Ecological selection for small microbial genomes along a temperate-to-thermal soil gradient

Abstract

Small bacterial and archaeal genomes provide insights into the minimal requirements for life¹ and are phylogenetically widespread². However, the precise environmental pressures that constrain genome size in free-living microorganisms are unknown. A study including isolates has shown that thermophiles and other bacteria with high optimum growth temperatures often have small genomes³. It is unclear whether this relationship extends generally to microorganisms in nature^4,5 and more specifically to microorganisms that inhabit complex and highly variable environments, such as soils^3,6,7. To understand the genomic traits of thermally adapted microorganisms, here we investigated metagenomes from a 45 °C gradient of temperate-to-thermal soils that lie over the ongoing Centralia, Pennsylvania (USA) coal-seam fire. We found that hot soils harboured distinct communities with small genomes and small cell sizes relative to those in ambient soils. Hot soils notably lacked genes that encode known two-component regulatory systems, and antimicrobial production and resistance genes. Our results provide field evidence for the inverse relationship between microbial genome size and temperature in a diverse, free-living community over a wide range of temperatures that support microbial life.