Ecosystem engineers drive differing microbial community composition in intertidal estuarine sediments

Intertidal systems are complex and dynamic environments with many interacting factors influencing biochemical characteristics and microbial communities. One key factor are the actions of resident fauna, many of which are regarded as ecosystem engineers because of their bioturbation, bioirrigation and sediment stabilising activities. The purpose of this investigation was to elucidate the evolutionary implications of the ecosystem engineering process by identifying, if any, aspects that act as selection pressures upon microbial communities. A mesocosm study was performed using the well characterised intertidal ecosystem engineers Corophium volutator, Hediste diversicolor, and microphytobenthos, in addition to manual turbation of sediments to compare effects of bioturbation, bioirrigation and stabilisation. A range of sediment functions and biogeochemical gradients were measured in conjunction with 16S rRNA sequencing and diatom taxonomy, with downstream bacterial metagenome function prediction, to identify selection pressures that incited change to microbial community composition and function. Bacterial communities were predominantly Proteobacteria, with the relative abundance of Bacteroidetes, Alphaproteobacteria and Verrucomicrobia being partially displaced by Deltaproteobacteria, Acidobacteria and Chloroflexi as dissolved oxygen concentration and redox potential decreased. Bacterial community composition was driven strongly by biogeochemistry; surface communities were affected by a combination of sediment functions and overlying water turbidity, and subsurface communities by biogeochemical gradients driven by sediment reworking. Diatom communities were dominated by Nitzschia laevis and Achnanthes sp., and assemblage composition was influenced by overlying water turbidity (manual or biogenic) rather than direct infaunal influences such as grazing.

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Microbial Communities Show Parallels at Sites with Distinct Litter and Soil Characteristics

Applied and Environmental Microbiology ◽

10.1128/aem.00527-11 ◽

2011 ◽

Vol 77 (21) ◽

pp. 7560-7567 ◽

Cited By ~ 17

Author(s):

Marketa Sagova-Mareckova ◽

Marek Omelka ◽

Ladislav Cermak ◽

Zdenek Kamenik ◽

Jana Olsovska ◽

...

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Composition ◽

Soil Ph ◽

Soil Chemistry ◽

High Performance ◽

Bacterial Community Composition ◽

Microbial Community Composition ◽

Carbon Sources ◽

Soil Extracts

ABSTRACTPlant and microbial community composition in connection with soil chemistry determines soil nutrient cycling. The study aimed at demonstrating links between plant and microbial communities and soil chemistry occurring among and within four sites: two pine forests with contrasting soil pH and two grasslands of dissimilar soil chemistry and vegetation. Soil was characterized by C and N content, particle size, and profiles of low-molecular-weight compounds determined by high-performance liquid chromatography (HPLC) of soil extracts. Bacterial and actinobacterial community composition was assessed by terminal restriction fragment length polymorphism (T-RFLP) and cloning followed by sequencing. Abundances of bacteria, fungi, and actinobacteria were determined by quantitative PCR. In addition, a pool of secondary metabolites was estimated byermresistance genes coding for rRNA methyltransferases. The sites were characterized by a stable proportion of C/N within each site, while on a larger scale, the grasslands had a significantly lower C/N ratio than the forests. A Spearman's test showed that soil pH was correlated with bacterial community composition not only among sites but also within each site. Bacterial, actinobacterial, and fungal abundances were related to carbon sources while T-RFLP-assessed microbial community composition was correlated with the chemical environment represented by HPLC profiles. Actinobacteria community composition was the only studied microbial characteristic correlated to all measured factors. It was concluded that the microbial communities of our sites were influenced primarily not only by soil abiotic characteristics but also by dominant litter quality, particularly, by percentage of recalcitrant compounds.

