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Zimmermann HH, Stoof-Leichsenring KR, Dinkel V, Harms L, Schulte L, Hütt MT, Nürnberg D, Tiedemann R, Herzschuh U. Marine ecosystem shifts with deglacial sea-ice loss inferred from ancient DNA shotgun sequencing. Nat Commun 2023; 14:1650. [PMID: 36964154 PMCID: PMC10039020 DOI: 10.1038/s41467-023-36845-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 02/20/2023] [Indexed: 03/26/2023] Open
Abstract
Sea ice is a key factor for the functioning and services provided by polar marine ecosystems. However, ecosystem responses to sea-ice loss are largely unknown because time-series data are lacking. Here, we use shotgun metagenomics of marine sedimentary ancient DNA off Kamchatka (Western Bering Sea) covering the last ~20,000 years. We traced shifts from a sea ice-adapted late-glacial ecosystem, characterized by diatoms, copepods, and codfish to an ice-free Holocene characterized by cyanobacteria, salmon, and herring. By providing information about marine ecosystem dynamics across a broad taxonomic spectrum, our data show that ancient DNA will be an important new tool in identifying long-term ecosystem responses to climate transitions for improvements of ocean and cryosphere risk assessments. We conclude that continuing sea-ice decline on the northern Bering Sea shelf might impact on carbon export and disrupt benthic food supply and could allow for a northward expansion of salmon and Pacific herring.
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Affiliation(s)
- Heike H Zimmermann
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems, D-14473, Potsdam, Germany
- Department of Glaciology and Climate, Geological Survey of Denmark and Greenland (GEUS), DK-1350, Copenhagen, Denmark
| | - Kathleen R Stoof-Leichsenring
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems, D-14473, Potsdam, Germany
| | - Viktor Dinkel
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems, D-14473, Potsdam, Germany
- Constructor University Bremen, Computational Systems Biology, Bremen, D-28759, Germany
| | - Lars Harms
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Data Science Support, D-27568, Bremerhaven, Germany
| | - Luise Schulte
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems, D-14473, Potsdam, Germany
| | - Marc-Thorsten Hütt
- Constructor University Bremen, Computational Systems Biology, Bremen, D-28759, Germany
| | - Dirk Nürnberg
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Ocean circulation and climate dynamics, D-24148, Kiel, Germany
| | - Ralf Tiedemann
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Marine Geology, D-27568, Bremerhaven, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, D-28334, Bremen, Germany
| | - Ulrike Herzschuh
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Polar Terrestrial Environmental Systems, D-14473, Potsdam, Germany.
- University of Potsdam, Institute of Biochemistry and Biology, D-14476, Potsdam, Germany.
- University of Potsdam, Institute of Environmental Sciences and Geography, D-14476, Potsdam, Germany.
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2
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Frolov EN, Lebedinsky AV, Elcheninov AG, Kublanov IV. Taxonomic proposal for a deep branching bacterial phylogenetic lineage: transfer of the family Thermodesulfobiaceae to Thermodesulfobiales ord. nov., Thermodesulfobiia classis nov. and Thermodesulfobiota phyl. nov. Syst Appl Microbiol 2023; 46:126388. [PMID: 36493506 DOI: 10.1016/j.syapm.2022.126388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/20/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022]
Abstract
The family Thermodesulfobiaceae, comprising one genus Thermodesulfobium with two validly published species, is currently assigned to order Thermoanaerobacterales within the class Clostridia of the phylum Bacillota. At the same time, the very first 16S rRNA gene sequence-based phylogenetic studies of representatives of the genus pointed out great differences between Thermodesulfobium and other members of the phylum Bacillota. Subsequent studies of new Thermodesulfobium representatives supported deep phylogenetic branching of this lineage within bacterial tree, implying that it represents a novel phylum. The results of the phylogenomic analysis performed in the frames of the present work confirm previous findings and suggest that Thermodesulfobium represents a distinct phylum-level lineage. Thus, we propose the transfer of the family Thermodesulfobiaceae to the new order Thermodesulfobiales within the new class Thermodesulfobiia and the new phylum Thermodesulfobiota.
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Affiliation(s)
- Evgenii N Frolov
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology, Russian Academy of Sciences, 60-let Oktyabrya prospect, 7, bld. 2, 119071 Moscow, Russia.
| | - Alexander V Lebedinsky
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology, Russian Academy of Sciences, 60-let Oktyabrya prospect, 7, bld. 2, 119071 Moscow, Russia
| | - Alexander G Elcheninov
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology, Russian Academy of Sciences, 60-let Oktyabrya prospect, 7, bld. 2, 119071 Moscow, Russia
| | - Ilya V Kublanov
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology, Russian Academy of Sciences, 60-let Oktyabrya prospect, 7, bld. 2, 119071 Moscow, Russia
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3
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Kochetkova TV, Podosokorskaya OA, Elcheninov AG, Kublanov IV. Diversity of Thermophilic Prokaryotes Inhabiting Russian Natural Hot Springs. Microbiology (Reading) 2022. [DOI: 10.1134/s0026261722010064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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4
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Frolov EN, Gololobova AV, Klyukina AA, Bonch-Osmolovskaya EA, Pimenov NV, Chernyh NA, Merkel AY. Diversity and Activity of Sulfate-Reducing Prokaryotes in Kamchatka Hot Springs. Microorganisms 2021; 9:2072. [PMID: 34683394 PMCID: PMC8539903 DOI: 10.3390/microorganisms9102072] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/25/2021] [Accepted: 09/28/2021] [Indexed: 12/26/2022] Open
Abstract
Microbial communities of the Kamchatka Peninsula terrestrial hot springs were studied using radioisotopic and cultural approaches, as well as by the amplification and sequencing of dsrB and 16S rRNA genes fragments. Radioisotopic experiments with 35S-labeled sulfate showed that microbial communities of the Kamchatka hot springs are actively reducing sulfate. Both the cultivation experiments and the results of dsrB and 16S rRNA genes fragments analyses indicated the presence of microorganisms participating in the reductive part of the sulfur cycle. It was found that sulfate-reducing prokaryotes (SRP) belonging to Desulfobacterota, Nitrospirota and Firmicutes phyla inhabited neutral and slightly acidic hot springs, while bacteria of phylum Thermodesulofobiota preferred moderately acidic hot springs. In high-temperature acidic springs sulfate reduction was mediated by archaea of the phylum Crenarchaeota, chemoorganoheterotrophic representatives of genus Vulcanisaeta being the most probable candidates. The 16S rRNA taxonomic profiling showed that in most of the studied communities SRP was present only as a minor component. Only in one microbial community, the representatives of genus Vulcanisaeta comprised a significant group. Thus, in spite of comparatively low sulfate concentrations in terrestrial hot springs of the Kamchatka, phylogenetically and metabolically diverse groups of sulfate-reducing prokaryotes are operating there coupling carbon and sulfur cycles in these habitats.
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Affiliation(s)
- Evgenii N. Frolov
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312 Moscow, Russia; (A.V.G.); (A.A.K.); (E.A.B.-O.); (N.V.P.); (N.A.C.); (A.Y.M.)
| | - Alexandra V. Gololobova
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312 Moscow, Russia; (A.V.G.); (A.A.K.); (E.A.B.-O.); (N.V.P.); (N.A.C.); (A.Y.M.)
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, 119991 Moscow, Russia
| | - Alexandra A. Klyukina
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312 Moscow, Russia; (A.V.G.); (A.A.K.); (E.A.B.-O.); (N.V.P.); (N.A.C.); (A.Y.M.)
| | - Elizaveta A. Bonch-Osmolovskaya
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312 Moscow, Russia; (A.V.G.); (A.A.K.); (E.A.B.-O.); (N.V.P.); (N.A.C.); (A.Y.M.)
- Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory, 119991 Moscow, Russia
| | - Nikolay V. Pimenov
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312 Moscow, Russia; (A.V.G.); (A.A.K.); (E.A.B.-O.); (N.V.P.); (N.A.C.); (A.Y.M.)
| | - Nikolay A. Chernyh
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312 Moscow, Russia; (A.V.G.); (A.A.K.); (E.A.B.-O.); (N.V.P.); (N.A.C.); (A.Y.M.)
| | - Alexander Y. Merkel
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 60 let Oktjabrja pr-t, 7, bld. 2, 117312 Moscow, Russia; (A.V.G.); (A.A.K.); (E.A.B.-O.); (N.V.P.); (N.A.C.); (A.Y.M.)
