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Denitratimonas tolerans gen. nov., sp. nov., a denitrifying bacterium isolated from a bioreactor for tannery wastewater treatment

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Abstract

A denitrifying bacterium, designated strain E4-1T, was isolated from a bioreactor for tannery wastewater treatment, and its taxonomic position was investigated using a polyphasic approach. Strain E4-1T, a facultative anaerobic bacterium, was observed to grow between 0 and 12 % (w/v) NaCl, between pH 3.0 and 12.0. Cells were found to be oxidase-positive and catalase-negative. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain E4-1T forms a distinct lineage with respect to closely related genera in the family Xanthomonadaceae, and is closely related to Chiayiivirga, Aquimonas and Dokdonella, and the levels of 16S rRNA gene sequence similarity with respect to the type species of related genera are less than 93.9 %. The predominant respiratory quinone was determined to be ubiquinone-8 (Q-8) and the major cellular fatty acids were determined to be iso-C15:0, iso-C17:1 ω9c, iso-C11:0 and iso-C11:0 3OH. Based on physiological, biochemical and chemotaxonomic properties together with results of comparative 16S rRNA gene sequence analysis, strain E4-1T is considered to represent a novel species in a new genus, for which the name Denitratimonas tolerans gen. nov., sp. nov. is proposed. The type strain is E4-1T (=KACC 17565T = NCAIM B 025327T).

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References

  • Atlas RM (1993) Handbook of Microbiological Media. In: L. C. Parks (eds): CRC Press, Boca Raton, FL

  • Auling G, Busse HJ, Pilz F, Webb L, Kneifel H, Claus D (1991) Rapid differentiation by polyamine analysis of Xanthomonas strains from phytopathogenic pseudomonads and other members of the class Proteobacteria interacting with plants. Int J Syst Bacteriol 41:223–228

    Article  CAS  Google Scholar 

  • Busse HJ, Kämpfer P, Moore ERB, Nuutinen J, Tsitko IV, Denner EBM, Vauterin L, Valens M, Rossellό-Mora R, Salkinoja-Salonen MS (2002) Thermomonas haemolytica gen. nov., sp. nov., a γ-proteobacterium from kaolin slurry. Int J Syst Evol Microbiol 52:473–483

    Article  CAS  PubMed  Google Scholar 

  • Christensen P, Cook FD (1978) Lysobacter, a new genus of nonfruiting, gliding bacteria with a high base ratio. Int J Syst Bacteriol 28:367–393

    Article  Google Scholar 

  • Collins MD, Jones D (1981) Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implications. Microbiol Rev 45:316–354

    CAS  PubMed  PubMed Central  Google Scholar 

  • Craigie J (1931) Studies on the serological reactions of the flagella of B. typhosus. J Immunol 21:417

    Google Scholar 

  • Cunha S, Tiago I, Pires AL, Da Costa MS, Verissimo A (2006) Dokdonella fugitiva sp. nov., a gammaproteobacterium isolated from potting soil. Syst Appl Microbiol 29:191–196

    Article  CAS  PubMed  Google Scholar 

  • DeLong EF (1992) Archaea in coastal marine environments. Proc Natl Acad Sci USA 89:5685–5689

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • 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 39:224–229

    Article  Google Scholar 

  • Famintzin A (1982) Eine neue Bacterienform: nevskia ramosa. Bull Acad Imp Sci St Petersb New Ser 2(34):481–486 (in German)

    Google Scholar 

  • Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376

    Article  CAS  PubMed  Google Scholar 

  • Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Article  Google Scholar 

  • Finkmann W, Altendorf K, Stackebrandt E, Lipski A (2000) Characterization of N2O-producing Xanthomonas-like isolates from biofilters as Stenotrophomonas nitritireducens sp. nov., Luteimonas mephitis gen. nov., sp. nov. and Pseudoxanthomonas broegbernensis gen. nov., sp. nov. Int J Syst Evol Microbiol 50:273–282

