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Pouliot J, Galand PE, Lovejoy C, Vincent WF. Vertical structure of archaeal communities and the distribution of ammonia monooxygenase A gene variants in two meromictic High Arctic lakes. Environ Microbiol 2009; 11:687-99. [PMID: 19207564 DOI: 10.1111/j.1462-2920.2008.01846.x] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The distribution of archaeal amoA and 16S rRNA genes was evaluated in two marine-derived, meromictic lakes in the Canadian High Arctic: Lake A and Lake C1 on the northern coast of Ellesmere Island. The amoA gene was recorded in both lakes, with highest copy numbers in the oxycline. Sequence analysis showed that amoA from the two lakes shared 94% similarity, indicating at least two phylogenetically distinct clusters. Clone libraries of archaeal 16S rRNA genes from Lake A revealed strong vertical differences in archaeal community diversity and composition down the water column. The oxic layer was dominated by one group of Euryarchaeota affiliated to the Lake Dagow Sediment (LDS) cluster. This group was absent from the oxycline, which had an extremely low archaeal diversity of two phylotypes. Both belonged to the Crenarchaeota Marine Group I (MGI), the marine group that has been linked to archaeal amoA; however, there was a low ratio of amoA to MGI copy numbers, suggesting that many MGI Archaea did not carry the amoA gene. The anoxic zone contained representatives of the RC-V (Rice Cluster-V) and LDS clusters of Euryarchaeota. These results show the strong vertical differentiation of archaeal communities in polar meromictic lakes, and they suggest archaeal nitrification within the oxycline of these highly stratified waters.
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Affiliation(s)
- Jérémie Pouliot
- Département de Biologie and Québec-Océan, Université Laval, Québec, QC, Canada
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52
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Nakagawa S, Takai K. Deep-sea vent chemoautotrophs: diversity, biochemistry and ecological significance. FEMS Microbiol Ecol 2008; 65:1-14. [DOI: 10.1111/j.1574-6941.2008.00502.x] [Citation(s) in RCA: 229] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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53
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Davis RE, Moyer CL. Extreme spatial and temporal variability of hydrothermal microbial mat communities along the Mariana Island Arc and southern Mariana back-arc system. ACTA ACUST UNITED AC 2008. [DOI: 10.1029/2007jb005413] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Richard E. Davis
- Biology Department; Western Washington University; Bellingham Washington USA
| | - Craig L. Moyer
- Biology Department; Western Washington University; Bellingham Washington USA
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54
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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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55
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Pagé A, Tivey MK, Stakes DS, Reysenbach AL. Temporal and spatial archaeal colonization of hydrothermal vent deposits. Environ Microbiol 2008; 10:874-84. [DOI: 10.1111/j.1462-2920.2007.01505.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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56
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Biochemical characterization of DNA-binding proteins from Pyrobaculum aerophilum and Aeropyrum pernix. Extremophiles 2007; 12:235-46. [DOI: 10.1007/s00792-007-0120-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2007] [Accepted: 10/24/2007] [Indexed: 11/25/2022]
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The Campylobacter jejuni NADH:ubiquinone oxidoreductase (complex I) utilizes flavodoxin rather than NADH. J Bacteriol 2007; 190:915-25. [PMID: 18065531 DOI: 10.1128/jb.01647-07] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Campylobacter jejuni encodes 12 of the 14 subunits that make up the respiratory enzyme NADH:ubiquinone oxidoreductase (also called complex I). The two nuo genes not present in C. jejuni encode the NADH dehydrogenase, and in their place in the operon are the novel genes designated Cj1575c and Cj1574c. A series of mutants was generated in which each of the 12 nuo genes (homologues to known complex I subunits) was disrupted or deleted. Each of the nuo mutants will not grow in amino acid-based medium unless supplemented with an alternative respiratory substrate such as formate. Unlike the nuo genes, Cj1574c is an essential gene and could not be disrupted unless an intact copy of the gene was provided at an unrelated site on the chromosome. A nuo deletion mutant can efficiently respire formate but is deficient in alpha-ketoglutarate respiratory activity compared to the wild type. In C. jejuni, alpha-ketoglutarate respiration is mediated by the enzyme 2-oxoglutarate:acceptor oxidoreductase; mutagenesis of this enzyme abolishes alpha-ketoglutarate-dependent O2 uptake and fails to reduce the electron transport chain. The electron acceptor for 2-oxoglutarate:acceptor oxidoreductase was determined to be flavodoxin, which was also determined to be an essential protein in C. jejuni. A model is presented in which CJ1574 mediates electron flow into the respiratory transport chain from reduced flavodoxin and through complex I.
