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Zhou J, Wu C, Pang S, Yang L, Yao M, Li X, Xia S, Rittmann BE. Dissimilatory and Cytoplasmic Antimonate Reductions in a Hydrogen-Based Membrane Biofilm Reactor. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:14808-14816. [PMID: 36201672 DOI: 10.1021/acs.est.2c04939] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
A hydrogen-based membrane biofilm reactor (H2-MBfR) was operated to investigate the bioreduction of antimonate [Sb(V)] in terms of Sb(V) removal, the fate of Sb, and the pathways of reduction metabolism. The MBfR achieved up to 80% Sb(V) removal and an Sb(V) removal flux of 0.55 g/m2·day. Sb(V) was reduced to Sb(III), which mainly formed Sb2O3 precipitates in the biofilm matrix, although some Sb(III) was retained intracellularly. High Sb(V) loading caused stress that deteriorated performance that was not recovered when the high Sb(V) loading was removed. The biofilm community consisted of DSbRB (dissimilatory Sb-reduction bacteria), SbRB (Sb-resistant bacteria), and DIRB (dissimilatory iron-reducing bacteria). Dissimilatory antimonate reduction, mediated by the respiratory arsenate reductase ArrAB, was the main reduction route, but respiratory reduction coexisted with cytoplasmic Sb(V)-reduction mediated by arsenate reductase ArsC. Increasing Sb(V) loading caused stress that led to increases in the expression of arsC gene and intracellular accumulation of Sb(III). By illuminating the roles of the dissimilatory and cytoplasmic Sb(V) reduction mechanism in the biofilms of the H2-MBfR, this study reveals that the Sb(V) loading should be controlled to avoid stress that deteriorates Sb(V) reduction.
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Affiliation(s)
- Jingzhou Zhou
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai200092, China
| | - Chengyang Wu
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai200092, China
| | - Si Pang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai200092, China
| | - Lin Yang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai200092, China
| | - Mengying Yao
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai200092, China
| | - Xiaodi Li
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai200092, China
| | - Siqing Xia
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai200092, China
- Shanghai Institute of Pollution Control and Ecological Security, Shanghai200092, China
| | - Bruce E Rittmann
- Biodesign Swette Center for Environmental Biotechnology, Arizona State University, Tempe, Arizona85287-5701, United States
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Zhan Y, Yang MR, Zhang S, Pan H, Wang WD, Yan L. Phylogenetic diversity contributes more to sediment magnetism than abundance during incubation of iron-reducing sediment from a non-active volcanic lake in Northeast China. J Appl Microbiol 2021; 131:1813-1829. [PMID: 33772951 DOI: 10.1111/jam.15086] [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: 11/06/2020] [Revised: 01/18/2021] [Accepted: 03/22/2021] [Indexed: 12/01/2022]
Abstract
AIM This study aimed to analyse bacterial community and biomineralization products from Wudalianchi non-active volcanic field and the relationship between magnetization and bacterial community. METHODS AND RESULTS Eighteen sediment samples obtained from Wenbo Lake, high-throughput sequencing and quantitative PCR (qPCR) were separately employed to investigate the bacterial community composition dynamics and abundance variation of the sediment sample with the highest iron-reducing capacity during incubation. The mineralization products were characterized by transmission electron microscopy, scanning electron microscopy, X-ray diffraction (XRD), Raman spectroscopy, vibrating sample magnetometer (VSM) and variable-temperature magnetism analyses. The results showed that the highest iron reduction rate was 98·06%. Seven phyla were identified as dominant bacterial phyla during the incubation process. Iron-reducing bacteria (FeRB) including Geobacter, Desulfosporosinus and Clostridium were involved in the iron mineralization process. The 16S rDNA copy numbers of sediment decreased quickly and then stayed steady during the incubation. Bacteria with rod-shaped and spheroid species were involved in extracellular iron reduction to produce magnetic particles with massive aggregation and columnar structures on the mineral surface morphologies. The materials produced by the microbial community over the incubation period were sequentially identified as siderite, magnetite and maghemite. The magnetism of the mineral samples gradually increased from 0·31748 to 33·58423 emu g-1 with increased incubation time. The final products showed relatively stable magnetism under 0-400 K. Meanwhile, the saturation magnetization (MS ) of the mineralized substance was tightly associated with bacterial diversity (P < 0·05). CONCLUSIONS Bacterial community varied during incubation of iron-reducing sediment of volcanic lake. Various iron mineral crystals were in turn formed extracellularly by FeRB. The magnetism of mineralized products was tightly associated with bacterial community. SIGNIFICANCE AND IMPACT OF THE STUDY These results not only help us to better understand the iron mineralization of FeRB in the volcanic lake sediments but also provide basic information for the future application of FeRB in environmental bioremediation.