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Application of Methods for Identifying Broiler Chicken Gut Bacterial Species Linked with Increased Energy Metabolism

Applied and Environmental Microbiology ◽

10.1128/aem.01384-07 ◽

2007 ◽

Vol 74 (3) ◽

pp. 783-791 ◽

Cited By ~ 105

Author(s):

Valeria A. Torok ◽

Kathy Ophel-Keller ◽

Maylene Loo ◽

Robert J. Hughes

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Composition ◽

Bacterial Species ◽

Bacterial Community Composition ◽

Microbial Community Composition ◽

Metabolizable Energy ◽

Principal Coordinates ◽

Improved Performance ◽

Gut Microbial Community

ABSTRACT A high-throughput microbial profiling tool based on terminal restriction fragment length polymorphism was developed to monitor the poultry gut microbiota in response to dietary manipulations. Gut microbial communities from the duodena, jejuna, ilea, and ceca of 48 birds fed either a barley control diet or barley diet supplemented with exogenous enzymes for degrading nonstarch polysaccharide were characterized by using multivariate statistical methods. Analysis of samples showed that gut microbial communities varied significantly among gut sections, except between the duodenum and jejunum. Significant diet-associated differences in gut microbial communities were detected within the ileum and cecum only. The dissimilarity in bacterial community composition between diets was 73 and 66% within the ileum and cecum, respectively. Operational taxonomic units, representing bacterial species or taxonomically related groups, contributing to diet-associated differences were identified. Several bacterial species contributed to differences between diet-related gut microbial community composition, with no individual bacterial species contributing more than 1 to 5% of the total. Using canonical analysis of principal coordinates biplots, we correlated differences in gut microbial community composition within the ileum and cecum to improved performance, as measured by apparent metabolizable energy. This is the first report that directly links differences in the composition of the gut microbial community with improved performance, which implies that the presence of specific beneficial and/or absence of specific detrimental bacterial species may contribute to the improved performance in these birds.

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Colonization in the Photic Zone and Subsequent Changes during Sinking Determine Bacterial Community Composition in Marine Snow

Applied and Environmental Microbiology ◽

10.1128/aem.02570-14 ◽

2014 ◽

Vol 81 (4) ◽

pp. 1463-1471 ◽

Cited By ~ 45

Author(s):

Stefan Thiele ◽

Bernhard M. Fuchs ◽

Rudolf Amann ◽

Morten H. Iversen

Keyword(s):

Microbial Community ◽

Bacterial Community ◽

Microbial Communities ◽

Community Composition ◽

Bacterial Community Composition ◽

Microbial Community Composition ◽

Marine Snow ◽

Free Living ◽

Fluorescence Maximum

ABSTRACTDue to sampling difficulties, little is known about microbial communities associated with sinking marine snow in the twilight zone. A drifting sediment trap was equipped with a viscous cryogel and deployed to collect intact marine snow from depths of 100 and 400 m off Cape Blanc (Mauritania). Marine snow aggregates were fixed and washedin situto prevent changes in microbial community composition and to enable subsequent analysis using catalyzed reporter deposition fluorescencein situhybridization (CARD-FISH). The attached microbial communities collected at 100 m were similar to the free-living community at the depth of the fluorescence maximum (20 m) but different from those at other depths (150, 400, 550, and 700 m). Therefore, the attached microbial community seemed to be “inherited” from that at the fluorescence maximum. The attached microbial community structure at 400 m differed from that of the attached community at 100 m and from that of any free-living community at the tested depths, except that collected near the sediment at 700 m. The differences between the particle-associated communities at 400 m and 100 m appeared to be due to internal changes in the attached microbial community rather thande novocolonization, detachment, or grazing during the sinking of marine snow. The new sampling method presented here will facilitate future investigations into the mechanisms that shape the bacterial community within sinking marine snow, leading to better understanding of the mechanisms which regulate biogeochemical cycling of settling organic matter.