    Article  CAS  PubMed  Google Scholar 

  • Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416

    Article  Google Scholar 

  • Hamana K, Sakamoto A, Tachiyanagi S, Terauchi E (2003) Polyamine profiles of some members of the gamma subclass of the class Proteobacteria: polyamine analysis of twelve recently described genera. Microbiol Cult Collect 19:3–11

    Google Scholar 

  • Hamana K, Sato W, Gouma K, Yu J, Ino Y, Umemura Y, Mochizuki C, Takatsuka K, Kigure Y et al (2006) Cellular polyamine catalogues of the five classes of the phylum Proteobacteria: distributions of homospermidine within the class Alphaproteobacteria, hydroxyputrescine within the class Betaproteobacteria, norspermidine within the class Gammaproteobacteria, and spermine within the classes Deltaproteobacteria and Epsilonproteobacteria. Ann Gunma Health Sci 27:1–16

    Google Scholar 

  • Hsu YH, Lai WA, Lin SY, Hameed A, Shahina M, Shen FT, Zhu ZL, Young LS, Young CC (2013) Chiayiivirga flava gen. nov., sp. nov., a novel bacterium of the family Xanthomonadaceae isolated from an agricultural soil and emended description of the genus Dokdonella. Int J Syst Evol Microbiol 63:3293–3300

    Article  CAS  PubMed  Google Scholar 

  • Im WT, Liu QM, Yang JE, Kim MS, Kim SY, Lee ST, Yi TH (2010) Panacagrimonas perspica gen. nov., sp. nov., a novel member of Gammaproteobacteria isolated from soil of Ginseng field. J Microbiol 48:262–266

    Article  PubMed  Google Scholar 

  • Jin L, Jim KK, Im WT, Yang HC, Lee ST (2007) Aspromonas composti gen. nov., sp. nov., a novel member of the family Xanthomonadaceae. Int J Syst Evol Microbiol 57:1876–7880

    Article  PubMed  Google Scholar 

  • Johansen JE, Binnerup SJ, Kroer N, Molbak L (2005) Luteibacter rhizovicinus gen. nov., sp. nov., a yellow-pigmented gammaproteobacterium isolated from the rhizosphere of barley (Hordeum vulgare L.). Int J Syst Evol Microbiol 55:2285–2291

    Article  CAS  PubMed  Google Scholar 

  • Kämpfer P, Martin E, Lodders N, Langer S, Schumann P, Jäckel U, Busse HJ (2010) Pseudofulvimonas gallinarii gen. nov., sp. nov., a new member of the family Xanthomonadaceae. Int J Syst Evol Microbiol 60:1427–1431

    Article  PubMed  Google Scholar 

  • Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Yi H, Won S, Chun J (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721

    Article  CAS  PubMed  Google Scholar 

  • Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions though comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    Article  CAS  PubMed  Google Scholar 

  • Kwon SW, Kim BY, Weon HY, Baek YK, Go SJ (2007) Arenimonas donghaensis gen. nov., sp. nov., isolated from seashore sand. Int J Syst Evol Microbiol 57:954–958

    Article  CAS  PubMed  Google Scholar 

  • Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948

    Article  CAS  PubMed  Google Scholar 

  • Lee EM, Jeon CO, Choi I, Chang KS, Kim CJ (2005) Silanimonas lenta gen. nov., sp. nov., a slightly thermophilic and alkaliphilic gammaproteobacterium isolated from a hot spring. Int J Syst Evol Microbiol 55:385–389

    Article  CAS  PubMed  Google Scholar 

  • Li Y, Zhang J, Chen Q, Yang G, Cai S, He J, Zhou S, Li SP (2013) Dokdonella kunshanensis sp. nov., isolated from activated sludge and emended description of the genus Dokdonella. Int J Syst Evol Microbiol 63:1519–1523

    Article  CAS  PubMed  Google Scholar 

  • Ludwig W, Strunk O, Klugbauer S, Klugbauer N, Weizenegger M, Neumaier J, Bachleitner M, Schleifer KH (1998) Bacterial phylogeny based on comparative sequence analysis. Electrophoresis 19:554–568

    Article  CAS  PubMed  Google Scholar 

  • Mandel M, Reese ET (1960) Induction of cellulase in fungi by cellobiose. J Bacteriol 79:816