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58
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Uncultured archaea in deep marine subsurface sediments: have we caught them all? ISME JOURNAL 2007; 2:3-18. [PMID: 18180743 DOI: 10.1038/ismej.2007.90] [Citation(s) in RCA: 292] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Deep marine subsurface sediments represent a novel archaeal biosphere with unknown physiology; the sedimentary subsurface harbors numerous novel phylogenetic lineages of archaea that are at present uncultured. Archaeal 16S rRNA analyses of deep subsurface sediments demonstrate their global occurrence and wide habitat range, including deep subsurface sediments, methane seeps and organic-rich coastal sediments. These subsurface archaeal lineages were discovered by PCR of extracted environmental DNA; their detection ultimately depends on the specificity of the archaeal PCR 16S rRNA primers. Surprisingly high mismatch frequencies for some archaeal PCR primers result in amplification bias against the corresponding archaeal lineages; this review presents some examples. Obviously, most archaeal 16S rRNA PCR primers were developed either before the discovery of these deep subsurface archaeal lineages, or without taking their sequence variants into account. PCR surveys with multiple primer combinations, revision and updates of primers whenever possible, and increasing use of PCR-independent methods in molecular microbial ecology will contribute to a more comprehensive view of subsurface archaeal communities.
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Culture-dependent and -independent characterization of microbial communities associated with a shallow submarine hydrothermal system occurring within a coral reef off Taketomi Island, Japan. Appl Environ Microbiol 2007; 73:7642-56. [PMID: 17921273 DOI: 10.1128/aem.01258-07] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Microbial communities in a shallow submarine hydrothermal system near Taketomi Island, Japan, were investigated using cultivation-based and molecular techniques. The main hydrothermal activity occurred in a craterlike basin (depth, approximately 23 m) on the coral reef seafloor. The vent fluid (maximum temperature, >52 degrees C) contained 175 microM H2S and gas bubbles mainly composed of CH4 (69%) and N2 (29%). A liquid serial dilution cultivation technique targeting a variety of metabolism types quantified each population in the vent fluid and in a white microbial mat located near the vent. The most abundant microorganisms cultivated from both the fluid and the mat were autotrophic sulfur oxidizers, including mesophilic Thiomicrospira spp. and thermophilic Sulfurivirga caldicuralii. Methane oxidizers were the second most abundant organisms in the fluid; one novel type I methanotroph exhibited optimum growth at 37 degrees C, and another novel type I methanotroph exhibited optimum growth at 45 degrees C. The number of hydrogen oxidizers cultivated only from the mat was less than the number of sulfur and methane oxidizers, although a novel mesophilic hydrogen-oxidizing member of the Epsilonproteobacteria was isolated. Various mesophilic to hyperthermophilic heterotrophs, including sulfate-reducing Desulfovibrio spp., iron-reducing Deferribacter sp., and sulfur-reducing Thermococcus spp., were also cultivated. Culture-independent 16S rRNA gene clone analysis of the vent fluid and mat revealed highly diverse archaeal communities. In the bacterial community, S. caldicuralii was identified as the predominant phylotype in the fluid (clonal frequency, 25%). Both bacterial clone libraries indicated that there were bacterial communities involved in sulfur, hydrogen, and methane oxidation and sulfate reduction. Our results indicate that there are unique microbial communities that are sustained by active chemosynthetic primary production rather than by photosynthetic production in a shallow hydrothermal system where sunlight is abundant.
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Coolen MJL, Abbas B, van Bleijswijk J, Hopmans EC, Kuypers MMM, Wakeham SG, Sinninghe Damsté JS. Putative ammonia-oxidizing Crenarchaeota in suboxic waters of the Black Sea: a basin-wide ecological study using 16S ribosomal and functional genes and membrane lipids. Environ Microbiol 2007; 9:1001-16. [PMID: 17359272 DOI: 10.1111/j.1462-2920.2006.01227.x] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Within the upper 400 m at western, central and eastern stations in the world's largest stratified basin, the Black Sea, we studied the qualitative and quantitative distribution of putative nitrifying Archaea based on their genetic markers (16S rDNA, amoA encoding for the alpha-subunit of archaeal ammonia monooxygenase), and crenarchaeol, the specific glycerol diphytanyl glycerol tetraether of pelagic Crenarchaeota within the Group I.1a. Marine Crenarchaeota were the most abundant Archaea (up to 98% of the total archaeal 16S rDNA copies) in the suboxic layers with oxygen levels as low as 1 microM including layers where previously anammox bacteria were described. Different marine crenarchaeotal phylotypes (both 16S rDNA and amoA) were found at the upper part of the suboxic zone as compared with the base of the suboxic zone and the upper 15-30 m of the anoxic waters with prevailing sulfide concentrations of up to 30 microM. Crenarchaeol concentrations were higher in the sulfidic chemocline as compared with the suboxic zone. These results indicate an abundance of putative nitrifying Archaea at very low oxygen levels within the Black Sea and might form an important source of nitrite for the anammox reaction.
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Affiliation(s)
- Marco J L Coolen
- Royal Netherlands Institute for Sea Research, Department of Marine Biogeochemistry and Toxicology, PO Box 59, 1790 AB Den Burg, the Netherlands.
