed

Leung, Marcus H Y; Wilkins, David; Li, Ellen K T; Kong, Fred K F; Lee, Patrick K H

2014-11-01

Subway systems are indispensable for urban societies, but microbiological characteristics of subway aerosols are relatively unknown. Previous studies investigating microbial compositions in subways employed methodologies that underestimated the diversity of microbial exposure for commuters, with little focus on factors governing subway air microbiology, which may have public health implications. Here, a culture-independent approach unraveling the bacterial diversity within the urban subway network in Hong Kong is presented. Aerosol samples from multiple subway lines and outdoor locations were collected. Targeting the 16S rRNA gene V4 region, extensive taxonomic diversity was found, with the most common bacterial genera in the subway environment among those associated with skin. Overall, subway lines harbored different phylogenetic communities based on α- and β-diversity comparisons, and closer inspection suggests that each community within a line is dependent on architectural characteristics, nearby outdoor microbiomes, and connectedness with other lines. Microbial diversities and assemblages also varied depending on the day sampled, as well as the time of day, and changes in microbial communities between peak and nonpeak commuting hours were attributed largely to increases in skin-associated genera in peak samples. Microbial diversities within the subway were influenced by temperature and relative humidity, while carbon dioxide levels showed a positive correlation with abundances of commuter-associated genera. This Hong Kong data set and communities from previous studies conducted in the United States formed distinct community clusters, indicating that additional work is required to unravel the mechanisms that shape subway microbiomes around the globe. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems

PubMed Central

Perez-Garcia, Octavio; Lear, Gavin; Singhal, Naresh

2016-01-01

We review approaches to characterize metabolic interactions within microbial communities using Stoichiometric Metabolic Network (SMN) models for applications in environmental and industrial biotechnology. SMN models are computational tools used to evaluate the metabolic engineering potential of various organisms. They have successfully been applied to design and optimize the microbial production of antibiotics, alcohols and amino acids by single strains. To date however, such models have been rarely applied to analyze and control the metabolism of more complex microbial communities. This is largely attributed to the diversity of microbial community functions, metabolisms, and interactions. Here, we firstly review different types of microbial interaction and describe their relevance for natural and engineered environmental processes. Next, we provide a general description of the essential methods of the SMN modeling workflow including the steps of network reconstruction, simulation through Flux Balance Analysis (FBA), experimental data gathering, and model calibration. Then we broadly describe and compare four approaches to model microbial interactions using metabolic networks, i.e., (i) lumped networks, (ii) compartment per guild networks, (iii) bi-level optimization simulations, and (iv) dynamic-SMN methods. These approaches can be used to integrate and analyze diverse microbial physiology, ecology and molecular community data. All of them (except the lumped approach) are suitable for incorporating species abundance data but so far they have been used only to model simple communities of two to eight different species. Interactions based on substrate exchange and competition can be directly modeled using the above approaches. However, interactions based on metabolic feedbacks, such as product inhibition and synthropy require extensions to current models, incorporating gene regulation and compounding accumulation mechanisms. SMN models of microbial interactions can be used to analyze complex “omics” data and to infer and optimize metabolic processes. Thereby, SMN models are suitable to capitalize on advances in high-throughput molecular and metabolic data generation. SMN models are starting to be applied to describe microbial interactions during wastewater treatment, in-situ bioremediation, microalgae blooms methanogenic fermentation, and bioplastic production. Despite their current challenges, we envisage that SMN models have future potential for the design and development of novel growth media, biochemical pathways and synthetic microbial associations. PMID:27242701

Estimating and comparing microbial diversity in the presence of sequencing errors

PubMed Central

Chiu, Chun-Huo

2016-01-01

Estimating and comparing microbial diversity are statistically challenging due to limited sampling and possible sequencing errors for low-frequency counts, producing spurious singletons. The inflated singleton count seriously affects statistical analysis and inferences about microbial diversity. Previous statistical approaches to tackle the sequencing errors generally require different parametric assumptions about the sampling model or about the functional form of frequency counts. Different parametric assumptions may lead to drastically different diversity estimates. We focus on nonparametric methods which are universally valid for all parametric assumptions and can be used to compare diversity across communities. We develop here a nonparametric estimator of the true singleton count to replace the spurious singleton count in all methods/approaches. Our estimator of the true singleton count is in terms of the frequency counts of doubletons, tripletons and quadrupletons, provided these three frequency counts are reliable. To quantify microbial alpha diversity for an individual community, we adopt the measure of Hill numbers (effective number of taxa) under a nonparametric framework. Hill numbers, parameterized by an order q that determines the measures’ emphasis on rare or common species, include taxa richness (q = 0), Shannon diversity (q = 1, the exponential of Shannon entropy), and Simpson diversity (q = 2, the inverse of Simpson index). A diversity profile which depicts the Hill number as a function of order q conveys all information contained in a taxa abundance distribution. Based on the estimated singleton count and the original non-singleton frequency counts, two statistical approaches (non-asymptotic and asymptotic) are developed to compare microbial diversity for multiple communities. (1) A non-asymptotic approach refers to the comparison of estimated diversities of standardized samples with a common finite sample size or sample completeness. This approach aims to compare diversity estimates for equally-large or equally-complete samples; it is based on the seamless rarefaction and extrapolation sampling curves of Hill numbers, specifically for q = 0, 1 and 2. (2) An asymptotic approach refers to the comparison of the estimated asymptotic diversity profiles. That is, this approach compares the estimated profiles for complete samples or samples whose size tends to be sufficiently large. It is based on statistical estimation of the true Hill number of any order q ≥ 0. In the two approaches, replacing the spurious singleton count by our estimated count, we can greatly remove the positive biases associated with diversity estimates due to spurious singletons and also make fair comparisons across microbial communities, as illustrated in our simulation results and in applying our method to analyze sequencing data from viral metagenomes. PMID:26855872

Comparison of bacterial communities from lava cave microbial mats to overlying surface soils from Lava Beds National Monument, USA

PubMed Central

Read, Kaitlyn J. H.; Hughes, Evan M.; Spilde, Michael N.

2017-01-01

Subsurface habitats harbor novel diversity that has received little attention until recently. Accessible subsurface habitats include lava caves around the world that often support extensive microbial mats on ceilings and walls in a range of colors. Little is known about lava cave microbial diversity and how these subsurface mats differ from microbial communities in overlying surface soils. To investigate these differences, we analyzed bacterial 16S rDNA from 454 pyrosequencing from three colors of microbial mats (tan, white, and yellow) from seven lava caves in Lava Beds National Monument, CA, USA, and compared them with surface soil overlying each cave. The same phyla were represented in both surface soils and cave microbial mats, but the overlap in shared OTUs (operational taxonomic unit) was only 11.2%. Number of entrances per cave and temperature contributed to observed differences in diversity. In terms of species richness, diversity by mat color differed, but not significantly. Actinobacteria dominated in all cave samples, with 39% from caves and 21% from surface soils. Proteobacteria made up 30% of phyla from caves and 36% from surface soil. Other major phyla in caves were Nitrospirae (7%) followed by minor phyla (7%), compared to surface soils with Bacteroidetes (8%) and minor phyla (8%). Many of the most abundant sequences could not be identified to genus, indicating a high degree of novelty. Surface soil samples had more OTUs and greater diversity indices than cave samples. Although surface soil microbes immigrate into underlying caves, the environment selects for microbes able to live in the cave habitats, resulting in very different cave microbial communities. This study is the first comprehensive comparison of bacterial communities in lava caves with the overlying soil community. PMID:28199330

Predator identity more than predator richness structures aquatic microbial assemblages in Sarracenia purpurea leaves.

PubMed

Canter, Erin J; Cuellar-Gempeler, Catalina; Pastore, Abigail I; Miller, Thomas E; Mason, Olivia U

2018-03-01

The importance of predators in influencing community structure is a well-studied area of ecology. However, few studies test ecological hypotheses of predation in multi-predator microbial communities. The phytotelmic community found within the water-filled leaves of the pitcher plant, Sarracenia purpurea, exhibits a simple trophic structure that includes multiple protozoan predators and microbial prey. Using this system, we sought to determine whether different predators target distinct microorganisms, how interactions among protozoans affect resource (microorganism) use, and how predator diversity affects prey community diversity. In particular, we endeavored to determine if protozoa followed known ecological patterns such as keystone predation or generalist predation. For these experiments, replicate inquiline microbial communities were maintained for seven days with five protozoan species. Microbial community structure was determined by 16S rRNA gene amplicon sequencing (iTag) and analysis. Compared to the control (no protozoa), two ciliates followed patterns of keystone predation by increasing microbial evenness. In pairwise competition treatments with a generalist flagellate, prey communities resembled the microbial communities of the respective keystone predator in monoculture. The relative abundance of the most common bacterial Operational Taxonomic Unit (OTU) in our system decreased compared to the control in the presence of these ciliates. This OTU was 98% similar to a known chitin degrader and nitrate reducer, important functions for the microbial community and the plant host. Collectively, the data demonstrated that predator identity had a greater effect on prey diversity and composition than overall predator diversity. © 2018 by the Ecological Society of America.

An Integrated Insight into the Relationship between Soil Microbial Community and Tobacco Bacterial Wilt Disease

PubMed Central

Yang, Hongwu; Li, Juan; Xiao, Yunhua; Gu, Yabing; Liu, Hongwei; Liang, Yili; Liu, Xueduan; Hu, Jin; Meng, Delong; Yin, Huaqun

2017-01-01

The soil microbial communities play an important role in plant health, however, the relationship between the below-ground microbiome and above-ground plant health remains unclear. To reveal such a relationship, we analyzed soil microbial communities through sequencing of 16S rRNA gene amplicons from 15 different tobacco fields with different levels of wilt disease in the central south part of China. We found that plant health was related to the soil microbial diversity as plants may benefit from the diverse microbial communities. Also, those 15 fields were grouped into ‘healthy’ and ‘infected’ samples based upon soil microbial community composition analyses such as unweighted paired-group method with arithmetic means (UPGMA) and principle component analysis, and furthermore, molecular ecological network analysis indicated that some potential plant-beneficial microbial groups, e.g., Bacillus and Actinobacteria could act as network key taxa, thus reducing the chance of plant soil-borne pathogen invasion. In addition, we propose that a more complex soil ecology network may help suppress tobacco wilt, which was also consistent with highly diversity and composition with plant-beneficial microbial groups. This study provides new insights into our understanding the relationship between the soil microbiome and plant health. PMID:29163453

Host Ecology Rather Than Host Phylogeny Drives Amphibian Skin Microbial Community Structure in the Biodiversity Hotspot of Madagascar

PubMed Central

Bletz, Molly C.; Archer, Holly; Harris, Reid N.; McKenzie, Valerie J.; Rabemananjara, Falitiana C. E.; Rakotoarison, Andolalao; Vences, Miguel

2017-01-01

Host-associated microbiotas of vertebrates are diverse and complex communities that contribute to host health. In particular, for amphibians, cutaneous microbial communities likely play a significant role in pathogen defense; however, our ecological understanding of these communities is still in its infancy. Here, we take advantage of the fully endemic and locally species-rich amphibian fauna of Madagascar to investigate the factors structuring amphibian skin microbiota on a large scale. Using amplicon-based sequencing, we evaluate how multiple host species traits and site factors affect host bacterial diversity and community structure. Madagascar is home to over 400 native frog species, all of which are endemic to the island; more than 100 different species are known to occur in sympatry within multiple rainforest sites. We intensively sampled frog skin bacterial communities, from over 800 amphibians from 89 species across 30 sites in Madagascar during three field visits, and found that skin bacterial communities differed strongly from those of the surrounding environment. Richness of bacterial operational taxonomic units (OTUs) and phylogenetic diversity differed among host ecomorphs, with arboreal frogs exhibiting lower richness and diversity than terrestrial and aquatic frogs. Host ecomorphology was the strongest factor influencing microbial community structure, with host phylogeny and site parameters (latitude and elevation) explaining less but significant portions of the observed variation. Correlation analysis and topological congruency analyses revealed little to no phylosymbiosis for amphibian skin microbiota. Despite the observed geographic variation and low phylosymbiosis, we found particular OTUs that were differentially abundant between particular ecomorphs. For example, the genus Pigmentiphaga (Alcaligenaceae) was significantly enriched on arboreal frogs, Methylotenera (Methylophilaceae) was enriched on aquatic frogs, and Agrobacterium (Rhizobiaceae) was enriched on terrestrial frogs. The presence of shared bacterial OTUs across geographic regions for selected host genera suggests the presence of core microbial communities which in Madagascar, might be driven more strongly by a species’ preference for specific microhabitats than by the physical, physiological or biochemical properties of their skin. These results corroborate that both host and environmental factors are driving community assembly of amphibian cutaneous microbial communities, and provide an improved foundation for elucidating their role in disease resistance. PMID:28861051

Metagenomics Reveals the Influence of Land Use and Rain on the Benthic Microbial Communities in a Tropical Urban Waterway

PubMed Central

2018-01-01

ABSTRACT Growing demands for potable water have led to extensive reliance on waterways in tropical megacities. Attempts to manage these waterways in an environmentally sustainable way generally lack an understanding of microbial processes and how they are influenced by urban factors, such as land use and rain. Here, we describe the composition and functional potential of benthic microbial communities from an urban waterway network and analyze the effects of land use and rain perturbations on these communities. With a sequence depth of 3 billion reads from 48 samples, these metagenomes represent nearly full coverage of microbial communities. The predominant taxa in these waterways were Nitrospira and Coleofasciculus, indicating the presence of nitrogen and carbon fixation in this system. Gene functions from carbohydrate, protein, and nucleic acid metabolism suggest the presence of primary and secondary productivity in such nutrient-deficient systems. Comparison of microbial communities by land use type and rain showed that while there are significant differences in microbial communities in land use, differences due to rain perturbations were rain event specific. The more diverse microbial communities in the residential areas featured a higher abundance of reads assigned to genes related to community competition. However, the less diverse communities from industrial areas showed a higher abundance of reads assigned to specialized functions such as organic remediation. Finally, our study demonstrates that microbially diverse populations in well-managed waterways, where contaminant levels are within defined limits, are comparable to those in other relatively undisturbed freshwater systems. IMPORTANCE Unravelling the microbial metagenomes of urban waterway sediments suggest that well-managed urban waterways have the potential to support diverse sedimentary microbial communities, similar to those of undisturbed natural freshwaters. Despite the fact that these urban waterways are well managed, our study shows that environmental pressures from land use and rain perturbations play a role in shaping the structure and functions of microbial communities in these waterways. We propose that although pulsed disturbances, such as rain perturbations, influence microbial communities, press disturbances, including land usage history, have a long-term and stronger influence on microbial communities. Our study found that the functions of microbial communities were less affected by environmental factors than the structure of microbial communities was, indicating that core microbial functions largely remain conserved in challenging environments. PMID:29896568

Metagenomics Reveals the Influence of Land Use and Rain on the Benthic Microbial Communities in a Tropical Urban Waterway.

PubMed

Saxena, Gourvendu; Mitra, Suparna; Marzinelli, Ezequiel M; Xie, Chao; Wei, Toh Jun; Steinberg, Peter D; Williams, Rohan B H; Kjelleberg, Staffan; Lauro, Federico M; Swarup, Sanjay

2018-01-01

Growing demands for potable water have led to extensive reliance on waterways in tropical megacities. Attempts to manage these waterways in an environmentally sustainable way generally lack an understanding of microbial processes and how they are influenced by urban factors, such as land use and rain. Here, we describe the composition and functional potential of benthic microbial communities from an urban waterway network and analyze the effects of land use and rain perturbations on these communities. With a sequence depth of 3 billion reads from 48 samples, these metagenomes represent nearly full coverage of microbial communities. The predominant taxa in these waterways were Nitrospira and Coleofasciculus , indicating the presence of nitrogen and carbon fixation in this system. Gene functions from carbohydrate, protein, and nucleic acid metabolism suggest the presence of primary and secondary productivity in such nutrient-deficient systems. Comparison of microbial communities by land use type and rain showed that while there are significant differences in microbial communities in land use, differences due to rain perturbations were rain event specific. The more diverse microbial communities in the residential areas featured a higher abundance of reads assigned to genes related to community competition. However, the less diverse communities from industrial areas showed a higher abundance of reads assigned to specialized functions such as organic remediation. Finally, our study demonstrates that microbially diverse populations in well-managed waterways, where contaminant levels are within defined limits, are comparable to those in other relatively undisturbed freshwater systems. IMPORTANCE Unravelling the microbial metagenomes of urban waterway sediments suggest that well-managed urban waterways have the potential to support diverse sedimentary microbial communities, similar to those of undisturbed natural freshwaters. Despite the fact that these urban waterways are well managed, our study shows that environmental pressures from land use and rain perturbations play a role in shaping the structure and functions of microbial communities in these waterways. We propose that although pulsed disturbances, such as rain perturbations, influence microbial communities, press disturbances, including land usage history, have a long-term and stronger influence on microbial communities. Our study found that the functions of microbial communities were less affected by environmental factors than the structure of microbial communities was, indicating that core microbial functions largely remain conserved in challenging environments.

Bacterial community and groundwater quality changes in an anaerobic aquifer during groundwater recharge with aerobic recycled water.

PubMed

Ginige, Maneesha P; Kaksonen, Anna H; Morris, Christina; Shackelton, Mark; Patterson, Bradley M

2013-09-01

Managed aquifer recharge offers the opportunity to manage groundwater resources by storing water in aquifers when in surplus and thus increase the amount of groundwater available for abstraction during high demand. The Water Corporation of Western Australia (WA) is undertaking a Groundwater Replenishment Trial to evaluate the effects of recharging aerobic recycled water (secondary treated wastewater subjected to ultrafiltration, reverse osmosis, and ultraviolet disinfection) into the anaerobic Leederville aquifer in Perth, WA. Using culture-independent methods, this study showed the presence of Actinobacteria, Alphaproteobacteria, Bacilli, Betaproteobacteria, Cytophaga, Flavobacteria, Gammaproteobacteria, and Sphingobacteria, and a decrease in microbial diversity with an increase in depth of aquifer. Assessment of physico-chemical and microbiological properties of groundwater before and after recharge revealed that recharging the aquifer with aerobic recycled water resulted in elevated redox potentials in the aquifer and increased bacterial numbers, but reduced microbial diversity. The increase in bacterial numbers and reduced microbial diversity in groundwater could be a reflection of an increased denitrifier and sulfur-oxidizing populations in the aquifer, as a result of the increased availability of nitrate, oxygen, and residual organic matter. This is consistent with the geochemical data that showed pyrite oxidation and denitrification within the aquifer after recycled water recharge commenced. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

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

Wieder, William R.; Allison, Steven D.; Davidson, Eric A.

Microbes influence soil organic matter (SOM) decomposition and the long-term stabilization of carbon (C) in soils. We contend that by revising the representation of microbial processes and their interactions with the physicochemical soil environment, Earth system models (ESMs) may make more realistic global C cycle projections. Explicit representation of microbial processes presents considerable challenges due to the scale at which these processes occur. Thus, applying microbial theory in ESMs requires a framework to link micro-scale process-level understanding and measurements to macro-scale models used to make decadal- to century-long projections. Here, we review the diversity, advantages, and pitfalls of simulating soilmore » biogeochemical cycles using microbial-explicit modeling approaches. We present a roadmap for how to begin building, applying, and evaluating reliable microbial-explicit model formulations that can be applied in ESMs. Drawing from experience with traditional decomposition models we suggest: (1) guidelines for common model parameters and output that can facilitate future model intercomparisons; (2) development of benchmarking and model-data integration frameworks that can be used to effectively guide, inform, and evaluate model parameterizations with data from well-curated repositories; and (3) the application of scaling methods to integrate microbial-explicit soil biogeochemistry modules within ESMs. With contributions across scientific disciplines, we feel this roadmap can advance our fundamental understanding of soil biogeochemical dynamics and more realistically project likely soil C response to environmental change at global scales.« less

Microbial Functional Gene Diversity with a Shift of Subsurface Redox Conditions during In Situ Uranium Reduction

PubMed Central

Liang, Yuting; Van Nostrand, Joy D.; N′Guessan, Lucie A.; Peacock, Aaron D.; Deng, Ye; Long, Philip E.; Resch, C. Tom; Wu, Liyou; He, Zhili; Li, Guanghe; Hazen, Terry C.; Lovley, Derek R.

2012-01-01

To better understand the microbial functional diversity changes with subsurface redox conditions during in situ uranium bioremediation, key functional genes were studied with GeoChip, a comprehensive functional gene microarray, in field experiments at a uranium mill tailings remedial action (UMTRA) site (Rifle, CO). The results indicated that functional microbial communities altered with a shift in the dominant metabolic process, as documented by hierarchical cluster and ordination analyses of all detected functional genes. The abundance of dsrAB genes (dissimilatory sulfite reductase genes) and methane generation-related mcr genes (methyl coenzyme M reductase coding genes) increased when redox conditions shifted from Fe-reducing to sulfate-reducing conditions. The cytochrome genes detected were primarily from Geobacter sp. and decreased with lower subsurface redox conditions. Statistical analysis of environmental parameters and functional genes indicated that acetate, U(VI), and redox potential (Eh) were the most significant geochemical variables linked to microbial functional gene structures, and changes in microbial functional diversity were strongly related to the dominant terminal electron-accepting process following acetate addition. The study indicates that the microbial functional genes clearly reflect the in situ redox conditions and the dominant microbial processes, which in turn influence uranium bioreduction. Microbial functional genes thus could be very useful for tracking microbial community structure and dynamics during bioremediation. PMID:22327592

Microbial Life in Ridge Flank Crustal Fluids at Baby Bare Seamount, Juan de Fuca Ridge

NASA Astrophysics Data System (ADS)

Huber, J. A.; Johnson, H. P.; Butterfield, D. A.; Baross, J. A.

2005-12-01

To determine the microbial community diversity within old oceanic crust, a novel sampling strategy was used to collect crustal fluids at Baby Bare Seamount, a 3.5 Ma old outcrop located in the northeast Pacific Ocean on the eastern flank of the Juan de Fuca Ridge. Stainless steel probes were driven directly into the igneous ocean crust to obtain samples of ridge flank crustal fluids. Genetic signatures and enrichment cultures of microorganisms demonstrate that these crustal fluids host a microbial community composed of species indigenous to the subseafloor, including anaerobic thermophiles, and species from other deep-sea habitats, such as seawater and sediments. Evidence using molecular techniques indicates the presence of a relatively small but active microbial population, dominated by bacteria. The microbial community diversity found in the crustal fluids may indicate habitat variability in old oceanic crust, with inputs of nutrients from seawater, sediment pore-water fluids and possibly hydrothermal sources. This report further supports the presence of an indigenous microbial community in ridge flank crustal fluids and advances our understanding of the potential physiological and phylogenetic diversity of this community.

Diversity of Arbuscular Mycorrhizal Fungi in a Brazilian Atlantic Forest Toposequence.

PubMed

Bonfim, Joice Andrade; Vasconcellos, Rafael Leandro Figueiredo; Gumiere, Thiago; de Lourdes Colombo Mescolotti, Denise; Oehl, Fritz; Nogueira Cardoso, Elke Jurandy Bran

2016-01-01

The diversity of arbuscular mycorrhizal fungi (AMF) was studied in the Atlantic Forest in Serra do Mar Park (SE Brazil), based on seven host plants in relationship to their soil environment, altitude and seasonality. The studied plots along an elevation gradient are located at 80, 600, and 1,000 m. Soil samples (0-20 cm) were collected in four seasons from SE Brazilian winter 2012 to autumn 2013. AMF spores in rhizosperic soils were morphologically classified and chemical, physical and microbiological soil caracteristics were determined. AMF diversity in roots was evaluated using the NS31/AM1 primer pair, with subsequent cloning and sequencing. In the rhizosphere, 58 AMF species were identified. The genera Acaulospora and Glomus were predominant. However, in the roots, only 14 AMF sequencing groups were found and all had high similarity to Glomeraceae. AMF species identities varied between altitudes and seasons. There were species that contributed the most to this variation. Some soil characteristics (pH, organic matter, microbial activity and microbial biomass carbon) showed a strong relationship with the occurrence of certain species. The highest AMF species diversity, based on Shannon's diversity index, was found for the highest altitude. Seasonality did not affect the diversity. Our results show a high AMF diversity, higher than commonly found in the Atlantic Forest. The AMF detected in roots were not identical to those detected in rhizosperic soil and differences in AMF communities were found in different altitudes even in geographically close-lying sites.

MICROBIAL DIVERSITY IN SURFACE SEDIMENTS: A COMPARISON OF TWO ESTUARINE CONTINUUMS

EPA Science Inventory

The microbial diversity in estuarine sediments of the Altamaha and Savannah Rivers in Georgia were compared temporally and spatially using phospholipid fatty acid (PLFA) analysis. Surface sediment samples collected along a salinity gradient were also analyzed for ATP, TOC, and C ...

Loss of soil microbial diversity may increase insecticide uptake by crop

USDA-ARS?s Scientific Manuscript database

Belowground biodiversity is essential for soil functioning, but the effect of belowground biodiversity loss on food safety is unknown. We investigated the loss of soil microbial diversity on insecticides accumulation in Brassica. We manipulated soil biodiversity using the dilution-to-extinction appr...

Changing bacterial profile of Sundarbans, the world heritage mangrove: impact of anthropogenic interventions.

PubMed

Chakraborty, Arpita; Bera, Amit; Mukherjee, Arghya; Basak, Pijush; Khan, Imroze; Mondal, Arindam; Roy, Arunava; Bhattacharyya, Anish; SenGupta, Sohan; Roy, Debojyoti; Nag, Sudip; Ghosh, Abhrajyoti; Chattopadhyay, Dhrubajyoti; Bhattacharyya, Maitree

2015-04-01

Mangrove microbial communities and their associated activities have profound impact on biogeochemical cycles. Although microbial composition and structure are known to be influenced by biotic and abiotic factors in the mangrove sediments, finding direct correlations between them remains a challenge. In this study we have explored sediment bacterial diversity of the Sundarbans, a world heritage site using a culture-independent molecular approach. Bacterial diversity was analyzed from three different locations with a history of exposure to differential anthropogenic activities. 16S rRNA gene libraries were constructed and partial sequencing of the clones was performed to identify the microbial strains. We identified bacterial strains known to be involved in a variety of biodegradation/biotransformation processes including hydrocarbon degradation, and heavy metal resistance. Canonical Correspondence Analysis of the environmental and exploratory datasets revealed correlations between the ecological indices associated with pollutant levels and bacterial diversity across the sites. Our results indicate that sites with similar exposure of anthropogenic intervention reflect similar patterns of microbial diversity besides spatial commonalities.

Gut microbial profile analysis by MiSeq sequencing of pancreatic carcinoma patients in China

PubMed Central

Xie, Haiyang; Li, Ang; Lu, Haifeng; Xu, Shaoyan; Zhou, Lin; Zhang, Hua; Cui, Guangying; Chen, Xinhua; Liu, Yuanxing; Wu, Liming; Qin, Nan; Sun, Ranran; Wang, Wei; Li, Lanjuan; Wang, Weilin; Zheng, Shusen

2017-01-01

Pancreatic carcinoma (PC) is a lethal cancer. Gut microbiota is associated with some risk factors of PC, e.g. obesity and types II diabetes. However, the specific gut microbial profile in clinical PC in China has never been reported. This prospective study collected 85 PC and 57 matched healthy controls (HC) to analyze microbial characteristics by MiSeq sequencing. The results showed that gut microbial diversity was decreased in PC with an unique microbial profile, which partly attributed to its decrease of alpha diversity. Microbial alterations in PC featured by the increase of certain pathogens and lipopolysaccharides-producing bacteria, and the decrease of probiotics and butyrate-producing bacteria. Microbial community in obstruction cases was separated from the un-obstructed cases. Streptococcus was associated with the bile. Furthermore, 23 microbial functions e.g. Leucine and LPS biosynthesis were enriched, while 13 functions were reduced in PC. Importantly, based on 40 genera associated with PC, microbial markers achieves a high classification power with AUC of 0.842. In conclusion, gut microbial profile was unique in PC, providing a microbial marker for non-invasive PC diagnosis. PMID:29221120

Pyrosequencing reveals highly diverse and species-specific microbial communities in sponges from the Red Sea

PubMed Central

Lee, On On; Wang, Yong; Yang, Jiangke; Lafi, Feras F; Al-Suwailem, Abdulaziz; Qian, Pei-Yuan

2011-01-01

Marine sponges are associated with a remarkable array of microorganisms. Using a tag pyrosequencing technology, this study was the first to investigate in depth the microbial communities associated with three Red Sea sponges, Hyrtios erectus, Stylissa carteri and Xestospongia testudinaria. We revealed highly diverse sponge-associated bacterial communities with up to 1000 microbial operational taxonomic units (OTUs) and richness estimates of up to 2000 species. Altogether, 26 bacterial phyla were detected from the Red Sea sponges, 11 of which were absent from the surrounding sea water and 4 were recorded in sponges for the first time. Up to 100 OTUs with richness estimates of up to 300 archaeal species were revealed from a single sponge species. This is by far the highest archaeal diversity ever recorded for sponges. A non-negligible proportion of unclassified reads was observed in sponges. Our results demonstrated that the sponge-associated microbial communities remained highly consistent in the same sponge species from different locations, although they varied at different degrees among different sponge species. A significant proportion of the tag sequences from the sponges could be assigned to one of the sponge-specific clusters previously defined. In addition, the sponge-associated microbial communities were consistently divergent from those present in the surrounding sea water. Our results suggest that the Red Sea sponges possess highly sponge-specific or even sponge-species-specific microbial communities that are resistant to environmental disturbance, and much of their microbial diversity remains to be explored. PMID:21085196

Soil microbial diversity in the vicinity of desert shrubs.

PubMed

Saul-Tcherkas, Vered; Unc, Adrian; Steinberger, Yosef

2013-04-01

Water and nutrient availability are the major limiting factors of biological activity in arid and semiarid ecosystems. Therefore, perennial plants have developed different ecophysiological adaptations to cope with harsh conditions. The chemical profile of the root exudates varies among plant species and this can induce variability in associated microbial populations. We examined the influence of two shrubs species, Artemisia sieberi and Noaea mucronata, on soil microbial diversity. Soil samples were collected monthly, from December 2006 to November 2007, near canopies of both shrubs (0-10-cm depth). Samples were used for abiotic tests and determination of soil bacterial diversity. No significant differences were found in the abiotic variables (soil moisture, total organic matter, and total soluble nitrogen (TSN)) between soil samples collected from under the two shrubs during the study period. No obvious differences in the Shannon-Weaver index, evenness values, or total phylogenetic distances were found for the soil microbial communities. However, detailed denaturing gradient gel electrophoresis (DGGE) clustering as well as taxonomic diversity analyses indicated clear shifts in the soil microbial community composition. These shifts were governed by seasonal variability in water availability and, significantly, by plant species type.

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.

Metaproteogenomic Profiling of Microbial Communities Colonizing Actively Venting Hydrothermal Chimneys

PubMed Central

Pjevac, Petra; Meier, Dimitri V.; Markert, Stephanie; Hentschker, Christian; Schweder, Thomas; Becher, Dörte; Gruber-Vodicka, Harald R.; Richter, Michael; Bach, Wolfgang; Amann, Rudolf; Meyerdierks, Anke

2018-01-01

At hydrothermal vent sites, chimneys consisting of sulfides, sulfates, and oxides are formed upon contact of reduced hydrothermal fluids with oxygenated seawater. The walls and surfaces of these chimneys are an important habitat for vent-associated microorganisms. We used community proteogenomics to investigate and compare the composition, metabolic potential and relative in situ protein abundance of microbial communities colonizing two actively venting hydrothermal chimneys from the Manus Basin back-arc spreading center (Papua New Guinea). We identified overlaps in the in situ functional profiles of both chimneys, despite differences in microbial community composition and venting regime. Carbon fixation on both chimneys seems to have been primarily mediated through the reverse tricarboxylic acid cycle and fueled by sulfur-oxidation, while the abundant metabolic potential for hydrogen oxidation and carbon fixation via the Calvin–Benson–Bassham cycle was hardly utilized. Notably, the highly diverse microbial community colonizing the analyzed black smoker chimney had a highly redundant metabolic potential. In contrast, the considerably less diverse community colonizing the diffusely venting chimney displayed a higher metabolic versatility. An increased diversity on the phylogenetic level is thus not directly linked to an increased metabolic diversity in microbial communities that colonize hydrothermal chimneys. PMID:29696004

Centralized Drinking Water Treatment Operations Shape Bacterial and Fungal Community Structure.

PubMed

Ma, Xiao; Vikram, Amit; Casson, Leonard; Bibby, Kyle

2017-07-05

Drinking water microbial communities impact opportunistic pathogen colonization and corrosion of water distribution systems, and centralized drinking water treatment represents a potential control for microbial community structure in finished drinking water. In this article, we examine bacterial and fungal abundance and diversity, as well as the microbial community taxonomic structure following each unit operation in a conventional surface water treatment plant. Treatment operations drove the microbial composition more strongly than sampling time. Both bacterial and fungal abundance and diversity decreased following sedimentation and filtration; however, only bacterial abundance and diversity was significantly impacted by free chlorine disinfection. Similarly, each treatment step was found to shift bacterial and fungal community beta-diversity, with the exception of disinfection on the fungal community structure. We observed the enrichment of bacterial and fungal taxa commonly found in drinking water distribution systems through the treatment process, for example, Sphingomonas following filtration and Leptospirillium and Penicillium following disinfection. Study results suggest that centralized drinking water treatment processes shape the final drinking water microbial community via selection of community members and that the bacterial community is primarily driven by disinfection while the eukaryotic community is primarily controlled by physical treatment processes.

Abundance and diversity of microbial inhabitants in European spacecraft-associated clean rooms.

