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Rowe AR, Yoshimura M, LaRowe DE, Bird LJ, Amend JP, Hashimoto K, Nealson KH, Okamoto A. In situ
electrochemical enrichment and isolation of a magnetite-reducing bacterium from a high pH serpentinizing spring. Environ Microbiol 2017; 19:2272-2285. [DOI: 10.1111/1462-2920.13723] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 03/05/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Annette R. Rowe
- Department of Earth Sciences; University of Southern California; Los Angeles CA 90089 USA
| | - Miho Yoshimura
- Department of Applied and Chemical Engineering; University of Tokyo; Tokyo Japan
| | - Doug E. LaRowe
- Department of Earth Sciences; University of Southern California; Los Angeles CA 90089 USA
| | - Lina J. Bird
- Department of Earth Sciences; University of Southern California; Los Angeles CA 90089 USA
| | - Jan P. Amend
- Department of Earth Sciences; University of Southern California; Los Angeles CA 90089 USA
- Department of Biological Sciences; University of Southern California; Los Angeles CA 90089 USA
| | - Kazuhito Hashimoto
- Center for Green Research on Energy and Environmental Materials; National Institute for Material Sciences; Tsukuba Ibaraki 305-0047 Japan
| | - Kenneth H. Nealson
- Department of Earth Sciences; University of Southern California; Los Angeles CA 90089 USA
| | - Akihiro Okamoto
- Center for Green Research on Energy and Environmental Materials; National Institute for Material Sciences; Tsukuba Ibaraki 305-0047 Japan
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Postec A, Quéméneur M, Bes M, Mei N, Benaïssa F, Payri C, Pelletier B, Monnin C, Guentas-Dombrowsky L, Ollivier B, Gérard E, Pisapia C, Gérard M, Ménez B, Erauso G. Microbial diversity in a submarine carbonate edifice from the serpentinizing hydrothermal system of the Prony Bay (New Caledonia) over a 6-year period. Front Microbiol 2015; 6:857. [PMID: 26379636 PMCID: PMC4551099 DOI: 10.3389/fmicb.2015.00857] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 08/06/2015] [Indexed: 01/10/2023] Open
Abstract
Active carbonate chimneys from the shallow marine serpentinizing Prony Hydrothermal Field were sampled 3 times over a 6 years period at site ST09. Archaeal and bacterial communities composition was investigated using PCR-based methods (clone libraries, Denaturating Gel Gradient Electrophoresis, quantitative PCR) targeting 16S rRNA genes, methyl coenzyme M reductase A and dissimilatory sulfite reductase subunit B genes. Methanosarcinales (Euryarchaeota) and Thaumarchaea were the main archaeal members. The Methanosarcinales, also observed by epifluorescent microscopy and FISH, consisted of two phylotypes that were previously solely detected in two other serpentinitzing ecosystems (The Cedars and Lost City Hydrothermal Field). Surprisingly, members of the hyperthermophilic order Thermococcales were also found which may indicate the presence of a hot subsurface biosphere. The bacterial community mainly consisted of Firmicutes, Chloroflexi, Alpha-, Gamma-, Beta-, and Delta-proteobacteria and of the candidate division NPL-UPA2. Members of these taxa were consistently found each year and may therefore represent a stable core of the indigenous bacterial community of the PHF chimneys. Firmicutes isolates representing new bacterial taxa were obtained by cultivation under anaerobic conditions. Our study revealed diverse microbial communities in PHF ST09 related to methane and sulfur compounds that share common populations with other terrestrial or submarine serpentinizing ecosystems.