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61
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La Duc MT, Benardini JN, Kempf MJ, Newcombe DA, Lubarsky M, Venkateswaran K. Microbial diversity of Indian Ocean hydrothermal vent plumes: microbes tolerant of desiccation, peroxide exposure, and ultraviolet and gamma-irradiation. ASTROBIOLOGY 2007; 7:416-31. [PMID: 17480169 DOI: 10.1089/ast.2006.0060] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The microbial diversity of Kali chimney plumes, part of a hydrothermal vent field in the Rodriguez Triple Junction, Indian Ocean (depth approximately 2,240 m), was examined in an attempt to discover "extremotolerant" microorganisms that have evolved unique resistance capabilities to this harsh environment. Water and sediment samples were collected from the vent and from sediments located at various distances (2-20 m) away from and surrounding the chimney. Samples were screened for hypertolerant microbes that are able to withstand multiple stresses. A total of 46 isolates were selected for exposure to a number of perturbations, such as heat shock, desiccation, H(2)O(2), and ultraviolet (UV) and gamma-irradiation. The survival of Psychrobacter sp. L0S3S-03b following exposure to >1,000 J/m(2) UV(254) radiation was particularly intriguing amid a background of varying levels of resistance. Vegetative cells of this non-spore-forming microbe not only survived all of the treatments, but also exhibited a 90% lethal dose of 30 s when exposed to simulated martian UV radiation and a 100% lethal dose of 2 min when exposed to full spectrum UV, which is comparable to findings for bacterial endospores.
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Affiliation(s)
- Myron T La Duc
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California 91109, USA.
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62
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Nakagawa T, Mori K, Kato C, Takahashi R, Tokuyama T. Distribution of Cold-Adapted Ammonia-Oxidizing Microorganisms in the Deep-Ocean of the Northeastern Japan Sea. Microbes Environ 2007. [DOI: 10.1264/jsme2.22.365] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Tatsunori Nakagawa
- Department of Agricultural and Biological Chemistry, College of Bioresource Sciences, Nihon University
| | - Koji Mori
- Biological Resource Center (NBRC), Department of Biotechnology, National Institute of Technology and Evaluation (NITE)
| | - Chiaki Kato
- Extremobiosphere Research Center, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Reiji Takahashi
- Department of Agricultural and Biological Chemistry, College of Bioresource Sciences, Nihon University
| | - Tatsuaki Tokuyama
- Department of Agricultural and Biological Chemistry, College of Bioresource Sciences, Nihon University
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63
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Huber JA, Butterfield DA, Baross JA. Diversity and distribution of subseafloor Thermococcales populations in diffuse hydrothermal vents at an active deep-sea volcano in the northeast Pacific Ocean. ACTA ACUST UNITED AC 2006. [DOI: 10.1029/2005jg000097] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Julie A. Huber
- School of Oceanography and Center for Astrobiology and Early Evolution; University of Washington; Seattle Washington USA
| | - David A. Butterfield
- Joint Institute for the Study of Atmosphere and Ocean; University of Washington; Seattle Washington USA
| | - John A. Baross
- School of Oceanography and Center for Astrobiology and Early Evolution; University of Washington; Seattle Washington USA
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64
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Takai K, Suzuki M, Nakagawa S, Miyazaki M, Suzuki Y, Inagaki F, Horikoshi K. Sulfurimonas paralvinellae sp. nov., a novel mesophilic, hydrogen- and sulfur-oxidizing chemolithoautotroph within the Epsilonproteobacteria isolated from a deep-sea hydrothermal vent polychaete nest, reclassification of Thiomicrospira denitrificans as Sulfurimonas denitrificans comb. nov. and emended description of the genus Sulfurimonas. Int J Syst Evol Microbiol 2006; 56:1725-1733. [PMID: 16901999 DOI: 10.1099/ijs.0.64255-0] [Citation(s) in RCA: 193] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel mesophilic bacterium, strain GO25(T), was isolated from a nest of hydrothermal vent polychaetes, Paralvinella sp., at the Iheya North field in the Mid-Okinawa Trough. Cells were motile short rods with a single polar flagellum. Growth was observed between 4 and 35 degrees C (optimum 30 degrees C; 13-16 h doubling time) and between pH 5.4 and 8.6 (optimum pH 6.1). The isolate was a facultatively anaerobic chemolithoautotroph capable of growth using molecular hydrogen, elemental sulfur or thiosulfate as the sole energy source, carbon dioxide as the sole carbon source, ammonium or nitrate as the sole nitrogen source and elemental sulfur, thiosulfate or yeast extract as the sole sulfur source. Strain GO25(T) represents the first deep-sea epsilonproteobacterium capable of growth by both hydrogen and sulfur oxidation. Nitrate or molecular oxygen (up to 10 % partial pressure) could serve as the sole electron acceptor to support growth. Metabolic products of nitrate reduction shifted in response to the electron donor provided. The G+C content of genomic DNA was 37.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the novel isolate belonged to the genus Sulfurimonas and was most closely related to Sulfurimonas autotrophica OK10(T) (96.3 % sequence similarity). DNA-DNA hybridization demonstrated that the novel isolate could be differentiated genotypically from Sulfurimonas autotrophica OK10(T). On the basis of the physiological and molecular properties of the novel isolate, the name Sulfurimonas paralvinellae sp. nov. is proposed, with strain GO25(T) (=JCM 13212(T)=DSM 17229(T)) as the type strain. Thiomicrospira denitrificans DSM 1251(T) (=ATCC 33889(T)) is phylogenetically associated with Sulfurimonas autotrophica OK10(T) and Sulfurimonas paralvinellae GO25(T). Based on the phylogenetic relationship between Thiomicrospira denitrificans DSM 1251(T), Sulfurimonas autotrophica OK10(T) and Sulfurimonas paralvinellae GO25(T), we propose the reclassification of Thiomicrospira denitrificans as Sulfurimonas denitrificans comb. nov. (type strain DSM 1251(T)=ATCC 33889(T)). In addition, an emended description of the genus Sulfurimonas is proposed.
