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 favouring the accumulation of diversity (as predicted by DBD). However, as niches become increasingly filled, diversity hits a plateau (as predicted by EC).
Highlights
The majority of the genetic diversity on Earth is encoded by microbes (Hug et al, 2016; Lapierre and Gogarten, 2009; Tara Oceans coordinators et al, 2015) and the functioning of all Earth’s ecosystems is reliant on diverse microbial communities (Falkowski et al, 2008)
We used generalized linear mixed models (GLMMs) to estimate the diversity slope at each taxonomic level in the Earth Microbiome Project (EMP) data, which revealed a tendency towards positive slopes with significant variation explained by the random effects of lineage, environment, and their interaction (Table 1, Figure 2, Figure 2—figure supplement 1–16, Supplementary file 1 Section 1)
Using ~10 million individual marker sequences from the EMP, we demonstrate an overall trend for diversity in focal lineages to be positively associated with overall community diversity, albeit with significant variation across lineages and environments
Summary
The majority of the genetic diversity on Earth is encoded by microbes (Hug et al, 2016; Lapierre and Gogarten, 2009; Tara Oceans coordinators et al, 2015) and the functioning of all Earth’s ecosystems is reliant on diverse microbial communities (Falkowski et al, 2008). In an early study of 49 animal (vertebrate and invertebrate) community samples, Elton, 1946 plotted the number of species versus the number of genera and observed a ~ 1:1 ratio in each individual sample, but a ~ 4:1 ratio when all samples were pooled. He took this observation as evidence for competitive exclusion preventing related species, more likely to overlap in niche space, to co-exist.
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