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Affiliation(s)
- Anne Postec
- Aix-Marseille Université, Centre National de la Recherche Scientifique/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography, UM 110Marseille, France
| | - Marianne Quéméneur
- Aix-Marseille Université, Centre National de la Recherche Scientifique/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography, UM 110Marseille, France
| | - Méline Bes
- Aix-Marseille Université, Centre National de la Recherche Scientifique/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography, UM 110Marseille, France
| | - Nan Mei
- Aix-Marseille Université, Centre National de la Recherche Scientifique/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography, UM 110Marseille, France
| | - Fatma Benaïssa
- Aix-Marseille Université, Centre National de la Recherche Scientifique/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography, UM 110Marseille, France
| | - Claude Payri
- Institut pour la Recherche et le Développement Centre de NouméaNouméa-Nouvelle-Calédonie, France
| | - Bernard Pelletier
- Institut pour la Recherche et le Développement Centre de NouméaNouméa-Nouvelle-Calédonie, France
| | - Christophe Monnin
- Géosciences Environnement Toulouse, Université de Toulouse/Centre National de la Recherche Scientifique/IRDToulouse, France
| | - Linda Guentas-Dombrowsky
- Aix-Marseille Université, Centre National de la Recherche Scientifique/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography, UM 110Marseille, France
- Institut pour la Recherche et le Développement Centre de NouméaNouméa-Nouvelle-Calédonie, France
| | - Bernard Ollivier
- Aix-Marseille Université, Centre National de la Recherche Scientifique/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography, UM 110Marseille, France
| | - Emmanuelle Gérard
- Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, Centre National de la Recherche Scientifique, UMR7154Paris, France
| | - Céline Pisapia
- Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, Centre National de la Recherche Scientifique, UMR7154Paris, France
| | - Martine Gérard
- Institut de Minéralogie et de Physique des Milieux Condensés, Université Pierre et Marie CurieParis, France
| | - Bénédicte Ménez
- Institut de Physique du Globe de Paris, Sorbonne Paris Cité, Université Paris Diderot, Centre National de la Recherche Scientifique, UMR7154Paris, France
| | - Gaël Erauso
- Aix-Marseille Université, Centre National de la Recherche Scientifique/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography, UM 110Marseille, France
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Méhay S, Früh-Green GL, Lang SQ, Bernasconi SM, Brazelton WJ, Schrenk MO, Schaeffer P, Adam P. Record of archaeal activity at the serpentinite-hosted Lost City Hydrothermal Field. GEOBIOLOGY 2013; 11:570-92. [PMID: 24118888 DOI: 10.1111/gbi.12062] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 09/06/2013] [Indexed: 05/22/2023]
Abstract
Samples of young, outer surfaces of brucite-carbonate deposits from the ultramafic-hosted Lost City hydrothermal field were analyzed for DNA and lipid biomarker distributions and for carbon and hydrogen stable isotope compositions of the lipids. Methane-cycling archaeal communities, notably the Lost City Methanosarcinales (LCMS) phylotype, are specifically addressed. Lost City is unlike all other hydrothermal systems known to date and is characterized by metal- and CO2 -poor, high pH fluids with high H2 and CH4 contents resulting from serpentinization processes at depth. The archaeal fraction of the microbial community varies widely within the Lost City chimneys, from 1-81% and covaries with concentrations of hydrogen within the fluids. Archaeal lipids include isoprenoid glycerol di- and tetraethers and C25 and C30 isoprenoid hydrocarbons (pentamethylicosane derivatives - PMIs - and squalenoids). In particular, unsaturated PMIs and squalenoids, attributed to the LCMS archaea, were identified for the first time in the carbonate deposits at Lost City and probably record processes exclusively occurring at the surface of the chimneys. The carbon isotope compositions of PMIs and squalenoids are remarkably heterogeneous across samples and show highly (13) C-enriched signatures reaching δ(13) C values of up to +24.6‰. Unlike other environments in which similar structural and isotopic lipid heterogeneity has been observed and attributed to diversity in the archaeal assemblage, the lipids here appear to be synthesized solely by the LCMS. Some of the variations in lipid isotope signatures may, in part, be due to unusual isotopic fractionation during biosynthesis under extreme conditions. However, we argue that the diversity in archaeal abundances, lipid structure and carbon isotope composition rather reflects the ability of the LCMS archaeal biofilms to adapt to chemical gradients in the hydrothermal chimneys and possibly to perform either methanotrophy or methanogenesis using dissolved inorganic carbon, methane or formate as a function of the prevailing environmental conditions.
