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Vortsepneva E, Chevaldonné P, Klyukina A, Naduvaeva E, Todt C, Zhadan A, Tzetlin A, Kublanov I. Microbial associations of shallow-water Mediterranean marine cave Solenogastres (Mollusca). PeerJ 2022; 9:e12655. [PMID: 35003936 PMCID: PMC8684320 DOI: 10.7717/peerj.12655] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 11/29/2021] [Indexed: 12/26/2022] Open
Abstract
The first cave-dwelling Solenogastres—marine shell-less worm-like mollusks—were sampled from Mediterranean marine caves floor silt in the Marseille area. The mollusks were 1.5 mm in length, had a transparent body with shiny spicules and appear to represent a new Tegulaherpia species. Electron microscopy revealed a high number of microbial cells, located on the surface of the spicules as well as in the cuticle of Tegulaherpia sp. The observed microbial cells varied in morphology and were unequally distributed through the cuticle, reaching a highest density on the dorsal and lateral sides and being practically absent on the ventral side. Next Generation Sequencing (NGS) of V4 region of 16S rRNA gene amplicons, obtained from the DNA samples of whole bodies of Tegulaherpia sp. revealed three dominating microorganisms, two of which were bacteria of Bacteroidetes and Nitrospirae phyla, while the third one represented archaea of Thaumarchaeota phylum. The Operational Taxonomic Unit (OTU), affiliated with Bacteroidetes was an uncultured bacteria of the family Saprospiraceae (93–95% of Bacteroidetes and 25–44% of the total community, depending on sample), OTU, affiliated with Nitrospirae belonged to the genus Nitrospira (8–30% of the community), while the thaumarchaeal OTU was classified as Candidatus Nitrosopumilus (11–15% of the community). Members of these three microbial taxa are known to form associations with various marine animals such as sponges or snails where they contribute to nitrogen metabolism or the decomposition of biopolymers. A similar role is assumed to be played by the microorganisms associated with Tegulaherpia sp.
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Affiliation(s)
- Elena Vortsepneva
- Invertebrate Zoology Department, Biological Faculty, M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Pierre Chevaldonné
- IMBE, CNRS, Aix Marseille University, IRD, Avignon University, Station Marine d'Endoume, Marseille, France
| | - Alexandra Klyukina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Elizaveta Naduvaeva
- Invertebrate Zoology Department, Biological Faculty, M. V. Lomonosov Moscow State University, Moscow, Russia
| | | | - Anna Zhadan
- White Sea Biological Station, Biological Faculty, M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Alexander Tzetlin
- Invertebrate Zoology Department, Biological Faculty, M. V. Lomonosov Moscow State University, Moscow, Russia.,White Sea Biological Station, Biological Faculty, M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Ilya Kublanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
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2
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Chistyakova N, Antonova A, Elizarov I, Fabritchnyi P, Afanasov M, Korolenko M, Gracheva M, Pchelina D, Sergueev I, Leupold O, Steinbrügge R, Gavrilov S, Kublanov I, Rusakov V. Mössbauer, Nuclear Forward Scattering, and Raman Spectroscopic Approaches in the Investigation of Bioinduced Transformations of Mixed-Valence Antimony Oxide. J Phys Chem A 2021; 125:139-145. [PMID: 33389998 DOI: 10.1021/acs.jpca.0c08865] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mössbauer spectroscopy, nuclear forward scattering, and Raman spectroscopy were applied to study redox transformations of the synthesized mixed-valence (III/V) antimony oxide. The transformations were induced by a culture of a hyperthermophilic archaeon of the genus Pyrobaculum. The applied methods allowed us to reveal the minor decrease of ca. 11.0 ± 1.2% of the antimony(V) content of the mixed-valence oxide with the concomitant increase of antimony(III). The method sensitivities for the quantitative assessment of the Sb(III/V) ratio have been considered.