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Affiliation(s)
- Y Zhan
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, PR China.,Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Xianyang, PR China
| | - M R Yang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, PR China
| | - S Zhang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, PR China
| | - H Pan
- Institute of Volcano and Spring, Heilongjiang Academy of Science, Wudalianchi, PR China
| | - W D Wang
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, PR China
| | - L Yan
- Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in Cold Region, College of Life Science and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, PR China
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Pillot G, Davidson S, Auria R, Combet-Blanc Y, Godfroy A, Liebgott PP. Production of Current by Syntrophy Between Exoelectrogenic and Fermentative Hyperthermophilic Microorganisms in Heterotrophic Biofilm from a Deep-Sea Hydrothermal Chimney. MICROBIAL ECOLOGY 2020; 79:38-49. [PMID: 31079197 DOI: 10.1007/s00248-019-01381-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2018] [Accepted: 04/12/2019] [Indexed: 06/09/2023]
Abstract
To study the role of exoelectrogens within the trophic network of deep-sea hydrothermal vents, we performed successive subcultures of a hyperthermophilic community from a hydrothermal chimney sample on a mix of electron donors in a microbial fuel cell system. Electrode (the electron acceptor) was swapped every week to enable fresh development from spent media as inoculum. The MFC at 80 °C yielded maximum current production increasing from 159 to 247 mA m-2 over the subcultures. The experiments demonstrated direct production of electric current from acetate, pyruvate, and H2 and indirect production from yeast extract and peptone through the production of H2 and acetate from fermentation. The microorganisms found in on-electrode communities were mainly affiliated to exoelectrogenic Archaeoglobales and Thermococcales species, whereas in liquid media, the communities were mainly affiliated to fermentative Bacillales and Thermococcales species. The work shows interactions between fermentative microorganisms degrading complex organic matter into fermentation products that are then used by exoelectrogenic microorganisms oxidizing these reduced compounds while respiring on a conductive support. The results confirmed that with carbon cycling, the syntrophic relations between fermentative microorganisms and exoelectrogens could enable some microbes to survive as biofilm in extremely unstable conditions. Graphical Abstract Schematic representation of cross-feeding between fermentative and exoelectrogenic microbes on the surface of the conductive support. B, Bacillus/Geobacillus spp.; Tc, Thermococcales; Gg, Geoglobus spp.; Py, pyruvate; Ac, acetate.
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Affiliation(s)
- Guillaume Pillot
- Aix-Marseille Université, IRD, CNRS, MIO, UM110, Marseille, France
- Université du Sud Toulon-Var, IRD, CNRS, MIO, UM 110, La Garde, France
| | - Sylvain Davidson
- Aix-Marseille Université, IRD, CNRS, MIO, UM110, Marseille, France
- Université du Sud Toulon-Var, IRD, CNRS, MIO, UM 110, La Garde, France
| | - Richard Auria
- Aix-Marseille Université, IRD, CNRS, MIO, UM110, Marseille, France
- Université du Sud Toulon-Var, IRD, CNRS, MIO, UM 110, La Garde, France
| | - Yannick Combet-Blanc
- Aix-Marseille Université, IRD, CNRS, MIO, UM110, Marseille, France
- Université du Sud Toulon-Var, IRD, CNRS, MIO, UM 110, La Garde, France
| | - Anne Godfroy
- IFREMER, CNRS, Laboratoire de Microbiologie des Environnements Extrêmes - UMR6197, Ifremer, Université de Bretagne Occidentale, Centre de Brest, CS10070, Plouzané, France
| | - Pierre-Pol Liebgott
- Aix-Marseille Université, IRD, CNRS, MIO, UM110, Marseille, France.
- Université du Sud Toulon-Var, IRD, CNRS, MIO, UM 110, La Garde, France.
