Unraveling mechanisms of microbial community assembly using naturally replicated microbiomes

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Microbial consortia fulfill important functions for human health, industrial biotechnology and global climate regulation. It is often believed that the species and functional composition of microbial communities is controlled by neutral as well as deterministic assembly processes. The proposed research aims at obtaining a systematic understanding of the relative impact of these processes depending on the taxonomic diversity of the community, the degree of functional specialization of individual taxa, and the scale of ecological organization. Specifically, it will test the hypotheses that(i) neutral processes are more important for more taxon-rich communities, whereas deterministic processes are more important for taxon-poor communities of the same size.(ii) neutral processes are more important for substrate generalists, whereas deterministic processes are more important for substrate specialists. (iii) neutral processes are more important within functional groups, whereas deterministic processes are more important between functional groups. To test these hypotheses the proposed research will make use of a unique system, microbial consortia that have recently been discovered within tiny water droplets at Pitch Lake, the largest natural oil seep of the world situated in Trinidad and Tobago. These microbiomes are ideal for the study of community assembly as they represent naturally replicated communities that have evolved for a long period in isolation and within a spatially and temporally homogeneous environment. The project will proceed by isolating and determining the taxonomic composition of 100 water droplet communities using amplicon sequencing of the 16S rRNA gene. Individual taxa will then be assigned to groups of similar ecological function based on their functional genes, which will be determined by sequencing the mini-metagenomes of several water droplets microbiomes using single-cell techniques. Finally, stochastic simulations will be applied to generate synthetic communities with neutral taxon and functional group patterns. This allows for a statistical comparison of neutral and observed data and for a discrimination between neutral and deterministic processes with respect to community size, substrate specialization and the level of ecological organization. The obtained insights will further advance our ability to predict and manage complex microbial communities.