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Affiliation(s)
- Nataliya Chistyakova
- Department of Physics, Lomonosov Moscow State University, Leninskie Gory 1-2, Moscow 119991, Russian Federation
| | - Angelina Antonova
- Department of Physics, Lomonosov Moscow State University, Leninskie Gory 1-2, Moscow 119991, Russian Federation
| | - Ivan Elizarov
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology, Russian Academy of Sciences, Prospekt 60 Letiya Oktyabrya 7, bld. 2, Moscow 117312, Russian Federation
| | - Pavel Fabritchnyi
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-3, Moscow 119234, Russian Federation
| | - Mikhail Afanasov
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-3, Moscow 119234, Russian Federation
| | - Mikhail Korolenko
- Department of Chemistry, Lomonosov Moscow State University, Leninskie Gory 1-3, Moscow 119234, Russian Federation
| | - Maria Gracheva
- Department of Physics, Lomonosov Moscow State University, Leninskie Gory 1-2, Moscow 119991, Russian Federation
| | - Diana Pchelina
- Department of Physics, Lomonosov Moscow State University, Leninskie Gory 1-2, Moscow 119991, Russian Federation
| | - Ilya Sergueev
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Olaf Leupold
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - René Steinbrügge
- Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg, Germany
| | - Sergey Gavrilov
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology, Russian Academy of Sciences, Prospekt 60 Letiya Oktyabrya 7, bld. 2, Moscow 117312, Russian Federation
| | - Ilya Kublanov
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology, Russian Academy of Sciences, Prospekt 60 Letiya Oktyabrya 7, bld. 2, Moscow 117312, Russian Federation
| | - Vyacheslav Rusakov
- Department of Physics, Lomonosov Moscow State University, Leninskie Gory 1-2, Moscow 119991, Russian Federation
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3
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Slobodkin A, Slobodkina G, Allioux M, Alain K, Jebbar M, Shadrin V, Kublanov I, Toshchakov S, Bonch-Osmolovskaya E. Genomic Insights into the Carbon and Energy Metabolism of a Thermophilic Deep-Sea Bacterium Deferribacter autotrophicus Revealed New Metabolic Traits in the Phylum Deferribacteres. Genes (Basel) 2019; 10:genes10110849. [PMID: 31717820 PMCID: PMC6896113 DOI: 10.3390/genes10110849] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 10/22/2019] [Accepted: 10/23/2019] [Indexed: 01/12/2023] Open
Abstract
Information on the biochemical pathways of carbon and energy metabolism in representatives of the deep lineage bacterial phylum Deferribacteres are scarce. Here, we report the results of the sequencing and analysis of the high-quality draft genome of the thermophilic chemolithoautotrophic anaerobe Deferribacter autotrophicus. Genomic data suggest that CO2 assimilation is carried out by recently proposed reversible tricarboxylic acid cycle (“roTCA cycle”). The predicted genomic ability of D. autotrophicus to grow due to the oxidation of carbon monoxide was experimentally proven. CO oxidation was coupled with the reduction of nitrate to ammonium. Utilization of CO most likely involves anaerobic [Ni, Fe]-containing CO dehydrogenase. This is the first evidence of CO oxidation in the phylum Deferribacteres. The genome of D. autotrophicus encodes a Nap-type complex of nitrate reduction. However, the conversion of produced nitrite to ammonium proceeds via a non-canonical pathway with the participation of hydroxylamine oxidoreductase (Hao) and hydroxylamine reductase. The genome contains 17 genes of putative multiheme c-type cytochromes and “e-pilin” genes, some of which are probably involved in Fe(III) reduction. Genomic analysis indicates that the roTCA cycle of CO2 fixation and putative Hao-enabled ammonification may occur in several members of the phylum Deferribacteres.
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Affiliation(s)
- Alexander Slobodkin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (G.S.); (V.S.); (I.K.); (S.T.); (E.B.-O.)
