Widespread horizontal transfer and strong selection enhance microbial adaptation in Antarctic soils

Terrestrial Antarctica harbors compositionally diverse and functionally distinct microbial life. Yet the ecological and evolutionary processes enabling these communities to adapt to the polyextreme conditions of the continent remain largely unknown. Here, we address how horizontal gene transfer (HGT) and de novo mutations influence adaptation of microbial communities in 16 proglacial and mountainous Antarctic soils, from a combination of short- and long-read datasets. Phylogenetic reconciliation and mobile genetic element analysis of 676 metagenome-assembled genomes show that HGT events occur frequently within these microbial communities. While the transferred genes are distributed across diverse functional categories, those involved in energy metabolism are exchanged at relatively higher frequency. The genes for aerotrophy, i.e. the consumption of atmospheric trace gases to provide energy, carbon, and hydration, are among the most frequently and widely disseminated. Approximately a quarter of all carbon monoxide (CO) dehydrogenases and [NiFe]-hydrogenases that catalyze atmospheric CO and hydrogen (H ₂ ) oxidation are predicted to be horizontally acquired and are often closely associated with mobile genetic elements. In parallel, analysis of polymorphisms in protein-encoding genes suggests widespread purifying selection, demonstrated by a predominance of synonymous mutations. This selection is particularly intense for aerotrophy genes, providing further evidence that this process is critical for microbial survival in Antarctica. The genetic variation of hydrogenases is tightly associated with their predicted protein structures, with intense selection acting on critical sites that preserve their stability and function in Antarctic environments. Together, these findings show that previously unrecognised eco-evolutionary dynamics shape the composition and function of Antarctic desert microbial communities, and confirm aerotrophy is a strongly selected and horizontally disseminated trait.