title: 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.
authors.affiliation: 1] Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of Oslo, Blindern, Oslo, Norway [2] Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.
authors.forename: Camilla L
authors.initials: CL
authors.lastname: Nesbø
authors.affiliation: 1] Department of Cell Biology, Yale School of Medicine, Yale University, New Haven, CT, USA [2] Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA.
authors.forename: Kristen
authors.initials: K
authors.lastname: S Swithers
authors.affiliation: Department of Biology and Centre for Geobiology, University of Bergen, Bergen, Norway.
authors.forename: Håkon
authors.initials: H
authors.lastname: Dahle
authors.affiliation: Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of Oslo, Blindern, Oslo, Norway.
authors.forename: Thomas H A
authors.initials: TH
authors.lastname: Haverkamp
authors.affiliation: Department of Biology and Centre for Geobiology, University of Bergen, Bergen, Norway.
authors.forename: Nils-Kåre
authors.initials: NK
authors.lastname: Birkeland
authors.affiliation: Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Tatiana
authors.initials: T
authors.lastname: Sokolova
authors.affiliation: Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Ilya
authors.initials: I
authors.lastname: Kublanov
authors.affiliation: 1] Department of Biological Sciences, Dartmouth College, Hanover, NH, USA [2] Department of Computer Science, Dartmouth College, Hanover, NH, USA.
authors.forename: Olga
authors.initials: O
authors.lastname: Zhaxybayeva
mesh_terms: D001315:Australia; D005075:Biological Evolution; D004269:DNA, Bacterial / Q000235:genetics*; D051456:Gene Flow; D014644:Genetic Variation; D016680:Genome, Bacterial; D007558:Italy; D007564:Japan; D009656:North America; D009659:North Sea; D061329:Oil and Gas Fields / Q000382:microbiology*; D010578:Petroleum / Q000382:microbiology*; D020124:Thermotoga maritima / Q000145:classification* / Q000235:genetics*; D013997:Time Factors
chemical_list: D004269:DNA, Bacterial; D010578:Petroleum