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Rozanov AS, Korzhuk AV, Shekhovtsov SV, Vasiliev GV, Peltek SE. Microorganisms of Two Thermal Pools on Kunashir Island, Russia. BIOLOGY 2021; 10:924. [PMID: 34571800 PMCID: PMC8468003 DOI: 10.3390/biology10090924] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 11/18/2022]
Abstract
The Kuril Archipelago is a part of the Circum-Pacific Belt (Ring of Fire). These islands have numerous thermal springs. There are very few studies on these microbial communities, and none of them have been conducted by modern molecular biological methods. Here we performed the first metagenomic study on two thermophilic microbial communities of Kunashir Island. Faust Lake is hot (48 °C) and highly acidic (pH 2.0). We constructed 28 metagenome-assembled genomes as well as 17 16S ribosomal RNA sequences. We found that bottom sediments of Faust Lake are dominated by a single species of red algae belonging to the Cyanidiaceae family. Archaeans in Faust Lake are more diverse than bacteria but less abundant. The Tretyakovsky Thermal Spring is also hot (52 °C) but only weakly acidic (pH 6.0). It has much higher microbial diversity (233 metagenome-assembled genomes; 93 16S ribosomal RNAs) and is dominated by bacteria, with only several archaeans and one fungus. Despite their geographic proximity, these two thermal springs were found to not share any species. A comparison of these two lakes with other thermal springs of the Circum-Pacific Belt revealed that only a few members of the communities are shared among different locations.
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Affiliation(s)
- Aleksei S. Rozanov
- Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences (ICG SB RAS), 630090 Novosibirsk, Russia; (S.V.S.); (G.V.V.); (S.E.P.)
| | - Anton V. Korzhuk
- Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences (ICG SB RAS), 630090 Novosibirsk, Russia; (S.V.S.); (G.V.V.); (S.E.P.)
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Sergei V. Shekhovtsov
- Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences (ICG SB RAS), 630090 Novosibirsk, Russia; (S.V.S.); (G.V.V.); (S.E.P.)
| | - Gennady V. Vasiliev
- Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences (ICG SB RAS), 630090 Novosibirsk, Russia; (S.V.S.); (G.V.V.); (S.E.P.)
| | - Sergei E. Peltek
- Institute of Cytology and Genetics of Siberian Branch of Russian Academy of Sciences (ICG SB RAS), 630090 Novosibirsk, Russia; (S.V.S.); (G.V.V.); (S.E.P.)
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6
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Mueller RC, Peach JT, Skorupa DJ, Copié V, Bothner B, Peyton BM. An emerging view of the diversity, ecology and function of Archaea in alkaline hydrothermal environments. FEMS Microbiol Ecol 2021; 97:6021323. [PMID: 33501490 DOI: 10.1093/femsec/fiaa246] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 12/01/2020] [Indexed: 11/15/2022] Open
Abstract
The described diversity within the domain Archaea has recently expanded due to advances in sequencing technologies, but many habitats that likely harbor novel lineages of archaea remain understudied. Knowledge of archaea within natural and engineered hydrothermal systems, such as hot springs and engineered subsurface habitats, has been steadily increasing, but the majority of the work has focused on archaea living in acidic or circumneutral environments. The environmental pressures exerted by the combination of high temperatures and high pH likely select for divergent communities and distinct metabolic pathways from those observed in acidic or circumneutral systems. In this review, we examine what is currently known about the archaea found in thermoalkaline environments, focusing on the detection of novel lineages and knowledge of the ecology, metabolic pathways and functions of these populations and communities. We also discuss the potential of emerging multi-omics approaches, including proteomics and metabolomics, to enhance our understanding of archaea within extreme thermoalkaline systems.
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Affiliation(s)
- Rebecca C Mueller
- Department of Chemical and Biological Engineering, Montana State University,Bozeman, MT 59717, PO Box 173920, USA.,Thermal Biology Institute, Montana State University, Bozeman, MT 59717, PO Box 173142, USA
| | - Jesse T Peach
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, PO Box 173400, USA
| | - Dana J Skorupa
- Department of Chemical and Biological Engineering, Montana State University,Bozeman, MT 59717, PO Box 173920, USA.,Thermal Biology Institute, Montana State University, Bozeman, MT 59717, PO Box 173142, USA
| | - Valerie Copié
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, PO Box 173400, USA.,Thermal Biology Institute, Montana State University, Bozeman, MT 59717, PO Box 173142, USA
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, PO Box 173400, USA.,Thermal Biology Institute, Montana State University, Bozeman, MT 59717, PO Box 173142, USA
| | - Brent M Peyton
- Department of Chemical and Biological Engineering, Montana State University,Bozeman, MT 59717, PO Box 173920, USA.,Thermal Biology Institute, Montana State University, Bozeman, MT 59717, PO Box 173142, USA
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7
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Meziti A, Nikouli E, Hatt JK, Konstantinidis KT, Kormas KA. Time series metagenomic sampling of the Thermopyles, Greece, geothermal springs reveals stable microbial communities dominated by novel sulfur-oxidizing chemoautotrophs. Environ Microbiol 2021; 23:3710-3726. [PMID: 33350070 DOI: 10.1111/1462-2920.15373] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/19/2020] [Indexed: 11/29/2022]
Abstract
Geothermal springs are essentially unaffected by environmental conditions aboveground as they are continuously supplied with subsurface water with little variability in chemistry. Therefore, changes in their microbial community composition and function, especially over a long period, are expected to be limited but this assumption has not yet been rigorously tested. Toward closing this knowledge gap, we applied whole metagenome sequencing to 17 water samples collected between 2010 and 2016 from the Thermopyles sulfur-rich geothermal springs in central Greece. As revealed by 16S rRNA gene fragments recovered in the metagenomes, Epsilonproteobacteria-related operational taxonomic units (OTUs) dominated most samples and grouping of samples based on OTU abundances exhibited no apparent seasonal pattern. Similarities between samples regarding functional gene content were high, with all samples sharing >70% similarity in functional pathways. These community-wide patterns were further confirmed by analysis of metagenome-assembled genomes (MAGs), which showed that novel species and genera of the chemoautotrophic Campylobacterales order dominated the springs. These MAGs carried different pathways for thiosulfate or sulfide oxidation coupled to carbon fixation pathways. Overall, our study showed that even in the long term, functions of microbial communities in a moderately hot terrestrial spring remain stable, presumably driving the corresponding stability in community structure.
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Affiliation(s)
- A Meziti
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, 38446, Greece.,School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science and Technology Building, 311 Ferst Drive, Atlanta, GA, 30332, USA
| | - E Nikouli
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, 38446, Greece.,School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science and Technology Building, 311 Ferst Drive, Atlanta, GA, 30332, USA
| | - J K Hatt
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science and Technology Building, 311 Ferst Drive, Atlanta, GA, 30332, USA
| | - K T Konstantinidis
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Ford Environmental Science and Technology Building, 311 Ferst Drive, Atlanta, GA, 30332, USA.,School of Biological Sciences, Georgia Institute of Technology, Ford Environmental Sciences and Technology Building, 311 Ferst Drive, Atlanta, GA, 30332, USA
| | - K A Kormas
- Department of Ichthyology and Aquatic Environment, University of Thessaly, Volos, 38446, Greece
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8
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Peltek SE, Bryanskaya AV, Uvarova YE, Rozanov AS, Ivanisenko TV, Ivanisenko VA, Lazareva EV, Saik OV, Efimov VM, Zhmodik SM, Taran OP, Slynko NM, Shekhovtsov SV, Parmon VN, Dobretsov NL, Kolchanov NA. Young «oil site» of the Uzon Caldera as a habitat for unique microbial life. BMC Microbiol 2020; 20:349. [PMID: 33228530 PMCID: PMC7685581 DOI: 10.1186/s12866-020-02012-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 10/15/2020] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The Uzon Caldera is one of the places on our planet with unique geological, ecological, and microbiological characteristics. Uzon oil is the youngest on Earth. Uzon oil has unique composition, with low proportion of heavy fractions and relatively high content of saturated hydrocarbons. Microbial communities of the «oil site» have a diverse composition and live at high temperatures (up to 97 °C), significant oscillations of Eh and pH, and high content of sulfur, sulfides, arsenic, antimony, and mercury in water and rocks. RESULTS The study analyzed the composition, structure and unique genetics characteristics of the microbial communities of the oil site, analyzed the metabolic pathways in the communities. Metabolic pathways of hydrocarbon degradation by microorganisms have been found. The study found statistically significant relationships between geochemical parameters, taxonomic composition and the completeness of metabolic pathways. It was demonstrated that geochemical parameters determine the structure and metabolic potential of microbial communities. CONCLUSIONS There were statistically significant relationships between geochemical parameters, taxonomic composition, and the completeness of metabolic pathways. It was demonstrated that geochemical parameters define the structure and metabolic potential of microbial communities. Metabolic pathways of hydrocarbon oxidation was found to prevail in the studied communities, which corroborates the hypothesis on abiogenic synthesis of Uzon hydrothermal petroleum.
