The assembly and functions of microbial communities on complex substrates

Abstract

Microbes form diverse and complex communities to influence the health and function of all ecosystems on earth. However, key ecological and evolutionary processes that allow microbial communities to form and maintain their diversity, and how this diversity further affects ecosystem function, are largely underexplored. This is especially true for natural microbial communities that harbor large numbers of species whose interactions are often the result of long term evolutionary processes of co-occurring organisms. In this thesis, I make use of "common garden experiments" -- introducing varying microbial communities to the same environments -- to investigate how the assembly and functions of natural microbial communities are affected by the diversity of communities, as well as the chemical nature of substrates that they assemble on. In the first project, I present an experimental workflow that streamlines the generation of self-assembled microbial communities with a wide range of diversity, measurements of community function in "common gardens", followed by subsequent isolation of the most abundant taxa from these communities via dilution-to-extinction. This high-throughput workflow is applied to assess how interactions scale with organismal diversity to affect the function of microbial communities from the coastal ocean. In the second project, I use a combination of theoretical models and an ex vivo experimental framework to examine how the volume and content of gas produced by gut microbiota assembling on different prebiotic substrates ("gardens") are influenced by the chemical nature of the substrate and the composition of the gut microbiota itself. As a whole, this body of work represents a small step towards finding common organization principles in microbial community assembly and their functional consequences.