PubMed

Stieglmeier, Michaela; Rettberg, Petra; Barczyk, Simon; Bohmeier, Maria; Pukall, Rüdiger; Wirth, Reinhard; Moissl-Eichinger, Christine

2012-06-01

The determination of the microbial load of a spacecraft en route to interesting extraterrestrial environments is mandatory and currently based on the culturable, heat-shock-surviving portion of microbial contaminants. Our study compared these classical bioburden measurements as required by NASA's and ESA's guidelines for the microbial examination of flight hardware, with molecular analysis methods (16S rRNA gene cloning and quantitative PCR) to further develop our understanding of the diversity and abundance of the microbial communities of spacecraft-associated clean rooms. Three samplings of the Herschel Space Observatory and its surrounding clean rooms were performed in two different European facilities. Molecular analyses detected a broad diversity of microbes typically found in the human microbiome with three bacterial genera (Staphylococcus, Propionibacterium, and Brevundimonas) common to all three locations. Bioburden measurements revealed a low, but heterogeneous, abundance of spore-forming and other heat-resistant microorganisms. Total cell numbers estimated by quantitative real-time PCR were typically 3 orders of magnitude greater than those determined by viable counts, which indicates a tendency for traditional methods to underestimate the extent of clean room bioburden. Furthermore, the molecular methods allowed the detection of a much broader diversity than traditional culture-based methods.

Microbial composition in microcosms amended with natural and mineral fertilizers under different water regimes

NASA Astrophysics Data System (ADS)

Brad, Traian; Chiriac, Cecilia; Szekeres, Edina; Coman, Cristian; Rudi, Knut; Sandor, Mignon

2017-04-01

Twenty microcosm enclosures containing two types of soil (i.e. a rich Chernozemic and a poorer soil) were fertilized with mineral (NPK-complex) and organic (Gülle, manure and a green fertilizer) materials and placed under dry and wet water regimes. After 10, 20 and 30 days of the experiment, soil samples were analyzed for the structure and composition of microbial communities using next generation sequencing techniques (Illumina) and statistical analysis. The differences between bacteria communities in different soil types, and in different fertilization and hydric treatments were analyzed using quantitative phylogenetic distances and the ANOSIM test. The two types of soil especially selected for the structure of microbial communities, while moisture and the type of fertilizer appeared to have a smaller influence on microbial diversity in microcosms. The alpha-diversity indices (species richness, evenness and phylogenetic diversity) had higher values for the poorer soil compared to the rich Chernozemic soil. For both soil types, the highest bacteria diversity values were obtained after fertilization with manure. The microbial communities in the analyzed soils were complex and dominated by sequences belonging to Actinobacteria, Proteobacteria, Acidobacteria and Firmicutes.

Effects of Resource Chemistry on the Composition and Function of Stream Hyporheic Biofilms

PubMed Central

Hall, E. K.; Besemer, K.; Kohl, L.; Preiler, C.; Riedel, K.; Schneider, T.; Wanek, W.; Battin, T. J.

2012-01-01

Fluvial ecosystems process large quantities of dissolved organic matter as it moves from the headwater streams to the sea. In particular, hyporheic sediments are centers of high biogeochemical reactivity due to their elevated residence time and high microbial biomass and activity. However, the interaction between organic matter and microbial dynamics in the hyporheic zone remains poorly understood. We evaluated how variance in resource chemistry affected the microbial community and its associated activity in experimentally grown hyporheic biofilms. To do this we fed beech leaf leachates that differed in chemical composition to a series of bioreactors filled with sediment from a sub-alpine stream. Differences in resource chemistry resulted in differences in diversity and phylogenetic origin of microbial proteins, enzyme activity, and microbial biomass stoichiometry. Specifically, increased lignin, phenolics, and manganese in a single leachate resulted in increased phenoloxidase and peroxidase activity, elevated microbial biomass carbon:nitrogen ratio, and a greater proportion of proteins of Betaproteobacteria origin. We used this model system to attempt to link microbial form (community composition and metaproteome) with function (enzyme activity) in order to better understand the mechanisms that link resource heterogeneity to ecosystem function in stream ecosystems. PMID:22347877

Effects of resource chemistry on the composition and function of stream hyporheic biofilms.

USGS Publications Warehouse

Hall, E.K.; Besemer, K.; Kohl, L.; Preiler, C.; Reidel, K.; Schneider, T.; Wanek, W.; Battin, T.J.

2012-01-01

Fluvial ecosystems process large quantities of dissolved organic matter as it moves from the headwater streams to the sea. In particular, hyporheic sediments are centers of high biogeochemical reactivity due to their elevated residence time and high microbial biomass and activity. However, the interaction between organic matter and microbial dynamics in the hyporheic zone remains poorly understood. We evaluated how variance in resource chemistry affected the microbial community and its associated activity in experimentally grown hyporheic biofilms. To do this we fed beech leaf leachates that differed in chemical composition to a series of bioreactors filled with sediment from a sub-alpine stream. Differences in resource chemistry resulted in differences in diversity and phylogenetic origin of microbial proteins, enzyme activity, and microbial biomass stoichiometry. Specifically, increased lignin, phenolics, and manganese in a single leachate resulted in increased phenoloxidase and peroxidase activity, elevated microbial biomass carbon:nitrogen ratio, and a greater proportion of proteins of Betaproteobacteria origin. We used this model system to attempt to link microbial form (community composition and metaproteome) with function (enzyme activity) in order to better understand the mechanisms that link resource heterogeneity to ecosystem function in stream ecosystems.

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.

Bacterial diversity in goat milk from the Guanzhong area of China.

PubMed

Zhang, Fuxin; Wang, Zhaoxia; Lei, Feiyan; Wang, Bini; Jiang, Shuaiming; Peng, Qiannan; Zhang, Jiachao; Shao, Yuyu

2017-10-01

In this study, the V3 and V4 regions of the 16S rRNA gene from metagenomic DNA were sequenced to identify differences in microbial diversity in raw milk of Saanen and Guanzhong goats from the Guanzhong area of China. The results showed that Proteobacteria was the predominant phylum, accounting for 71.31% of all phyla identified in milk from the 2 breeds, and Enterobacter was the predominant genus (24.69%) within the microbial community. Microbial alpha diversity from Saanen goat milk was significantly higher than that of Guanzhong goat milk based on bioinformatic analysis of indices of Chao1, Shannon, Simpson, observed species, and the abundance-based coverage estimator. Functional genes and their likely metabolic pathways were predicted, which demonstrated that the functional genes present in the bacteria in goat milk were enriched in pathways for amino acid metabolism and carbohydrate metabolism, which represented 11.93 and 11.23% of functional genes, respectively. Physicochemical properties such as pH, protein, fat, and AA levels were also determined and correlations made with microbial diversity. We detected a significant difference in the content of lactose and 6 AA, which were higher in Saanen milk than in Guanzhong milk, and positively correlated with microbial carbohydrate metabolism and AA metabolism. Lactococcus, Lactobacillus, Bifidobacterium, Enterococcus, and Streptococcus, which are lactose-utilizing genera, were more abundant in Saanen milk than in Guanzhong milk. Higher levels of lactose in Saanen goat milk may explain its greater microbial diversity. We also demonstrated that most of the AA metabolism-related bacterial genera (e.g., Massilia, Bacteroides, Lysobacter) were enriched in Saanen goat milk. In this research, both probiotic and pathogenic bacteria were identified in goat milk, which provided the microbial information necessary to direct the utilization of beneficial microbial resources and prevent the development of harmful organisms in goat milk. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Temperature mediates continental-scale diversity of microbes in forest soils

PubMed Central

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

2016-01-01

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

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.

Comparison of Microbial Communities Isolated from Feces of Asymptomatic Salmonella-Shedding and Non-Salmonella Shedding Dairy Cows

PubMed Central

Haley, Bradd J.; Pettengill, James; Gorham, Sasha; Ottesen, Andrea; Karns, Jeffrey S.; Van Kessel, Jo Ann S.

2016-01-01

In the United States Salmonella enterica subsp. enterica serotypes Kentucky and Cerro are frequently isolated from asymptomatic dairy cows. However, factors that contribute to colonization of the bovine gut by these two serotypes have not been identified. To investigate associations between Salmonella status and bacterial diversity, as well as the diversity of the microbial community in the dairy cow hindgut, the bacterial and archaeal communities of fecal samples from cows on a single dairy farm were determined by high-throughput sequencing of 16S rRNA gene amplicons. Fecal grab samples were collected from two Salmonella-positive cows and two Salmonella-negative cows on five sampling dates (n = 20 cows), and 16S rRNA gene amplicons from these samples were sequenced on the Illumina MiSeq platform. A high level of alpha (within) and beta diversity (between) samples demonstrated that microbial profiles of dairy cow hindguts are quite diverse. To determine whether Salmonella presence, sampling year, or sampling date explained a significant amount of the variation in microbial diversity, we performed constrained ordination analyses (distance based RDA) on the unifrac distance matrix produced with QIIME. Results indicated that there was not a significant difference in the microbial diversity associated with Salmonella presence (P > 0.05), but there were significant differences between sampling dates and years (Pseudo-F = 2.157 to 4.385, P < 0.05). Based on these data, it appears that commensal Salmonella infections with serotypes Cerro and Kentucky in dairy cows have little or no association with changes in the abundance of major bacterial groups in the hindgut. Rather, our results indicated that temporal dynamics and other undescribed parameters associated with them were the most influential drivers of the differences in microbial diversity and community structure in the dairy cow hindgut. PMID:27313565

Changes in microbial and nutrient composition associated with rumen content compost incubation.

PubMed

Shrestha, Karuna; Shrestha, Pramod; Adetutu, Eric M; Walsh, Kerry B; Harrower, Keith M; Ball, Andrew S; Midmore, David J

2011-02-01

Physico-chemical and microbiological investigations were carried out on rumen content material composted for nine months, fresh vermicasts (obtained after passing the same compost through the guts of a mixture of three species of earthworms: Eisenia fetida, Lumbricus rubellus and Perionyx excavates) and microbially enhanced extracts derived from rumen compost, vermicast and vermicast leachate incubated for up to 48 h. Compared to composted rumen contents, vermicast was only improved in terms of microbial biomass C, while vermicast leached extract was significantly higher in NH(4)(+)-N,PO(4)(-)-P, humic acid, bacterial counts and total microbial activity compared to rumen compost extract. Although no difference between treatments was observed in genetic diversity as indicated by DGGE analysis, community level functional diversity of vermicast leached extract (Biolog™) was higher than that of composted rumen contents, vermicast and rumen compost extract indicating an enhancement of microbial activity rather than diversity due to liquid incubation. Copyright © 2010 Elsevier Ltd. All rights reserved.

Microbial community related to lysozyme digestion process for boosting waste activated sludge biodegradability.

PubMed

Xin, Xiao-Dong; He, Jun-Guo; Qiu, Wei; Tang, Jian; Liu, Tian-Tian

2015-01-01

Waste activated sludge from a lab-scale sequencing batch reactor was used to investigate the potential relation of microbial community with lysozyme digestion process for sludge solubilization. The results showed the microbial community shifted conspicuously as sludge suffered lysozyme digestion. Soluble protein and polysaccharide kept an increasing trend in solution followed with succession of microbial community. The rise of lysozyme dosage augmented the dissimilarity among communities in various digested sludge. A negative relationship presented between community diversity and lysozyme digestion process under various lysozyme/TS from 0 to 240min (correlation coefficient R(2) exceeded 0.9). Pareto-Lorenz curves demonstrated that microbial community tended to be even with sludge disintegration process by lysozyme. Finally, with diversity (H) decrease and community distribution getting even, the SCOD/TCOD increased steadily in solution which suggested the sludge with high community diversity and uneven population distribution might have tremendous potential for improving their biodegradability by lysozyme digestion. Copyright © 2014 Elsevier Ltd. All rights reserved.

MicRhoDE: a curated database for the analysis of microbial rhodopsin diversity and evolution

PubMed Central

Boeuf, Dominique; Audic, Stéphane; Brillet-Guéguen, Loraine; Caron, Christophe; Jeanthon, Christian

2015-01-01

Microbial rhodopsins are a diverse group of photoactive transmembrane proteins found in all three domains of life and in viruses. Today, microbial rhodopsin research is a flourishing research field in which new understandings of rhodopsin diversity, function and evolution are contributing to broader microbiological and molecular knowledge. Here, we describe MicRhoDE, a comprehensive, high-quality and freely accessible database that facilitates analysis of the diversity and evolution of microbial rhodopsins. Rhodopsin sequences isolated from a vast array of marine and terrestrial environments were manually collected and curated. To each rhodopsin sequence are associated related metadata, including predicted spectral tuning of the protein, putative activity and function, taxonomy for sequences that can be linked to a 16S rRNA gene, sampling date and location, and supporting literature. The database currently covers 7857 aligned sequences from more than 450 environmental samples or organisms. Based on a robust phylogenetic analysis, we introduce an operational classification system with multiple phylogenetic levels ranging from superclusters to species-level operational taxonomic units. An integrated pipeline for online sequence alignment and phylogenetic tree construction is also provided. With a user-friendly interface and integrated online bioinformatics tools, this unique resource should be highly valuable for upcoming studies of the biogeography, diversity, distribution and evolution of microbial rhodopsins. Database URL: http://micrhode.sb-roscoff.fr. PMID:26286928

MicRhoDE: a curated database for the analysis of microbial rhodopsin diversity and evolution.

PubMed

Boeuf, Dominique; Audic, Stéphane; Brillet-Guéguen, Loraine; Caron, Christophe; Jeanthon, Christian

2015-01-01

Microbial rhodopsins are a diverse group of photoactive transmembrane proteins found in all three domains of life and in viruses. Today, microbial rhodopsin research is a flourishing research field in which new understandings of rhodopsin diversity, function and evolution are contributing to broader microbiological and molecular knowledge. Here, we describe MicRhoDE, a comprehensive, high-quality and freely accessible database that facilitates analysis of the diversity and evolution of microbial rhodopsins. Rhodopsin sequences isolated from a vast array of marine and terrestrial environments were manually collected and curated. To each rhodopsin sequence are associated related metadata, including predicted spectral tuning of the protein, putative activity and function, taxonomy for sequences that can be linked to a 16S rRNA gene, sampling date and location, and supporting literature. The database currently covers 7857 aligned sequences from more than 450 environmental samples or organisms. Based on a robust phylogenetic analysis, we introduce an operational classification system with multiple phylogenetic levels ranging from superclusters to species-level operational taxonomic units. An integrated pipeline for online sequence alignment and phylogenetic tree construction is also provided. With a user-friendly interface and integrated online bioinformatics tools, this unique resource should be highly valuable for upcoming studies of the biogeography, diversity, distribution and evolution of microbial rhodopsins. Database URL: http://micrhode.sb-roscoff.fr. © The Author(s) 2015. Published by Oxford University Press.

Taxonomic and functional diversity provides insight into microbial pathways and stress responses in the saline Qinghai Lake, China.

PubMed

Huang, Qiuyuan; Briggs, Brandon R; Dong, Hailiang; Jiang, Hongchen; Wu, Geng; Edwardson, Christian; De Vlaminck, Iwijn; Quake, Stephen

2014-01-01

Microbe-mediated biogeochemical cycles contribute to the global climate system and have sensitive responses and feedbacks to environmental stress caused by climate change. Yet, little is known about the effects of microbial biodiversity (i.e., taxonmic and functional diversity) on biogeochemical cycles in ecosytems that are highly sensitive to climate change. One such sensitive ecosystem is Qinghai Lake, a high-elevation (3196 m) saline (1.4%) lake located on the Tibetan Plateau, China. This study provides baseline information on the microbial taxonomic and functional diversity as well as the associated stress response genes. Illumina metagenomic and metatranscriptomic datasets were generated from lake water samples collected at two sites (B and E). Autotrophic Cyanobacteria dominated the DNA samples, while heterotrophic Proteobacteria dominated the RNA samples at both sites. Photoheterotrophic Loktanella was also present at both sites. Photosystem II was the most active pathway at site B; while, oxidative phosphorylation was most active at site E. Organisms that expressed photosystem II or oxidative phosphorylation also expressed genes involved in photoprotection and oxidative stress, respectively. Assimilatory pathways associated with the nitrogen cycle were dominant at both sites. Results also indicate a positive relationship between functional diversity and the number of stress response genes. This study provides insight into the stress resilience of microbial metabolic pathways supported by greater taxonomic diversity, which may affect the microbial community response to climate change.

Taxonomic and Functional Diversity Provides Insight into Microbial Pathways and Stress Responses in the Saline Qinghai Lake, China

PubMed Central

Dong, Hailiang; Jiang, Hongchen; Wu, Geng; Edwardson, Christian; De Vlaminck, Iwijn; Quake, Stephen

2014-01-01

Microbe-mediated biogeochemical cycles contribute to the global climate system and have sensitive responses and feedbacks to environmental stress caused by climate change. Yet, little is known about the effects of microbial biodiversity (i.e., taxonmic and functional diversity) on biogeochemical cycles in ecosytems that are highly sensitive to climate change. One such sensitive ecosystem is Qinghai Lake, a high-elevation (3196 m) saline (1.4%) lake located on the Tibetan Plateau, China. This study provides baseline information on the microbial taxonomic and functional diversity as well as the associated stress response genes. Illumina metagenomic and metatranscriptomic datasets were generated from lake water samples collected at two sites (B and E). Autotrophic Cyanobacteria dominated the DNA samples, while heterotrophic Proteobacteria dominated the RNA samples at both sites. Photoheterotrophic Loktanella was also present at both sites. Photosystem II was the most active pathway at site B; while, oxidative phosphorylation was most active at site E. Organisms that expressed photosystem II or oxidative phosphorylation also expressed genes involved in photoprotection and oxidative stress, respectively. Assimilatory pathways associated with the nitrogen cycle were dominant at both sites. Results also indicate a positive relationship between functional diversity and the number of stress response genes. This study provides insight into the stress resilience of microbial metabolic pathways supported by greater taxonomic diversity, which may affect the microbial community response to climate change. PMID:25365331

Analysis of bacterial and archaeal diversity in coastal microbial mats using massive parallel 16S rRNA gene tag sequencing.

PubMed

Bolhuis, Henk; Stal, Lucas J

2011-11-01

Coastal microbial mats are small-scale and largely closed ecosystems in which a plethora of different functional groups of microorganisms are responsible for the biogeochemical cycling of the elements. Coastal microbial mats play an important role in coastal protection and morphodynamics through stabilization of the sediments and by initiating the development of salt-marshes. Little is known about the bacterial and especially archaeal diversity and how it contributes to the ecological functioning of coastal microbial mats. Here, we analyzed three different types of coastal microbial mats that are located along a tidal gradient and can be characterized as marine (ST2), brackish (ST3) and freshwater (ST3) systems. The mats were sampled during three different seasons and subjected to massive parallel tag sequencing of the V6 region of the 16S rRNA genes of Bacteria and Archaea. Sequence analysis revealed that the mats are among the most diverse marine ecosystems studied so far and consist of several novel taxonomic levels ranging from classes to species. The diversity between the different mat types was far more pronounced than the changes between the different seasons at one location. The archaeal community for these mats have not been studied before and revealed a strong reaction on a short period of draught during summer resulting in a massive increase in halobacterial sequences, whereas the bacterial community was barely affected. We concluded that the community composition and the microbial diversity were intrinsic of the mat type and depend on the location along the tidal gradient indicating a relation with salinity.

Recovery of microbial diversity and activity during bioremediation following chemical oxidation of diesel contaminated soils.

PubMed

Sutton, Nora B; Langenhoff, Alette A M; Lasso, Daniel Hidalgo; van der Zaan, Bas; van Gaans, Pauline; Maphosa, Farai; Smidt, Hauke; Grotenhuis, Tim; Rijnaarts, Huub H M

2014-03-01

To improve the coupling of in situ chemical oxidation and in situ bioremediation, a systematic analysis was performed of the effect of chemical oxidation with Fenton's reagent, modified Fenton's reagent, permanganate, or persulfate, on microbial diversity and activity during 8 weeks of incubation in two diesel-contaminated soils (peat and fill). Chemical oxidant and soil type affected the microbial community diversity and biodegradation activity; however, this was only observed following treatment with Fenton's reagent and modified Fenton's reagent, and in the biotic control without oxidation. Differences in the highest overall removal efficiencies of 69 % for peat (biotic control) and 59 % for fill (Fenton's reagent) were partially explained by changes in contaminant soil properties upon oxidation. Molecular analysis of 16S rRNA and alkane monooxygenase (alkB) gene abundances indicated that oxidation with Fenton's reagent and modified Fenton's reagent negatively affected microbial abundance. However, regeneration occurred, and final relative alkB abundances were 1-2 orders of magnitude higher in chemically treated microcosms than in the biotic control. 16S rRNA gene fragment fingerprinting with DGGE and prominent band sequencing illuminated microbial community composition and diversity differences between treatments and identified a variety of phylotypes within Alpha-, Beta-, and Gammaproteobacteria. Understanding microbial community dynamics during coupled chemical oxidation and bioremediation is integral to improved biphasic field application.

Microbial diversity and biogeochemistry of the Guaymas Basin deep-sea hydrothermal plume.

PubMed

Dick, Gregory J; Tebo, Bradley M

2010-05-01

Hydrothermal plumes are hot spots of microbial biogeochemistry in the deep ocean, yet little is known about the diversity or ecology of microorganisms inhabiting plumes. Recent biogeochemical evidence shows that Mn(II) oxidation in the Guaymas Basin (GB) hydrothermal plume is microbially mediated and suggests that the plume microbial community is distinct from deep-sea communities. Here we use a molecular approach to compare microbial diversity in the GB plume and in background deep seawater communities, and cultivation to identify Mn(II)-oxidizing bacteria from plumes and sediments. Despite dramatic differences in Mn(II) oxidation rates between plumes and background seawater, microbial diversity and membership were remarkably similar. All bacterial clone libraries were dominated by Gammaproteobacteria and archaeal clone libraries were dominated by Crenarchaeota. Two lineages, both phylogenetically related to methanotrophs and/or methylotrophs, were consistently over-represented in the plume. Eight Mn(II)-oxidizing bacteria were isolated, but none of these or previously identified Mn(II) oxidizers were abundant in clone libraries. Taken together with Mn(II) oxidation rates measured in laboratory cultures and in the field, these results suggest that Mn(II) oxidation in the GB hydrothermal plume is mediated by genome-level dynamics (gene content and/or expression) of microorganisms that are indigenous and abundant in the deep sea but have yet to be unidentified as Mn(II) oxidizers.

Methodological flaws introduce strong bias into molecular analysis of microbial populations.

PubMed

Krakat, N; Anjum, R; Demirel, B; Schröder, P

2017-02-01

In this study, we report how different cell disruption methods, PCR primers and in silico analyses can seriously bias results from microbial population studies, with consequences for the credibility and reproducibility of the findings. Our results emphasize the pitfalls of commonly used experimental methods that can seriously weaken the interpretation of results. Four different cell lysis methods, three commonly used primer pairs and various computer-based analyses were applied to investigate the microbial diversity of a fermentation sample composed of chicken dung. The fault-prone, but still frequently used, amplified rRNA gene restriction analysis was chosen to identify common weaknesses. In contrast to other studies, we focused on the complete analytical process, from cell disruption to in silico analysis, and identified potential error rates. This identified a wide disagreement of results between applied experimental approaches leading to very different community structures depending on the chosen approach. The interpretation of microbial diversity data remains a challenge. In order to accurately investigate the taxonomic diversity and structure of prokaryotic communities, we suggest a multi-level approach combining DNA-based and DNA-independent techniques. The identified weaknesses of commonly used methods to study microbial diversity can be overcome by a multi-level approach, which produces more reliable data about the fate and behaviour of microbial communities of engineered habitats such as biogas plants, so that the best performance can be ensured. © 2016 The Society for Applied Microbiology.

Models of microbiome evolution incorporating host and microbial selection.

PubMed

Zeng, Qinglong; Wu, Steven; Sukumaran, Jeet; Rodrigo, Allen

2017-09-25

Numerous empirical studies suggest that hosts and microbes exert reciprocal selective effects on their ecological partners. Nonetheless, we still lack an explicit framework to model the dynamics of both hosts and microbes under selection. In a previous study, we developed an agent-based forward-time computational framework to simulate the neutral evolution of host-associated microbial communities in a constant-sized, unstructured population of hosts. These neutral models allowed offspring to sample microbes randomly from parents and/or from the environment. Additionally, the environmental pool of available microbes was constituted by fixed and persistent microbial OTUs and by contributions from host individuals in the preceding generation. In this paper, we extend our neutral models to allow selection to operate on both hosts and microbes. We do this by constructing a phenome for each microbial OTU consisting of a sample of traits that influence host and microbial fitnesses independently. Microbial traits can influence the fitness of hosts ("host selection") and the fitness of microbes ("trait-mediated microbial selection"). Additionally, the fitness effects of traits on microbes can be modified by their hosts ("host-mediated microbial selection"). We simulate the effects of these three types of selection, individually or in combination, on microbiome diversities and the fitnesses of hosts and microbes over several thousand generations of hosts. We show that microbiome diversity is strongly influenced by selection acting on microbes. Selection acting on hosts only influences microbiome diversity when there is near-complete direct or indirect parental contribution to the microbiomes of offspring. Unsurprisingly, microbial fitness increases under microbial selection. Interestingly, when host selection operates, host fitness only increases under two conditions: (1) when there is a strong parental contribution to microbial communities or (2) in the absence of a strong parental contribution, when host-mediated selection acts on microbes concomitantly. We present a computational framework that integrates different selective processes acting on the evolution of microbiomes. Our framework demonstrates that selection acting on microbes can have a strong effect on microbial diversities and fitnesses, whereas selection on hosts can have weaker outcomes.

The microbial community in decaying fallen logs varies with critical period in an alpine forest.

PubMed

Chang, Chenhui; Wu, Fuzhong; Yang, Wanqin; Xu, Zhenfeng; Cao, Rui; He, Wei; Tan, Bo; Justine, Meta Francis

2017-01-01

Little information has been available on the shifts in the microbial community in decaying fallen logs during critical periods in cold forests. Minjiang fir (Abies faxoniana) fallen logs in decay classes I-V were in situ incubated on the forest floor of an alpine forest in the eastern Tibet Plateau. The microbial community was investigated during the seasonal snow cover period (SP), snow thawing period (TP), early growing season (EG) and late growing season (LG) using Phosphorous Lipid Fatty Acid (PLFA) analysis. Total microbial biomass and microbial diversity in fallen logs were much more affected by critical period than decay class, whereas decay class had a stronger effect on microbial diversity than on microbial biomass. Abundant microbial biomass and microbial diversity in logs even without the cover of snow were observed in winter, which could not be linked to thermal insulation by snow cover. The freshly decayed logs functioned as an excellent buffer of environmental variation for microbial organisms during the sharp fluctuations in temperature in winter. We also found distinct decay patterns along with seasonality for heartwood, sapwood and bark, which requires further detailed research. Gram- bacteria mainly dominated the shifts in microbial community composition from SP to EG, while fungi and Gram+ bacteria mainly dominated it from SP to TP. Based on previous work and the present study, we conclude that fallen logs on the forest floor alter ecological processes by influencing microbial communities on woody debris and beneath the soil and litter. Our study also emphasizes the need to maintain a number of fallen logs, especially fresh ones, on the forest floor.

The microbial community in decaying fallen logs varies with critical period in an alpine forest

PubMed Central

Chang, Chenhui; Wu, Fuzhong; Xu, Zhenfeng; Cao, Rui; He, Wei; Tan, Bo; Justine, Meta Francis

2017-01-01

Little information has been available on the shifts in the microbial community in decaying fallen logs during critical periods in cold forests. Minjiang fir (Abies faxoniana) fallen logs in decay classes I-V were in situ incubated on the forest floor of an alpine forest in the eastern Tibet Plateau. The microbial community was investigated during the seasonal snow cover period (SP), snow thawing period (TP), early growing season (EG) and late growing season (LG) using Phosphorous Lipid Fatty Acid (PLFA) analysis. Total microbial biomass and microbial diversity in fallen logs were much more affected by critical period than decay class, whereas decay class had a stronger effect on microbial diversity than on microbial biomass. Abundant microbial biomass and microbial diversity in logs even without the cover of snow were observed in winter, which could not be linked to thermal insulation by snow cover. The freshly decayed logs functioned as an excellent buffer of environmental variation for microbial organisms during the sharp fluctuations in temperature in winter. We also found distinct decay patterns along with seasonality for heartwood, sapwood and bark, which requires further detailed research. Gram- bacteria mainly dominated the shifts in microbial community composition from SP to EG, while fungi and Gram+ bacteria mainly dominated it from SP to TP. Based on previous work and the present study, we conclude that fallen logs on the forest floor alter ecological processes by influencing microbial communities on woody debris and beneath the soil and litter. Our study also emphasizes the need to maintain a number of fallen logs, especially fresh ones, on the forest floor. PMID:28787465

Wetlands for Wastewater: a Visual Approach to Microbial Dynamics

NASA Astrophysics Data System (ADS)

Joubert, L.; Wolfaardt, G.; Du Plessis, K.

2007-12-01

The complex character of distillery wastewater comprises high concentrations of sugars, lignins, hemicelluloses, dextrans, resins, polyphenols and organic acids which are recalcitrant to biodegradation. Microorganisms play a key role in the production and degradation of organic matter, environmental pollutants, and cycling of nutrients and metals. Due to their short life cycles microbes respond rapidly to external nutrient loading, with major consequences for the stability of biological systems. We evaluated the feasibility of wetlands to treat winery and distillery effluents in experimental systems based on constructed wetlands, including down-scaled on-site distillery wetlands, small-scale controlled greenhouse systems, and bench-scale mesocosms. Chemical, visual and molecular fingerprinting (t-RFLP) techniques were applied to study the dynamics of planktonic and attached (biofilm) communities at various points in wetlands of different size, retention time and geological substrate, and under influence of shock nutrient loadings. Variable- Pressure Scanning Electron Microscopy (VP-SEM) was applied to visualize microbial colonization, morphotype diversity and distribution, and 3D biofilm architecture. Cross-taxon and predator-prey interactions were markedly influenced by organic loading, while the presence of algae affected microbial community composition and biofilm structure. COD removal varied with geological substrate, and was positively correlated with retention time in gravel wetlands. Planktonic and biofilm communities varied markedly in different regions of the wetland and over time, as indicated by whole-community t-RFLP and VP-SEM. An integrative visual approach to community dynamics enhanced data retrieval not afforded by molecular techniques alone. The high microbial diversity along spatial and temporal gradients, and responsiveness to the physico-chemical environment, suggest that microbial communities maintain metabolic function by modifying species composition in response to fluctuations in their environment. It seems apparent that microbial community plasticity may indeed be the distinguishing characteristic of a successful wetland system.

Copper immobilization by biochar and microbial community abundance in metal-contaminated soils.

PubMed

Moore, Francisca; González, María-Eugenia; Khan, Naser; Curaqueo, Gustavo; Sanchez-Monedero, Miguel; Rilling, Joaquín; Morales, Esteban; Panichini, Marcelo; Mutis, Ana; Jorquera, Milko; Mejias, Jaime; Hirzel, Juan; Meier, Sebastián

2018-03-01

Biochar (BC) is gaining attention as a soil amendment that can remediate metal polluted soils. The simultaneous effects of BC on copper (Cu) mobility, microbial activities in soil using metallophytes have scarcely been addressed. The objective of this study was to evaluate the effects of biochar BCs on Cu immobilization and over soil microbial communities in a Cu-contaminated soil evaluated over a two-year trial. A Cu-contaminated soil (338mgkg -1 ) was incubated with chicken manure biochar (CMB) or oat hull biochar (OHB) at rates of 1 and 5% w/w. Metallophyte Oenothera picensis was grown over one season (six months). The above process was repeated for 3 more consecutive seasons using the same soils. The BCs increased the soil pH and decreased the Cu exchangeable fraction Cu by 5 and 10 times (for OHB and CMB, respectively) by increasing the Cu bound in organic matter and residual fractions, and its effects were consistent across all seasons evaluated. BCs provided favorable habitat for microorganisms that was evident in increased microbial activity. The DHA activity was increased in all BC treatments, reaching a maximum of 7 and 6 times higher than control soils in CMB and OHB. Similar results were observed in microbial respiration, which increased 53% in OHB and 61% in CMB with respect to control. The BCs produced changes in microbial communities in all seasons evaluated. The fungal and bacterial richness were increased by CMB and OHB treatments; however, no clear effects were observed in the microbial diversity estimators. The physiochemical and microbiological effects produced by BC result in an increase of plant biomass production, which was on average 3 times higher than control treatments. However, despite being a metallophyte, O. picensis did not uptake Cu efficiently. Root and shoot Cu concentrations decreased or changed insignificantly in most BC treatments. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

GIBBs: A new soil biology index to quantify beneficial bacteria in the soil

USDA-ARS?s Scientific Manuscript database

Microbial diversity has been linked to soil resilience and health but few microbial indices explicitly link diversity to function. Many of the thousands of bacteria species present in soils enhance plant nutrition, confer stress tolerance, and promote plant growth and productivity through specific m...

