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

Summary Small bacterial and archaeal genomes provide insights into the minimal requirements for life 1 and seem to be widespread on the microbial phylogenetic tree 2 . We know that evolutionary processes, mainly selection and drift, can result in microbial genome reduction 3,4 . However, we do not know the precise environmental pressures that constrain genome size in free-living microorganisms. A study including isolates 5 has shown that bacteria with high optimum growth temperatures, including thermophiles, often have small genomes 6 . It is unclear how well this relationship may extend generally to microorganisms in nature 7,8 , and in particular to those microbes inhabiting complex and highly variable environments like soil 3,6,9 . To understand the genomic traits of thermally-adapted microorganisms, here we investigated bacterial and archaeal metagenomes from a 45°C gradient of temperate-to-thermal soils overlying the ongoing Centralia, Pennsylvania (USA) coal seam fire. There was a strong relationship between average genome size and temperature: hot soils had small genomes relative to ambient soils (Pearson’s r = −0.910, p < 0.001). There was also an inverse relationship between soil temperature and cell size (Pearson’s r = −0.65, p = 0.021), providing evidence that cell and genome size in the wild are together constrained by temperature. Notably, hot soils had different community structures than ambient soils, implicating ecological selection for thermo-tolerant cells that had small genomes, rather than contemporary genome streamlining within the local populations. Hot soils notably lacked genes for described two-component regulatory systems and antimicrobial production and resistance. Our work provides field evidence for the inverse relationship between microbial genome size and temperature requirements in a diverse, free-living community over a wide range of temperatures that support microbial life. Our findings demonstrate that ecological selection for thermophiles and thermo-tolerant microorganisms can result in smaller average genome sizes in situ , possibly because they have small genomes reminiscent of a more ancestral state.