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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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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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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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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Temperature mediates continental-scale diversity of microbes in forest soils

Nature Communications, Journal Year: 2016, Volume and Issue: 7(1)

Published: July 5, 2016

Abstract Climate warming is increasingly leading to marked changes in plant and animal biodiversity, but it remains unclear how temperatures affect microbial particularly terrestrial soils. Here we show that, accordance with metabolic theory of ecology, taxonomic phylogenetic diversity soil bacteria, fungi nitrogen fixers are all better predicted by variation environmental temperature than pH. However, the rates turnover across global gradients substantially lower those recorded for trees animals, suggesting that plant, communities differential responses climate change. To best our knowledge, this first study demonstrating different groups has significantly other major taxa, which important implications assessing effects human-caused climate, land use factors.

Language: Английский

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High-Throughput Metagenomic Technologies for Complex Microbial Community Analysis: Open and Closed Formats

mBio, Journal Year: 2015, Volume and Issue: 6(1)

Published: Jan. 27, 2015

Understanding the structure, functions, activities and dynamics of microbial communities in natural environments is one grand challenges 21st century science. To address this challenge, over past decade, numerous technologies have been developed for interrogating communities, which some are amenable to exploratory work (e.g., high-throughput sequencing phenotypic screening) others depend on reference genes or genomes phylogenetic functional gene arrays). Here, we provide a critical review synthesis most commonly applied "open-format" "closed-format" detection technologies. We discuss their characteristics, advantages, disadvantages within context environmental applications focus analysis complex systems, such as those soils, diversity high few. In addition, crucial issues considerations associated with applying complementary molecular important ecological questions.

Language: Английский

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Metagenomics meets time series analysis: unraveling microbial community dynamics

Current Opinion in Microbiology, Journal Year: 2015, Volume and Issue: 25, P. 56 - 66

Published: May 22, 2015

Language: Английский

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Network succession reveals the importance of competition in response to emulsified vegetable oil amendment for uranium bioremediation

Environmental Microbiology, Journal Year: 2015, Volume and Issue: 18(1), P. 205 - 218

Published: July 14, 2015

Summary Discerning network interactions among different species/populations in microbial communities has evoked substantial interests recent years, but little information is available about temporal dynamics of response to environmental perturbations. Here, we modified the random matrix theory‐based approach discern succession groundwater emulsified vegetable oil ( EVO ) amendment for uranium bioremediation. Groundwater from one control and seven monitor wells were analysed with a functional gene array GeoChip 3.0), molecular ecological networks fMENs at time points reconstructed. Our results showed that dramatically altered by amendment. Dynamic resilient was evident: fairly simple initial stage (Day 0), increasingly complex middle period (Days 4, 17, 31), most Day 80, then decreasingly later (140–269 days). Unlike previous studies other habitats, negative predominated time‐series fMEN , suggesting strong competition species systems after injection. Particularly, several keystone sulfate‐reducing bacteria their neighbours. These provide mechanistic understanding decreased phylogenetic diversity during

Language: Английский

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