Diversity of marine microbes in a changing Mediterranean Sea

Unicellular microbes are fundamental players in the ecosystem functioning and biogeochemistry of the Mediterranean Sea. Due to the unique hydrological, geological and geomorphological features, the basin is a biodiversity hot-spot of multicellular organisms, and likewise can harbor peculiar assemblages of microbes if compared to other oceans. However, we still know little about the diversity of Mediterranean microbes, due to past methodological constraints only recently conquerable with next generation sequencing of DNA and metagenomics. This review aims at summarizing the knowledge on microbial diversity in the basin, by focusing on prokaryotes (bacteria and archaea) in pelagic and benthic habitats. Richness of bacterioplankton and archaeoplankton assemblages is high in surface and deep waters, and shows consistent horizontal and vertical patterns. Members of the SAR11 clade of Alphaproteobacteria dominate surface bacterial assemblages, followed by other Alphaproteobacteria, Cyanobacteria, Bacteroidetes and uncultured Gammaproteobacteria, with a different contribution according to distance from land and human impact. Meso- and bathypelagic bacterial assemblages are conversely dominated by Gammaproteobacteria, the most representative being the Mediterranean Alteromonas macleodii “deep-ecotype”, followed by other taxa such as Delta- and Betaproteobacteria, Acidobacteria, Planctomycetes and Chloroflexi. Archaeoplankton richness is lower, and assemblages differ between water layers, with higher abundance and diversity of Euryarchaeota in the surface, and of Crenarchaeota Marine Group (MG) I, among which specific Mediterranean ecotypes, in deeper layers. In the sediments, abundance and richness of bacteria are always higher than archaea. Surface benthic bacterial assemblages are dominated by Gamma- and Deltaproteobacteria, followed by Acidobacteria and Planctomycetes, and display community composition changes between coastal and deep-sea settings. Benthic archaea show dominance of Crenarchaeota MGI in deep-sea sediments, but their phylogenetic diversity is still poorly known. Pelagic and benthic assemblages include a large proportion of rare taxa, the contribution of which to the ecosystem functioning is unknown. Continuing the exploration of Mediterranean microbes will provide a “next generation” body of knowledge, which needs to be put into the context of climate change and the anthropogenic pressure affecting this highly vulnerable basin.