Stochastic Assembly Leads to Alternative Communities with Distinct Functions in a Bioreactor Microbial Community

Zhou, Jizhong; Liu, Wenzong; Deng, Ye; Jiang, Yi-Huei; Xue, Kai; He, Zhili; Van Nostrand, Joy D.; Wu, Liyou; Yang, Yunfeng; Wang, Aijie; Handelsman, Jo

doi:10.1128/mbio.00584-12

Stochastic Assembly Leads to Alternative Communities with Distinct Functions in a Bioreactor Microbial Community

Journal Article · Tue Mar 05 00:00:00 EST 2013 · mBio (Online)

DOI:https://doi.org/10.1128/mbio.00584-12· OSTI ID:1626112

Zhou, Jizhong ^[1]; Liu, Wenzong ^[2]; Deng, Ye ^[3]; Jiang, Yi-Huei ^[3]; Xue, Kai ^[3]; He, Zhili ^[3]; Van Nostrand, Joy D. ^[3]; Wu, Liyou ^[3]; Yang, Yunfeng ^[4]; Wang, Aijie ^[5]; Handelsman, Jo

Tsinghua Univ., Beijing (China). State Key Joint Lab. of Environment Simulation and Pollution Control. School of Environment; Univ. of Oklahoma, Norman, OK (United States). Inst. for Environmental Genomics. Dept. of Microbiology and Plant Biology; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Earth Sciences Division; DOE/OSTI
Univ. of Oklahoma, Norman, OK (United States). Inst. for Environmental Genomics. Dept. of Microbiology and Plant Biology; Harbin Inst. of Technology (China). State Key Lab. of Urban Water Resource and Environment
Univ. of Oklahoma, Norman, OK (United States). Inst. for Environmental Genomics. Dept. of Microbiology and Plant Biology
Tsinghua Univ., Beijing (China). State Key Joint Lab. of Environment Simulation and Pollution Control. School of Environment
Harbin Inst. of Technology (China). State Key Lab. of Urban Water Resource and Environment

The processes and mechanisms of community assembly and its relationships to community functioning are central issues in ecology. Both deterministic and stochastic factors play important roles in shaping community composition and structure, but the connection between community assembly and ecosystem functioning remains elusive, especially in microbial communities. Here, we used microbial electrolysis cell reactors as a model system to examine the roles of stochastic assembly in determining microbial community structure and functions. Under identical environmental conditions with the same source community, ecological drift (i.e., initial stochastic colonization) and subsequent biotic interactions created dramatically different communities with little overlap among 14 identical reactors, indicating that stochastic assembly played dominant roles in determining microbial community structure. Neutral community modeling analysis revealed that deterministic factors also played significant roles in shaping microbial community structure in these reactors. Most importantly, the newly formed communities differed substantially in community functions (e.g., H₂ production), which showed strong linkages to community structure. This study is the first to demonstrate that stochastic assembly plays a dominant role in determining not only community structure but also ecosystem functions. Elucidating the links among community assembly, biodiversity, and ecosystem functioning is critical to understanding ecosystem functioning, biodiversity preservation, and ecosystem management.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1626112

Journal Information:: mBio (Online), Journal Name: mBio (Online) Journal Issue: 2 Vol. 4; ISSN 2150-7511

Publisher:: American Society for Microbiology (ASM)Copyright Statement

Country of Publication:: United States

Language:: English

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Neutral mechanisms and niche differentiation in steady-state insular microbial communities revealed by single cell analysis: Non-equilibria systems Liu, Zishu; Cichocki, Nicolas; Hübschmann, Thomas Environmental Microbiology, Vol. 21, Issue 1 https://doi.org/10.1111/1462-2920.14437	journal	November 2018
Microbial functional diversity covaries with permafrost thaw-induced environmental heterogeneity in tundra soil Yuan, Mengting M.; Zhang, Jin; Xue, Kai Global Change Biology, Vol. 24, Issue 1 https://doi.org/10.1111/gcb.13820	journal	September 2017
Transient invaders can induce shifts between alternative stable states of microbial communities Amor, Daniel R.; Ratzke, Christoph; Gore, Jeff Science Advances, Vol. 6, Issue 8 https://doi.org/10.1126/sciadv.aay8676	journal	February 2020
pH Influences the Importance of Niche-Related and Neutral Processes in Lacustrine Bacterioplankton Assembly Ren, Lijuan; Jeppesen, Erik; He, Dan Applied and Environmental Microbiology, Vol. 81, Issue 9 https://doi.org/10.1128/aem.04042-14	journal	February 2015
High-Throughput Metagenomic Technologies for Complex Microbial Community Analysis: Open and Closed Formats Zhou, Jizhong; He, Zhili; Yang, Yunfeng mBio, Vol. 6, Issue 1 https://doi.org/10.1128/mbio.02288-14	journal	January 2015
Dynamic linear models guide design and analysis of microbiota studies within artificial human guts Silverman, Justin D.; Durand, Heather K.; Bloom, Rachael J. Microbiome, Vol. 6, Issue 1 https://doi.org/10.1186/s40168-018-0584-3	journal	November 2018
What Shapes the Phylogenetic Structure of Anuran Communities in a Seasonal Environment? The Influence of Determinism at Regional Scale to Stochasticity or Antagonistic Forces at Local Scale Martins, Clarissa de Araújo; Roque, Fabio de Oliveira; Santos, Bráulio A. PLOS ONE, Vol. 10, Issue 6 https://doi.org/10.1371/journal.pone.0130075	journal	June 2015
Effects of initial microbial biomass abundance on respiration during pine litter decomposition Albright, Michaeline B. N.; Runde, Andreas; Lopez, Deanna PLOS ONE, Vol. 15, Issue 2 https://doi.org/10.1371/journal.pone.0224641	journal	February 2020
Nexus of Stochastic and Deterministic Processes on Microbial Community Assembly in Biological Systems Yuan, Heyang; Mei, Ran; Liao, Junhui Frontiers in Microbiology, Vol. 10 https://doi.org/10.3389/fmicb.2019.01536	journal	July 2019
Competition and niche separation of pelagic bacteria in freshwater habitats Pernthaler, Jakob Wiley-Blackwell Publishing, Inc. https://doi.org/10.5167/uzh-147652	text	January 2017
Subsea tunnel reinforced sprayed concrete subjected to deterioration harbours distinct microbial communities Karačić, Sabina; Wilén, Britt-Marie; Suarez, Carolina Taylor & Francis https://doi.org/10.6084/m9.figshare.7700483	text	January 2019
Subsea tunnel reinforced sprayed concrete subjected to deterioration harbours distinct microbial communities Karačić, Sabina; Wilén, Britt-Marie; Suarez, Carolina Taylor & Francis https://doi.org/10.6084/m9.figshare.7700483.v1	text	January 2019
Multistability and regime shifts in microbial communities explained by competition for essential nutrients Dubinkina, Veronika; Fridman, Yulia; Pandey, Parth Pratim eLife, Vol. 8 https://doi.org/10.7554/elife.49720	journal	November 2019

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