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Affiliation(s)
- Sergey E Peltek
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
| | - Alla V Bryanskaya
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090.
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090.
| | - Yuliya E Uvarova
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
| | - Aleksey S Rozanov
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
| | - Timofey V Ivanisenko
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
- Novosibirsk State University, Pirogova str., 2, Novosibirsk, Russia, 630090
| | - Vladimir A Ivanisenko
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
| | - Elena V Lazareva
- The V.S. Sobolev Institute of Geology and Mineralogy SB RAS, pr. Koptyuga, 3, Novosibirsk, Russia, 630090
| | - Olga V Saik
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
| | - Vadim M Efimov
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
- Novosibirsk State University, Pirogova str., 2, Novosibirsk, Russia, 630090
| | - Sergey M Zhmodik
- The V.S. Sobolev Institute of Geology and Mineralogy SB RAS, pr. Koptyuga, 3, Novosibirsk, Russia, 630090
| | - Oxana P Taran
- Institute of Chemistry and Chemical Technology SB RAS, FRC Krasnoyarsk Science Center SB RAS, Akademgorodok, 50/24, Krasnoyarsk, Russia, 660036
- Siberian Federal University, Svobodny ave. 79, Krasnoyarsk, Russia, 660041
- Boreskov Institute of Catalysis SB RAS, pr. Lavrentieva 5, Novosibirsk, Russia, 630090
| | - Nikolay M Slynko
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
| | - Sergey V Shekhovtsov
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
| | - Valentin N Parmon
- Boreskov Institute of Catalysis SB RAS, pr. Lavrentieva 5, Novosibirsk, Russia, 630090
| | - Nikolay L Dobretsov
- Trofimuk Institute of Petroleum Geology and Geophysics SB RAS, pr. Koptyuga, 3, Novosibirsk, Russia, 630090
| | - Nikolay A Kolchanov
- Laboratory of Molecular Biotechnologies of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
- Kurchatov Genomics Center of Federal research center Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Aven., Novosibirsk, Russia, 630090
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9
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Willis G, Nancucheo I, Hedrich S, Giaveno A, Donati E, Johnson DB. Enrichment and isolation of acid-tolerant sulfate-reducing microorganisms in the anoxic, acidic hot spring sediments from Copahue volcano, Argentina. FEMS Microbiol Ecol 2020; 95:5610214. [PMID: 31665270 DOI: 10.1093/femsec/fiz175] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 10/28/2019] [Indexed: 01/21/2023] Open
Abstract
The geothermal Copahue-Caviahue (GCC) system (Argentina) is an extreme acidic environment, dominated by the activity of Copahue volcano. Environments characterised by low pH values, such as volcanic areas, are of particular interest for the search of acidophilic microorganisms with application in biotechnological processes. In this work, sulfate-reducing microorganisms were investigated in geothermal acidic, anaerobic zones from GCC system. Sediment samples from Agua del Limón (AL1), Las Máquinas (LMa2), Las Maquinitas (LMi) and Baño 9 (B9-2, B9-3) were found to be acidic (pH values 2.1-3.0) to moderate acidic (5.1-5.2), containing small total organic carbon values, and ferric iron precipitates. The organic electron donor added to the enrichment was completely oxidised to CO2. Bacteria related to 'Desulfobacillus acidavidus' strain CL4 were found to be dominant (67-83% of the total number of clones) in the enrichment cultures, and their presence was confirmed by their isolation on overlay plates. Other bacteria were also detected with lower abundance (6-20% of the total number of clones), with representatives of the genera Acidithiobacillus, Sulfobacillus, Alicyclobacillus and Athalassotoga/Mesoaciditoga. These enrichment and isolates found at low pH confirm the presence of anaerobic activities in the acidic sediments from the geothermal Copahue-Caviahue system.
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Affiliation(s)
- Graciana Willis
- CINDEFI (CONICET-UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 47 y 115, 1900 La Plata, Argentina
| | - Ivan Nancucheo
- Facultad de Ingeniería y Tecnología, Universidad San Sebastián, Lientur 1457, Concepción 4080871, Chile
| | - Sabrina Hedrich
- Federal Institute for Geosciences and Natural Resources, Resource Geochemistry, Stilleweg 2, 30655 Hannover, Germany
| | - Alejandra Giaveno
- PROBIEN (CONICET-UNCo), Departamento de Química, Facultad de Ingeniería, Universidad Nacional del Comahue, Buenos Aires 1400, 8300 Neuquén, Argentina
| | - Edgardo Donati
- CINDEFI (CONICET-UNLP), Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 47 y 115, 1900 La Plata, Argentina
| | - David Barrie Johnson
- School of Natural Sciences, Bangor University, Deiniol Road, Bangor, LL57 2UW, UK
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10
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Panosyan H, Margaryan A, Birkeland NK. Geothermal springs in Armenia and Nagorno-Karabakh: potential sources of hydrolase-producing thermophilic bacilli. Extremophiles 2020; 24:519-536. [PMID: 32390108 DOI: 10.1007/s00792-020-01173-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 04/27/2020] [Indexed: 02/02/2023]
Abstract
In recent years, scientists have increasingly focused on the microbial diversity of high-altitude hot springs to explore the biotechnological applications of extremophiles. In this regard, a total of 107 thermophilic bacilli were isolated from 9 high-altitude mineralized geothermal springs (of temperatures ranging from 27.5 to 70 °C) located within the territory of Armenia and Nagorno-Karabakh. The isolated bacilli were phylogenetically profiled and studied for their potential to produce extracellular hydrolytic enzymes (protease, amylase, and lipase). The identification of isolates based on 16S rRNA gene sequences revealed their relationship to members of more than 22 distinct species, of 8 different genera, namely Aeribacillus, Anoxybacillus, Bacillus, Brevibacillus, Geobacillus, Parageobacillus, Paenibacillus and Ureibacillus. Bacillus licheniformis, Parageobacillus toebii and Anoxybacillus flavithermus were found to be the most abundant species in the springs that were studied. Some of the isolated bacilli shared less than 91-97% sequence identity with their closest match in GenBank, indicating that Armenian geothermal springs harbor novel bacilli, at least at the species level. 71% of the isolates actively produced at least one or more extracellular proteases, amylases, or lipases. In total, 22 strains (28.6%) were efficient producers of all three types of thermostable enzymes.
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Affiliation(s)
- Hovik Panosyan
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, Alex Manoogian 1, 0025, Yerevan, Armenia.
| | - Armine Margaryan
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, Alex Manoogian 1, 0025, Yerevan, Armenia
| | - Nils-Kåre Birkeland
- Department of Biological Sciences, University of Bergen, P.O. Box 7803, 5020, Bergen, Norway
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11
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Chalupa J, Pocik O, Halecky M, Kozliak E. Thermophilic waste air treatment of an airborne ethyl acetate/toluene mixture in a bubble column reactor: Stability towards temperature changes. JOURNAL OF HAZARDOUS MATERIALS 2020; 384:120744. [PMID: 31812476 DOI: 10.1016/j.jhazmat.2019.120744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 05/04/2019] [Accepted: 06/05/2019] [Indexed: 06/10/2023]
Abstract
Thermophilic waste air treatment in a lab-scale bubble column reactor (BCR) was used to remove an ethyl acetate/toluene mixture under both mesophilic and thermophilic conditions, at 30-50 °C. Additional tests, e.g., toluene mass transfer measurement and monitoring of microbial population development, explained the observed bioreactor response to the conducted loading tests and temperature changes. The maximum overall elimination capacity at thermophilic conditions (50 °C) was 136.9 g·m-3 h-1, however hysteresis in elimination capacity was observed in response to ascending/descending temperature and inlet concentration changes. Representatives of genera Cupriavidus, Variovorax and order Rhodospirillales were found to be predominant in the degrading microbial population, depending on the operating temperature. Thermobacillus and Blastocatella were abundant at high (50 °C) and low (30 °C) temperatures, respectively. The observed gradual shift in microbial population caused a small yet significant gradual change in developing a preference for toluene at the expense of ethyl acetate, which explains the observed hysteresis. Yet, the whole bioreactor removal efficiency remained similar at the same temperature, thus demonstrating the advantages of using thermophiles in bioreactors with temperature variation, such as robustness and flexibility.
