The recognition that all macroorganisms live in symbiotic association with microbial communities has opened up a new field in biology. While most attention in the first CRC 1182 funding phase was placed on bacteria as members of the microbiome, we suggest here that selfish genetic elements (SGEs), including phages, are major players in shaping microbial community composition and function.
PI Rainey (C4.1) has performed a year-long experiment that involved perturbation of a primary evolutionary process (recombination mediated by lateral gene transfer) combined with metagenome sequencing and measures of community function. The results have provided direct insight into the impact of SGEs on the eco-evolutionary dynamics in microbial communities and associated effects on metabolism and function.
PI Lachnit (C4.2) has explored “phage-therapy” in Hydra. A switch from oligotrophic to eutrophic environmental conditions causes changes in bacterial community composition and expression of a disease phenotype in Hydra, which can be rescued by the addition of phages.
PI Hentschel (C4.3) has taken a viromics approach to characterize the diversity and specificity of phages in marine sponge species. Using a nested sampling design, it was shown that each sponge individual of the four species investigated harbours its own unique virome.
From these and other studies, it has become clear that phages are integral and specific elements of animal microbiomes that may hold yet to be identified regulatory roles for microbiome composition and function.
In the second funding phase, PIs Rainey, Lachnit, and Hentschel will join forces to assess how phages and other SGEs affect eco-evolutionary dynamics within metaorganisms and the resulting consequences on metabolism and life-history characteristics. We will explore two major goals which are
(i) the role of SGEs as master regulators of microbial community composition and function, and
(ii), the role of SGEs as promoters of novel microbial functions.
A carefully co-designed experiment, hereafter termed the “Metaorganism Evolution Experiment” (MEE) will be performed to obtain high resolution, time-resolved metagenomics data linking the dynamics of genes to metaorganism function. Moreover, we will test whether the experimentally altered microbiomes confer a fitness advantage to the metaorganism. The generality and also the specific details of the effects are dissected across three distinct metaorganism models: C. elegans (nematode), Hydra vulgaris (cnidarian) and Halichondria panicea (sponge).
Our studies will contribute to the CRC 1182 by moving phages and other SGEs to the forefront of research and by combining an eco-evolutionary approach with metagenomic analyses to characterize the evolution of metaorganism function.