1
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Smedile F, Foustoukos DI, Patwardhan S, Mullane K, Schlegel I, Adams MW, Schut GJ, Giovannelli D, Vetriani C. Adaptations to high pressure of Nautilia sp. strain PV-1, a piezophilic Campylobacterium (aka Epsilonproteobacterium) isolated from a deep-sea hydrothermal vent. Environ Microbiol 2022; 24:6164-6183. [PMID: 36271901 PMCID: PMC10092268 DOI: 10.1111/1462-2920.16256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 10/20/2022] [Indexed: 01/12/2023]
Abstract
Physiological and gene expression studies of deep-sea bacteria under pressure conditions similar to those experienced in their natural habitat are critical for understanding growth kinetics and metabolic adaptations to in situ conditions. The Campylobacterium (aka Epsilonproteobacterium) Nautilia sp. strain PV-1 was isolated from hydrothermal fluids released from an active deep-sea hydrothermal vent at 9° N on the East Pacific Rise. Strain PV-1 is a piezophilic, moderately thermophilic, chemolithoautotrophic anaerobe that conserves energy by coupling the oxidation of hydrogen to the reduction of nitrate or elemental sulfur. Using a high-pressure-high temperature continuous culture system, we established that strain PV-1 has the shortest generation time of all known piezophilic bacteria and we investigated its protein expression pattern in response to different hydrostatic pressure regimes. Proteogenomic analyses of strain PV-1 grown at 20 and 5 MPa showed that pressure adaptation is not restricted to stress response or homeoviscous adaptation but extends to enzymes involved in central metabolic pathways. Protein synthesis, motility, transport, and energy metabolism are all affected by pressure, although to different extents. In strain PV-1, low-pressure conditions induce the synthesis of phage-related proteins and an overexpression of enzymes involved in carbon fixation.
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Affiliation(s)
- Francesco Smedile
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, USA.,Institute of Polar Science (ISP-CNR), Messina, Italy
| | - Dionysis I Foustoukos
- Earth and Planets Laboratory, Carnegie Institution of Washington, Washington, District of Columbia, USA
| | - Sushmita Patwardhan
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, USA
| | - Kelli Mullane
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, USA.,Marine Biology Research Division, Scripps Institution of Oceanography, La Jolla, California, USA
| | - Ian Schlegel
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA
| | - Michael W Adams
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Gerrit J Schut
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Donato Giovannelli
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, USA.,Department of Biology, University of Naples "Federico II", Naples, Italy
| | - Costantino Vetriani
- Department of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey, USA.,Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, USA
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2
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Zeng X, Alain K, Shao Z. Microorganisms from deep-sea hydrothermal vents. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:204-230. [PMID: 37073341 PMCID: PMC10077256 DOI: 10.1007/s42995-020-00086-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 11/17/2020] [Indexed: 05/03/2023]
Abstract
With a rich variety of chemical energy sources and steep physical and chemical gradients, hydrothermal vent systems offer a range of habitats to support microbial life. Cultivation-dependent and independent studies have led to an emerging view that diverse microorganisms in deep-sea hydrothermal vents live their chemolithoautotrophic, heterotrophic, or mixotrophic life with versatile metabolic strategies. Biogeochemical processes are mediated by microorganisms, and notably, processes involving or coupling the carbon, sulfur, hydrogen, nitrogen, and metal cycles in these unique ecosystems. Here, we review the taxonomic and physiological diversity of microbial prokaryotic life from cosmopolitan to endemic taxa and emphasize their significant roles in the biogeochemical processes in deep-sea hydrothermal vents. According to the physiology of the targeted taxa and their needs inferred from meta-omics data, the media for selective cultivation can be designed with a wide range of physicochemical conditions such as temperature, pH, hydrostatic pressure, electron donors and acceptors, carbon sources, nitrogen sources, and growth factors. The application of novel cultivation techniques with real-time monitoring of microbial diversity and metabolic substrates and products are also recommended. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-020-00086-4.