- Campus de Luminy, Bâtiment OCEANOMED, Mediterranean Institute of Oceanography, 13288, Marseille Cedex 09, France.
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Slobodkin A, Slobodkina G, Allioux M, Alain K, Jebbar M, Shadrin V, Kublanov I, Toshchakov S, Bonch-Osmolovskaya E. Genomic Insights into the Carbon and Energy Metabolism of a Thermophilic Deep-Sea Bacterium Deferribacter autotrophicus Revealed New Metabolic Traits in the Phylum Deferribacteres. Genes (Basel) 2019; 10:genes10110849. [PMID: 31717820 PMCID: PMC6896113 DOI: 10.3390/genes10110849] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 10/22/2019] [Accepted: 10/23/2019] [Indexed: 01/12/2023] Open
Abstract
Information on the biochemical pathways of carbon and energy metabolism in representatives of the deep lineage bacterial phylum Deferribacteres are scarce. Here, we report the results of the sequencing and analysis of the high-quality draft genome of the thermophilic chemolithoautotrophic anaerobe Deferribacter autotrophicus. Genomic data suggest that CO2 assimilation is carried out by recently proposed reversible tricarboxylic acid cycle (“roTCA cycle”). The predicted genomic ability of D. autotrophicus to grow due to the oxidation of carbon monoxide was experimentally proven. CO oxidation was coupled with the reduction of nitrate to ammonium. Utilization of CO most likely involves anaerobic [Ni, Fe]-containing CO dehydrogenase. This is the first evidence of CO oxidation in the phylum Deferribacteres. The genome of D. autotrophicus encodes a Nap-type complex of nitrate reduction. However, the conversion of produced nitrite to ammonium proceeds via a non-canonical pathway with the participation of hydroxylamine oxidoreductase (Hao) and hydroxylamine reductase. The genome contains 17 genes of putative multiheme c-type cytochromes and “e-pilin” genes, some of which are probably involved in Fe(III) reduction. Genomic analysis indicates that the roTCA cycle of CO2 fixation and putative Hao-enabled ammonification may occur in several members of the phylum Deferribacteres.
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Affiliation(s)
- Alexander Slobodkin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (G.S.); (V.S.); (I.K.); (S.T.); (E.B.-O.)
- Correspondence:
| | - Galina Slobodkina
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (G.S.); (V.S.); (I.K.); (S.T.); (E.B.-O.)
| | - Maxime Allioux
- Univ Brest, CNRS, Ifremer, LIA1211, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, F-29280 Plouzané, France; (M.A.); (K.A.); (M.J.)
| | - Karine Alain
- Univ Brest, CNRS, Ifremer, LIA1211, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, F-29280 Plouzané, France; (M.A.); (K.A.); (M.J.)
| | - Mohamed Jebbar
- Univ Brest, CNRS, Ifremer, LIA1211, Laboratoire de Microbiologie des Environnements Extrêmes LM2E, F-29280 Plouzané, France; (M.A.); (K.A.); (M.J.)
| | - Valerian Shadrin
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (G.S.); (V.S.); (I.K.); (S.T.); (E.B.-O.)
| | - Ilya Kublanov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (G.S.); (V.S.); (I.K.); (S.T.); (E.B.-O.)
| | - Stepan Toshchakov
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (G.S.); (V.S.); (I.K.); (S.T.); (E.B.-O.)
| | - Elizaveta Bonch-Osmolovskaya
- Winogradsky Institute of Microbiology, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (G.S.); (V.S.); (I.K.); (S.T.); (E.B.-O.)
