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Nexus of Stochastic and Deterministic Processes on Microbial Community Assembly in Biological Systems

Microbial community assembly in engineered biological systems is often simultaneously influenced by stochastic and deterministic processes, and the nexus of these two mechanisms remains to be further investigated. Here, three lab-scale activated sludge reactors were seeded with identical inoculum an...

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Autores principales: Yuan, Heyang, Mei, Ran, Liao, Junhui, Liu, Wen-Tso
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6621641/
https://www.ncbi.nlm.nih.gov/pubmed/31333629
http://dx.doi.org/10.3389/fmicb.2019.01536
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author Yuan, Heyang
Mei, Ran
Liao, Junhui
Liu, Wen-Tso
author_facet Yuan, Heyang
Mei, Ran
Liao, Junhui
Liu, Wen-Tso
author_sort Yuan, Heyang
collection PubMed
description Microbial community assembly in engineered biological systems is often simultaneously influenced by stochastic and deterministic processes, and the nexus of these two mechanisms remains to be further investigated. Here, three lab-scale activated sludge reactors were seeded with identical inoculum and operated in parallel under eight different sludge retention time (SRT) by sequentially reducing the SRT from 15 days to 1 day. Using 16S rRNA gene amplicon sequencing data, the microbial populations at the start-up (15-day SRT) and SRT-driven (≤10-day SRT) phases were observed to be noticeably different. Clustering results demonstrated ecological succession at the start-up phase with no consistent successional steps among the three reactors, suggesting that stochastic processes played an important role in the community assembly during primary succession. At the SRT-driven phase, the three reactors shared 31 core operational taxonomic units (OTUs). Putative primary acetate utilizers and secondary metabolizers were proposed based on K-means clustering, network and synchrony analysis. The shared core populations accounted for 65% of the total abundance, indicating that the microbial communities at the SRT-driven phase were shaped predominantly by deterministic processes. Sloan’s Neutral model and a null model analysis were performed to disentangle and quantify the relative influence of stochastic and deterministic processes on community assembly. The increased estimated migration rate in the neutral community model and the higher percentage of stochasticity in the null model implied that stochastic community assembly was intensified by strong deterministic factors. This was confirmed by the significantly different α- and β-diversity indices at SRTs shorter than 2 days and the observation that over half of the core OTUs were unshared or unsynchronized. Overall, this study provided quantitative insights into the nexus of stochastic and deterministic processes on microbial community assembly in a biological process.
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spelling pubmed-66216412019-07-22 Nexus of Stochastic and Deterministic Processes on Microbial Community Assembly in Biological Systems Yuan, Heyang Mei, Ran Liao, Junhui Liu, Wen-Tso Front Microbiol Microbiology Microbial community assembly in engineered biological systems is often simultaneously influenced by stochastic and deterministic processes, and the nexus of these two mechanisms remains to be further investigated. Here, three lab-scale activated sludge reactors were seeded with identical inoculum and operated in parallel under eight different sludge retention time (SRT) by sequentially reducing the SRT from 15 days to 1 day. Using 16S rRNA gene amplicon sequencing data, the microbial populations at the start-up (15-day SRT) and SRT-driven (≤10-day SRT) phases were observed to be noticeably different. Clustering results demonstrated ecological succession at the start-up phase with no consistent successional steps among the three reactors, suggesting that stochastic processes played an important role in the community assembly during primary succession. At the SRT-driven phase, the three reactors shared 31 core operational taxonomic units (OTUs). Putative primary acetate utilizers and secondary metabolizers were proposed based on K-means clustering, network and synchrony analysis. The shared core populations accounted for 65% of the total abundance, indicating that the microbial communities at the SRT-driven phase were shaped predominantly by deterministic processes. Sloan’s Neutral model and a null model analysis were performed to disentangle and quantify the relative influence of stochastic and deterministic processes on community assembly. The increased estimated migration rate in the neutral community model and the higher percentage of stochasticity in the null model implied that stochastic community assembly was intensified by strong deterministic factors. This was confirmed by the significantly different α- and β-diversity indices at SRTs shorter than 2 days and the observation that over half of the core OTUs were unshared or unsynchronized. Overall, this study provided quantitative insights into the nexus of stochastic and deterministic processes on microbial community assembly in a biological process. Frontiers Media S.A. 2019-07-04 /pmc/articles/PMC6621641/ /pubmed/31333629 http://dx.doi.org/10.3389/fmicb.2019.01536 Text en Copyright © 2019 Yuan, Mei, Liao and Liu. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Yuan, Heyang
Mei, Ran
Liao, Junhui
Liu, Wen-Tso
Nexus of Stochastic and Deterministic Processes on Microbial Community Assembly in Biological Systems
title Nexus of Stochastic and Deterministic Processes on Microbial Community Assembly in Biological Systems
title_full Nexus of Stochastic and Deterministic Processes on Microbial Community Assembly in Biological Systems
title_fullStr Nexus of Stochastic and Deterministic Processes on Microbial Community Assembly in Biological Systems
title_full_unstemmed Nexus of Stochastic and Deterministic Processes on Microbial Community Assembly in Biological Systems
title_short Nexus of Stochastic and Deterministic Processes on Microbial Community Assembly in Biological Systems
title_sort nexus of stochastic and deterministic processes on microbial community assembly in biological systems
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6621641/
https://www.ncbi.nlm.nih.gov/pubmed/31333629
http://dx.doi.org/10.3389/fmicb.2019.01536
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