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Affiliation(s)
- Xiang Zeng
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005 China
- LIA/IRP 1211 MicrobSea, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Plouzané, France
| | - Karine Alain
- Laboratoire de Microbiologie des Environnements Extrêmes LM2E UMR6197, Univ Brest, CNRS, IFREMER, F-29280 Plouzané, France
- LIA/IRP 1211 MicrobSea, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Plouzané, France
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005 China
- LIA/IRP 1211 MicrobSea, Sino-French International Laboratory of Deep-Sea Microbiology, 29280 Plouzané, France
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3
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Seafloor Incubation Experiment with Deep-Sea Hydrothermal Vent Fluid Reveals Effect of Pressure and Lag Time on Autotrophic Microbial Communities. Appl Environ Microbiol 2021; 87:AEM.00078-21. [PMID: 33608294 PMCID: PMC8091007 DOI: 10.1128/aem.00078-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/10/2021] [Indexed: 12/03/2022] Open
Abstract
Diverse microbial communities drive biogeochemical cycles in Earth’s ocean, yet studying these organisms and processes is often limited by technological capabilities, especially in the deep ocean. In this study, we used a novel marine microbial incubator instrument capable of in situ experimentation to investigate microbial primary producers at deep-sea hydrothermal vents. Depressurization and sample processing delays may impact the outcome of shipboard microbial incubations of samples collected from the deep sea. To address this knowledge gap, we developed a remotely operated vehicle (ROV)-powered incubator instrument to carry out and compare results from in situ and shipboard RNA stable isotope probing (RNA-SIP) experiments to identify the key chemolithoautotrophic microbes and metabolisms in diffuse, low-temperature venting fluids from Axial Seamount. All the incubations showed microbial uptake of labeled bicarbonate primarily by thermophilic autotrophic Epsilonbacteraeota that oxidized hydrogen coupled with nitrate reduction. However, the in situ seafloor incubations showed higher abundances of transcripts annotated for aerobic processes, suggesting that oxygen was lost from the hydrothermal fluid samples prior to shipboard analysis. Furthermore, transcripts for thermal stress proteins such as heat shock chaperones and proteases were significantly more abundant in the shipboard incubations, suggesting that depressurization induced thermal stress in the metabolically active microbes in these incubations. Together, the results indicate that while the autotrophic microbial communities in the shipboard and seafloor experiments behaved similarly, there were distinct differences that provide new insight into the activities of natural microbial assemblages under nearly native conditions in the ocean. IMPORTANCE Diverse microbial communities drive biogeochemical cycles in Earth’s ocean, yet studying these organisms and processes is often limited by technological capabilities, especially in the deep ocean. In this study, we used a novel marine microbial incubator instrument capable of in situ experimentation to investigate microbial primary producers at deep-sea hydrothermal vents. We carried out identical stable isotope probing experiments coupled to RNA sequencing both on the seafloor and on the ship to examine thermophilic, microbial autotrophs in venting fluids from an active submarine volcano. Our results indicate that microbial communities were significantly impacted by the effects of depressurization and sample processing delays, with shipboard microbial communities being more stressed than seafloor incubations. Differences in metabolism were also apparent and are likely linked to the chemistry of the fluid at the beginning of the experiment. Microbial experimentation in the natural habitat provides new insights into understanding microbial activities in the ocean.