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5
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Toner BM, Rouxel OJ, Santelli CM, Bach W, Edwards KJ. Iron Transformation Pathways and Redox Micro-Environments in Seafloor Sulfide-Mineral Deposits: Spatially Resolved Fe XAS and δ(57/54)Fe Observations. Front Microbiol 2016; 7:648. [PMID: 27242685 PMCID: PMC4862312 DOI: 10.3389/fmicb.2016.00648] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/18/2016] [Indexed: 11/13/2022] Open
Abstract
Hydrothermal sulfide chimneys located along the global system of oceanic spreading centers are habitats for microbial life during active venting. Hydrothermally extinct, or inactive, sulfide deposits also host microbial communities at globally distributed sites. The main goal of this study is to describe Fe transformation pathways, through precipitation and oxidation-reduction (redox) reactions, and examine transformation products for signatures of biological activity using Fe mineralogy and stable isotope approaches. The study includes active and inactive sulfides from the East Pacific Rise 9°50'N vent field. First, the mineralogy of Fe(III)-bearing precipitates is investigated using microprobe X-ray absorption spectroscopy (μXAS) and X-ray diffraction (μXRD). Second, laser-ablation (LA) and micro-drilling (MD) are used to obtain spatially-resolved Fe stable isotope analysis by multicollector-inductively coupled plasma-mass spectrometry (MC-ICP-MS). Eight Fe-bearing minerals representing three mineralogical classes are present in the samples: oxyhydroxides, secondary phyllosilicates, and sulfides. For Fe oxyhydroxides within chimney walls and layers of Si-rich material, enrichments in both heavy and light Fe isotopes relative to pyrite are observed, yielding a range of δ(57)Fe values up to 6‰. Overall, several pathways for Fe transformation are observed. Pathway 1 is characterized by precipitation of primary sulfide minerals from Fe(II)aq-rich fluids in zones of mixing between vent fluids and seawater. Pathway 2 is also consistent with zones of mixing but involves precipitation of sulfide minerals from Fe(II)aq generated by Fe(III) reduction. Pathway 3 is direct oxidation of Fe(II) aq from hydrothermal fluids to form Fe(III) precipitates. Finally, Pathway 4 involves oxidative alteration of pre-existing sulfide minerals to form Fe(III). The Fe mineralogy and isotope data do not support or refute a unique biological role in sulfide alteration. The findings reveal a dynamic range of Fe transformation pathways consistent with a continuum of micro-environments having variable redox conditions. These micro-environments likely support redox cycling of Fe and S and are consistent with culture-dependent and -independent assessments of microbial physiology and genetic diversity of hydrothermal sulfide deposits.
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Affiliation(s)
- Brandy M. Toner
- Département des Ressources Physiques et Écosystèmes de Fond de Mer, Water, and Climate, University of Minnesota-Twin CitiesSt. Paul, MN, USA
| | - Olivier J. Rouxel
- Department of Deep-sea Physical Resources and Ecosystems, Centre de Brest, Institut Français de Recherche pour l'Exploitation de la MerPlouzané, France
| | - Cara M. Santelli
- Department of Earth Sciences, University of Minnesota-Twin CitiesMinneapolis, MN, USA
| | - Wolfgang Bach
- Department of Geosciences and MARUM, University of BremenBremen, Germany
| | - Katrina J. Edwards
- Department of Biological Sciences, University of Southern CaliforniaLos Angeles, CA, USA
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Ferry JG. Acetate Metabolism in Anaerobes from the Domain Archaea. Life (Basel) 2015; 5:1454-71. [PMID: 26068860 PMCID: PMC4500148 DOI: 10.3390/life5021454] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 06/01/2015] [Indexed: 01/26/2023] Open
Abstract
Acetate and acetyl-CoA play fundamental roles in all of biology, including anaerobic prokaryotes from the domains Bacteria and Archaea, which compose an estimated quarter of all living protoplasm in Earth's biosphere. Anaerobes from the domain Archaea contribute to the global carbon cycle by metabolizing acetate as a growth substrate or product. They are components of anaerobic microbial food chains converting complex organic matter to methane, and many fix CO2 into cell material via synthesis of acetyl-CoA. They are found in a diversity of ecological habitats ranging from the digestive tracts of insects to deep-sea hydrothermal vents, and synthesize a plethora of novel enzymes with biotechnological potential. Ecological investigations suggest that still more acetate-metabolizing species with novel properties await discovery.
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Affiliation(s)
- James G Ferry
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.