    Google Scholar 

  • Mergaert J, Cnockaert MC, Swings J (2002) Fulvimonas soli gen. nov., sp. nov., a γ-proteobacterium isolated from soil after enrichment on acetylated 400 starch plastic. Int J Syst Evol Microbiol 52:1285–1289

    CAS  PubMed  Google Scholar 

  • Mesbah M, Premachandran U, Whitman WB (1989) Precise measurement of the G + C content of deoxyribonucleic acid by high performance liquid chromatography. Int J Syst Bacteriol 39:159–167

    Article  CAS  Google Scholar 

  • Minnikin DE, O’Donella AG, Goodfellow M, Alderson G, Athalye M, Schaal K, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241

    Article  CAS  Google Scholar 

  • Moore DD, Dowhan D (1995) Preparation and analysis of DNA. In: Ausubel FW, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K (eds) Current protocols in molecular biology. Wiley, New York, pp 2–11

    Google Scholar 

  • Murray RGE, Doetsch RN, Robinow CF (1994) Determination and cytological light microscopy. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington DC, pp 31–32

    Google Scholar 

  • Nalin R, Simonet P, Vogel TM, Normand P (1999) Rhodanobacter lindaniclasticus gen. nov., sp. nov., a lindane-degrading bacterium. Int J Syst Bacteriol 49:19–23

    Article  PubMed  Google Scholar 

  • Palleroni NJ, Bradbury JF (1993) Stenotrophomonas a new bacterial genus for Xanthomonas maltophilia (Hugh 1980) Swings et al. 1983. Int J Syst Evol Microbiol 43:606–609

    CAS  Google Scholar 

  • Saddler GS, Bradbury JF (2005) Family I. Xanthomonadaceae fam. nov. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM (eds) Bergy’s manual of systematic bacteriology, (The Proteobacteria), Partt B (The Gammaproteobacteria), vol vol 2, 2nd edn. Springer, New York, pp 63–65

    Chapter  Google Scholar 

  • Saha P, Krishnamurthi S, Mayilraj S, Prasad GS, Bora TC, Chakrabarti T (2005) Aquimonas voraii gen. nov., sp. nov., a novel gammaproteobacterium isolated from a worm spring of Assam. India. Int J Syst Evol Microbiol 55:1491–1495

    Article  CAS  PubMed  Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  • Schaal KP (1986) Genus Actinomyces Harz 1877, 133AL. In: Sneath PHA, Mair NS, Sharpe ME, Holt JG (eds) Bergey’s Manual of Systematic Bacteriology, vol vol 2. Williams & Wilkins, Baltimore, pp 1383–1418

    Google Scholar 

  • Scherer P, Kneifel H (1983) Distribution of polyamines in methanogenic bacteria. J Bacteriol 154:1315–1322

    CAS  PubMed  PubMed Central  Google Scholar 

  • Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, DC, pp 607–654

    Google Scholar 

  • Swings J, Gillis M, Kersters K, De Vos P, Gossele F, De Ley J (1980) Frateuria, a new genus for Acetobacter aurantius. Int J Syst Evol Microbiol 30:547–556

    CAS  Google Scholar 

  • Tamaoka J, Komagata K (1984) Determination of DNA base composition by reverse-phase high performance liquid chromatography. FEMS Microbiol Lett 25:125–128

    Article  CAS  Google Scholar 

  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA 5: molecular evolutionary genetics anal maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tóth E, Kovács G, Schumann P, Kovács AL, Steiner U, Halbritter A, Márialigeti K (2001) Schineria larvae gen. nov., sp. nov., isolated from the 1st and 2nd larval stage of Wohlfahrtia magnifica (Diptera: Sarcophagidae). Int J Syst Evol Microbiol 51:401–407

    Article  PubMed  Google Scholar 

  • Tóth EM, Schumann P, Borsodi AK, Kéki Z, Kovács AL, Márialigeti K (2008) Wohlfahrtiimonas chitiniclastica gen. nov., sp. nov., a new gammaproteobacterium isolated from Wohlfahrtia magnifica (Diptera: Sarcophagidae). Int J Syst Evol Microbiol 58:976–981