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4
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Wang S, Jiang L, Hu Q, Liu X, Yang S, Shao Z. Elemental sulfur reduction by a deep-sea hydrothermal vent Campylobacterium Sulfurimonas sp. NW10. Environ Microbiol 2020; 23:965-979. [PMID: 32974951 DOI: 10.1111/1462-2920.15247] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/22/2020] [Indexed: 01/10/2023]
Abstract
Sulfurimonas species (class Campylobacteria, phylum Campylobacterota) were globally distributed and especially predominant in deep-sea hydrothermal environments. They were previously identified as chemolithoautotrophic sulfur-oxidizing bacteria (SOB), whereas little is known about their potential in sulfur reduction. In this report, we found that the elemental sulfur reduction is quite common in different species of genus Sulfurimonas. To gain insights into the sulfur reduction mechanism, growth tests, morphology observation, as well as genomic and transcriptomic analyses were performed on a deep-sea hydrothermal vent bacterium Sulfurimonas sp. NW10. Scanning electron micrographs and dialysis tubing tests confirmed that elemental sulfur reduction occurred without direct contact of cells with sulfur particles while direct access strongly promoted bacterial growth. Furthermore, we demonstrated that most species of Sulfurimonas probably employ both periplasmic and cytoplasmic polysulfide reductases, encoded by genes psrA1 B1 CDE and psrA2 B2 , respectively, to accomplish cyclooctasulfur reduction. This is the first report showing two different sulfur reduction pathways coupled to different energy conservations could coexist in one sulfur-reducing microorganism, and demonstrates that most bacteria of Sulfurimonas could employ both periplasmic and cytoplasmic polysulfide reductases to perform cyclooctasulfur reduction. The capability of sulfur reduction coupling with hydrogen oxidation may partially explain the prevalenceof Sulfurimonas in deep-sea hydrothermal vent environments.
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Affiliation(s)
- Shasha Wang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, 361005, China.,Fujian Key Laboratory of Marine Genetic Resources, Xiamen, 361005, China.,Department of Bioengineering and Biotechnology, College of Chemical Engineering, Huaqiao University, Xiamen, 361021, China
| | - Lijing Jiang
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, 361005, China.,Fujian Key Laboratory of Marine Genetic Resources, Xiamen, 361005, China
| | - Qitao Hu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, 361005, China.,Fujian Key Laboratory of Marine Genetic Resources, Xiamen, 361005, China
| | - Xuewen Liu
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, 361005, China.,Fujian Key Laboratory of Marine Genetic Resources, Xiamen, 361005, China
| | - Suping Yang
- Department of Bioengineering and Biotechnology, College of Chemical Engineering, Huaqiao University, Xiamen, 361021, China
| | - Zongze Shao
- Key Laboratory of Marine Genetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, China.,State Key Laboratory Breeding Base of Marine Genetic Resources, Xiamen, 361005, China.,Fujian Key Laboratory of Marine Genetic Resources, Xiamen, 361005, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, China
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5
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Nagata R, Takaki Y, Tame A, Nunoura T, Muto H, Mino S, Sawayama S, Takai K, Nakagawa S. Lebetimonas natsushimae sp. nov., a novel strictly anaerobic, moderately thermophilic chemoautotroph isolated from a deep-sea hydrothermal vent polychaete nest in the Mid-Okinawa Trough. Syst Appl Microbiol 2017; 40:352-356. [PMID: 28690052 DOI: 10.1016/j.syapm.2017.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 06/02/2017] [Accepted: 06/05/2017] [Indexed: 10/19/2022]
Abstract
A moderately thermophilic, strictly anaerobic, chemoautotrophic bacterium, designated strain HS1857T, was isolated from a deep-sea hydrothermal vent at the Noho site in the Mid-Okinawa Trough. Strain HS1857T grew between 35 and 63°C (optimum 55°C), in the presence of 10-55gl-1 NaCl (optimum 25gl-1), and pH 5.5-7.1 (optimum 6.4). Growth occurred with molecular hydrogen as the electron donor and elemental sulfur, nitrate, or selenate as the electron acceptors. Formate could serve as an alternative electron donor with nitrate as an electron acceptor. During growth with nitrate as the electron acceptor, strain HS1857T produced ammonium and formed a biofilm. CO2 was utilized as the sole carbon source. The G+C content of the genomic DNA was 33.2mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain HS1857T is a member of the order Nautiliales, showing a sequence similarity of 95.0% with Lebetimonas acidiphila Pd55T. The fatty acid composition was similar to that of L. acidiphila, which was dominated by C18:0 (47.0%) and C18:1 (23.7%). Based on the genomic, chemotaxonomic, phenotypic characteristics, the name Lebetimonas natsushimae sp. nov., is proposed. The type strain is HS1857T (=NBRC 112478T=DSM 104102T).
