The role of the microbiome in individual and community adaptation

Most eukaryotes live in close interaction with microorganisms (the microbiome) and together they form a meta-organism in which natural selection occurs (hologenome theory of evolution). When in association with hosts, the microbiome is involved in the development and regulation of the immune response. It also plays a role in disease protection and in controlling host nutrition, which might lead to changes in host behaviour. When free-living, microbes regulate biogeochemical cycles, recycling the nutrients essential for life on earth. Soils harbour the greatest diversity of microorganisms and the functioning of this microbiome, either as free-living microbial communities or in association with other soil organisms and plants, determines soil health.

Modes of adaptation
Directly linked to the hologenome theory of evolution, where the hologenome of the meta-organism (host + microbes) should be considered as the unit where natural selection occurs. Given the high microbial diversity, as well as the high plasticity and rates of evolution at the population level, the host can adapt much faster to changes in environmental condition simply by altering its microbiome. Similar responses are observed in soils, where the interaction between soil microbes and plants might be modulated in response to stress conditions. As the soil microbiome study is directed at ‘healthy’ soil functioning, it has direct connections with sustainable agricultural practices and thereby with the UG theme Sustainable Society.

Adaptive diversity and diversification
Bacterial symbionts (acting as commensalistic or mutualistic species) are recruited from the environmental species pool. For example, the bacteria that become endophytes in plants are recruited from the rhizosphere bacteria, which in turn are a subset of bulk soil. As these three environments impose very different demands on the bacteria involved, often requiring distinct metabolic adaptations this theme could prove to be a model for fast genetic adaptation (or even speciation) and for the evolution of symbiotic interactions as termite-protist, ruminant-gut bacteria, etc.

Architecture of adaptive systems
The microbiome theme has strong connections. The stability of the interactions is based on mutual benefit and the capability of the different species to maintain the interactions by keeping on providing the benefits for the ‘other’ species, or by ending the interaction by withholding the benefits or by treating the ‘other’ species as hostile.

Coordinator(s): Joanna Salles, Theo Elzenga