Genomically and ecologically cohesive subspecies as biologically meaningful units in the global ocean microbiome

Abstract Microbial diversity is organised into operationally defined species. However, it remains unclear whether these, or finer-scale groups represent biologically meaningful units in natural communities. Here, we implement a scalable, cultivation-independent framework to identify 724 genomically discrete and ecologically cohesive subspecies across 270 species in the global ocean microbiome. Their diversification is underpinned by gene-specific, nucleotide-level selection on the core genomic backbone and by variable restructuring of gene content, both of which proceed in a subspecies-specific manner. In over half of the species tested, subspecies were significantly associated with distinct environmental conditions, most frequently temperature. This coupling of genomic discreteness and ecological cohesiveness positions these subspecies as biologically meaningful units, a fundamental level at which ecological and evolutionary processes jointly drive divergence and structure microbial diversity in the oceans.