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Affiliation(s)
- Jan Chalupa
- University of Chemistry and Technology, Prague, Department of Biotechnology, Technicka 5, 166 28, Prague, Czech Republic
| | - Ondrej Pocik
- University of Chemistry and Technology, Prague, Department of Biotechnology, Technicka 5, 166 28, Prague, Czech Republic
| | - Martin Halecky
- University of Chemistry and Technology, Prague, Department of Biotechnology, Technicka 5, 166 28, Prague, Czech Republic.
| | - Evguenii Kozliak
- Department of Chemistry, University of North Dakota, Grand Forks, North Dakota, USA
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12
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Carrizo D, Sánchez-García L, Rodriguez N, Gómez F. Lipid Biomarker and Carbon Stable Isotope Survey on the Dallol Hydrothermal System in Ethiopia. ASTROBIOLOGY 2019; 19:1474-1489. [PMID: 31112043 PMCID: PMC6921156 DOI: 10.1089/ast.2018.1963] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The remote Dallol Hot Springs, an active hydrothermal system in the volcanic region of Danakil (Ethiopia), is an interesting yet poorly studied polyextreme environment for investigating the limits of life. Here, we explored the presence of signs of life in five samples of sinter deposits at Dallol, by means of lipid biomarkers and stable isotope composition. The results reveal the existence of biological material with predominance of (presently or recently active) microbial sources, according to the relative abundance of low-over-high molecular weight moieties (n-alkanes, n-carboxylic acids, or n-alkanols), and the detection of diverse microbial-diagnostic compounds (i.e., monomethyl alkanes; C16:1 ω7, C18:1 ω9, C18:1 ω10, C18:2 ω6,9 and iso/anteiso C15 and C17 carboxylic acids; or short-chained dicarboxylic acids). The molecular lipid patterns at Dallol suggest a microbial community largely composed of thermophilic members of the Aquificae, Thermotogae, Chroroflexi, or Proteobacteria phyla, as well as microbial consortia of phototrophs (e.g., Cyanobacteria-Chloroflexi) in lower-temperature and higher-pH niches. Autotrophic sources most likely using the Calvin cycle, together with the acetyl coenzyme A (CoA) pathway, were inferred from the depleted bulk δ13C ratios (-25.9/-22.6‰), while sulfate-reducing bacteria were considered according to enriched sulfate (7.3/11.7‰) and total sulfur (20.5/8.2‰) δ34S ratios. The abundance of functionalized hydrocarbons (i.e., n-carboxylic acids and n-alkanols) and the distinct even-over-odd predominance/preference on the typically odd n-alkanes (CPIalkanes ≤ 1) pointed to active or recent microbial metabolisms. This study documents the detection of biosignatures in the polyextreme environment of Dallol and raises the possibility of finding life or its remnants in other remote locations on Earth, where the harsh environmental conditions would lead to expect otherwise. These findings are relevant for understanding the limits of life and have implications for searching for hypothetical life vestiges in extreme environments beyond Earth.
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Affiliation(s)
- Daniel Carrizo
- Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid, Spain
- Address correspondence to: Daniel Carrizo, Centro de Astrobiología (CSIC-INTA), Carretera de Ajalvir km 4, Torrejón de Ardoz, 28850, Madrid, Spain
| | | | - Nuria Rodriguez
- Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid, Spain
| | - Felipe Gómez
- Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid, Spain
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13
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A novel thermophilic Aeribacillus bacteriophage AP45 isolated from the Valley of Geysers, Kamchatka: genome analysis suggests the existence of a new genus within the Siphoviridae family. Extremophiles 2019; 23:599-612. [PMID: 31376001 DOI: 10.1007/s00792-019-01119-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 07/21/2019] [Indexed: 12/12/2022]
Abstract
A novel thermophilic bacteriophage AP45 and its host strain Aeribacillus sp. CEMTC656 were isolated from the Valley of Geysers, Kamchatka Peninsula, Russia. Bacteriophage AP45 was identified as a member of the Siphoviridae family by electron microscopy. It showed high thermostability and had a slow cycle of reproduction. The AP45 genome had 51,606 base pairs (bp) and contained 71 open reading frames (ORFs), 40 of them encoding proteins of predicted function. Genes encoding DNA and RNA polymerases were not identified, indicating that AP45 used host polymerases. Based on the ORF65 encoding putative endolysin, the recombinant protein rAP45Lys was developed and its peptidoglycan-hydrolyzing activity was demonstrated. The AP45 genome exhibited limited identity to other phage sequences; the highest identity, 36%, was with the genome of the thermophilic Geobacillus myovirus D6E. The majority of putative proteins encoded by the AP45 genome had higher similarity to proteins from bacteria belonging to the Bacillaceae family, than to bacteriophages. In addition, more than half of the putative ORFs in the AP45 genome were highly similar to prophage sequences of A. pallidus strain 8m3, which was isolated in north-east China. The AP45 phage and revealed prophages might be members of a new genus belonging to the Siphoviridae family.
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14
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Wilkins LGE, Ettinger CL, Jospin G, Eisen JA. Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia. Sci Rep 2019; 9:3059. [PMID: 30816235 PMCID: PMC6395817 DOI: 10.1038/s41598-019-39576-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 01/17/2019] [Indexed: 12/21/2022] Open
Abstract
Culture-independent methods have contributed substantially to our understanding of global microbial diversity. Recently developed algorithms to construct whole genomes from environmental samples have further refined, corrected and revolutionized understanding of the tree of life. Here, we assembled draft metagenome-assembled genomes (MAGs) from environmental DNA extracted from two hot springs within an active volcanic ecosystem on the Kamchatka peninsula, Russia. This hydrothermal system has been intensively studied previously with regard to geochemistry, chemoautotrophy, microbial isolation, and microbial diversity. We assembled genomes of bacteria and archaea using DNA that had previously been characterized via 16S rRNA gene clone libraries. We recovered 36 MAGs, 29 of medium to high quality, and inferred their placement in a phylogenetic tree consisting of 3,240 publicly available microbial genomes. We highlight MAGs that were taxonomically assigned to groups previously underrepresented in available genome data. This includes several archaea (Korarchaeota, Bathyarchaeota and Aciduliprofundum) and one potentially new species within the bacterial genus Sulfurihydrogenibium. Putative functions in both pools were compared and are discussed in the context of their diverging geochemistry. This study adds comprehensive information about phylogenetic diversity and functional potential within two hot springs in the caldera of Kamchatka.
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Affiliation(s)
- Laetitia G E Wilkins
- Department of Environmental Sciences, Policy & Management, University of California, Berkeley, CA, 94720, USA. .,Genome Center, University of California, Davis, CA, 95616, USA.
| | | | | | - Jonathan A Eisen
- Genome Center, University of California, Davis, CA, 95616, USA.,Department of Evolution and Ecology, University of California, Davis, CA, 95616, USA.,Department of Medical Microbiology and Immunology, University of California, Davis, CA, 95616, USA
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15
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Calditol-linked membrane lipids are required for acid tolerance in Sulfolobus acidocaldarius. Proc Natl Acad Sci U S A 2018; 115:12932-12937. [PMID: 30518563 DOI: 10.1073/pnas.1814048115] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Archaea have many unique physiological features of which the lipid composition of their cellular membranes is the most striking. Archaeal ether-linked isoprenoidal membranes can occur as bilayers or monolayers, possess diverse polar head groups, and a multiplicity of ring structures in the isoprenoidal cores. These lipid structures are proposed to provide protection from the extreme temperature, pH, salinity, and nutrient-starved conditions that many archaea inhabit. However, many questions remain regarding the synthesis and physiological role of some of the more complex archaeal lipids. In this study, we identify a radical S-adenosylmethionine (SAM) protein in Sulfolobus acidocaldarius required for the synthesis of a unique cyclopentyl head group, known as calditol. Calditol-linked glycerol dibiphytanyl glycerol tetraethers (GDGTs) are membrane spanning lipids in which calditol is ether bonded to the glycerol backbone and whose production is restricted to a subset of thermoacidophilic archaea of the Sulfolobales order within the Crenarchaeota phylum. Several studies have focused on the enzymatic mechanism for the synthesis of the calditol moiety, but to date no protein that catalyzes this reaction has been discovered. Phylogenetic analyses of this putative calditol synthase (Cds) reveal the genetic potential for calditol-GDGT synthesis in phyla other than the Crenarchaeota, including the Korarchaeota and Marsarchaeota. In addition, we identify Cds homologs in metagenomes predominantly from acidic ecosystems. Finally, we demonstrate that deletion of calditol synthesis renders S. acidocaldarius sensitive to extremely low pH, indicating that calditol plays a critical role in protecting archaeal cells from acidic stress.