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7
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Callac N, Rouxel O, Lesongeur F, Liorzou C, Bollinger C, Pignet P, Chéron S, Fouquet Y, Rommevaux-Jestin C, Godfroy A. Biogeochemical insights into microbe-mineral-fluid interactions in hydrothermal chimneys using enrichment culture. Extremophiles 2015; 19:597-617. [PMID: 25778451 DOI: 10.1007/s00792-015-0742-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/01/2015] [Indexed: 10/23/2022]
Abstract
Active hydrothermal chimneys host diverse microbial communities exhibiting various metabolisms including those involved in various biogeochemical cycles. To investigate microbe-mineral-fluid interactions in hydrothermal chimney and the driver of microbial diversity, a cultural approach using a gas-lift bioreactor was chosen. An enrichment culture was performed using crushed active chimney sample as inoculum and diluted hydrothermal fluid from the same vent as culture medium. Daily sampling provided time-series access to active microbial diversity and medium composition. Active archaeal and bacterial communities consisted mainly of sulfur, sulfate and iron reducers and hydrogen oxidizers with the detection of Thermococcus, Archaeoglobus, Geoglobus, Sulfurimonas and Thermotoga sequences. The simultaneous presence of active Geoglobus sp. and Archaeoglobus sp. argues against competition for available carbon sources and electron donors between sulfate and iron reducers at high temperature. This approach allowed the cultivation of microbial populations that were under-represented in the initial environmental sample. The microbial communities are heterogeneously distributed within the gas-lift bioreactor; it is unlikely that bulk mineralogy or fluid chemistry is the drivers of microbial community structure. Instead, we propose that micro-environmental niche characteristics, created by the interaction between the mineral grains and the fluid chemistry, are the main drivers of microbial diversity in natural systems.
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Affiliation(s)
- Nolwenn Callac
- Laboratoire de Microbiologie des Environnements Extrêmes, Université de Bretagne Occidentale, UEB, IUEM, UMR 6197, Place Nicolas Copernic, 29280, Plouzané, France,
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8
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The Geoglobus acetivorans genome: Fe(III) reduction, acetate utilization, autotrophic growth, and degradation of aromatic compounds in a hyperthermophilic archaeon. Appl Environ Microbiol 2014; 81:1003-12. [PMID: 25416759 DOI: 10.1128/aem.02705-14] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Geoglobus acetivorans is a hyperthermophilic anaerobic euryarchaeon of the order Archaeoglobales isolated from deep-sea hydrothermal vents. A unique physiological feature of the members of the genus Geoglobus is their obligate dependence on Fe(III) reduction, which plays an important role in the geochemistry of hydrothermal systems. The features of this organism and its complete 1,860,815-bp genome sequence are described in this report. Genome analysis revealed pathways enabling oxidation of molecular hydrogen, proteinaceous substrates, fatty acids, aromatic compounds, n-alkanes, and organic acids, including acetate, through anaerobic respiration linked to Fe(III) reduction. Consistent with the inability of G. acetivorans to grow on carbohydrates, the modified Embden-Meyerhof pathway encoded by the genome is incomplete. Autotrophic CO2 fixation is enabled by the Wood-Ljungdahl pathway. Reduction of insoluble poorly crystalline Fe(III) oxide depends on the transfer of electrons from the quinone pool to multiheme c-type cytochromes exposed on the cell surface. Direct contact of the cells and Fe(III) oxide particles could be facilitated by pilus-like appendages. Genome analysis indicated the presence of metabolic pathways for anaerobic degradation of aromatic compounds and n-alkanes, although an ability of G. acetivorans to grow on these substrates was not observed in laboratory experiments. Overall, our results suggest that Geoglobus species could play an important role in microbial communities of deep-sea hydrothermal vents as lithoautotrophic producers. An additional role as decomposers would close the biogeochemical cycle of carbon through complete mineralization of various organic compounds via Fe(III) respiration.