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Affiliation(s)
- Ken Takai
- Subground Animalcule Retrieval (SUGAR) Program, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Masae Suzuki
- Subground Animalcule Retrieval (SUGAR) Program, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Satoshi Nakagawa
- Subground Animalcule Retrieval (SUGAR) Program, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Masayuki Miyazaki
- Subground Animalcule Retrieval (SUGAR) Program, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Yohey Suzuki
- Subground Animalcule Retrieval (SUGAR) Program, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Fumio Inagaki
- Subground Animalcule Retrieval (SUGAR) Program, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Koki Horikoshi
- Subground Animalcule Retrieval (SUGAR) Program, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
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Nakagawa T, Takai K, Suzuki Y, Hirayama H, Konno U, Tsunogai U, Horikoshi K. Geomicrobiological exploration and characterization of a novel deep-sea hydrothermal system at the TOTO caldera in the Mariana Volcanic Arc. Environ Microbiol 2006; 8:37-49. [PMID: 16343320 DOI: 10.1111/j.1462-2920.2005.00884.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Novel hydrothermal activities accompanying effluent white smokers and elemental sulfur chimney structures at the north-east lava dome of the TOTO caldera depression in the Mariana Volcanic Arc have been explored and characterized by geochemical and microbiological surveys. White smoker hydrothermal fluids were observed in the potential hydrothermal activity centre of the field and represented the maximal temperature of 170 degrees C and the lowest pH of 1.6. The chimney structures, all consisting of elemental sulfur (sulfur chimney), were also unique to the TOTO caldera hydrothermal field. Microbial community structures in a sulfur chimney and its formation hydrothermal fluid with a high concentration of hydrogen sulfide (15 mM) have been investigated by culture-dependent and -independent analyses. 16S rRNA gene clone analysis and fluorescence in situ hybridization (FISH) analysis revealed that epsilon-Proteobacteria dominated the microbial communities in the sulfur chimney structure and formed a dense microbial mat covering the sulfur chimney surface. Archaeal phylotypes were consistently minor components in the communities and related to the genera Thermococcus, Pyrodictium, Aeropyrum, and the uncultivated archaeal group of 'deep-sea hydrothermal vent euryarchaeotal group'. Cultivation analysis suggested that the chemolithoautotrophs might play a significant ecological role as primary producers utilizing gas and sulfur compounds provided from hydrothermal fluids.
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Affiliation(s)
- Tatsunori Nakagawa
- Subground Animalcule Retrieval SUGAR Project, Japan Agency for Marine-Earth Science and Technology, JAMSTEC, Yokosuka 237-0061, Japan
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Campbell BJ, Engel AS, Porter ML, Takai K. The versatile ε-proteobacteria: key players in sulphidic habitats. Nat Rev Microbiol 2006; 4:458-68. [PMID: 16652138 DOI: 10.1038/nrmicro1414] [Citation(s) in RCA: 430] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The epsilon-proteobacteria have recently been recognized as globally ubiquitous in modern marine and terrestrial ecosystems, and have had a significant role in biogeochemical and geological processes throughout Earth's history. To place this newly expanded group, which consists mainly of uncultured representatives, in an evolutionary context, we present an overview of the taxonomic classification for the class, review ecological and metabolic data in key sulphidic habitats and consider the ecological and geological potential of the epsilon-proteobacteria in modern and ancient systems. These integrated perspectives provide a framework for future culture- and genomic-based studies.
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Affiliation(s)
- Barbara J Campbell
- College of Marine Studies, University of Delaware, Lewes, Delaware 19958, USA.
