Evolutionary stasis and homogeneous selection structure microbial communities in the deep subseafloor sedimentary biosphere

The subseafloor biosphere, one of the Earth's largest and most stable microbial habitats, mainly consists of energy-limited sediments where microbial life persists over geological timescales. However, the mechanisms governing microbial community assembly and evolution under condition of extreme energy limitation remains unclear. Here, we analysed a 296 m sediment core off the Shimokita Peninsula using amplicon sequencing, metagenomics, and genome-resolved analyses from 31 depth intervals spanning ~480 kyr. The microbial community composition was governed primarily by homogeneous selection, consistent with persistent environmental uniformity during burial. Genome-resolved analyses of 224 high-quality metagenome-assembled genomes revealed highy conserved gene repertoires and uniformly low ratios of non-synonymous-to-synonymous substitutions, suggesting strong purifying selection with minimal genomic changes over this timescale. Our results indicate that evolutionary stasis is a pervasive feature of microbial life in deep subseafloor sediments, and propose a conceptual framework linking long-term environmental stability to genomic preservation in the Earth's most persistent biosphere.