Functional Gene Diversity and Metabolic Potential of the Microbial Community in an Estuary-Shelf Environment

PubMed Central

Wang, Yu; Zhang, Rui; He, Zhili; Van Nostrand, Joy D.; Zheng, Qiang; Zhou, Jizhong; Jiao, Nianzhi

2017-01-01

Microbes play crucial roles in various biogeochemical processes in the ocean, including carbon (C), nitrogen (N), and phosphorus (P) cycling. Functional gene diversity and the structure of the microbial community determines its metabolic potential and therefore its ecological function in the marine ecosystem. However, little is known about the functional gene composition and metabolic potential of bacterioplankton in estuary areas. The East China Sea (ECS) is a dynamic marginal ecosystem in the western Pacific Ocean that is mainly affected by input from the Changjiang River and the Kuroshio Current. Here, using a high-throughput functional gene microarray (GeoChip), we analyzed the functional gene diversity, composition, structure, and metabolic potential of microbial assemblages in different ECS water masses. Four water masses determined by temperature and salinity relationship showed different patterns of functional gene diversity and composition. Generally, functional gene diversity [Shannon–Weaner’s H and reciprocal of Simpson’s 1/(1-D)] in the surface water masses was higher than that in the bottom water masses. The different presence and proportion of functional genes involved in C, N, and P cycling among the bacteria of the different water masses showed different metabolic preferences of the microbial populations in the ECS. Genes involved in starch metabolism (amyA and nplT) showed higher proportion in microbial communities of the surface water masses than of the bottom water masses. In contrast, a higher proportion of genes involved in chitin degradation was observed in microorganisms of the bottom water masses. Moreover, we found a higher proportion of nitrogen fixation (nifH), transformation of hydroxylamine to nitrite (hao) and ammonification (gdh) genes in the microbial communities of the bottom water masses compared with those of the surface water masses. The spatial variation of microbial functional genes was significantly correlated with salinity, temperature, and chlorophyll based on canonical correspondence analysis, suggesting a significant influence of hydrologic conditions on water microbial communities. Our data provide new insights into better understanding of the functional potential of microbial communities in the complex estuarine-coastal environmental gradient of the ECS. PMID:28680420

Accurate, multi-kb reads resolve complex populations and detect rare microorganisms.

PubMed

Sharon, Itai; Kertesz, Michael; Hug, Laura A; Pushkarev, Dmitry; Blauwkamp, Timothy A; Castelle, Cindy J; Amirebrahimi, Mojgan; Thomas, Brian C; Burstein, David; Tringe, Susannah G; Williams, Kenneth H; Banfield, Jillian F

2015-04-01

Accurate evaluation of microbial communities is essential for understanding global biogeochemical processes and can guide bioremediation and medical treatments. Metagenomics is most commonly used to analyze microbial diversity and metabolic potential, but assemblies of the short reads generated by current sequencing platforms may fail to recover heterogeneous strain populations and rare organisms. Here we used short (150-bp) and long (multi-kb) synthetic reads to evaluate strain heterogeneity and study microorganisms at low abundance in complex microbial communities from terrestrial sediments. The long-read data revealed multiple (probably dozens of) closely related species and strains from previously undescribed Deltaproteobacteria and Aminicenantes (candidate phylum OP8). Notably, these are the most abundant organisms in the communities, yet short-read assemblies achieved only partial genome coverage, mostly in the form of short scaffolds (N50 = ∼ 2200 bp). Genome architecture and metabolic potential for these lineages were reconstructed using a new synteny-based method. Analysis of long-read data also revealed thousands of species whose abundances were <0.1% in all samples. Most of the organisms in this "long tail" of rare organisms belong to phyla that are also represented by abundant organisms. Genes encoding glycosyl hydrolases are significantly more abundant than expected in rare genomes, suggesting that rare species may augment the capability for carbon turnover and confer resilience to changing environmental conditions. Overall, the study showed that a diversity of closely related strains and rare organisms account for a major portion of the communities. These are probably common features of many microbial communities and can be effectively studied using a combination of long and short reads. © 2015 Sharon et al.; Published by Cold Spring Harbor Laboratory Press.

The ecology and diversity of microbial eukaryotes in geothermal springs.

PubMed

Oliverio, Angela M; Power, Jean F; Washburne, Alex; Cary, S Craig; Stott, Matthew B; Fierer, Noah

2018-04-16

Decades of research into the Bacteria and Archaea living in geothermal spring ecosystems have yielded great insight into the diversity of life and organismal adaptations to extreme environmental conditions. Surprisingly, while microbial eukaryotes (protists) are also ubiquitous in many environments, their diversity across geothermal springs has mostly been ignored. We used high-throughput sequencing to illuminate the diversity and structure of microbial eukaryotic communities found in 160 geothermal springs with broad ranges in temperature and pH across the Taupō Volcanic Zone in New Zealand. Protistan communities were moderately predictable in composition and varied most strongly across gradients in pH and temperature. Moreover, this variation mirrored patterns observed for bacterial and archaeal communities across the same spring samples, highlighting that there are similar ecological constraints across the tree of life. While extreme pH values were associated with declining protist diversity, high temperature springs harbored substantial amounts of protist diversity. Although protists are often overlooked in geothermal springs and other extreme environments, our results indicate that such environments can host distinct and diverse protistan communities.

Current approaches to exploit actinomycetes as a source of novel natural products.

PubMed

Genilloud, Olga; González, Ignacio; Salazar, Oscar; Martín, Jesus; Tormo, José Rubén; Vicente, Francisca

2011-03-01

For decades, microbial natural products have been one of the major sources of novel drugs for pharmaceutical companies, and today all evidence suggests that novel molecules with potential therapeutic applications are still waiting to be discovered from these natural sources, especially from actinomycetes. Any appropriate exploitation of the chemical diversity of these microbial sources relies on proper understanding of their biological diversity and other related key factors that maximize the possibility of successful identification of novel molecules. Without doubt, the discovery of platensimycin has shown that microbial natural products can continue to deliver novel scaffolds if appropriate tools are put in place to reveal them in a cost-effective manner. Whereas today innovative technologies involving exploitation of uncultivated environmental diversity, together with chemical biology and in silico approaches, are seeing rapid development in natural products research, maximization of the chances of exploiting chemical diversity from microbial collections is still essential for novel drug discovery. This work provides an overview of the integrated approaches developed at the former Basic Research Center of Merck Sharp and Dohme in Spain to exploit the diversity and biosynthetic potential of actinomycetes, and includes some examples of those that were successfully applied to the discovery of novel antibiotics.

Exploring microbial diversity in volcanic environments: a review of methods in DNA extraction.

PubMed

Herrera, Aude; Cockell, Charles S

2007-07-01

The last decade has been marked by a large number of studies focused on understanding the distribution of microorganisms in volcanic environments. These studies are motivated by the desire to elucidate how the geochemically extreme conditions of such environments can influence microbial diversity both on the surface and in the subsurface of the Earth. The exploration of microbial community diversity has generally not relied on culture-dependent methods, but has been carried out using environmental DNA extraction. Because of the large diversity of chemically and physically complex samples, extracting DNA from volcanic environments is technically challenging. In view of the emerging literature, and our own experience in the optimisation of methods for DNA extraction from volcanic materials, it is timely to provide a methodological comparison. This review highlights and discusses new insights and methods published on DNA extraction methods from volcanic samples, considering the different volcanic environments. A description of a recent method for DNA extraction from basalt and obsidian glass rock samples from Iceland is included. Finally, we discuss these approaches in the wider context of modern work to understand the microbial diversity of volcanic environments.

Increasing the Size of the Microbial Biomass Altered Bacterial Community Structure which Enhances Plant Phosphorus Uptake

PubMed Central

Shen, Pu; Murphy, Daniel Vaughan; George, Suman J.; Lapis-Gaza, Hazel; Xu, Minggang

2016-01-01

Agricultural production can be limited by low phosphorus (P) availability, with soil P being constrained by sorption and precipitation reactions making it less available for plant uptake. There are strong links between carbon (C) and nitrogen (N) availability and P cycling within soil P pools, with microorganisms being an integral component of soil P cycling mediating the availability of P to plants. Here we tested a conceptual model that proposes (i) the addition of readily-available organic substrates would increase the size of the microbial biomass thus exhausting the pool of easily-available P and (ii) this would cause the microbial biomass to access P from more recalcitrant pools. In this model it is hypothesised that the size of the microbial population is regulating access to less available P rather than the diversity of organisms contained within this biomass. To test this hypothesis we added mixtures of simple organic compounds that reflect typical root exudates at different C:N ratios to a soil microcosm experiment and assessed changes in soil P pools, microbial biomass and bacterial diversity measures. We report that low C:N ratio (C:N = 12.5:1) artificial root exudates increased the size of the microbial biomass while high C:N ratio (C:N = 50:1) artificial root exudates did not result in a similar increase in microbial biomass. Interestingly, addition of the root exudates did not alter bacterial diversity (measured via univariate diversity indices) but did alter bacterial community structure. Where C, N and P supply was sufficient to support plant growth the increase observed in microbial biomass occurred with a concurrent increase in plant yield. PMID:27893833

Microbial Diversity in Sediment Ecosystems (Evaporites Domes, Microbial Mats, and Crusts) of Hypersaline Laguna Tebenquiche, Salar de Atacama, Chile.

PubMed

Fernandez, Ana B; Rasuk, Maria C; Visscher, Pieter T; Contreras, Manuel; Novoa, Fernando; Poire, Daniel G; Patterson, Molly M; Ventosa, Antonio; Farias, Maria E

2016-01-01

We combined nucleic acid-based molecular methods, biogeochemical measurements, and physicochemical characteristics to investigate microbial sedimentary ecosystems of Laguna Tebenquiche, Atacama Desert, Chile. Molecular diversity, and biogeochemistry of hypersaline microbial mats, rhizome-associated concretions, and an endoevaporite were compared with: The V4 hypervariable region of the 16S rRNA gene was amplified by pyrosequencing to analyze the total microbial diversity (i.e., bacteria and archaea) in bulk samples, and in addition, in detail on a millimeter scale in one microbial mat and in one evaporite. Archaea were more abundant than bacteria. Euryarchaeota was one of the most abundant phyla in all samples, and particularly dominant (97% of total diversity) in the most lithified ecosystem, the evaporite. Most of the euryarchaeal OTUs could be assigned to the class Halobacteria or anaerobic and methanogenic archaea. Planctomycetes potentially also play a key role in mats and rhizome-associated concretions, notably the aerobic organoheterotroph members of the class Phycisphaerae. In addition to cyanobacteria, members of Chromatiales and possibly the candidate family Chlorotrichaceae contributed to photosynthetic carbon fixation. Other abundant uncultured taxa such as the candidate division MSBL1, the uncultured MBGB, and the phylum Acetothermia potentially play an important metabolic role in these ecosystems. Lithifying microbial mats contained calcium carbonate precipitates, whereas endoevoporites consisted of gypsum, and halite. Biogeochemical measurements revealed that based on depth profiles of O2 and sulfide, metabolic activities were much higher in the non-lithifying mat (peaking in the least lithified systems) than in lithifying mats with the lowest activity in endoevaporites. This trend in decreasing microbial activity reflects the increase in salinity, which may play an important role in the biodiversity.

Microbial Diversity in Sediment Ecosystems (Evaporites Domes, Microbial Mats, and Crusts) of Hypersaline Laguna Tebenquiche, Salar de Atacama, Chile

PubMed Central

Fernandez, Ana B.; Rasuk, Maria C.; Visscher, Pieter T.; Contreras, Manuel; Novoa, Fernando; Poire, Daniel G.; Patterson, Molly M.; Ventosa, Antonio; Farias, Maria E.

2016-01-01

We combined nucleic acid-based molecular methods, biogeochemical measurements, and physicochemical characteristics to investigate microbial sedimentary ecosystems of Laguna Tebenquiche, Atacama Desert, Chile. Molecular diversity, and biogeochemistry of hypersaline microbial mats, rhizome-associated concretions, and an endoevaporite were compared with: The V4 hypervariable region of the 16S rRNA gene was amplified by pyrosequencing to analyze the total microbial diversity (i.e., bacteria and archaea) in bulk samples, and in addition, in detail on a millimeter scale in one microbial mat and in one evaporite. Archaea were more abundant than bacteria. Euryarchaeota was one of the most abundant phyla in all samples, and particularly dominant (97% of total diversity) in the most lithified ecosystem, the evaporite. Most of the euryarchaeal OTUs could be assigned to the class Halobacteria or anaerobic and methanogenic archaea. Planctomycetes potentially also play a key role in mats and rhizome-associated concretions, notably the aerobic organoheterotroph members of the class Phycisphaerae. In addition to cyanobacteria, members of Chromatiales and possibly the candidate family Chlorotrichaceae contributed to photosynthetic carbon fixation. Other abundant uncultured taxa such as the candidate division MSBL1, the uncultured MBGB, and the phylum Acetothermia potentially play an important metabolic role in these ecosystems. Lithifying microbial mats contained calcium carbonate precipitates, whereas endoevoporites consisted of gypsum, and halite. Biogeochemical measurements revealed that based on depth profiles of O2 and sulfide, metabolic activities were much higher in the non-lithifying mat (peaking in the least lithified systems) than in lithifying mats with the lowest activity in endoevaporites. This trend in decreasing microbial activity reflects the increase in salinity, which may play an important role in the biodiversity. PMID:27597845

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

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.

Understanding the degradation of Congo red and bacterial diversity in an air-cathode microbial fuel cell being evaluated for simultaneous azo dye removal from wastewater and bioelectricity generation.

PubMed

Sun, Jian; Li, Youming; Hu, Yongyou; Hou, Bin; Zhang, Yaping; Li, Sizhe

2013-04-01

We investigated the mechanism of Congo red degradation and bacterial diversity in a single-chambered microbial fuel cell (MFC) incorporating a microfiltration membrane and air-cathode. The MFC was operated continuously for more than 4 months using a mixture of Congo red and glucose as fuel. We demonstrated that the Congo red azo bonds were reduced at the anode to form aromatic amines. This is consistent with the known mechanism of anaerobic biodegradation of azo dyes. The MFC developed a less dense biofilm at the anode in the presence of Congo red compared to its absence indicating that Congo red degradation negatively affected biofilm formation. Denaturing gradient gel electrophoresis and direct 16S ribosomal DNA gene nucleotide sequencing revealed that the microbial communities differed depending on whether Congo red was present in the MFC. Geobacter-like species known to generate electricity were detected in the presence or absence of Congo red. In contrast, Azospirillum, Methylobacterium, Rhodobacter, Desulfovibrio, Trichococcus, and Bacteroides species were only detected in its presence. These species were most likely responsible for degrading Congo red.

Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments.

PubMed

Trembath-Reichert, Elizabeth; Case, David H; Orphan, Victoria J

2016-01-01

Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range of Deltaproteobacteria diversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seep sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. Many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed to many co-occurrences containing putatively heterotrophic, candidate phyla such as OD1, Atribacteria, MBG-B, and Hyd24-12 and the potential for complex sulfur cycling involving Epsilon-, Delta-, and Gammaproteobacteria in methane seep ecosystems.

Improved bacteriophage genome data is necessary for integrating viral and bacterial ecology.

PubMed

Bibby, Kyle

2014-02-01

The recent rise in "omics"-enabled approaches has lead to improved understanding in many areas of microbial ecology. However, despite the importance that viruses play in a broad microbial ecology context, viral ecology remains largely not integrated into high-throughput microbial ecology studies. A fundamental hindrance to the integration of viral ecology into omics-enabled microbial ecology studies is the lack of suitable reference bacteriophage genomes in reference databases-currently, only 0.001% of bacteriophage diversity is represented in genome sequence databases. This commentary serves to highlight this issue and to promote bacteriophage genome sequencing as a valuable scientific undertaking to both better understand bacteriophage diversity and move towards a more holistic view of microbial ecology.

A Comparison of Microbial Community Structures by Depth and Season Under Switchgrass

NASA Astrophysics Data System (ADS)

Fansler, S. J.; Smith, J. L.; Bolton, H.; Bailey, V. L.

2008-12-01

As part of a multidisciplinary study of C sequestration in switchgrass production systems, the soil microbial community structure was monitored at 6 different depths (reaching 90 cm) in both spring and autumn. Microbial community structure was assessed using ribosomal intergenic spacer analysis (RISA), and primers were used specific to either bacteria or fungi, generating microbial community fingerprints for each taxonomic group. Diverse microbial communities for both groups were detected throughout the soil profile. It is notable that while community structure clearly changed with depth, there was the deepest soil samples still retained relatively diverse communities. Seasonally, differences are clearly evident within plots at the surface. As the plots were replicated, significant differences in the community fingerprints with depth and season are reported.

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.

Daily Changes in Composition and Diversity of the Intestinal Microbiota in Patients with Anorexia Nervosa: A Series of Three Cases.

PubMed

Kleiman, Susan C; Glenny, Elaine M; Bulik-Sullivan, Emily C; Huh, Eun Young; Tsilimigras, Matthew C B; Fodor, Anthony A; Bulik, Cynthia M; Carroll, Ian M

2017-09-01

Anorexia nervosa, a severe psychiatric illness, is associated with an intestinal microbial dysbiosis. Individual microbial signatures dominate in healthy samples, even over time and under controlled conditions, but whether microbial markers of the disorder overcome inter-individual variation during the acute stage of illness or renourishment is unknown. We characterized daily changes in the intestinal microbiota in three acutely ill patients with anorexia nervosa over the entire course of hospital-based renourishment and found significant, patient-specific changes in microbial composition and diversity. This preliminary case series suggests that even in a state of pathology, individual microbial signatures persist in accounting for the majority of intestinal microbial variation. Copyright © 2017 John Wiley & Sons, Ltd and Eating Disorders Association. Copyright © 2017 John Wiley & Sons, Ltd and Eating Disorders Association.

Microbial community phylogenetic and trait diversity declines with depth in a marine oxygen minimum zone.

PubMed

Bryant, Jessica A; Stewart, Frank J; Eppley, John M; DeLong, Edward F

2012-07-01

Oxygen minimum zones (OMZs) are natural physical features of the world's oceans. They create steep physiochemical gradients in the water column, which most notably include a dramatic draw down in oxygen concentrations over small vertical distances (<100 m). Microbial communities within OMZs play central roles in ocean and global biogeochemical cycles, yet we still lack a fundamental understanding of how microbial biodiversity is distributed across OMZs. Here, we used metagenomic sequencing to investigate microbial diversity across a vertical gradient in the water column during three seasons in the Eastern Tropical South Pacific (ETSP) OMZ. Based on analysis of small subunit ribosomal RNA (SSU rRNA) gene fragments, we found that both taxonomic and phylogenetic diversity declined steeply along the transition from oxygen-rich surface water to the permanent OMZ. We observed similar declines in the diversity of protein-coding gene categories, suggesting a decrease in functional (trait) diversity with depth. Metrics of functional and trait dispersion indicated that microbial communities are phylogenetically and functionally more overdispersed in oxic waters, but clustered within the OMZ. These dispersion patterns suggest that community assembly drivers (e.g., competition, environmental filtering) vary strikingly across the oxygen gradient. To understand the generality of our findings, we compared OMZ results to two marine depth gradients in subtropical oligotrophic sites and found that the oligotrophic sites did not display similar patterns, likely reflecting unique features found in the OMZ. Finally, we discuss how our results may relate to niche theory, diversity-energy relationships and stress gradients.

Ecological effects of soil properties and metal concentrations on the composition and diversity of microbial communities associated with land use patterns in an electronic waste recycling region.

PubMed

Wu, Wencheng; Dong, Changxun; Wu, Jiahui; Liu, Xiaowen; Wu, Yingxin; Chen, Xianbin; Yu, Shixiao

2017-12-01

Soil microbes play vital roles in ecosystem functions, and soil microbial communities may be strongly structured by land use patterns associated with electronic waste (e-waste) recycling activities, which can increase the heavy metal concentration in soils. In this study, a suite of soils from five land use types (paddy field, vegetable field, dry field, forest field, and e-waste recycling site) were collected in Longtang Town, Guangdong Province, South China. Soil physicochemical properties and heavy metal concentrations were measured, and the indigenous microbial assemblages were profiled using 16S rRNA high-throughput sequencing and clone library analyses. The results showed that mercury concentration was positively correlated with both Faith's PD and Chao1 estimates, suggesting that the soil microbial alpha diversity was predominantly regulated by mercury. In addition, redundancy analysis indicated that available phosphorus, soil moisture, and mercury were the three major drivers affecting the microbial assemblages. Overall, the microbial composition was determined primarily by land use patterns, and this study provides a novel insight on the composition and diversity of microbial communities in soils associated with e-waste recycling activities. Copyright © 2017 Elsevier B.V. All rights reserved.

Microbial Diversity of Septic Tank Effluent and a Soil Biomat▿ †

PubMed Central

Tomaras, Jill; Sahl, Jason W.; Siegrist, Robert L.; Spear, John R.

2009-01-01

Microbial diversity of septic tank effluent (STE) and the biomat that is formed as a result of STE infiltration on soil were characterized by 16S rRNA gene sequence analysis. Results indicate that microbial communities are different within control soil, STE, and the biomat and that microbes found in STE are not found in the biomat. The development of a stable soil biomat appears to provide the best on-site water treatment or protection for subsequent groundwater interactions of STE. PMID:19304840

Microbial diversity of septic tank effluent and a soil biomat.

PubMed

Tomaras, Jill; Sahl, Jason W; Siegrist, Robert L; Spear, John R

2009-05-01

Microbial diversity of septic tank effluent (STE) and the biomat that is formed as a result of STE infiltration on soil were characterized by 16S rRNA gene sequence analysis. Results indicate that microbial communities are different within control soil, STE, and the biomat and that microbes found in STE are not found in the biomat. The development of a stable soil biomat appears to provide the best on-site water treatment or protection for subsequent groundwater interactions of STE.

Exploration of Microbial Diversity and Community Structure of Lonar Lake: The Only Hypersaline Meteorite Crater Lake within Basalt Rock

PubMed Central

Paul, Dhiraj; Kumbhare, Shreyas V.; Mhatre, Snehit S.; Chowdhury, Somak P.; Shetty, Sudarshan A.; Marathe, Nachiket P.; Bhute, Shrikant; Shouche, Yogesh S.

2016-01-01

Lonar Lake is a hypersaline and hyperalkaline soda lake and the only meteorite impact crater in the world situated in basalt rocks. Although culture-dependent studies have been reported, a comprehensive understanding of microbial community composition and structure in Lonar Lake remains elusive. In the present study, microbial community structure associated with Lonar Lake sediment and water samples was investigated using high-throughput sequencing. Microbial diversity analysis revealed the existence of diverse, yet largely consistent communities. Proteobacteria (30%), Actinobacteria (24%), Firmicutes (11%), and Cyanobacteria (5%) predominated in the sequencing survey, whereas Bacteroidetes (1.12%), BD1-5 (0.5%), Nitrospirae (0.41%), and Verrucomicrobia (0.28%) were detected in relatively minor abundances in the Lonar Lake ecosystem. Within the Proteobacteria phylum, the Gammaproteobacteria represented the most abundantly detected class (21–47%) within sediment samples, but only a minor population in the water samples. Proteobacteria and Firmicutes were found at significantly higher abundance (p ≥ 0.05) in sediment samples, whereas members of Actinobacteria, Candidate division TM7 and Cyanobacteria (p ≥ 0.05) were significantly abundant in water samples. Compared to the microbial communities of other hypersaline soda lakes, those of Lonar Lake formed a distinct cluster, suggesting a different microbial community composition and structure. Here we report for the first time, the difference in composition of indigenous microbial communities between the sediment and water samples of Lonar Lake. An improved census of microbial community structure in this Lake ecosystem provides a foundation for exploring microbial biogeochemical cycling and microbial function in hypersaline lake environments. PMID:26834712

Differences in Temperature and Water Chemistry Shape Distinct Diversity Patterns in Thermophilic Microbial Communities

PubMed Central

Chiriac, Cecilia M.; Szekeres, Edina; Rudi, Knut; Baricz, Andreea; Hegedus, Adriana; Dragoş, Nicolae

2017-01-01

ABSTRACT This report describes the biodiversity and ecology of microbial mats developed in thermal gradients (20 to 65°C) in the surroundings of three drillings (Chiraleu [CH], Ciocaia [CI], and Mihai Bravu [MB]) tapping a hyperthermal aquifer in Romania. Using a metabarcoding approach, 16S rRNA genes were sequenced from both DNA and RNA transcripts (cDNA) and compared. The relationships between the microbial diversity and the physicochemical factors were explored. Additionally, the cDNA data were used for in silico functionality predictions, bringing new insights into the functional potential and dynamics of these communities. The results showed that each hot spring determined the formation of distinct microbial communities. In the CH mats (40 to 53°C), the abundance of Cyanobacteria decreased with temperature, opposite to those of Chloroflexi and Proteobacteria. Ectothiorhodospira, Oscillatoria, and methanogenic archaea dominated the CI communities (20 to 65°C), while the MB microbial mats (53 to 65°C) were mainly composed of Chloroflexi, Hydrogenophilus, Thermi, and Aquificae. Alpha-diversity was negatively correlated with the increase in water temperature, while beta-diversity was shaped in each hot spring by the unique combination of physicochemical parameters, regardless of the type of nucleic acid analyzed (DNA versus cDNA). The rank correlation analysis revealed a unique model that associated environmental data with community composition, consisting in the combined effect of Na+, K+, HCO3−, and PO43− concentrations, together with temperature and electrical conductivity. These factors seem to determine the grouping of samples according to location, rather than with the similarities in thermal regimes, showing that other parameters beside temperature are significant drivers of biodiversity. IMPORTANCE Hot spring microbial mats represent a remarkable manifestation of life on Earth and have been intensively studied for decades. Moreover, as hot spring areas are isolated and have a limited exchange of organisms, nutrients, and energy with the surrounding environments, hot spring microbial communities can be used in model studies to elucidate the colonizing potential within extreme settings. Thus, they are of great importance in evolutionary biology, microbial ecology, and exobiology. In spite of all the efforts that have been made, the current understanding of the influence of temperature and water chemistry on the microbial community composition, diversity, and abundance in microbial mats is limited. In this study, the composition and diversity of microbial communities developed in thermal gradients in the vicinity of three hot springs from Romania were investigated, each having particular physicochemical characteristics. Our results expose new factors that could determine the formation of these ecosystems, expanding the current knowledge in this regard. PMID:28821552

Land cover and forest connectivity alter the interactions among host, pathogen and skin microbiome.

PubMed

Becker, C G; Longo, A V; Haddad, C F B; Zamudio, K R

2017-08-30

Deforestation has detrimental consequences on biodiversity, affecting species interactions at multiple scales. The associations among vertebrates, pathogens and their commensal/symbiotic microbial communities (i.e. microbiomes) have important downstream effects for biodiversity conservation, yet we know little about how deforestation contributes to changes in host microbial diversity and pathogen abundance. Here, we tested the effects of landcover, forest connectivity and infection by the chytrid fungus Batrachochytrium dendrobatidis ( Bd ) on amphibian skin bacterial diversity along deforestation gradients in Brazilian landscapes. If disturbance to natural habitat alters skin microbiomes as it does in vertebrate host communities, then we would expect higher host bacterial diversity in natural forest habitats. Bd infection loads are also often higher in these closed-canopy forests, which may in turn impact skin-associated bacterial communities. We found that forest corridors shaped composition of host skin microbiomes; high forest connectivity predicted greater similarity of skin bacterial communities among host populations. In addition, we found that host skin bacterial diversity and Bd loads increased towards natural vegetation. Because symbiotic bacteria can potentially buffer hosts from Bd infection, we also evaluated the bi-directional microbiome- Bd link but failed to find a significant effect of skin bacterial diversity reducing Bd infections. Although weak, we found support for Bd increasing bacterial diversity and/or for core bacteria dominance reducing Bd loads. Our research incorporates a critical element in the study of host microbiomes by linking environmental heterogeneity of landscapes to the host-pathogen-microbiome triangle. © 2017 The Author(s).

Scalable Biomarker Discovery for Diverse High-Dimensional Phenotypes

DTIC Science & Technology

2015-11-23

bytes: Computational analysis methods for microbial communities," University of Oregon BioBE center seminar. Eugene, OR, 2013 35- "From microbial...analysis methods for microbial communities," University of Oregon BioBE center seminar. Eugene, OR, 2013 • "From microbial surveys to mechanisms of

Microbial-Catalyzed Biotransformation of Multifunctional Triterpenoids Derived from Phytonutrients

PubMed Central

Shah, Syed Adnan Ali; Tan, Huey Ling; Sultan, Sadia; Mohd Faridz, Muhammad Afifi Bin; Mohd Shah, Mohamad Azlan Bin; Nurfazilah, Sharifah; Hussain, Munawar

2014-01-01

Microbial-catalyzed biotransformations have considerable potential for the generation of an enormous variety of structurally diversified organic compounds, especially natural products with complex structures like triterpenoids. They offer efficient and economical ways to produce semi-synthetic analogues and novel lead molecules. Microorganisms such as bacteria and fungi could catalyze chemo-, regio- and stereospecific hydroxylations of diverse triterpenoid substrates that are extremely difficult to produce by chemical routes. During recent years, considerable research has been performed on the microbial transformation of bioactive triterpenoids, in order to obtain biologically active molecules with diverse structures features. This article reviews the microbial modifications of tetranortriterpenoids, tetracyclic triterpenoids and pentacyclic triterpenoids. PMID:25003642

Diversity and Biosynthetic Potential of Culturable Microbes Associated with Toxic Marine Animals

PubMed Central

Chau, Rocky; Kalaitzis, John A.; Wood, Susanna A.; Neilan, Brett A.

2013-01-01

Tetrodotoxin (TTX) is a neurotoxin that has been reported from taxonomically diverse organisms across 14 different phyla. The biogenic origin of tetrodotoxin is still disputed, however, TTX biosynthesis by host-associated bacteria has been reported. An investigation into the culturable microbial populations from the TTX-associated blue-ringed octopus Hapalochlaena sp. and sea slug Pleurobranchaea maculata revealed a surprisingly high microbial diversity. Although TTX was not detected among the cultured isolates, PCR screening identifiedsome natural product biosynthesis genes putatively involved in its assembly. This study is the first to report on the microbial diversity of culturable communities from H. maculosa and P. maculata and common natural product biosynthesis genes from their microbiota. We also reassess the production of TTX reported from three bacterial strains isolated from the TTX-containing gastropod Nassarius semiplicatus. PMID:23917066

Diversity and biosynthetic potential of culturable microbes associated with toxic marine animals.

PubMed

Chau, Rocky; Kalaitzis, John A; Wood, Susanna A; Neilan, Brett A

2013-08-02

Tetrodotoxin (TTX) is a neurotoxin that has been reported from taxonomically diverse organisms across 14 different phyla. The biogenic origin of tetrodotoxin is still disputed, however, TTX biosynthesis by host-associated bacteria has been reported. An investigation into the culturable microbial populations from the TTX-associated blue-ringed octopus Hapalochlaena sp. and sea slug Pleurobranchaea maculata revealed a surprisingly high microbial diversity. Although TTX was not detected among the cultured isolates, PCR screening identifiedsome natural product biosynthesis genes putatively involved in its assembly. This study is the first to report on the microbial diversity of culturable communities from H. maculosa and P. maculata and common natural product biosynthesis genes from their microbiota. We also reassess the production of TTX reported from three bacterial strains isolated from the TTX-containing gastropod Nassarius semiplicatus.

Changes in the Bacterial Community of Soil from a Neutral Mine Drainage Channel

PubMed Central

Pereira, Letícia Bianca; Vicentini, Renato; Ottoboni, Laura M. M.

2014-01-01

Mine drainage is an important environmental disturbance that affects the chemical and biological components in natural resources. However, little is known about the effects of neutral mine drainage on the soil bacteria community. Here, a high-throughput 16S rDNA pyrosequencing approach was used to evaluate differences in composition, structure, and diversity of bacteria communities in samples from a neutral drainage channel, and soil next to the channel, at the Sossego copper mine in Brazil. Advanced statistical analyses were used to explore the relationships between the biological and chemical data. The results showed that the neutral mine drainage caused changes in the composition and structure of the microbial community, but not in its diversity. The Deinococcus/Thermus phylum, especially the Meiothermus genus, was in large part responsible for the differences between the communities, and was positively associated with the presence of copper and other heavy metals in the environmental samples. Other important parameters that influenced the bacterial diversity and composition were the elements potassium, sodium, nickel, and zinc, as well as pH. The findings contribute to the understanding of bacterial diversity in soils impacted by neutral mine drainage, and demonstrate that heavy metals play an important role in shaping the microbial population in mine environments. PMID:24796430

Longitudinal analysis of microbiota in microalga Nannochloropsis salina cultures

DOE PAGES

Geng, Haifeng; Sale, Kenneth L.; Tran-Gyamfi, Mary Bao; ...

