Denitrification as an important taxonomic marker within the genus Halomonas

Systematic and Applied Microbiology

Volumn 33, Issue 2, 2010, Pages 85-93

  González Domenech, Carmen M ^a   Martínez Checa, Fernando ^a   Béjar, Victoria ^a   Quesada, Emilia ^a  

^a UNIVERSITY OF GRANADA   (Spain)

Author keywords

Denitrification; Halomonas; Phylogeny.; Taxonomy

Indexed keywords

BACTERIAL PROTEIN; PROTEIN NARH; PROTEIN NIRS; PROTEIN NOSZ; RNA 16S; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL STRAIN; BACTERIUM ISOLATION; CONTROLLED STUDY; DENITRIFICATION; DENITRIFYING BACTERIUM; DNA BASE COMPOSITION; EVOLUTIONARY HOMOLOGY; GENOTYPE PHENOTYPE CORRELATION; HALOMONAS; HALOMONAS CERINA; HALOMONAS DENITRIFICANS; HALOMONAS KOREENSIS; HALOMONAS VENTOSA; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; RNA SEQUENCE; SEQUENCE HOMOLOGY; TAXONOMIC IDENTIFICATION; UNINDEXED SEQUENCE;

BACTERIAL PROTEINS; BACTERIAL TYPING TECHNIQUES; BASE COMPOSITION; CLUSTER ANALYSIS; DNA, BACTERIAL; DNA, RIBOSOMAL; HALOMONAS; MOLECULAR SEQUENCE DATA; NITRATES; NITRITES; NITROGEN; PHYLOGENY; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA;

HALOMONAS; HALOMONAS KOREENSIS; HALOMONAS VENTOSAE;

EID: 77950368373     PISSN: 07232020     EISSN: 16180984     Source Type: Journal    
DOI: 10.1016/j.syapm.2009.12.001     Document Type: Article

References (59)

