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- Volume 65, Issue 6
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f Tepidicaulis marinus gen. nov., sp. nov., a marine bacterium that reduces nitrate to nitrous oxide under strictly microaerobic conditions
- Authors: Mio Takeuchi1 , Takao Yamagishi1 , Yoichi Kamagata2 , Kenshiro Oshima3 , Masahira Hattori3 , Taiki Katayama1 , Satoshi Hanada2 , Hideyuki Tamaki2 , Katsumi Marumo4,† , Hiroto Maeda5 , Munetomo Nedachi6 , Wataru Iwasaki3,7 , Yuichi Suwa8 , Susumu Sakata1
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- VIEW AFFILIATIONS
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1 1Institute for Geo-resources and Environments, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan 2 2Bioproduction Research Institute, AIST, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan 3 3The Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwa-no-ha, Kashiwa, Chiba 277-8561, Japan 4 4Institute of Geology and Geoinformation, AIST, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8567, Japan 5 5Department of Physics and Astronomy Graduate School of Science and Engineering/Faculty of Science, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-8580, Japan 6 6The United Graduate School of Agricultural Sciences, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-8580, Japan 7 7Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan 8 8Department of Biological Science, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan
- Correspondence Mio Takeuchi [email protected]
- First Published Online: 01 June 2015, International Journal of Systematic and Evolutionary Microbiology 65: 1749-1754, doi: 10.1099/ijs.0.000167
- Subject: NEW TAXA - Proteobacteria
- Cover date:




Tepidicaulis marinus gen. nov., sp. nov., a marine bacterium that reduces nitrate to nitrous oxide under strictly microaerobic conditions, Page 1 of 1
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A moderately thermophilic, aerobic, stalked bacterium (strain MA2T) was isolated from marine sediments in Kagoshima Bay, Japan. Phylogenetic analysis of 16S rRNA gene sequences indicated that strain MA2T was most closely related to the genera Rhodobium , Parvibaculum , and Rhodoligotrophos (92–93 % similarity) within the class Alphaproteobacteria . Strain MA2T was a Gram-stain-negative and stalked dimorphic bacteria. The temperature range for growth was 16–48 °C (optimum growth at 42 °C). This strain required yeast extract and NaCl (>1 %, w/v) for growth, tolerated up to 11 % (w/v) NaCl, and was capable of utilizing various carbon sources. The major cellular fatty acid and major respiratory quinone were C18 : 1ω7c and ubiquinone-10, respectively. The DNA G+C content was 60.7 mol%. Strain MA2T performed denitrification and produced N2O from nitrate under strictly microaerobic conditions. Strain MA2T possessed periplasmic nitrate reductase (Nap) genes but not membrane-bound nitrate reductase (Nar) genes. On the basis of this morphological, physiological, biochemical and genetic information a novel genus and species, Tepidicaulis marinus gen. nov., sp. nov., are proposed, with MA2T ( = NBRC 109643T = DSM 27167T) as the type strain of the species.
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†
Present address: Faculty of Science, Toyama University, 3190 Gofuku, Toyama-shi, Toyama 930-8555, Japan.
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The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene of strain MA2T is AB821371. The draft genome sequence has been deposited in DDBJ/EMBL/GenBank under the accession numbers BBIO01000001–BBIO01000046.
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Three supplementary figures are available with the online Supplementary Material.
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Abbreviations: OMZ oxygen minimum zone; PE paired-end; SE single-end.