- Correspondence:
| | - Galina Slobodkina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (G.S.); (V.S.); (I.K.); (S.T.); (E.B.-O.)
| | - Maxime Allioux
- Univ Brest, CNRS, Ifremer, LIA1211, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, F-29280 Plouzané, France; (M.A.); (K.A.); (M.J.)
| | - Karine Alain
- Univ Brest, CNRS, Ifremer, LIA1211, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, F-29280 Plouzané, France; (M.A.); (K.A.); (M.J.)
| | - Mohamed Jebbar
- Univ Brest, CNRS, Ifremer, LIA1211, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, F-29280 Plouzané, France; (M.A.); (K.A.); (M.J.)
| | - Valerian Shadrin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (G.S.); (V.S.); (I.K.); (S.T.); (E.B.-O.)
| | - Ilya Kublanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (G.S.); (V.S.); (I.K.); (S.T.); (E.B.-O.)
| | - Stepan Toshchakov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (G.S.); (V.S.); (I.K.); (S.T.); (E.B.-O.)
| | - Elizaveta Bonch-Osmolovskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (G.S.); (V.S.); (I.K.); (S.T.); (E.B.-O.)
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Haverkamp THA, Geslin C, Lossouarn J, Podosokorskaya OA, Kublanov I, Nesbø CL. Thermosipho spp. Immune System Differences Affect Variation in Genome Size and Geographical Distributions. Genome Biol Evol 2018; 10:2853-2866. [PMID: 30239713 PMCID: PMC6211235 DOI: 10.1093/gbe/evy202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/12/2018] [Indexed: 01/24/2023] Open
Abstract
Thermosipho species inhabit thermal environments such as marine hydrothermal vents, petroleum reservoirs, and terrestrial hot springs. A 16S rRNA phylogeny of available Thermosipho spp. sequences suggested habitat specialists adapted to living in hydrothermal vents only, and habitat generalists inhabiting oil reservoirs, hydrothermal vents, and hotsprings. Comparative genomics of 15 Thermosipho genomes separated them into three distinct species with different habitat distributions: The widely distributed T. africanus and the more specialized, T. melanesiensis and T. affectus. Moreover, the species can be differentiated on the basis of genome size (GS), genome content, and immune system composition. For instance, the T. africanus genomes are largest and contained the most carbohydrate metabolism genes, which could explain why these isolates were obtained from ecologically more divergent habitats. Nonetheless, all the Thermosipho genomes, like other Thermotogae genomes, show evidence of genome streamlining. GS differences between the species could further be correlated to differences in defense capacities against foreign DNA, which influence recombination via HGT. The smallest genomes are found in T. affectus that contain both CRISPR-cas Type I and III systems, but no RM system genes. We suggest that this has caused these genomes to be almost devoid of mobile elements, contrasting the two other species genomes that contain a higher abundance of mobile elements combined with different immune system configurations. Taken together, the comparative genomic analyses of Thermosipho spp. revealed genetic variation allowing habitat differentiation within the genus as well as differentiation with respect to invading mobile DNA.
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Affiliation(s)
- Thomas H A Haverkamp
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway.,Norwegian Veterinary Institute, Oslo, Norway
| | - Claire Geslin
- Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Institut Universitaire Européen de la Mer (IUEM) - UMR 6197, Université de Bretagne Occidentale (UBO), Plouzané, France.,CNRS, IUEM - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Plouzané, France.,Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Technopôle Pointe du diable, Plouzané, France
| | - Julien Lossouarn
- Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Institut Universitaire Européen de la Mer (IUEM) - UMR 6197, Université de Bretagne Occidentale (UBO), Plouzané, France.,CNRS, IUEM - UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Plouzané, France.,Ifremer, UMR 6197, Laboratoire de Microbiologie des Environnements Extrêmes (LMEE), Technopôle Pointe du diable, Plouzané, France
| | - Olga A Podosokorskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Ilya Kublanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of Sciences, Moscow, Russia.,Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Camilla L Nesbø
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, Norway.,Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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5
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Abstract
Thermophilic microorganisms are capable of growing on polymeric substrates and have been intensively studied for their enzymes, thermostable hydrolases (glycosidases, proteinases, lipases), which have important applications in many fields of bioindustry: production of detergents, food processing, paper and textile industry, biofuel formation from organic wastes, etc.1. The advantages of thermostable enzymes application are in their higher stability not only against temperature, but also against high or low pH, presence of detergents, etc. High temperature increases solubility of substrates2, thus making them more available, and significantly decreases the contamination risks. Many highly stable hydrolases, produced by thermophilic bacteria and archaea have been discovered3–6; however, due to continuous industrial demand and our knowledge that natural environments are a significant reservoir of genetic and hence functional diversity7, new thermophilic organisms producing hydrolytic enzymes are still of high interest. Here we present our achievements in isolation of novel thermophilic bacteria and archaea with various hydrolytic activities.
