sp. nov., an endospore-forming, Mn-oxidizing, moderately halophilic bacterium isolated from deep subseafloor basaltic crust Free

Abstract

A facultatively anaerobic bacterium, designated strain 1MBB1, was isolated from basaltic breccia collected from 341 m below the seafloor by seafloor drilling of Rigil Guyot during Integrated Ocean Drilling Program Expedition 330. The cells were straight rods, 0.5 μm wide and 1–3 μm long, that occurred singly and in chains. Strain 1MBB1 stained Gram-positive. Catalase and oxidase were produced. The isolate grew optimally at 30 °C and pH 7.5, and could grow with up to 12 % (w/v) NaCl. The DNA G+C content was 40.5 mol%. The major cellular fatty acids were C ω11 (26.5 %), anteiso-C (19.5 %), C (18.7 %) and iso-C (10.4 %), and the cell-wall diamino acid was -diaminopimelic acid. Endospores of strain 1MBB1 oxidized Mn(II) to Mn(IV), and siderophore production by vegetative cells was positive. Phylogenetic analysis of the 16S rRNA gene indicated that strain 1MBB1 was a member of the family , with CV53 and LMG 21837 being the closest phylogenetic neighbours (96.5 and 96.2 % similarity, respectively). This is the first novel species described from deep subseafloor basaltic crust. On the basis of our polyphasic analysis, we conclude that strain 1MBB1 represents a novel species of the genus , for which we propose the name Bacillus sp. nov. The type strain is 1MBB1 ( = NCMA B78 = LMG 28275).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.000211
2015-06-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/65/6/1992.html?itemId=/content/journal/ijsem/10.1099/ijs.0.000211&mimeType=html&fmt=ahah

