Genome size variation between pelagic and benthic communities across prokaryotic taxonomy and environmental gradients in the Baltic Sea

Microbial genome size can be used as a predictor to explain the ecology and metabolism of Bacteria and Archaea across major biomes. Despite their ecological significance, the contribution of microbial genome size to differences in metabolic potential of benthic and pelagic prokaryotes are poorly studied. Here, we investigated how taxonomy and microbial genome size varies between benthic and pelagic habitats across environmental gradients of the brackish Baltic Sea. We also explored the relationships between that variation, the environmental heterogeneity, and microbial functions in these habitats. By analyzing Baltic metagenomes and MAGs, we observe that pelagic brackish Bacteria and Archaea present smaller genome sizes on average than pelagic marine and freshwater prokaryotes. Moreover, we found that prokaryotic genome sizes in Baltic sediments (3.47 Mbp) are significantly bigger than in the water column (2.96 Mbp). These differences in genome size persisted in Bacteria from the phyla level to the order level. For pelagic prokaryotes, the smallest genomes coded for a higher number of module steps per Mbp than bigger genomes for most of the functions, such as aminoacid metabolism and central carbohydrate metabolism. However, we observed that nitrogen metabolism was almost absent in pelagic genomes and was mostly present in benthic genomes. Finally, we also show that Bacteria inhabiting Baltic sediments and water column not only differ in taxonomy, but also in their metabolic potential, such as the Wood-Ljungdahl pathway or presence of different hydrogenases. ### Competing Interest Statement The authors have declared no competing interest.