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16
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Rüffel V, Maar M, Dammbrück MN, Hauröder B, Neu TR, Meier J. Thermodesulfobium sp. strain 3baa, an acidophilic sulfate reducing bacterium forming biofilms triggered by mineral precipitation. Environ Microbiol 2018; 20:3717-3731. [PMID: 30105784 DOI: 10.1111/1462-2920.14374] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 08/01/2018] [Accepted: 08/05/2018] [Indexed: 01/22/2023]
Abstract
Sulfate reducing prokaryotes are promising candidates for the remediation of acidic metal-rich waste waters. However, only few acidophilic species have been described to date. Chemolithoautotrophic strain 3baa was isolated from sediments of an acidic mine pit lake. Based on its 16S-rRNA gene sequence it belongs to the genus Thermodesulfobium. It was identified as an acidophile growing in artificial pore water medium in the range of pH 2.6-6.6. Though the highest sulfate reduction rates were obtained at the lower end of this range, elongated cells and extended lag phases demonstrated acid stress. Sulfate reduction at low pH was accompanied by the formation of mineral precipitates strongly adhering to solid surfaces. A structural investigation by laser scanning microscopy, electron microscopy and X-ray microanalysis revealed the formation of Al hydroxides and Fe sulfides which were densely populated by cells. Al hydroxides precipitated first, enabling initial cell attachment. Colonization of solid surfaces coincided with increased sulfate reducing activity indicating more favourable growth conditions within biofilms compared with free-living cells. These findings point out the importance of cell-mineral interaction for biofilm formation and contribute to our understanding how sulfate reducing prokaryotes thrive in both natural and engineered systems at low pH.
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Affiliation(s)
- Viola Rüffel
- Institute for Integrated Natural Sciences, University Koblenz-Landau, 56070, Koblenz, Germany
| | - Mona Maar
- Institute for Integrated Natural Sciences, University Koblenz-Landau, 56070, Koblenz, Germany
| | - Markus N Dammbrück
- Institute for Integrated Natural Sciences, University Koblenz-Landau, 56070, Koblenz, Germany
| | - Bärbel Hauröder
- Department of Pathology, Electron Microscopy, Bundeswehr Central Hospital Coblenz, 56070, Koblenz, Germany
| | - Thomas R Neu
- Department of River Ecology, Helmholtz Centre of Environmental Research - UFZ, 39114, Magdeburg, Germany
| | - Jutta Meier
- Institute for Integrated Natural Sciences, University Koblenz-Landau, 56070, Koblenz, Germany
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17
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Mardanov AV, Gumerov VM, Beletsky AV, Ravin NV. Microbial diversity in acidic thermal pools in the Uzon Caldera, Kamchatka. Antonie Van Leeuwenhoek 2017; 111:35-43. [PMID: 28815328 DOI: 10.1007/s10482-017-0924-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 08/07/2017] [Indexed: 11/27/2022]
Abstract
Microbial communities of four acidic thermal pools in the Uzon Caldera, Kamchatka, Russia, were studied using amplification and pyrosequencing of 16S rRNA gene fragments. The sites differed in temperature and pH: 1805 (60 °C, pH 3.7), 1810 (90 °C, pH 4.1), 1818 (80 °C, pH 3.5), and 1807 (86 °C, pH 5.6). Archaea of the order Sulfolobales were present among the dominant groups in all four pools. Acidilobales dominated in pool 1818 but were a minor fraction at the higher temperature in pool 1810. Uncultivated Archaea of the Hot Thaumarchaeota-related clade were present in significant quantities in pools 1805 and 1807, but they were not abundant in pools 1810 and 1818, where high temperatures were combined with low pH. Nanoarchaeota were present in all pools, but were more abundant in pools 1810 and 1818. A similar abundance pattern was observed for Halobacteriales. Thermophilic Bacteria were less diverse and were mostly represented by aerobic hydrogen- and sulfur-oxidizers of the phylum Aquificae and sulfur-oxidising Proteobacteria of the genus Acidithiobacillus. Thus we showed that extremely acidic hot pools contain diverse microbial communities comprising different metabolic groups of prokaryotes, including putative lithoautotrophs using energy sources of volcanic origin, and various facultative and obligate heterotrophs.
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Affiliation(s)
- Andrey V Mardanov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prosp., 33-2, Moscow, Russia, 119071
| | - Vadim M Gumerov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prosp., 33-2, Moscow, Russia, 119071
| | - Alexey V Beletsky
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prosp., 33-2, Moscow, Russia, 119071
| | - Nikolai V Ravin
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Prosp., 33-2, Moscow, Russia, 119071.
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18
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Merkel AY, Pimenov NV, Rusanov II, Slobodkin AI, Slobodkina GB, Tarnovetckii IY, Frolov EN, Dubin AV, Perevalova AA, Bonch-Osmolovskaya EA. Microbial diversity and autotrophic activity in Kamchatka hot springs. Extremophiles 2016; 21:307-317. [DOI: 10.1007/s00792-016-0903-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Accepted: 11/27/2016] [Indexed: 12/26/2022]
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19
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Brumm PJ, Gowda K, Robb FT, Mead DA. The Complete Genome Sequence of Hyperthermophile Dictyoglomus turgidum DSM 6724™ Reveals a Specialized Carbohydrate Fermentor. Front Microbiol 2016; 7:1979. [PMID: 28066333 PMCID: PMC5167688 DOI: 10.3389/fmicb.2016.01979] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 11/25/2016] [Indexed: 11/13/2022] Open
Abstract
Here we report the complete genome sequence of the chemoorganotrophic, extremely thermophilic bacterium, Dictyoglomus turgidum, which is a Gram negative, strictly anaerobic bacterium. D. turgidum and D. thermophilum together form the Dictyoglomi phylum. The two Dictyoglomus genomes are highly syntenic, and both are distantly related to Caldicellulosiruptor spp. D. turgidum is able to grow on a wide variety of polysaccharide substrates due to significant genomic commitment to glycosyl hydrolases, 16 of which were cloned and expressed in our study. The GH5, GH10, and GH42 enzymes characterized in this study suggest that D. turgidum can utilize most plant-based polysaccharides except crystalline cellulose. The DNA polymerase I enzyme was also expressed and characterized. The pure enzyme showed improved amplification of long PCR targets compared to Taq polymerase. The genome contains a full complement of DNA modifying enzymes, and an unusually high copy number (4) of a new, ancestral family of polB type nucleotidyltransferases designated as MNT (minimal nucleotidyltransferases). Considering its optimal growth at 72°C, D. turgidum has an anomalously low G+C content of 39.9% that may account for the presence of reverse gyrase, usually associated with hyperthermophiles.
