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Article

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

1
Microbial Ecology Cluster, Genomics Research in Ecology and Evolution in Nature (GREEN), Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, 9747 AG Groningen, The Netherlands
2
Department of Plant Science, The Pennsylvania State University, University Park, PA 16802, USA
3
Huck Institute of Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
*
Authors to whom correspondence should be addressed.
Senior Author.
Microorganisms 2020, 8(6), 798; https://doi.org/10.3390/microorganisms8060798
Received: 11 March 2020 / Revised: 13 May 2020 / Accepted: 20 May 2020 / Published: 26 May 2020
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. View Full-Text
Keywords: 16S rRNA gene; community turnover; ecological modeling; selection; dispersal; drift 16S rRNA gene; community turnover; ecological modeling; selection; dispersal; drift
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MDPI and ACS Style

Jia, X.; Dini-Andreote, F.; Falcão Salles, J. Comparing the Influence of Assembly Processes Governing Bacterial Community Succession Based on DNA and RNA Data. Microorganisms 2020, 8, 798. https://doi.org/10.3390/microorganisms8060798

AMA Style

Jia X, Dini-Andreote F, Falcão Salles J. Comparing the Influence of Assembly Processes Governing Bacterial Community Succession Based on DNA and RNA Data. Microorganisms. 2020; 8(6):798. https://doi.org/10.3390/microorganisms8060798

Chicago/Turabian Style

Jia, Xiu, Francisco Dini-Andreote, and Joana Falcão Salles. 2020. "Comparing the Influence of Assembly Processes Governing Bacterial Community Succession Based on DNA and RNA Data" Microorganisms 8, no. 6: 798. https://doi.org/10.3390/microorganisms8060798

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