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Affiliation(s)
- Ryousuke Nagata
- Laboratory of Marine Environmental Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Yoshihiro Takaki
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Akihiro Tame
- Department of Technical Services, Marine Works Japan, Ltd., Yokosuka, Japan
| | - Takuro Nunoura
- Marine Functional Biology Group, Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Hisashi Muto
- Laboratory of Marine Environmental Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Sayaka Mino
- Laboratory of Microbiology, Faculty of Fisheries Sciences, Hokkaido University, Hakodate, Japan
| | - Shigeki Sawayama
- Laboratory of Marine Environmental Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Satoshi Nakagawa
- Laboratory of Marine Environmental Microbiology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan; Department of Subsurface Geobiological Analysis and Research (D-SUGAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan.
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6
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Florentino AP, Stams AJM, Sánchez-Andrea I. Genome Sequence of Desulfurella amilsii Strain TR1 and Comparative Genomics of Desulfurellaceae Family. Front Microbiol 2017; 8:222. [PMID: 28265263 PMCID: PMC5317093 DOI: 10.3389/fmicb.2017.00222] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 01/31/2017] [Indexed: 11/13/2022] Open
Abstract
The acidotolerant sulfur reducer Desulfurella amilsii was isolated from sediments of Tinto River, an extremely acidic environment. Its ability to grow in a broad range of pH and to tolerate certain heavy metals offers potential for metal recovery processes. Here we report its high-quality draft genome sequence and compare it to the available genome sequences of other members of Desulfurellaceae family: D. acetivorans. D. multipotens, Hippea maritima. H. alviniae, H. medeae, and H. jasoniae. For most species, pairwise comparisons for average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH) revealed ANI values from 67.5 to 80% and DDH values from 12.9 to 24.2%. D. acetivorans and D. multipotens, however, surpassed the estimated thresholds of species definition for both DDH (98.6%) and ANI (88.1%). Therefore, they should be merged to a single species. Comparative analysis of Desulfurellaceae genomes revealed different gene content for sulfur respiration between Desulfurella and Hippea species. Sulfur reductase is only encoded in D. amilsii, in which it is suggested to play a role in sulfur respiration, especially at low pH. Polysulfide reductase is only encoded in Hippea species; it is likely that this genus uses polysulfide as electron acceptor. Genes encoding thiosulfate reductase are present in all the genomes, but dissimilatory sulfite reductase is only present in Desulfurella species. Thus, thiosulfate respiration via sulfite is only likely in this genus. Although sulfur disproportionation occurs in Desulfurella species, the molecular mechanism behind this process is not yet understood, hampering a genome prediction. The metabolism of acetate in Desulfurella species can occur via the acetyl-CoA synthetase or via acetate kinase in combination with phosphate acetyltransferase, while in Hippea species, it might occur via the acetate kinase. Large differences in gene sets involved in resistance to acidic conditions were not detected among the genomes. Therefore, the regulation of those genes, or a mechanism not yet known, might be responsible for the unique ability of D. amilsii. This is the first report on comparative genomics of sulfur-reducing bacteria, which is valuable to give insight into this poorly understood metabolism, but of great potential for biotechnological purposes and of environmental significance.