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67
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Abstract
The domain Archaea represents a third line of evolutionary descent, separate from Bacteria and Eucarya. Initial studies seemed to limit archaea to various extreme environments. These included habitats at the extreme limits that allow life on earth, in terms of temperature, pH, salinity, and anaerobiosis, which were the homes to hyper thermo philes, extreme (thermo)acidophiles, extreme halophiles, and methanogens. Typical environments from which pure cultures of archaeal species have been isolated include hot springs, hydrothermal vents, solfataras, salt lakes, soda lakes, sewage digesters, and the rumen. Within the past two decades, the use of molecular techniques, including PCR-based amplification of 16S rRNA genes, has allowed a culture-independent assessment of microbial diversity. Remarkably, such techniques have indicated a wide distribution of mostly uncultured archaea in normal habitats, such as ocean waters, lake waters, and soil. This review discusses organisms from the domain Archaea in the context of the environments where they have been isolated or detected. For organizational purposes, the domain has been separated into the traditional groups of methanogens, extreme halophiles, thermoacidophiles, and hyperthermophiles, as well as the uncultured archaea detected by molecular means. Where possible, we have correlated known energy-yielding reactions and carbon sources of the archaeal types with available data on potential carbon sources and electron donors and acceptors present in the environments. From the broad distribution, metabolic diversity, and sheer numbers of archaea in environments from the extreme to the ordinary, the roles that the Archaea play in the ecosystems have been grossly underestimated and are worthy of much greater scrutiny.Key words: Archaea, methanogen, extreme halophile, hyperthermophile, thermoacidophile, uncultured archaea, habitats.
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Affiliation(s)
- Bonnie Chaban
- Department of Microbiology and Immunology, Queen's University, Kingston, ON, Canada
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69
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Takai K, Nakagawa S, Reysenbach AL, Hoek J. Microbial ecology of mid-ocean ridges and back-arc basins. ACTA ACUST UNITED AC 2006. [DOI: 10.1029/166gm10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2023]
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70
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Nakagawa S, Takai K, Inagaki F, Chiba H, Ishibashi JI, Kataoka S, Hirayama H, Nunoura T, Horikoshi K, Sako Y. Variability in microbial community and venting chemistry in a sediment-hosted backarc hydrothermal system: Impacts of subseafloor phase-separation. FEMS Microbiol Ecol 2005; 54:141-55. [PMID: 16329980 DOI: 10.1016/j.femsec.2005.03.007] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2004] [Revised: 03/10/2005] [Accepted: 03/16/2005] [Indexed: 11/26/2022] Open
Abstract
Phase-separation and -segregation (boiling/distillation of subseafloor hydrothermal fluids) represent the primary mechanisms causing intra-field variations in vent fluid compositions. To determine whether this geochemical process affects the formation of microbial communities, we examined the microbial communities at three different vent sites located within a few tens meters of one another. In addition to chimney structures, colonization devices capturing subseafloor communities entrained by the vent fluids were studied, using culture-dependent and -independent methods. Microbiological analyses demonstrated the occurrence of distinctive microbial communities in each of the hydrothermal niches. Within a chimney structure, there was a transition from a mixed community of mesophiles and thermophiles in the exterior parts to thermophiles in the interior. Beside the transition within a chimney structure, intra-field variations in microbial communities in vent fluids were apparent. Geochemical analysis demonstrated that different vent fluids have distinctive end-member compositions as a consequence of subseafloor phase-separation and -segregation, which were designated gas-depleted, normal and gas-enriched fluids. In comparison to gas-depleted and normal fluids, gas-enriched fluids harbored more abundant chemolithoautotrophs with gaseous component-dependent energy metabolism, such as hydrogenotrophic methanogenesis. Subseafloor phase-separation and -segregation may play a key role in supplying energy and carbon sources to vent-associated chemolithoautotrophs and subvent microbial communities.
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Affiliation(s)
- Satoshi Nakagawa
- Laboratory of Marine Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Japan.
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Takai K, Campbell BJ, Cary SC, Suzuki M, Oida H, Nunoura T, Hirayama H, Nakagawa S, Suzuki Y, Inagaki F, Horikoshi K. Enzymatic and genetic characterization of carbon and energy metabolisms by deep-sea hydrothermal chemolithoautotrophic isolates of Epsilonproteobacteria. Appl Environ Microbiol 2005; 71:7310-20. [PMID: 16269773 PMCID: PMC1287660 DOI: 10.1128/aem.71.11.7310-7320.2005] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The carbon and energy metabolisms of a variety of cultured chemolithoautotrophic Epsilonproteobacteria from deep-sea hydrothermal environments were characterized by both enzymatic and genetic analyses. All the Epsilonproteobacteria tested had all three key reductive tricarboxylic acid (rTCA) cycle enzymatic activities--ATP-dependent citrate lyase, pyruvate:ferredoxin oxidoreductase, and 2-oxoglutarate:ferredoxin oxidoreductase--while they had no ribulose 1,5-bisphosphate carboxylase (RubisCO) activity, the key enzyme in the Calvin-Benson cycle. These results paralleled the successful amplification of the key rTCA cycle genes aclB, porAB, and oorAB and the lack of success at amplifying the form I and II RubisCO genes, cbbL and cbbM. The combination of enzymatic and genetic analyses demonstrates that the Epsilonproteobacteria tested use the rTCA cycle for carbon assimilation. The energy metabolisms of deep-sea Epsilonproteobacteria were also well specified by the enzymatic and genetic characterization: hydrogen-oxidizing strains had evident soluble acceptor:methyl viologen hydrogenase activity and hydrogen uptake hydrogenase genes (hyn operon), while sulfur-oxidizing strains lacked both the enzyme activity and the genes. Although the energy metabolism of reduced sulfur compounds was not genetically analyzed and was not fully clarified, sulfur-oxidizing Epsilonproteobacteria showed enzyme activity of a potential sulfite:acceptor oxidoreductase for a direct oxidation pathway to sulfate but no activity of AMP-dependent adenosine 5'-phosphate sulfate reductase for a indirect oxidation pathway. No activity of thiosulfate-oxidizing enzymes was detected. The enzymatic and genetic characteristics described here were consistent with cellular carbon and energy metabolisms and suggest that molecular tools may have great potential for in situ elucidation of the ecophysiological roles of deep-sea Epsilonproteobacteria.
