1887

Abstract

A moderately halophilic, Gram-stain-negative, aerobic bacterium, strain D1-1, belonging to the genus , was isolated from soil sampled at Pentha beach, Odisha, India. Phylogenetic trees reconstructed based on 16S rRNA genes and multilocus sequence analysis of and genes revealed that strain D1-1 belonged to the genus and was most closely related to YKJ-16 (98.1 %) followed by Al12 (97.5 %), CPS11 (97.5 %), 5CR (97.4 %) and DSM 735 (97.2 %) on the basis of 16S rRNA gene sequence similarity. Sequence identities with other species within the genus were lower than 97.0 %. The digital DNA–DNA hybridization (dDDH) and average nucleotide identity (ANI) values of 22.4–30 % and 79.5–85.4 % with close relatives of DSM 735, . YKJ-16, Al12 and 5CR were lower than the threshold recommended for species delineation (70 % and 95–96 % for dDDH and ANI, respectively). Further, strain D1-1 formed yellow-coloured colonies; cells were rod-shaped, motile with optimum growth at 30 °C (range, 4–45 °C) and 2–8 % NaCl (w/v; grew up to 24 % NaCl). The major fatty acids were summed feature 8 (C 7/C 6), summed feature 3 (C 7/C 6) and C and the main respiratory quinone was ubiquinone Q-9 in line with description of the genus. Based on its chemotaxonomic and phylogenetic characteristics and genome uniqueness, strain D1-1 represents a novel species in the genus , for which we propose the name sp. nov., within the family . The type strain is D1-1 (=JCM 33602=KACC 21317=NAIMCC-B-2254).

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2020-12-22
2024-03-29
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References