2016-03-08

Here, large-scale open microalgae cultivation has tremendous potential to make a significant contribution to replacing petroleum-based fuels with biofuels. Open algal cultures are unavoidably inhabited with a diversity of microbes that live on, influence, and shape the fate of these ecosystems. However, there is little understanding of the resilience and stability of the microbial communities in engineered semicontinuous algal systems. To evaluate the dynamics and resilience of the microbial communities in microalgae biofuel cultures, we conducted a longitudinal study on open systems to compare the temporal profiles of the microbiota from two multigenerational algal cohorts, which include one seeded withmore » the microbiota from an in-house culture and the other exogenously seeded with a natural-occurring consortia of bacterial species harvested from the Pacific Ocean. From these month-long, semicontinuous open microalga Nannochloropsis salina cultures, we sequenced a time-series of 46 samples, yielding 8804 operational taxonomic units derived from 9,160,076 high-quality partial 16S rRNA sequences. We provide quantitative evidence that clearly illustrates the development of microbial community is associated with microbiota ancestry. In addition, N. salina growth phases were linked with distinct changes in microbial phylotypes. Alteromonadeles dominated the community in the N. salina exponential phase whereas Alphaproteobacteria and Flavobacteriia were more prevalent in the stationary phase. We also demonstrate that the N. salina-associated microbial community in open cultures is diverse, resilient, and dynamic in response to environmental perturbations. This knowledge has general implications for developing and testing design principles of cultivated algal systems.« less

Diversity is the question, not the answer

DOE PAGES

Shade, Ashley

2016-09-16

Local diversity (within-sample or alpha diversity) is often implicated as a cause of success or failure of a microbial community. However, the relationships between diversity and emergent properties of a community, such as its stability, productivity or invasibility, are much more nuanced. In this paper, I argue that diversity without context provides limited insights into the mechanisms underpinning community patterns. I provide examples from traditional and microbial ecology to discuss common complications and assumptions about within-sample diversity that may prevent us from digging deeper into the more specific mechanisms underpinning community outcomes. I suggest that measurement of diversity should servemore » as a starting point for further inquiry of ecological mechanisms rather than an 'answer' to community outcomes.« less

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

Shade, Ashley

Local diversity (within-sample or alpha diversity) is often implicated as a cause of success or failure of a microbial community. However, the relationships between diversity and emergent properties of a community, such as its stability, productivity or invasibility, are much more nuanced. In this paper, I argue that diversity without context provides limited insights into the mechanisms underpinning community patterns. I provide examples from traditional and microbial ecology to discuss common complications and assumptions about within-sample diversity that may prevent us from digging deeper into the more specific mechanisms underpinning community outcomes. I suggest that measurement of diversity should servemore » as a starting point for further inquiry of ecological mechanisms rather than an 'answer' to community outcomes.« less

Nitrogen deposition and management practices increase soil microbial biomass carbon but decrease diversity in Moso bamboo plantations

PubMed Central

Li, Quan; Song, Xinzhang; Gu, Honghao; Gao, Fei

2016-01-01

Because microbial communities play a key role in carbon (C) and nitrogen (N) cycling, changes in the soil microbial community may directly affect ecosystem functioning. However, the effects of N deposition and management practices on soil microbes are still poorly understood. We studied the effects of these two factors on soil microbial biomass carbon (MBC) and community composition in Moso bamboo plantations using high-throughput sequencing of the 16S rRNA gene. Plantations under conventional (CM) or intensive management (IM) were subjected to one of four N treatments for 30 months. IM and N addition, both separately and in combination, significantly increased soil MBC while decreasing bacterial diversity. However, increases in soil MBC were inhibited when N addition exceeded 60 kg N∙ha−1∙yr−1. IM increased the relative abundances of Actinobacteria and Crenarchaeota but decreased that of Acidobacteria. N addition increased the relative abundances of Acidobacteria, Crenarchaeota, and Actinobacteria but decreased that of Proteobacteria. Soil bacterial diversity was significantly related to soil pH, C/N ratio, and nitrogen and available phosphorus content. Management practices exerted a greater influence over regulation of the soil MBC and microbial diversity compared to that of N deposition in Moso bamboo plantations. PMID:27302857

Modeling microbial diversity in anaerobic digestion through an extended ADM1 model.

PubMed

Ramirez, Ivan; Volcke, Eveline I P; Rajinikanth, Rajagopal; Steyer, Jean-Philippe

2009-06-01

The anaerobic digestion process comprises a whole network of sequential and parallel reactions, of both biochemical and physicochemical nature. Mathematical models, aiming at understanding and optimization of the anaerobic digestion process, describe these reactions in a structured way, the IWA Anaerobic Digestion Model No. 1 (ADM1) being the most well established example. While these models distinguish between different microorganisms involved in different reactions, to our knowledge they all neglect species diversity between organisms with the same function, i.e. performing the same reaction. Nevertheless, available experimental evidence suggests that the structure and properties of a microbial community may be influenced by process operation and on their turn also determine the reactor functioning. In order to adequately describe these phenomena, mathematical models need to consider the underlying microbial diversity. This is demonstrated in this contribution by extending the ADM1 to describe microbial diversity between organisms of the same functional group. The resulting model has been compared with the traditional ADM1 in describing experimental data of a pilot-scale hybrid Upflow Anaerobic Sludge Filter Bed (UASFB) reactor, as well as in a more detailed simulation study. The presented model is further shown useful in assessing the relationship between reactor performance and microbial community structure in mesophilic CSTRs seeded with slaughterhouse wastewater when facing increasing levels of ammonia.

Metagenomics analysis of microbial communities associated with a traditional rice wine starter culture (Xaj-pitha) of Assam, India.

PubMed

Bora, Sudipta Sankar; Keot, Jyotshna; Das, Saurav; Sarma, Kishore; Barooah, Madhumita

2016-12-01

This is the first report on the microbial diversity of xaj-pitha, a rice wine fermentation starter culture through a metagenomics approach involving Illumine-based whole genome shotgun (WGS) sequencing method. Metagenomic DNA was extracted from rice wine starter culture concocted by Ahom community of Assam and analyzed using a MiSeq ® System. A total of 2,78,231 contigs, with an average read length of 640.13 bp, were obtained. Data obtained from the use of several taxonomic profiling tools were compared with previously reported microbial diversity studies through the culture-dependent and culture-independent method. The microbial community revealed the existence of amylase producers, such as Rhizopus delemar, Mucor circinelloides, and Aspergillus sp. Ethanol producers viz., Meyerozyma guilliermondii, Wickerhamomyces ciferrii, Saccharomyces cerevisiae, Candida glabrata, Debaryomyces hansenii, Ogataea parapolymorpha, and Dekkera bruxellensis, were found associated with the starter culture along with a diverse range of opportunistic contaminants. The bacterial microflora was dominated by lactic acid bacteria (LAB). The most frequent occurring LAB was Lactobacillus plantarum, Lactobacillus brevis, Leuconostoc lactis, Weissella cibaria, Lactococcus lactis, Weissella para mesenteroides, Leuconostoc pseudomesenteroides, etc. Our study provided a comprehensive picture of microbial diversity associated with rice wine fermentation starter and indicated the superiority of metagenomic sequencing over previously used techniques.

Effects of different soil management practices on soil properties and microbial diversity

NASA Astrophysics Data System (ADS)

Gajda, Anna M.; Czyż, Ewa A.; Dexter, Anthony R.; Furtak, Karolina M.; Grządziel, Jarosław; Stanek-Tarkowska, Jadwiga

2018-01-01

The effects of different tillage systems on the properties and microbial diversity of an agricultural soil was investigated. In doing so, soil physical, chemical and biological properties were analysed in 2013-2015, on a long-term field experiment on a loamy sand at the IUNG-PIB Experimental Station in Grabów, Poland. Winter wheat was grown under two tillage treatments: conventional tillage using a mouldboard plough and traditional soil tillage equipment, and reduced tillage based on soil crushing-loosening equipment and a rigid-tine cultivator. Chopped wheat straw was used as a mulch on both treatments. Reduced tillage resulted in increased water content throughout the whole soil profile, in comparison with conventional tillage. Under reduced tillage, the content of readily dispersible clay was also reduced, and, therefore, soil stability was increased in the toplayers, compared with conventional tillage. In addition, the beneficial effects of reduced tillage were reflected in higher soil microbial activity as measured with dehydrogenases and hydrolysis of fluorescein diacetate, compared with conventional tillage. Moreover, the polimerase chain reaction - denaturing gradient gel electrophoresis analysis showed that soil under reduced till-age had greater diversity of microbial communities, compared with conventionally-tilled soil. Finally, reduced tillage increased organic matter content, stability in water and microbial diversity in the top layer of the soil.

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.

Spatial and seasonal variation in diversity and structure of microbial biofilms on marine plastics in Northern European waters.

PubMed

Oberbeckmann, Sonja; Loeder, Martin G J; Gerdts, Gunnar; Osborn, A Mark

2014-11-01

Plastic pollution is now recognised as a major threat to marine environments and marine biota. Recent research highlights that diverse microbial species are found to colonise plastic surfaces (the plastisphere) within marine waters. Here, we investigate how the structure and diversity of marine plastisphere microbial community vary with respect to season, location and plastic substrate type. We performed a 6-week exposure experiment with polyethylene terephthalate (PET) bottles in the North Sea (UK) as well as sea surface sampling of plastic polymers in Northern European waters. Scanning electron microscopy revealed diverse plastisphere communities comprising prokaryotic and eukaryotic microorganisms. Denaturing gradient gel electrophoresis (DGGE) and sequencing analysis revealed that plastisphere microbial communities on PET fragments varied both with season and location and comprised of bacteria belonging to Bacteroidetes, Proteobacteria, Cyanobacteria and members of the eukaryotes Bacillariophyceae and Phaeophyceae. Polymers sampled from the sea surface mainly comprised polyethylene, polystyrene and polypropylene particles. Variation within plastisphere communities on different polymer types was observed, but communities were primarily dominated by Cyanobacteria. This research reveals that the composition of plastisphere microbial communities in marine waters varies with season, geographical location and plastic substrate type. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Microbial network, phylogenetic diversity and community membership in the active layer across a permafrost thaw gradient.

PubMed

Mondav, Rhiannon; McCalley, Carmody K; Hodgkins, Suzanne B; Frolking, Steve; Saleska, Scott R; Rich, Virginia I; Chanton, Jeff P; Crill, Patrick M

2017-08-01

Biogenic production and release of methane (CH 4 ) from thawing permafrost has the potential to be a strong source of radiative forcing. We investigated changes in the active layer microbial community of three sites representative of distinct permafrost thaw stages at a palsa mire in northern Sweden. The palsa site (intact permafrost and low radiative forcing signature) had a phylogenetically clustered community dominated by Acidobacteria and Proteobacteria. The bog (thawing permafrost and low radiative forcing signature) had lower alpha diversity and midrange phylogenetic clustering, characteristic of ecosystem disturbance affecting habitat filtering. Hydrogenotrophic methanogens and Acidobacteria dominated the bog shifting from palsa-like to fen-like at the waterline. The fen (no underlying permafrost, high radiative forcing signature) had the highest alpha, beta and phylogenetic diversity, was dominated by Proteobacteria and Euryarchaeota and was significantly enriched in methanogens. The Mire microbial network was modular with module cores consisting of clusters of Acidobacteria, Euryarchaeota or Xanthomonodales. Loss of underlying permafrost with associated hydrological shifts correlated to changes in microbial composition, alpha, beta and phylogenetic diversity associated with a higher radiative forcing signature. These results support the complex role of microbial interactions in mediating carbon budget changes and climate feedback in response to climate forcing. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Microbial diversity in Brazilian mangrove sediments – a mini review

PubMed Central

Ghizelini, Angela Michelato; Mendonça-Hagler, Leda Cristina Santana; Macrae, Andrew

2012-01-01

The importance and protection of mangrove ecosystems has been recognized in Brazilian Federal law since 1965. Being protected in law, however, has not always guaranteed their protection in practice. Mangroves are found in coastal and estuarine locations, which are prime real estate for the growth of cities, ports and other economic activities important for Brazilian development. In this mini-review we introduce what mangroves are and why they are so important. We give a brief overview of the microbial diversity found in mangrove sediments and then focus on diversity studies from Brazilian mangroves. We highlight the breadth and depth of knowledge about mangrove microbial communities gained from studying Brazilian mangroves. We report on the exciting findings of molecular microbial ecology methods that have been very successfully applied to study bacterial communities. We note that there have been fewer studies that focus on fungal communities and that fungal diversity studies deserve more attention. The review ends with a look at how a combination of new molecular biology methods and isolation studies are being developed to monitor and conserve mangrove ecosystems and their associated microbial communities. These recent studies are having a global impact and we hope they will help to protect and re-establish mangrove ecosystems. PMID:24031949

Nitrogen deposition and management practices increase soil microbial biomass carbon but decrease diversity in Moso bamboo plantations

NASA Astrophysics Data System (ADS)

Li, Quan; Song, Xinzhang; Gu, Honghao; Gao, Fei

2016-06-01

Because microbial communities play a key role in carbon (C) and nitrogen (N) cycling, changes in the soil microbial community may directly affect ecosystem functioning. However, the effects of N deposition and management practices on soil microbes are still poorly understood. We studied the effects of these two factors on soil microbial biomass carbon (MBC) and community composition in Moso bamboo plantations using high-throughput sequencing of the 16S rRNA gene. Plantations under conventional (CM) or intensive management (IM) were subjected to one of four N treatments for 30 months. IM and N addition, both separately and in combination, significantly increased soil MBC while decreasing bacterial diversity. However, increases in soil MBC were inhibited when N addition exceeded 60 kg N•ha-1•yr-1. IM increased the relative abundances of Actinobacteria and Crenarchaeota but decreased that of Acidobacteria. N addition increased the relative abundances of Acidobacteria, Crenarchaeota, and Actinobacteria but decreased that of Proteobacteria. Soil bacterial diversity was significantly related to soil pH, C/N ratio, and nitrogen and available phosphorus content. Management practices exerted a greater influence over regulation of the soil MBC and microbial diversity compared to that of N deposition in Moso bamboo plantations.

Shift in the Microbial Ecology of a Hospital Hot Water System following the Introduction of an On-Site Monochloramine Disinfection System

PubMed Central

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

2014-01-01

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

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

PubMed

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

2014-01-01

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

Shifts of tundra bacterial and archaeal communities along a permafrost thaw gradient in Alaska.

PubMed

Deng, Jie; Gu, Yunfu; Zhang, Jin; Xue, Kai; Qin, Yujia; Yuan, Mengting; Yin, Huaqun; He, Zhili; Wu, Liyou; Schuur, Edward A G; Tiedje, James M; Zhou, Jizhong

2015-01-01

Understanding the response of permafrost microbial communities to climate warming is crucial for evaluating ecosystem feedbacks to global change. This study investigated soil bacterial and archaeal communities by Illumina MiSeq sequencing of 16S rRNA gene amplicons across a permafrost thaw gradient at different depths in Alaska with thaw progression for over three decades. Over 4.6 million passing 16S rRNA gene sequences were obtained from a total of 97 samples, corresponding to 61 known classes and 470 genera. Soil depth and the associated soil physical-chemical properties had predominant impacts on the diversity and composition of the microbial communities. Both richness and evenness of the microbial communities decreased with soil depth. Acidobacteria, Verrucomicrobia, Alpha- and Gamma-Proteobacteria dominated the microbial communities in the upper horizon, whereas abundances of Bacteroidetes, Delta-Proteobacteria and Firmicutes increased towards deeper soils. Effects of thaw progression were absent in microbial communities in the near-surface organic soil, probably due to greater temperature variation. Thaw progression decreased the abundances of the majority of the associated taxa in the lower organic soil, but increased the abundances of those in the mineral soil, including groups potentially involved in recalcitrant C degradation (Actinomycetales, Chitinophaga, etc.). The changes in microbial communities may be related to altered soil C sources by thaw progression. Collectively, this study revealed different impacts of thaw in the organic and mineral horizons and suggests the importance of studying both the upper and deeper soils while evaluating microbial responses to permafrost thaw. © 2014 John Wiley & Sons Ltd.

[Carbon source metabolic diversity of soil microbial community under different climate types in the area affected by Wenchuan earthquake].

PubMed

Zhang, Guang-Shuai; Lin, Yong-Ming; Ma, Rui-Feng; Deng, Hao-Jun; Du, Kun; Wu, Cheng-Zhen; Hong, Wei

2015-02-01

The MS8.0 Wenchuan earthquake in 2008 led to huge damage to land covers in northwest Sichuan, one of the critical fragile eco-regions in China which can be divided into Semi-arid dry hot climate zone (SDHC) and Subtropical humid monsoon climate zone (SHMC). Using the method of Bilog-ECO-microplate technique, this paper aimed to determine the functional diversity of soil microbial community in the earthquake-affected areas which can be divided into undamaged area (U), recover area (R) and damaged area without recovery (D) under different climate types, in order to provide scientific basis for ecological recovery. The results indicated that the average-well-color-development (AWCD) in undamaged area and recovery area showed SDHC > SHMC, which was contrary to the AWCD in the damaged area without recovery. The AWCD of damaged area without recovery was the lowest in both climate zones. The number of carbon source utilization types of soil microbial in SHMC zone was significantly higher than that in SDHC zone. The carbon source utilization types in both climate zones presented a trend of recover area > undamaged area > damaged area without recovery. The carbon source metabolic diversity characteristic of soil microbial community was significantly different in different climate zones. The diversity index and evenness index both showed a ranking of undamaged area > recover area > damaged area without recovery. In addition, the recovery area had the highest richness index. The soil microbial carbon sources metabolism characteristic was affected by soil nutrient, aboveground vegetation biomass and vegetation coverage to some extent. In conclusion, earthquake and its secondary disasters influenced the carbon source metabolic diversity characteristic of soil microbial community mainly through the change of aboveground vegetation and soil environmental factors.

Sequencing Insights into Microbial Communities in the Water and Sediments of Fenghe River, China.

PubMed

Lu, Sidan; Sun, Yujiao; Zhao, Xuan; Wang, Lei; Ding, Aizhong; Zhao, Xiaohui

2016-07-01

The connection between microbial community structure and spatial variation and pollution in river waters has been widely investigated. However, water and sediments together have rarely been explored. In this study, Illumina high-throughput sequencing was performed to analyze microbes in 24 water and sediment samples from natural to anthropogenic sources and from headstream to downstream areas. These data were used to assess variability in microbial community structure and diversity along in the Fenghe River, China. The relationship between bacterial diversity and environmental parameters was statistically analyzed. An average of 1682 operational taxonomic units was obtained. Microbial diversity increased from the headstream to downstream and tended to be greater in sediment compared with water. The water samples near the headstream endured relatively low Shannon and Chao1 indices. These diversity indices and the number of observed species in the water and sediment samples increase downstream. The parameters also differ in the two river tributaries. Community structures shift based on the extent of nitrogen pollution variation in the sediment and water samples. The four most dominant genera in the water community were Escherichia, Acinetobacter, Comamonadaceae, and Pseudomonas. In the sediments, the most dominant genera were Stramenopiles, Flavobacterium, Pseudomonas, and Comamonadaceae. The number of ammonia-oxidizing archaea in the headstream water slightly differed from that in the sediment but varied considerably in the downstream sediments. Statistical analysis showed that community variation is correlated with changes in ammonia nitrogen, total nitrogen, and nitrate nitrogen. This study identified different microbial community structures in river water and sediments. Overall this study emphasized the need to elucidate spatial variations in bacterial diversity in water and sediments associated with physicochemical gradients and to show the effects of such variation on waterborne microbial community structures.

Sulfur-oxidizing bacteria dominate the microbial diversity shift during the pyrite and low-grade pyrolusite bioleaching process.

PubMed

Han, Yifan; Ma, Xiaomei; Zhao, Wei; Chang, Yunkang; Zhang, Xiaoxia; Wang, Xingbiao; Wang, Jingjing; Huang, Zhiyong

2013-10-01

The microbial ecology of the pyrite-pyrolusite bioleaching system and its interaction with ore has not been well-described. A 16S rRNA gene clone library was created to evaluate changes in the microbial community at different stages of the pyrite-pyrolusite bioleaching process in a shaken flask. The results revealed that the bacterial community was disturbed after 5 days of the reaction. Phylogenetic analysis of 16S rRNA sequences demonstrated that the predominant microorganisms were members of a genus of sulfur-oxidizing bacteria, Thiomonas sp., that subsequently remained dominant during the bioleaching process. Compared with iron-oxidizing bacteria, sulfur-oxidizing bacteria were more favorable to the pyrite-pyrolusite bioleaching system. Decreased pH due to microbial acid production was an important condition for bioleaching efficiency. Iron-oxidizing bacteria competed for pyrite reduction power with Mn(IV) in pyrolusite under specific conditions. These results extend our knowledge of microbial dynamics during pyrite-pyrolusite bioleaching, which is a key issue to improve commercial applications. Copyright © 2013 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Marine sources influence fog bioaerosol composition in Namibia and Maine

NASA Astrophysics Data System (ADS)

Evans, S. E.; Dueker, E.; Logan, J. R. V.; Weathers, K. C.

2017-12-01

Organic aerosol particles act as condensation nuclei for fogs and clouds (CCN) and are main determinants of fog evolution, chemical processing, and overall aerosol-fog-cloud interactions. Recent work has confirmed the presence of marine bioaerosols, but little is known about their sources, transport, taxonomic diversity or viability. The few studies that have characterized bioaerosols in fog have been limited to culture-based approaches that capture only a fraction of microbial diversity. We characterized fungal and bacterial communities in the fog in two iconic fog systems, the Coast of Maine (USA) and the Namib Desert (Namibia). The biology of fog in both systems was diverse and distinct, by geography, from dry aerosols, and from local sources. The local environment had a dominant influence on fog in both the Namib and Maine; in particular, the biology of fog in Maine, which was collected near the coast, was more similar to microbial communities from the ocean surface. In both systems, differences between pre- and post-fog aerosol communities suggest that fog events can significantly alter microbial aerosol diversity and composition. This insight into the microbial composition of fog indicates that its origin and frequency has the potential to influence the number and diversity of microorganisms that settle in a given environment, and the composition of microbial aerosol communities in ambient or clear conditions. Here we suggest that fog microbes can possess specific traits that enhance nucleation, altering the transport and deposition of marine- and soil-derived organic matter in terrestrial systems.

Microbial diversity of extreme habitats in human homes.

PubMed

Savage, Amy M; Hills, Justin; Driscoll, Katherine; Fergus, Daniel J; Grunden, Amy M; Dunn, Robert R

2016-01-01

High-throughput sequencing techniques have opened up the world of microbial diversity to scientists, and a flurry of studies in the most remote and extreme habitats on earth have begun to elucidate the key roles of microbes in ecosystems with extreme conditions. These same environmental extremes can also be found closer to humans, even in our homes. Here, we used high-throughput sequencing techniques to assess bacterial and archaeal diversity in the extreme environments inside human homes (e.g., dishwashers, hot water heaters, washing machine bleach reservoirs, etc.). We focused on habitats in the home with extreme temperature, pH, and chemical environmental conditions. We found a lower diversity of microbes in these extreme home environments compared to less extreme habitats in the home. However, we were nonetheless able to detect sequences from a relatively diverse array of bacteria and archaea. Habitats with extreme temperatures alone appeared to be able to support a greater diversity of microbes than habitats with extreme pH or extreme chemical environments alone. Microbial diversity was lowest when habitats had both extreme temperature and one of these other extremes. In habitats with both extreme temperatures and extreme pH, taxa with known associations with extreme conditions dominated. Our findings highlight the importance of examining interactive effects of multiple environmental extremes on microbial communities. Inasmuch as taxa from extreme environments can be both beneficial and harmful to humans, our findings also suggest future work to understand both the threats and opportunities posed by the life in these habitats.

Biogeochemistry of microbial coal-bed methane

USGS Publications Warehouse

Strc, D.; Mastalerz, Maria; Dawson, K.; MacAlady, J.; Callaghan, A.V.; Wawrik, B.; Turich, C.; Ashby, M.

2011-01-01

Microbial methane accumulations have been discovered in multiple coal-bearing basins over the past two decades. Such discoveries were originally based on unique biogenic signatures in the stable isotopic composition of methane and carbon dioxide. Basins with microbial methane contain either low-maturity coals with predominantly microbial methane gas or uplifted coals containing older, thermogenic gas mixed with more recently produced microbial methane. Recent advances in genomics have allowed further evaluation of the source of microbial methane, through the use of high-throughput phylogenetic sequencing and fluorescent in situ hybridization, to describe the diversity and abundance of bacteria and methanogenic archaea in these subsurface formations. However, the anaerobic metabolism of the bacteria breaking coal down to methanogenic substrates, the likely rate-limiting step in biogenic gas production, is not fully understood. Coal molecules are more recalcitrant to biodegradation with increasing thermal maturity, and progress has been made in identifying some of the enzymes involved in the anaerobic degradation of these recalcitrant organic molecules using metagenomic studies and culture enrichments. In recent years, researchers have attempted lab and subsurface stimulation of the naturally slow process of methanogenic degradation of coal. Copyright ?? 2011 by Annual Reviews. All rights reserved.

Microbial Diversity of a Brazilian Coastal Region Influenced by an Upwelling System and Anthropogenic Activity

PubMed Central

Cury, Juliano C.; Araujo, Fabio V.; Coelho-Souza, Sergio A.; Peixoto, Raquel S.; Oliveira, Joana A. L.; Santos, Henrique F.; Dávila, Alberto M. R.; Rosado, Alexandre S.

2011-01-01

Background Upwelling systems are characterised by an intense primary biomass production in the surface (warmest) water after the outcrop of the bottom (coldest) water, which is rich in nutrients. Although it is known that the microbial assemblage plays an important role in the food chain of marine systems and that the upwelling systems that occur in southwest Brazil drive the complex dynamics of the food chain, little is known about the microbial composition present in this region. Methodology/Principal Findings We carried out a molecular survey based on SSU rRNA gene from the three domains of the phylogenetic tree of life present in a tropical upwelling region (Arraial do Cabo, Rio de Janeiro, Brazil). The aim was to analyse the horizontal and vertical variations of the microbial composition in two geographically close areas influenced by anthropogenic activity (sewage disposal/port activity) and upwelling phenomena, respectively. A lower estimated diversity of microorganisms of the three domains of the phylogenetic tree of life was found in the water of the area influenced by anthropogenic activity compared to the area influenced by upwelling phenomena. We observed a heterogenic distribution of the relative abundance of taxonomic groups, especially in the Archaea and Eukarya domains. The bacterial community was dominated by Proteobacteria, Cyanobacteria and Bacteroidetes phyla, whereas the microeukaryotic community was dominated by Metazoa, Fungi, Alveolata and Stramenopile. The estimated archaeal diversity was the lowest of the three domains and was dominated by uncharacterised marine Crenarchaeota that were most closely related to Marine Group I. Conclusions/Significance The variety of conditions and the presence of different microbial assemblages indicated that the area of Arraial do Cabo can be used as a model for detailed studies that contemplate the correlation between pollution-indicating parameters and the depletion of microbial diversity in areas close to anthropogenic activity; functional roles and geochemical processes; phylogeny of the uncharacterised diversity; and seasonal variations of the microbial assemblages. PMID:21304582

Diversity, Stability, and Reproducibility in Stochastically Assembled Microbial Ecosystems

NASA Astrophysics Data System (ADS)

Goyal, Akshit; Maslov, Sergei

2018-04-01

Microbial ecosystems are remarkably diverse, stable, and usually consist of a mixture of core and peripheral species. Here we propose a conceptual model exhibiting all these emergent properties in quantitative agreement with real ecosystem data, specifically species abundance and prevalence distributions. Resource competition and metabolic commensalism drive the stochastic ecosystem assembly in our model. We demonstrate that even when supplied with just one resource, ecosystems can exhibit high diversity, increasing stability, and partial reproducibility between samples.

[Effects of re-vegetation on soil microbial functional diversity in purple soils at different re-vegetation stages on sloping-land in Hengyang, Hunan Province, China.

PubMed

Wen, Dong Xin; Yang, Ning; Yang, Man Yuan

2016-08-01

The aim of the study was to explore the effects of re-vegetation on soil microbial functio-nal diversity in purple soils at different re-vegetation stages on sloping-land in Hengyang, Hunan Province, China. By using the spatial series to replace time series, four typical sampling plots, grass (Setaria viridi, GS), frutex and grass (Lagerstroemia indica-Setaria viridi, FG), frutex (Vitex negundo var. cannabifolia+Robinia pseudoacacia, FX), as well as arbor and frutex (Liquidamdar formosana+Melia azedarach-Vitex negundo var. cannabifolia, AF) community were selected to study the soil microbial functional diversity by using the Biolog-ECO micro-plate technique. The four communities in purple soils on sloping-land were similar and denoted four different re-vegetation stages. The results showed that the soil microbial metabolic activity increased after re-vegetation significantly, and the average well color development (AWCD) which represented soil microbial activity and functional diversity followed the order of AF community＞FX community＞FG community＞GS community at different re-vegetation stages, and followed the order of 0-10 cm ＞10-20 cm in different soil layers. Principal component analysis (PCA) identified that FG and FX community had similar C sources utilization mode and metabolic function, and GS and AF community were diffe-rent. The carbohydrates, amino acids, intermediate metabolites, and secondary metabolites were the main carbon sources separating the two principal component factors. The Shannon species richness index (H), Shannon evenness index (E), Simpson dominance index (D), McIntosh index (U) at four re-vegetation stages were the highest in AF community, the second in FG and FX community, and the lowest in GS community. The results of correlation analysis indicated that the content of soil water content (SWC), soil total organic carbon (STOC), total nitrogen (TN), total phospho-rus (TP) and available phosphorus (AP) had important influence on the soil microbial metabolic function and functional diversity indices. There existed significant correlation between the activities of urease (URE), alk-phosphatase (APE), invertase (INV), catalase (CAT) and the soil microbial metabolic function and functional diversity indices. All the results indicated that re-vegetation could enhance the soil microbial metabolic function, which was beneficial to the reproduction of soil micro-organisms, thereby promoting an increase of soil carbon source utilization intensity.

Microbial community structure and diversity in a municipal solid waste landfill.

PubMed

Wang, Xiaolin; Cao, Aixin; Zhao, Guozhu; Zhou, Chuanbin; Xu, Rui

2017-08-01

Municipal solid waste (MSW) landfills are the most prevalent waste disposal method and constitute one of the largest sources of anthropogenic methane emissions in the world. Microbial activities in disposed waste play a crucial role in greenhouse gas emissions; however, only a few studies have examined metagenomic microbial profiles in landfills. Here, the MiSeq high-throughput sequencing method was applied for the first time to examine microbial diversity of the cover soil and stored waste located at different depths (0-150cm) in a typical MSW landfill in Yangzhou City, East China. The abundance of microorganisms in the cover soil (0-30cm) was the lowest among all samples, whereas that in stored waste decreased from the top to the middle layer (30-90cm) and then increased from the middle to the bottom layer (90-150cm). In total, 14 phyla and 18 genera were found in the landfill. A microbial diversity analysis showed that Firmicutes, Proteobacteria, and Bacteroidetes were the dominant phyla, whereas Halanaerobium, Methylohalobius, Syntrophomonas, Fastidiosipila, and Spirochaeta were the dominant genera. Methylohalobius (methanotrophs) was more abundant in the cover layers of soil than in stored waste, whereas Syntrophomonas and Fastidiosipila, which affect methane production, were more abundant in the middle to bottom layers (90-150cm) in stored waste. A canonical correlation analysis showed that microbial diversity in the landfill was most strongly correlated with the conductivity, organic matter, and moisture content of the stored waste. Copyright © 2017 Elsevier Ltd. All rights reserved.

Variations of soil microbial community structures beneath broadleaved forest trees in temperate and subtropical climate zones

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

Yang, Sihang; Zhang, Yuguang; Cong, Jing

Global warming has shifted climate zones poleward or upward. Furthermore, understanding the responses and mechanism of microbial community structure and functions relevant to natural climate zone succession is challenged by the high complexity of microbial communities. Here, we examined soil microbial community in three broadleaved forests located in the Wulu Mountain (WLM, temperate climate), Funiu Mountain (FNM, at the border of temperate and subtropical climate zones), or Shennongjia Mountain (SNJ, subtropical climate). Although plant species richness decreased with latitudes, the microbial taxonomic α-diversity increased with latitudes, concomitant with increases in soil total and available nitrogen and phosphorus contents. Phylogenetic NRImore » (Net Relatedness Index) values increased from 0.718 in temperate zone (WLM) to 1.042 in subtropical zone (SNJ), showing a shift from over dispersion to clustering likely caused by environmental filtering such as low pH and nutrients. Similarly, taxonomybased association networks of subtropical forest samples were larger and tighter, suggesting clustering. In contrast, functional α-diversity was similar among three forests, but functional gene networks of the FNM forest significantly (P < 0.050) differed from the others. A significant correlation (R = 0.616, P < 0.001) between taxonomic and functional β-diversity was observed only in the FNM forest, suggesting low functional redundancy at the border of climate zones. Using a strategy of space-fortime substitution, we predict that poleward climate range shift will lead to decreased microbial taxonomic α-diversities in broadleaved forest.« less

Variations of soil microbial community structures beneath broadleaved forest trees in temperate and subtropical climate zones

DOE PAGES

Yang, Sihang; Zhang, Yuguang; Cong, Jing; ...

2017-02-10

Global warming has shifted climate zones poleward or upward. Furthermore, understanding the responses and mechanism of microbial community structure and functions relevant to natural climate zone succession is challenged by the high complexity of microbial communities. Here, we examined soil microbial community in three broadleaved forests located in the Wulu Mountain (WLM, temperate climate), Funiu Mountain (FNM, at the border of temperate and subtropical climate zones), or Shennongjia Mountain (SNJ, subtropical climate). Although plant species richness decreased with latitudes, the microbial taxonomic α-diversity increased with latitudes, concomitant with increases in soil total and available nitrogen and phosphorus contents. Phylogenetic NRImore » (Net Relatedness Index) values increased from 0.718 in temperate zone (WLM) to 1.042 in subtropical zone (SNJ), showing a shift from over dispersion to clustering likely caused by environmental filtering such as low pH and nutrients. Similarly, taxonomybased association networks of subtropical forest samples were larger and tighter, suggesting clustering. In contrast, functional α-diversity was similar among three forests, but functional gene networks of the FNM forest significantly (P < 0.050) differed from the others. A significant correlation (R = 0.616, P < 0.001) between taxonomic and functional β-diversity was observed only in the FNM forest, suggesting low functional redundancy at the border of climate zones. Using a strategy of space-fortime substitution, we predict that poleward climate range shift will lead to decreased microbial taxonomic α-diversities in broadleaved forest.« less

Evaluation of bacterial pathogen diversity, abundance and health risks in urban recreational water by amplicon next-generation sequencing and quantitative PCR.

PubMed

Cui, Qijia; Fang, Tingting; Huang, Yong; Dong, Peiyan; Wang, Hui

2017-07-01

The microbial quality of urban recreational water is of great concern to public health. The monitoring of indicator organisms and several pathogens alone is not sufficient to accurately and comprehensively identify microbial risks. To assess the levels of bacterial pathogens and health risks in urban recreational water, we analyzed pathogen diversity and quantified four pathogens in 46 water samples collected from waterbodies in Beijing Olympic Forest Park in one year. The pathogen diversity revealed by 16S rRNA gene targeted next-generation sequencing (NGS) showed that 16 of 40 genera and 13 of 76 reference species were present. The most abundant species were Acinetobacter johnsonii, Mycobacterium avium and Aeromonas spp. Quantitative polymerase chain reaction (qPCR) of Escherichia coli (uidA), Aeromonas (aerA), M. avium (16S rRNA), Pseudomonas aeruginosa (oaa) and Salmonella (invA) showed that the aerA genes were the most abundant, occurring in all samples with concentrations of 10 4-6 genome copies/100mL, followed by oaa, invA and M. avium. In total, 34.8% of the samples harbored all genes, indicating the prevalence of these pathogens in this recreational waterbody. Based on the qPCR results, a quantitative microbial risk assessment (QMRA) showed that the annual infection risks of Salmonella, M. avium and P. aeruginosa in five activities were mostly greater than the U.S. EPA risk limit for recreational contacts, and children playing with water may be exposed to the greatest infection risk. Our findings provide a comprehensive understanding of bacterial pathogen diversity and pathogen abundance in urban recreational water by applying both NGS and qPCR. Copyright © 2016. Published by Elsevier B.V.