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Reduction of Perchlorate and Nitrate by Microbial Communities in Vadose Soil

Applied and Environmental Microbiology ◽

10.1128/aem.71.7.3928-3934.2005 ◽

2005 ◽

Vol 71 (7) ◽

pp. 3928-3934 ◽

Cited By ~ 46

Author(s):

Mamie Nozawa-Inoue ◽

Kate M. Scow ◽

Dennis E. Rolston

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Composition ◽

Denaturing Gradient Gel Electrophoresis ◽

Bacterial Community Composition ◽

Microbial Community Composition ◽

16S Rrna Genes ◽

Rrna Genes ◽

Human Thyroid ◽

Perchlorate Reduction

ABSTRACT Perchlorate contamination is a concern because of the increasing frequency of its detection in soils and groundwater and its presumed inhibitory effect on human thyroid hormone production. Although significant perchlorate contamination occurs in the vadose (unsaturated) zone, little is known about perchlorate biodegradation potential by indigenous microorganisms in these soils. We measured the effects of electron donor (acetate and hydrogen) and nitrate addition on perchlorate reduction rates and microbial community composition in microcosm incubations of vadose soil. Acetate and hydrogen addition enhanced perchlorate reduction, and a longer lag period was observed for hydrogen (41 days) than for acetate (14 days). Initially, nitrate suppressed perchlorate reduction, but once perchlorate started to be degraded, the process was stimulated by nitrate. Changes in the bacterial community composition were observed in microcosms enriched with perchlorate and either acetate or hydrogen. Denaturing gradient gel electrophoresis analysis and partial sequencing of 16S rRNA genes recovered from these microcosms indicated that formerly reported perchlorate-reducing bacteria were present in the soil and that microbial community compositions were different between acetate- and hydrogen-amended microcosms. These results indicate that there is potential for perchlorate bioremediation by native microbial communities in vadose soil.

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Effect of River Ecological Restoration on Biofilm Microbial Community Composition

Water ◽

10.3390/w11061244 ◽

2019 ◽

Vol 11 (6) ◽

pp. 1244 ◽

Cited By ~ 4

Author(s):

Qiaoyan Lin ◽

Raju Sekar ◽

Rob Marrs ◽

Yixin Zhang

Keyword(s):

Microbial Community ◽

Bacterial Community ◽

Microbial Communities ◽

Community Composition ◽

Organic Pollutants ◽

Habitat Restoration ◽

Bacterial Community Composition ◽

Microbial Community Composition ◽

Reference Conditions ◽

Urban Rivers

Across the world, there have been increasing attempts to restore good ecological condition to degraded rivers through habitat restoration. Microbial communities developing as biofilms play an important role in river ecosystem functioning by driving organic matter decomposition and ecosystem respiration. However, little is known about the structure and function of microbial communities in riverine systems and how these change when habitat restoration is implemented. Here, we compared the biofilm bacterial community composition using 16S rRNA genes targeted high-throughput Illumina Miseq sequencing in three river types, degraded urban rivers, urban rivers undergoing habitat restoration and forested rivers (our reference conditions). We aimed to determine: (i) the biofilm bacterial community composition affected by habitat restoration (ii) the difference in bacterial diversity in restored rivers, and (iii) correlations between environmental variables and bacterial community composition. The results showed that both water quality and biofilm bacterial community structure were changed by habitat restoration. In rivers where habitat had been restored, there was an increase in dissolved oxygen, a reduction in organic pollutants, a reduction in bacterial diversity and a related developing pattern of microbial communities, which is moving towards that of the reference conditions (forested rivers). River habitat management stimulated the processing of organic pollutants through the variation in microbial community composition, however, a big difference in bacterial structure still existed between the restored rivers and the reference forest rivers. Thus, habitat restoration is an efficient way of modifying the biofilm microbial community composition for sustainable freshwater management. It will, however, take a much longer time for degraded rivers to attain a similar ecosystem quality as the “pristine” forest sites than the seven years of restoration studied here.

