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Comparing the Influence of Assembly Processes Governing Bacterial Community Succession Based on DNA and RNA Data

Quantifying which assembly processes structure microbiomes can assist prediction, manipulation, and engineering of community outcomes. However, the relative importance of these processes might depend on whether DNA or RNA are used, as they differ in stability. We hypothesized that RNA-inferred commu...

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Autores principales: Jia, Xiu, Dini-Andreote, Francisco, Falcão Salles, Joana
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7355735/
https://www.ncbi.nlm.nih.gov/pubmed/32466517
http://dx.doi.org/10.3390/microorganisms8060798
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author Jia, Xiu
Dini-Andreote, Francisco
Falcão Salles, Joana
author_facet Jia, Xiu
Dini-Andreote, Francisco
Falcão Salles, Joana
author_sort Jia, Xiu
collection PubMed
description Quantifying which assembly processes structure microbiomes can assist prediction, manipulation, and engineering of community outcomes. However, the relative importance of these processes might depend on whether DNA or RNA are used, as they differ in stability. We hypothesized that RNA-inferred community responses to (a)biotic fluctuations are faster than those inferred by DNA; the relative influence of variable selection is stronger in RNA-inferred communities (environmental factors are spatiotemporally heterogeneous), whereas homogeneous selection largely influences DNA-inferred communities (environmental filters are constant). To test these hypotheses, we characterized soil bacterial communities by sequencing both 16S rRNA amplicons from the extracted DNA and RNA transcripts across distinct stages of soil primary succession and quantified the relative influence of each assembly process using ecological null model analysis. Our results revealed that variations in α-diversity and temporal turnover were higher in RNA- than in DNA-inferred communities across successional stages, albeit there was a similar community composition; in line with our hypotheses, the assembly of RNA-inferred community was more closely associated with environmental variability (variable selection) than using the standard DNA-based approach, which was largely influenced by homogeneous selection. This study illustrates the need for benchmarking approaches to properly elucidate how community assembly processes structure microbial communities.
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spelling pubmed-73557352020-07-23 Comparing the Influence of Assembly Processes Governing Bacterial Community Succession Based on DNA and RNA Data Jia, Xiu Dini-Andreote, Francisco Falcão Salles, Joana Microorganisms Article Quantifying which assembly processes structure microbiomes can assist prediction, manipulation, and engineering of community outcomes. However, the relative importance of these processes might depend on whether DNA or RNA are used, as they differ in stability. We hypothesized that RNA-inferred community responses to (a)biotic fluctuations are faster than those inferred by DNA; the relative influence of variable selection is stronger in RNA-inferred communities (environmental factors are spatiotemporally heterogeneous), whereas homogeneous selection largely influences DNA-inferred communities (environmental filters are constant). To test these hypotheses, we characterized soil bacterial communities by sequencing both 16S rRNA amplicons from the extracted DNA and RNA transcripts across distinct stages of soil primary succession and quantified the relative influence of each assembly process using ecological null model analysis. Our results revealed that variations in α-diversity and temporal turnover were higher in RNA- than in DNA-inferred communities across successional stages, albeit there was a similar community composition; in line with our hypotheses, the assembly of RNA-inferred community was more closely associated with environmental variability (variable selection) than using the standard DNA-based approach, which was largely influenced by homogeneous selection. This study illustrates the need for benchmarking approaches to properly elucidate how community assembly processes structure microbial communities. MDPI 2020-05-26 /pmc/articles/PMC7355735/ /pubmed/32466517 http://dx.doi.org/10.3390/microorganisms8060798 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Jia, Xiu
Dini-Andreote, Francisco
Falcão Salles, Joana
Comparing the Influence of Assembly Processes Governing Bacterial Community Succession Based on DNA and RNA Data
title Comparing the Influence of Assembly Processes Governing Bacterial Community Succession Based on DNA and RNA Data
title_full Comparing the Influence of Assembly Processes Governing Bacterial Community Succession Based on DNA and RNA Data
title_fullStr Comparing the Influence of Assembly Processes Governing Bacterial Community Succession Based on DNA and RNA Data
title_full_unstemmed Comparing the Influence of Assembly Processes Governing Bacterial Community Succession Based on DNA and RNA Data
title_short Comparing the Influence of Assembly Processes Governing Bacterial Community Succession Based on DNA and RNA Data
title_sort comparing the influence of assembly processes governing bacterial community succession based on dna and rna data
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7355735/
https://www.ncbi.nlm.nih.gov/pubmed/32466517
http://dx.doi.org/10.3390/microorganisms8060798
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