    Article  PubMed  Google Scholar 

  • Van Den Mooter M, Swings J (1990) Numerical analysis of 295 phenotypic features of 266 Xanthomonas strains and related strains and an improved taxonomy of the genus. Int J Syst Evol Microbiol 40:348–369

    Google Scholar 

  • Wells JM, Raju BC, Hung HY, Weisburg WG, Mandelco Paul L, Brenner DJ (1987) Xylella fastidiosa gen. nov., sp. nov.: gram-negative, xylem-limited, fastidious plant bacteria related to Xanthomonas spp. Int J Syst Evol Microbiol 37:136–143

    CAS  Google Scholar 

  • Weon HY, Yoo SH, Kim YJ, Lee CM, Kim BY, Jeon YA, Hong SB, Anandham R, Kwon SW (2009) Rudaea cellulosilytica gen. nov., sp. nov., isolated from soil. Int J Syst Evol Microbiol 59:2308–2312

    Article  CAS  PubMed  Google Scholar 

  • Woo SG, Srinivasan S, Kim MK, Lee M (2012) Rhodanobacter caeni sp. nov., isolated from sludge from a sewage disposal plant. Int J Syst Evol Microbiol 62:2815–2821

    Article  PubMed  Google Scholar 

  • Xie CH, Yokota A (2005) Dyella japonica gen. nov., sp. nov., a γ-proteobacterium isolated from soil. Int J Syst Evol Microbiol 55:753–756

    Article  CAS  PubMed  Google Scholar 

  • Yang P, De Vos P, Kersters K, Swings J (1993) Polyamine patterns as chemotaxonomic markers for the genus Xanthomonas. Int J Syst Bacteriol 43:709–714

    Article  Google Scholar 

  • Yoo SH, Weon HY, Anandham R, Kim BY, Hong SB, Jeon YA, Koo BS, Kwon SW (2009) Dokdonella soli sp. nov., a gammaproteobacterium isolated from soil. Int J Syst Evol Microbiol 59:1965–1968

    Article  CAS  PubMed  Google Scholar 

  • Yoon JH, Kang SJ, Oh TK (2006) Dokdonella koreensis gen. nov., sp. nov., isolated from soil. Int J Syst Evol Microbiol 56:145–150

    Article  CAS  PubMed  Google Scholar 

  • Young CC, Kämpfer P, Ho MJ, Busse HJ, Huber BE, Arun AB, Shen FT, Lai WA, Rekha PD (2007) Arenimonas malthae sp. nov., a gammaproteobacterium isolated from an oilcontaminated site. Int J Syst Evol Microbiol 57:2790–2793

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

This work was supported by a grant from the Regional Subgenebank Support Program of Rural Development Administration, Korea. It was also supported by National Research Foundation (NRF) of Korea (grant No. 2011-0016521) and the Cooperative R&D between Industry, Academy, and Research Institute of the Korea Small and Medium Business Administration (grant No. 00047293).

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Authors and Affiliations

  1. Department of Microbial & Nano Materials, College of Science & Technology, Mokwon University, 88 Doanbuk-ro, Seo-gu, Daejeon, 35349, Republic of Korea

    Song-Ih Han, Ju-Ok Kim, Ye-Rim Lee & Kyung-Sook Whang

  2. Department of Environmental Engineering, Korea Maritime University, Busan, 606-791, Republic of Korea

    Kalu I. Ekpeghere & Sung-Cheol Koh

  3. Institute of Microbial Ecology and Resources, Mokwon University, Daejeon, 35349, Republic of Korea

    Kyung-Sook Whang

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  1. Song-Ih Han
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Han, SI., Kim, JO., Lee, YR. et al. Denitratimonas tolerans gen. nov., sp. nov., a denitrifying bacterium isolated from a bioreactor for tannery wastewater treatment. Antonie van Leeuwenhoek 109, 785–792 (2016). https://doi.org/10.1007/s10482-016-0678-5

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