Microbes are essential components of the world's oceans, playing crucial roles in biogeochemical cycles, food webs, and global climate. Understanding microbial populations is fundamental for comprehending microbes' adaptations to different niches and their role in the ecosystem. Despite the importance of microbial population genomics, this field is still in its infancy. Here, we investigate the population genomics of microbial species retrieved from short- and long-read marine metagenomes. Firstly, we investigated the genomic differentiation of 495 abundant prokaryotic short-read metagenome-assembled genomes (MAGs) over 12 and 7 years in two neighboring stations in the Mediterranean Sea and across the global surface ocean. The Single Nucleotide Variants (SNVs) analysis indicated a stronger population differentiation at large spatial scales, potentially modulated by temperature and salinity, compared to long temporal scales. Population structure was also detected in both time series, with evidence of positive selection in diverse genes. Secondly, long-read metagenomes from the Mediterranean Sea allowed us to recover MAGs of higher quality than short-read counterparts, some of them being single-contig complete genomes. Specific long-read MAGs featured clear population structure linked to different seasons. Adaptive genes were identified in different species, representing the adaptation of diverse populations to varying environmental conditions. Our work contributes to a better understanding of the spatiotemporal structure of marine microbial populations

ASLO Aquatic Sciences Meeting, Resilience and Recovery in Aquatic Systems, 4-9 June 2023, Palma de Mallorca, Spain