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Campbell BJ, Polson SW, Zeigler Allen L, Williamson SJ, Lee CK, Wommack KE, Cary SC. Diffuse flow environments within basalt- and sediment-based hydrothermal vent ecosystems harbor specialized microbial communities. Front Microbiol 2013; 4:182. [PMID: 23898323 PMCID: PMC3721025 DOI: 10.3389/fmicb.2013.00182] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 06/17/2013] [Indexed: 02/01/2023] Open
Abstract
Hydrothermal vents differ both in surface input and subsurface geochemistry. The effects of these differences on their microbial communities are not clear. Here, we investigated both alpha and beta diversity of diffuse flow-associated microbial communities emanating from vents at a basalt-based hydrothermal system along the East Pacific Rise (EPR) and a sediment-based hydrothermal system, Guaymas Basin. Both Bacteria and Archaea were targeted using high throughput 16S rRNA gene pyrosequencing analyses. A unique aspect of this study was the use of a universal set of 16S rRNA gene primers to characterize total and diffuse flow-specific microbial communities from varied deep-sea hydrothermal environments. Both surrounding seawater and diffuse flow water samples contained large numbers of Marine Group I (MGI) Thaumarchaea and Gammaproteobacteria taxa previously observed in deep-sea systems. However, these taxa were geographically distinct and segregated according to type of spreading center. Diffuse flow microbial community profiles were highly differentiated. In particular, EPR dominant diffuse flow taxa were most closely associated with chemolithoautotrophs, and off axis water was dominated by heterotrophic-related taxa, whereas the opposite was true for Guaymas Basin. The diversity and richness of diffuse flow-specific microbial communities were strongly correlated to the relative abundance of Epsilonproteobacteria, proximity to macrofauna, and hydrothermal system type. Archaeal diversity was higher than or equivalent to bacterial diversity in about one third of the samples. Most diffuse flow-specific communities were dominated by OTUs associated with Epsilonproteobacteria, but many of the Guaymas Basin diffuse flow samples were dominated by either OTUs within the Planctomycetes or hyperthermophilic Archaea. This study emphasizes the unique microbial communities associated with geochemically and geographically distinct hydrothermal diffuse flow environments.
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Affiliation(s)
- Barbara J Campbell
- Department of Biological Sciences, Life Science Facility, Clemson University Clemson, SC, USA
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Takaki Y, Shimamura S, Nakagawa S, Fukuhara Y, Horikawa H, Ankai A, Harada T, Hosoyama A, Oguchi A, Fukui S, Fujita N, Takami H, Takai K. Bacterial lifestyle in a deep-sea hydrothermal vent chimney revealed by the genome sequence of the thermophilic bacterium Deferribacter desulfuricans SSM1. DNA Res 2010; 17:123-37. [PMID: 20189949 PMCID: PMC2885270 DOI: 10.1093/dnares/dsq005] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The complete genome sequence of the thermophilic sulphur-reducing bacterium, Deferribacter desulfuricans SMM1, isolated from a hydrothermal vent chimney has been determined. The genome comprises a single circular chromosome of 2 234 389 bp and a megaplasmid of 308 544 bp. Many genes encoded in the genome are most similar to the genes of sulphur- or sulphate-reducing bacterial species within Deltaproteobacteria. The reconstructed central metabolisms showed a heterotrophic lifestyle primarily driven by C1 to C3 organics, e.g. formate, acetate, and pyruvate, and also suggested that the inability of autotrophy via a reductive tricarboxylic acid cycle may be due to the lack of ATP-dependent citrate lyase. In addition, the genome encodes numerous genes for chemoreceptors, chemotaxis-like systems, and signal transduction machineries. These signalling networks may be linked to this bacterium's versatile energy metabolisms and may provide ecophysiological advantages for D. desulfuricans SSM1 thriving in the physically and chemically fluctuating environments near hydrothermal vents. This is the first genome sequence from the phylum Deferribacteres.
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Affiliation(s)
- Yoshihiro Takaki
- Microbial Genome Research Group, Extremobiosphere Research Program, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa 237-0061, Japan.