1. Alefounder P.R., Ferguson S.J. Electron transport-linked nitrous oxide synthesis and reduction by Paracoccus denitrificans monitored with an electrode. Biochem. Biophys. Res. Commun. 1982, 104:1149-1155.
2. Arahal D.R., Castillo A.M., Ludwig W., Schleifer K.H., Ventosa A. Proposal of Cobetia marina gen. nov., comb. nov., within the family Halomonadaceae, to include the species Halomonas marina. Syst. Appl. Microbiol. 2002, 25:207-211.
3. Arahal D.R., Ludwig W., Schleifer K.H., Ventosa A. Phylogeny of the family Halomonadaceae based on 23S and 16S rDNA sequence analyses. Int. J. Syst. Evol. Microbiol. 2002, 52:241-249.
4. Arahal D.R., Vreeland R.H., Litchfield C.D., Mormile M.R., Tindall B.J., Oren A., Béjar V., Quesada E., Ventosa A. Recommended minimal standards for describing new taxa of the family Halomonadaceae. Int. J. Syst. Evol. Microbiol. 2007, 57:2436-2446.
5. Ben Ali Gam Z., Abdelkafi S., Casalot L., Tholozan J.L., Oueslati R., Labat M. Modicisalibacter tunisiensis gen. nov., sp. nov., an aerobic, moderately halophilic bacterium isolated from an oilfield-water injection sample, and emended description of the family Halomonadaceae Franzmann et al. 1989 emend Dobson and Franzmann 1996 emend Ntougias et al. Int. J. Syst. Evol. Microbiol. 2007, 57(2007):2307-2313.
6. Berendes F., Gottschalk G., Heine-dobbernack E., Moore E.R.B., Tindall B.J. Halomonas desiderata sp. nov., a new alkaliphilic, halotolerant and denitrifying bacterium isolated from a municipal sewage works. Syst. Appl. Microbiol. 1996, 19:158-167.
7. Bouchotroch S., Quesada E., Del Moral A., Llamas I., Béjar V. Halomonas maura sp. nov., a novel moderately halophilic, exopolysaccharide-producing bacterium. Int. J. Syst. Evol. Microbiol. 2001, 51:1625-1632.
8. Braker G., Zhou J., Wu L., Devol A.H., Tiedje J.M. Nitrite reductase genes (nirK and nirS) as functional markers to investigate diversity of denitrifying bacteria in pacific northwest marine sediment communities. Appl. Environ. Microbiol. 2000, 66:2096-2104.
9. Brettar I., Höfle M.G. Nitrous oxide producing heterotrophic bacteria from the water column of the central Baltic: abundance and molecular identification. Mar. Ecol. Prog. Ser. 1993, 94:253-265.
10. Burland T.G. DNASTAR's lasergene sequence analysis software. Methods Mol. Biol. 2000, 132:71-91.
11. Callies E., Mannheim E. Classification of the Flavobacterium-Cytophaga complex on the basis of respiratory quinones and fumarate respiration. Int. J. Syst. Bacteriol. 1978, 28:14-19.
12. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 2000, 17:540-552.
13. Delorme S., Philippot L., Edel-Hermann V., Deulvot C., Mougel C., Lemanceau P. Comparative genetic diversity of the narG, nosZ, and 16S rRNA genes in fluorescent pseudomonads. Appl. Environ. Microbiol. 2003, 69:1004-1012.
14. Dobson S.J., Franzmann P.D. Unification of the genera Deleya, Halomonas and Halovibrio and the species Paracoccus halodenitrificans into a single genus, Halomonas, and placement of the genus Zymobacter in the family Halomonadaceae. Int. J. Syst. Bacteriol. 1996, 46:550-558.
15. Euzeby, J.P., 2009. List of Prokaryotic Names with Standing in Nomenclature. http://www.bacterio.cict.fr/.
16. Felsenstein J. PHYLIP (Phylogenetic inference package), version 3,8. Distributed by the author 2008, Department of Genome Sciences, University of Washington, Seattle, USA.
17. Garriga M., Ehrmann M.A., Arnau J., Hugas M., Vogel R.F. Carnimonas nigrificans gen. nov., sp. nov., a bacterial causative agent for black spot formation on cured meat products. Int. J. Syst. Bacteriol. 1998, 48:677-686.
18. Gauthier M.J., Lafay B., Christen R., Fernandez L., Acquaviva M., Bonin P., Bertrand J.C. Marinobacter hydrocarbonoclasticus gen. nov., sp. nov., a new, extremely halotolerant, hydrocarbondegrading marine bacterium. Int. J. Syst. Bacteriol. 1992, 42:568-576.
19. González-Domenech C.M., Béjar V., Martínez-Checa F., Quesada E. Halomonas nitroreducens sp. nov., a novel nitrate- and nitrite-reducing species. Int. J. Syst. Evol. Microbiol. 2008, 58:872-876.
