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

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

SUBMITTER: Justice NB

PROVIDER: S-EPMC5626985 | biostudies-literature | 2017 Oct

REPOSITORIES: biostudies-literature

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

Justice N B NB Sczesnak A A Hazen T C TC Arkin A P AP

Applied and environmental microbiology 20170929 20

A central goal of microbial ecology is to identify and quantify the forces that lead to observed population distributions and dynamics. However, these forces, which include environmental selection, dispersal, and organism interactions, are often difficult to assess in natural environments. Here, we present a method that links microbial community structures with selective and stochastic forces through highly replicated subsampling and enrichment of a single environmental inoculum. Specifically, g ...[more]

PMID: 28778896

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Project description:Background and aimsHydroperiod drives plant community composition in wetlands, resulting in distinct zonation patterns. Here, we explored the role of seed germination traits in shaping wetland community assembly along a hydroperiod gradient. Specifically, we tested the hypothesis that seeds of reed, mudflat, swamp, shallow- and deep-water communities only germinate under a specific set of environmental factors characterized by the community-specific optimal conditions for seedling survival and growth.MethodsIn a three-factorial experiment, we tested the seed germination response of 50 species typical for temperate wetlands of Europe to temperature fluctuations (constant vs. fluctuating temperature), illumination (light vs. darkness) and oxygen availability (aerobic vs. hypoxia). Phylogenetic principal component analysis, cluster analysis and phylogenetic linear regressions were used to confirm the community-specific seed germination niches.Key resultsOur study revealed the presence of five distinct, community-specific seed germination niches that reflect adaptations made by the study communities to decreasing light intensity, temperature fluctuations and oxygen availability along the hydroperiod gradient. Light as a germination trigger was found to be important in mudflats, swamps and shallow water, whereas the seeds of reed and deep-water species were able to germinate in darkness. A fluctuating temperature is only required for seed germination in mudflat species. Germination of species in the communities at the higher end of the hydroperiod gradient (reed and mudflat) demonstrated a strict requirement for oxygen, whereas swamp, shallow- and deep-water species also germinated under hypoxia.ConclusionsOur study supports the recent argument that the inclusion of seed germination traits in community ecology adds significant insights to community response to the abiotic and biotic environment. Furthermore, the close relationship between seed germination adaptations and community assembly could help reach a better understanding of the existing patterns of wetland plant distribution at local scales and wetland vegetation dynamics, as well as facilitate nature conservation measures and aquatic habitat restoration.

Dataset Information

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

Publications

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

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