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

PubMed

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

2016-09-29

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

Microbial Functional Diversity, Biomass and Activity as Affected by Soil Surface Mulching in a Semiarid Farmland

PubMed Central

Shen, Yufang; Chen, Yingying; Li, Shiqing

2016-01-01

Mulching is widely used to increase crop yield in semiarid regions in northwestern China, but little is known about the effect of different mulching systems on the microbial properties of the soil, which play an important role in agroecosystemic functioning and nutrient cycling. Based on a 4-year spring maize (Zea mays L.) field experiment at Changwu Agricultural and Ecological Experimental Station, Shaanxi, we evaluated the responses of soil microbial activity and crop to various management systems. The treatments were NMC (no mulching with inorganic N fertilizer), GMC (gravel mulching with inorganic N fertilizer), FMC (plastic-film mulching with inorganic N fertilizer) and FMO (plastic-film mulching with inorganic N fertilizer and organic manure addition). The results showed that the FMO soil had the highest contents of microbial biomass carbon and nitrogen, dehydrogenase activity, microbial activity and Shannon diversity index. The relative use of carbohydrates and amino acids by microbes was highest in the FMO soil, whereas the relative use of polymers, phenolic compounds and amines was highest in the soil in the NMC soil. Compared with the NMC, an increased but no significant trend of biomass production and nitrogen accumulation was observed under the GMC treatment. The FMC and FMO led a greater increase in biomass production than GMC and NMC. Compare with the NMC treatment, FMC increased grain yield, maize biomass and nitrogen accumulation by 62.2, 62.9 and 86.2%, but no significant difference was found between the FMO and FMC treatments. Some soil biological properties, i.e. microbial biomass carbon, microbial biomass nitrogen, being sensitive to the mulching and organic fertilizer, were significant correlated with yield and nitrogen availability. Film mulching over gravel mulching can serve as an effective measure for crop production and nutrient cycling, and plus organic fertilization additions may thus have improvements in the biological quality of the soil and its sustainability in the rainfall-limited semiarid region. PMID:27414400

Microbial Ecology and Evolution in the Acid Mine Drainage Model System.

PubMed

Huang, Li-Nan; Kuang, Jia-Liang; Shu, Wen-Sheng

2016-07-01

Acid mine drainage (AMD) is a unique ecological niche for acid- and toxic-metals-adapted microorganisms. These low-complexity systems offer a special opportunity for the ecological and evolutionary analyses of natural microbial assemblages. The last decade has witnessed an unprecedented interest in the study of AMD communities using 16S rRNA high-throughput sequencing and community genomic and postgenomic methodologies, significantly advancing our understanding of microbial diversity, community function, and evolution in acidic environments. This review describes new data on AMD microbial ecology and evolution, especially dynamics of microbial diversity, community functions, and population genomes, and further identifies gaps in our current knowledge that future research, with integrated applications of meta-omics technologies, will fill. Copyright © 2016 Elsevier Ltd. All rights reserved.

The effect of cigarette smoking on the oral and nasal microbiota.

PubMed

Yu, Guoqin; Phillips, Stephen; Gail, Mitchell H; Goedert, James J; Humphrys, Michael S; Ravel, Jacques; Ren, Yanfang; Caporaso, Neil E

2017-01-17

The goal of the study was to investigate whether cigarette smoking alters oral and nasal microbial diversity, composition, and structure. Twenty-three current smokers and 20 never smokers were recruited. From each subject, nine samples including supra and subgingiva plaque scrapes, saliva, swabs from five soft oral tissue sites, and one nasal swab from both the anterior nares were collected. 16S rRNA V3-V4 region was sequenced for microbial profiles. We found that alpha diversity was lower in smokers than in nonsmokers in the buccal mucosa, but in other sample sites, microbial diversity and composition were not significantly different by smoking status. Microbial profiles differed significantly among eight oral sites. This study investigates the effect of cigarette smoking on different sites of the oral cavity and shows a potential effect of cigarette smoking on the buccal mucosa microbiota. The marked heterogeneity of the oral microbial ecosystem that we found may contribute to the stability of the oral microbiota in most sites when facing environmental perturbations such as that caused by cigarette smoking.

Arctic gypsum endoliths: a biogeochemical characterization of a viable and active microbial community

NASA Astrophysics Data System (ADS)

Ziolkowski, L. A.; Mykytczuk, N. C. S.; Omelon, C. R.; Johnson, H.; Whyte, L. G.; Slater, G. F.

2013-11-01

Extreme environmental conditions such as those found in the polar regions on Earth are thought to test the limits of life. Microorganisms living in these environments often seek protection from environmental stresses such as high UV exposure, desiccation and rapid temperature fluctuations, with one protective habitat found within rocks. Such endolithic microbial communities, which often consist of bacteria, fungi, algae and lichens, are small-scale ecosystems comprised of both producers and consumers. However, the harsh environmental conditions experienced by polar endolithic communities are thought to limit microbial diversity and therefore the rate at which they cycle carbon. In this study, we characterized the microbial community diversity, turnover rate and microbe-mineral interactions of a gypsum-based endolithic community in the polar desert of the Canadian high Arctic. 16S/18S/23S rRNA pyrotag sequencing demonstrated the presence of a diverse community of phototrophic and heterotrophic bacteria, archaea, algae and fungi. Stable carbon isotope analysis of the viable microbial membranes, as phospholipid fatty acids and glycolipid fatty acids, confirmed the diversity observed by molecular techniques and indicated that present-day atmospheric carbon is assimilated into the microbial community biomass. Uptake of radiocarbon from atmospheric nuclear weapons testing during the 1960s into microbial lipids was used as a pulse label to determine that the microbial community turns over carbon on the order of 10 yr, equivalent to 4.4 g C m-2 yr-1 gross primary productivity. Scanning electron microscopy (SEM) micrographs indicated that mechanical weathering of gypsum by freeze-thaw cycles leads to increased porosity, which ultimately increases the habitability of the rock. In addition, while bacteria were adhered to these mineral surfaces, chemical analysis by micro-X-ray fluorescence (μ-XRF) spectroscopy suggests little evidence for microbial alteration of minerals, which contrasts with other endolithic habitats. While it is possible that these communities turn over carbon quickly and leave little evidence of microbe-mineral interaction, an alternative hypothesis is that the soluble and friable nature of gypsum and harsh conditions lead to elevated erosion rates, limiting microbial residence times in this habitat. Regardless, this endolithic community represents a microbial system that does not rely on a nutrient pool from the host gypsum cap rock, instead receiving these elements from allochthonous debris to maintain a more diverse and active community than might have been predicted in the polar desert of the Canadian high Arctic.

Microbial community diversity associated with moonmilk deposits in a karstic cave system in Ireland

NASA Astrophysics Data System (ADS)

Rooney, D.; Hutchens, E.; Clipson, Nick; McDermott, Frank

2009-04-01

Microbial ecology in subterranean systems has yet to be fully studied. Cave systems present highly unusual and extreme habitats, where microbial activity can potentially play a major role in nutrient cycling and possibly contribute to the formation of characteristic subaerial structures. How microorganisms actually function in cave systems, and what ecological roles they may perform, has yet to be widely addressed, although recent studies using molecular techniques combined with analytical geochemistry have begun to answer some questions surrounding subterranean microbial ecology (Northup et al., 2003). Moonmilk has a ‘cottage-cheese' like consistency, comprised of fine crystal aggregates of carbonate minerals, commonly calcite, hydromagnesite and gypsum, and is believed to be at least partially precipitated by microbial activity (Baskar et al., 2006). Microbial metabolic processes have been implicated in the formation of moonmilk, probably a result of biochemical corrosion of bedrock under high moisture conditions. Mineral weathering via bacterial activity has become accepted as a major influence on subsurface geochemistry and formation of belowground structures (Summers-Engel et al., 2004). While many studies focus on bacterial communities in subterranean systems, fungal community structure is also likely to be important in cave systems, given the important role fungi play in the transformations of organic and inorganic substrates (Gadd, 2004) and the significant role of fungi in mineral dissolution and secondary mineral formation (Burford et al., 2003). In general, it is agreed that both biotic and abiotic processes influence moonmilk formation, yet the diversity of the microbial community associated with moonmilk formations has not been characterised to date. Ballinamintra Cave (Waterford County, Ireland) is largely protected from human influence due to accessibility difficulties and thereby offers an opportunity to study microbial community structure that has been unaltered by human disturbance or practices. The aim of this study was to examine microbial community diversity associated with moonmilk deposits at Ballynamintra Cave, Ireland using automated ribosomal intergenic spacer analysis (ARISA). The results revealed considerable bacterial and fungal diversity associated with moonmilk in a karstic cave system, suggesting that the microbial community implicated in moonmilk formation may be more diverse than previously thought. These results suggest that microbes may have important functional roles in subterranean environments. Although the moonmilk in this study was largely comprised of calcite, microbial involvement in calcite precipitation could result in the bioavailability of a range of organic compounds for subsequent microbial metabolism. References: Baskar, S., Baskar, R., Mauclaire, L., and McKenzie, J.A. 2006. Microbially induced calcite precipitation in culture experiments: Possible origin for stalactites in Sahastradhara caves, Dehradun, India. Current Science 90: 58-64. Burford, E.P., Fomina, M., Gadd, G. 2003. Fungal involvement in bioweathering and biotrasformations of rocks and minerals. Min Mag 67(6):1172-1155. Engel, A.S., Stern, L.A., Bennett, P.C. 2004. Microbial contributions to cave formation: new insights into sulfuric acid speleogenesis. Geology 32(5): 369-372. Gadd, G.M. (2004). Mycotransformation of organic and inorganic substrates. Mycologist 18: 60-70. Northup, D., Barns, S.M., Yu, Laura, E., Spilde, M.N., Schelble, R.T., Dano, K.E., Crossey, L.J., Connolly, C.A., Boston, P.J., and Dahm, C.N. 2003. Diverse microbial communities inhabiting ferromanganese deposits in Lechuguilla and Spider Caves. Environmental Microbiology 5(11): 1071-1086.

Fungal endophyte communities reflect environmental structuring across a Hawaiian landscape

PubMed Central

Zimmerman, Naupaka B.; Vitousek, Peter M.

2012-01-01

We surveyed endophytic fungal communities in leaves of a single tree species (Metrosideros polymorpha) across wide environmental gradients (500–5,500 mm of rain/y; 10–22 °C mean annual temperature) spanning short geographic distances on Mauna Loa Volcano, Hawai’i. Using barcoded amplicon pyrosequencing at 13 sites (10 trees/site; 10 leaves/tree), we found very high levels of diversity within sites (a mean of 551 ± 134 taxonomic units per site). However, among-site diversity contributed even more than did within-site diversity to the overall richness of more than 4,200 taxonomic units observed in M. polymorpha, and this among-site variation in endophyte community composition correlated strongly with temperature and rainfall. These results are consistent with suggestions that foliar endophytic fungi are hyperdiverse. They further suggest that microbial diversity may be even greater than has been assumed and that broad-scale environmental controls such as temperature and rainfall can structure eukaryotic microbial diversity. Appropriately constrained study systems across strong environmental gradients present a useful means to understand the environmental factors that structure the diversity of microbial communities. PMID:22837398

Microbial Diversity in Deep-sea Methane Seep Sediments Presented by SSU rRNA Gene Tag Sequencing

PubMed Central

Nunoura, Takuro; Takaki, Yoshihiro; Kazama, Hiromi; Hirai, Miho; Ashi, Juichiro; Imachi, Hiroyuki; Takai, Ken

2012-01-01

Microbial community structures in methane seep sediments in the Nankai Trough were analyzed by tag-sequencing analysis for the small subunit (SSU) rRNA gene using a newly developed primer set. The dominant members of Archaea were Deep-sea Hydrothermal Vent Euryarchaeotic Group 6 (DHVEG 6), Marine Group I (MGI) and Deep Sea Archaeal Group (DSAG), and those in Bacteria were Alpha-, Gamma-, Delta- and Epsilonproteobacteria, Chloroflexi, Bacteroidetes, Planctomycetes and Acidobacteria. Diversity and richness were examined by 8,709 and 7,690 tag-sequences from sediments at 5 and 25 cm below the seafloor (cmbsf), respectively. The estimated diversity and richness in the methane seep sediment are as high as those in soil and deep-sea hydrothermal environments, although the tag-sequences obtained in this study were not sufficient to show whole microbial diversity in this analysis. We also compared the diversity and richness of each taxon/division between the sediments from the two depths, and found that the diversity and richness of some taxa/divisions varied significantly along with the depth. PMID:22510646

Functions and Unique Diversity of Genes and Microorganisms Involved in Arsenite Oxidation from the Tailings of a Realgar Mine

PubMed Central

E, Guoji; Wang, Jianing; Wang, Nian; Chen, Xiaoming; Mu, Yao; Li, Hao; Yang, Ye; Liu, Yichen; Wang, Yanxin

2016-01-01

ABSTRACT The tailings of the Shimen realgar mine have unique geochemical features. Arsenite oxidation is one of the major biogeochemical processes that occurs in the tailings. However, little is known about the functional and molecular aspects of the microbial community involved in arsenite oxidation. Here, we fully explored the functional and molecular features of the microbial communities from the tailings of the Shimen realgar mine. We collected six samples of tailings from sites A, B, C, D, E, and F. Microcosm assays indicated that all of the six sites contain both chemoautotrophic and heterotrophic arsenite-oxidizing microorganisms; their activities differed considerably from each other. The microbial arsenite-oxidizing activities show a positive correlation with soluble arsenic concentrations. The microbial communities of the six sites contain 40 phyla of bacteria and 2 phyla of archaea that show extremely high diversity. Soluble arsenic, sulfate, pH, and total organic carbon (TOC) are the key environmental factors that shape the microbial communities. We further identified 114 unique arsenite oxidase genes from the samples; all of them code for new or new-type arsenite oxidases. We also isolated 10 novel arsenite oxidizers from the samples, of which 4 are chemoautotrophic and 6 are heterotrophic. These data highlight the unique diversities of the arsenite-oxidizing microorganisms and their oxidase genes from the tailings of the Shimen realgar mine. To the best of our knowledge, this is the first report describing the functional and molecular features of microbial communities from the tailings of a realgar mine. IMPORTANCE This study focused on the functional and molecular characterizations of microbial communities from the tailings of the Shimen realgar mine. We fully explored, for the first time, the arsenite-oxidizing activities and the functional gene diversities of microorganisms from the tailings, as well as the correlation of the microbial activities/diversities with environmental factors. The findings of this study help us to better understand the diversities of the arsenite-oxidizing bacteria and the geochemical cycle of arsenic in the tailings of the Shimen realgar mine and gain insights into the microbial mechanisms by which the secondary minerals of the tailings were formed. This work also offers a set of unique arsenite-oxidizing bacteria for basic research of the molecular regulation of arsenite oxidation in bacterial cells and for the environmentally friendly bioremediation of arsenic-contaminated groundwater. PMID:27663031

Functions and Unique Diversity of Genes and Microorganisms Involved in Arsenite Oxidation from the Tailings of a Realgar Mine.

PubMed

Zeng, Xian-Chun; E, Guoji; Wang, Jianing; Wang, Nian; Chen, Xiaoming; Mu, Yao; Li, Hao; Yang, Ye; Liu, Yichen; Wang, Yanxin

2016-12-15

The tailings of the Shimen realgar mine have unique geochemical features. Arsenite oxidation is one of the major biogeochemical processes that occurs in the tailings. However, little is known about the functional and molecular aspects of the microbial community involved in arsenite oxidation. Here, we fully explored the functional and molecular features of the microbial communities from the tailings of the Shimen realgar mine. We collected six samples of tailings from sites A, B, C, D, E, and F. Microcosm assays indicated that all of the six sites contain both chemoautotrophic and heterotrophic arsenite-oxidizing microorganisms; their activities differed considerably from each other. The microbial arsenite-oxidizing activities show a positive correlation with soluble arsenic concentrations. The microbial communities of the six sites contain 40 phyla of bacteria and 2 phyla of archaea that show extremely high diversity. Soluble arsenic, sulfate, pH, and total organic carbon (TOC) are the key environmental factors that shape the microbial communities. We further identified 114 unique arsenite oxidase genes from the samples; all of them code for new or new-type arsenite oxidases. We also isolated 10 novel arsenite oxidizers from the samples, of which 4 are chemoautotrophic and 6 are heterotrophic. These data highlight the unique diversities of the arsenite-oxidizing microorganisms and their oxidase genes from the tailings of the Shimen realgar mine. To the best of our knowledge, this is the first report describing the functional and molecular features of microbial communities from the tailings of a realgar mine. This study focused on the functional and molecular characterizations of microbial communities from the tailings of the Shimen realgar mine. We fully explored, for the first time, the arsenite-oxidizing activities and the functional gene diversities of microorganisms from the tailings, as well as the correlation of the microbial activities/diversities with environmental factors. The findings of this study help us to better understand the diversities of the arsenite-oxidizing bacteria and the geochemical cycle of arsenic in the tailings of the Shimen realgar mine and gain insights into the microbial mechanisms by which the secondary minerals of the tailings were formed. This work also offers a set of unique arsenite-oxidizing bacteria for basic research of the molecular regulation of arsenite oxidation in bacterial cells and for the environmentally friendly bioremediation of arsenic-contaminated groundwater. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Comparative evaluation of microbial diversity and metabolite profiles in doenjang, a fermented soybean paste, during the two different industrial manufacturing processes.

PubMed

Lee, Sunmin; Lee, Sarah; Singh, Digar; Oh, Ji Young; Jeon, Eun Jung; Ryu, Hyung SeoK; Lee, Dong Wan; Kim, Beom Seok; Lee, Choong Hwan

2017-04-15

Two different doenjang manufacturing processes, the industrial process (IP) and the modified industrial process (mIP) with specific microbial assortments, were subjected to metabolite profiling using liquid chromatography-mass spectrometry (LC-MS) and gas chromatography time-of-flight mass spectrometry (GC-TOF-MS). The multivariate analyses indicated that both primary and secondary metabolites exhibited distinct patterns according to the fermentation processes (IP and mIP). Microbial community analysis for doenjang using denaturing gradient gel electrophoresis (DGGE), exhibited that both bacteria and fungi contributed proportionally for each step in the process viz., soybean, steaming, drying, meju fermentation, cooling, brining, and aging. Further, correlation analysis indicated that Aspergillus population was linked to sugar metabolism, Bacillus spp. with that of fatty acids, whereas Tetragenococcus and Zygosaccharomyces were found associated with amino acids. These results suggest that the components and quality of doenjang are critically influenced by the microbial assortments in each process. Copyright © 2016 Elsevier Ltd. All rights reserved.

Using soil health to assess ecotoxicological impacts of pollutants on soil microflora.

PubMed

Bécaert, Valérie; Deschênes, Louise

2006-01-01

Microorganisms are essential for a properly functioning soil ecosystem. However, few methods allow an ecotoxicological evaluation of pollutant impact on the soil microbial community. This review proposes the use of the concept of soil health as an ecotoxicological evaluation tool for soil microflora. Initially limited to sustainable agriculture, the concept of soil health is now being applied to novel situations including contaminated and remediated soils. A large amount of work has been published in the last few decades on soil health indicators, and a review of the most relevant studies is presented here. The most cited work is that of the S-5518 committee set up in 1997 by the Soil Science Society of America (SSSA), which proposed to define soil quality as being "the capacity of a soil to function within the limits of an ecosystem, to support biological production, to maintain environmental quality and to support fauna and flora health." The soil health indicators reviewed here are the ones based on this definition because it relates well to sustainability and durability of the soil functions. Several indicators proposed in these studies could be employed in the evaluation of the ecotoxicological impact of pollutants on the soil microbial community, including microbial diversity, microbial activity, and functional stability. However, research is still required to unify the concept, to set threshold values, and to standardize methodologies.

Evaluation of the ruminal bacterial diversity of cattle fed diets containing citrus pulp pellets (CPP) using bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP)

USDA-ARS?s Scientific Manuscript database

The rumen microbial ecosystem has been extensively studied, but remains a mystery from a quantitative perspective. Dietary components and changes cause shifts in the ruminal microflora that can affect animal health and productivity, but the majority of these changes remain unknown. The objective of ...

Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics [Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics and NanoSIMS.

DOE PAGES

Burow, Luke C.; Woebken, Dagmar; Marshall, Ian PG; ...

2012-11-29

Photosynthetic microbial mats possess extraordinary phylogenetic and functional diversity that makes linking specific pathways with individual microbial populations a daunting task. Close metabolic and spatial relationships between Cyanobacteria and Chloroflexi have previously been observed in diverse microbial mats. Here in this paper, we report that an expressed metabolic pathway for the anoxic catabolism of photosynthate involving Cyanobacteria and Chloroflexi in microbial mats can be reconstructed through metatranscriptomic sequencing of mats collected at Elkhorn Slough, Monterey Bay, CA, USA. In this reconstruction, Microcoleus spp., the most abundant cyanobacterial group in the mats, ferment photosynthate to organic acids, CO 2 and Hmore » 2 through multiple pathways, and an uncultivated lineage of the Chloroflexi take up these organic acids to store carbon as polyhydroxyalkanoates. The metabolic reconstruction is consistent with metabolite measurements and single cell microbial imaging with fluorescence in situ hybridization and NanoSIMS.« less

Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics [Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics and NanoSIMS.

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

Burow, Luke C.; Woebken, Dagmar; Marshall, Ian PG

Photosynthetic microbial mats possess extraordinary phylogenetic and functional diversity that makes linking specific pathways with individual microbial populations a daunting task. Close metabolic and spatial relationships between Cyanobacteria and Chloroflexi have previously been observed in diverse microbial mats. Here in this paper, we report that an expressed metabolic pathway for the anoxic catabolism of photosynthate involving Cyanobacteria and Chloroflexi in microbial mats can be reconstructed through metatranscriptomic sequencing of mats collected at Elkhorn Slough, Monterey Bay, CA, USA. In this reconstruction, Microcoleus spp., the most abundant cyanobacterial group in the mats, ferment photosynthate to organic acids, CO 2 and Hmore » 2 through multiple pathways, and an uncultivated lineage of the Chloroflexi take up these organic acids to store carbon as polyhydroxyalkanoates. The metabolic reconstruction is consistent with metabolite measurements and single cell microbial imaging with fluorescence in situ hybridization and NanoSIMS.« less

Evaluating three trace metal contaminated sites: a field and laboratory investigation.

PubMed

Murray, P; Ge, Y; Hendershot, W H

2000-01-01

Selecting guidelines to evaluate elevated metals in urban brownfields is hindered by the lack of information for these sites on ecosystem structure and function. A study was performed to compare three trace metal-contaminated sites in the metropolitan Montreal area. The goal was to obtain an idea of the organisms that may be present on urban brownfields and to measure if elevated metals alter the presence and activity of the indigenous biota. Field and laboratory studies were conducted using simple methodologies to determine the extent to which microbial activity affected by trace metal content, to assess diversity of plant and soil invertebrate communities and to measure phytoaccumulation of trace metals. It was found that microbial activity, as measured by substrate-induced respiration (SIR) and nitrification, was not affected by the levels of soil Cd, Cu, Ni, Pb and Zn recorded on the sites. Seven of the 12 invertebrate groups collected were sampled on soils with similar Cd, Cu, Ni, Pb and Zn concentrations. Diversity of plant species increased as a function of the length of time the sites had been inactive. Levels of metals in plant tissue were influenced by soil characteristics and not by total soil Cd, Cu, Ni, Pb and Zn.

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.

Microbial community variation and functions to excess sludge reduction in a novel gravel contact oxidation reactor.

PubMed

Lin, Shanshan; Jin, Y; Fu, L; Quan, C; Yang, Y S

2009-06-15

Excess biomass produced within the degradation processes of organic pollutants is creating environmental challenges. The gravel contact oxidation reactor (GCOR) filled with crushed stone globular aggregates as carriers, has been demonstrated capable of reducing the excess sludge effectively in some pilot and small-scale engineering studies. In order to evaluate the variation and structure of the microbial community and their functions to excess sludge reduction in GCOR, a conventional activated sludge reactor (ASR) was studied as a comparison. The 16S rDNA library of the universal bacteria was constructed, Shannon's diversity index (H) and Species evenness (E) were calculated with distance-based operational taxonomic unit and richness (DOTUR) for microbial diversity. Real-time quantity PCR and optical microscope were used for absolute bacterial DNA concentration and eukarya identification, respectively. Meanwhile, the suspended solid index in GCOR and ASR was detected for assessing the excess sludge production. The results indicated that the most abundant bacteria in GCOR were those related to the beta-Proteobacteria group, then gamma-Proteobacteria and to Cytophaga-Flexibacter-Bacteriode (CFB). In the ASR samples major bacteria were in the closest match with gamma-Proteobacteria, then beta-Proteobacteria and CFB. Shannon's index (H) was higher (3.41) for diversity of bacteria extracted from the carrier samples in GCOR than that (2.71) from the sludge sample in ASR. Species evenness (E) for the isolates from GCOR and ASR samples was 0.97 and 0.96, respectively. Comparison of the universal bacteria population in GCOR and ASR shows that the total bacterial DNA concentration on the GCOR carriers were 8.98 x 10(5) microg/ microl, twice that in ASR of 4.67 x 10(5) microg/ microl under normal operation of two reactors. But the MLSS in GCOR was only 4.5mg/L, 25 times less than that in ASR of 115.4 mg/L. The most representative eukarya were protozoa both in GCOR (15 no. per 20 ml) and in ASR (15 no. per 20 ml); the next abundant group was attachment plants 10 no. per 20 ml in GCOR and 4 no. per 20 ml in ASR, respectively. Rotifers and copepoda belonging to metazoan were only present in GCOR (8 no. per 20 ml for both rotifers and copepoda). The microbial diversity and population difference both in the GCOR carriers and ASR sludge indicated that the diverse microbes, a large amount of biomass forming longer microbial food chains attached on the carriers may be the main functions for the excess sludge reduction in GCOR.

Methane Seep Carbonates Host Distinct, Diverse, and Dynamic Microbial Assemblages

PubMed Central

Pasulka, Alexis L.; Marlow, Jeffrey J.; Grupe, Benjamin M.; Levin, Lisa A.

2015-01-01

ABSTRACT Marine methane seeps are globally distributed geologic features in which reduced fluids, including methane, are advected upward from the subsurface. As a result of alkalinity generation during sulfate-coupled methane oxidation, authigenic carbonates form slabs, nodules, and extensive pavements. These carbonates shape the landscape within methane seeps, persist long after methane flux is diminished, and in some cases are incorporated into the geologic record. In this study, microbial assemblages from 134 native and experimental samples across 5,500 km, representing a range of habitat substrates (carbonate nodules and slabs, sediment, bottom water, and wood) and seepage conditions (active and low activity), were analyzed to address two fundamental questions of seep microbial ecology: (i) whether carbonates host distinct microbial assemblages and (ii) how sensitive microbial assemblages are to habitat substrate type and temporal shifts in methane seepage flux. Through massively parallel 16S rRNA gene sequencing and statistical analysis, native carbonates are shown to be reservoirs of distinct and highly diverse seep microbial assemblages. Unique coupled transplantation and colonization experiments on the seafloor demonstrated that carbonate-associated microbial assemblages are resilient to seep quiescence and reactive to seep activation over 13 months. Various rates of response to simulated seep quiescence and activation are observed among similar phylogenies (e.g., Chloroflexi operational taxonomic units) and similar metabolisms (e.g., putative S oxidizers), demonstrating the wide range of microbial sensitivity to changes in seepage flux. These results imply that carbonates do not passively record a time-integrated history of seep microorganisms but rather host distinct, diverse, and dynamic microbial assemblages. PMID:26695630

A computationally simplistic poly-phasic approach to explore microbial communities from the Yucatan aquifer as a potential sources of novel natural products.

PubMed

Marfil-Santana, Miguel David; O'Connor-Sánchez, Aileen; Ramírez-Prado, Jorge Humberto; De Los Santos-Briones, Cesar; López-Aguiar; Lluvia, Korynthia; Rojas-Herrera, Rafael; Lago-Lestón, Asunción; Prieto-Davó, Alejandra

2016-11-01

The need for new antibiotics has sparked a search for the microbes that might potentially produce them. Current sequencing technologies allow us to explore the biotechnological potential of microbial communities in diverse environments without the need for cultivation, benefitting natural product discovery in diverse ways. A relatively recent method to search for the possible production of novel compounds includes studying the diverse genes belonging to polyketide synthase pathways (PKS), as these complex enzymes are an important source of novel therapeutics. In order to explore the biotechnological potential of the microbial community from the largest underground aquifer in the world located in the Yucatan, we used a polyphasic approach in which a simple, non-computationally intensive method was coupled with direct amplification of environmental DNA to assess the diversity and novelty of PKS type I ketosynthase (KS) domains. Our results suggest that the bioinformatic method proposed can indeed be used to assess the novelty of KS enzymes; nevertheless, this in silico study did not identify some of the KS diversity due to primer bias and stringency criteria outlined by the metagenomics pipeline. Therefore, additionally implementing a method involving the direct cloning of KS domains enhanced our results. Compared to other freshwater environments, the aquifer was characterized by considerably less diversity in relation to known ketosynthase domains; however, the metagenome included a family of KS type I domains phylogenetically related, but not identical, to those found in the curamycin pathway, as well as an outstanding number of thiolases. Over all, this first look into the microbial community found in this large Yucatan aquifer and other fresh water free living microbial communities highlights the potential of these previously overlooked environments as a source of novel natural products.

Maintenance of Distal Intestinal Structure in the Face of Prolonged Fasting: A Comparative Examination of Species From Five Vertebrate Classes.

PubMed

McCue, Marshall D; Passement, Celeste A; Meyerholz, David K

2017-12-01

It was recently shown that fasting alters the composition of microbial communities residing in the distal intestinal tract of animals representing five classes of vertebrates [i.e., fishes (tilapia), amphibians (toads), reptiles (leopard geckos), birds (quail), and mammals (mice)]. In this study, we tested the hypothesis that the extent of tissue reorganization in the fasted distal intestine was correlated with the observed changes in enteric microbial diversity. Segments of intestine adjacent to those used for the microbiota study were examined histologically to quantify cross-sectional and mucosal surface areas and thicknesses of mucosa, submucosa, and tunica muscularis. We found no fasting-induced differences in the morphology of distal intestines of the mice (3 days), quail (7 days), or geckos (28 days). The toads, which exhibited a general increase in phylogenetic diversity of their enteric microbiota with fasting, also exhibited reduced mucosal circumference at 14 and 21 days of fasting. Tilapia showed increased phylogenetic diversity of their enteric microbiota, and showed a thickened tunica muscularis at 21 days of fasting; but this morphological change was not related to microbial diversity or absorptive surface area, and thus, is unlikely to functionally match the changes in their microbiome. Given that fasting caused significant increases and reductions in the enteric microbial diversity of mice and quail, respectively, but no detectable changes in distal intestine morphology, we conclude that reorganization is not the primary factor shaping changes in microbial diversity within the fasted colon, and the observed modest structural changes are more related to the fasted state. Anat Rec, 300:2208-2219, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Insights into Diversity and Imputed Metabolic Potential of Bacterial Communities in the Continental Shelf of Agatti Island

PubMed Central

Dhar, Sunil Kumar; Jani, Kunal; Apte, Deepak A.; Shouche, Yogesh S.; Sharma, Avinash

2015-01-01

Marine microbes play a key role and contribute largely to the global biogeochemical cycles. This study aims to explore microbial diversity from one such ecological hotspot, the continental shelf of Agatti Island. Sediment samples from various depths of the continental shelf were analyzed for bacterial diversity using deep sequencing technology along with the culturable approach. Additionally, imputed metagenomic approach was carried out to understand the functional aspects of microbial community especially for microbial genes important in nutrient uptake, survival and biogeochemical cycling in the marine environment. Using culturable approach, 28 bacterial strains representing 9 genera were isolated from various depths of continental shelf. The microbial community structure throughout the samples was dominated by phylum Proteobacteria and harbored various bacterioplanktons as well. Significant differences were observed in bacterial diversity within a short region of the continental shelf (1–40 meters) i.e. between upper continental shelf samples (UCS) with lesser depths (i.e. 1–20 meters) and lower continental shelf samples (LCS) with greater depths (i.e. 25–40 meters). By using imputed metagenomic approach, this study also discusses several adaptive mechanisms which enable microbes to survive in nutritionally deprived conditions, and also help to understand the influence of nutrition availability on bacterial diversity. PMID:26066038

Insights into Diversity and Imputed Metabolic Potential of Bacterial Communities in the Continental Shelf of Agatti Island.

PubMed

Kumbhare, Shreyas V; Dhotre, Dhiraj P; Dhar, Sunil Kumar; Jani, Kunal; Apte, Deepak A; Shouche, Yogesh S; Sharma, Avinash

2015-01-01

Marine microbes play a key role and contribute largely to the global biogeochemical cycles. This study aims to explore microbial diversity from one such ecological hotspot, the continental shelf of Agatti Island. Sediment samples from various depths of the continental shelf were analyzed for bacterial diversity using deep sequencing technology along with the culturable approach. Additionally, imputed metagenomic approach was carried out to understand the functional aspects of microbial community especially for microbial genes important in nutrient uptake, survival and biogeochemical cycling in the marine environment. Using culturable approach, 28 bacterial strains representing 9 genera were isolated from various depths of continental shelf. The microbial community structure throughout the samples was dominated by phylum Proteobacteria and harbored various bacterioplanktons as well. Significant differences were observed in bacterial diversity within a short region of the continental shelf (1-40 meters) i.e. between upper continental shelf samples (UCS) with lesser depths (i.e. 1-20 meters) and lower continental shelf samples (LCS) with greater depths (i.e. 25-40 meters). By using imputed metagenomic approach, this study also discusses several adaptive mechanisms which enable microbes to survive in nutritionally deprived conditions, and also help to understand the influence of nutrition availability on bacterial diversity.

