1887

Abstract

A facultatively anaerobic organoheterotroph, designated JAM-BA0302, was isolated from a deep subseafloor sediment at a depth of 247.1 m below the seafloor off the Shimokita Peninsula of Japan in the north-western Pacific Ocean (Site C9001 , water depth 1180 m). Cells of strain JAM-BA0302 showed gliding motility and were thin, long rods with peritrichous fimbriae-like structures. Growth occurred at 4–37 °C (optimum 30 °C; doubling time 8 h), at pH 5.4–8.3 (optimum pH 7.5) and with 5–60 g NaCl l (optimum 20–25 g l). The isolate utilized proteinaceous substrates such as yeast extract, tryptone, casein and Casamino acids with O respiration or fermentation. Strain JAM-BA0302 was a piezotolerant bacterium that could grow at pressures as high as 25 MPa under aerobic conditions and 10 MPa under anaerobic conditions. The G+C content of the genomic DNA was 43.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain JAM-BA0302 was most closely related to yet-undescribed strains recently isolated from various marine sedimentary environments (>99.6 % 16S rRNA gene sequence similarity) and was moderately related to DQHS-4, isolated from a sea cucumber farm sediment (95.5 % 16S rRNA gene sequence similarity) within the . The phylogenetic analysis suggested that the isolate should belong to the genus However, low DNA–DNA relatedness (<11 %) and many physiological and molecular properties differentiated the isolate from those previously described. We propose here a novel species of the genus , with the name sp. nov. The type strain is JAM-BA0302 ( = JCM 15547  = NCIMB 14481).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.044065-0
2013-05-01
2021-05-17
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/63/5/1602.html?itemId=/content/journal/ijsem/10.1099/ijs.0.044065-0&mimeType=html&fmt=ahah

References

  1. Aoike K. ( 2007 ). CDEX Laboratory Operation Report: CK06–06 D/V Chikyu shakedown cruise offshore Shimokita: Yokohama (CDEX-JAMSTEC). http://sio7.jamstec.go.jp/JAMSTEC-exp-report/902/CK06-06_CR.pdf.
  2. Bale S. J., Goodman K., Rochelle P. A., Marchesi J. R., Fry J. C., Weightman A. J., Parkes R. J. ( 1997 ). Desulfovibrio profundus sp. nov., a novel barophilic sulfate-reducing bacterium from deep sediment layers in the Japan Sea. . Int J Syst Bacteriol 47, 515521. [CrossRef] [PubMed]
    [Google Scholar]
  3. Batzke A., Engelen B., Sass H., Cypionka H. ( 2007 ). Phylogenetic and physiological diversity of cultured deep-biosphere bacteria from Equatorial Pacific Ocean and Peru Margin sediments. . Geomicrobiol J 24, 261273. [CrossRef]
    [Google Scholar]
  4. Biddle J. F., Lipp J. S., Lever M. A., Lloyd K. G., Sørensen K. B., Anderson R., Fredricks H. F., Elvert M., Kelly T. J. & other authors ( 2006 ). Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru. . Proc Natl Acad Sci U S A 103, 38463851. [CrossRef] [PubMed]
    [Google Scholar]
  5. D’Hondt S., Rutherford S., Spivack A. J. ( 2002 ). Metabolic activity of subsurface life in deep-sea sediments. . Science 295, 20672070. [CrossRef] [PubMed]
    [Google Scholar]
  6. D’Hondt S., Jørgensen B. B., Miller D. J., Batzke A., Blake R., Cragg B. A., Cypionka H., Dickens G. R., Ferdelman T. & other authors ( 2004 ). Distributions of microbial activities in deep subseafloor sediments. . Science 306, 22162221. [CrossRef] [PubMed]
    [Google Scholar]
  7. D’Hondt S., Spivack A. J., Pockalny R., Ferdelman T. G., Fischer J. P., Kallmeyer J., Abrams L. J., Smith D. C., Graham D. & other authors ( 2009 ). Subseafloor sedimentary life in the South Pacific Gyre. . Proc Natl Acad Sci U S A 106, 1165111656.[PubMed] [CrossRef]