© 2015 IUMS | Published by the Microbiology Society
-
Albuquerque L. , Rainey F. A. , Pena A. , Tiago I. , Veríssimo A. , Nobre M. F. , da Costa M. S. . ( 2010; ). Tepidamorphus gemmatus gen. nov., sp. nov., a slightly thermophilic member of the Alphaproteobacteria . . Syst Appl Microbiol 33:, 60––66. [CrossRef] [PubMed]
-
Bazylinski D. A. , Blakemore R. P. . ( 1983; ). Denitrification and assimilatory nitrate reduction in Aquaspirillum magnetotacticum . . Appl Environ Microbiol 46:, 1118––1124.[PubMed]
-
Bell L. C. , Richardson D. J. , Ferguson S. J. . ( 1990; ). Periplasmic and membrane-bound respiratory nitrate reductases in Thiosphaera pantotropha: the periplasmic enzyme catalyzes the first step in aerobic denitrification. . FEBS Lett 265:, 85––87. [CrossRef] [PubMed]
-
Blakemore R. P. , Maratea D. , Wolfe R. S. . ( 1979; ). Isolation and pure culture of a freshwater magnetic spirillum in chemically defined medium. . J Bacteriol 140:, 720––729.[PubMed]
-
Bowman J. P. . ( 2006; ). The methanotrophs—the families Methylococcaceae and Methylocystaceae . . In The Prokaryotes, vol. 5, pp. 266––289. Edited by Dworkin M. , Falkow S. , Rosenberg E. . . New York:: Springer;. [CrossRef]
-
Brettar I. , Christen R. , Bötel J. , Lünsdorf H. , Höfle M. G. . ( 2007; ). Anderseniella baltica gen. nov., sp. nov., a novel marine bacterium of the Alphaproteobacteria isolated from sediment in the central Baltic Sea. . Int J Syst Evol Microbiol 57:, 2399––2405. [CrossRef] [PubMed]
-
Felsenstein J. . ( 1981; ). Evolutionary trees from DNA sequences: a maximum likelihood approach. . J Mol Evol 17:, 368––376. [CrossRef] [PubMed]
-
Frette L. , Gejlsbjerg B. , Westermann P. . ( 1997; ). Aerobic denitrifiers isolated from an alternating activated sludge system. . FEMS Microbiol Ecol 24:, 363––370. [CrossRef]
-
Fukuda W. , Yamada K. , Miyoshi Y. , Okuno H. , Atomi H. , Imanaka T. . ( 2012; ). Rhodoligotrophos appendicifer gen. nov., sp. nov., an appendaged bacterium isolated from a freshwater Antarctic lake. . Int J Syst Evol Microbiol 62:, 1945––1950. [CrossRef] [PubMed]
-
Hanada S. , Takaichi S. , Matsuura K. , Nakamura K. . ( 2002; ). Roseiflexus castenholzii gen. nov., sp. nov., a thermophilic, filamentous, photosynthetic bacterium that lacks chlorosomes. . Int J Syst Evol Microbiol 52:, 187––193.[PubMed] [CrossRef]
-
Hiraishi A. , Urata K. , Satoh T. . ( 1995; ). A new genus of marine budding phototrophic bacteria, Rhodobium gen. nov., which includes Rhodobium orientis sp. nov. and Rhodobium marinum comb. nov.. Int J Syst Bacteriol 45:, 226––234. [CrossRef] [PubMed]
-
Ishibashi J.-I. , Nakaseama M. , Seguchi M. , Yamashita T. , Doi S. , Sakamoto T. , Shimada K. , Shimada N. , Noguchi T. et al. ( 2008; ). Marine shallow-water hydrothermal activity and mineralization at the Wakamiko Crater in Kagoshima Bay, South Kyushu, Japan. . J Volcanol Geotherm Res 173:, 84––98. [CrossRef]
-
Kamagata Y. , Mikami E. . ( 1991; ). Isolation and characterization of a novel thermophilic Methanosaeta strain. . Int J Syst Evol Microbiol 41:, 191––196.
-
Katsuyama C. , Kondo N. , Suwa Y. , Yamagishi T. , Itoh M. , Ohte N. , Kimura H. , Nagaosa K. , Kato K. . ( 2008; ). Denitrification activity and relevant bacteria revealed by nitrite reductase gene fragments in soil of temperate mixed forest. . Microbes Environ 23:, 337––345. [CrossRef] [PubMed]
-
Lai Q. , Wang L. , Liu Y. , Yuan J. , Sun F. , Shao Z. . ( 2011; ). Parvibaculum indicum sp. nov., isolated from deep-sea water. . Int J Syst Evol Microbiol 61:, 271––274. [CrossRef] [PubMed]
-
Nevison C. , Butler J. H. , Elkins J. W. . ( 2003; ). Global distribution of N2O and the AN2O-AOU yield in the subsurface ocean. . Global Biogeochem Cycles 17:, 1119, 30-1––30-18. [CrossRef]
-
Okada N. , Nomura N. , Nakajima-Kambe T. , Uchiyama H. . ( 2005; ). Characterization of the aerobic denitrification in Mesorhizobium sp. strain NH-14 in comparison with that in related rhizobia. . Microbes Environ 20:, 208––215. [CrossRef]
-
Osborn A. M. , Moore E. R. , Timmis K. N. . ( 2000; ). An evaluation of terminal-restriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics. . Environ Microbiol 2:, 39––50. [CrossRef] [PubMed]
-
Patureau D. , Godon J. J. , Dabert P. , Bouchez T. , Bernet N. , Delgenes J. P. , Moletta R. . ( 1998; ). Microvirgula aerodenitrificans gen. nov., sp. nov., a new gram-negative bacterium exhibiting co-respiration of oxygen and nitrogen oxides up to oxygen-saturated conditions. . Int J Syst Bacteriol 48:, 775––782. [CrossRef] [PubMed]
-
Pruesse E. , Quast C. , Knittel K. , Fuchs B. M. , Ludwig W. , Peplies J. , Glöckner F. O. . ( 2007; ). silva: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with arb . . Nucleic Acids Res 35:, 7188––7196. [CrossRef] [PubMed]
-
Ravishankara A. R. , Daniel J. S. , Portmann R. W. . ( 2009; ). Nitrous oxide (N2O): the dominant ozone-depleting substance emitted in the 21st century. . Science 326:, 123––125. [CrossRef] [PubMed]
-
Robertson L. A. , Kuenen J. G. . ( 1983; ). Thiosphaera pantotropha gen. nov., sp. nov., a facultatively anaerobic, facultatively autotrophic sulphur bacterium. . J Gen Microbiol 129:, 2847––2855.