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Affiliation(s)
- Phillip J Brumm
- C5-6 Technologies LLCFitchburg, WI, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-MadisonMadison, WI, USA
| | - Krishne Gowda
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-MadisonMadison, WI, USA; Lucigen CorporationMiddleton, WI, USA
| | - Frank T Robb
- Department of Microbiology and Immunology, Institute of Marine and Environmental Technology, University of Maryland Baltimore, MD, USA
| | - David A Mead
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin-MadisonMadison, WI, USA; Varigen Biosciences CorporationMadison, WI, USA
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20
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Geesey GG, Barkay T, King S. Microbes in mercury-enriched geothermal springs in western North America. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 569-570:321-331. [PMID: 27344121 DOI: 10.1016/j.scitotenv.2016.06.080] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 06/11/2016] [Accepted: 06/12/2016] [Indexed: 06/06/2023]
Abstract
Because geothermal environments contain mercury (Hg) from natural sources, microorganisms that evolved in these systems have likely adapted to this element. Knowledge of the interactions between microorganisms and Hg in geothermal systems may assist in understanding the long-term evolution of microbial adaptation to Hg with relevance to other environments where Hg is introduced from anthropogenic sources. A number of microbiological studies with supporting geochemistry have been conducted in geothermal systems across western North America. Approximately 1 in 5 study sites include measurements of Hg. Of all prokaryotic taxa reported across sites with microbiological and accompanying physicochemical data, 42% have been detected at sites in which Hg was measured. Genes specifying Hg reduction and detoxification by microorganisms were detected in a number of hot springs across the region. Archaeal-like sequences, representing two crenarchaeal orders and one order each of the Euryarchaeota and Thaumarchaeota, dominated in metagenomes' MerA (the mercuric reductase protein) inventories, while bacterial homologs were mostly found in one deeply sequenced metagenome. MerA homologs were more frequently found in metagenomes of microbial communities in acidic springs than in circumneutral or high pH geothermal systems, possibly reflecting higher bioavailability of Hg under acidic conditions. MerA homologs were found in hot springs prokaryotic isolates affiliated with Bacteria and Archaea taxa. Acidic sites with high Hg concentrations contain more of Archaea than Bacteria taxa, while the reverse appears to be the case in circumneutral and high pH sites with high Hg concentrations. However, MerA was detected in only a small fraction of the Archaea and Bacteria taxa inhabiting sites containing Hg. Nevertheless, the presence of MerA homologs and their distribution patterns in systems, in which Hg has yet to be measured, demonstrates the potential for detoxification by Hg reduction in these geothermal systems, particularly the low pH springs that are dominated by Archaea.
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Affiliation(s)
- Gill G Geesey
- Department of Microbiology and Immunology, Thermal Biology Institute, Montana State University, Bozeman, MT 59717-3520, USA.
| | - Tamar Barkay
- Department of Biochemistry and Microbiology, Graduate Program in Ecology and Evolution, Rutgers University, New Brunswick, NJ 08901-8525, USA.
| | - Sue King
- 2908 3rd Avenue North, Great Falls, MT 59401, USA.
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21
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Kochetkova TV, Kublanov IV, Toshchakov SV, Osburn MR, Novikov AA, Bonch-Osmolovskaya EA, Perevalova AA. Thermogladius calderae gen. nov., sp. nov., an anaerobic, hyperthermophilic crenarchaeote from a Kamchatka hot spring. Int J Syst Evol Microbiol 2016; 66:1407-1412. [DOI: 10.1099/ijsem.0.000916] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Tatiana V. Kochetkova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS,33/2 Leninsky prospect, 119071, Moscow,Russia
| | - Ilya V. Kublanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS,33/2 Leninsky prospect, 119071, Moscow,Russia
| | - Stepan V. Toshchakov
- Immanuel Kant Baltic Federal University,Botkina str. 3, 236016, Kaliningrad,Russia
| | - Magdalena R. Osburn
- Department of Earth and Planetary Sciences, Northwestern University,Evanston, IL,USA
| | - Andrei A. Novikov
- Gubkin Russian State University of Oil and Gas,Leninskiy Prospect 65, 119991, Moscow,Russia
| | | | - Anna A. Perevalova
- Winogradsky Institute of Microbiology, Research Center of Biotechnology RAS,33/2 Leninsky prospect, 119071, Moscow,Russia
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22
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Gaisin VA, Grouzdev DS, Namsaraev ZB, Sukhacheva MV, Gorlenko VM, Kuznetsov BB. Biogeography of thermophilic phototrophic bacteria belonging toRoseiflexusgenus. FEMS Microbiol Ecol 2016; 92:fiw012. [DOI: 10.1093/femsec/fiw012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/27/2016] [Indexed: 11/14/2022] Open
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23
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Chernyh NA, Mardanov AV, Gumerov VM, Miroshnichenko ML, Lebedinsky AV, Merkel AY, Crowe D, Pimenov NV, Rusanov II, Ravin NV, Moran MA, Bonch-Osmolovskaya EA. Microbial life in Bourlyashchy, the hottest thermal pool of Uzon Caldera, Kamchatka. Extremophiles 2015; 19:1157-71. [DOI: 10.1007/s00792-015-0787-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 08/30/2015] [Indexed: 11/29/2022]
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24
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Menzel P, Gudbergsdóttir SR, Rike AG, Lin L, Zhang Q, Contursi P, Moracci M, Kristjansson JK, Bolduc B, Gavrilov S, Ravin N, Mardanov A, Bonch-Osmolovskaya E, Young M, Krogh A, Peng X. Comparative Metagenomics of Eight Geographically Remote Terrestrial Hot Springs. MICROBIAL ECOLOGY 2015; 70:411-424. [PMID: 25712554 DOI: 10.1007/s00248-015-0576-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 01/23/2015] [Indexed: 06/04/2023]
Abstract
Hot springs are natural habitats for thermophilic Archaea and Bacteria. In this paper, we present the metagenomic analysis of eight globally distributed terrestrial hot springs from China, Iceland, Italy, Russia, and the USA with a temperature range between 61 and 92 (∘)C and pH between 1.8 and 7. A comparison of the biodiversity and community composition generally showed a decrease in biodiversity with increasing temperature and decreasing pH. Another important factor shaping microbial diversity of the studied sites was the abundance of organic substrates. Several species of the Crenarchaeal order Thermoprotei were detected, whereas no single bacterial species was found in all samples, suggesting a better adaptation of certain archaeal species to different thermophilic environments. Two hot springs show high abundance of Acidithiobacillus, supporting the idea of a true thermophilic Acidithiobacillus species that can thrive in hyperthermophilic environments. Depending on the sample, up to 58 % of sequencing reads could not be assigned to a known phylum, reinforcing the fact that a large number of microorganisms in nature, including those thriving in hot environments remain to be isolated and characterized.
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Affiliation(s)
- Peter Menzel
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark
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Urbieta MS, Porati GW, Segretín AB, González-Toril E, Giaveno MA, Donati ER. Copahue Geothermal System: A Volcanic Environment with Rich Extreme Prokaryotic Biodiversity. Microorganisms 2015; 3:344-63. [PMID: 27682093 PMCID: PMC5023244 DOI: 10.3390/microorganisms3030344] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Revised: 06/09/2015] [Accepted: 06/15/2015] [Indexed: 01/25/2023] Open
Abstract
The Copahue geothermal system is a natural extreme environment located at the northern end of the Cordillera de los Andes in Neuquén province in Argentina. The geochemistry and consequently the biodiversity of the area are dominated by the activity of the Copahue volcano. The main characteristic of Copahue is the extreme acidity of its aquatic environments; ponds and hot springs of moderate and high temperature as well as Río Agrio. In spite of being an apparently hostile location, the prokaryotic biodiversity detected by molecular ecology techniques as well as cultivation shows a rich and diverse environment dominated by acidophilic, sulphur oxidising bacteria or archaea, depending on the conditions of the particular niche studied. In microbial biofilms, found in the borders of the ponds where thermal activity is less intense, the species found are completely different, with a high presence of cyanobacteria and other photosynthetic species. Our results, collected during more than 10 years of work in Copahue, have enabled us to outline geomicrobiological models for the different environments found in the ponds and Río Agrio. Besides, Copahue seems to be the habitat of novel, not yet characterised autochthonous species, especially in the domain Archaea.
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Affiliation(s)
- María Sofía Urbieta
- CINDEFI (CCT La Plata-CONICET, Facultad de Ciencias Exactas-UNLP), calle 50 entre 115 y 116 N° 227 La Plata, Buenos Aires B8508, Argentina.
| | - Graciana Willis Porati
- CINDEFI (CCT La Plata-CONICET, Facultad de Ciencias Exactas-UNLP), calle 50 entre 115 y 116 N° 227 La Plata, Buenos Aires B8508, Argentina.
| | - Ana Belén Segretín
- CINDEFI (CCT La Plata-CONICET, Facultad de Ciencias Exactas-UNLP), calle 50 entre 115 y 116 N° 227 La Plata, Buenos Aires B8508, Argentina.
| | - Elena González-Toril
- Centro de Astrobiología, Instituto Nacional de Técnica Aeroespacial (INTA-CSIC), Carretera de Ajalvir Km. 4, 28850, Torrejón de Ardoz, Madrid 28850, Spain.
| | - María Alejandra Giaveno
- Laboratorio de Biolixiviación, Departamentoo de Química-Facultad de Ingeniería, Universidad Nacional del Comahue, PROBIEN (CONICET-UNCo) Buenos Aires 1400 (8300) Neuquén, Argentina.
| | - Edgardo Rubén Donati
- CINDEFI (CCT La Plata-CONICET, Facultad de Ciencias Exactas-UNLP), calle 50 entre 115 y 116 N° 227 La Plata, Buenos Aires B8508, Argentina.