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Affiliation(s)
- Ken Takai
- Subground Animalcule Retrieval Program, Extremobiosphere Research Center, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan.
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72
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Nakagawa S, Takai K, Inagaki F, Hirayama H, Nunoura T, Horikoshi K, Sako Y. Distribution, phylogenetic diversity and physiological characteristics of epsilon-Proteobacteria in a deep-sea hydrothermal field. Environ Microbiol 2005; 7:1619-32. [PMID: 16156735 DOI: 10.1111/j.1462-2920.2005.00856.x] [Citation(s) in RCA: 173] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Epsilon-Proteobacteria is increasingly recognized as an ecologically significant group of bacteria, particularly in deep-sea hydrothermal environments. In this study, we studied the spatial distribution, diversity and physiological characteristics of the epsilon-Proteobacteria in various microbial habitats in the vicinity of a deep-sea hydrothermal vent occurring in the Iheya North field in the Mid-Okinawa Trough, by using culture-dependent and -independent approaches. The habitats studied were inside and outside hydrothermal plume, and annelid polychaete tubes. In addition, we deployed colonization devices near the vent emission. The polychaete tubes harboured physiologically and phylogenetically diverse microbial community. The in situ samplers were predominantly colonized by epsilon-Proteobacteria. Energy metabolism of epsilon-Proteobacteria isolates was highly versatile. Tree topology generated from the metabolic traits was significantly different (P = 0.000) from that of 16S rRNA tree, indicating current 16S rRNA gene-based analyses do not provide sufficient information to infer the physiological characteristics of epsilon-Proteobacteria. Nevertheless, culturability of epsilon-Proteobacteria in various microbial habitats differed among the phylogenetic subgroups. Members of Sulfurimonas were characterized by the robust culturability, and the other phylogenetic subgroups appeared to lose culturability in seawater, probably because of the sensitivity to oxygen. These results provide new insight into the ecophysiological characteristics of the deep-sea hydrothermal vent epsilon-Proteobacteria, which has never been assessed by comparative analysis of the 16S rRNA genes.
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Affiliation(s)
- Satoshi Nakagawa
- Laboratory of Marine Microbiology, Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Kyoto 606-8502, Japan.
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73
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Mehta MP, Huber JA, Baross JA. Incidence of novel and potentially archaeal nitrogenase genes in the deep Northeast Pacific Ocean. Environ Microbiol 2005; 7:1525-34. [PMID: 16156726 DOI: 10.1111/j.1462-2920.2005.00836.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Archaea have been detected throughout the oceanic water column and are quantitatively important members of picoplankton in the deep ocean. Two common groups, group I Crenarchaeota and group II Euryarchaeota, are consistently detected in warm hydrothermal fluid and are assumed to have been drawn into the subseafloor, mixed with hydrothermal fluid and then expelled. However, because they remain resistant to cultivation, very little is known about their physiology. Here we show that cold deep-seawater from the axial valley of Endeavour Segment on the Juan de Fuca Ridge contains not only groups I and II archaea as expected, but also unique potentially archaeal nitrogenase (nifH) genes, which are required for nitrogen fixation. These nifH genes are phylogenetically distinct and have dissimilar G+C content compared with those of hydrothermal vent archaea, suggesting that they belong to non-thermophilic deep-sea archaea. Furthermore, this sample did not contain mcrA genes, which are present in methanogens, the only known archaeal nitrogen fixers. These nifH genes were not detected in upper water column samples, or in a deep-seawater sample 100 km away from the spreading axis of the Juan de Fuca Ridge. We propose that these unique nifH genes may be localized to archaea that circulate through the nitrogen-poor subseafloor at the mid-ocean ridge as part of their life cycle.
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Affiliation(s)
- Mausmi P Mehta
- University of Washington, School of Oceanography, Seattle, WA 98195, USA.