References

  1. Bagheri M., Didari M., Amoozegar M.A., Schumann P., Sánchez-Porro C., Mehrshad M., Ventosa A. ( 2012;). Bacillus iranensis sp. nov., a moderate halophile from a hypersaline lake. Int J Syst Evol Microbiol 62 811816. [CrossRef]
    [Google Scholar]
  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]
    [Google Scholar]
  3. Barnes S.P., Bradbrook S.D., Cragg B.A., Marchesi J.R., Weightman A.J., Fry J.C., Parkes R.J. ( 1998;). Isolation of sulfate-reducing bacteria from deep sediment layers of the Pacific Ocean. Geomicrobiol J 15 6783. [CrossRef]
    [Google Scholar]
  4. 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]
  5. Biddle J.F., House C.H., Brenchley J.E. ( 2005;). Microbial stratification in deeply buried marine sediment reflects changes in sulfate/methane profiles. Geobiology 3 287295. [CrossRef]
    [Google Scholar]
  6. Butler A. ( 2005;). Marine siderophores and microbial iron mobilization. Biometals 18 369374. [CrossRef]
    [Google Scholar]
  7. Cashion P., Holder-Franklin M.A., McCully J., Franklin M. ( 1977;). A rapid method for the base ratio determination of bacterial DNA. Anal Biochem 81 461466. [CrossRef]
    [Google Scholar]
  8. Chao Y., Zhang T. ( 2011;). Optimization of fixation methods for observation of bacterial cell morphology and surface ultrastructures by atomic force microscopy. Appl Microbiol Biotechnol 92 381392. [CrossRef]
    [Google Scholar]
  9. Dick G.J., Lee Y.E., Tebo B.M. ( 2006;). Manganese(II)-oxidizing Bacillus spores in Guaymas Basin hydrothermal sediments and plumes. Appl Environ Microbiol 72 31843190. [CrossRef]
    [Google Scholar]
  10. Drummond A.J., Ashton B., Buxton S., Cheung M., Cooper A., Duran C., Field M., Heled J., Kearse M., other authors. ( 2011). Geneious v5.4. Available from http://www.geneious.com .
  11. Fichtel K., Mathes F., Könneke M., Cypionka H., Engelen B. ( 2012;). Isolation of sulfate-reducing bacteria from sediments above the deep-subseafloor aquifer. Front Microbiol 3 65. [CrossRef]
    [Google Scholar]
  12. Francis C.A., Tebo B.M. ( 2002;). Enzymatic manganese(II) oxidation by metabolically dormant spores of diverse Bacillus species. Appl Environ Microbiol 68 874880. [CrossRef]
    [Google Scholar]
  13. Heberling C., Lowell R.P., Liu L., Fisk M.R. ( 2010;). Extent of the microbial biosphere in the oceanic crust. Geochem Geophys Geosyst 11 Q08003. [CrossRef]
    [Google Scholar]
  14. Heyrman J., Vanparys B., Logan N.A., Balcaen A., Rodríguez-Díaz M., Felske A., De Vos P. ( 2004;). Bacillus novalis sp. nov., Bacillus vireti sp. nov., Bacillus soli sp. nov., Bacillus bataviensis sp. nov. and Bacillus drentensis sp. nov., from the Drentse A grasslands. Int J Syst Evol Microbiol 54 4757. [CrossRef]
    [Google Scholar]
  15. Inagaki F., Suzuki M., Takai K., Oida H., Sakamoto T., Aoki K., Nealson K.H., Horikoshi K. ( 2003;). Microbial communities associated with geological horizons in coastal subseafloor sediments from the Sea of Okhotsk. Appl Environ Microbiol 69 72247235. [CrossRef]
    [Google Scholar]
  16. Kallmeyer J., Pockalny R., Adhikari R.R., Smith D.C., D'Hondt S. ( 2012;). Global distribution of microbial abundance and biomass in subseafloor sediment. Proc Natl Acad Sci U S A 109 1621316216. [CrossRef]
    [Google Scholar]
  17. Kanso S., Greene A.C., Patel B.K.C. ( 2002;). Bacillus subterraneus sp. nov., an iron- and manganese-reducing bacterium from a deep subsurface Australian thermal aquifer. Int J Syst Evol Microbiol 52 869874. [CrossRef]
    [Google Scholar]
  18. Koppers A.A.P., Yamazaki T., Geldmacher J., Expedition 330 Scientists. ( 2012). Proceedings of the Integrated Ocean Drilling Program vol. 330 Tokyo, Japan: Integrated Ocean Drilling Program Management International, Inc;.
    [Google Scholar]
  19. Krumbein W.E., Altmann H.J. ( 1973;). A new method for the detection and enumeration of manganese oxidizing and respiring microorganisms. Helgol Wiss Meeresunters 25 347356. [CrossRef]
    [Google Scholar]
  20. Lane D.J. ( 1991;). 16S/23S rRNA sequencing. . In Nucleic Acid Technology in Bacterial Systematics, pp. 115175. Edited by Stackebrandt E., Goodfellow M. Chichester: Wiley;.
    [Google Scholar]
  21. 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]
    [Google Scholar]
  22. Logan N.A., Berge O., Bishop A.H., Busse H.-J., De Vos P., Fritze D., Heyndrickx M., Kämpfer P., Rabinovitch L., other authors. ( 2009;). Proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria. Int J Syst Evol Microbiol 59 21142121. [CrossRef]
    [Google Scholar]
  23. Lomstein B.A., Langerhuus A.T., D'Hondt S., Jørgensen B.B., Spivack A.J. ( 2012;). Endospore abundance, microbial growth and necromass turnover in deep sub-seafloor sediment. Nature 484 101104. [CrossRef]
    [Google Scholar]
  24. Martin J.D., Ito Y., Homann V.V., Haygood M.G., Butler A. ( 2006;). Structure and membrane affinity of new amphiphilic siderophores produced by Ochrobactrum sp. SP18. J Biol Inorg Chem 11 633641. [CrossRef]
    [Google Scholar]
  25. Mayhew L.E., Swanner E.D., Martin A.P., Templeton A.S. ( 2008;). Phylogenetic relationships and functional genes: distribution of a gene (mnxG) encoding a putative manganese-oxidizing enzyme in Bacillus species. Appl Environ Microbiol 74 72657271. [CrossRef]
    [Google Scholar]
  26. Mesbah M., Premachandran U., Whitman W.B. ( 1989;). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39 159167. [CrossRef]
    [Google Scholar]
  27. 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 submarinus sp. nov. Appl Environ Microbiol 69 33113316. [CrossRef]
    [Google Scholar]
  28. Rosson R.A., Nealson K.H. ( 1982;). Manganese binding and oxidation by spores of a marine bacillus. J Bacteriol 151 10271034.
    [Google Scholar]
  29. Schumann P. ( 2011;). Peptidoglycan structure. Methods Microbiol 38 101129. [CrossRef]
    [Google Scholar]
  30. Schwyn B., Neilands J.B. ( 1987;). Universal chemical assay for the detection and determination of siderophores. Anal Biochem 160 4756. [CrossRef]
    [Google Scholar]
  31. Smith A., Popa R., Fisk M., Nielsen M., Wheat C.G., Jannasch H.W., Fisher A.T., Becker K., Sievert S.M., Flores G. ( 2011;). In situ enrichment of ocean crust microbes on igneous minerals and glasses using an osmotic flow-through device. Geochem Geophys Geosyst 12 Q06007. [CrossRef]
    [Google Scholar]
  32. 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]
    [Google Scholar]
  33. Tebo B.M., Clement B.G., Dick G.J. ( 2007;). Biotransformations of manganese. . In Manual of Environmental Microbiology , 3rd edn.., pp. 12231238. Edited by Hurst C. J., Crawford R. L., Garland J. L., Lipson D. A., Mills A. L., Stetzenbach L. D. ., Washington, DC: American Society for Microbiology;.
    [Google Scholar]
  34. Tiago I., Pires C., Mendes V., Morais P.V., da Costa M.S., Veríssimo A. ( 2006;). Bacillus foraminis sp. nov., isolated from a non-saline alkaline groundwater. Int J Syst Evol Microbiol 56 25712574. [CrossRef]
    [Google Scholar]
  35. Toffin L., Bidault A., Pignet P., Tindall B.J., Slobodkin A., Kato C., Prieur D. ( 2004a;). Shewanella profunda sp. nov., isolated from deep marine sediment of the Nankai Trough. Int J Syst Evol Microbiol 54 19431949. [CrossRef]
    [Google Scholar]
  36. Toffin L., Webster G., Weightman A.J., Fry J.C., Prieur D. ( 2004b;). Molecular monitoring of culturable bacteria from deep-sea sediment of the Nankai Trough, Leg 190 Ocean Drilling Program. FEMS Microbiol Ecol 48 357367. [CrossRef]
    [Google Scholar]
  37. Ventosa A., Quesada E., Rodriguez-Valera F., Ruiz-Berraquero F., Ramos-Cormenzana A. ( 1982;). Numerical taxonomy of moderately halophilic Gram-negative rods. J Gen Microbiol 128 19591968.
    [Google Scholar]
  38. Zimbro M.J., Power D.A., Miller S.M., Wilson G.E., Johnson J.A. ( 2009). Difco and BBL Manual: Manual of Biological Culture Media , 2nd edn.., Franklin Lakes, NJ: Becton Dickinson;.
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.000211
Loading
/content/journal/ijsem/10.1099/ijs.0.000211
Loading

Data & Media loading...

Supplements

Supplementary Data

PDF

Most cited Most Cited RSS feed