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Wübbeler JH, Hiessl S, Meinert C, Poehlein A, Schuldes J, Daniel R, Steinbüchel A. The genome of Variovorax paradoxus strain TBEA6 provides new understandings for the catabolism of 3,3'-thiodipropionic acid and hence the production of polythioesters. J Biotechnol 2015; 209:85-95. [PMID: 26073999 DOI: 10.1016/j.jbiotec.2015.06.390] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 06/01/2015] [Accepted: 06/09/2015] [Indexed: 11/30/2022]
Abstract
The betaproteobacterium Variovorax paradoxus strain TBEA6 is capable of using 3,3'-thiodipropionic acid (TDP) as sole carbon and energy source for growth. This thioether is employed for several industrial applications. It can be applied as precursor for the biotechnical production of polythioesters (PTE), which represent persistent bioplastics. Consequently, the genome of V. paradoxus strain TBEA6 was sequenced. The draft genome sequence comprises approximately 7.2Mbp and 6852 predicted open reading frames. Furthermore, transposon mutagenesis to unravel the catabolism of TDP in strain TBEA6 was performed. Screening of 20,000 mutants mapped the insertions of Tn5::mob in 32 mutants, which all showed no growth with TDP as sole carbon source. Based on the annotated genome sequence together with transposon-induced mutagenesis, defined gene deletions, in silico analyses and comparative genomics, a comprehensive pathway for the catabolism of TDP is proposed: TDP is imported via the tripartite tricarboxcylate transport system and/or the TRAP-type dicarboxylate transport system. The initial cleavage of TDP into 3-hydroxypropionic acid (3HP) and 3-mercaptopropionic acid (3MP), which serves as precursor substrate for PTE synthesis, is most probably performed by the FAD-dependent oxidoreductase Fox. 3HP is presumably catabolized via malonate semialdehyde, whereas 3MP is oxygenated by the 3MP-dioxygenase Mdo yielding 3-sulfinopropionic acid (3SP). Afterwards, 3SP is linked to coenzyme A. The next step is the abstraction of sulfite by a desulfinase, and the resulting propionyl-CoA enters the central metabolism. Sulfite is oxidized to sulfate by the sulfite-oxidizing enzyme SoeABC and is subsequently excreted by the cells by the sulfate exporter Pse.
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Affiliation(s)
- Jan Hendrik Wübbeler
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Sebastian Hiessl
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Christina Meinert
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Jörg Schuldes
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, 48149 Münster, Germany; Faculty of Biology, King Abdulaziz University, Jeddah, Saudi Arabia.
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Comparison of the microbial communities of hot springs waters and the microbial biofilms in the acidic geothermal area of Copahue (Neuquén, Argentina). Extremophiles 2015; 19:437-50. [DOI: 10.1007/s00792-015-0729-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 01/05/2015] [Indexed: 10/24/2022]
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Rozanov AS, Bryanskaya AV, Malup TK, Meshcheryakova IA, Lazareva EV, Taran OP, Ivanisenko TV, Ivanisenko VA, Zhmodik SM, Kolchanov NA, Peltek SE. Molecular analysis of the benthos microbial community in Zavarzin thermal spring (Uzon Caldera, Kamchatka, Russia). BMC Genomics 2014; 15 Suppl 12:S12. [PMID: 25563397 PMCID: PMC4303939 DOI: 10.1186/1471-2164-15-s12-s12] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background Geothermal areas are of great interest for the study of microbial communities. The results of such investigations can be used in a variety of fields (ecology, microbiology, medicine) to answer fundamental questions, as well as those with practical benefits. Uzon caldera is located in the Uzon-Geyser depression that is situated in the centre of the Karym-Semyachin region of the East Kamchatka graben-synclinorium. The microbial communities of Zavarzin spring are well studied; however, its benthic microbial mat has not been previously described. Results Pyrosequencing of the V3 region of the 16S rRNA gene was used to study the benthic microbial community of the Zavarzin thermal spring (Uzon Caldera, Kamchatka). The community is dominated by bacteria (>95% of all sequences), including thermophilic, chemoorganotrophic Caldiserica (33.0%) and Dictyoglomi (24.8%). The benthic community and the previously examined planktonic community of Zavarzin spring have qualitatively similar, but quantitatively different, compositions. Conclusions In this study, we performed a metagenomic analysis of the benthic microbial mat of Zavarzin spring. We compared this benthic community to microbial communities found in the water and of an integral probe consisting of water and bottom sediments. Various phylogenetic groups of microorganisms, including potentially new ones, represent the full-fledged trophic system of Zavarzin. A thorough geochemical study of the spring was performed.
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Archaeal and bacterial diversity in five different hydrothermal ponds in the Copahue region in Argentina. Syst Appl Microbiol 2014; 37:429-41. [DOI: 10.1016/j.syapm.2014.05.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 05/24/2014] [Accepted: 05/26/2014] [Indexed: 11/18/2022]
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Biosignatures in chimney structures and sediment from the Loki’s Castle low-temperature hydrothermal vent field at the Arctic Mid-Ocean Ridge. Extremophiles 2014; 18:545-60. [DOI: 10.1007/s00792-014-0640-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 03/02/2014] [Indexed: 11/26/2022]
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Lebedinsky AV, Mardanov AV, Kublanov IV, Gumerov VM, Beletsky AV, Perevalova AA, Bidzhieva SK, Bonch-Osmolovskaya EA, Skryabin KG, Ravin NV. Analysis of the complete genome of Fervidococcus fontis confirms the distinct phylogenetic position of the order Fervidicoccales and suggests its environmental function. Extremophiles 2013; 18:295-309. [DOI: 10.1007/s00792-013-0616-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 12/05/2013] [Indexed: 12/30/2022]
Affiliation(s)
- Alexander V Lebedinsky
- Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospekt 60-let Oktyabrya, 7/2, Moscow, 117312, Russia,
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Brandt U, Hiessl S, Schuldes J, Thürmer A, Wübbeler JH, Daniel R, Steinbüchel A. Genome-guided insights into the versatile metabolic capabilities of the mercaptosuccinate-utilizing β-proteobacterium Variovorax paradoxus strain B4. Environ Microbiol 2013; 16:3370-86. [PMID: 24245581 DOI: 10.1111/1462-2920.12340] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 11/12/2013] [Indexed: 10/26/2022]
Abstract
Variovorax paradoxus B4 is able to utilize 2-mercaptosuccinate (MS) as sole carbon, sulfur and energy source. The whole genome of V. paradoxus B4 was sequenced, annotated and evaluated with special focus on genomic elements related to MS metabolism. The genome encodes two chromosomes harbouring 5 795 261 and 1 353 255 bp. A total of 6753 putative protein-coding sequences were identified. Based on the genome and in combination with results from previous studies, a putative pathway for the degradation of MS could be postulated. The putative molybdopterin oxidoreductase identified during transposon mutagenesis probably catalyses the conversion of MS first into sulfinosuccinate and then into sulfosuccinate by successive transfer of oxygen atoms. Subsequently, the cleavage of sulfosuccinate yields oxaloacetate and sulfite, while the latter is oxidized to sulfate. The expression of the putative molybdopterin oxidoreductase was induced by MS, but not by gluconate, as confirmed by reverse transcriptase polymerase chain reaction. Further, in silico studies combined with experiments and comparative genomics revealed high metabolic diversity of strain B4. It bears a high potential as plant growth-promoting bacterium and as candidate for degradation and detoxification of xenobiotics and other hardly degradable substances. Additionally, the strain is of special interest for production of polythioesters with sulfur-containing precursors as MS.