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74
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Wang P, Xiao X, Wang F. Phylogenetic analysis of Archaea in the deep-sea sediments of west Pacific Warm Pool. Extremophiles 2005; 9:209-17. [PMID: 15761691 DOI: 10.1007/s00792-005-0436-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2004] [Accepted: 01/14/2005] [Indexed: 10/25/2022]
Abstract
Archaea are known to play important roles in carbon cycling in marine sediments. The main compositions of archaeal community in five deep-sea sediment samples collected from west Pacific Warm Pool area (WP-0, WP-1, WP-2, WP-3, WP-4), and in five sediment layers (1 cm-, 3 cm-, 6 cm-, 10 cm-, 12 cm- layer) of the 12 cm sediment core of WP-0 were checked and compared by denaturing gradient gel electrophoresis and 16 S rRNA gene sequencing. It was revealed that all the deep-sea sediment samples checked contained members of non-thermophilic marine group I crenarchaeota as the predominant archaeal group. To further detect groups of archaea possibly relating with C1 metabolism, PCR amplification was carried out using primers targeting methane-oxidizing archaea. Although no methane-oxidizing archaea was detected, a group of novel archaea (named as WPA) was instead identified from all these five WP samples by clone analysis. They could be placed in the euryarchaeota kingdom, separated into two distinct groups, the main group was peripherally related with methanogens, the other group related with Thermoplasma. The vertical distributions of WPA, archaea and bacteria along the WP-0 sediment column were determined by quantitative-PCR. It was found that bacteria dominated at all depths, the numbers of bacteria were 10-10(4) times more than those of archaea. The proportion of archaea versus bacteria had a depth related increasing tendency, it was lowest at the first layer (0.01%), reached highest at the 12 cm- layer (10%). WPA only constituted a small proportion of the archaeal community (0.05% to 5%) of west Pacific Warm Pool sediment.
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Affiliation(s)
- Peng Wang
- College of Marine Life Science, Ocean University of China, Qingdao, PR China
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75
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Inagaki F, Tsunogai U, Suzuki M, Kosaka A, Machiyama H, Takai K, Nunoura T, Nealson KH, Horikoshi K. Characterization of C1-metabolizing prokaryotic communities in methane seep habitats at the Kuroshima Knoll, southern Ryukyu Arc, by analyzing pmoA, mmoX, mxaF, mcrA, and 16S rRNA genes. Appl Environ Microbiol 2005; 70:7445-55. [PMID: 15574947 PMCID: PMC535202 DOI: 10.1128/aem.70.12.7445-7455.2004] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Samples from three submerged sites (MC, a core obtained in the methane seep area; MR, a reference core obtained at a distance from the methane seep; and HC, a gas-bubbling carbonate sample) at the Kuroshima Knoll in the southern Ryuku arc were analyzed to gain insight into the organisms present and the processes involved in this oxic-anoxic methane seep environment. 16S rRNA gene analyses by quantitative real-time PCR and clone library sequencing revealed that the MC core sediments contained abundant archaea (approximately 34% of the total prokaryotes), including both mesophilic methanogens related to the genus Methanolobus and ANME-2 members of the Methanosarcinales, as well as members of the delta-Proteobacteria, suggesting that both anaerobic methane oxidation and methanogenesis occurred at this site. In addition, several functional genes connected with methane metabolism were analyzed by quantitative competitive-PCR, including the genes encoding particulate methane monooxygenase (pmoA), soluble methane monooxygenase (mmoX), methanol dehydrogenese (mxaF), and methyl coenzyme M reductase (mcrA). In the MC core sediments, the most abundant gene was mcrA (2.5 x 10(6) copies/g [wet weight]), while the pmoA gene of the type I methanotrophs (5.9 x 10(6) copies/g [wet weight]) was most abundant at the surface of the MC core. These results indicate that there is a very complex environment in which methane production, anaerobic methane oxidation, and aerobic methane oxidation all occur in close proximity. The HC carbonate site was rich in gamma-Proteobacteria and had a high copy number of mxaF (7.1 x 10(6) copies/g [wet weight]) and a much lower copy number of the pmoA gene (3.2 x 10(2) copies/g [wet weight]). The mmoX gene was never detected. In contrast, the reference core contained familiar sequences of marine sedimentary archaeal and bacterial groups but not groups specific to C1 metabolism. Geochemical characterization of the amounts and isotopic composition of pore water methane and sulfate strongly supported the notion that in this zone both aerobic methane oxidation and anaerobic methane oxidation, as well as methanogenesis, occur.
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Affiliation(s)
- Fumio Inagaki
- Subground Animalcule Retrieval (SUGAR) Project, Frontier Research System for Extremophiles, Yokosuka, Japan.
