Abstract
Despite their discovery over 25 years ago, the Marine Group II Euryarchaea (MGII) have remained a difficult group of organisms to study, lacking cultured isolates and genome references. The MGII have been identified in marine samples from around the world and evidence supports a photoheterotrophic lifestyle combining phototrophy via proteorhodopsins with the remineralization of high molecular weight organic matter. Divided between two Orders, the MGII have distinct ecological patterns that are not understood based on the limited number of available genomes. Here, we present the comparative genomic analysis of 322 MGII genomes, providing the most detailed view of these mesophilic archaea to-date. This analysis identified 17 distinct Family level clades including nine clades that previously lacked reference genomes. The metabolic potential and ecological distribution of the MGII genera revealed distinct roles in the environment, identifying algal-saccharide-degrading coastal genera, protein-degrading oligotrophic surface ocean genera, and mesopelagic genera lacking proteorhodopsins common in all other families. This study redefines the MGII and provides an avenue for understanding the role these organisms play in the cycling of organic matter throughout the water column.