Microbial diversity in degraded and non-degraded petroleum samples and comparison across oil reservoirs at local and global scales.

PubMed

Sierra-Garcia, Isabel Natalia; Dellagnezze, Bruna M; Santos, Viviane P; Chaves B, Michel R; Capilla, Ramsés; Santos Neto, Eugenio V; Gray, Neil; Oliveira, Valeria M

2017-01-01

Microorganisms have shown their ability to colonize extreme environments including deep subsurface petroleum reservoirs. Physicochemical parameters may vary greatly among petroleum reservoirs worldwide and so do the microbial communities inhabiting these different environments. The present work aimed at the characterization of the microbiota in biodegraded and non-degraded petroleum samples from three Brazilian reservoirs and the comparison of microbial community diversity across oil reservoirs at local and global scales using 16S rRNA clone libraries. The analysis of 620 16S rRNA bacterial and archaeal sequences obtained from Brazilian oil samples revealed 42 bacterial OTUs and 21 archaeal OTUs. The bacterial community from the degraded oil was more diverse than the non-degraded samples. Non-degraded oil samples were overwhelmingly dominated by gammaproteobacterial sequences with a predominance of the genera Marinobacter and Marinobacterium. Comparisons of microbial diversity among oil reservoirs worldwide suggested an apparent correlation of prokaryotic communities with reservoir temperature and depth and no influence of geographic distance among reservoirs. The detailed analysis of the phylogenetic diversity across reservoirs allowed us to define a core microbiome encompassing three bacterial classes (Gammaproteobacteria, Clostridia, and Bacteroidia) and one archaeal class (Methanomicrobia) ubiquitous in petroleum reservoirs and presumably owning the abilities to sustain life in these environments.

Soil bacterial diversity in degraded and restored lands of Northeast Brazil.

PubMed

Araújo, Ademir Sérgio Ferreira; Borges, Clovis Daniel; Tsai, Siu Mui; Cesarz, Simone; Eisenhauer, Nico

2014-11-01

Land degradation deteriorates biological productivity and affects environmental, social, and economic sustainability, particularly so in the semi-arid region of Northeast Brazil. Although some studies exist reporting gross measures of soil microbial parameters and processes, limited information is available on how land degradation and restoration strategies influence the diversity and composition of soil microbial communities. In this study we compare the structure and diversity of bacterial communities in degraded and restored lands in Northeast Brazil and determine the soil biological and chemical properties influencing bacterial communities. We found that land degradation decreased the diversity of soil bacteria as indicated by both reduced operational taxonomic unit (OTU) richness and Shannon index. Soils under native vegetation and restoration had significantly higher bacterial richness and diversity than degraded soils. Redundancy analysis revealed that low soil bacterial diversity correlated with a high respiratory quotient, indicating stressed microbial communities. By contrast, soil bacterial communities in restored land positively correlated with high soil P levels. Importantly, however, we found significant differences in the soil bacterial community composition under native vegetation and in restored land, which may indicate differences in their functioning despite equal levels of bacterial diversity.

Microbial island biogeography: isolation shapes the life history characteristics but not diversity of root-symbiotic fungal communities.

PubMed

Davison, John; Moora, Mari; Öpik, Maarja; Ainsaar, Leho; Ducousso, Marc; Hiiesalu, Inga; Jairus, Teele; Johnson, Nancy; Jourand, Philippe; Kalamees, Rein; Koorem, Kadri; Meyer, Jean-Yves; Püssa, Kersti; Reier, Ülle; Pärtel, Meelis; Semchenko, Marina; Traveset, Anna; Vasar, Martti; Zobel, Martin

2018-06-08

Island biogeography theory is one of the most influential paradigms in ecology. That island characteristics, including remoteness, can profoundly modulate biological diversity has been borne out by studies of animals and plants. By contrast, the processes influencing microbial diversity in island systems remain largely undetermined. We sequenced arbuscular mycorrhizal (AM) fungal DNA from plant roots collected on 13 islands worldwide and compared AM fungal diversity on islands with existing data from mainland sites. AM fungal communities on islands (even those >6000 km from the closest mainland) comprised few endemic taxa and were as diverse as mainland communities. Thus, in contrast to patterns recorded among macro-organisms, efficient dispersal appears to outweigh the effects of taxogenesis and extinction in regulating AM fungal diversity on islands. Nonetheless, AM fungal communities on more distant islands comprised a higher proportion of previously cultured and large-spored taxa, indicating that dispersal may be human-mediated or require tolerance of significant environmental stress, such as exposure to sunlight or high salinity. The processes driving large-scale patterns of microbial diversity are a key consideration for attempts to conserve and restore functioning ecosystems in this era of rapid global change.

Alternative cytoskeletal landscapes: cytoskeletal novelty and evolution in basal excavate protists

PubMed Central

Dawson, Scott C.; Paredez, Alexander R.

2016-01-01

Microbial eukaryotes encompass the majority of eukaryotic evolutionary and cytoskeletal diversity. The cytoskeletal complexity observed in multicellular organisms appears to be an expansion of components present in genomes of diverse microbial eukaryotes such as the basal lineage of flagellates, the Excavata. Excavate protists have complex and diverse cytoskeletal architectures and life cycles – essentially alternative cytoskeletal “landscapes” – yet still possess conserved microtubule- and actin-associated proteins. Comparative genomic analyses have revealed that a subset of excavates, however, lack many canonical actin-binding proteins central to actin cytoskeleton function in other eukaryotes. Overall, excavates possess numerous uncharacterized and “hypothetical” genes, and may represent an undiscovered reservoir of novel cytoskeletal genes and cytoskeletal mechanisms. The continued development of molecular genetic tools in these complex microbial eukaryotes will undoubtedly contribute to our overall understanding of cytoskeletal diversity and evolution. PMID:23312067

Hydrothermal activity lowers trophic diversity in Antarctic hydrothermal sediments

NASA Astrophysics Data System (ADS)

Bell, James B.; Reid, William D. K.; Pearce, David A.; Glover, Adrian G.; Sweeting, Christopher J.; Newton, Jason; Woulds, Clare

2017-12-01

Hydrothermal sediments are those in which hydrothermal fluid is discharged through sediments and are one of the least studied deep-sea ecosystems. We present a combination of microbial and biochemical data to assess trophodynamics between and within hydrothermal and background areas of the Bransfield Strait (1050-1647 m of depth). Microbial composition, biomass, and fatty acid signatures varied widely between and within hydrothermally active and background sites, providing evidence of diverse metabolic activity. Several species had different feeding strategies and trophic positions between hydrothermally active and inactive areas, and the stable isotope values of consumers were not consistent with feeding morphology. Niche area and the diversity of microbial fatty acids was lowest at the most hydrothermally active site, reflecting trends in species diversity. Faunal uptake of chemosynthetically produced organics was relatively limited but was detected at both hydrothermal and non-hydrothermal sites, potentially suggesting that hydrothermal activity can affect trophodynamics over a much wider area than previously thought.

The Impact of Climate Change on Microbial Communities and Carbon Cycling in High Arctic Permafrost Soil from Spitsbergen, Northern Norway

NASA Astrophysics Data System (ADS)

de Leon, K. C.; Schwery, D.; Yoshikawa, K.; Christiansen, H. H.; Pearce, D.

2014-12-01

Permafrost-affected soils are among the most fragile ecosystems in which current microbial controls on organic matter decomposition are changing as a result of climate change. Warmer conditions in the high Arctic will lead to a deepening of the seasonal active layer of permafrost, provoking changes in microbial processes and possibly resulting in exacerbated carbon degradation under increasing anoxic conditions. The viable and non-viable fractions of the microbial community in a permafrost soil from Adventdalen, Spitsbergen, Norway were subjected to a comprehensive investigation using culture-dependent and culture-independent methods. Molecular analyses using FISH (with CTC-DAPI) and amplified rDNA restriction analysis (ARDRA) on a 257cm deep core, revealed the presence of all major microbial soil groups, with the active layer having more viable cells, and a higher microbial community diversity. Carbon dioxide (CO2) and methane (CH4) flux measurements were performed to show the amount of C stored in the sample. We demonstrated that the microbial community composition from the soil in the center of the core was most likely influenced by small scale variations in environmental conditions. Community structure showed distinct shift of presence of bacterial groups along the vertical temperature gradient profile and microbial counts and diversity was found to be highest in the surface layers, decreasing with depth. It was observed that soil properties driving microbial diversity and functional potential varied across the permafrost table. Data on the variability of CO2 and CH4 distribution described in peat structure heterogeneity are important for modeling emissions on a larger scale. Furthermore, linking microbial biomass to gas distribution may elucidate the cause of peak CO2 and CH4 and their changes in relation to environmental change and peat composition.

Functional Microbial Diversity Explains Groundwater Chemistry in a Pristine Aquifer

EPA Science Inventory

Microbial communities inhabiting anoxic aquifers catalyze critical biogeochemical reactions in the subsurface, yet little is known about how their community structure correlates with groundwater chemistry. In this study, we described the composition of microbial communities in th...

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.

Soil fertility and plant diversity enhance microbial performance in metal-polluted soils.

PubMed

Stefanowicz, Anna M; Kapusta, Paweł; Szarek-Łukaszewska, Grażyna; Grodzińska, Krystyna; Niklińska, Maria; Vogt, Rolf D

2012-11-15

This study examined the effects of soil physicochemical properties (including heavy metal pollution) and vegetation parameters on soil basal respiration, microbial biomass, and the activity and functional richness of culturable soil bacteria and fungi. In a zinc and lead mining area (S Poland), 49 sites were selected to represent all common plant communities and comprise the area's diverse soil types. Numerous variables describing habitat properties were reduced by PCA to 7 independent factors, mainly representing subsoil type (metal-rich mining waste vs. sand), soil fertility (exchangeable Ca, Mg and K, total C and N, organic C), plant species richness, phosphorus content, water-soluble heavy metals (Zn, Cd and Pb), clay content and plant functional diversity (based on graminoids, legumes and non-leguminous forbs). Multiple regression analysis including these factors explained much of the variation in most microbial parameters; in the case of microbial respiration and biomass, it was 86% and 71%, respectively. The activity of soil microbes was positively affected mainly by soil fertility and, apparently, by the presence of mining waste in the subsoil. The mining waste contained vast amounts of trace metals (total Zn, Cd and Pb), but it promoted microbial performance due to its inherently high content of macronutrients (total Ca, Mg, K and C). Plant species richness had a relatively strong positive effect on all microbial parameters, except for the fungal component. In contrast, plant functional diversity was practically negligible in its effect on microbes. Other explanatory variables had only a minor positive effect (clay content) or no significant influence (phosphorus content) on microbial communities. The main conclusion from this study is that high nutrient availability and plant species richness positively affected the soil microbes and that this apparently counteracted the toxic effects of metal contamination. Copyright © 2012 Elsevier B.V. All rights reserved.

Diffuse flow environments within basalt- and sediment-based hydrothermal vent ecosystems harbor specialized microbial communities.

PubMed

Campbell, Barbara J; Polson, Shawn W; Zeigler Allen, Lisa; Williamson, Shannon J; Lee, Charles K; Wommack, K Eric; Cary, S Craig

2013-01-01

Hydrothermal vents differ both in surface input and subsurface geochemistry. The effects of these differences on their microbial communities are not clear. Here, we investigated both alpha and beta diversity of diffuse flow-associated microbial communities emanating from vents at a basalt-based hydrothermal system along the East Pacific Rise (EPR) and a sediment-based hydrothermal system, Guaymas Basin. Both Bacteria and Archaea were targeted using high throughput 16S rRNA gene pyrosequencing analyses. A unique aspect of this study was the use of a universal set of 16S rRNA gene primers to characterize total and diffuse flow-specific microbial communities from varied deep-sea hydrothermal environments. Both surrounding seawater and diffuse flow water samples contained large numbers of Marine Group I (MGI) Thaumarchaea and Gammaproteobacteria taxa previously observed in deep-sea systems. However, these taxa were geographically distinct and segregated according to type of spreading center. Diffuse flow microbial community profiles were highly differentiated. In particular, EPR dominant diffuse flow taxa were most closely associated with chemolithoautotrophs, and off axis water was dominated by heterotrophic-related taxa, whereas the opposite was true for Guaymas Basin. The diversity and richness of diffuse flow-specific microbial communities were strongly correlated to the relative abundance of Epsilonproteobacteria, proximity to macrofauna, and hydrothermal system type. Archaeal diversity was higher than or equivalent to bacterial diversity in about one third of the samples. Most diffuse flow-specific communities were dominated by OTUs associated with Epsilonproteobacteria, but many of the Guaymas Basin diffuse flow samples were dominated by either OTUs within the Planctomycetes or hyperthermophilic Archaea. This study emphasizes the unique microbial communities associated with geochemically and geographically distinct hydrothermal diffuse flow environments.

Diffuse flow environments within basalt- and sediment-based hydrothermal vent ecosystems harbor specialized microbial communities

PubMed Central

Campbell, Barbara J.; Polson, Shawn W.; Zeigler Allen, Lisa; Williamson, Shannon J.; Lee, Charles K.; Wommack, K. Eric; Cary, S. Craig

2013-01-01

Hydrothermal vents differ both in surface input and subsurface geochemistry. The effects of these differences on their microbial communities are not clear. Here, we investigated both alpha and beta diversity of diffuse flow-associated microbial communities emanating from vents at a basalt-based hydrothermal system along the East Pacific Rise (EPR) and a sediment-based hydrothermal system, Guaymas Basin. Both Bacteria and Archaea were targeted using high throughput 16S rRNA gene pyrosequencing analyses. A unique aspect of this study was the use of a universal set of 16S rRNA gene primers to characterize total and diffuse flow-specific microbial communities from varied deep-sea hydrothermal environments. Both surrounding seawater and diffuse flow water samples contained large numbers of Marine Group I (MGI) Thaumarchaea and Gammaproteobacteria taxa previously observed in deep-sea systems. However, these taxa were geographically distinct and segregated according to type of spreading center. Diffuse flow microbial community profiles were highly differentiated. In particular, EPR dominant diffuse flow taxa were most closely associated with chemolithoautotrophs, and off axis water was dominated by heterotrophic-related taxa, whereas the opposite was true for Guaymas Basin. The diversity and richness of diffuse flow-specific microbial communities were strongly correlated to the relative abundance of Epsilonproteobacteria, proximity to macrofauna, and hydrothermal system type. Archaeal diversity was higher than or equivalent to bacterial diversity in about one third of the samples. Most diffuse flow-specific communities were dominated by OTUs associated with Epsilonproteobacteria, but many of the Guaymas Basin diffuse flow samples were dominated by either OTUs within the Planctomycetes or hyperthermophilic Archaea. This study emphasizes the unique microbial communities associated with geochemically and geographically distinct hydrothermal diffuse flow environments. PMID:23898323

Wastewater treatment plant effluent introduces recoverable shifts in microbial community composition in urban streams

NASA Astrophysics Data System (ADS)

Ledford, S. H.; Price, J. R.; Ryan, M. O.; Toran, L.; Sales, C. M.

2017-12-01

New technologies are allowing for intense scrutiny of the impact of land use on microbial communities in stream networks. We used a combination of analytical chemistry, real-time polymerase chain reaction (qPCR) and targeted amplicon sequencing for a preliminary study on the impact of wastewater treatment plant effluent discharge on urban streams. Samples were collected on two dates above and below treatment plants on the Wissahickon Creek, and its tributary, Sandy Run, in Montgomery County, PA, USA. As expected, effluent was observed to be a significant source of nutrients and human and non-specific fecal associated taxa. There was an observed increase in the alpha diversity at locations immediately below effluent outflows, which contributed many taxa involved in wastewater treatment processes and nutrient cycling to the stream's microbial community. Unexpectedly, modeling of microbial community shifts along the stream was not controlled by concentrations of measured nutrients. Furthermore, partial recovery, in the form of decreasing abundances of bacteria and nutrients associated with wastewater treatment plant processes, nutrient cycling bacteria, and taxa associated with fecal and sewage sources, was observed between effluent sources. Antecedent moisture conditions impacted overall microbial community diversity, with higher diversity occurring after rainfall. These findings hint at resilience in stream microbial communities to recover from wastewater treatment plant effluent and are vital to understanding the impacts of urbanization on microbial stream communities.

Soil and plant factors driving the community of soil-borne microorganisms across chronosequences of secondary succession of chalk grasslands with a neutral pH.

PubMed

Kuramae, Eiko; Gamper, Hannes; van Veen, Johannes; Kowalchuk, George

2011-08-01

Although soil pH has been shown to be an important factor driving microbial communities, relatively little is known about the other potentially important factors that shape soil-borne microbial community structure. This study examined plant and microbial communities across a series of neutral pH fields (pH=7.0-7.5) representing a chronosequence of secondary succession after former arable fields were taken out of production. These fields ranged from 17 to >66 years since the time of abandonment, and an adjacent arable field was included as a reference. Hierarchical clustering analysis, nonmetric multidimensional scaling and analysis of similarity of 52 different plant species showed that the plant community composition was significantly different in the different chronosequences, and that plant species richness and diversity increased with time since abandonment. The microbial community structure, as analyzed by phylogenetic microarrays (PhyloChips), was significantly different in arable field and the early succession stage, but no distinct microbial communities were observed for the intermediate and the late succession stages. The most determinant factors in shaping the soil-borne microbial communities were phosphorous and NH(4)(+). Plant community composition and diversity did not have a significant effect on the belowground microbial community structure or diversity. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

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

The performance and microbial diversity of temperature-phased hyperthermophilic and thermophilic anaerobic digestion system fed with organic waste.

PubMed

Lee, M Y; Cheon, J H; Hidaka, T; Tsuno, H

2008-01-01

The objective of this study was to evaluate the performances and microbial diversities for development of the effective hyperthermophilic digester system that consists of a hyperthermophilic reactor and hyperthermophilic or thermophilic reactor in series. Lab-scale reactors were operated continuously fed with artificial kitchen garbage. The effect of temperature on the acidification step was firstly investigated. Results indicated that 20.8% of COD solubilization was achieved at 70 degrees C, with 12.6% at 80 degrees C. The average protein solubilization reached 31% at 80 degrees C. Methane conversion efficiency following the acidification was around 85% on average at 55 degrees C, but decreased with increasing temperature and methane gas was not produced over 73 degrees C. As well, bacteria affiliated with the methanogens dominated the population below 65 degrees C, while those affiliated with acidogens were predominant over 73 degrees C. These results indicated that the hyperthermophilic process has considerable benefits to treat wastewater or waste containing high concentration of protein.

Marine Protists Are Not Just Big Bacteria.

PubMed

Keeling, Patrick J; Campo, Javier Del

2017-06-05

The study of marine microbial ecology has been completely transformed by molecular and genomic data: after centuries of relative neglect, genomics has revealed the surprising extent of microbial diversity and how microbial processes transform ocean and global ecosystems. But the revolution is not complete: major gaps in our understanding remain, and one obvious example is that microbial eukaryotes, or protists, are still largely neglected. Here we examine various ways in which protists might be better integrated into models of marine microbial ecology, what challenges this will present, and why understanding the limitations of our tools is a significant concern. In part this is a technical challenge - eukaryotic genomes are more difficult to characterize - but eukaryotic adaptations are also more dependent on morphology and behaviour than they are on the metabolic diversity that typifies bacteria, and these cannot be inferred from genomic data as readily as metabolism can be. We therefore cannot simply follow in the methodological footsteps of bacterial ecology and hope for similar success. Understanding microbial eukaryotes will require different approaches, including greater emphasis on taxonomically and trophically diverse model systems. Molecular sequencing will continue to play a role, and advances in environmental sequence tag studies and single-cell methods for genomic and transcriptomics offer particular promise. Copyright © 2017 Elsevier Ltd. All rights reserved.

Bacterial dynamics in steady-state biofilters: beyond functional stability.

PubMed

Cabrol, Léa; Malhautier, Luc; Poly, Franck; Lepeuple, Anne-Sophie; Fanlo, Jean-Louis

2012-01-01

The spatial and temporal dynamics of microbial community structure and function were surveyed in duplicated woodchip-biofilters operated under constant conditions for 231 days. The contaminated gaseous stream for treatment was representative of composting emissions, included ammonia, dimethyl disulfide and a mixture of five oxygenated volatile organic compounds. The community structure and diversity were investigated by denaturing gradient gel electrophoresis on 16S rRNA gene fragments. During the first 42 days, microbial acclimatization revealed the influence of operating conditions and contaminant loading on the biofiltration community structure and diversity, as well as the limited impact of inoculum compared to the greater persistence of the endogenous woodchip community. During long-term operation, a high and stable removal efficiency was maintained despite a highly dynamic microbial community, suggesting the probable functional redundancy of the community. Most of the contaminant removal occurred in the first compartment, near the gas inlet, where the microbial diversity was the highest. The stratification of the microbial structures along the filter bed was statistically correlated to the longitudinal distribution of environmental conditions (selective pressure imposed by contaminant concentrations) and function (contaminant elimination capacity), highlighting the central role of the bacterial community. The reproducibility of microbial succession in replicates suggests that the community changes were presumably driven by a deterministic process.

Greater temporal changes of sediment microbial community than its waterborne counterpart in Tengchong hot springs, Yunnan Province, China

PubMed Central

Wang, Shang; Dong, Hailiang; Hou, Weiguo; Jiang, Hongchen; Huang, Qiuyuan; Briggs, Brandon R.; Huang, Liuqin

2014-01-01

Temporal variation in geochemistry can cause changes in microbial community structure and diversity. Here we studied temporal changes of microbial communities in Tengchong hot springs of Yunnan Province, China in response to geochemical variations by using microbial and geochemical data collected in January, June and August of 2011. Greater temporal variations were observed in individual taxa than at the whole community structure level. Water and sediment communities exhibited different temporal variation patterns. Water communities were largely stable across three sampling times and dominated by similar microbial lineages: Hydrogenobaculum in moderate-temperature acidic springs, Sulfolobus in high-temperature acidic springs, and Hydrogenobacter in high-temperature circumneutral to alkaline springs. Sediment communities were more diverse and responsive to changing physicochemical conditions. Most of the sediment communities in January and June were similar to those in waters. However, the August sediment community was more diverse and contained more anaerobic heterotrophs than the January and June: Desulfurella and Acidicaldus in moderate-temperature acidic springs, Ignisphaera and Desulfurococcus in high-temperature acidic springs, the candidate division OP1 and Fervidobacterium in alkaline springs, and Thermus and GAL35 in neutral springs. Temporal variations in physicochemical parameters including temperature, pH, and dissolved organic carbon may have triggered the observed microbial community shifts. PMID:25524763

Microbial activity and community diversity in a variable charge soil as affected by cadmium exposure levels and time*

PubMed Central

Shentu, Jia-li; He, Zhen-li; Yang, Xiao-e; Li, Ting-qiang

2008-01-01

Effects of cadmium (Cd) on microbial biomass, activity and community diversity were assessed in a representative variable charge soil (Typic Aquult) using an incubation study. Cadmium was added as Cd(NO3)2 to reach a concentration range of 0~16 mg Cd/kg soil. Soil extractable Cd generally increased with Cd loading rate, but decreased with incubation time. Soil microbial biomass was enhanced at low Cd levels (0.5~1 mg/kg), but was inhibited consistently with increasing Cd rate. The ratio of microbial biomass C/N varied with Cd treatment levels, decreasing at low Cd rate (<0.7 mg/kg available Cd), but increasing progressively with Cd loading. Soil respiration was restrained at low Cd loading (<1 mg/kg), and enhanced at higher Cd levels. Soil microbial metabolic quotient (MMQ) was generally greater at high Cd loading (1~16 mg/kg). However, the MMQ is also affected by other factors. Cd contamination reduces species diversity of soil microbial communities and their ability to metabolize different C substrates. Soils with higher levels of Cd contamination showed decreases in indicator phospholipids fatty acids (PLFAs) for Gram-negative bacteria and actinomycetes, while the indicator PLFAs for Gram-positive bacteria and fungi increased with increasing levels of Cd contamination. PMID:18357628

Microbial diversity in biofilm infections of the urinary tract with the use of sonication techniques.

PubMed

Holá, Veronika; Ruzicka, Filip; Horka, Marie

2010-08-01

Infections of the urinary tract account for >40% of nosocomial infections; most of these are infections in catheterized patients. Bacterial colonization of the urinary tract and catheters causes not only the particular infection but also a number of complications, for example blockage of catheters with crystallic deposits of bacterial origin, generation of gravels and pyelonephritis. Infections of urinary catheters are only rarely single-species infections. The longer a patient is catheterized, the higher the diversity of biofilm microbial communities. The aims of this study were to investigate the microbial diversity on the catheters and to compare the ability to form biofilm among isolated microbial species. The next aim was to discriminate particular causative agents of infections of the urinary tract and their importance as biofilm formers in the microbial community on the urinary catheter. We examined catheters from 535 patients and isolated 1555 strains of microorganisms. Most of the catheters were infected by three or more microorganisms; only 12.5% showed monomicrobial infection. Among the microorganisms isolated from the urinary catheters, there were significant differences in biofilm-forming ability, and we therefore conclude that some microbial species have greater potential to cause a biofilm-based infection, whereas others can be only passive members of the biofilm community.

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...

Functional Gene Differences in Soil Microbial Communities from Conventional, Low-Input, and Organic Farmlands

PubMed Central

Xue, Kai; Wu, Liyou; Deng, Ye; He, Zhili; Van Nostrand, Joy; Robertson, Philip G.; Schmidt, Thomas M.

2013-01-01

Various agriculture management practices may have distinct influences on soil microbial communities and their ecological functions. In this study, we utilized GeoChip, a high-throughput microarray-based technique containing approximately 28,000 probes for genes involved in nitrogen (N)/carbon (C)/sulfur (S)/phosphorus (P) cycles and other processes, to evaluate the potential functions of soil microbial communities under conventional (CT), low-input (LI), and organic (ORG) management systems at an agricultural research site in Michigan. Compared to CT, a high diversity of functional genes was observed in LI. The functional gene diversity in ORG did not differ significantly from that of either CT or LI. Abundances of genes encoding enzymes involved in C/N/P/S cycles were generally lower in CT than in LI or ORG, with the exceptions of genes in pathways for lignin degradation, methane generation/oxidation, and assimilatory N reduction, which all remained unchanged. Canonical correlation analysis showed that selected soil (bulk density, pH, cation exchange capacity, total C, C/N ratio, NO3−, NH4+, available phosphorus content, and available potassium content) and crop (seed and whole biomass) variables could explain 69.5% of the variation of soil microbial community composition. Also, significant correlations were observed between NO3− concentration and denitrification genes, NH4+ concentration and ammonification genes, and N2O flux and denitrification genes, indicating a close linkage between soil N availability or process and associated functional genes. PMID:23241975

Actinobacterial Diversity in Volcanic Caves and Associated Geomicrobiological Interactions

PubMed Central

Riquelme, Cristina; Marshall Hathaway, Jennifer J.; Enes Dapkevicius, Maria de L. N.; Miller, Ana Z.; Kooser, Ara; Northup, Diana E.; Jurado, Valme; Fernandez, Octavio; Saiz-Jimenez, Cesareo; Cheeptham, Naowarat

2015-01-01

Volcanic caves are filled with colorful microbial mats on the walls and ceilings. These volcanic caves are found worldwide, and studies are finding vast bacteria diversity within these caves. One group of bacteria that can be abundant in volcanic caves, as well as other caves, is Actinobacteria. As Actinobacteria are valued for their ability to produce a variety of secondary metabolites, rare and novel Actinobacteria are being sought in underexplored environments. The abundance of novel Actinobacteria in volcanic caves makes this environment an excellent location to study these bacteria. Scanning electron microscopy (SEM) from several volcanic caves worldwide revealed diversity in the morphologies present. Spores, coccoid, and filamentous cells, many with hair-like or knobby extensions, were some of the microbial structures observed within the microbial mat samples. In addition, the SEM study pointed out that these features figure prominently in both constructive and destructive mineral processes. To further investigate this diversity, we conducted both Sanger sequencing and 454 pyrosequencing of the Actinobacteria in volcanic caves from four locations, two islands in the Azores, Portugal, and Hawai'i and New Mexico, USA. This comparison represents one of the largest sequencing efforts of Actinobacteria in volcanic caves to date. The diversity was shown to be dominated by Actinomycetales, but also included several newly described orders, such as Euzebyales, and Gaiellales. Sixty-two percent of the clones from the four locations shared less than 97% similarity to known sequences, and nearly 71% of the clones were singletons, supporting the commonly held belief that volcanic caves are an untapped resource for novel and rare Actinobacteria. The amplicon libraries depicted a wider view of the microbial diversity in Azorean volcanic caves revealing three additional orders, Rubrobacterales, Solirubrobacterales, and Coriobacteriales. Studies of microbial ecology in volcanic caves are still very limited. To rectify this deficiency, the results from our study help fill in the gaps in our knowledge of actinobacterial diversity and their potential roles in the volcanic cave ecosystems. PMID:26696966

Diversity and composition of vaginal microbiota of pregnant women at risk for transmitting Group B Streptococcus treated with intrapartum penicillin.

PubMed

Roesch, Luiz Fernando Wurdig; Silveira, Rita C; Corso, Andréa L; Dobbler, Priscila Thiago; Mai, Volker; Rojas, Bruna S; Laureano, Álvaro M; Procianoy, Renato S

2017-01-01

Administering intravenous antibiotics during labor to women at risk for transmitting Group B Streptococcus (GBS) can prevent infections in newborns. However, the impact of intrapartum antibiotic prophylaxis on mothers' microbial community composition is largely unknown. We compared vaginal microbial composition in pregnant women experiencing preterm birth at ≤ 32 weeks gestation that received intrapartum antibiotic prophylaxis with that in controls. Microbiota in vaginal swabs collected shortly before delivery from GBS positive women that received penicillin intravenously during labor or after premature rupture of membranes was compared to controls. Microbiota was analyzed by 16S rRNA sequencing using the PGM Ion Torrent to determine the effects of penicillin use during hospitalization and GBS status on its composition. Penicillin administration was associated with an altered vaginal microbial community composition characterized by increased microbial diversity. Lactobacillus sp. contributed only 13.1% of the total community in the women that received penicillin compared to 88.1% in the controls. Streptococcus sp. were present in higher abundance in GBS positive woman compared to controls, with 60% of the total vaginal microbiota in severe cases identified as Streptococcus sp. Vaginal communities of healthy pregnant women were dominated by Lactobacillus sp. and contained low diversity, while Group B Streptococcus positive women receiving intrapartum antibiotic prophylaxis had a modified vaginal microbiota composition with low abundance of Lactobacillus but higher microbial diversity.

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

[Changes in soil organic carbon and soil microbial functional diversity of Carya cathayensis plantations under intensive managements].

PubMed

Wu, Jia-Sen; Qian, Jin-Fang; Tong, Zhi-Peng; Huang, Jian-Qin; Zhao, Ke-Li

2014-09-01

The change characteristics of soil organic carbon and microbial function diversity in Chinese hickory Carya cathayensis stands with different intensive-management durations (5, 10, 15 and 20 years) were studied. The results showed that soil total organic carbon (TOC), microbial biomass carbon (MBC), water-soluble organic carbon (WSOC) decreased significantly, while the stability of soil C pool increased significantly after the conversion from evergreen and deciduous broadleaf forest to intensively-managed forest (IMF). TOC, MBC and WSOC in the hickory forest soil decreased by 28.4%, 34.1% and 53.3% with 5-year intensive management, and by 38.6%, 48.9% and 64.1% with 20-year intensive management, respectively. The proportions of carboxyl C, phenolic C and aromatic C in the hickory forest soil all increased significantly, and the aromaticity of soil organic C increased by 23.0%. Soil microbial functional diversity decreased greatly af- ter intensive management of Chinese hickory forest. Significant differences in average well color development (AWCD) were found between the 0- and 5-year treatments and the 10-, 15- and 20- year treatments. The microbial diversity indexes (H) and evenness indexes (E) in the 0- and 5-year treatments were much greater than in the 10- and 20-year treatments. Correlation analysis showed that there were significant correlations among soil TOC, WSOC, MBC, AWCD, H and E.

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

PubMed

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

2018-04-06

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

An Overview of Electron Acceptors in Microbial Fuel Cells

PubMed Central

Ucar, Deniz; Zhang, Yifeng; Angelidaki, Irini

2017-01-01

Microbial fuel cells (MFC) have recently received increasing attention due to their promising potential in sustainable wastewater treatment and contaminant removal. In general, contaminants can be removed either as an electron donor via microbial catalyzed oxidization at the anode or removed at the cathode as electron acceptors through reduction. Some contaminants can also function as electron mediators at the anode or cathode. While previous studies have done a thorough assessment of electron donors, cathodic electron acceptors and mediators have not been as well described. Oxygen is widely used as an electron acceptor due to its high oxidation potential and ready availability. Recent studies, however, have begun to assess the use of different electron acceptors because of the (1) diversity of redox potential, (2) needs of alternative and more efficient cathode reaction, and (3) expanding of MFC based technologies in different areas. The aim of this review was to evaluate the performance and applicability of various electron acceptors and mediators used in MFCs. This review also evaluated the corresponding performance, advantages and disadvantages, and future potential applications of select electron acceptors (e.g., nitrate, iron, copper, perchlorate) and mediators. PMID:28469607

Application of Ion Torrent Sequencing to the Assessment of the Effect of Alkali Ballast Water Treatment on Microbial Community Diversity

PubMed Central

Fujimoto, Masanori; Moyerbrailean, Gregory A.; Noman, Sifat; Gizicki, Jason P.; Ram, Michal L.; Green, Phyllis A.; Ram, Jeffrey L.