    [Google Scholar]
  8. DeLong E. F. ( 1992 ). Archaea in coastal marine environments. . Proc Natl Acad Sci U S A 89, 56855689. [CrossRef] [PubMed]
    [Google Scholar]
  9. Ezaki T., Hashimoto Y., Yabuuchi E. ( 1989 ). Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. . Int J Syst Bacteriol 39, 224229. [CrossRef]
    [Google Scholar]
  10. Felsenstein J. ( 1981 ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17, 368376. [CrossRef] [PubMed]
    [Google Scholar]
  11. Fry J. C., Parkes R. J., Cragg B. A., Weightman A. J., Webster G. ( 2008 ). Prokaryotic biodiversity and activity in the deep subseafloor biosphere. . FEMS Microbiol Ecol 66, 181196. [CrossRef] [PubMed]
    [Google Scholar]
  12. Futagami T., Morono Y., Terada T., Kaksonen A. H., Inagaki F. ( 2009 ). Dehalogenation activities and distribution of reductive dehalogenase homologous genes in marine subsurface sediments. . Appl Environ Microbiol 75, 69056909. [CrossRef] [PubMed]
    [Google Scholar]
  13. Holmes D. E., Nevin K. P., Woodard T. L., Peacock A. D., Lovley D. R. ( 2007 ). Prolixibacter bellariivorans gen. nov., sp. nov., a sugar-fermenting, psychrotolerant anaerobe of the phylum Bacteroidetes, isolated from a marine-sediment fuel cell. . Int J Syst Evol Microbiol 57, 701707. [CrossRef] [PubMed]
    [Google Scholar]
  14. Inagaki F. ( 2010 ). Deep subseafloor microbial communities. . In Encyclopedia of Life Sciences, pp. 110. Chichester:: John Wiley & Sons, Ltd;. [CrossRef]
    [Google Scholar]
  15. Inagaki F., Nakagawa S. ( 2008;). Spatial distribution of subseafloor life: diversity and biogeography. . In Links Between Geological Processes, Microbial Activities and Evolution of Life, pp. 135158. Edited by Dilek Y., Furnes H., Muehlenbachs K. . Dordrecht, The Netherlands:: Springer Science;. [CrossRef]
    [Google Scholar]
  16. Inagaki F., Nunoura T., Nakagawa S., Teske A., Lever M., Lauer A., Suzuki M., Takai K., Delwiche M. & other authors ( 2006 ). Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin. . Proc Natl Acad Sci U S A 103, 28152820. [CrossRef] [PubMed]
    [Google Scholar]
  17. Irgens R. L. ( 1977 ). Meniscus, a new genus of aerotolerant, gas-vacuolated bacteria. . Int J Syst Bacteriol 27, 3843. [CrossRef]
    [Google Scholar]
  18. Jørgensen B. B., Boetius A. ( 2007 ). Feast and famine – microbial life in the deep-sea bed. . Nat Rev Microbiol 5, 770781. [CrossRef] [PubMed]
    [Google Scholar]
  19. Kendall M. M., Liu Y., Sieprawska-Lupa M., Stetter K. O., Whitman W. B., Boone D. R. ( 2006 ). Methanococcus aeolicus sp. nov., a mesophilic, methanogenic archaeon from shallow and deep marine sediments. . Int J Syst Evol Microbiol 56, 15251529. [CrossRef] [PubMed]
    [Google Scholar]
  20. Kobayashi T., Koide O., Mori K., Shimamura S., Matsuura T., Miura T., Takaki Y., Morono Y., Nunoura T. & other authors ( 2008 ). Phylogenetic and enzymatic diversity of deep subseafloor aerobic microorganisms in organics- and methane-rich sediments off Shimokita Peninsula. . Extremophiles 12, 519527. [CrossRef] [PubMed]
    [Google Scholar]
  21. Komagata K., Suzuki K. ( 1987 ). Lipid and cell-wall analysis in bacterial systematics. . Methods Microbiol 19, 161207. [CrossRef]
    [Google Scholar]
  22. Lane D. J. ( 1985 ). 16S/23S sequencing. . In Nucleic Acid Techniques in Bacterial Systematics, pp. 115176. Edited by Stackebrandt E., Goodfellow M. . New York:: John Wiley & Sons;.
