Does diversity beget diversity in microbiomes

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. Two contrasting hypotheses have been put forward to explain how species interactions could influence diversity. 9Ecological Controls9 (EC) predicts a negative relationship, where the evolution or migration of novel types is constrained as available niches become filled. In contrast, 9Diversity Begets Diversity9 (DBD) predicts a positive relationship, with existing diversity promoting the accumulation of further diversity via niche construction and other interactions. Using the Earth Microbiome Project, the largest standardized survey of global biodiversity to date, we provide evidence that DBD is strongest in less diverse biomes, such as the animal gut, but weaker in more diverse biomes, such as soil, presumably because most available niches are filled. Also consistent with niche adaptation, resident genera that are strongly specialized for a particular environment show a stronger DBD relationship than do generalists or migrants from another environment. In contrast with the Black Queen Hypothesis that predicts a negative correlation between genome size and community metabolic interactions, we find that genera with larger genomes exhibit a stronger DBD response, which could be due to a higher potential for interactions and niche construction offered by more diverse gene repertoires. Our results highlight the importance of species interactions in shaping microbiome diversity, and the need to account for such interactions in the study of microbial genomes, physiology, and ecological function.