-
Robertson L. A. , Dalsgaard T. , Revsbech N.-P. , Kuenen J. G. . ( 1995; ). Confirmation of ‘aerobic denitrification’ in batch cultures, using gas chromatography and 15N mass spectrometry. . FEMS Microbiol Ecol 18:, 113––120. [CrossRef]
-
Rönner U. , Sörensson F. . ( 1985; ). Denitrification rates in the low-oxygen waters of the stratified baltic proper. . Appl Environ Microbiol 50:, 801––806.[PubMed]
-
Rosario-Passapera R. , Keddis R. , Wong R. , Lutz R. A. , Starovoytov V. , Vetriani C. . ( 2012; ). Parvibaculum hydrocarboniclasticum sp. nov., a mesophilic, alkane-oxidizing alphaproteobacterium isolated from a deep-sea hydrothermal vent on the East Pacific Rise. . Int J Syst Evol Microbiol 62:, 2921––2926. [CrossRef] [PubMed]
-
Saitou N. , Nei M. . ( 1987; ). The neighbor-joining method: a new method for reconstructing phylogenetic trees. . Mol Biol Evol 4:, 406––425.[PubMed]
-
Schleheck D. , Tindall B. J. , Rosselló-Mora R. , Cook A. M. . ( 2004; ). Parvibaculum lavamentivorans gen. nov., sp. nov., a novel heterotroph that initiates catabolism of linear alkylbenzenesulfonate. . Int J Syst Evol Microbiol 54:, 1489––1497. [CrossRef] [PubMed]
-
Schloss P. D. , Westcott S. L. , Ryabin T. , Hall J. R. , Hartmann M. , Hollister E. B. , Lesniewski R. A. , Oakley B. B. , Parks D. H. et al. ( 2009; ). Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. . Appl Environ Microbiol 75:, 7537––7541. [CrossRef] [PubMed]
-
Scholten E. , Lukow T. , Auling G. , Kroppenstedt R. M. , Rainey F. A. , Diekmann H. . ( 1999; ). Thauera mechernichensis sp. nov., an aerobic denitrifier from a leachate treatment plant. . Int J Syst Bacteriol 49:, 1045––1051. [CrossRef] [PubMed]
-
Sears H. J. , Spiro S. , Richardson D. J. . ( 1997; ). Effect of carbon substrate and aeration on nitrate reduction and expression of the periplasmic and membrane-bound nitrate reductases in carbon-limited continuous cultures of Paracoccus denitrificans Pd1222. . Microbiology 143:, 3767––3774. [CrossRef]
-
Smith C. J. , Nedwell D. B. , Dong L. F. , Osborn A. M. . ( 2007; ). Diversity and abundance of nitrate reductase genes (narG and napA), nitrite reductase genes (nirS and nrfA), and their transcripts in estuarine sediments. . Appl Environ Microbiol 73:, 3612––3622. [CrossRef] [PubMed]
-
Srinivas T. N. , Kumar P. A. , Sasikala Ch. , Ramana ChV. , Imhoff J. F. . ( 2007; ). Rhodobium gokarnense sp. nov., a novel phototrophic alphaproteobacterium from a saltern. . Int J Syst Evol Microbiol 57:, 932––935. [CrossRef] [PubMed]
-
Stewart V. , Lu Y. , Darwin A. J. . ( 2002; ). Periplasmic nitrate reductase (NapABC enzyme) supports anaerobic respiration by Escherichia coli K-12. . J Bacteriol 184:, 1314––1323. [CrossRef] [PubMed]
-
Takaya N. , Catalan-Sakairi M. A. B. , Sakaguchi Y. , Kato I. , Zhou Z. , Shoun H. . ( 2003; ). Aerobic denitrifying bacteria that produce low levels of nitrous oxide. . Appl Environ Microbiol 69:, 3152––3157. [CrossRef] [PubMed]
-
Takeuchi M. , Yoshioka H. , Seo Y. , Tanabe S. , Tamaki H. , Kamagata Y. , Takahashi H. A. , Igari S. , Mayumi D. , Sakata S. . ( 2011; ). A distinct freshwater-adapted subgroup of ANME-1 dominates active archaeal communities in terrestrial subsurfaces in Japan. . Environ Microbiol 13:, 3206––3218. [CrossRef] [PubMed]