    [Google Scholar]
  23. Lee Y.-J., Wagner I. D., Brice M. E., Kevbrin V. V., Mills G. L., Romanek C. S., Wiegel J. ( 2005 ). Thermosediminibacter oceani gen. nov., sp. nov. and Thermosediminibacter litoriperuensis sp. nov., new anaerobic thermophilic bacteria isolated from Peru Margin. . Extremophiles 9, 375383. [CrossRef] [PubMed]
    [Google Scholar]
  24. Lipp J. S., Morono Y., Inagaki F., Hinrichs K. U. ( 2008 ). Significant contribution of Archaea to extant biomass in marine subsurface sediments. . Nature 454, 991994. [CrossRef] [PubMed]
    [Google Scholar]
  25. Ludwig W., Strunk O., Westram R., Richter L., Meier H., Yadhukumar, Buchner A., Lai T., Steppi S. & other authors ( 2004 ). arb: a software environment for sequence data. . Nucleic Acids Res 32, 13631371. [CrossRef] [PubMed]
    [Google Scholar]
  26. Marmur J., Doty P. ( 1962 ). Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. . J Mol Biol 5, 109118. [CrossRef] [PubMed]
    [Google Scholar]
  27. MIDI ( 1999 ). Sherlock Microbial Identification System, operating manual version 3.0. . Newark, DE:: MIDI, Inc.;
  28. Mikucki J. A., Liu Y., Delwiche M., Colwell F. S., Boone D. R. ( 2003 ). Isolation of a methanogen from deep marine sediments that contain methane hydrates, and description of Methanoculleus submarines sp. nov.. Appl Environ Microbiol 69, 33113316. [CrossRef] [PubMed]
    [Google Scholar]
  29. Minnikin D. E., O’Donnell A. G., Goodfellow M., Alderson G., Athalye M., Schaal K., Parlett J. H. ( 1984 ). An integrated procedure for extracting bacterial isoprenoid quinones and polar lipids. . J Microbiol Methods 2, 233241. [CrossRef]
    [Google Scholar]
  30. Morono Y., Terada T., Masui N., Inagaki F. ( 2009 ). Discriminative detection and enumeration of microbial life in marine subsurface sediments. . ISME J 3, 503511. [CrossRef] [PubMed]
    [Google Scholar]
  31. Nakagawa S., Inagaki F., Suzuki Y., Steinsbu B. O., Lever M. A., Takai K., Engelen B., Sako Y., Wheat C. G., Horikoshi K. ( 2006 ). Microbial community in black rust exposed to hot ridge flank crustal fluids. . Appl Environ Microbiol 72, 67896799. [CrossRef] [PubMed]
    [Google Scholar]
  32. Parkes R. J., Cragg B. A., Wellsbury P. ( 2000 ). Recent studies on bacterial populations and processes in subseafloor sediments: a review. . Hydrogeol J 8, 1128. [CrossRef]
    [Google Scholar]
  33. Parkes R. J., Sellek G., Webster G., Martin D., Anders E., Weightman A. J., Sass H. ( 2009 ). Culturable prokaryotic diversity of deep, gas hydrate sediments: first use of a continuous high-pressure, anaerobic, enrichment and isolation system for subseafloor sediments (DeepIsoBUG). . Environ Microbiol 11, 31403153. [CrossRef] [PubMed]
    [Google Scholar]
  34. Porter K. G., Feig Y. S. ( 1980 ). The use of DAPI for identifying and counting aquatic microflora. Limnol Oceanogr 25, 943948. [CrossRef]
    [Google Scholar]
  35. Qu J.-H., Yuan H.-L., Yang J.-S., Li H.-F., Chen N. ( 2009 ). Lacibacter cauensis gen. nov., sp. nov., a novel member of the phylum Bacteroidetes isolated from sediment of a eutrophic lake. . Int J Syst Evol Microbiol 59, 11531157. [CrossRef] [PubMed]
    [Google Scholar]
  36. Qu L., Zhu F., Hong X., Gao W., Chen J., Sun X. ( 2011 ). Sunxiuqinia elliptica gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from sediment of a sea cucumber farm. . Int J Syst Evol Microbiol 61, 28852889. [CrossRef] [PubMed]
    [Google Scholar]
  37. Saitou N., Nei M. ( 1987 ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4, 406425.[PubMed]
    [Google Scholar]
  38. Stackebrandt E., Goebel B. M. ( 1994 ). Taxonomic note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. . Int J Syst Bacteriol 44, 846849. [CrossRef]
