Microbiome community assembly in the gut: disentangling the role of priority effects, evolution and genotype-by-environment interactions using the water flea Daphnia magna as a model system

In the proposed PhD research, we will use the water flea Daphnia magna as a model system, and aim at obtaining insight into the community assembly of the microbiome and how it is impacted by evolution. The community assembly of the microbiome is the result of an interaction between the source community of free-living bacteria (further called “environmental source community”) and the features of the host accumulating bacteria via the uptake through filter-feeding. Evolution can interfere with gut microbiome assembly in at least three different ways, which we here want to study in separate work packages. First, we want to establish the role of the host genotype (cf. evolution of the host population) on the recruitment of bacteria from the environmental source community. Second, we also will quantify to what extent microbiome community assembly can be impacted by adaptation of the bacteria to the local conditions in the Daphnia gut, either through de novo mutations within specific lineages or lineage sorting among closely related lineages (which can also be viewed as “community dynamics”, given that in bacteria there is a continuum of largely independent lineages with varying relatedness). More specifically, we will study the degree to which evolution-mediated priority effects contribute to shaping the gut microbiome of Daphnia. And last, we will study how evolution of bacteria in response to global change stressors, either prior to colonization of the gut or in the gut itself, impacts the microbiome and host phenotype.