Stochastic Community Assembly: Does It Matter in Microbial Ecology?

Microbiology and Molecular Biology Reviews, Journal Year: 2017, Volume and Issue: 81(4)

Published: Oct. 12, 2017

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

Language: Английский

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Disentangling mechanisms that mediate the balance between stochastic and deterministic processes in microbial succession

Proceedings of the National Academy of Sciences, Journal Year: 2015, Volume and Issue: 112(11)

Published: March 2, 2015

Significance Across ecology, and particularly within microbial there is limited understanding of the mechanisms governing relative influences stochastic deterministic processes. Filling this knowledge gap a major challenge that requires development novel conceptual paradigms, experiments, ecological models. Here we ( i ) present model couples stochastic/deterministic balance to primary secondary succession, thereby integrating previously isolated domains; ii evaluate over 105 years ecosystem development, revealing systematic shift in type strength selection; iii couple empirical data with new simulation elucidate underlying characterize their scale dependency. The insights framework provided here represent nexus for cross-system integration.

Language: Английский

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microeco: an R package for data mining in microbial community ecology

FEMS Microbiology Ecology, Journal Year: 2020, Volume and Issue: 97(2)

Published: Dec. 15, 2020

A large amount of sequencing data is produced in microbial community ecology studies using the high-throughput technique, especially amplicon-sequencing-based data. After conducting initial bioinformatic analysis amplicon data, performing subsequent statistics and mining based on operational taxonomic unit assignment tables still complicated time-consuming. To address this problem, we present an integrated R package-'microeco' as pipeline for treating environmental This package was developed R6 class system combines a series commonly used advanced approaches research. The includes classes preprocessing, taxa abundance plotting, venn diagram, alpha diversity analysis, beta differential test indicator taxon null model network functional analysis. Each designed to provide set that can be easily accessible users. Compared with other packages field, microeco fast, flexible modularized use provides powerful convenient tools researchers. installed from CRAN (The Comprehensive Archive Network) or github (https://github.com/ChiLiubio/microeco).

Language: Английский

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A quantitative framework reveals ecological drivers of grassland microbial community assembly in response to warming

Nature Communications, Journal Year: 2020, Volume and Issue: 11(1)

Published: Sept. 18, 2020

Abstract Unraveling the drivers controlling community assembly is a central issue in ecology. Although it generally accepted that selection, dispersal, diversification and drift are major processes, defining their relative importance very challenging. Here, we present framework to quantitatively infer mechanisms by phylogenetic bin-based null model analysis (iCAMP). iCAMP shows high accuracy (0.93–0.99), precision (0.80–0.94), sensitivity (0.82–0.94), specificity (0.95–0.98) on simulated communities, which 10–160% higher than those from entire community-based approach. Application of grassland microbial communities response experimental warming reveals dominant roles homogeneous selection (38%) ‘drift’ (59%). Interestingly, decreases over time, enhances primarily imposed Bacillales. In addition, has correlations with drought plant productivity under control. provides an effective robust tool quantify should also be useful for animal

Language: Английский

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Soil pH mediates the balance between stochastic and deterministic assembly of bacteria

The ISME Journal, Journal Year: 2018, Volume and Issue: 12(4), P. 1072 - 1083

Published: March 1, 2018

Little is known about the factors affecting relative influences of stochastic and deterministic processes that govern assembly microbial communities in successional soils. Here, we conducted a meta-analysis bacterial using six different soil datasets distributed across regions. Different relationships between pH age these allowed us to separate (i.e., time) from pH. We found extreme acidic or alkaline conditions lead phylogenetically more clustered through processes, whereas close neutral less with stochasticity. suggest influence pH, rather than age, main driving force producing trends phylogenetic bacteria, also balance along Given had much stronger association community did evaluated whether inferred was maintained when studying globally samples collected without regard for age. This dataset confirmed strong suggesting on occurs globally. Extreme likely exert stringent limits survival fitness, imposing selective pressures ecological evolutionary time. Taken together, findings degree which vs. shape consequence

Language: Английский

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Balance between community assembly processes mediates species coexistence in agricultural soil microbiomes across eastern China

The ISME Journal, Journal Year: 2019, Volume and Issue: 14(1), P. 202 - 216

Published: Oct. 14, 2019

Language: Английский

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A general framework for quantitatively assessing ecological stochasticity

Proceedings of the National Academy of Sciences, Journal Year: 2019, Volume and Issue: 116(34), P. 16892 - 16898

Published: Aug. 7, 2019

Understanding the community assembly mechanisms controlling biodiversity patterns is a central issue in ecology. Although it generally accepted that both deterministic and stochastic processes play important roles assembly, quantifying their relative importance challenging. Here we propose general mathematical framework to quantify ecological stochasticity under different situations which factors drive communities more similar or dissimilar than null expectation. An index, normalized ratio (NST), was developed with 50% as boundary point between (<50%) (>50%) assembly. NST tested simulated by considering abiotic filtering, competition, environmental noise, spatial scales. All approaches showed limited performance at large scales very high noise. However, all of other scenarios, accuracy (0.90 1.00) precision (0.91 0.99), averages 0.37 higher (0.1 0.7) 0.33 (0.0 1.8) previous approaches. also applied estimate succession groundwater microbial response organic carbon (vegetable oil) injection. Our results shifted from (NST = 21%) 70%) right after input. As vegetable oil consumed, gradually returned be 27%). In addition, our demonstrated model algorithms similarity metrics had strong effects on stochasticity.

Language: Английский

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Estimating and mapping ecological processes influencing microbial community assembly

Frontiers in Microbiology, Journal Year: 2015, Volume and Issue: 6

Published: May 1, 2015

Ecological community assembly is governed by a combination of (i) selection resulting from among-taxa differences in performance; (ii) dispersal organismal movement; and (iii) ecological drift stochastic changes population sizes. The relative importance nature these processes can vary across environments. Selection be homogeneous or variable, while rate, we conceptualize extreme rates as two categories; limitation results limited exchange organisms among communities, homogenizing high levels organism exchange. To estimate the influence spatial variation each process extend recently developed statistical framework, use simulation model to evaluate accuracy extended framework examine subsurface microbial communities over geologic formations. For degree which it influenced selection, variable limitation, dispersal. Our analyses revealed that influences substantially even within formation. We further identify environmental features associated with process, allowed mapping ecological-process-influences. maps provide new lens through systems understood; system investigated here they was rate at redox conditions change depth.

Language: Английский

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Global diversity and biogeography of bacterial communities in wastewater treatment plants

Nature Microbiology, Journal Year: 2019, Volume and Issue: 4(7), P. 1183 - 1195

Published: May 13, 2019

Language: Английский

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The Gut Microbiota of Rural Papua New Guineans: Composition, Diversity Patterns, and Ecological Processes

Cell Reports, Journal Year: 2015, Volume and Issue: 11(4), P. 527 - 538

Published: April 1, 2015

Although recent research revealed an impact of westernization on diversity and composition the human gut microbiota, exact consequences metacommunity characteristics are insufficiently understood, underlying ecological mechanisms have not been elucidated. Here, we compared fecal microbiota adults from two non-industrialized regions in Papua New Guinea (PNG) with that United States (US) residents. Guineans harbor communities greater bacterial diversity, lower inter-individual variation, vastly different abundance profiles, lineages undetectable US A quantification processes govern community assembly identified dispersal as dominant process shapes microbiome PNG but US. These findings suggest alterations detected industrialized societies might arise modern lifestyle factors limiting dispersal, which has implications for health development strategies aimed to redress westernization.

Language: Английский

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