    [Google Scholar]
  39. Stackebrandt E., Frederiksen W., Garrity G. M., Grimont P. A. D., Kämpfer P., Maiden M. C. J., Nesme X., Rosselló-Mora R., Swings J. & other authors ( 2002 ). Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. . Int J Syst Evol Microbiol 52, 10431047. [CrossRef] [PubMed]
    [Google Scholar]
  40. Takai K., Inoue A., Horikoshi K. ( 1999 ). Thermaerobacter marianensis gen. nov., sp. nov., an aerobic extremely thermophilic marine bacterium from the 11,000 m deep Mariana Trench. . Int J Syst Bacteriol 49, 619628. [CrossRef] [PubMed]
    [Google Scholar]
  41. Takai K., Komatsu T., Horikoshi K. ( 2001 ). Hydrogenobacter subterraneus sp. nov., an extremely thermophilic, heterotrophic bacterium unable to grow on hydrogen gas, from deep subsurface geothermal water. . Int J Syst Evol Microbiol 51, 14251435.[PubMed]
    [Google Scholar]
  42. Takai K., Moyer C. L., Miyazaki M., Nogi Y., Hirayama H., Nealson K. H., Horikoshi K. ( 2005 ). Marinobacter alkaliphilus sp. nov., a novel alkaliphilic bacterium isolated from subseafloor alkaline serpentine mud from Ocean Drilling Program Site 1200 at South Chamorro Seamount, Mariana Forearc. . Extremophiles 9, 1727. [CrossRef] [PubMed]
    [Google Scholar]
  43. Takai K., Nakamura K., Toki T., Tsunogai U., Miyazaki M., Miyazaki J., Hirayama H., Nakagawa S., Nunoura T., Horikoshi K. ( 2008 ). Cell proliferation at 122°C and isotopically heavy CH4 production by a hyperthermophilic methanogen under high-pressure cultivation. . Proc Natl Acad Sci U S A 105, 1094910954. [CrossRef] [PubMed]
    [Google Scholar]
  44. Tamaoka J., Komagata K. ( 1984 ). Determination of DNA base composition by reversed-phase high-performance liquid chromatography. . FEMS Microbiol Lett 25, 125128. [CrossRef]
    [Google Scholar]
  45. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S. ( 2011 ). mega5: Molecular Evolutionary Genetics Analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. . Mol Biol Evol 28, 27312739. [CrossRef] [PubMed]
    [Google Scholar]
  46. Teske A. ( 2006 ). Microbial communities of deep marine subsurface sediments: Molecular and cultivation surveys. . Geomicrobiol J 23, 357368. [CrossRef]
    [Google Scholar]
  47. Toffin L., Bidault A., Pignet P., Tindall B. J., Slobodkin A., Kato C., Prieur D. ( 2004 ). Shewanella profunda sp. nov., isolated from deep marine sediment of the Nankai Trough. . Int J Syst Evol Microbiol 54, 19431949. [CrossRef] [PubMed]
    [Google Scholar]
  48. Tomaru H., Fehn U., Lu Z., Takeuchi R., Inagaki F., Imachi H., Kotani R., Matsumoto R., Aoike K. ( 2009 ). Dating of dissolved iodine in pore waters from the gas hydrate occurrence offshore Shimokita Peninsula, Japan: 129I results from the D/V Chikyu shakedown cruise. . Resource Geol 59, 359373. [CrossRef]
    [Google Scholar]
  49. Wayne L. G., Brenner D. J., Colwell R. R., Grimont P. A. D., Kandler O., Krichevsky M. I., Moore L. H., Moore W. E. C., Murray R. G. E. & other authors ( 1987 ). International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. . Int J Syst Bacteriol 37, 463464. [CrossRef]
    [Google Scholar]
  50. Whitman W. B., Coleman D. C., Wiebe W. J. ( 1998 ). Prokaryotes: the unseen majority. . Proc Natl Acad Sci U S A 95, 65786583. [CrossRef] [PubMed]
    [Google Scholar]
  51. Zillig W., Holz I., Janekovic D., Klenk H.-P., Imsel E., Trent J., Wunderl S., Forjaz V. H., Coutinho R., Ferreira T. ( 1990 ). Hyperthermus butylicus, a hyperthermophilic sulfur-reducing archaebacterium that ferments peptides. . J Bacteriol 172, 39593965.[PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.044065-0
Loading
/content/journal/ijsem/10.1099/ijs.0.044065-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error