Periodic Reporting for period 2 - MicroEcoEvol (Ecological and evolutionary forces shaping microbial diversity in freshwater blooms)
Reporting period: 2017-06-01 to 2018-05-31
In this project we attempted to (i) characterize the evolutionary dynamics of natural Microcystis populations by investigating both ecological and evolutionary responses to selective pressure and (ii) dissect the impact of the different selective pressures (environmental and biological factors) that may shape Microcystis populations. The aims of this project will be achieved using a unique multidisciplinary approach mixing ecology and evolution, and combining observations from natural time-courses in lakes, in situ experiments in microcosms within lakes, and in vitro experiments in the lab. This project will be the first to comprehensively and simultaneously quantify both ecological and evolutionary responses of a bacterial population in real time, and in a natural setting.
Two cyanobacterial genera, Microcystis (M) and Dolichospermum (D), were frequently observed simultaneously (during bloom events in lake Champlain) and might have partially overlapping niches. In a second study, we determined the intra-genus variability and the ecological niche of the different strains. Within each genus, we identified strains differentially associated with specific environmental conditions. In general, we found that niche similarity between strains (as measured by co-occurrence over time) declined with genetic distance. This pattern is consistent with habitat filtering – in which closely related taxa are ecologically similar, and therefore tend to co-occur under similar environmental conditions. However, in contrast with this general pattern, we found that similarity in certain niche dimensions (notably nutrient) did not decline linearly with genetic distance, and instead showed a complex polynomial relationship. This observation suggests the importance of processes other than habitat filtering – such as competition between closely related taxa, or convergent trait evolution in distantly related taxa – in shaping particular traits in microbial communities (Tromas et al., 2018).
In a third study, we analyzed 76 Microcystis genomes from cultures to investigate the Microcystis population structure; i.e whether Microcystis consists of a single recombining population, or whether there are ecologically-specialized sub-populations. We found that indeed several genomic clusters correspond to named species and monophyletic groups whereas others are paraphyletic, distributed across genomic clusters. We also observed a higher recombination rate within clusters than between clusters supporting the species coherence of monophyletic groups. This work is in progress.
In a fourth study, we analyzed the Microcystis /cyanophage infection dynamic and the role of phages (virus infecting bacteria) in terminating blooms using CRISPR array information. In this analysis, based on 62 metagenomic samples between 2006 and 2016, we found evidence in arms race dynamic between phages, especially during the intensive sampling (2015-2016) where samples were taken every 1-3 days. However, the overall pattern showed that Microcystis population remains abundant over time, which could be explained by the maintenance of a highly diverse CRISPR arrays within Microcystis genomes. This work is in progress.
In this project, we used a reverse ecology approach, i.e extracting genomic information from natural environments and obtain novel comprehension of an organism’s ecology. We improved our understanding of a complex freshwater microbial community. We used for example the microbial genomic information with machine learning approaches to develop predictive tools and define cyanobacterial sub-population ecological niches. Finally, this project lead to a better understanding of Microcystis population structure and cyanobacterial predators (bacteria and phages), leading to a better understanding of how these predators impact bloom termination.