Genetic exchange shapes ultra-small Patescibacteria metabolic capacities in the terrestrial subsurface

Genomic fluidity and diversity in bacteria are mainly governed by horizontal gene transfer (HGT), leading to a variety of genome structures and physiological diversity. The predominantly uncultivated Patescibacteria comprise highly diverse bacteria that consistently exhibit small cell and genome sizes. Despite strong pressures to reduce genetic content, we predict that these ultra-small bacteria use HGT to the same extent as other bacteria and that HGT may help facilitate recovery and maintenance of critical metabolic functions, niche exploitation, and putative symbiont-host interactions. Here, we determine the contribution of gene exchange to the evolution and diversification of Patescibacteria, despite the constraints of streamlining. We provide evidence of gene gains in Patescibacteria genomes recovered from aquifer environments and describe the large extent to which ultra-small bacterial genomes are subjected to HGT. Results suggest distinct metabolic functions acquired by Patescibacteria compared to general groundwater communities, suggesting specific evolutionary pressures on gene transfer dynamics occurring in ultra-small prokaryotes.