2014-01-01

The impact of NaOH as a ballast water treatment (BWT) on microbial community diversity was assessed using the 16S rRNA gene based Ion Torrent sequencing with its new 400 base chemistry. Ballast water samples from a Great Lakes ship were collected from the intake and discharge of both control and NaOH (pH 12) treated tanks and were analyzed in duplicates. One set of duplicates was treated with the membrane-impermeable DNA cross-linking reagent propidium mono-azide (PMA) prior to PCR amplification to differentiate between live and dead microorganisms. Ion Torrent sequencing generated nearly 580,000 reads for 31 bar-coded samples and revealed alterations of the microbial community structure in ballast water that had been treated with NaOH. Rarefaction analysis of the Ion Torrent sequencing data showed that BWT using NaOH significantly decreased microbial community diversity relative to control discharge (p<0.001). UniFrac distance based principal coordinate analysis (PCoA) plots and UPGMA tree analysis revealed that NaOH-treated ballast water microbial communities differed from both intake communities and control discharge communities. After NaOH treatment, bacteria from the genus Alishewanella became dominant in the NaOH-treated samples, accounting for <0.5% of the total reads in intake samples but more than 50% of the reads in the treated discharge samples. The only apparent difference in microbial community structure between PMA-processed and non-PMA samples occurred in intake water samples, which exhibited a significantly higher amount of PMA-sensitive cyanobacteria/chloroplast 16S rRNA than their corresponding non-PMA total DNA samples. The community assembly obtained using Ion Torrent sequencing was comparable to that obtained from a subset of samples that were also subjected to 454 pyrosequencing. This study showed the efficacy of alkali ballast water treatment in reducing ballast water microbial diversity and demonstrated the application of new Ion Torrent sequencing techniques to microbial community studies. PMID:25222021

Application of ion torrent sequencing to the assessment of the effect of alkali ballast water treatment on microbial community diversity.

PubMed

Fujimoto, Masanori; Moyerbrailean, Gregory A; Noman, Sifat; Gizicki, Jason P; Ram, Michal L; Green, Phyllis A; Ram, Jeffrey L

2014-01-01

The impact of NaOH as a ballast water treatment (BWT) on microbial community diversity was assessed using the 16S rRNA gene based Ion Torrent sequencing with its new 400 base chemistry. Ballast water samples from a Great Lakes ship were collected from the intake and discharge of both control and NaOH (pH 12) treated tanks and were analyzed in duplicates. One set of duplicates was treated with the membrane-impermeable DNA cross-linking reagent propidium mono-azide (PMA) prior to PCR amplification to differentiate between live and dead microorganisms. Ion Torrent sequencing generated nearly 580,000 reads for 31 bar-coded samples and revealed alterations of the microbial community structure in ballast water that had been treated with NaOH. Rarefaction analysis of the Ion Torrent sequencing data showed that BWT using NaOH significantly decreased microbial community diversity relative to control discharge (p<0.001). UniFrac distance based principal coordinate analysis (PCoA) plots and UPGMA tree analysis revealed that NaOH-treated ballast water microbial communities differed from both intake communities and control discharge communities. After NaOH treatment, bacteria from the genus Alishewanella became dominant in the NaOH-treated samples, accounting for <0.5% of the total reads in intake samples but more than 50% of the reads in the treated discharge samples. The only apparent difference in microbial community structure between PMA-processed and non-PMA samples occurred in intake water samples, which exhibited a significantly higher amount of PMA-sensitive cyanobacteria/chloroplast 16S rRNA than their corresponding non-PMA total DNA samples. The community assembly obtained using Ion Torrent sequencing was comparable to that obtained from a subset of samples that were also subjected to 454 pyrosequencing. This study showed the efficacy of alkali ballast water treatment in reducing ballast water microbial diversity and demonstrated the application of new Ion Torrent sequencing techniques to microbial community studies.

Characterization of Bacterial, Archaeal and Eukaryote Symbionts from Antarctic Sponges Reveals a High Diversity at a Three-Domain Level and a Particular Signature for This Ecosystem.

PubMed

Rodríguez-Marconi, Susana; De la Iglesia, Rodrigo; Díez, Beatriz; Fonseca, Cássio A; Hajdu, Eduardo; Trefault, Nicole

2015-01-01

Sponge-associated microbial communities include members from the three domains of life. In the case of bacteria, they are diverse, host specific and different from the surrounding seawater. However, little is known about the diversity and specificity of Eukarya and Archaea living in association with marine sponges. This knowledge gap is even greater regarding sponges from regions other than temperate and tropical environments. In Antarctica, marine sponges are abundant and important members of the benthos, structuring the Antarctic marine ecosystem. In this study, we used high throughput ribosomal gene sequencing to investigate the three-domain diversity and community composition from eight different Antarctic sponges. Taxonomic identification reveals that they belong to families Acarnidae, Chalinidae, Hymedesmiidae, Hymeniacidonidae, Leucettidae, Microcionidae, and Myxillidae. Our study indicates that there are different diversity and similarity patterns between bacterial/archaeal and eukaryote microbial symbionts from these Antarctic marine sponges, indicating inherent differences in how organisms from different domains establish symbiotic relationships. In general, when considering diversity indices and number of phyla detected, sponge-associated communities are more diverse than the planktonic communities. We conclude that three-domain microbial communities from Antarctic sponges are different from surrounding planktonic communities, expanding previous observations for Bacteria and including the Antarctic environment. Furthermore, we reveal differences in the composition of the sponge associated bacterial assemblages between Antarctic and tropical-temperate environments and the presence of a highly complex microbial eukaryote community, suggesting a particular signature for Antarctic sponges, different to that reported from other ecosystems.

Microbial diversity and composition of the sediment in the drinking water reservoir Saidenbach (Saxonia, Germany).

PubMed

Röske, Kerstin; Sachse, René; Scheerer, Carola; Röske, Isolde

2012-02-01

Sediments contain a huge number and diversity of microorganisms that are important for the flux of material and are pivotal to all major biogeochemical cycles. Sediments of reservoirs are affected by a wide spectrum of allochthous and autochthonous influences providing versatile environments along the flow of water within the reservoir. Here we report on the microbial diversity in sediments of the mesotrophic drinking water reservoir Saidenbach, Germany, featuring a pronounced longitudinal gradient in sediment composition in the reservoir system. Three sampling sites were selected along the gradient, and the microbial communities in two sediment depths were characterized using catalysed reporter deposition fluorescence in situ hybridization (CARD-FISH) and a bar-coded pyrosequencing approach. Multivariate statistic was used to reveal relationships between sequence diversity and the environmental conditions. The microbial communities were tremendously diverse with a Shannon index of diversity (H') ranging from 6.7 to 7.1. 18,986 sequences could be classified into 37 phyla including candidate divisions, but the full extent of genetic diversity was not captured. While CARD-FISH gave an overview about the community composition, more detailed information was gained by pyrosequencing. Bacteria were more abundant than Archaea. The dominating phylum in all samples was Proteobacteria, especially Betaproteobacteria and Deltaproteobacteria. Furthermore, sequences of Bacteroidetes, Verrucomicrobia, Acidobacteria, Chlorobi, Nitrospira, Spirochaetes, Gammaproteobacteria, Alphaproteobacteria, Chloroflexi, and Gemmatimonadetes were found. The site ammonium concentration, water content and organic matter content revealed to be strongest environmental predictors explaining the observed significant differences in the community composition between sampling sites. Copyright © 2011 Elsevier GmbH. All rights reserved.

The Bacterial and Fungal Diversity of an Aged PAH- and Heavy Metal-Contaminated Soil is Affected by Plant Cover and Edaphic Parameters.

PubMed

Bourceret, Amélia; Cébron, Aurélie; Tisserant, Emilie; Poupin, Pascal; Bauda, Pascale; Beguiristain, Thierry; Leyval, Corinne

2016-04-01

Industrial wasteland soils with aged PAH and heavy metal contaminations are environments where pollutant toxicity has been maintained for decades. Although the communities may be well adapted to the presence of stressors, knowledge about microbial diversity in such soils is scarce. Soil microbial community dynamics can be driven by the presence of plants, but the impact of plant development on selection or diversification of microorganisms in these soils has not been established yet. To test these hypotheses, aged-contaminated soil samples from a field trial were collected. Plots planted with alfalfa were compared to bare soil plots, and bacterial and fungal diversity and abundance were assessed after 2 and 6 years. Using pyrosequencing of 16S rRNA gene and ITS amplicons, we showed that the bacterial community was dominated by Proteobacteria, Actinobacteria, and Bacteroidetes and was characterized by low Acidobacteria abundance, while the fungal community was mainly represented by members of the Ascomycota. The short-term toxic impact of pollutants usually reduces the microbial diversity, yet in our samples bacterial and fungal species richness and diversity was high suggesting that the community structure and diversity adapted to the contaminated soil over decades. The presence of plants induced higher bacterial and fungal diversity than in bare soil. It also increased the relative abundance of bacterial members of the Actinomycetales, Rhizobiales, and Xanthomonadales orders and of most fungal orders. Multivariate analysis showed correlations between microbial community structure and heavy metal and PAH concentrations over time, but also with edaphic parameters (C/N, pH, phosphorus, and nitrogen concentrations).

Analyzing the relation between the microbial diversity of DaQu and the turbidity spoilage of traditional Chinese vinegar.

PubMed

Li, Pan; Li, Sha; Cheng, Lili; Luo, Lixin

2014-07-01

Vinegar is a traditional fermented condiment, and the microbial diversity of DaQu makes the quality of vinegar products. Recently, turbidity spoilage of vinegar sharply tampered with the quality of vinegar. In this study, the relation between the microbial diversity of DaQu and turbidity spoilage of vinegar was analyzed by plating technique, PCR-denaturing gradient gel electrophoresis (DGGE), and high-performance liquid chromatography (HPLC). The 16S rRNA sequencing and DGGE analysis indicated that Bacillus (Bacillus subtilis, Bacillus amyloliquefaciens, and Bacillus thuringiensis) and Lactobacillus (including Lactobacillus acidipiscis and Lactobacillus pobuzihii) species were the dominant contaminants in vinegar products. Meanwhile, DGGE analysis showed that the dominant bacteria in DaQu belonged to genera Bacillus, Lactobacillus, Pseudomonas, Weissella, Saccharopolyspora, Enterobacter, and Pantoea. However, only two yeast species (Pichia kudriavzevii and Saccharomycopsis fibuligera) and seven mold species including Aspergillus oryzae, Aspergillus niger, Aspergillus candidus, Rhizopus microspores, Eurotium herbariorum, Absidia corymbifera, and Eupenicillium javanicum were detected in the DaQu. The population level of fungi was below 5 log CFU/g in DaQu. The chemical and physical properties of vinegar and sediments were also determined. On the basis of a combined microbial diversity-chemical analysis, we demonstrated that turbidity spoilage of vinegar was a result of cooperation among the low population level and abundance of fungal species in DaQu, the suitable climate conditions, and the contaminants in vinegar. This is the first report to analyze the relation between the microbial diversity of DaQu and turbidity spoilage of vinegar.

Bacterial diversity in the rhizosphere of cucumbers grown in soils covering a wide range of cucumber cropping histories and environmental conditions.

PubMed

Tian, Yongqiang; Gao, Lihong

2014-11-01

Rhizosphere microorganisms in soils are important for plant growth. However, the importance of rhizosphere microorganisms is still underestimated since many microorganisms associated with plant roots cannot be cultured and since the microbial diversity in the rhizosphere can be influenced by several factors, such as the cropping history, biogeography, and agricultural practice. Here, we characterized the rhizosphere bacterial diversity of cucumber plants grown in soils covering a wide range of cucumber cropping histories and environmental conditions by using pyrosequencing of bacterial 16S rRNA genes. We also tested the effects of compost addition and/or bacterial inoculation on the bacterial diversity in the rhizosphere. We identified an average of approximately 8,883 reads per sample, corresponding to around 4,993 molecular operational taxonomic units per sample. The Proteobacteria was the most abundant phylum in almost all soils. The abundances of the phyla Bacteroidetes, Actinobacteria, Firmicutes, Acidobacteria, and Verrucomicrobia varied among the samples, and together with Proteobacteria, these phyla were the six most abundant phyla in almost all analyzed samples. Analyzing all the sample libraries together, the predominant genera found were Flavobacterium, Ohtaekwangia, Opitutus, Gp6, Steroidobacter, and Acidovorax. Overall, compost and microbial amendments increased shoot biomass when compared to untreated soils. However, compost addition decreased the bacterial α-diversity in most soils (but for three soils compost increased diversity), and no statistical effect of microbial amendment on the bacterial α-diversity was found. Moreover, soil amendments did not significantly influence the bacterial β-diversity. Soil organic content appeared more important than compost and microbial amendments in shaping the structure of bacterial communities in the rhizosphere of cucumber.

Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach

PubMed Central

Gontang, Erin A.; Aylward, Frank O.; Carlos, Camila; Glavina del Rio, Tijana; Chovatia, Mansi; Fern, Alison; Lo, Chien-Chi; Malfatti, Stephanie A.; Tringe, Susannah G.; Currie, Cameron R.; Kolter, Roberto

2017-01-01

Investigations of gut microbiomes have shed light on the diversity and genetic content of these communities, and helped shape our understanding of how host-associated microorganisms influence host physiology, behavior, and health. Despite the importance of gut microbes to metazoans, our understanding of the changes in diversity and composition across the alimentary tract, and the source of the resident community are limited. Here, using community metagenomics and 16S rRNA gene sequencing, we assess microbial community diversity and coding potential in the foregut, midgut, and hindgut of a juvenile Panchlora cockroach, which resides in the refuse piles of the leaf-cutter ant species Atta colombica. We found a significant shift in the microbial community structure and coding potential throughout the three gut sections of Panchlora sp., and through comparison with previously generated metagenomes of the cockroach’s food source and niche, we reveal that this shift in microbial community composition is influenced by the ecosystems in which Panchlora sp. occurs. While the foregut is composed of microbes that likely originate from the symbiotic fungus gardens of the ants, the midgut and hindgut are composed of a microbial community that is likely cockroach-specific. Analogous to mammalian systems, the midgut and hindgut appear to be dominated by Firmicutes and Bacteroidetes with the capacity for polysaccharide degradation, suggesting they may assist in the degradation of dietary plant material. Our work underscores the prominence of community changes throughout gut microbiomes and highlights ecological factors that underpin the structure and function of the symbiotic microbial communities of metazoans. PMID:28545131

Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach

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

Gontang, Erin A.; Aylward, Frank O.; Carlos, Camila

Investigations of gut microbiomes have shed light on the diversity and genetic content of these communities, and helped shape our understanding of how host-associated microorganisms influence host physiology, behavior, and health. Despite the importance of gut microbes to metazoans, our understanding of the changes in diversity and composition across the alimentary tract, and the source of the resident community are limited. Here, using community metagenomics and 16S rRNA gene sequencing, we assess microbial community diversity and coding potential in the foregut, midgut, and hindgut of a juvenile Panchlora cockroach, which resides in the refuse piles of the leaf-cutter ant speciesmore » Atta colombica. We found a significant shift in the microbial community structure and coding potential throughout the three gut sections of Panchlora sp., and through comparison with previously generated metagenomes of the cockroach's food source and niche, we reveal that this shift in microbial community composition is influenced by the ecosystems in which Panchlora sp. occurs. While the foregut is composed of microbes that likely originate from the symbiotic fungus gardens of the ants, the midgut and hindgut are composed of a microbial community that is likely cockroach-specific. Analogous to mammalian systems, the midgut and hindgut appear to be dominated by Firmicutes and Bacteroidetes with the capacity for polysaccharide degradation, suggesting they may assist in the degradation of dietary plant material. Our work underscores the prominence of community changes throughout gut microbiomes and highlights ecological factors that underpin the structure and function of the symbiotic microbial communities of metazoans.« less

Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach

DOE PAGES

Gontang, Erin A.; Aylward, Frank O.; Carlos, Camila; ...

2017-05-18

Investigations of gut microbiomes have shed light on the diversity and genetic content of these communities, and helped shape our understanding of how host-associated microorganisms influence host physiology, behavior, and health. Despite the importance of gut microbes to metazoans, our understanding of the changes in diversity and composition across the alimentary tract, and the source of the resident community are limited. Here, using community metagenomics and 16S rRNA gene sequencing, we assess microbial community diversity and coding potential in the foregut, midgut, and hindgut of a juvenile Panchlora cockroach, which resides in the refuse piles of the leaf-cutter ant speciesmore » Atta colombica. We found a significant shift in the microbial community structure and coding potential throughout the three gut sections of Panchlora sp., and through comparison with previously generated metagenomes of the cockroach's food source and niche, we reveal that this shift in microbial community composition is influenced by the ecosystems in which Panchlora sp. occurs. While the foregut is composed of microbes that likely originate from the symbiotic fungus gardens of the ants, the midgut and hindgut are composed of a microbial community that is likely cockroach-specific. Analogous to mammalian systems, the midgut and hindgut appear to be dominated by Firmicutes and Bacteroidetes with the capacity for polysaccharide degradation, suggesting they may assist in the degradation of dietary plant material. Our work underscores the prominence of community changes throughout gut microbiomes and highlights ecological factors that underpin the structure and function of the symbiotic microbial communities of metazoans.« less

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.

Increased microbial functional diversity under long-term organic and integrated fertilization in a paddy soil.

PubMed

Ding, Long-Jun; Su, Jian-Qiang; Sun, Guo-Xin; Wu, Jin-Shui; Wei, Wen-Xue

2018-02-01

Microbes play key roles in diverse biogeochemical processes including nutrient cycling. However, responses of soil microbial community and functional genes to long-term integrated fertilization (chemical combined with organic fertilization) remain unclear. Here, we used pyrosequencing and a microarray-based GeoChip to explore the shifts of microbial community and functional genes in a paddy soil which received over 21-year fertilization with various regimes, including control (no fertilizer), rice straw (R), rice straw plus chemical fertilizer nitrogen (NR), N and phosphorus (NPR), NP and potassium (NPKR), and reduced rice straw plus reduced NPK (L-NPKR). Significant shifts of the overall soil bacterial composition only occurred in the NPKR and L-NPKR treatments, with enrichment of certain groups including Bradyrhizobiaceae and Rhodospirillaceae families that benefit higher productivity. All fertilization treatments significantly altered the soil microbial functional structure with increased diversity and abundances of genes for carbon and nitrogen cycling, in which NPKR and L-NPKR exhibited the strongest effect, while R exhibited the least. Functional gene structure and abundance were significantly correlated with corresponding soil enzymatic activities and rice yield, respectively, suggesting that the structural shift of the microbial functional community under fertilization might promote soil nutrient turnover and thereby affect yield. Overall, this study indicates that the combined application of rice straw and balanced chemical fertilizers was more pronounced in shifting the bacterial composition and improving the functional diversity toward higher productivity, providing a microbial point of view on applying a cost-effective integrated fertilization regime with rice straw plus reduced chemical fertilizers for sustainable nutrient management.

Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach.

PubMed

Gontang, Erin A; Aylward, Frank O; Carlos, Camila; Glavina Del Rio, Tijana; Chovatia, Mansi; Fern, Alison; Lo, Chien-Chi; Malfatti, Stephanie A; Tringe, Susannah G; Currie, Cameron R; Kolter, Roberto

2017-01-01

Investigations of gut microbiomes have shed light on the diversity and genetic content of these communities, and helped shape our understanding of how host-associated microorganisms influence host physiology, behavior, and health. Despite the importance of gut microbes to metazoans, our understanding of the changes in diversity and composition across the alimentary tract, and the source of the resident community are limited. Here, using community metagenomics and 16S rRNA gene sequencing, we assess microbial community diversity and coding potential in the foregut, midgut, and hindgut of a juvenile Panchlora cockroach, which resides in the refuse piles of the leaf-cutter ant species Atta colombica. We found a significant shift in the microbial community structure and coding potential throughout the three gut sections of Panchlora sp., and through comparison with previously generated metagenomes of the cockroach's food source and niche, we reveal that this shift in microbial community composition is influenced by the ecosystems in which Panchlora sp. occurs. While the foregut is composed of microbes that likely originate from the symbiotic fungus gardens of the ants, the midgut and hindgut are composed of a microbial community that is likely cockroach-specific. Analogous to mammalian systems, the midgut and hindgut appear to be dominated by Firmicutes and Bacteroidetes with the capacity for polysaccharide degradation, suggesting they may assist in the degradation of dietary plant material. Our work underscores the prominence of community changes throughout gut microbiomes and highlights ecological factors that underpin the structure and function of the symbiotic microbial communities of metazoans.

Increasing ecological inference from high throughput sequencing of fungi in the environment through a tagging approach

Treesearch

D. Lee Taylor; Michael G. Booth; Jack W. McFarland; Ian C. Herriott; Niall J. Lennon; Chad Nusbaum; Thomas G. Marr

2008-01-01

High throughput sequencing methods are widely used in analyses of microbial diversity but are generally applied to small numbers of samples, which precludes charaterization of patterns of microbial diversity across space and time. We have designed a primer-tagging approach that allows pooling and subsequent sorting of numerous samples, which is directed to...

Bacterial Diversity in Microbial Mats and Sediments from the Atacama Desert.

PubMed

Rasuk, Maria Cecilia; Fernández, Ana Beatriz; Kurth, Daniel; Contreras, Manuel; Novoa, Fernando; Poiré, Daniel; Farías, María Eugenia

2016-01-01

The Atacama Desert has extreme environmental conditions that allow the development of unique microbial communities. The present paper reports the bacterial diversity of microbial mats and sediments and its mineralogical components. Some physicochemical conditions of the water surrounding these ecosystems have also been studied trying to determine their influence on the diversity of these communities. In that way, mats and sediments distributed among different hypersaline lakes located in salt flats of the Atacama Desert were subjected to massive parallel sequencing of the V4 region of the 16S rRNA genes of Bacteria. A higher diversity in sediment than in mat samples have been found. Lakes that harbor microbial mats have higher salinity than lakes where mats are absent. Proteobacteria and/or Bacteroidetes are the major phyla represented in all samples. An interesting item is the finding of a low proportion or absence of Cyanobacteria sequences in the ecosystems studied, suggesting the possibility that other groups may be playing an essential role as primary producers in these extreme environments. Additionally, the large proportion of 16S rRNA gene sequences that could not be classified at the level of phylum indicates potential new phyla present in these ecosystems.

[Influence of PCR cycle number on microbial diversity analysis through next generation sequencing].

PubMed

An, Yunhe; Gao, Lijuan; Li, Junbo; Tian, Yanjie; Wang, Jinlong; Zheng, Xuejuan; Wu, Huijuan

2016-08-25

Using of high throughput sequencing technology to study the microbial diversity in complex samples has become one of the hottest issues in the field of microbial diversity research. In this study, the soil and sheep rumen chyme samples were used to extract DNA, respectively. Then the 25 ng total DNA was used to amplify the 16S rRNA V3 region with 20, 25, 30 PCR cycles, and the final sequencing library was constructed by mixing equal amounts of purified PCR products. Finally, the operational taxonomic unit (OUT) amount, rarefaction curve, microbial number and species were compared through data analysis. It was found that at the same amount of DNA template, the proportion of the community composition was not the best with more numbers of PCR cycle, although the species number was much more. In all, when the PCR cycle number is 25, the number of species and proportion of the community composition were the most optimal both in soil or chyme samples.

Modeling microbial community structure and functional diversity across time and space.

PubMed

Larsen, Peter E; Gibbons, Sean M; Gilbert, Jack A

2012-07-01

Microbial communities exhibit exquisitely complex structure. Many aspects of this complexity, from the number of species to the total number of interactions, are currently very difficult to examine directly. However, extraordinary efforts are being made to make these systems accessible to scientific investigation. While recent advances in high-throughput sequencing technologies have improved accessibility to the taxonomic and functional diversity of complex communities, monitoring the dynamics of these systems over time and space - using appropriate experimental design - is still expensive. Fortunately, modeling can be used as a lens to focus low-resolution observations of community dynamics to enable mathematical abstractions of functional and taxonomic dynamics across space and time. Here, we review the approaches for modeling bacterial diversity at both the very large and the very small scales at which microbial systems interact with their environments. We show that modeling can help to connect biogeochemical processes to specific microbial metabolic pathways. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Phylogenetic conservatism of thermal traits explains dispersal limitation and genomic differentiation of Streptomyces sister-taxa.

PubMed

Choudoir, Mallory J; Buckley, Daniel H

2018-06-07

The latitudinal diversity gradient is a pattern of biogeography observed broadly in plants and animals but largely undocumented in terrestrial microbial systems. Although patterns of microbial biogeography across broad taxonomic scales have been described in a range of contexts, the mechanisms that generate biogeographic patterns between closely related taxa remain incompletely characterized. Adaptive processes are a major driver of microbial biogeography, but there is less understanding of how microbial biogeography and diversification are shaped by dispersal limitation and drift. We recently described a latitudinal diversity gradient of species richness and intraspecific genetic diversity in Streptomyces by using a geographically explicit culture collection. Within this geographically explicit culture collection, we have identified Streptomyces sister-taxa whose geographic distribution is delimited by latitude. These sister-taxa differ in geographic distribution, genomic diversity, and ecological traits despite having nearly identical SSU rRNA gene sequences. Comparative genomic analysis reveals genomic differentiation of these sister-taxa consistent with restricted gene flow across latitude. Furthermore, we show phylogenetic conservatism of thermal traits between the sister-taxa suggesting that thermal trait adaptation limits dispersal and gene flow across climate regimes as defined by latitude. Such phylogenetic conservatism of thermal traits is commonly associated with latitudinal diversity gradients for plants and animals. These data provide further support for the hypothesis that the Streptomyces latitudinal diversity gradient was formed as a result of historical demographic processes defined by dispersal limitation and driven by paleoclimate dynamics.

454 pyrosequencing analysis of bacterial diversity revealed by a comparative study of soils from mining subsidence and reclamation areas.

PubMed

Li, Yuanyuan; Chen, Longqian; Wen, Hongyu; Zhou, Tianjian; Zhang, Ting; Gao, Xiali

2014-03-28

Significant alteration in the microbial community can occur across reclamation areas suffering subsidence from mining. A reclamation site undergoing fertilization practices and an adjacent coal-excavated subsidence site (sites A and B, respectively) were examined to characterize the bacterial diversity using 454 high-throughput 16S rDNA sequencing. The dominant taxonomic groups in both the sites were Proteobacteria, Acidobacteria, Bacteroidetes, Betaproteobacteria, Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, Deltaproteobacteria, Chloroflexi, and Firmicutes. However, the bacterial communities' abundance, diversity, and composition differed significantly between the sites. Site A presented higher bacterial diversity and more complex community structures than site B. The majority of sequences related to Proteobacteria, Gemmatimonadetes, Chloroflexi, Nitrospirae, Firmicutes, Betaproteobacteria, Deltaproteobacteria, and Anaerolineae were from site A; whereas those related to Actinobacteria, Planctomycetes, Bacteroidetes, Verrucomicrobia, Gammaproteobacteria, Nitriliruptoria, Alphaproteobacteria, and Phycisphaerae originated from site B. The distribution of some bacterial groups and subgroups in the two sites correlated with soil properties and vegetation due to reclamation practice. Site A exhibited enriched bacterial community, soil organic matter (SOM), and total nitrogen (TN), suggesting the presence of relatively diverse microorganisms. SOM and TN were important factors shaping the underlying microbial communities. Furthermore, the specific plant functional group (legumes) was also an important factor influencing soil microbial community composition. Thus, the effectiveness of 454 pyrosequencing in analyzing soil bacterial diversity was validated and an association between land ecological system restoration, mostly mediated by microbial communities, and an improvement in soil properties in coalmining reclamation areas was suggested.

Taxonomic and Functional Differences between Microbial Communities in Qinghai Lake and Its Input Streams

PubMed Central

Ren, Ze; Wang, Fang; Qu, Xiaodong; Elser, James J.; Liu, Yang; Chu, Limin

2017-01-01

Understanding microbial communities in terms of taxon and function is essential to decipher the biogeochemical cycling in aquatic ecosystems. Lakes and their input streams are highly linked. However, the differences between microbial assemblages in streams and lakes are still unclear. In this study, we conducted an intensive field sampling of microbial communities from lake water and stream biofilms in the Qinghai Lake watershed, the largest lake in China. We determined bacterial communities using high-throughput 16S rRNA gene sequencing and predicted functional profiles using PICRUSt to determine the taxonomic and functional differences between microbial communities in stream biofilms and lake water. The results showed that stream biofilms and lake water harbored distinct microbial communities. The microbial communities were different taxonomically and functionally between stream and lake. Moreover, streams biofilms had a microbial network with higher connectivity and modularity than lake water. Functional beta diversity was strongly correlated with taxonomic beta diversity in both the stream and lake microbial communities. Lake microbial assemblages displayed greater predicted metabolic potentials of many metabolism pathways while the microbial assemblages in stream biofilms were more abundant in xenobiotic biodegradation and metabolism and lipid metabolism. Furthermore, lake microbial assemblages had stronger predicted metabolic potentials in amino acid metabolism, carbon fixation, and photosynthesis while stream microbial assemblages were higher in carbohydrate metabolism, oxidative phosphorylation, and nitrogen metabolism. This study adds to our knowledge of stream-lake linkages from the functional and taxonomic composition of microbial assemblages. PMID:29213266

Profiling soil microbial communities with next-generation sequencing: the influence of DNA kit selection and technician technical expertise.

PubMed

Soliman, Taha; Yang, Sung-Yin; Yamazaki, Tomoko; Jenke-Kodama, Holger

2017-01-01

Structure and diversity of microbial communities are an important research topic in biology, since microbes play essential roles in the ecology of various environments. Different DNA isolation protocols can lead to data bias and can affect results of next-generation sequencing. To evaluate the impact of protocols for DNA isolation from soil samples and also the influence of individual handling of samples, we compared results obtained by two researchers (R and T) using two different DNA extraction kits: (1) MO BIO PowerSoil ® DNA Isolation kit (MO_R and MO_T) and (2) NucleoSpin ® Soil kit (MN_R and MN_T). Samples were collected from six different sites on Okinawa Island, Japan. For all sites, differences in the results of microbial composition analyses (bacteria, archaea, fungi, and other eukaryotes), obtained by the two researchers using the two kits, were analyzed. For both researchers, the MN kit gave significantly higher yields of genomic DNA at all sites compared to the MO kit (ANOVA; P  < 0.006). In addition, operational taxonomic units for some phyla and classes were missed in some cases: Micrarchaea were detected only in the MN_T and MO_R analyses; the bacterial phylum Armatimonadetes was detected only in MO_R and MO_T; and WIM5 of the phylum Amoebozoa of eukaryotes was found only in the MO_T analysis. Our results suggest the possibility of handling bias; therefore, it is crucial that replicated DNA extraction be performed by at least two technicians for thorough microbial analyses and to obtain accurate estimates of microbial diversity.

Representing life in the Earth system with soil microbial functional traits in the MIMICS model

NASA Astrophysics Data System (ADS)

Wieder, W. R.; Grandy, A. S.; Kallenbach, C. M.; Taylor, P. G.; Bonan, G. B.

2015-06-01

Projecting biogeochemical responses to global environmental change requires multi-scaled perspectives that consider organismal diversity, ecosystem processes, and global fluxes. However, microbes, the drivers of soil organic matter decomposition and stabilization, remain notably absent from models used to project carbon (C) cycle-climate feedbacks. We used a microbial trait-based soil C model with two physiologically distinct microbial communities, and evaluate how this model represents soil C storage and response to perturbations. Drawing from the application of functional traits used to model other ecosystems, we incorporate copiotrophic and oligotrophic microbial functional groups in the MIcrobial-MIneral Carbon Stabilization (MIMICS) model; these functional groups are akin to "gleaner" vs. "opportunist" plankton in the ocean, or r- vs. K-strategists in plant and animal communities. Here we compare MIMICS to a conventional soil C model, DAYCENT (the daily time-step version of the CENTURY model), in cross-site comparisons of nitrogen (N) enrichment effects on soil C dynamics. MIMICS more accurately simulates C responses to N enrichment; moreover, it raises important hypotheses involving the roles of substrate availability, community-level enzyme induction, and microbial physiological responses in explaining various soil biogeochemical responses to N enrichment. In global-scale analyses, we show that MIMICS projects much slower rates of soil C accumulation than a conventional soil biogeochemistry in response to increasing C inputs with elevated carbon dioxide (CO2) - a finding that would reduce the size of the land C sink estimated by the Earth system. Our findings illustrate that tradeoffs between theory and utility can be overcome to develop soil biogeochemistry models that evaluate and advance our theoretical understanding of microbial dynamics and soil biogeochemical responses to environmental change.

Plant Community and Nitrogen Deposition as Drivers of Alpha and Beta Diversities of Prokaryotes in Reconstructed Oil Sand Soils and Natural Boreal Forest Soils

PubMed Central

Prescott, Cindy E.; Renaut, Sébastien; Terrat, Yves; Grayston, Sue J.