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MESH Headings
- Archaea/classification
- Archaea/genetics
- Archaea/metabolism
- Bacteria/classification
- Bacteria/genetics
- Bacteria/metabolism
- Biota
- Carbon/analysis
- DNA, Archaeal/chemistry
- DNA, Archaeal/genetics
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Genes, rRNA
- Hot Springs/microbiology
- Hydrogen/analysis
- Lipids/analysis
- RNA, Archaeal/genetics
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
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Affiliation(s)
- S Méhay
- Department of Earth Sciences, ETH Zurich, Zurich, Switzerland
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6
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Abstract
Carbonate chimneys at the Lost City hydrothermal field are coated in biofilms dominated by a single phylotype of archaea known as Lost City Methanosarcinales. In this study, we have detected surprising physiological complexity in single-species biofilms, which is typically indicative of multispecies biofilm communities. Multiple cell morphologies were visible within the biofilms by transmission electron microscopy, and some cells contained intracellular membranes that may facilitate methane oxidation. Both methane production and oxidation were detected at 70 to 80°C and pH 9 to 10 in samples containing the single-species biofilms. Both processes were stimulated by the presence of hydrogen (H2), indicating that methane production and oxidation are part of a syntrophic interaction. Metagenomic data included a sequence encoding AMP-forming acetyl coenzyme A synthetase, indicating that acetate may play a role in the methane-cycling syntrophy. A wide range of nitrogen fixation genes were also identified, many of which were likely acquired via lateral gene transfer (LGT). Our results indicate that cells within these single-species biofilms may have differentiated into multiple physiological roles to form multicellular communities linked by metabolic interactions and LGT. Communities similar to these Lost City biofilms are likely to have existed early in the evolution of life, and we discuss how the multicellular characteristics of ancient hydrogen-fueled biofilm communities could have stimulated ecological diversification, as well as unity of biochemistry, during the earliest stages of cellular evolution. Our previous work at the Lost City hydrothermal field has shown that its carbonate chimneys host microbial biofilms dominated by a single uncultivated “species” of archaea. In this paper, we integrate evidence from these previous studies with new data on the metabolic activity and cellular morphology of these archaeal biofilms. We conclude that the archaeal biofilm must contain cells that are physiologically and possibly genetically differentiated with respect to each other. These results are especially interesting considering the possibility that the first cells originated and evolved in hydrothermal systems similar to Lost City.
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Narihiro T, Sekiguchi Y. Oligonucleotide primers, probes and molecular methods for the environmental monitoring of methanogenic archaea. Microb Biotechnol 2011; 4:585-602. [PMID: 21375721 PMCID: PMC3819009 DOI: 10.1111/j.1751-7915.2010.00239.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Accepted: 11/12/2010] [Indexed: 11/28/2022] Open
Abstract
For the identification and quantification of methanogenic archaea (methanogens) in environmental samples, various oligonucleotide probes/primers targeting phylogenetic markers of methanogens, such as 16S rRNA, 16S rRNA gene and the gene for the α-subunit of methyl coenzyme M reductase (mcrA), have been extensively developed and characterized experimentally. These oligonucleotides were designed to resolve different groups of methanogens at different taxonomic levels, and have been widely used as hybridization probes or polymerase chain reaction primers for membrane hybridization, fluorescence in situ hybridization, rRNA cleavage method, gene cloning, DNA microarray and quantitative polymerase chain reaction for studies in environmental and determinative microbiology. In this review, we present a comprehensive list of such oligonucleotide probes/primers, which enable us to determine methanogen populations in an environment quantitatively and hierarchically, with examples of the practical applications of the probes and primers.
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Affiliation(s)
- Takashi Narihiro
- International Patent Organism Depositary (IPOD), Tsukuba, Ibaraki 305‐8566, Japan
| | - Yuji Sekiguchi
- Bio‐medical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305‐8566, Japan
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8
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Crépeau V, Cambon Bonavita MA, Lesongeur F, Randrianalivelo H, Sarradin PM, Sarrazin J, Godfroy A. Diversity and function in microbial mats from the Lucky Strike hydrothermal vent field. FEMS Microbiol Ecol 2011; 76:524-40. [DOI: 10.1111/j.1574-6941.2011.01070.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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9
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Archaea and bacteria with surprising microdiversity show shifts in dominance over 1,000-year time scales in hydrothermal chimneys. Proc Natl Acad Sci U S A 2010; 107:1612-7. [PMID: 20080654 DOI: 10.1073/pnas.0905369107] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Lost City Hydrothermal Field, an ultramafic-hosted system located 15 km west of the Mid-Atlantic Ridge, has experienced at least 30,000 years of hydrothermal activity. Previous studies have shown that its carbonate chimneys form by mixing of approximately 90 degrees C, pH 9-11 hydrothermal fluids and cold seawater. Flow of methane and hydrogen-rich hydrothermal fluids in the porous interior chimney walls supports archaeal biofilm communities dominated by a single phylotype of Methanosarcinales. In this study, we have extensively sampled the carbonate-hosted archaeal and bacterial communities by obtaining sequences of >200,000 amplicons of the 16S rRNA V6 region and correlated the results with isotopic ((230)Th) ages of the chimneys over a 1,200-year period. Rare sequences in young chimneys were commonly more abundant in older chimneys, indicating that members of the rare biosphere can become dominant members of the ecosystem when environmental conditions change. These results suggest that a long history of selection over many cycles of chimney growth has resulted in numerous closely related species at Lost City, each of which is preadapted to a particular set of reoccurring environmental conditions. Because of the unique characteristics of the Lost City Hydrothermal Field, these data offer an unprecedented opportunity to study the dynamics of a microbial ecosystem's rare biosphere over a thousand-year time scale.
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