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Antarctic Water Tracks: Microbial Community Responses to Variation in Soil Moisture, pH, and Salinity

Frontiers in Microbiology ◽

10.3389/fmicb.2021.616730 ◽

2021 ◽

Vol 12 ◽

Author(s):

Scott F. George ◽

Noah Fierer ◽

Joseph S. Levy ◽

Byron Adams

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Composition ◽

Environmental Conditions ◽

Microbial Community Composition ◽

Soil Microbial Communities ◽

Vapor Flow ◽

Arid Soils ◽

Opposite Pattern ◽

Dry Valley

Ice-free soils in the McMurdo Dry Valleys select for taxa able to cope with challenging environmental conditions, including extreme chemical water activity gradients, freeze-thaw cycling, desiccation, and solar radiation regimes. The low biotic complexity of Dry Valley soils makes them well suited to investigate environmental and spatial influences on bacterial community structure. Water tracks are annually wetted habitats in the cold-arid soils of Antarctica that form briefly each summer with moisture sourced from snow melt, ground ice thaw, and atmospheric deposition via deliquescence and vapor flow into brines. Compared to neighboring arid soils, water tracks are highly saline and relatively moist habitats. They represent a considerable area (∼5–10 km2) of the Dry Valley terrestrial ecosystem, an area that is expected to increase with ongoing climate change. The goal of this study was to determine how variation in the environmental conditions of water tracks influences the composition and diversity of microbial communities. We found significant differences in microbial community composition between on- and off-water track samples, and across two distinct locations. Of the tested environmental variables, soil salinity was the best predictor of community composition, with members of the Bacteroidetes phylum being relatively more abundant at higher salinities and the Actinobacteria phylum showing the opposite pattern. There was also a significant, inverse relationship between salinity and bacterial diversity. Our results suggest water track formation significantly alters dry soil microbial communities, likely influencing subsequent ecosystem functioning. We highlight how Dry Valley water tracks could be a useful model system for understanding the potential habitability of transiently wetted environments found on the surface of Mars.

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Soil microbial communities in microaggregates are less affected by top-down effects of collembolans than those in macroaggregates

10.5194/egusphere-egu21-10345 ◽

2021 ◽

Author(s):

Amandine Erktan ◽

MD Ekramul Haque ◽

Jérôme Cortet ◽

Paul Henning Krogh ◽

Stefan Scheu

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Composition ◽

Trophic Interactions ◽

Phospholipid Fatty Acid ◽

Microbial Community Composition ◽

Soil Microbial Communities ◽

Trophic Levels ◽

Soil Matrix ◽

Fungal Abundance

<p>Trophic regulation of microbial communities is receiving growing interest in soil ecology. Most studies investigated the effect of higher trophic levels on microbial communities at the bulk soil level. However, microbes are not equally accessible to consumers. They may be hidden in small pores and thus protected from consumers, suggesting that trophic regulation may depend on the localization of microbes within the soil matrix. As microaggregates (< 250 &#181;m) usually are more stable than macroaggregates (> 250 &#181;m) and embedded in the latter, we posit that they will be less affected by trophic regulations than larger aggregates. We quantified the effect of four contrasting species of collembolans (Ceratophysella denticulata, Protaphorura fimata, Folsomia candida, Sinella curviseta) on the microbial community composition in macro- (250 &#181;m &#8211; 2mm) and microaggregates (50 &#8211; 250 &#181;m). To do so, we re-built consumer-prey systems comprising remaining microbial background (post-autoclaving), fungal prey (Chaetomium globosum), and collembolan species (added as single species or combined). After three months, we quantified microbial community composition using phospholipid fatty acid markers (PLFAs). We found that the microbial communities in macroaggregates were more affected by the addition of collembolans than the communities in microaggregates. In particular, the fungal-to-bacterial (F:B) ratio significantly decreased in soil macroaggregates in the presence of collembolans. In the microaggregates, the F:B ratio remained lower and unaffected by collembolan inoculation. Presumably, fungal hyphae were more abundant in macroaggregates because they offered more habitat space for them, and the collembolans reduced fungal abundance because they consumed them. On the contrary, microaggregates presumably contained microbial communities protected from consumers. In addition, collembolans increased the formation of macroaggregates but did not influence their stability, despite their negative effect on fungal abundance, a well-known stabilizing agent. Overall, we show that trophic interactions between microbial communities and collembolans depend on the aggregate size class considered and, in return, soil macroaggregation is affected by these trophic interactions.</p>