20. González-Domenech C.M., Martínez-Checa F., Quesada E., Béjar V. Halomonas cerina sp. nov., a moderately halophilic, denitrifying, exopolysaccharide-producing bacterium. Int. J. Syst. Evol. Microbiol. 2008, 58:803-809.
21. González-Domenech C.M., Martínez-Checa F., Quesada E., Béjar V. Halomonas fontilapidosi sp. nov., a moderately halophilic, denitrifying bacterium. Int. J. Syst. Evol. Microbiol. 2009, 59:1290-1296.
22. Goregues C.M., Michotey V.D., Bonin P.C. Molecular, biochemical, and physiological approaches for understanding the ecology of denitrification. Microb. Ecol. 2005, 49:198-208.
23. Heylen K., Gevers D., Vanparys B., Wittebolle L., Geets J., Boon N., De Vos P. The incidence of nirS and nirK and their genetic heterogeneity in cultivated denitrifiers. Environ. Microbiol. 2006, 8:2012-2021.
24. Jeong H., Yim J.H., Lee C., Choi S.H., Park Y.K., Yoon S.H., Hur C.G., Kang H.Y., Kim D., Lee H.H., Park K.H., Park S.H., Park H.S., Lee H.K., Oh T.K., Kim J.F. Genomic blueprint of Hahella chejuensis, a marine microbe producing an algicidal agent. Nucleic Acids Res. 2005, 33:7066-7073.
25. Jones C.M., Stres B., Rosenquist M., Hallin S. Phylogenetic analysis of nitrite, nitric oxide, and nitrous oxide respiratory enzymes reveal a complex evolutionary history for denitrification. Mol. Biol. Evol. 2008, 25:1955-1966.
26. Kim K.K., Jin L., Yang H.C., Lee S.T. Halomonas gomseomensis sp. nov., Halomonas janggokensis sp. nov., Halomonas salaria sp. nov. and Halomonas denitrificans sp. nov., moderately halophilic bacteria isolated from saline water. Int. J. Syst. Evol. Microbiol. 2007, 57:675-681.
27. Kimura M. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 1980, 16:111-120.
28. Lee H.K., Chun J., Moon E.Y., Ko S.H., Lee D.S., Lee H.S., Bae K.S. Hahella chejuensis gen. nov., sp. nov., an extracellular-polysaccharide-producing marine bacterium. Int. J. Syst. Evol. Microbiol. 2001, 51:661-666.
29. Lehmann K.B., Neumann R. Atlas und Grundriss der Bakteriologie und Lehrbuch der speziellen bakteriologischen Diagnostik 1896, 1st edn. J.F. Lehmann (Ed.).
30. Lemanceau P., Samson R., Alabouvette C. Recherches sur la re'sistance des sols aux maladies XV. Comparison des populations de Pseudomonas fluorescents dans un sol résistant et un sol sensible aux fusarioses vasculaires. Agronomie 1988, 8:243-249.
31. Lim J.M., Yoon J.H., Lee J.C., Jeon C.O., Park D.J., Sung C., Kim C.J. Halomonas koreensis sp. nov., a novel moderately halophilic bacterium isolated from a solar saltern in Korea. Int. J. Syst. Evol. Microbiol. 2004, 54:2037-2042.
32. Marmur J., Doty P. Determination of the base composition of deoxyribonucleic acid from its thermal denaturation temperature. J. Mol. Biol. 1962, 5:109-118.
33. Martínez-Cánovas M.J., Quesada E., Llamas I., Béjar V. Halomonas ventosae sp. nov., a moderately halophilic, denitrifying, exopolysaccharide-producing bacterium. Int. J. Syst. Evol. Microbiol. 2004, 54:733-737.
34. Mata J.A., Martínez-Cánovas M.J., Quesada E., Béjar V. A detailed phenotypic characterisation of the type strains of Halomonas species. Syst. Appl. Microbiol. 2002, 25:360-375.
35. Migula W. System der Bakterien 1900, Vol. 2. Gustav Fischer, Jena.
36. Mormile M.R., Romine M.F., Garcia M.T., Ventosa A., Bailey T.J., Peyton B.M. Halomonas campisalis sp. nov., a denitrifying, moderately haloalkaliphilic bacterium. Syst. Appl. Microbiol. 1999, 22:551-558.
37. Ntougias S., Zervakis G.I., Fasseas C. Halotalea alkalilenta gen. nov., sp. nov., a novel osmotolerant and alkalitolerant bacterium from alkaline olive mill wastes, and emended description of the family Halomonadaceae Franzmann et al. 1989, emend. Dobson and Franzmann 1996. Int. J. Syst. Evol. Microbiol. 2007, 57:1975-1983.
38. Okamoto T., Taguchi H., Nakamura K., Ikenaga H., Kuraishi H., Yamasato K. Zymobacter palmae gen. nov., sp. nov., a new ethanol-fermenting peritrichous bacterium isolated from palm sap. Arch. Microbiol. 1993, 160:333-337.
39. Oren A. Microbial life at high salt concentrations: phylogenetic and metabolic diversity. Saline Syst. 2008, 4:2.
40. Owen R.J., Hill L.R. The estimation of base compositions, base pairing and genome size of bacterial deoxyribonucleic acids. Identification Methods for Microbiologists 1979, 277-296. Academic Press, London. 2nd ed. F.A. Skinner, D.W. Lovelock (Eds.).
