Microbial evolution and population genomics in a changing ocean (MINIME)

The global ocean harbours an astronomical number of microbes that have a fundamental role in the global biogeochemical cycles that guarantee the functioning of the Earth system. During the last decade, a plethora of omics approaches coupled to global oceanographic campaigns started to unveil the magnitude of the functional and taxonomic diversity of global-ocean microbes. Yet, the diversity of microbes at the population level, that is, the variation normally found among genomes belonging to the same species, has remained virtually unexplored.
Understanding this fine-grained “population genomic” diversity is fundamental, as it can unveil variation associated to differential niche adaptation that could be crucial in order to understand ecosystem function and community reactions to climate change. Furthermore, this population genomic diversity can help us understanding the processes of evolution at short timescales (months, years, decades). This is especially relevant in microbes, as their massive populations sizes and fast reproductive rates can allow them to evolve faster that animals and plants. Overall, comprehending the magnitude of the population genomic diversity in microbes as well as the evolution of their populations over short timescales represent two fundamental challenges for microbiology, evolutionary biology, biological oceanography and global change research.
This project, MINIME, addresses these two challenges by 1) investigating the population genomic diversity of microbial strains over 12 years in two coastal time series in the Mediterranean Sea using metagenomics and contrasting the results against the global ocean using data from campaigns such as Malaspina and TARA Oceans, 2) Analysing evolutionary processes occurring over 12 years using the DNA collected in both time series as an evolutionary record, 3) Examining experimentally the fine-grained evolutionary response of marine microbes to main global change stressors in the ocean (increased temperature and C0concentrations).
MINIME is divided into four “Research Streams”: 1) Population genomics, 2) Cross-species genomics, 3) Microbial evolution in the ocean, & 4) Evolution of microbes in a changing ocean. MINIME takes advantage of a unique juncture characterized by a) having access to two of the longest marine metagenomic time-series to date, b) having access to global-ocean metagenomic data, & c) new omics and bioinformatic approaches as well as high performance computing. MINIME will move forward the research frontier in ocean microbiology by exploring topics that are considered of high scientific interest and potentially high societal impact: the microdiversity of wild microbes, their evolution during short timescales (months, years, decades) and their response to global change. Understanding the genomic diversity of wild microbes in terms of existing diversity and evolution of new diversity can provide answers on whether or not microbial populations harbour enough genetic variation to be resistant to global change stressors and also, on whether global change may generate changes in the structure of microbial assemblages that could impact ocean ecosystem function. Given the large amount of ecosystem services that microbes provide to our society, it is fundamental to start comprehending how susceptible they are to global change.

Financed by the Spanish Agencia Estatal de Investigación: PID2019-105775RB-I00
PI: Ramiro Logares