Complete genome sequence of a urea-degrading Microbacterium sp. HM-570 reveals its deep-sea symbiotic lifestyle within sponge from the Western Pacific.

Microbacterium sp. HM-570 (16S rDNA sequence similarity 99.03% with the closest species Microbacterium lacus A5E-52T) is a sponge-associated bacterium isolated from deep-sea sponge, collected at the Hakugan seamount in Western Pacific. Here we report the complete genome sequence of strain HM-570, which consists of a single circular chromosome without no detectable plasmids. Genomic annotations revealed genetic features consistent with deep-sea stress tolerance and host-associated lifestyle, including genes putatively involved in stress responses and heavy-metal resistance, as well as multiple secondary-metabolite biosynthetic gene clusters. The genome also encodes several vitamin-biosynthesis pathways (e.g., riboflavin and folate) which may support the sponge host by supplementing essential vitamins and a set of eukaryotic-like repeat proteins that may be involved in host association, such as attachment and immune modulation. In addition, HM-570 carries genes associated with urea degradation (ureABC, ureDFG, urtABCDE, uca and atzF), and growth-based experiment confirmed urea degradation in vitro. Together, these data suggest that strain HM-570 represents a genomically distinct Microbacterium lineage with potential functional roles in nutrient cycling and stress tolerance within deep-sea sponge-associated microbial communities.