2017-01-01

ABSTRACT The Athabasca oil sand deposit is one of the largest single oil deposits in the world. Following surface mining, companies are required to restore soil-like profiles that can support the previous land capabilities. The objective of this study was to assess whether the soil prokaryotic alpha diversity (α-diversity) and β-diversity in oil sand soils reconstructed 20 to 30 years previously and planted to one of three vegetation types (coniferous or deciduous trees and grassland) were similar to those found in natural boreal forest soils subject to wildfire disturbance. Prokaryotic α-diversity and β-diversity were assessed using massively parallel sequencing of 16S rRNA genes. The β-diversity, but not the α-diversity, differed between reconstructed and natural soils. Bacteria associated with an oligotrophic lifestyle were more abundant in natural forest soils, whereas bacteria associated with a copiotrophic lifestyle were more abundant in reconstructed soils. Ammonia-oxidizing archaea were most abundant in reconstructed soils planted with grasses. Plant species were the main factor influencing α-diversity in natural and in reconstructed soils. Nitrogen deposition, pH, and plant species were the main factors influencing the β-diversity of the prokaryotic communities in natural and reconstructed soils. The results highlight the importance of nitrogen deposition and aboveground-belowground relationships in shaping soil microbial communities in natural and reconstructed soils. IMPORTANCE Covering over 800 km2, land disturbed by the exploitation of the oil sands in Canada has to be restored. Here, we take advantage of the proximity between these reconstructed ecosystems and the boreal forest surrounding the oil sand mining area to study soil microbial community structure and processes in both natural and nonnatural environments. By identifying key characteristics shaping the structure of soil microbial communities, this study improved our understanding of how vegetation, soil characteristics and microbial communities interact and drive soil functions. PMID:28213542

Plant Community and Nitrogen Deposition as Drivers of Alpha and Beta Diversities of Prokaryotes in Reconstructed Oil Sand Soils and Natural Boreal Forest Soils.

PubMed

Masse, Jacynthe; Prescott, Cindy E; Renaut, Sébastien; Terrat, Yves; Grayston, Sue J

2017-05-01

The Athabasca oil sand deposit is one of the largest single oil deposits in the world. Following surface mining, companies are required to restore soil-like profiles that can support the previous land capabilities. The objective of this study was to assess whether the soil prokaryotic alpha diversity (α-diversity) and β-diversity in oil sand soils reconstructed 20 to 30 years previously and planted to one of three vegetation types (coniferous or deciduous trees and grassland) were similar to those found in natural boreal forest soils subject to wildfire disturbance. Prokaryotic α-diversity and β-diversity were assessed using massively parallel sequencing of 16S rRNA genes. The β-diversity, but not the α-diversity, differed between reconstructed and natural soils. Bacteria associated with an oligotrophic lifestyle were more abundant in natural forest soils, whereas bacteria associated with a copiotrophic lifestyle were more abundant in reconstructed soils. Ammonia-oxidizing archaea were most abundant in reconstructed soils planted with grasses. Plant species were the main factor influencing α-diversity in natural and in reconstructed soils. Nitrogen deposition, pH, and plant species were the main factors influencing the β-diversity of the prokaryotic communities in natural and reconstructed soils. The results highlight the importance of nitrogen deposition and aboveground-belowground relationships in shaping soil microbial communities in natural and reconstructed soils. IMPORTANCE Covering over 800 km 2 , land disturbed by the exploitation of the oil sands in Canada has to be restored. Here, we take advantage of the proximity between these reconstructed ecosystems and the boreal forest surrounding the oil sand mining area to study soil microbial community structure and processes in both natural and nonnatural environments. By identifying key characteristics shaping the structure of soil microbial communities, this study improved our understanding of how vegetation, soil characteristics and microbial communities interact and drive soil functions. Copyright © 2017 American Society for Microbiology.

Correlation between vegetation and underground microbial communities on a micro-landscape of the Tibetan Plateau

NASA Astrophysics Data System (ADS)

Zhang, G.; Hu, A.; Wang, J.

2016-12-01

Aboveground vegetation and underground microbes are tightly associated and form a systematic entity to maintain terrestrial ecosystem functions; however, the roles and relative importance of vegetation to corresponding underlying microbial community remain clearly unresolved. Here we studied the vegetation and corresponding underground microbial communities along an elevation range of 704-3,760 m a.s.l on the Tibetan Plateau, which covering from a tropical forest to frigid shrub meadow ecosystem. By substituting space for time, we explored how the alteration of vegetation and abiotic environments jointly affect the underlying microbial communities. We found that vegetation showed a hump-shaped elevational pattern in diversity, while microbial community exhibited a two-section elevational pattern at a tipping point of 2400m elevation where vegetation diversity approximately peaks. The statistical analyses and regression modelling of the measures of underground microbial community including biomass, diversity, phylogenetic structure and community composition provided evidences of this threshold. Our findings highlighted that vegetation is a good predictor of underground microbial communities. Further statistical analyses suggested that alteration of vegetation and environmental filtering processes might be the vital driving forces jointly structuring underground microbial communities along an elevational gradient. Specifically, vegetation is a major contributor to underground microbes primarily through soil pH below the threshold (that is, in tropical and subtropical zones), while vegetation could directly influence underground microbes and also partly through its effects on several abiotic factors such as soil pH and WSOC above the threshold (that is, in temperate and frigid zones). These insights into the alteration of vegetation types and corresponding underground microbial communities provide new perspective on the aboveground and belowground interactions in forest ecosystems.

The Microbiome Structure of Oklahoma Cropland and Prairie Soils and its Response to Seasonal Forcing and Management Practices

NASA Astrophysics Data System (ADS)

Cornell, C. R.; Peterson, B.; Zhou, J.; Xiao, X.; Wawrik, B.

2017-12-01

Greenhouse gases (GHG) emissions from soils are primarily the consequence of microbial processes. Agricultural management of soils is known to affect the structure of microbial communities, and it is likely that dominant GHG emitting microbial activities are impacted via requisite practices. To gain better insight into the impact of seasonal forcing and management practices on the microbiome structure in Oklahoma agricultural soils, a seasonal study was conducted. Over a year period, samples were collected bi-weekly during wet months, and monthly during dry months from two grassland and two managed agricultural sites in El Reno, Oklahoma. Microbial community structure was determined in quadruplicate for each site and time point via 16S rRNA gene sequencing. Measures of soil water content, subsoil nitrate, ammonium, organic matter, total nitrogen, and biomass were also taken for each time point. Data analysis revealed several important trends, indicating greater microbial diversity in native grassland and distinct microbial community changes in response to management practices. The native grassland soils also contained greater microbial biomass than managed soils and both varied in response to rainfall events. Native grassland soils harbor more diverse microbial communities, with the diversity and biomass decreasing along a gradient of agricultural management intensity. These data indicate that microbial community structure in El Reno soils occurs along a continuum in which native grasslands and highly managed agricultural soils (tilling and manure application) form end members. Integration with measurements from eddy flux towers into modelling efforts using the DeNitrification-DeComposition (DNDC) model is currently being explored to improve predictions of GHG emissions from grassland soils.

Decoding the Principles of Emergence and Resiliency in Biological Collective Systems - A Multi-Scale Approach: Final Report

DTIC Science & Technology

2018-02-15

models and approaches are also valid using other invasive and non - invasive technologies. Finally, we illustrate and experimentally evaluate this...2017 Project Outline q  Pattern formation diversity in wild microbial societies q  Experimental and mathematical analysis methodology q  Skeleton...chemotaxis, nutrient degradation, and the exchange of amino acids between cells. Using both quantitative experimental methods and several theoretical

Phylogenetic and Functional Diversity of Total (DNA) and Expressed (RNA) Bacterial Communities in Urban Green Infrastructure Bioswale Soils.

PubMed

Gill, Aman S; Lee, Angela; McGuire, Krista L

2017-08-15

New York City (NYC) is pioneering green infrastructure with the use of bioswales and other engineered soil-based habitats to provide stormwater infiltration and other ecosystem functions. In addition to avoiding the environmental and financial costs of expanding traditional built infrastructure, green infrastructure is thought to generate cobenefits in the form of diverse ecological processes performed by its plant and microbial communities. Yet, although plant communities in these habitats are closely managed, we lack basic knowledge about how engineered ecosystems impact the distribution and functioning of soil bacteria. We sequenced amplicons of the 16S ribosomal subunit, as well as seven genes associated with functional pathways, generated from both total (DNA-based) and expressed (RNA) soil communities in the Bronx, NYC, NY, in order to test whether bioswale soils host characteristic bacterial communities with evidence for enriched microbial functioning, compared to nonengineered soils in park lawns and tree pits. Bioswales had distinct, phylogenetically diverse bacterial communities, including taxa associated with nutrient cycling and metabolism of hydrocarbons and other pollutants. Bioswale soils also had a significantly greater diversity of genes involved in several functional pathways, including carbon fixation ( cbbL-R [ cbbL gene, red-like subunit] and apsA ), nitrogen cycling ( noxZ and amoA ), and contaminant degradation ( bphA ); conversely, no functional genes were significantly more abundant in nonengineered soils. These results provide preliminary evidence that urban land management can shape the diversity and activity of soil communities, with positive consequences for genetic resources underlying valuable ecological functions, including biogeochemical cycling and degradation of common urban pollutants. IMPORTANCE Management of urban soil biodiversity by favoring taxa associated with decontamination or other microbial metabolic processes is a powerful prospect, but it first requires an understanding of how engineered soil habitats shape patterns of microbial diversity. This research adds to our understanding of urban microbial biogeography by providing data on soil bacteria in bioswales, which had relatively diverse and compositionally distinct communities compared to park and tree pit soils. Bioswales also contained comparatively diverse pools of genes related to carbon sequestration, nitrogen cycling, and contaminant degradation, suggesting that engineered soils may serve as effective reservoirs of functional microbial biodiversity. We also examined both total (DNA-based) and expressed (RNA) communities, revealing that total bacterial communities (the exclusive targets in the vast majority of soil studies) were poor predictors of expressed community diversity, pointing to the value of quantifying RNA, especially when ecological functioning is considered. Copyright © 2017 American Society for Microbiology.

Phylogenetic and Functional Diversity of Total (DNA) and Expressed (RNA) Bacterial Communities in Urban Green Infrastructure Bioswale Soils

PubMed Central

Lee, Angela; McGuire, Krista L.

2017-01-01

ABSTRACT New York City (NYC) is pioneering green infrastructure with the use of bioswales and other engineered soil-based habitats to provide stormwater infiltration and other ecosystem functions. In addition to avoiding the environmental and financial costs of expanding traditional built infrastructure, green infrastructure is thought to generate cobenefits in the form of diverse ecological processes performed by its plant and microbial communities. Yet, although plant communities in these habitats are closely managed, we lack basic knowledge about how engineered ecosystems impact the distribution and functioning of soil bacteria. We sequenced amplicons of the 16S ribosomal subunit, as well as seven genes associated with functional pathways, generated from both total (DNA-based) and expressed (RNA) soil communities in the Bronx, NYC, NY, in order to test whether bioswale soils host characteristic bacterial communities with evidence for enriched microbial functioning, compared to nonengineered soils in park lawns and tree pits. Bioswales had distinct, phylogenetically diverse bacterial communities, including taxa associated with nutrient cycling and metabolism of hydrocarbons and other pollutants. Bioswale soils also had a significantly greater diversity of genes involved in several functional pathways, including carbon fixation (cbbL-R [cbbL gene, red-like subunit] and apsA), nitrogen cycling (noxZ and amoA), and contaminant degradation (bphA); conversely, no functional genes were significantly more abundant in nonengineered soils. These results provide preliminary evidence that urban land management can shape the diversity and activity of soil communities, with positive consequences for genetic resources underlying valuable ecological functions, including biogeochemical cycling and degradation of common urban pollutants. IMPORTANCE Management of urban soil biodiversity by favoring taxa associated with decontamination or other microbial metabolic processes is a powerful prospect, but it first requires an understanding of how engineered soil habitats shape patterns of microbial diversity. This research adds to our understanding of urban microbial biogeography by providing data on soil bacteria in bioswales, which had relatively diverse and compositionally distinct communities compared to park and tree pit soils. Bioswales also contained comparatively diverse pools of genes related to carbon sequestration, nitrogen cycling, and contaminant degradation, suggesting that engineered soils may serve as effective reservoirs of functional microbial biodiversity. We also examined both total (DNA-based) and expressed (RNA) communities, revealing that total bacterial communities (the exclusive targets in the vast majority of soil studies) were poor predictors of expressed community diversity, pointing to the value of quantifying RNA, especially when ecological functioning is considered. PMID:28576763

Molecular analysis of microbial diversity in corrosion samples from energy transmission towers.

PubMed

Oliveira, Valéria M; Lopes-Oliveira, Patrícia F; Passarini, Michel R Z; Menezes, Claudia B A; Oliveira, Walter R C; Rocha, Adriano J; Sette, Lara D

2011-04-01

Microbial diversity in corrosion samples from energy transmission towers was investigated using molecular methods. Ribosomal DNA fragments were used to assemble gene libraries. Sequence analysis indicated 10 bacterial genera within the phyla Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. In the two libraries generated from corroded screw-derived samples, the genus Acinetobacter was the most abundant. Acinetobacter and Clostridium spp. dominated, with similar percentages, in the libraries derived from corrosion scrapings. Fungal clones were affiliated with 14 genera belonging to the phyla Ascomycota and Basidiomycota; of these, Capnobotryella and Fellomyces were the most abundant fungi observed. Several of the microorganisms had not previously been associated with biofilms and corrosion, reinforcing the need to use molecular techniques to achieve a more comprehensive assessment of microbial diversity in environmental samples.

Molecular analysis of meso- and thermophilic microbiota associated with anaerobic biowaste degradation

PubMed Central

2012-01-01

Background Microbial anaerobic digestion (AD) is used as a waste treatment process to degrade complex organic compounds into methane. The archaeal and bacterial taxa involved in AD are well known, whereas composition of the fungal community in the process has been less studied. The present study aimed to reveal the composition of archaeal, bacterial and fungal communities in response to increasing organic loading in mesophilic and thermophilic AD processes by applying 454 amplicon sequencing technology. Furthermore, a DNA microarray method was evaluated in order to develop a tool for monitoring the microbiological status of AD. Results The 454 sequencing showed that the diversity and number of bacterial taxa decreased with increasing organic load, while archaeal i.e. methanogenic taxa remained more constant. The number and diversity of fungal taxa increased during the process and varied less in composition with process temperature than bacterial and archaeal taxa, even though the fungal diversity increased with temperature as well. Evaluation of the microarray using AD sample DNA showed correlation of signal intensities with sequence read numbers of corresponding target groups. The sensitivity of the test was found to be about 1%. Conclusions The fungal community survives in anoxic conditions and grows with increasing organic loading, suggesting that Fungi may contribute to the digestion by metabolising organic nutrients for bacterial and methanogenic groups. The microarray proof of principle tests suggest that the method has the potential for semiquantitative detection of target microbial groups given that comprehensive sequence data is available for probe design. PMID:22727142

Improved Flotation Technique for Microscopy of In Situ Soil and Sediment Microorganisms

PubMed Central

Bone, T. L.; Balkwill, D. L.

1986-01-01

An improved flotation method for microscopy of in situ soil and sediment microorganisms was developed. Microbial cells were released into gellike flotation films that were stripped from soil and sediment aggregates as these aggregates were submerged in 0.5% solutions of polyvinylpyrrolidone. The use of polyvinylpyrrolidone solutions instead of water facilitated the release of films from saturated samples such as aquifer sediments as well as from typical surface soils. In situ microbial morphological characteristics could then be surveyed rapidly by light microscopy of films stained with acridine orange. This method effectively determined the ranges of morphological diversity in a variety of sample types. It also detected microcolonies and other spatial relationships among microbial cells. Only a small fraction (3.4 to 10.1%) of the microflora was released into the flotation films, but plating and direct evaluations by microscopy showed that this fraction was representative of the total population. Images PMID:16347005

Printing-assisted surface modifications of patterned ultrafiltration membranes

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

Wardrip, Nathaniel C.; Dsouza, Melissa; Urgun-Demirtas, Meltem

Understanding and restricting microbial surface attachment will enhance wastewater treatment with membranes. We report a maskless lithographic patterning technique for the generation of patterned polymer coatings on ultrafiltration membranes. Polyethylene glycol, zwitterionic, or negatively charged hydrophilic polymer compositions in parallel- or perpendicular-striped patterns with respect to feed flow were evaluated using wastewater. Membrane fouling was dependent on the orientation and chemical composition of the coatings. Modifications reduced alpha diversity in the attached microbial community (Shannon indices decreased from 2.63 to 1.89) which nevertheless increased with filtration time. Sphingomonas species, which condition membrane surfaces and facilitate cellular adhesion, were depleted inmore » all modified membranes. Microbial community structure was significantly different between control, different patterns, and different chemistries. Lastly, this study broadens the tools for surface modification of membranes with polymer coatings and for understanding and optimization of antifouling surfaces.« less

Heavy Metal Phytoremediation: Microbial Indicators of Soil Health for the Assessment of Remediation Efficiency

NASA Astrophysics Data System (ADS)

Epelde, Lur; Ma Becerril, José; Alkorta, Itziar; Garbisu, Carlos

Phytoremediation is an effective, non-intrusive, inexpensive, aesthetically pleasing, socially accepted, promising phytotechnology for the remediation of polluted soils. The objective of any soil remediation process must be not only to remove the contaminant(s) from the soil but, most importantly, to restore the continued capacity of the soil to perform or function according to its potential (i.e., to recover soil health). Hence, indicators of soil health are needed to properly assess the efficiency of a phytoremediation process. Biological indicators of soil health, especially those related to the size, activity and diversity of the soil microbial communities, are becoming increasingly used, due to their sensitivity and capacity to provide information that integrates many environmental factors. In particular, microbial indicators of soil health are valid tools to evaluate the success of metal phytoremediation procedures such as phytoextraction and phytostabilization processes.

Printing-assisted surface modifications of patterned ultrafiltration membranes

DOE PAGES

Wardrip, Nathaniel C.; Dsouza, Melissa; Urgun-Demirtas, Meltem; ...

2016-10-17

Understanding and restricting microbial surface attachment will enhance wastewater treatment with membranes. We report a maskless lithographic patterning technique for the generation of patterned polymer coatings on ultrafiltration membranes. Polyethylene glycol, zwitterionic, or negatively charged hydrophilic polymer compositions in parallel- or perpendicular-striped patterns with respect to feed flow were evaluated using wastewater. Membrane fouling was dependent on the orientation and chemical composition of the coatings. Modifications reduced alpha diversity in the attached microbial community (Shannon indices decreased from 2.63 to 1.89) which nevertheless increased with filtration time. Sphingomonas species, which condition membrane surfaces and facilitate cellular adhesion, were depleted inmore » all modified membranes. Microbial community structure was significantly different between control, different patterns, and different chemistries. Lastly, this study broadens the tools for surface modification of membranes with polymer coatings and for understanding and optimization of antifouling surfaces.« less

Exploring the Impacts of Anthropogenic Disturbance on Seawater and Sediment Microbial Communities in Korean Coastal Waters Using Metagenomics Analysis

PubMed Central

Won, Nam-Il; Kim, Ki-Hwan; Kang, Ji Hyoun; Park, Sang Rul; Lee, Hyuk Je

2017-01-01

The coastal ecosystems are considered as one of the most dynamic and vulnerable environments under various anthropogenic developments and the effects of climate change. Variations in the composition and diversity of microbial communities may be a good indicator for determining whether the marine ecosystems are affected by complex forcing stressors. DNA sequence-based metagenomics has recently emerged as a promising tool for analyzing the structure and diversity of microbial communities based on environmental DNA (eDNA). However, few studies have so far been performed using this approach to assess the impacts of human activities on the microbial communities in marine systems. In this study, using metagenomic DNA sequencing (16S ribosomal RNA gene), we analyzed and compared seawater and sediment communities between sand mining and control (natural) sites in southern coastal waters of Korea to assess whether anthropogenic activities have significantly affected the microbial communities. The sand mining sites harbored considerably lower levels of microbial diversities in the surface seawater community during spring compared with control sites. Moreover, the sand mining areas had distinct microbial taxonomic group compositions, particularly during spring season. The microbial groups detected solely in the sediment load/dredging areas (e.g., Marinobacter, Alcanivorax, Novosphingobium) are known to be involved in degradation of toxic chemicals such as hydrocarbon, oil, and aromatic compounds, and they also contain potential pathogens. This study highlights the versatility of metagenomics in monitoring and diagnosing the impacts of human disturbance on the environmental health of marine ecosystems from eDNA. PMID:28134828

Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH

PubMed Central

Twing, Katrina I.; Brazelton, William J.; Kubo, Michael D. Y.; Hyer, Alex J.; Cardace, Dawn; Hoehler, Tori M.; McCollom, Tom M.; Schrenk, Matthew O.

2017-01-01

Serpentinization is a widespread geochemical process associated with aqueous alteration of ultramafic rocks that produces abundant reductants (H2 and CH4) for life to exploit, but also potentially challenging conditions, including high pH, limited availability of terminal electron acceptors, and low concentrations of inorganic carbon. As a consequence, past studies of serpentinites have reported low cellular abundances and limited microbial diversity. Establishment of the Coast Range Ophiolite Microbial Observatory (California, U.S.A.) allowed a comparison of microbial communities and physicochemical parameters directly within serpentinization-influenced subsurface aquifers. Samples collected from seven wells were subjected to a range of analyses, including solute and gas chemistry, microbial diversity by 16S rRNA gene sequencing, and metabolic potential by shotgun metagenomics, in an attempt to elucidate what factors drive microbial activities in serpentinite habitats. This study describes the first comprehensive interdisciplinary analysis of microbial communities in hyperalkaline groundwater directly accessed by boreholes into serpentinite rocks. Several environmental factors, including pH, methane, and carbon monoxide, were strongly associated with the predominant subsurface microbial communities. A single operational taxonomic unit (OTU) of Betaproteobacteria and a few OTUs of Clostridia were the almost exclusive inhabitants of fluids exhibiting the most serpentinized character. Metagenomes from these extreme samples contained abundant sequences encoding proteins associated with hydrogen metabolism, carbon monoxide oxidation, carbon fixation, and acetogenesis. Metabolic pathways encoded by Clostridia and Betaproteobacteria, in particular, are likely to play important roles in the ecosystems of serpentinizing groundwater. These data provide a basis for further biogeochemical studies of key processes in serpentinite subsurface environments. PMID:28298908

Exploring the Impacts of Anthropogenic Disturbance on Seawater and Sediment Microbial Communities in Korean Coastal Waters Using Metagenomics Analysis.

PubMed

Won, Nam-Il; Kim, Ki-Hwan; Kang, Ji Hyoun; Park, Sang Rul; Lee, Hyuk Je

2017-01-27

The coastal ecosystems are considered as one of the most dynamic and vulnerable environments under various anthropogenic developments and the effects of climate change. Variations in the composition and diversity of microbial communities may be a good indicator for determining whether the marine ecosystems are affected by complex forcing stressors. DNA sequence-based metagenomics has recently emerged as a promising tool for analyzing the structure and diversity of microbial communities based on environmental DNA (eDNA). However, few studies have so far been performed using this approach to assess the impacts of human activities on the microbial communities in marine systems. In this study, using metagenomic DNA sequencing (16S ribosomal RNA gene), we analyzed and compared seawater and sediment communities between sand mining and control (natural) sites in southern coastal waters of Korea to assess whether anthropogenic activities have significantly affected the microbial communities. The sand mining sites harbored considerably lower levels of microbial diversities in the surface seawater community during spring compared with control sites. Moreover, the sand mining areas had distinct microbial taxonomic group compositions, particularly during spring season. The microbial groups detected solely in the sediment load/dredging areas (e.g., Marinobacter, Alcanivorax, Novosphingobium) are known to be involved in degradation of toxic chemicals such as hydrocarbon, oil, and aromatic compounds, and they also contain potential pathogens. This study highlights the versatility of metagenomics in monitoring and diagnosing the impacts of human disturbance on the environmental health of marine ecosystems from eDNA.

Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH.

PubMed

Twing, Katrina I; Brazelton, William J; Kubo, Michael D Y; Hyer, Alex J; Cardace, Dawn; Hoehler, Tori M; McCollom, Tom M; Schrenk, Matthew O

2017-01-01

Serpentinization is a widespread geochemical process associated with aqueous alteration of ultramafic rocks that produces abundant reductants (H 2 and CH 4 ) for life to exploit, but also potentially challenging conditions, including high pH, limited availability of terminal electron acceptors, and low concentrations of inorganic carbon. As a consequence, past studies of serpentinites have reported low cellular abundances and limited microbial diversity. Establishment of the Coast Range Ophiolite Microbial Observatory (California, U.S.A.) allowed a comparison of microbial communities and physicochemical parameters directly within serpentinization-influenced subsurface aquifers. Samples collected from seven wells were subjected to a range of analyses, including solute and gas chemistry, microbial diversity by 16S rRNA gene sequencing, and metabolic potential by shotgun metagenomics, in an attempt to elucidate what factors drive microbial activities in serpentinite habitats. This study describes the first comprehensive interdisciplinary analysis of microbial communities in hyperalkaline groundwater directly accessed by boreholes into serpentinite rocks. Several environmental factors, including pH, methane, and carbon monoxide, were strongly associated with the predominant subsurface microbial communities. A single operational taxonomic unit (OTU) of Betaproteobacteria and a few OTUs of Clostridia were the almost exclusive inhabitants of fluids exhibiting the most serpentinized character. Metagenomes from these extreme samples contained abundant sequences encoding proteins associated with hydrogen metabolism, carbon monoxide oxidation, carbon fixation, and acetogenesis. Metabolic pathways encoded by Clostridia and Betaproteobacteria, in particular, are likely to play important roles in the ecosystems of serpentinizing groundwater. These data provide a basis for further biogeochemical studies of key processes in serpentinite subsurface environments.

Ecosystem development in roadside grasslands: biotic control, plant–soil interactions and dispersal limitations

PubMed Central

García-Palacios, Pablo; Bowker, Matthew A.; Maestre, Fernando T.; Soliveres, Santiago; Valladares, Fernando; Papadopoulos, Jorge; Escudero, Adrián

2015-01-01

Roadside grasslands undergoing secondary succession are abundant, and represent ecologically meaningful examples of novel, human-created ecosystems. Interactions between plant and soil communities (hereafter plant–soil interactions) are of major importance in understanding the role of biotic control in ecosystem functioning, but little is known about these links in the context of ecosystem restoration and succession. The assessment of the key biotic communities and interactions driving ecosystem development will help practitioners to better allocate the limited resources devoted to roadside grassland restoration. We surveyed roadside grasslands from three successional stages (0–2, 7–9 and > 20 years) in two Mediterranean regions of Spain. Structural equation modeling was used to evaluate how interactions between plants, biological soil crusts [BSCs], and soil microbial functional diversity [soil microorganisms] affect indicators of ecosystem development and restoration: plant similarity to the reference ecosystem, erosion control and soil C storage and N accumulation. Changes in plant community composition along the successional gradient exerted the strongest influence on these indicators. High BSC cover was associated with high soil stability, and high soil microbial functional diversity from late-successional stages was associated with high soil fertility. Contrary to our expectations, the indirect effects of plants, mediated by either BSCs or soil microorganisms, were very weak in both regions, suggesting a minor role for plant–soil interactions upon ecosystem development indicators over long periods. Our results suggest that natural vegetation dynamics effectively improved ecosystem development within a time frame of 20 years in the grasslands evaluated. They also indicate that this time could be shortened if management actions focus on: 1) maintain well-conserved natural areas close to roadsides to enhance plant compositional changes towards late-successional stages, 2) increase BSC cover in areas under strong erosion risk, to avoid soil loss, and 3) enhance soil microbial functional diversity in resource-limited areas, to enhance soil C and N accumulation. PMID:22073661

Ecosystem development in roadside grasslands: Biotic control, plant-soil interactions, and dispersal limitations

USGS Publications Warehouse

Garcia-Palacios, P.; Bowker, M.A.; Maestre, F.T.; Soliveres, S.; Valladares, F.; Papadopoulos, J.; Escudero, A.

2011-01-01

Roadside grasslands undergoing secondary succession are abundant, and represent ecologically meaningful examples of novel, human-created ecosystems. Interactions between plant and soil communities (hereafter plant-soil interactions) are of major importance in understanding the role of biotic control in ecosystem functioning, but little is known about these links in the context of ecosystem restoration and succession. The assessment of the key biotic communities and interactions driving ecosystem development will help practitioners to better allocate the limited resources devoted to roadside grassland restoration. We surveyed roadside grasslands from three successional stages (0-2, 7-9, and > 20 years) in two Mediterranean regions of Spain. Structural equation modeling was used to evaluate how interactions between plants, biological soil crusts (BSCs), and soil microbial functional diversity (soil microorganisms) affect indicators of ecosystem development and restoration: plant similarity to the reference ecosystem, erosion control, and soil C storage and N accumulation. Changes in plant community composition along the successional gradient exerted the strongest influence on these indicators. High BSC cover was associated with high soil stability, and high soil microbial functional diversity from late-successional stages was associated with high soil fertility. Contrary to our expectations, the indirect effects of plants, mediated by either BSCs or soil microorganisms, were very weak in both regions, suggesting a minor role for plant-soil interactions upon ecosystem development indicators over long periods. Our results suggest that natural vegetation dynamics effectively improved ecosystem development within a time frame of 20 years in the grasslands evaluated. They also indicate that this time could be shortened if management actions focus on: (1) maintaining wellconserved natural areas close to roadsides to enhance plant compositional changes towards late-successional stages, (2) increasing BSC cover in areas under strong erosion risk, to avoid soil loss, and (3) enhancing soil microbial functional diversity in resource-limited areas, to enhance soil C and N accumulation. ?? 2011 by the Ecological Society of America.

[Observation of genetic diversity in dental plaque of elder people with root caries].

PubMed

Ma, Shan-fen; Liang, Jing-ping; Jiang, Yun-tao; Zhu, Cai-lian

2011-08-01

Bacterial community in dental plaque of elder people was analyzed to learn about the microhabitat composition and diversity. Dental plaque samples were collected from 25 elders. PCR-based denaturing gradient gel electrophoresis (PCR-DGGE) was used to evaluate the microbial diversity by displaying PCR-generated 16SrDNA fragments that migrate at different distances, reflecting the different sequence of fragment. SPSS12.0 software was used to analyze the variance of genotypes between different groups of bacteria. Genotypes of bacteria in dental plaques in the root caries group was significantly more than the other two groups. Crown caries group and caries-free group had no significant difference. The genetic diversity of the dental plaque microflora in the root caries group is significantly higher than coronal caries group and caries-free group.

Differences in carbon source usage by dental plaque in children with and without early childhood caries

PubMed Central

Zhao, Yan; Zhong, Wen-Jie; Xun, Zhe; Zhang, Qian; Song, Ye-Qing; Liu, Yun-Song; Chen, Feng

2017-01-01

Early childhood caries (ECC) is a considerable pediatric and public health problem worldwide. Preceding studies have focused primarily on bacterial diversity at the taxonomic level. Although these studies have provided significant information regarding the connection between dental caries and oral microbiomes, further comprehension of this microbial community’s ecological relevance is limited. This study identified the carbon source metabolic differences in dental plaque between children with and without ECC. We compared the microbial community functional diversity in 18 caries-free subjects with 18 severe ECC patients based on sole carbon source usage using a Biolog assay. The anaerobic microbial community in the ECC patients displayed greater metabolic activity than that of the control group. Specific carbon source metabolism differed significantly between the two groups. Subjects from the two groups were well distinguished by cluster and principal component analyses based on discriminative carbon sources. Our results implied that the microbial functional diversity between the ECC patients and healthy subjects differed significantly. In addition, the Biolog assay furthered our understanding of oral microbiomes as a composite of functional abilities, thus enabling us to identify the ecologically relevant functional differences among oral microbial communities.

Changes in microbial communities along redox gradients in polygonized Arctic wet tundra soils

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

Lipson, David A.; Raab, Theodore K.; Parker, Melanie

2015-08-01

Summary This study investigated how microbial community structure and diversity varied with depth and topography in ice wedge polygons of wet tundra of the Arctic Coastal Plain in northern Alaska and what soil variables explain these patterns. We observed strong changes in community structure and diversity with depth, and more subtle changes between areas of high and low topography, with the largest differences apparent near the soil surface. These patterns are most strongly correlated with redox gradients (measured using the ratio of reduced Fe to total Fe in acid extracts as a proxy): conditions grew more reducing with depth andmore » were most oxidized in shallow regions of polygon rims. Organic matter and pH also changed with depth and topography but were less effective predictors of the microbial community structure and relative abundance of specific taxa. Of all other measured variables, lactic acid concentration was the best, in combination with redox, for describing the microbial community. We conclude that redox conditions are the dominant force in shaping microbial communities in this landscape. Oxygen and other electron acceptors allowed for the greatest diversity of microbes: at depth the community was reduced to a simpler core of anaerobes,« less

Microbial community differentiation between active and inactive sulfide chimneys of the Kolumbo submarine volcano, Hellenic Volcanic Arc.

PubMed

Christakis, Christos A; Polymenakou, Paraskevi N; Mandalakis, Manolis; Nomikou, Paraskevi; Kristoffersen, Jon Bent; Lampridou, Danai; Kotoulas, Georgios; Magoulas, Antonios

2018-01-01

Over the last decades, there has been growing interest about the ecological role of hydrothermal sulfide chimneys, their microbial diversity and associated biotechnological potential. Here, we performed dual-index Illumina sequencing of bacterial and archaeal communities on active and inactive sulfide chimneys collected from the Kolumbo hydrothermal field, situated on a geodynamic convergent setting. A total of 15,701 OTUs (operational taxonomic units) were assigned to 56 bacterial and 3 archaeal phyla, 133 bacterial and 16 archaeal classes. Active chimney communities were dominated by OTUs related to thermophilic members of Epsilonproteobacteria, Aquificae and Deltaproteobacteria. Inactive chimney communities were dominated by an OTU closely related to the archaeon Nitrosopumilus sp., and by members of Gammaproteobacteria, Deltaproteobacteria, Planctomycetes and Bacteroidetes. These lineages are closely related to phylotypes typically involved in iron, sulfur, nitrogen, hydrogen and methane cycling. Overall, the inactive sulfide chimneys presented highly diverse and uniform microbial communities, in contrast to the active chimney communities, which were dominated by chemolithoautotrophic and thermophilic lineages. This study represents one of the most comprehensive investigations of microbial diversity in submarine chimneys and elucidates how the dissipation of hydrothermal activity affects the structure of microbial consortia in these extreme ecological niches.

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.