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Affiliation(s)
- Anna P Florentino
- Laboratory of Microbiology, Wageningen UniversityWageningen, Netherlands; Sub-department of Environmental Technology, Wageningen UniversityWageningen, Netherlands
| | - Alfons J M Stams
- Laboratory of Microbiology, Wageningen UniversityWageningen, Netherlands; Centre of Biological Engineering, University of MinhoBraga, Portugal
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7
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Colonization of Black Smokers by Hyperthermophilic Microorganisms. Trends Microbiol 2017; 25:92-99. [DOI: 10.1016/j.tim.2016.11.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 10/10/2016] [Accepted: 11/02/2016] [Indexed: 11/19/2022]
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8
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Florentino AP, Weijma J, Stams AJM, Sánchez-Andrea I. Ecophysiology and Application of Acidophilic Sulfur-Reducing Microorganisms. BIOTECHNOLOGY OF EXTREMOPHILES: 2016. [DOI: 10.1007/978-3-319-13521-2_5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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9
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Grosche A, Sekaran H, Pérez-Rodríguez I, Starovoytov V, Vetriani C. Cetia pacifica gen. nov., sp. nov., a chemolithoautotrophic, thermophilic, nitrate-ammonifying bacterium from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 2015; 65:1144-1150. [DOI: 10.1099/ijs.0.000070] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A thermophilic, anaerobic, chemolithoautotrophic bacterium, strain TB-6T, was isolated from a deep-sea hydrothermal vent located on the East Pacific Rise at 9° N. The cells were Gram-staining-negative and rod-shaped with one or more polar flagella. Cell size was approximately 1–1.5 µm in length and 0.5 µm in width. Strain TB-6T grew between 45 and 70 °C (optimum 55–60 °C), 0 and 35 g NaCl l−1 (optimum 20–30 g l−1) and pH 4.5 and 7.5 (optimum pH 5.5–6.0). Generation time under optimal conditions was 2 h. Growth of strain TB-6T occurred with H2 as the energy source, CO2 as the carbon source and nitrate or sulfur as electron acceptors, with formation of ammonium or hydrogen sulfide, respectively. Acetate, (+)-d-glucose, Casamino acids, sucrose and yeast extract were not used as carbon and energy sources. Inhibition of growth occurred in the presence of lactate, peptone and tryptone under a H2/CO2 (80 : 20; 200 kPa) gas phase. Thiosulfate, sulfite, arsenate, selenate and oxygen were not used as electron acceptors. The G+C content of the genomic DNA was 36.8 mol%. Phylogenetic analysis of the 16S rRNA gene of strain TB-6T showed that this organism branched separately from the three most closely related genera,
Caminibacter
,
Nautilia
and
Lebetimonas
, within the family
Nautiliaceae
. Strain TB-6T contained several unique fatty acids in comparison with other members of the family
Nautiliaceae
. Based on experimental evidence, it is proposed that the organism represents a novel species and genus within the family
Nautiliaceae
, Cetia pacifica, gen. nov., sp. nov. The type strain is TB-6T ( = DSM 27783T = JCM 19563T).