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11
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Li Y, Li F, Zhang X, Qin S, Zeng Z, Dang H, Qin Y. Vertical distribution of bacterial and archaeal communities along discrete layers of a deep-sea cold sediment sample at the East Pacific Rise (approximately 13 degrees N). Extremophiles 2008; 12:573-85. [PMID: 18418544 DOI: 10.1007/s00792-008-0159-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2007] [Accepted: 03/10/2008] [Indexed: 11/25/2022]
Abstract
The community structure and vertical distribution of prokaryotes in a deep-sea (ca. 3,191 m) cold sediment sample (ca. 43 cm long) collected at the East Pacific Rise (EPR) approximately 13 degrees N were studied with 16SrDNA-based molecular analyses. Total community DNA was extracted from each of four discrete layers EPRDS-1, -2, -3 and -4 (from top to bottom) and 16S rDNA were amplified by PCR. Cluster analysis of DGGE profiles revealed that the bacterial communities shifted sharply between EPRDS-1 and EPRDS-2 in similarity coefficient at merely 49%. Twenty-three sequences retrieved from DGGE bands fell into 11 groups based on BLAST and bootstrap analysis. The dominant groups in the bacterial communities were Chloroflexi, Gamma proteobacteria, Actinobacterium and unidentified bacteria, with their corresponding percentages varying along discrete layers. Pairwise Fst (F-statistics) values between the archaeal clone libraries indicated that the archaeal communities changed distinctly between EPRDS-2 and EPRDS-3. Sequences from the archaeal libraries were divided to eight groups. Crenarchaea Marine Group I (MGI) was prevalent in EPRDS-1 at 83%, while Uncultured Crenarchaea group II B (UCII B) abounded in EPRDS-4 at 61%. Our results revealed that the vertically stratified distribution of prokaryotic communities might be in response to the geochemical settings and suggested that the sampling area was influenced by hydrothermalism. The copresence of members related to hydrothermalism and cold deep-sea environments in the microbial community indicated that the area might be a transitional region from hydrothermal vents to cold deep-sea sediments.
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Affiliation(s)
- Youxun Li
- Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China
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12
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Slobodkina GB, Chernyh NA, Slobodkin AI, Subbotina IV, Bonch-Osmolovskaya EA, Lebedinsky AV. PCR-based identification of hyperthermophilic archaea of the family Thermococcaceae. Appl Environ Microbiol 2004; 70:5701-3. [PMID: 15345465 PMCID: PMC520901 DOI: 10.1128/aem.70.9.5701-5703.2004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A method for rapid detection and identification of hyperthermophilic archaea of the family Thermococcaceae based on PCR amplification of 16S rRNA gene fragments with primers TcPc 173F (5'-TCCCCCATAGGYCTGRGGTACTGGAAGGTC-3') and TcPc 589R (5'-GCCGTGRGATTTCGCCAGGGACTTACGGGC-3') was developed and used for identification of new isolates.
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Affiliation(s)
- Galina B Slobodkina
- Institute of Microbiology, Russian Academy of Sciences, prospekt 60-letiya Oktyabrya 7/2, Moscow, 117312 Russia
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13
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Nakagawa T, Ishibashi JI, Maruyama A, Yamanaka T, Morimoto Y, Kimura H, Urabe T, Fukui M. Analysis of dissimilatory sulfite reductase and 16S rRNA gene fragments from deep-sea hydrothermal sites of the Suiyo Seamount, Izu-Bonin Arc, Western Pacific. Appl Environ Microbiol 2004; 70:393-403. [PMID: 14711668 PMCID: PMC321305 DOI: 10.1128/aem.70.1.393-403.2004] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study describes the occurrence of unique dissimilatory sulfite reductase (DSR) genes at a depth of 1,380 m from the deep-sea hydrothermal vent field at the Suiyo Seamount, Izu-Bonin Arc, Western Pacific, Japan. The DSR genes were obtained from microbes that grew in a catheter-type in situ growth chamber deployed for 3 days on a vent and from the effluent water of drilled holes at 5 degrees C and natural vent fluids at 7 degrees C. DSR clones SUIYOdsr-A and SUIYOdsr-B were not closely related to cultivated species or environmental clones. Moreover, samples of microbial communities were examined by PCR-denaturing gradient gel electrophoresis (DGGE) analysis of the 16S rRNA gene. The sequence analysis of 16S rRNA gene fragments obtained from the vent catheter after a 3-day incubation revealed the occurrence of bacterial DGGE bands affiliated with the Aquificae and gamma- and epsilon-Proteobacteria as well as the occurrence of archaeal phylotypes affiliated with the Thermococcales and of a unique archaeon sequence that clustered with "Nanoarchaeota." The DGGE bands obtained from drilled holes and natural vent fluids from 7 to 300 degrees C were affiliated with the delta-Proteobacteria, genus Thiomicrospira, and Pelodictyon. The dominant DGGE bands retrieved from the effluent water of casing pipes at 3 and 4 degrees C were closely related to phylotypes obtained from the Arctic Ocean. Our results suggest the presence of microorganisms corresponding to a unique DSR lineage not detected previously from other geothermal environments.
