Understanding the ecological processes affecting freshwater sources is of capital importance in order to secure a sufficient supply of high quality water. Microorganisms hold a key position in freshwater ecosystems due to their ability to cycle and transform most bioactive compounds, but also in their trophic coupling to eukaryote predators. Both processes have a great impact on water quality, which has fueled a renewed interest in elucidating the spatio-temporal dynamics of the involved microbial taxa.
Our ability to study microbial communities has steadily increased over the last decades. Recently, we have become capable of distinguishing between closely related bacteria, even those belonging to the same species. This has revealed that freshwater bacterial species are actually composed of several subspecies or ecotypes, each with different optimum growth conditions, which replace one another as the environment changes. This intra-species diversity ensures that the species remains present under different environmental conditions, presumably enhancing the stability of the whole ecosystem.
The nature of this intra-species diversity is however unclear. Microbial species are difficult to define, as microorganisms can exchange genetic material via horizontal gene transfer. Because of this, some adaptive genes may not be exclusive of a single bacteria, but instead distributed across a common gene pool. Thus, each ecotype might not actually be a single entity, but a myriad of different bacteria all carrying the adaptive gene while differing otherwise. How are microbial species organized internally? What are the drivers of their diversification? Answering these questions could have large implications in the way we understand microbial species and ecosystems.
The ARAMIS project (Adaptive Radiation in Aquatic MIcrobial Species) aims to advance our understanding on the nature of microbial species, their evolution, and the ecological consequences of intra-species diversity. To achieve this, we collected genomic and metagenomic data from microbial communities in several lakes, and analyzed the internal dynamics of several cosmopolitan freshwater bacterial species through space, time and environmental gradients. We concluded that for some species ecotypes are indeed fuzzy, and that the drivers of intra-species diversification can operate at the gene level rather than the genome level. Furthermore, while this study focused on selection as the driver of intra-species diversification, we found an unexpected signal of dispersal limitation when comparing populations of the same species inhabiting geographically distant lakes.