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Affiliation(s)
- Ashley Grosche
- Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901, USA
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Hema Sekaran
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Ileana Pérez-Rodríguez
- Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901, USA
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Valentin Starovoytov
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
| | - Costantino Vetriani
- Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901, USA
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
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10
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Winkel M, Pjevac P, Kleiner M, Littmann S, Meyerdierks A, Amann R, Mußmann M. Identification and activity of acetate-assimilating bacteria in diffuse fluids venting from two deep-sea hydrothermal systems. FEMS Microbiol Ecol 2014; 90:731-46. [DOI: 10.1111/1574-6941.12429] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 09/10/2014] [Accepted: 09/16/2014] [Indexed: 12/01/2022] Open
Affiliation(s)
- Matthias Winkel
- Department of Molecular Ecology; Max Planck Institute for Marine Microbiology; Bremen Germany
| | - Petra Pjevac
- Department of Molecular Ecology; Max Planck Institute for Marine Microbiology; Bremen Germany
| | - Manuel Kleiner
- Department of Symbiosis; Max Planck Institute for Marine Microbiology; Bremen Germany
| | - Sten Littmann
- Department of Biogeochemistry; Max Planck Institute for Marine Microbiology; Bremen Germany
| | - Anke Meyerdierks
- Department of Molecular Ecology; Max Planck Institute for Marine Microbiology; Bremen Germany
| | - Rudolf Amann
- Department of Molecular Ecology; Max Planck Institute for Marine Microbiology; Bremen Germany
| | - Marc Mußmann
- Department of Molecular Ecology; Max Planck Institute for Marine Microbiology; Bremen Germany
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11
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Geochemistry and microbial ecology in alkaline hot springs of Ambitle Island, Papua New Guinea. Extremophiles 2014; 18:763-78. [DOI: 10.1007/s00792-014-0657-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Accepted: 05/18/2014] [Indexed: 11/30/2022]
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12
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Pérez-Rodríguez I, Bohnert KA, Cuebas M, Keddis R, Vetriani C. Detection and phylogenetic analysis of the membrane-bound nitrate reductase (Nar) in pure cultures and microbial communities from deep-sea hydrothermal vents. FEMS Microbiol Ecol 2013; 86:256-67. [PMID: 23889124 DOI: 10.1111/1574-6941.12158] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Revised: 05/17/2013] [Accepted: 06/04/2013] [Indexed: 11/28/2022] Open
Abstract
Over the past few years the relevance of nitrate respiration in microorganisms from deep-sea hydrothermal vents has become evident. In this study, we surveyed the membrane-bound nitrate reductase (Nar) encoding gene in three different deep-sea vent microbial communities from the East Pacific Rise and the Mid-Atlantic Ridge. Additionally, we tested pure cultures of vent strains for their ability to reduce nitrate and for the presence of the NarG-encoding gene in their genomes. By using the narG gene as a diagnostic marker for nitrate-reducing bacteria, we showed that nitrate reductases related to Gammaproteobacteria of the genus Marinobacter were numerically prevalent in the clone libraries derived from a black smoker and a diffuse flow vent. In contrast, NarG sequences retrieved from a community of filamentous bacteria located about 50 cm above a diffuse flow vent revealed the presence of a yet to be identified group of enzymes. 16S rRNA gene-inferred community compositions, in accordance with previous studies, showed a shift from Alpha- and Gammaproteobacteria to Epsilonproteobacteria as the vent fluids become warmer and more reducing. Based on these findings, we argue that Nar-catalyzed nitrate reduction is likely relevant in temperate and less reducing environments where Alpha- and Gammaproteobacteria are more abundant and where nitrate concentrations reflect that of background deep seawater.
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Affiliation(s)
- Ileana Pérez-Rodríguez
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA; Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA
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13
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Srinivasan V, Morowitz HJ, Huber H. What is an autotroph? Arch Microbiol 2011; 194:135-40. [DOI: 10.1007/s00203-011-0755-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2011] [Revised: 07/24/2011] [Accepted: 09/13/2011] [Indexed: 10/17/2022]
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14
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Giovannelli D, Ferriera S, Johnson J, Kravitz S, Pérez-Rodríguez I, Ricci J, O’Brien C, Voordeckers JW, Bini E, Vetriani C. Draft genome sequence of Caminibacter mediatlanticus strain TB-2, an epsilonproteobacterium isolated from a deep-sea hydrothermal vent. Stand Genomic Sci 2011; 5:135-43. [PMID: 22180817 PMCID: PMC3236049 DOI: 10.4056/sigs.2094859] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Caminibacter mediatlanticus strain TB-2T [1], is a thermophilic, anaerobic, chemolithoautotrophic bacterium, isolated from the walls of an active deep-sea hydrothermal vent chimney on the Mid-Atlantic Ridge and the type strain of the species. C. mediatlanticus is a Gram-negative member of the Epsilonproteobacteria (order Nautiliales) that grows chemolithoautotrophically with H2 as the energy source and CO2 as the carbon source. Nitrate or sulfur is used as the terminal electron acceptor, with resulting production of ammonium and hydrogen sulfide, respectively. In view of the widespread distribution, importance and physiological characteristics of thermophilic Epsilonproteobacteria in deep-sea geothermal environments, it is likely that these organisms provide a relevant contribution to both primary productivity and the biogeochemical cycling of carbon, nitrogen and sulfur at hydrothermal vents. Here we report the main features of the genome of C. mediatlanticus strain TB-2T.