-
Takeuchi M. , Katayama T. , Yamagishi T. , Hanada S. , Tamaki H. , Kamagata Y. , Oshima K. , Hattori M. , Marumo K. et al. ( 2014; a). Methyloceanibacter caenitepidi gen. nov., sp. nov., a facultatively methylotrophic bacterium isolated from marine sediments near a hydrothermal vent. . Int J Syst Evol Microbiol 64:, 462––468. [CrossRef] [PubMed]
-
Takeuchi M. , Kamagata Y. , Oshima K. , Hanada S. , Tamaki H. , Marumo K. , Maeda H. , Nedachi M. , Hattori M. et al. ( 2014; b). Methylocaldum marinum sp. nov., a thermotolerant, methane-oxidizing bacterium isolated from marine sediments, and emended description of the genus Methylocaldum. . Int J Syst Evol Microbiol 64:, 3240––3246. [CrossRef] [PubMed]
-
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:, 2731––2739. [CrossRef] [PubMed]
-
Taoka A. , Yoshimatsu K. , Kanemori M. , Fukumori Y. . ( 2003; ). Nitrate reductase from the magnetotactic bacterium Magnetospirillum magnetotacticum MS-1: purification and sequence analyses. . Can J Microbiol 49:, 197––206. [CrossRef] [PubMed]
-
Torres M. J. , Rubia M. I. , Bedmar E. J. , Delgado M. J. . ( 2011; ). Denitrification in Sinorhizobium meliloti . . Biochem Soc Trans 39:, 1886––1889. [CrossRef] [PubMed]
-
US EPA (2010). Methane and Nitrous Oxide Emissions from Natural Sources, US Environmental Protection Agency, Washington, DC, USA, available at: http://www.epa.gov/outreach/pdfs/Methane-and-Nitrous-Oxide-Emissions-From-Natural-Sources.pdf.
-
Weisburg W. G. , Barns S. M. , Pelletier D. A. , Lane D. J. . ( 1991; ). 16S ribosomal DNA amplification for phylogenetic study. . J Bacteriol 173:, 697––703.[PubMed]
-
Widdel F. , Pfennig N. . ( 1981; ). Studies on dissimilatory sulfate-reducing bacteria that decompose fatty acids. . Arch Microbiol 129:, 395––400. [CrossRef] [PubMed]
-
Yamanaka T. , Maeto K. , Akashi H. , Ishibashi J.-I. , Miyoshi Y. , Okamura K. , Noguchi T. , Kuwahara Y. , Toki T. et al. ( 2013; ). Shallow submarine hydrothermal activity with significant contribution of magmatic water producing talc chimneys in the Wakamiko Crater of Kagoshima Bay, southern Kyushu, Japan. . J Volcanol Geotherm Res 258:, 74––84. [CrossRef]
-
Yoshinaga I. , Amano T. , Yamagishi T. , Okada K. , Ueda S. , Sako Y. , Suwa Y. . ( 2011; ). Distribution and diversity of anaerobic ammonium oxidation (anammox) bacteria in the sediment of a eutrophic freshwater lake, Lake Kitaura, Japan. . Microbes Environ 26:, 189––197. [CrossRef] [PubMed]
-
Zhang H. , Hanada S. , Shigematsu T. , Shibuya K. , Kamagata Y. , Kanagawa T. , Kurane R. . ( 2000; ). Burkholderia kururiensis sp. nov., a trichloroethylene (TCE)-degrading bacterium isolated from an aquifer polluted with TCE. . Int J Syst Evol Microbiol 50:, 743––749. [CrossRef] [PubMed]
-
Zheng H. Y. , Liu Y. , Gao X. Y. , Ai G. M. , Miao L. L. , Liu Z. P. . ( 2012; ). Characterization of a marine origin aerobic nitrifying-denitrifying bacterium. . J Biosci Bioeng 114:, 33––37. [CrossRef] [PubMed]

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