Does diversity beget diversity in microbiomes?
Abstract
Microbes are embedded in complex communities where they engage in a wide array of intra- and inter-specific interactions. The extent to which these interactions drive or impede microbiome diversity is not well understood. Historically, two contrasting hypotheses have been suggested to explain how species interactions could influence diversity. 'Ecological Controls' (EC) predicts a negative relationship, where the evolution or migration of novel types is constrained as niches become filled. In contrast, 'Diversity Begets Diversity' (DBD) predicts a positive relationship, with existing diversity promoting the accumulation of further diversity via niche construction and other interactions. Using high-throughput amplicon sequencing data from the Earth Microbiome Project, we provide evidence that DBD is strongest in low-diversity biomes, but weaker in more diverse biomes, consistent with biotic interactions initially favoring the accumulation of diversity (as predicted by DBD). However, as niches become increasingly filled, diversity hits a plateau (as predicted by EC).
Data availability
All data is available from the Earth Microbiome Project (ftp.microbio.me), as detailed in the Methods. All computer code used for analysis are available at https://github.com/Naima16/dbd.git.
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Earth Microbiome Projectftp://ftp.microbio.me/emp/release1/otu_distributions/otu_summary.emp_deblur_90bp.subset_2k.rare_5000.tsv.
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Global Soil Datasetfigshare, 10.6084/m9.figshare.5611321.v3.
Article and author information
Author details
Funding
Natural Sciences and Engineering Research Council of Canada
- B. Jesse Shapiro
Canada Research Chairs
- B. Jesse Shapiro
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Detlef Weigel, Max Planck Institute for Developmental Biology, Germany
Publication history
- Received: May 18, 2020
- Accepted: November 19, 2020
- Accepted Manuscript published: November 20, 2020 (version 1)
- Version of Record published: December 22, 2020 (version 2)
- Version of Record updated: December 24, 2020 (version 3)
Copyright
© 2020, Madi et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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