  1. Franzmann PD, Wehmeyer U, Stackebrandt E. Halomonadaceae fam. nov., a new family of the class Proteobacteria to accommodate the genera Halomonas and Deleya . Syst Appl Microbiol 1988; 11:16–19 [View Article]
    [Google Scholar]
  2. Vreeland RH, Litchfield CD, Martin EL, Elliot E. Halomonas elongata, a new genus and species of extremely salt-tolerant bacteria. Int J Syst Bacteriol 1980; 30:485–495 [View Article]
    [Google Scholar]
  3. de la Haba RR, Márquez MC, Papke RT, Ventosa A, Carmen Márquez M, Thane Papke R. Multilocus sequence analysis of the family Halomonadaceae . Int J Syst Evol Microbiol 2012; 62:520–538 [View Article][PubMed]
    [Google Scholar]
  4. de la Haba RR, Arahal DR, Márquez MC, Ventosa A. Phylogenetic relationships within the family Halomonadaceae based on comparative 23S and 16S rRNA gene sequence analysis. Int J Syst Evol Microbiol 2010; 60:737–748 [View Article][PubMed]
    [Google Scholar]
  5. Kämpfer P, Rekha PD, Busse HJ, Arun AB, Priyanka P et al. Halomonas malpeensis sp. nov., isolated from rhizosphere sand of a coastal sand dune plant. Int J Syst Evol Microbiol 2018; 68:1037–1046 [View Article][PubMed]
    [Google Scholar]
  6. Oren A, Ventosa A. Subcommittee on the taxonomy of Halobacteriaceae and Subcommittee on the taxonomy of Halomonadaceae: minutes of the joint open meeting, 24 June 2013, Storrs, Connecticut, USA. Int J Syst Evol Microbiol 2013; 63:3540–3544 [View Article][PubMed]
    [Google Scholar]
  7. Arahal DR, Vreeland RH, Litchfield CD, Mormile MR, Tindall BJ et al. Recommended minimal standards for describing new taxa of the family Halomonadaceae . Int J Syst Evol Microbiol 2007; 57:2436–2446 [View Article][PubMed]
    [Google Scholar]
  8. DeLong EF. Archaea in coastal marine environments. Proc Natl Acad Sci U S A 1992; 89:5685–5689 [View Article][PubMed]
    [Google Scholar]
  9. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article][PubMed]
    [Google Scholar]
  10. Kumar S, Stecher G, Tamura K. mega7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
    [Google Scholar]
  11. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
    [Google Scholar]
  12. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  13. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
    [Google Scholar]
  14. Martínez-Cánovas MJ, 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 [View Article][PubMed]
    [Google Scholar]
  15. Lee JC, Kim SJ, Whang KS. Halomonas sediminicola sp. nov., a moderately halophilic bacterium isolated from a solar saltern sediment. Int J Syst Evol Microbiol 2016; 66:3865–3872 [View Article][PubMed]
    [Google Scholar]
  16. González-Domenech CM, 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 [View Article][PubMed]
    [Google Scholar]
  17. Ahn SJ, Burne RA. Effects of oxygen on biofilm formation and the AtlA autolysin of Streptococcus mutans . J Bacteriol 2007; 189:6293–6302 [View Article][PubMed]
    [Google Scholar]
  18. Mukherjee P, Mitra A, Roy M. Halomonas rhizobacteria of avicennia marina of indian sundarbans promote rice growth under saline and heavy metal stresses through exopolysaccharide production. Front Microbiol 2019; 10:1–18 [View Article]
    [Google Scholar]
  19. Cowan ST, Steel KJ. Manual for the Identification of Medical Bacteria Cambridge University Press; 1965
    [Google Scholar]
  20. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, D.C: American Society for Microbiology; 1994 pp 607–654
    [Google Scholar]
  21. Church DL. Biochemical tests for the identification of aerobic bacteria. In Leber AL. editor Clinical Microbiology Procedures Handbook Washington, DC: ASM Press; 2016
    [Google Scholar]
  22. Teather RM, Wood PJ. Use of Congo red-polysaccharide interactions in enumeration and characterization of cellulolytic bacteria from the bovine rumen. Appl Environ Microbiol 1982; 43:777–780 [View Article][PubMed]
    [Google Scholar]
  23. Lányi B. Classical and rapid identification methods for medically important bacteria. Methods Microbiol 1988; 19:1–67
    [Google Scholar]
  24. Cristea A, Baricz A, Leopold N, Floare CG, Borodi G et al. Polyhydroxybutyrate production by an extremely halotolerant Halomonas elongata strain isolated from the hypersaline meromictic Fără Fund Lake (Transylvanian Basin, Romania). J Appl Microbiol 2018; 125:1343–1357 [View Article][PubMed]
    [Google Scholar]
  25. Morra MJ, Dick WA. Mechanisms of H2S production from cysteine and cystine by microorganisms isolated from soil by selective enrichment. Appl Environ Microbiol 1991; 57:1413–1417 [View Article][PubMed]
    [Google Scholar]
  26. Véron M, Lenvoisé-Furet A, Beaune P. Anaerobic respiration of fumarate as a differential test between Campylobacter fetus and Campylobacter jejuni . Curr Microbiol 1981; 6:349–354 [View Article]
    [Google Scholar]
  27. Reiner K. Carbohydrate fermentation protocol. Am Soc Microbiol 20121–10
    [Google Scholar]
  28. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  29. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article][PubMed]
    [Google Scholar]
  30. Yoon SH, Ha S-min, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article]
    [Google Scholar]
  31. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
    [Google Scholar]
  32. Meier-Kolthoff JP, Klenk HP, Göker M. Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 2014; 64:352–356 [View Article][PubMed]
    [Google Scholar]
  33. Verma A, Ojha AK, Dastager SG, Natarajan R, Mayilraj S et al. Domibacillus mangrovi sp. nov. and Domibacillus epiphyticus sp. nov., isolated from marine habitats of the central west coast of India. Int J Syst Evol Microbiol 2017; 67:3063–3070 [View Article][PubMed]
    [Google Scholar]
  34. da Costa MS, Albuquerque L, Nobre MF, Wait R. The extraction and identification of respiratory lipoquinones of prokaryotes and their use in taxonomy. Elsevier Ltd 2011
    [Google Scholar]
  35. Verma A, Ojha AK, Kumari P, Sundharam SS, Mayilraj S et al. Luteimonas padinae sp. nov., an epiphytic bacterium isolated from an intertidal macroalga. Int J Syst Evol Microbiol 2016; 66:5444–5451 [View Article][PubMed]
    [Google Scholar]
  36. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [View Article][PubMed]
    [Google Scholar]
  37. Komagata K, Suzuki KI. Lipid and cell-wall analysis in bacterial systematics. Methods Microbiol 1988; 19:161–207
    [Google Scholar]
  38. Yoon JH, Lee KC, Kho YH, Kang KH, Kim CJ et al. Halomonas alimentaria sp. nov., isolated from jeotgal, a traditional Korean fermented seafood. Int J Syst Evol Microbiol 2002; 52:123–130 [View Article][PubMed]
    [Google Scholar]
  39. Montero-Calasanz MDC, Göker M, Rohde M, Spröer C, Schumann P et al. Chryseobacterium hispalense sp. nov., a plant-growth-promoting bacterium isolated from a rainwater pond in an olive plant nursery, and emended descriptions of Chryseobacterium defluvii, Chryseobacterium indologenes, Chryseobacterium wanjuense and Chryseobacterium gregarium . Int J Syst Evol Microbiol 2013; 63:4386–4395 [View Article][PubMed]
    [Google Scholar]
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