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6
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Gavrilov S, Podosokorskaya O, Alexeev D, Merkel A, Khomyakova M, Muntyan M, Altukhov I, Butenko I, Bonch-Osmolovskaya E, Govorun V, Kublanov I. Respiratory Pathways Reconstructed by Multi-Omics Analysis in Melioribacter roseus, Residing in a Deep Thermal Aquifer of the West-Siberian Megabasin. Front Microbiol 2017; 8:1228. [PMID: 28713355 PMCID: PMC5492636 DOI: 10.3389/fmicb.2017.01228] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 06/16/2017] [Indexed: 01/19/2023] Open
Abstract
Melioribacter roseus, a representative of recently proposed Ignavibacteriae phylum, is a metabolically versatile thermophilic bacterium, inhabiting subsurface biosphere of the West-Siberian megabasin and capable of growing on various substrates and electron acceptors. Genomic analysis followed by inhibitor studies and membrane potential measurements of aerobically grown M. roseus cells revealed the activity of aerobic respiratory electron transfer chain comprised of respiratory complexes I and IV, and an alternative complex III. Phylogeny reconstruction revealed that oxygen reductases belonged to atypical cc(o/b)o3-type and canonical cbb3–type cytochrome oxidases. Also, two molybdoenzymes of M. roseus were affiliated either with Ttr or Psr/Phs clades, but not with typical respiratory arsenate reductases of the Arr clade. Expression profiling, both at transcripts and protein level, allowed us to assign the role of the terminal respiratory oxidase under atmospheric oxygen concentration for the cc(o/b)o3 cytochrome oxidase, previously proposed to serve for oxygen detoxification only. Transcriptomic analysis revealed the involvement of both molybdoenzymes of M. roseus in As(V) respiration, yet differences in the genomic context of their gene clusters allow to hypothesize about their distinct roles in arsenate metabolism with the ‘Psr/Phs’-type molybdoenzyme being the most probable candidate respiratory arsenate reductase. Basing on multi-omics data, the pathways for aerobic and arsenate respiration were proposed. Our results start to bridge the vigorously increasing gap between homology-based predictions and experimentally verified metabolic processes, what is especially important for understudied microorganisms of novel lineages from deep subsurface environments of Eurasia, which remained separated from the rest of the biosphere for several geological periods.
