Evidence for extensive gene flow and Thermotoga subpopulations in subsurface and marine environments

Abstract

Oil reservoirs represent a nutrient-rich ecological niche of the deep biosphere. Although most oil reservoirs are occupied by microbial populations, when and how the microbes colonized these environments remains unanswered. To address this question, we compared 11 genomes of Thermotoga maritima-like hyperthermophilic bacteria from two environment types: subsurface oil reservoirs in the North Sea and Japan, and marine sites located in the Kuril Islands, Italy and the Azores. We complemented our genomes with Thermotoga DNA from publicly available subsurface metagenomes from North America and Australia. Our analysis revealed complex non-bifurcating evolutionary history of the isolates' genomes, suggesting high amounts of gene flow across all sampled locations, a conjecture supported by numerous recombination events. Genomes from the same type of environment tend to be more similar, and have exchanged more genes with each other than with geographically close isolates from different types of environments. Hence, Thermotoga populations of oil reservoirs do not appear isolated, a requirement of the 'burial and isolation' hypothesis, under which reservoir bacteria are descendants of the isolated communities buried with sediments that over time became oil reservoirs. Instead, our analysis supports a more complex view, where bacteria from subsurface and marine populations have been continuously migrating into the oil reservoirs and influencing their genetic composition. The Thermotoga spp. in the oil reservoirs in the North Sea and Japan probably entered the reservoirs shortly after they were formed. An Australian oil reservoir, on the other hand, was likely colonized very recently, perhaps during human reservoir development.

Comparative genomics and physiology of the genus Methanohalophilus, a prevalent methanogen in hydraulically fractured shale

“…The percentage of genes in the Methanohalophilus core genome is much lower than Thermotoga (>90% core genes, n = 11) , a bacterium that spans surface ( n = 4) and deeper ( n = 7) ecosystems (Nesbø et al, ). In fact, the relative abundance of genes in the core genome for Methanohalophilus is closer to Prochlorococcus , a highly abundant marine photosynthetic bacterial genus, with a core genome of about 50% ( n = 49) (Biller et al, ).…”

Two viruses, MCV1 and MCV2, which infect Marinitoga bacteria isolated from deep‐sea hydrothermal vents: functional and genomic analysis

“…In a recent study, it was shown that, for the hyperthermophilic Thermotogae , similarity of environment is more important for gene exchanges than the geographical proximity (Nesbø et al ., ). The authors compared 11 Thermotoga maritima ‐like genomes, isolated from two environment types (oil reservoirs and marine sites).…”

“…The authors compared 11 Thermotoga maritima ‐like genomes, isolated from two environment types (oil reservoirs and marine sites). They reported that the ‘ genomes from the same type of environment tended to be more similar, and exchanged more genes with each other than with geographically close isolates from different types of environments’ (Nesbø et al ., ). One likely vector for such exchanges could be viruses.…”

Insights into thermoadaptation and the evolution of mesophily from the bacterial phylum Thermotogae

“…For example, the archaeon Pyrococcus abyssi has a highly efficient DNA repair system that continuously repairs temperatureinduced DNA damage (Jolivet et al 2003). Very high levels of homologous recombination are observed in hyperthermophilic Thermotoga spp., where the ratio of nucleotide changes introduced by recombination relative to point mutation (r/m) is in the range 24-100 for genomes originating from geographically distant sites (Nesbø et al 2006a(Nesbø et al , 2015. This is in the upper range of values reported in a comparison of r/m across a large sample of mostly mesophilic Bacteria and Archaea (0.02-64), where values above 10 were interpreted as very high (Vos and Didelot 2009).…”