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76
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Takai K, Hirayama H, Nakagawa T, Suzuki Y, Nealson KH, Horikoshi K. Lebetimonas acidiphila gen. nov., sp. nov., a novel thermophilic, acidophilic, hydrogen-oxidizing chemolithoautotroph within the ‘Epsilonproteobacteria’, isolated from a deep-sea hydrothermal fumarole in the Mariana Arc. Int J Syst Evol Microbiol 2005; 55:183-189. [PMID: 15653874 DOI: 10.1099/ijs.0.63330-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel thermophilic, acidophilic bacterium, designated strain Pd55T, was isolated from a self-temperature-recordingin situcolonization system deployed in a hydrothermal diffusing flow (maximum temperature of 78 °C) at the TOTO caldera in the Mariana Arc. Cells of strain Pd55Twere motile, short rods with a single polar flagellum. Growth was observed between 30 and 68 °C (optimum growth at 50 °C; 120 min doubling time) and between (initial) pH 4·2 and 7·0 (optimum at pH 5·2). The isolate was a strictly anaerobic chemolithoautotroph capable of using molecular hydrogen as sole energy source and carbon dioxide as sole carbon source. Elemental sulfur served as the sole electron acceptor to support growth. The G+C content of the genomic DNA was 34·0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate was related to members of the generaNautiliaandCaminibacter, although it appeared to be a novel lineage prior to the divergence betweenNautiliaandCaminibacter. Strain Pd55Tcould also be differentiated fromNautiliaandCaminibacterspecies on the basis of its physiological properties. It is, therefore, proposed that strain Pd55T(=JCM 12420T=DSM 16356T) represents the type strain of a novel species in a new genus,Lebetimonas acidiphilagen. nov., sp. nov.
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Affiliation(s)
- Ken Takai
- Subground Animalcule Retrieval (SUGAR) Project, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Hisako Hirayama
- Subground Animalcule Retrieval (SUGAR) Project, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Tatsunori Nakagawa
- Subground Animalcule Retrieval (SUGAR) Project, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Yohey Suzuki
- Subground Animalcule Retrieval (SUGAR) Project, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Kenneth H Nealson
- Department of Earth Sciences, University of Southern California, 3651 Trousdale Pkwy, Los Angeles, CA 90089-0740, USA
- Subground Animalcule Retrieval (SUGAR) Project, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Koki Horikoshi
- Subground Animalcule Retrieval (SUGAR) Project, Japan Agency for Marine-Earth Science and Technology, 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
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77
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Takai K, Hirayama H, Nakagawa T, Suzuki Y, Nealson KH, Horikoshi K. Thiomicrospira thermophila sp. nov., a novel microaerobic, thermotolerant, sulfur-oxidizing chemolithomixotroph isolated from a deep-sea hydrothermal fumarole in the TOTO caldera, Mariana Arc, Western Pacific. Int J Syst Evol Microbiol 2004; 54:2325-2333. [PMID: 15545479 DOI: 10.1099/ijs.0.63284-0] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A novel thermotolerant bacterium, designated strain I78T, was isolated from a self-temperature-recording in situ colonization system deployed in a hydrothermal diffusing flow (maximal temperature 78 °C) at the TOTO caldera in the Mariana Arc, Western Pacific. Cells were highly motile curved rods with a single polar flagellum. Growth was observed at 15–55 °C (optimum 35–40 °C; 60 min doubling time) and pH 5·0–8·0 (optimum pH 6·0). The isolate was a microaerobic chemolithomixotroph capable of using thiosulfate, elemental sulfur or sulfide as the sole energy source, and molecular oxygen as the sole electron acceptor. The isolate was able to grow chemolithoautotrophically with carbon dioxide. Various organic substrates such as complex proteinaceous compounds, carbohydrates, organic acids, amino acids and sugars could also support growth as the carbon source instead of carbon dioxide with sulfur oxidation. The G+C content of the genomic DNA was 43·8 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belonged to the genus Thiomicrospira and was most closely related to Thiomicrospira crunogena strain TH-55T and Thiomicrospira sp. strain L-12, while DNA–DNA hybridization demonstrated that the novel isolate could be genetically differentiated from previously described strains of Thiomicrospira. On the basis of its physiological and molecular properties the isolate is representative of a novel Thiomicrospira species, for which the name Thiomicrospira thermophila sp. nov. is proposed (type strain, I78T=JCM 12397T=DSM 16397T).
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Affiliation(s)
- Ken Takai
- Subground Animalcule Retrieval (SUGAR) Project, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Hisako Hirayama
- Subground Animalcule Retrieval (SUGAR) Project, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Tatsunori Nakagawa
- Subground Animalcule Retrieval (SUGAR) Project, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Yohey Suzuki
- Subground Animalcule Retrieval (SUGAR) Project, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Kenneth H Nealson
- Department of Earth Sciences, University of Southern California, 3651 Trousdale Parkway, Los Angeles, CA 90089-0740, USA
- Subground Animalcule Retrieval (SUGAR) Project, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
| | - Koki Horikoshi
- Subground Animalcule Retrieval (SUGAR) Project, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka 237-0061, Japan
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