41. Owen R.J., Pitcher D. Current methods for estimating DNA base composition and levels of DNA-DNA hybridization. Chemical Methods in Bacterial Systematic 1985, 67-93. Academic Press, New York. M. Good-Fellow, E. Minnikin (Eds.).
42. Petri R., Imhoff J.F. The relationship of nitrate reducing bacteria on the basis of narH gene sequences and comparison of narH and 16S rDNA based phylogeny. Syst. Appl. Microbiol. 2000, 23:47-57.
43. Quesada E., Béjar V., Calvo C. Exopolysaccharide production by Volcaniella eurihalina. Experientia 1993, 49:1037-1041.
44. Rodríguez-Valera F., Ruiz-Berraquero F., Ramos-Cormenzana A. Characteristics of the heterotropic bacterial populations in hypersaline environments of different salt concentration. Microbiol. Ecol. 1981, 7:235-243.
45. Romano I., Giordano A., Lama L., Nicolaus B., Gambacorta A. Halomonas campaniensis sp. nov., a haloalkaliphilic bacterium isolated from a mineral pool of Campania Region, Italy. Syst. Appl. Microbiol. 2005, 28:610-618.
46. Sánchez-Porro C., de la Haba R.R., Soto-Ramírez N., Márquez M.C., Montalvo-Rodríguez R., Ventosa A. Description of Kushneria aurantia gen. nov., sp. nov., a novel member of the family Halomonadaceae, and a proposal for reclassification of Halomonas marisflavi as Kushneria marisflavi comb. nov., of Halomonas indalinina as Kushneria indalinina comb. nov. and of Halomonas avicenniae as Kushneria avicenniae comb. nov. Int. J. Syst. Evol. Bacteriol. 2009, 59:397-405.
47. Scala D.J., Kerkhof L.J. Nitrous oxide reductase (nosZ) gene-specific PCR primers for detection of denitrifiers and three nosZ genes from marine sediments. FEMS Microbiol. Lett. 1998, 162:61-68.
48. Scala D.J., Kerkhof L.J. Diversity of nitrous oxide reductase (nosZ) genes in continental shelf sediments. Appl. Environ. Microbiol. 1999, 65:1681-1687.
49. Sneath P.H.A., Sokal R.R. Numerical taxonomy: The Principles and Practice of Numerical Classification 1973, W.H. Freeman and Co. Ltd., San Francisco.
50. Sokal R.R., Michener C.D. A statistical method for evaluating systematic relationships. Univ. Kansas Sci. Bull. 1958, 38:1409-1438.
51. Stanier R.Y., Palleroni N.J., Duodoroff M. The aerobic pseudomonads: a taxonomic study. J. Gen. Micro Biol. 1966, 43:159-272.
52. Stover C.K., Pham X.Q.T., Erwin A.L., Mizoguchi S.D., Warrener P., Hickey M.J., Brinkman F.S., Hufnagle W.O., Kowalik D.J., Lagrou M., Garber R.L., Goltry L., Tolentino E., Westbrock-Wadman S., Yuan Y., Brody L.L., Coulter S.N., Folger K.R., Kas A., Larbig K., Lim R., Smith K., Spencer D., Wong G.K., Wu Z., Paulsen I.T., Reizer J., Saier M.H., Hancock R.E., Lory S., Olson M.V. Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen. Nature 2000, 406:959-964.
53. Tamura K., Dudley J., Nei M., Kumar S. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24:1596-1599.
54. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997, 25:4876-4882.
55. Ventosa A., Gutiérrez M.C., García M.T., Ruiz-Berraquero F. Classification of "Chromobacterium marismortui" in a new genus, Chromohalobacter gen. nov., as Chromohalobacter marismortui comb. nov., nom. rev. Int. J. Syst. Bacteriol. 1989, 39:382-386.
56. Wang Y.N., Cai H., Chi C.Q., Lu A.H., Lin X.G., Jiang Z.F., Wu X.L. Halomonas shengliensis sp. nov., a moderately halophilic, denitrifying, crude-oil-utilizing bacterium. Int. J. Syst. Evol. Microbiol. 2007, 57:1222-1226.
57. Wang Y.N., Cai H., Yu S.L., Wang Z.Y., Liu J., Wu X.L. Halomonas gudaonensis sp. nov., isolated from a saline soil contaminated by crude oil. Int. J. Syst. Evol. Microbiol. 2007, 57:911-915.
58. Yoon J.H., Lee K.C., Kho Y.H., Kang K.H., Kim C.J., Park Y.H. Halomonas alimentaria sp. nov., isolated from jeotgal, a traditional Korean fermented seafood. Int. J. Syst. Evol. Microbiol. 2002, 52:123-130.
59. Xu X.W., Wu Y.H., Zhou Z., Wang C.S., Zhou Y.G., Zhang H.B., Wang Y., Wu M. Halomonas saccharevitans sp. nov., Halomonas arcis sp. nov. and Halomonas subterranea sp. nov., halophilic bacteria isolated from hypersaline environments of China. Int. J. Syst. Evol. Microbiol. 2007, 57:1619-1624.