Genomic stasis over millions of years in subseafloor sediment

Abstract

One of the significant challenges in microbiology is to understand the extent and mechanisms of evolution within life beneath the surface of the Earth. The population bottleneck that microbes in deep marine sediment experience implies that mutational and population genetic forces could lead to higher levels of relaxed selection and an increase in pseudogenes. To investigate this hypothesis, a group of Thalassospira strains were isolated from subseafloor sediment that is 3 to 6 million years old, as reported by Orsi and colleagues in 2021. These isolates, representing lineages that have been buried for millions of years, offer an excellent opportunity to study the evolution of life beneath the seafloor over a long period. The existence of closely related strains from environments on the surface of the Earth enabled us to examine the impact of selection within each group. We discovered that isolates from beneath the seafloor show lineage-specific similarities to Thalassospira from the surface world, both in the overall intensity of selection on the genome and in the specific genes affected by mutation. We found no signs of increased relaxed selection or other notable genomic changes in the genomes of the Thalassospira isolates from beneath the seafloor, suggesting that these subseafloor isolates were awakened from a million-year near-stasis. The unique genomic characteristics of each Thalassospira lineage from beneath the seafloor must then reflect genetic changes that surface-inhabiting decendants acquired in the past 3–6 million years. Remarkably, Thalassospira lineages beneath the surface appear to have stably maintained their genomes in the midst of metabolic dormancy and extremely long generation times.