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Changes in the Active, Dead, and Dormant Microbial Community Structure across a Pleistocene Permafrost Chronosequence

Applied and Environmental Microbiology ◽

10.1128/aem.02646-18 ◽

2019 ◽

Vol 85 (7) ◽

Cited By ~ 17

Author(s):

Alexander Burkert ◽

Thomas A. Douglas ◽

Mark P. Waldrop ◽

Rachel Mackelprang

Keyword(s):

Microbial Community ◽

16S Rrna ◽

16S Rrna Gene ◽

Microbial Communities ◽

Community Composition ◽

Environmental Conditions ◽

Microbial Community Composition ◽

Rrna Gene ◽

Subzero Temperatures ◽

Dormant Cells

ABSTRACTPermafrost hosts a community of microorganisms that survive and reproduce for millennia despite extreme environmental conditions, such as water stress, subzero temperatures, high salinity, and low nutrient availability. Many studies focused on permafrost microbial community composition use DNA-based methods, such as metagenomics and 16S rRNA gene sequencing. However, these methods do not distinguish among active, dead, and dormant cells. This is of particular concern in ancient permafrost, where constant subzero temperatures preserve DNA from dead organisms and dormancy may be a common survival strategy. To circumvent this, we applied (i) LIVE/DEAD differential staining coupled with microscopy, (ii) endospore enrichment, and (iii) selective depletion of DNA from dead cells to permafrost microbial communities across a Pleistocene permafrost chronosequence (19,000, 27,000, and 33,000 years old). Cell counts and analysis of 16S rRNA gene amplicons from live, dead, and dormant cells revealed how communities differ between these pools, how they are influenced by soil physicochemical properties, and whether they change over geologic time. We found evidence that cells capable of forming endospores are not necessarily dormant and that members of the classBacilliwere more likely to form endospores in response to long-term stressors associated with permafrost environmental conditions than members of theClostridia, which were more likely to persist as vegetative cells in our older samples. We also found that removing exogenous “relic” DNA preserved within permafrost did not significantly alter microbial community composition. These results link the live, dead, and dormant microbial communities to physicochemical characteristics and provide insights into the survival of microbial communities in ancient permafrost.IMPORTANCEPermafrost soils store more than half of Earth’s soil carbon despite covering ∼15% of the land area (C. Tarnocai et al., Global Biogeochem Cycles 23:GB2023, 2009, https://doi.org/10.1029/2008GB003327). This permafrost carbon is rapidly degraded following a thaw (E. A. G. Schuur et al., Nature 520:171–179, 2015, https://doi.org/10.1038/nature14338). Understanding microbial communities in permafrost will contribute to the knowledge base necessary to understand the rates and forms of permafrost C and N cycling postthaw. Permafrost is also an analog for frozen extraterrestrial environments, and evidence of viable organisms in ancient permafrost is of interest to those searching for potential life on distant worlds. If we can identify strategies microbial communities utilize to survive in permafrost, it may yield insights into how life (if it exists) survives in frozen environments outside of Earth. Our work is significant because it contributes to an understanding of how microbial life adapts and survives in the extreme environmental conditions in permafrost terrains.