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Affiliation(s)
- Ulrike Brandt
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität, Corrensstraße 3, Münster, D-48149, Germany
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Diversity and abundance of the arsenite oxidase gene aioA in geothermal areas of Tengchong, Yunnan, China. Extremophiles 2013; 18:161-70. [DOI: 10.1007/s00792-013-0608-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 11/14/2013] [Indexed: 10/26/2022]
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Wagner ID, Varghese LB, Hemme CL, Wiegel J. Multilocus sequence analysis of Thermoanaerobacter isolates reveals recombining, but differentiated, populations from geothermal springs of the Uzon Caldera, Kamchatka, Russia. Front Microbiol 2013; 4:169. [PMID: 23801987 PMCID: PMC3689144 DOI: 10.3389/fmicb.2013.00169] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Accepted: 06/04/2013] [Indexed: 01/15/2023] Open
Abstract
Thermal environments have island-like characteristics and provide a unique opportunity to study population structure and diversity patterns of microbial taxa inhabiting these sites. Strains having ≥98% 16S rRNA gene sequence similarity to the obligately anaerobic Firmicutes Thermoanaerobacter uzonensis were isolated from seven geothermal springs, separated by up to 1600 m, within the Uzon Caldera (Kamchatka, Russian Far East). The intraspecies variation and spatial patterns of diversity for this taxon were assessed by multilocus sequence analysis (MLSA) of 106 strains. Analysis of eight protein-coding loci (gyrB, lepA, leuS, pyrG, recA, recG, rplB, and rpoB) revealed that all loci were polymorphic and that nucleotide substitutions were mostly synonymous. There were 148 variable nucleotide sites across 8003 bp concatenates of the protein-coding loci. While pairwise FST values indicated a small but significant level of genetic differentiation between most subpopulations, there was a negligible relationship between genetic divergence and spatial separation. Strains with the same allelic profile were only isolated from the same hot spring, occasionally from consecutive years, and single locus variant (SLV) sequence types were usually derived from the same spring. While recombination occurred, there was an “epidemic” population structure in which a particular T. uzonensis sequence type rose in frequency relative to the rest of the population. These results demonstrate spatial diversity patterns for an anaerobic bacterial species in a relative small geographic location and reinforce the view that terrestrial geothermal springs are excellent places to look for biogeographic diversity patterns regardless of the involved distances.
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Affiliation(s)
- Isaac D Wagner
- Department of Microbiology, University of Georgia Athens, GA, USA
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Microbial diversity and biochemical potential encoded by thermal spring metagenomes derived from the Kamchatka Peninsula. ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL 2013; 2013:136714. [PMID: 23533327 PMCID: PMC3600328 DOI: 10.1155/2013/136714] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 01/06/2013] [Indexed: 02/01/2023]
Abstract
Volcanic regions contain a variety of environments suitable for extremophiles. This study was focused on assessing and exploiting the prokaryotic diversity of two microbial communities derived from different Kamchatkian thermal springs by metagenomic approaches. Samples were taken from a thermoacidophilic spring near the Mutnovsky Volcano and from a thermophilic spring in the Uzon Caldera. Environmental DNA for metagenomic analysis was isolated from collected sediment samples by direct cell lysis. The prokaryotic community composition was examined by analysis of archaeal and bacterial 16S rRNA genes. A total number of 1235 16S rRNA gene sequences were obtained and used for taxonomic classification. Most abundant in the samples were members of Thaumarchaeota, Thermotogae, and Proteobacteria. The Mutnovsky hot spring was dominated by the Terrestrial Hot Spring Group, Kosmotoga, and Acidithiobacillus. The Uzon Caldera was dominated by uncultured members of the Miscellaneous Crenarchaeotic Group and Enterobacteriaceae. The remaining 16S rRNA gene sequences belonged to the Aquificae, Dictyoglomi, Euryarchaeota, Korarchaeota, Thermodesulfobacteria, Firmicutes, and some potential new phyla. In addition, the recovered DNA was used for generation of metagenomic libraries, which were subsequently mined for genes encoding lipolytic and proteolytic enzymes. Three novel genes conferring lipolytic and one gene conferring proteolytic activity were identified.
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Comparative genomic analysis of phylogenetically closely related Hydrogenobaculum sp. isolates from Yellowstone National Park. Appl Environ Microbiol 2013; 79:2932-43. [PMID: 23435891 DOI: 10.1128/aem.03591-12] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We describe the complete genome sequences of four closely related Hydrogenobaculum sp. isolates (≥ 99.7% 16S rRNA gene identity) that were isolated from the outflow channel of Dragon Spring (DS), Norris Geyser Basin, in Yellowstone National Park (YNP), WY. The genomes range in size from 1,552,607 to 1,552,931 bp, contain 1,667 to 1,676 predicted genes, and are highly syntenic. There are subtle differences among the DS isolates, which as a group are different from Hydrogenobaculum sp. strain Y04AAS1 that was previously isolated from a geographically distinct YNP geothermal feature. Genes unique to the DS genomes encode arsenite [As(III)] oxidation, NADH-ubiquinone-plastoquinone (complex I), NADH-ubiquinone oxidoreductase chain, a DNA photolyase, and elements of a type II secretion system. Functions unique to strain Y04AAS1 include thiosulfate metabolism, nitrate respiration, and mercury resistance determinants. DS genomes contain seven CRISPR loci that are almost identical but are different from the single CRISPR locus in strain Y04AAS1. Other differences between the DS and Y04AAS1 genomes include average nucleotide identity (94.764%) and percentage conserved DNA (80.552%). Approximately half of the genes unique to Y04AAS1 are predicted to have been acquired via horizontal gene transfer. Fragment recruitment analysis and marker gene searches demonstrated that the DS metagenome was more similar to the DS genomes than to the Y04AAS1 genome, but that the DS community is likely comprised of a continuum of Hydrogenobaculum genotypes that span from the DS genomes described here to an Y04AAS1-like organism, which appears to represent a distinct ecotype relative to the DS genomes characterized.
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Abstract
This review outlines information about the Gram-negative, aerobic bacterium Variovorax paradoxus. The genomes of these species have G+C contents of 66.5-69.4 mol%, and the cells form yellow colonies. Some strains of V. paradoxus are facultative lithoautotrophic, others are chemoorganotrophic. Many of them are associated with important catabolic processes including the degradation of toxic and/or complex chemical compounds. The degradation pathways or other skills related to the following compounds, respectively, are described in this review: sulfolane, 3-sulfolene, 2-mercaptosuccinic acid, 3,3'-thiodipropionic acid, aromatic sulfonates, alkanesulfonates, amino acids and other sulfur sources, polychlorinated biphenyls, dimethyl terephthalate, linuron, 2,4-dinitrotoluene, homovanillate, veratraldehyde, 2,4-dichlorophenoxyacetic acid, anthracene, poly(3-hydroxybutyrate), chitin, cellulose, humic acids, metal-EDTA complexes, yttrium, rare earth elements, As(III), trichloroethylene, capsaicin, 3-nitrotyrosine, acyl-homoserine lactones, 1-aminocyclopropane-1-carboxylate, methyl tert-butyl ether, geosmin, and 2-methylisoborneol. Strains of V. paradoxus are also engaged in mutually beneficial interactions with other plant and bacterial species in various ecosystems. This species comprises probably promising strains for bioremediation and other biotechnical applications. Lately, the complete genomes of strains S110 and EPS have been sequenced for further investigations.
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Song ZQ, Wang FP, Zhi XY, Chen JQ, Zhou EM, Liang F, Xiao X, Tang SK, Jiang HC, Zhang CL, Dong H, Li WJ. Bacterial and archaeal diversities in Yunnan and Tibetan hot springs, China. Environ Microbiol 2012; 15:1160-75. [PMID: 23126508 DOI: 10.1111/1462-2920.12025] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Revised: 09/17/2012] [Accepted: 10/09/2012] [Indexed: 11/27/2022]
Abstract
Thousands of hot springs are located in the north-eastern part of the Yunnan-Tibet geothermal zone, which is one of the most active geothermal areas in the world. However, a comprehensive and detailed understanding of microbial diversity in these hot springs is still lacking. In this study, bacterial and archaeal diversities were investigated in 16 hot springs (pH 3.2-8.6; temperature 47-96°C) in Yunnan Province and Tibet, China by using a barcoded 16S rRNA gene-pyrosequencing approach. Aquificae, Proteobacteria, Firmicutes, Deinococcus-Thermus and Bacteroidetes comprised the large portion of the bacterial communities in acidic hot springs. Non-acidic hot springs harboured more and variable bacterial phyla than acidic springs. Desulfurococcales and unclassified Crenarchaeota were the dominated groups in archaeal populations from most of the non-acidic hot springs; whereas, the archaeal community structure in acidic hot springs was simpler and characterized by Sulfolobales and Thermoplasmata. The phylogenetic analyses showed that Aquificae and Crenarchaeota were predominant in the investigated springs and possessed many phylogenetic lineages that have never been detected in other hot springs in the world. Thus findings from this study significantly improve our understanding of microbial diversity in terrestrial hot springs.
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Affiliation(s)
- Zhao-Qi Song
- Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Laboratory for Conservation and Utilization of Bio-resources, Yunnan Institute of Microbiology, Yunnan University, Kunming, 650091, China
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