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Affiliation(s)
- Donato Giovannelli
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA
- Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA
- Institute for Marine Science - ISMAR, National Research Council of Italy, Ancona, ITALY
| | - Steven Ferriera
- J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland, USA
| | - Justin Johnson
- J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland, USA
| | - Saul Kravitz
- J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, Maryland, USA
| | - Ileana Pérez-Rodríguez
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA
- Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA
| | - Jessica Ricci
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA
- Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA
| | - Charles O’Brien
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA
- Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA
| | - James W. Voordeckers
- Institute for Environmental Genomics, Department of Botany and Microbiology, University of Oklahoma, Norman, OK, USA
| | - Elisabetta Bini
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA
| | - Costantino Vetriani
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ, USA
- Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ, USA
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Extremophiles: from abyssal to terrestrial ecosystems and possibly beyond. Naturwissenschaften 2011; 98:253-79. [DOI: 10.1007/s00114-011-0775-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2010] [Revised: 02/17/2011] [Accepted: 02/18/2011] [Indexed: 01/27/2023]
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Pérez-Rodríguez I, Ricci J, Voordeckers JW, Starovoytov V, Vetriani C. Nautilia nitratireducens sp. nov., a thermophilic, anaerobic, chemosynthetic, nitrate-ammonifying bacterium isolated from a deep-sea hydrothermal vent. Int J Syst Evol Microbiol 2009; 60:1182-1186. [PMID: 19667392 DOI: 10.1099/ijs.0.013904-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A thermophilic, anaerobic, chemosynthetic bacterium, designated strain MB-1(T), was isolated from the walls of an active deep-sea hydrothermal vent chimney on the East Pacific Rise at degrees 50' N 10 degrees 17' W. The cells were Gram-negative-staining rods, approximately 1-1.5 mum long and 0.3-0.5 mum wide. Strain MB-1(T) grew at 25-65 degrees C (optimum 55 degrees C), with 10-35 g NaCl l(-1) (optimum 20 g l(-1)) and at pH 4.5-8.5 (optimum pH 7.0). Generation time under optimal conditions was 45.6 min. Growth occurred under chemolithoautotrophic conditions with H(2) as the energy source and CO(2) as the carbon source. Nitrate was used as the electron acceptor, with resulting production of ammonium. Thiosulfate, sulfur and selenate were also used as electron acceptors. No growth was observed in the presence of lactate, peptone or tryptone. Chemo-organotrophic growth occurred in the presence of acetate, formate, Casamino acids, sucrose, galactose and yeast extract under a N(2)/CO(2) gas phase. The G+C content of the genomic DNA was 36.0 mol%. Phylogenetic analysis of the 16S rRNA gene sequence indicated that this organism is closely related to Nautilia profundicola AmH(T), Nautilia abyssi PH1209(T) and Nautilia lithotrophica 525(T) (95, 94 and 93 % sequence identity, respectively). On the basis of phylogenetic, physiological and genetic considerations, it is proposed that the organism represents a novel species within the genus Nautilia, Nautilia nitratireducens sp. nov. The type strain is MB-1(T) (=DSM 22087(T) =JCM 15746(T)).
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Affiliation(s)
- Ileana Pérez-Rodríguez
- Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901, USA
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Jessica Ricci
- Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901, USA
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - James W Voordeckers
- Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901, USA
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | - Valentin Starovoytov
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ 08854, USA
| | - Costantino Vetriani
- Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, NJ 08901, USA
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
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