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Ecology and Host Identity Outweigh Evolutionary History in Shaping the Bat Microbiome

mSystems ◽

10.1128/msystems.00511-19 ◽

2019 ◽

Vol 4 (6) ◽

Cited By ~ 5

Author(s):

Holly L. Lutz ◽

Elliot W. Jackson ◽

Paul W. Webala ◽

Waswa S. Babyesiza ◽

Julian C. Kerbis Peterhans ◽

...

Keyword(s):

Microbial Community ◽

Bacterial Community ◽

Community Composition ◽

Evolutionary History ◽

Bacterial Community Composition ◽

Microbial Community Composition ◽

Anatomical Site ◽

Skin Microbiota ◽

Host Identity ◽

Host Ecology

ABSTRACT Recent studies of mammalian microbiomes have identified strong phylogenetic effects on bacterial community composition. Bats (Mammalia: Chiroptera) are among the most speciose mammals on the planet and the only mammal capable of true flight. We examined 1,236 16S rRNA amplicon libraries of the gut, oral, and skin microbiota from 497 Afrotropical bats (representing 9 families, 20 genera, and 31 species) to assess the extent to which host ecology and phylogeny predict microbial community similarity in bats. In contrast to recent studies of host-microbe associations in other mammals, we found no correlation between chiropteran phylogeny and bacterial community dissimilarity across the three anatomical sites sampled. For all anatomical sites, we found host species identity and geographic locality to be strong predictors of microbial community composition and observed a positive correlation between elevation and bacterial richness. Last, we identified significantly different bacterial associations within the gut microbiota of insectivorous and frugivorous bats. We conclude that the gut, oral, and skin microbiota of bats are shaped predominantly by ecological factors and do not exhibit the same degree of phylosymbiosis observed in other mammals. IMPORTANCE This study is the first to provide a comprehensive survey of bacterial symbionts from multiple anatomical sites across a broad taxonomic range of Afrotropical bats, demonstrating significant associations between the bat microbiome and anatomical site, geographic locality, and host identity—but not evolutionary history. This study provides a framework for future systems biology approaches to examine host-symbiont relationships across broad taxonomic scales, emphasizing the need to elucidate the interplay between host ecology and evolutionary history in shaping the microbiome of different anatomical sites.

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Impacts of Maize Domestication and Breeding on Rhizosphere Microbial Community Recruitment from a Nutrient Depleted Agricultural Soil

Scientific Reports ◽

10.1038/s41598-019-52148-y ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 11

Author(s):

Vanessa L. Brisson ◽

Jennifer E. Schmidt ◽

Trent R. Northen ◽

John P. Vogel ◽

Amélie C. M. Gaudin

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Community Composition ◽

Microbial Community Composition ◽

Microbial Community Analysis ◽

Agricultural System ◽

Community Members ◽

Genetic Groups ◽

Maize Domestication ◽

Rhizosphere Microbial Community

Abstract Maize domestication and breeding have resulted in drastic and well documented changes in aboveground traits, but belowground effects on root system functioning and rhizosphere microbial communities remain poorly understood, despite their critical importance for nutrient and water acquisition. We investigated the rhizosphere microbial community composition and structure of ten Zea mays accessions along an evolutionary transect (two teosinte, three inbred maize lines, and five modern maize hybrids) grown in nutrient depleted soil from a low input agricultural system. Microbial community analysis revealed significant differences in community composition between soil compartments (proximal vs. distal rhizosphere) and between plant genetic groups (teosinte, inbred, and modern hybrid). Only a small portion of the microbial community was differentially selected across plant genetic groups: 3.7% of prokaryotic community members and 4.9% of fungal community members were significantly associated with a specific plant genetic group. Indicator species analysis showed the greatest differentiation between modern hybrids and the other two plant genetic groups. Co-occurrence network analysis revealed that microbial co-occurrence patterns of the inbred maize lines’ rhizosphere were significantly more similar to those of the teosintes than to the modern hybrids. Our results suggest that advances in hybrid development significantly impacted rhizosphere microbial communities and network assembly.

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