Cultivated Kapaibacteriales reveal contrasting lake and groundwater lifestyles built on shared metabolic dependencies

Microbial lineages occupying contrasting habitats offer an opportunity to examine how habitat-associated genomic diversification coexists with evolutionarily conserved metabolic traits. Here, we investigated this relationship in Kapaibacteriales, a globally distributed but poorly characterized bacterial group. We obtained 29 axenic isolates representing three families and nine novel species from lakes and groundwater, providing the first cultivated members of the order from non-thermal habitats. Global metagenomic profiling and comparative genomics revealed marked differences in ecological distributions and genomic architectures between lake and groundwater populations. Lake populations were widespread, recurrently enriched during summer, and had compact genomes. In contrast, groundwater populations were geographically restricted and had larger genomes enriched in genes for signal transduction, transcriptional regulation, and mobile genetic elements. Despite this divergence, both groups shared predicted deficiencies in the biosynthesis of multiple amino acids, vitamins, and respiratory cofactors, including quinones and heme. These findings indicate that greater coding capacity need not confer greater biosynthetic self-sufficiency, and that metabolic dependencies can persist through ecological diversification, with implications for cultivating abundant but uncultured aquatic lineages.