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Affiliation(s)
- Tatsunori Nakagawa
- Department of Biological Science, Graduate School of Science, Tokyo Metropolitan University, Hachioji, Tokyo 192-0397, Japan
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14
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Schrenk MO, Kelley DS, Delaney JR, Baross JA. Incidence and diversity of microorganisms within the walls of an active deep-sea sulfide chimney. Appl Environ Microbiol 2003; 69:3580-92. [PMID: 12788766 PMCID: PMC161516 DOI: 10.1128/aem.69.6.3580-3592.2003] [Citation(s) in RCA: 157] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A large, intact sulfide chimney, designated Finn, was recovered from the Mothra Vent Field on the Juan de Fuca Ridge in 1998. Finn was venting 302 degrees C fluids on the seafloor and contained complex mineralogical zones surrounding a large open central conduit. Examination of microorganisms within these zones, followed by community analysis with oligonucleotide probes, showed that there were variations in the abundance and diversity of eubacteria and archaea from the exterior to the interior of the chimney. The microbial abundance based upon epifluorescence microscopy and quantitative fatty acid analyses varied from >10(8) cells/g of sulfide 2 to 10 cm within the chimney wall to <10(5) cells/g in interior zones. Direct microscopic observation indicated that microorganisms were attached to mineral surfaces throughout the structure. Whole-cell hybridization results revealed that there was a transition from a mixed community of eubacteria and archaea near the cool exterior of the chimney to primarily archaea near the warm interior. Archaeal diversity was examined in three zones of Finn by cloning and sequencing of the 16S rRNA gene. The majority of sequences from the exterior of the chimney were related to marine group I of the Crenarchaeota and uncultured Euryarchaeota from benthic marine environments. In contrast, clone libraries from interior regions of the chimney contained sequences closely related to methanogens, Thermococcales, and Archaeoglobales, in addition to uncultured crenarchaeal phylotypes obtained from deep subsurface sites. These observations of microbial communities within an active hydrothermal chimney provide insight into the microbial ecology within such structures and may facilitate follow-up exploration into expanding the known upper temperature limits of life.
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Affiliation(s)
- Matthew O Schrenk
- School of Oceanography and Astrobiology Program, University of Washington, Seattle, Washington 98195, USA.
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15
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Campbell BJ, Jeanthon C, Kostka JE, Luther GW, Cary SC. Growth and phylogenetic properties of novel bacteria belonging to the epsilon subdivision of the Proteobacteria enriched from Alvinella pompejana and deep-sea hydrothermal vents. Appl Environ Microbiol 2001; 67:4566-72. [PMID: 11571157 PMCID: PMC93204 DOI: 10.1128/aem.67.10.4566-4572.2001] [Citation(s) in RCA: 116] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recent molecular characterizations of microbial communities from deep-sea hydrothermal sites indicate the predominance of bacteria belonging to the epsilon subdivision of Proteobacteria (epsilon Proteobacteria). Here, we report the first enrichments and characterizations of four epsilon Proteobacteria that are directly associated with Alvinella pompejana, a deep sea hydrothermal vent polychete, or with hydrothermal vent chimney samples. These novel bacteria were moderately thermophilic sulfur-reducing heterotrophs growing on formate as the energy and carbon source. In addition, two of them (Am-H and Ex-18.2) could grow on sulfur lithoautrotrophically using hydrogen as the electron donor. Optimal growth temperatures of the bacteria ranged from 41 to 45 degrees C. Phylogenetic analysis of the small-subunit ribosomal gene of the two heterotrophic bacteria demonstrated 95% similarity to Sulfurospirillum arcachonense, an epsilon Proteobacteria isolated from an oxidized marine surface sediment. The autotrophic bacteria grouped within a deeply branching clade of the epsilon Proteobacteria, to date composed only of uncultured bacteria detected in a sample from a hydrothermal vent along the mid-Atlantic ridge. A molecular survey of various hydrothermal vent environments demonstrated the presence of two of these bacteria (Am-N and Am-H) in more than one geographic location and habitat. These results suggest that certain epsilon Proteobacteria likely fill important niches in the environmental habitats of deep-sea hydrothermal vents, where they contribute to overall carbon and sulfur cycling at moderate thermophilic temperatures.
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Affiliation(s)
- B J Campbell
- College of Marine Studies, University of Delaware, Lewes, Delaware 19958, USA
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