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Affiliation(s)
- Sergey Gavrilov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of SciencesMoscow, Russia
| | - Olga Podosokorskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of SciencesMoscow, Russia
| | - Dmitry Alexeev
- Saint Petersburg State University of Information Technologies, Mechanics and OpticsSt. Petersburg, Russia
| | - Alexander Merkel
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of SciencesMoscow, Russia
| | - Maria Khomyakova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of SciencesMoscow, Russia
| | - Maria Muntyan
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State UniversityMoscow, Russia
| | - Ilya Altukhov
- Federal Research and Clinical Centre of Physico-Chemical MedicineMoscow, Russia.,Moscow Institute of Physics and TechnologyDolgoprudny, Russia
| | - Ivan Butenko
- Federal Research and Clinical Centre of Physico-Chemical MedicineMoscow, Russia
| | - Elizaveta Bonch-Osmolovskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of SciencesMoscow, Russia
| | - Vadim Govorun
- Federal Research and Clinical Centre of Physico-Chemical MedicineMoscow, Russia.,Moscow Institute of Physics and TechnologyDolgoprudny, Russia
| | - Ilya Kublanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology, Russian Academy of SciencesMoscow, Russia.,Laboratory of Microbial Genomics, Immanuel Kant Baltic Federal UniversityKaliningrad, Russia
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Zarafeta D, Moschidi D, Ladoukakis E, Gavrilov S, Chrysina ED, Chatziioannou A, Kublanov I, Skretas G, Kolisis FN. Metagenomic mining for thermostable esterolytic enzymes uncovers a new family of bacterial esterases. Sci Rep 2016; 6:38886. [PMID: 27991516 PMCID: PMC5171882 DOI: 10.1038/srep38886] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 11/14/2016] [Indexed: 11/09/2022] Open
Abstract
Biocatalysts exerting activity against ester bonds have a broad range of applications in modern biotechnology. Here, we have identified a new esterolytic enzyme by screening a metagenomic sample collected from a hot spring in Kamchatka, Russia. Biochemical characterization of the new esterase, termed EstDZ2, revealed that it is highly active against medium chain fatty acid esters at temperatures between 25 and 60 °C and at pH values 7-8. The new enzyme is moderately thermostable with a half-life of more than six hours at 60 °C, but exhibits exquisite stability against high concentrations of organic solvents. Phylogenetic analysis indicated that EstDZ2 is likely an Acetothermia enzyme that belongs to a new family of bacterial esterases, for which we propose the index XV. One distinctive feature of this new family, is the presence of a conserved GHSAG catalytic motif. Multiple sequence alignment, coupled with computational modelling of the three-dimensional structure of EstDZ2, revealed that the enzyme lacks the largest part of the "cap" domain, whose extended structure is characteristic for the closely related Family IV esterases. Thus, EstDZ2 appears to be distinct from known related esterolytic enzymes, both in terms of sequence characteristics, as well as in terms of three-dimensional structure.
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Affiliation(s)
- Dimitra Zarafeta
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Danai Moschidi
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Efthymios Ladoukakis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Sergey Gavrilov
- Winogradsky Institute of Microbiology, Research Center for Biotechnology Russian Academy of Sciences, Moscow, Russian Federation
| | - Evangelia D. Chrysina
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Aristotelis Chatziioannou
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Ilya Kublanov
- Winogradsky Institute of Microbiology, Research Center for Biotechnology Russian Academy of Sciences, Moscow, Russian Federation
| | - Georgios Skretas
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Fragiskos N. Kolisis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
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8
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Nesbø CL, S Swithers K, Dahle H, Haverkamp THA, Birkeland NK, Sokolova T, Kublanov I, Zhaxybayeva O. Evidence for extensive gene flow and Thermotoga subpopulations in subsurface and marine environments. ISME J 2014; 9:1532-42. [PMID: 25500512 DOI: 10.1038/ismej.2014.238] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 11/03/2014] [Accepted: 11/10/2014] [Indexed: 11/09/2022]
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.
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Affiliation(s)
- Camilla L Nesbø
- 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
| | - Kristen S Swithers
- 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
| | - Håkon Dahle
- Department of Biology and Centre for Geobiology, University of Bergen, Bergen, Norway
| | - Thomas H A Haverkamp
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of Oslo, Blindern, Oslo, Norway
| | - Nils-Kåre Birkeland
- Department of Biology and Centre for Geobiology, University of Bergen, Bergen, Norway
| | - Tatiana Sokolova
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Ilya Kublanov
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
| | - Olga Zhaxybayeva
- 1] Department of Biological Sciences, Dartmouth College, Hanover, NH, USA [2] Department of Computer Science, Dartmouth College, Hanover, NH, USA
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