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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| Format: | Article |
| Language: | English |
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MDPI AG
2020-05-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/8/6/798 |
| _version_ | 1797566938102104064 |
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| author | Xiu Jia Francisco Dini-Andreote Joana Falcão Salles |
| author_facet | Xiu Jia Francisco Dini-Andreote Joana Falcão Salles |
| author_sort | Xiu Jia |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-10T19:34:31Z |
| format | Article |
| id | doaj.art-3c5d3c38a05c49f09f0af0678b5a6e81 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-10T19:34:31Z |
| publishDate | 2020-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-3c5d3c38a05c49f09f0af0678b5a6e812023-11-20T01:47:58ZengMDPI AGMicroorganisms2076-26072020-05-018679810.3390/microorganisms8060798Comparing the Influence of Assembly Processes Governing Bacterial Community Succession Based on DNA and RNA DataXiu Jia0Francisco Dini-Andreote1Joana Falcão Salles2Microbial 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 NetherlandsDepartment of Plant Science, The Pennsylvania State University, University Park, PA 16802, USAMicrobial 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 NetherlandsQuantifying 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.https://www.mdpi.com/2076-2607/8/6/79816S rRNA genecommunity turnoverecological modelingselectiondispersaldrift |
| spellingShingle | Xiu Jia Francisco Dini-Andreote Joana Falcão Salles Comparing the Influence of Assembly Processes Governing Bacterial Community Succession Based on DNA and RNA Data Microorganisms 16S rRNA gene community turnover ecological modeling selection dispersal drift |
| 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 | 16S rRNA gene community turnover ecological modeling selection dispersal drift |
| url | https://www.mdpi.com/2076-2607/8/6/798 |
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